Index: /issm/trunk/CMakeLists.txt =================================================================== --- /issm/trunk/CMakeLists.txt (revision 14310) +++ /issm/trunk/CMakeLists.txt (revision 14310) @@ -0,0 +1,74 @@ +# CMake version check. Version 2.6 is considered standard. +cmake_minimum_required (VERSION 2.6) + +# Project Information {{{ +# Project Name +project(ISSM) +set(ISSM_VERSION_MAJOR 4) +set(ISSM_VERSION_MINOR 1) +# }}} +# Contact Information {{{ +set(ISSM_EMAIL "issm@jpl.nasa.gov") +set(ISSM_WEBSITE "http://issm.jpl.nasa.gov") +# }}} + +# Environment Variables {{{ +# Out of source build can be done here. +set(CMAKE_BINARY_DIR ${ISSM_DIR}) +# }}} + +# Install Targets {{{ +# Install 'issm.exe' +#install(TARGETS issm RUNTIME) + +# Install 'libISSMCore.a' and 'libISSMOverload.a' +# install(TARGETS ISSMCore +# ISSMOverload +# ARCHIVE) +# }}} +# Optional Install {{{ +#if(${SHARED_LIBS} IS ON) +# install(TARGETS ISSMCore +# ISSMOverload +# LIBRARY) +#endif(${SHARED_LIBS} IS ON) +# }}} + +# Language Checks {{{ + +# 'C' language check. +include(CheckLanguage) + +check_language(C) +if(CMAKE_C_COMPILER) + enable_language(C) +else(CMAKE_C_COMPILER) + message(FATAL_ERROR "No C support found!") +endif(CMAKE_C_COMPILER) + +# 'C++' language check. +check_language(CXX) +if(CMAKE_CXX_COMPILER) + enable_language(CXX) +else(CMAKE_CXX_COMPILER) + message(FATA_ERROR "No C++ support found!") +endif(CMAKE_CXX_COMPILER) + +# 'Fortran' language check. +#check_language(Fortran) +#if(CMAKE_Fortran_COMPILER) +# enable_language(Fortran) +#else(CMAKE_Fortran_COMPILER) +# message(FATA_ERROR "No Fortran support") +#endif(CMAKE_Fortran_COMPILER) +# }}} + +# Subdirectories {{{ +add_subdirectory(src) +# }}} + +# Options {{{ +option(SHARED_LIBS "Set whether to produce shared libraries, or not. Default is no." + OFF) +# Questionable whether all options should be contained within this file or included from some other file. +# }}} Index: /issm/trunk/configs/config-arm-linux.sh =================================================================== --- /issm/trunk/configs/config-arm-linux.sh (revision 14309) +++ /issm/trunk/configs/config-arm-linux.sh (revision 14310) @@ -6,5 +6,6 @@ --host="arm-linux-androideabi" \ --enable-shared \ - --with-android=jni\ + --with-android=jni \ + --with-android-ndk=$ISSM_DIR/externalpackages/android/android-ndk/install \ --without-fortran \ --without-wrappers \ Index: /issm/trunk/configs/config-hoffman2.sh =================================================================== --- /issm/trunk/configs/config-hoffman2.sh (revision 14310) +++ /issm/trunk/configs/config-hoffman2.sh (revision 14310) @@ -0,0 +1,18 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=/u/local/intel/11.1/openmpi/1.4.5/include \ + --with-mpi-lib="-L/u/local/intel/11.1/openmpi/1.4.5/include -lmpi" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -L/u/local/intel/11.1/openmpi/1.4.5/lib -lmpi -lmpi_f77 -lmpi_cxx" Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 14309) +++ /issm/trunk/configure.ac (revision 14310) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([ISSM],[4.2.4],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([ISSM],[4.2.5],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 Index: /issm/trunk/externalpackages/adolc/install-dev.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-dev.sh (revision 14309) +++ /issm/trunk/externalpackages/adolc/install-dev.sh (revision 14310) @@ -6,4 +6,5 @@ git clone -b 2.3.x_ISSM git://git.mcs.anl.gov/adol-c.git adolc_issm +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad #Compile ADOL-C Index: /issm/trunk/externalpackages/adolc/install-update-dev.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-update-dev.sh (revision 14309) +++ /issm/trunk/externalpackages/adolc/install-update-dev.sh (revision 14310) @@ -15,4 +15,5 @@ cd adolc_issm git pull +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad autoreconf -f -i Index: sm/trunk/externalpackages/dakota/LHSDriver.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/LHSDriver.cpp.patch (revision 14309) +++ (revision ) @@ -1,8 +1,0 @@ -766c766 -< /*char output_string[32], message_string[32], title_string[32], ---- -> char output_string[32], message_string[32], title_string[32], -802c802 -< check_error(err_code, "lhs_files");*/ ---- -> check_error(err_code, "lhs_files"); Index: sm/trunk/externalpackages/dakota/NIDRProblemDescDB.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/NIDRProblemDescDB.C.patch (revision 14309) +++ (revision ) @@ -1,4 +1,0 @@ -95a96,98 -> -> //close the input file -> fclose(nidrin); Index: sm/trunk/externalpackages/dakota/NonDLocalReliability.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/NonDLocalReliability.C.patch (revision 14309) +++ (revision ) @@ -1,7 +1,0 @@ -2276a2277 -> // add sensitivity output to importance factors (jes, 8/06/10) -2280c2281,2282 -< << impFactor[i][j] << '\n'; ---- -> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) -> << fnGradsMeanX(i, j) << '\n'; Index: sm/trunk/externalpackages/dakota/NonDSampling.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/NonDSampling.C.patch (revision 14309) +++ (revision ) @@ -1,15 +1,0 @@ -656a657,658 -> -> -659a662,663 -> -> return; //don't compute for now, too expensive. -705c709 -< //calculate simple rank correlation coeff ---- -> //calculate simple correlation coeff -710a715 -> -1071a1077,1078 -> -> return; //don't output for now. Index: sm/trunk/externalpackages/dakota/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/NonDUnilevelRBDO.C.patch (revision 14309) +++ (revision ) @@ -1,10 +1,0 @@ -1052,1053c1052,1057 -< s << " Importance Factor for variable " << setw(11) -< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; ---- -> // add sensitivity output to importance factors (jes, 8/06/10) -> s << " Importance Factor for variable " << setiosflags(ios::left) -> << setw(11) << uv_labels[j].data() << " = " -> << resetiosflags(ios::adjustfield) << setw(write_precision+7) -> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) -> << fnGradsMeanX(i, j) << '\n'; Index: sm/trunk/externalpackages/dakota/ParallelLibrary.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/ParallelLibrary.C.patch (revision 14309) +++ (revision ) @@ -1,34 +1,0 @@ -134a135 -> initialized=0; //we run serially all the time! -165a167,197 -> /** This constructor is provided for the Issm software, to run serial -> * Dakota in a parallel MPI ring: */ -> ParallelLibrary::ParallelLibrary(char* serial_mode): worldRank(0), worldSize(1), -> mpirunFlag(false), ownMPIFlag(false), dryRunFlag(false), dummyFlag(false), -> stdOutputFlag(false), stdErrorFlag(false), startClock(0), -> stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL), -> writeRestartFilename(NULL), stopRestartEvals(0), -> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) -> { -> startClock = clock(); -> #ifdef DAKOTA_UTILIB -> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); -> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp -> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp -> #endif // DAKOTA_UTILIB -> -> // do not initialize MPI. Get worldRank/worldSize if available -> ParallelLevel pl; -> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! -> pl.serverIntraComm = MPI_COMM_NULL; -> Cout << "Running Dakota in serial mode on CPU 0, inside an MPI ring."; -> #else // mpi not available -> pl.serverIntraComm = MPI_COMM_NULL; -> Cout << "Running Dakota in serial mode.\n"; -> #endif // HAVE_MPI -> -> parallelLevels.insert(pl); -> currPLIter = parallelLevels.begin(); -> increment_parallel_configuration(); -> } -> Index: sm/trunk/externalpackages/dakota/ParallelLibrary.H.patch =================================================================== --- /issm/trunk/externalpackages/dakota/ParallelLibrary.H.patch (revision 14309) +++ (revision ) @@ -1,3 +1,0 @@ -346a347,348 -> /// library mode constructor, serial mode -> ParallelLibrary(char* serial_mode); Index: /issm/trunk/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 14310) @@ -0,0 +1,8 @@ +766c766 +< /*char output_string[32], message_string[32], title_string[32], +--- +> char output_string[32], message_string[32], title_string[32], +802c802 +< check_error(err_code, "lhs_files");*/ +--- +> check_error(err_code, "lhs_files"); Index: /issm/trunk/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 14310) @@ -0,0 +1,4 @@ +95a96,98 +> +> //close the input file +> fclose(nidrin); Index: /issm/trunk/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 14310) @@ -0,0 +1,7 @@ +2276a2277 +> // add sensitivity output to importance factors (jes, 8/06/10) +2280c2281,2282 +< << impFactor[i][j] << '\n'; +--- +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/4.2/NonDSampling.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 14310) @@ -0,0 +1,15 @@ +656a657,658 +> +> +659a662,663 +> +> return; //don't compute for now, too expensive. +705c709 +< //calculate simple rank correlation coeff +--- +> //calculate simple correlation coeff +710a715 +> +1071a1077,1078 +> +> return; //don't output for now. Index: /issm/trunk/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 14310) @@ -0,0 +1,10 @@ +1052,1053c1052,1057 +< s << " Importance Factor for variable " << setw(11) +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> // add sensitivity output to importance factors (jes, 8/06/10) +> s << " Importance Factor for variable " << setiosflags(ios::left) +> << setw(11) << uv_labels[j].data() << " = " +> << resetiosflags(ios::adjustfield) << setw(write_precision+7) +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 14310) @@ -0,0 +1,34 @@ +134a135 +> initialized=0; //we run serially all the time! +165a167,197 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dryRunFlag(false), dummyFlag(false), +> stdOutputFlag(false), stdErrorFlag(false), startClock(0), +> stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL), +> writeRestartFilename(NULL), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode on CPU 0, inside an MPI ring."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.insert(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> Index: /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 14310) @@ -0,0 +1,3 @@ +346a347,348 +> /// library mode constructor, serial mode +> ParallelLibrary(char* serial_mode); Index: /issm/trunk/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 14310) @@ -0,0 +1,5 @@ +109a110,113 +> +> //close the input file +> fclose(nidrin); +> Index: /issm/trunk/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 14310) @@ -0,0 +1,9 @@ +2218a2219 +> // add sensitivity output to importance factors (jes, 8/06/10) +2223c2224,2227 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/5.2/NonDSampling.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 14310) @@ -0,0 +1,14 @@ +438,439c438,440 +< if (!subIteratorFlag) +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +894,895c895,897 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/trunk/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 14310) @@ -0,0 +1,7 @@ +1046a1047 +> // add sensitivity output to importance factors (jes, 8/06/10) +1048c1049,1050 +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> << uv_labels[j].data() << " = " << impFactor[i][j] +> << " Sensitivity = " << fnGradsMeanX(i,j) << '\n'; Index: /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 14310) @@ -0,0 +1,36 @@ +178a179 +> initialized=0; //we run serially all the time! +214a216,248 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 MPI executable in serial mode on CPU 0 for ISSM."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 serial executable in serial mode for ISSM.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> Index: /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 14310) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the Issm software) +> ParallelLibrary(char* serial_mode); Index: /issm/trunk/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 14310) +++ /issm/trunk/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 14310) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/trunk/externalpackages/dakota/install-4.2-altix64-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/opt/intel/mkl/9.1.023/lib/64/libmkl.so \ + --with-lapack=/opt/intel/mkl/9.1.023/lib/64/libmkl_lapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-discover.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-discover.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-linux64-astrid.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-linux64-astrid.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib64/libblas.so.3.0.3 \ + --with-lapack=/usr/lib64/liblapack.so.3.0.3 +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-linux64-cloud.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib/libblas.so \ + --with-lapack=/usr/lib/liblapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib64/libblas.so.3.1.1 \ + --with-lapack=/usr/lib64/liblapack.so.3.1.1 +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-macosx64.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-macosx64.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 14310) @@ -0,0 +1,103 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ +--with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " + +#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ +#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" + +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-4.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-pleiades.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-4.2-pleiades.sh (revision 14310) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dakota/install-5.2-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.2-linux64-astrid.sh (revision 14310) +++ /issm/trunk/externalpackages/dakota/install-5.2-linux64-astrid.sh (revision 14310) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-plugin \ + --with-blas=/usr/lib64/libblas.so.3.0.3 \ + --with-lapack=/usr/lib64/liblapack.so.3.0.3 +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: sm/trunk/externalpackages/dakota/install-altix64-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas=/opt/intel/mkl/9.1.023/lib/64/libmkl.so \ - --with-lapack=/opt/intel/mkl/9.1.023/lib/64/libmkl_lapack.so -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-discover.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ ---with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-astrid.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas=/usr/lib64/libblas.so.3.0.3 \ - --with-lapack=/usr/lib64/liblapack.so.3.0.3 -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-linux64-cloud.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-cloud.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas=/usr/lib/libblas.so \ - --with-lapack=/usr/lib/liblapack.so -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-murdo.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas=/usr/lib64/libblas.so.3.1.1 \ - --with-lapack=/usr/lib64/liblapack.so.3.1.1 -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-macosx64.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ - --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-pleiades-petsc3.3.sh (revision 14309) +++ (revision ) @@ -1,103 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ ---with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " - -#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ -#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" -#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ -#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" - -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-pleiades.sh (revision 14309) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C ./NonDSampling.C.patch -patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ---with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk/externalpackages/dem/dem.m =================================================================== --- /issm/trunk/externalpackages/dem/dem.m (revision 14310) +++ /issm/trunk/externalpackages/dem/dem.m (revision 14310) @@ -0,0 +1,530 @@ +function [h,I]=dem(x,y,z,varargin) +%DEM Shaded relief image plot +% DEM(X,Y,Z) plots the Digital Elevation Model defined by X and Y +% coordinate vectors and elevation matrix Z, as a lighted image using +% specific "landcolor" and "seacolor" colormaps. DEM uses IMAGESC +% function which is much faster than SURFL when dealing with large +% high-resolution DEM. +% +% DEM(X,Y,Z,OPT) specifies options with OPT = [A,C,SCUT,ZMIN,ZMAX,ZCUT], +% where sorted optional scalars are: +% A = azimuth light (in degrees relative to North). Default is A = -45 +% for a natural northwestern illumination. +% C = controls contrast, as the exponent of the gradient value. Default +% is C = 1 for linear contrast; use C = 0 to remove lighting, +% C = 0.5 for moderate lighting, C = 2 or more for strong contrast. +% SCUT = controls lighting scale saturation with a median-style filter +% in % of elements. Default is SCUT = 0.2 (0.2% maximum gradient +% values is ignored). Use SCUT = 0 for full scale gradient. +% ZMIN,ZMAX = fixes min and max elevation values for colormap. Use NaN +% to keep real min and/or max data values. +% ZCUT = median-style filter to cut extremes values (in % of elements). +% Default is ZCUT = 0.5 to ignore the 0.5% of most min/max +% elevation values. Use ZCUT = 0 for full scale. +% Use OPT=[] to keep default values and define following arguments. +% +% DEM(...,CMAP) uses CMAP colormap instead of default (landcolor, if +% exists or jet). Note that defining CMAP disables the default SEACOLOR +% colormap attribution for Z<=0 elevations. +% +% DEM(...,NOVALUE) defines the values that will be replaced by NaN. This +% might be mandatory for DEM that use a value like -99999 or -32768 if +% you don't want a flat image... +% +% DEM(...,SEACOLOR) sets the colormap used for zero and negative values. +% Default is seacolor (if exists) or single color [0.7,0.9,1] (a light +% cyan) to simulate sea color. Use [] to apply colormap CMAP on the full +% elevation scale. +% +% DEM(...,'interp') interpolates linearly NaN values (fills the gaps). +% +% DEM(...,'lake') detects automaticaly flat areas different from sea +% level (non-zero elevations) and draws them as lake surfaces. +% +% DEM(...,'dec') plots classic basemap-style axis, considering +% coordinates as cartesian (decimal). +% +% DEM(...,'dms') plots geographic basemap-style axis in deg/min/sec, +% considering coordinates X as longitude and Y as latitude. Axis aspect +% ratio will be adjusted to approximatively preserve distances (this is +% not a real projection!). +% +% DEM(...,'scale') adds a legend to the right of graph, with elevation +% scale (colormap) and a distance scale if 'dms' option is used. +% +% [H,I]=DEM(...) returns graphic handle H and illuminated image as I, an +% MxNx3 matrix (if Z is MxN). +% +% Informations: +% - For optimization purpose, DEM will automatically decimate data to +% limit to a total of 1500x1500 pixels images. To avoid it, use option +% DEM(...,'nodecim') or DEM(...,'decim',N) where N is an integer, but +% be aware that large grids may require computer ressources and induce +% disk swap or memory errors. +% - Colormaps are Mx3 RGB matrix so it is easy to modify saturation +% (CMAP.^N), set darker (CMAP/N), lighter ((N - 1 + CMAP)/N), inverse +% it (flipud(CMAP)), etc... +% - To get free worldwide topographic data (SRTM), see READHGT function. +% +% Author: François Beauducel +% Created: 2007-05-17 +% Updated: 2013-01-05 + +% Copyright (c) 2013, François Beauducel, covered by BSD License. +% All rights reserved. +% +% Redistribution and use in source and binary forms, with or without +% modification, are permitted provided that the following conditions are +% met: +% +% * Redistributions of source code must retain the above copyright +% notice, this list of conditions and the following disclaimer. +% * Redistributions in binary form must reproduce the above copyright +% notice, this list of conditions and the following disclaimer in +% the documentation and/or other materials provided with the distribution +% +% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +% POSSIBILITY OF SUCH DAMAGE. + +if nargin < 3 + error('Not enough input arguments.'); +end + +% default OPT arguments +a = -45; +c = 1; +scut = 0.2; +zmin = NaN; +zmax = NaN; +zcut = 0.5; +grey = 0.2*[1,1,1]; +csea = []; +fs = 10; % tick label fontsize + +dec = 0; +dms = 0; +scale = 0; +inter = 0; +lake = 0; +decimflag = 0; +decim = 0; + +novalue_color = [0,0,0]; + +if ~isnumeric(x) | ~isnumeric(y) | ~isnumeric(z) + error('X,Y and Z must be numeric.') +end + +if all(size(x) ~= 1) | all(size(y) ~= 1) + error('X and Y must be vectors, not matrix.') +end + +if length(x) ~= size(z,2) | length(y) ~= size(z,1) + error('If Z has a size of [M,N], X must have a length of N, and Y a length of M.') +end + +if nargin > 3 + dec = any(strcmp(varargin,'dec')); + dms = any(strcmp(varargin,'dms')); + if dms & any(abs(y) > 91) + error('With DMS option Y must be in valid latitudes interval (decimal degrees).') + end + scale = any(strcmp(varargin,'scale')); + inter = any(strcmp(varargin,'interp')); + lake = any(strcmp(varargin,'lake')); + if any(strcmp(varargin,'nodecim')) + decim = 1; + decimflag = 1; + end + kdecim = find(strcmp(varargin,'decim')); + if ~isempty(kdecim) + decimflag = 1; + if (kdecim + 1) <= nargin & isnumeric(varargin{kdecim+1}) + decim = round(varargin{kdecim+1}); + decimflag = 2; + end + end +end +nargs = decimflag + dec + dms + scale + lake + inter; + +if (nargin - nargs) > 3 + opt = varargin{1}; + if ~isnumeric(opt) + error('OPT = [A,C,S,ZMIN,ZMAX] argument must be numeric.'); + end + if ~isempty(opt) + a = opt(1); + end + if length(opt) > 1 + c = opt(2); + if c < 0 + error('C argument must be positive.'); + end + end + if length(opt) > 2 + scut = opt(3); + if scut < 0 | scut >= 100 + error('SCUT argument must be a positive percentage.'); + end + end + if length(opt) > 4 + zmin = opt(4); + zmax = opt(5); + end + if length(opt) > 5 + zcut = opt(6); + if zcut < 0 | zcut >= 100 + error('ZCUT argument must be a positive percentage.'); + end + end +end + +if (nargin - nargs) < 5 + cmap = []; +else + cmap = varargin{2}; + if ~isnumeric(cmap) | (~isempty(cmap) & (size(cmap,2) ~= 3 | min(cmap(:)) < 0 | max(cmap(:)) > 1)) + error('CMAP must be a valid colormap (3-column [R,G,B] matrix with 0.0 to 1.0 values).') + end +end + +if (nargin - nargs) < 6 + novalue = NaN; +else + novalue = varargin{3}; + if ~isnumeric(novalue) | numel(novalue) > 1 + error('NOVALUE must be scalar.') + end +end + +if (nargin - nargs) < 7 + if isempty(cmap) + if exist('seacolor','file') + csea = seacolor(256); + else + csea = [.7,.9,1]; + end + end +else + csea = varargin{4}; + if ~isnumeric(csea) + error('Unknown option') + elseif (~isempty(csea) & (size(csea,2) ~= 3 | min(csea) < 0 | max(csea) > 1)) + error('SEACOLOR must be a valid [R,G,B] vector with 0.0 to 1.0 values).') + end +end + +if isempty(cmap) + if exist('landcolor','file') + cmap = landcolor.^1.3; + else + cmap = jet(256); + end +end + + + +% decimates data to avoid disk swap/out of memory... +nmax = 1500; +if decim + n = decim; +else + n = ceil(sqrt(numel(z))/nmax); +end +if n > 1 + x = x(1:n:end); + y = y(1:n:end); + z = z(1:n:end,1:n:end); + fprintf('DEM: on the plot data has been decimated by a factor of %d...\n',n); +end + +z = double(z); % necessary for most of the following calculations... +z(z==novalue) = NaN; + +if inter + z = fillgap(x,y,z); +end + +if isempty(csea) + k = (z~=0 & ~isnan(z)); +else + k = ~isnan(z); +end + +if isnan(zmin) + zmin = nmedian(z(k),zcut/100); +end +if isnan(zmax) + zmax = nmedian(z(k),1 - zcut/100); +end +dz = zmax - zmin; + +if dz > 0 + % builds the colormap: concatenates seacolor and landcolor around 0 + if ~isempty(csea) & zmin < 0 & zmax > 0 + l = size(csea,1); + r = size(cmap,1)*abs(zmin)/zmax/l; + cmap = cat(1,interp1(1:l,csea,linspace(1,l,round(l*r)),'*linear'),cmap); + end + + % normalisation of Z using CMAP and convertion to RGB + I = ind2rgb(uint16((z - zmin)*(length(cmap)/dz)),cmap); + + if c > 0 + % computes lighting from elevation gradient + [fx,fy] = gradient(z,x,y); + %fx = filter([1,0,0,0,-1],1,rf(z'))'; + %fy = filter([1,0,0,0,-1],1,rf(z)); + fxy = -fx*sind(a) - fy*cosd(a); + clear fx fy % free some memory... + + % lake option: zero gradient + if lake + dx = diff(z,1,2); + dy = diff(z,1,1); + u1 = ones(size(z,1),1); + u2 = ones(1,size(z,2)); + z(cat(1,u2,dy)==0 & cat(1,dy,u2)==0 & cat(2,dx,u1)==0 & cat(2,u1,dx)==0) = 0; + clear dx dy % free some memory... + end + + fxy(isnan(fxy)) = 0; + + % computes maximum absolute gradient (median-style), normalizes, saturates and duplicates in 3-D matrix + r = repmat(max(min(fxy/nmedian(abs(fxy),1 - scut/100),1),-1),[1,1,3]); + + % applies contrast using exponent + rp = (1 - abs(r)).^c; + I = I.*rp; + + % lighter for positive gradient + k = find(r > 0); + I(k) = I(k) + (1 - rp(k)); + + end + + % set novalues / NaN to black color + [i,j] = find(isnan(z)); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(novalue_color,size(i,1),1); + end + % set the seacolor for 0 values + if ~isempty(csea) + [i,j] = find(z==0); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(csea(end,:),size(i,1),1); + end + end + + hh = imagesc(x,y,I); +else + hh = imagesc(x,y,z); + colormap(cmap); + text(mean(x),mean(y),'SPLASH!','Color','c','FontWeight','bold','HorizontalAlignment','center') +end + +orient tall +axis xy, axis equal, axis tight + +xlim = [min(x),max(x)]; +ylim = [min(y),max(y)]; +zlim = [min(z(:)),max(z(:))]; + +% axis basemap style +if dec | dms + axis off + + if dms + % approximates X-Y aspect ratio for this latitude (< 20-m precision for 1x1° grid) + xyr = cos(mean(y)*pi/180); + else + xyr = 1; + end + set(gca,'DataAspectRatio',[1,xyr,1]) + bwy = 0.008*diff(ylim); % Y border width = 1% + bwx = bwy/xyr; % border width (in degree of longitude) + + % transparent borders + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(1) - bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(2) + bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch(xlim(1) - bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + patch(xlim(2) + bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + + dlon = {'E','W'}; + dlat = {'N','S'}; + + if dec + ddx = dtick(diff(xlim)); + ddy = dtick(diff(ylim)); + else + ddx = dtick(diff(xlim),1); + ddy = dtick(diff(ylim),1); + end + + xtick = (ddx*ceil(xlim(1)/ddx)):ddx:xlim(2); + for xt = xtick(1:2:end) + dt = ddx - max(0,xt + ddx - xlim(2)); + patch(repmat(xt + dt*[0,1,1,0]',[1,2]),[ylim(1) - bwy*[0,0,1,1];ylim(2) + bwy*[0,0,1,1]]','k','clipping','off') + text(xt,ylim(1) - bwy,deg2dms(xt,dlon,dec),'FontSize',fs,'HorizontalAlignment','center','VerticalAlignment','top'); + end + + ytick = (ddy*ceil(ylim(1)/ddy)):ddy:ylim(2); + for yt = ytick(1:2:end) + dt = ddy - max(0,yt + ddy - ylim(2)); + patch([xlim(1) - bwx*[0,0,1,1];xlim(2) + bwx*[0,0,1,1]]',repmat(yt + dt*[0,1,1,0]',[1,2]),'k','clipping','off') + text(xlim(1) - 1.1*bwx,yt,deg2dms(yt,dlat,dec),'FontSize',fs,'HorizontalAlignment','right','VerticalAlignment','middle'); + end +end + +% scale legend +if scale + %wsc = diff(xlim)*0.01; + wsc = bwx; + xsc = xlim(2) + wsc*4; + + % elevation scale (colorbar) + zscale = linspace(zlim(1),zlim(2),length(cmap)); + yscale = linspace(0,diff(ylim)/2,length(cmap)); + ysc = ylim(1); + ddz = dtick(dz*max(0.5*xyr*diff(xlim)/yscale(end),1)); + ztick = (ddz*ceil(zlim(1)/ddz)):ddz:zlim(2); + patch(xsc + repmat(wsc*[-1;1;1;-1],[1,length(cmap)]), ... + ysc + [repmat(yscale,[2,1]);repmat(yscale + diff(yscale(1:2)),[2,1])], ... + repmat(zscale,[4,1]), ... + 'EdgeColor','flat','LineWidth',.1,'FaceColor','flat','clipping','off') + colormap(cmap) + caxis([zmin,zmax]) + patch(xsc + wsc*[-1,1,1,-1],ysc + yscale(end)*[0,0,1,1],'k','FaceColor','none','Clipping','off') + text(xsc + 2*wsc + zeros(size(ztick)),ysc + (ztick - zlim(1))*0.5*diff(ylim)/diff(zlim),num2str(ztick'), ... + 'HorizontalAlignment','left','VerticalAlignment','middle','FontSize',8) + + % distance scale (in case of DMS only) + if dms + degkm = 6370*pi/180; + dkm = dtick(diff(ylim)*degkm); + ysc = ylim(2) - 0.5*dkm/degkm; + patch(xsc + wsc*[-1,-1,0,0],ysc + dkm*0.5*[-1,1,1,-1]/degkm,'k','FaceColor',grey,'clipping','off') + if dkm > 1 + skm = sprintf('%g km',dkm); + else + skm = sprintf('%g m',dkm*1000); + end + text(xsc,ysc,skm,'rotation',-90,'HorizontalAlignment','center','VerticalAlignment','bottom', ... + 'Color',grey,'FontWeight','bold') + end + +end + + +if nargout > 0 + h = hh; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function y = nmedian(x,n) +%NMEDIAN Generalized median filter +% NMEDIAN(X,N) sorts elemets of X and returns N-th value (N normalized). +% So: +% N = 0 is minimum value +% N = 0.5 is median value +% N = 1 is maximum value + +if nargin < 2 + n = 0.5; +end +y = sort(x(:)); +y = interp1(sort(y),n*(length(y)-1) + 1); + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function dd = dtick(dlim,deg) +%DTICK Tick intervals + +if nargin < 2 + deg = 0; +end + +if deg & dlim <= 2/60 + % less than 2 minutes: base 36 + m = 10^floor(log10(dlim*36))/36; +elseif deg & dlim <= 2 + % less than 2 degrees: base 6 + m = 10^floor(log10(dlim*6))/6; +else + % more than few degrees or not degrees: decimal rules + m = 10^floor(log10(dlim)); +end +p = ceil(dlim/m); +if p <= 1 + dd = .1*m; +elseif p == 2 + dd = .2*m; +elseif p <= 5 + dd = .5*m; +else + dd = m; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = deg2dms(x,ll,dec) +%DEG2DMS Degree/minute/second display + +if dec + s = sprintf('%7.7g',x); +else + xa = abs(x) + 1/360000; + sd = sprintf('%d%c',floor(xa),176); % ASCII char 176 is the degree sign + sm = ''; + ss = ''; + if mod(x,1) + sm = sprintf('%02d''',floor(mod(60*xa,60))); + sa = floor(mod(3600*xa,60)); + if sa + ss = sprintf('%02d"',sa); + else + if strcmp(sm,'00''') + sm = ''; + end + end + end + s = [sd,sm,ss,ll{1+int8(x<0)}]; +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function z = fillgap(x,y,z) +% GRIDDATA is not efficient for large arrays, but has great advantage to be +% included in Matlab core functions! To optimize interpolation, we +% reduce the number of relevant data by building a mask of surrounding +% pixels of novalue areas... playing with linear index! + +sz = size(z); +k = find(isnan(z)); +k(k == 1 | k == numel(z)) = []; % removes first and last index (if exist) +if ~isempty(k) + [xx,yy] = meshgrid(x,y); + mask = zeros(sz,'int8'); + k2 = ind90(sz,k); % k2 is linear index in the row order + % sets to 1 every previous and next index, both in column and row order + mask([k-1;k+1;ind90(fliplr(sz),[k2-1;k2+1])]) = 1; + mask(k) = 0; % removes the novalue index + kb = find(mask); % keeps only border values + z(k) = griddata(xx(kb),yy(kb),z(kb),xx(k),yy(k)); +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function k2 = ind90(sz,k) + +[i,j] = ind2sub(sz,k); +k2 = sub2ind(fliplr(sz),j,i); % switched i and j: k2 is linear index in row order Index: /issm/trunk/externalpackages/dem/landcolor.m =================================================================== --- /issm/trunk/externalpackages/dem/landcolor.m (revision 14310) +++ /issm/trunk/externalpackages/dem/landcolor.m (revision 14310) @@ -0,0 +1,78 @@ +function y = landcolor(n) +%LANDCOLOR Land colormap +% +% Author: Francois Beauducel +% $Revision: 1.0.0 $ $Date: 2012/05/17 11:22:44 $ + +J = [ ... +0.095678 0.53427 0.21682 +0.15785 0.5979 0.23274 +0.21286 0.64673 0.2514 +0.26411 0.68789 0.27268 +0.32959 0.72416 0.31308 +0.39794 0.75695 0.36038 +0.46153 0.7871 0.40624 +0.52108 0.81516 0.45135 +0.57702 0.84152 0.49547 +0.62973 0.86645 0.53891 +0.67946 0.89016 0.58187 +0.72647 0.91282 0.62427 +0.77095 0.93455 0.66619 +0.81306 0.95546 0.70772 +0.85292 0.97563 0.7489 +0.89066 0.99514 0.78976 +0.88379 0.98595 0.77038 +0.86389 0.96758 0.73236 +0.84615 0.94972 0.69623 +0.8303 0.93233 0.66186 +0.81612 0.91536 0.6291 +0.80341 0.8988 0.59784 +0.79201 0.8826 0.56795 +0.78191 0.86676 0.53946 +0.7729 0.85123 0.51224 +0.76479 0.83602 0.48615 +0.75747 0.8211 0.46111 +0.75084 0.80645 0.43704 +0.74506 0.79206 0.41414 +0.73981 0.77792 0.39211 +0.73501 0.76401 0.37089 +0.73068 0.75033 0.35052 +0.72683 0.73685 0.33106 +0.72042 0.72074 0.31228 +0.71032 0.70085 0.29417 +0.69761 0.67821 0.27694 +0.68489 0.65558 0.26026 +0.67235 0.63313 0.24418 +0.65997 0.61082 0.22889 +0.64775 0.58874 0.21406 +0.63568 0.56689 0.19983 +0.62376 0.54527 0.18622 +0.61197 0.52391 0.17299 +0.60033 0.50283 0.16046 +0.58881 0.48203 0.14832 +0.57742 0.46151 0.13667 +0.56616 0.44133 0.12555 +0.55502 0.4214 0.11472 +0.54398 0.4019 0.10456 +0.53306 0.38266 0.094633 +0.52226 0.36382 0.085242 +0.51155 0.3453 0.076179 +0.50095 0.32714 0.067515 +0.49045 0.30938 0.059259 +0.48005 0.29193 0.051294 +0.46973 0.27495 0.043796 +0.45951 0.25823 0.0365 +0.44938 0.24206 0.029715 +0.43934 0.22609 0.023063 +0.42938 0.21074 0.016949 +0.41951 0.19556 0.010917 +0.40971 0.18105 0.0054326 +0.4 0.16667 0 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/trunk/externalpackages/dem/license.txt =================================================================== --- /issm/trunk/externalpackages/dem/license.txt (revision 14310) +++ /issm/trunk/externalpackages/dem/license.txt (revision 14310) @@ -0,0 +1,24 @@ +Copyright (c) 2013, François Beauducel +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk/externalpackages/dem/seacolor.m =================================================================== --- /issm/trunk/externalpackages/dem/seacolor.m (revision 14310) +++ /issm/trunk/externalpackages/dem/seacolor.m (revision 14310) @@ -0,0 +1,58 @@ +function y = seacolor(n) +%SEACOLOR Sea colormap adapted from NGDC ETOPO1 +% +% Author: Francois Beauducel + +J = [ ... + 0.0392 0 0.4745 + 0.1020 0 0.5373 + 0.1020 0 0.5373 + 0.1490 0 0.5961 + 0.1490 0 0.5961 + 0.1059 0.0118 0.6510 + 0.1059 0.0118 0.6510 + 0.0627 0.0235 0.7059 + 0.0627 0.0235 0.7059 + 0.0196 0.0353 0.7569 + 0.0196 0.0353 0.7569 + 0 0.0549 0.7961 + 0 0.0549 0.7961 + 0 0.0863 0.8235 + 0 0.0863 0.8235 + 0 0.1176 0.8471 + 0 0.1176 0.8471 + 0 0.1529 0.8745 + 0 0.1529 0.8745 + 0.0471 0.2667 0.9059 + 0.0471 0.2667 0.9059 + 0.1020 0.4000 0.9412 + 0.1020 0.4000 0.9412 + 0.0745 0.4588 0.9569 + 0.0745 0.4588 0.9569 + 0.0549 0.5216 0.9765 + 0.0549 0.5216 0.9765 + 0.0824 0.6196 0.9882 + 0.0824 0.6196 0.9882 + 0.1176 0.6980 1.0000 + 0.1176 0.6980 1.0000 + 0.1686 0.7294 1.0000 + 0.1686 0.7294 1.0000 + 0.2157 0.7569 1.0000 + 0.2157 0.7569 1.0000 + 0.2549 0.7843 1.0000 + 0.2549 0.7843 1.0000 + 0.3098 0.8235 1.0000 + 0.3098 0.8235 1.0000 + 0.3686 0.8745 1.0000 + 0.3686 0.8745 1.0000 + 0.5412 0.8902 1.0000 + 0.5412 0.8902 1.0000 + 0.7373 0.9020 1.0000 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/trunk/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/trunk/externalpackages/export_fig/export_fig.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/export_fig.m (revision 14310) @@ -123,6 +123,6 @@ % -bookmark - option to indicate that a bookmark with the name of the % figure is to be created in the output file (pdf only). -% handle - The handle of the figure or axes (can be an array of handles -% of several axes, but these must be in the same figure) to be +% handle - The handle of the figure, axes or uipanels (can be an array of +% handles, but the objects must be in the same figure) to be % saved. Default: gcf. % @@ -166,17 +166,24 @@ % 09/05/12: Incorporate patch of Arcelia Arrieta (many thanks), to keep % tick marks fixed. - -function [im alpha] = export_fig(varargin) +% 12/12/12: Add support for isolating uipanels. Thanks to michael for +% suggesting it. + +function [im, alpha] = export_fig(varargin) % Make sure the figure is rendered correctly _now_ so that properties like % axes limits are up-to-date. drawnow; % Parse the input arguments -[fig options] = parse_args(nargout, varargin{:}); +[fig, options] = parse_args(nargout, varargin{:}); % Isolate the subplot, if it is one -cls = strcmp(get(fig(1), 'Type'), 'axes'); +cls = all(ismember(get(fig, 'Type'), {'axes', 'uipanel'})); if cls % Given handles of one or more axes, so isolate them from the rest fig = isolate_axes(fig); else + % Check we have a figure + if ~isequal(get(fig, 'Type'), 'figure'); + error('Handle must be that of a figure, axes or uipanel'); + end + % Get the old InvertHardcopy mode old_mode = get(fig, 'InvertHardcopy'); end @@ -198,5 +205,5 @@ end end -% MATLAB "feature": axes limits can change when printing +% MATLAB "feature": axes limits and tick marks can change when printing Hlims = findall(fig, 'Type', 'axes'); if ~cls @@ -282,5 +289,5 @@ % Crop the background if options.crop - [alpha v] = crop_background(alpha, 0); + [alpha, v] = crop_background(alpha, 0); A = A(v(1):v(2),v(3):v(4),:); end @@ -289,5 +296,5 @@ res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3; % Save the png - imwrite(A, [options.name '.png'], 'Alpha', alpha, 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); + imwrite(A, [options.name '.png'], 'Alpha', double(alpha), 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); % Clear the png bit options.png = false; @@ -325,5 +332,5 @@ tcol = 255; else - [A tcol] = print2array(fig, magnify, renderer); + [A, tcol] = print2array(fig, magnify, renderer); end % Crop the background @@ -460,5 +467,5 @@ return -function [fig options] = parse_args(nout, varargin) +function [fig, options] = parse_args(nout, varargin) % Parse the input arguments % Set the defaults @@ -542,5 +549,5 @@ end else - [p options.name ext] = fileparts(varargin{a}); + [p, options.name, ext] = fileparts(varargin{a}); if ~isempty(p) options.name = [p filesep options.name]; @@ -577,5 +584,5 @@ % Check whether transparent background is wanted (old way) -if isequal(get(fig, 'Color'), 'none') +if isequal(get(ancestor(fig, 'figure'), 'Color'), 'none') options.transparent = true; end @@ -667,7 +674,7 @@ return -function [A v] = crop_background(A, bcol) +function [A, v] = crop_background(A, bcol) % Map the foreground pixels -[h w c] = size(A); +[h, w, c] = size(A); if isscalar(bcol) && c > 1 bcol = bcol(ones(1, c)); Index: /issm/trunk/externalpackages/export_fig/ghostscript.m =================================================================== --- /issm/trunk/externalpackages/export_fig/ghostscript.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/ghostscript.m (revision 14310) @@ -1,3 +1,2 @@ -function varargout = ghostscript(cmd) %GHOSTSCRIPT Calls a local GhostScript executable with the input command % @@ -25,35 +24,35 @@ % Thanks to Jonas Dorn for the fix for the title of the uigetdir window on % Mac OS. - % Thanks to Nathan Childress for the fix to the default location on 64-bit % Windows systems. - % 27/4/11 - Find 64-bit Ghostscript on Windows. Thanks to Paul Durack and % Shaun Kline for pointing out the issue - % 4/5/11 - Thanks to David Chorlian for pointing out an alternative % location for gs on linux. +% 12/12/12 - Add extra executable name on Windows. Thanks to Ratish +% Punnoose for highlighting the issue. +function varargout = ghostscript(cmd) % Call ghostscript [varargout{1:nargout}] = system(sprintf('"%s" %s', gs_path, cmd)); return -function path = gs_path +function path_ = gs_path % Return a valid path % Start with the currently set path -path = user_string('ghostscript'); +path_ = user_string('ghostscript'); % Check the path works -if check_gs_path(path) +if check_gs_path(path_) return end % Check whether the binary is on the path if ispc - bin = {'gswin32c.exe', 'gswin64c.exe'}; + bin = {'gswin32c.exe', 'gswin64c.exe', 'gs'}; else bin = {'gs'}; end for a = 1:numel(bin) - path = bin{a}; - if check_store_gs_path(path) + path_ = bin{a}; + if check_store_gs_path(path_) return end @@ -76,5 +75,5 @@ path2 = [default_location dir_list(a).name executable{b}]; if exist(path2, 'file') == 2 - path = path2; + path_ = path2; ver_num = ver_num2; end @@ -82,5 +81,5 @@ end end - if check_store_gs_path(path) + if check_store_gs_path(path_) return end @@ -88,6 +87,6 @@ bin = {'/usr/bin/gs', '/usr/local/bin/gs'}; for a = 1:numel(bin) - path = bin{a}; - if check_store_gs_path(path) + path_ = bin{a}; + if check_store_gs_path(path_) return end @@ -110,7 +109,7 @@ for a = 1:numel(bin_dir) for b = 1:numel(bin) - path = [base bin_dir{a} bin{b}]; - if exist(path, 'file') == 2 - if check_store_gs_path(path) + path_ = [base bin_dir{a} bin{b}]; + if exist(path_, 'file') == 2 + if check_store_gs_path(path_) return end @@ -121,12 +120,12 @@ error('Ghostscript not found. Have you installed it from www.ghostscript.com?'); -function good = check_store_gs_path(path) +function good = check_store_gs_path(path_) % Check the path is valid -good = check_gs_path(path); +good = check_gs_path(path_); if ~good return end % Update the current default path to the path found -if ~user_string('ghostscript', path) +if ~user_string('ghostscript', path_) warning('Path to ghostscript installation could not be saved. Enter it manually in ghostscript.txt.'); return @@ -134,7 +133,7 @@ return -function good = check_gs_path(path) +function good = check_gs_path(path_) % Check the path is valid -[good message] = system(sprintf('"%s" -h', path)); +[good, message] = system(sprintf('"%s" -h', path_)); good = good == 0; return Index: /issm/trunk/externalpackages/export_fig/isolate_axes.m =================================================================== --- /issm/trunk/externalpackages/export_fig/isolate_axes.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/isolate_axes.m (revision 14310) @@ -5,11 +5,12 @@ % fh = isolate_axes(ah, vis) % -% This function will create a new figure containing the axes specified, and -% also their associated legends and colorbars. The axes specified must all -% be in the same figure, but they will generally only be a subset of the -% axes in the figure. +% This function will create a new figure containing the axes/uipanels +% specified, and also their associated legends and colorbars. The objects +% specified must all be in the same figure, but they will generally only be +% a subset of the objects in the figure. % % IN: -% ah - An array of axes handles, which must come from the same figure. +% ah - An array of axes and uipanel handles, which must come from the +% same figure. % vis - A boolean indicating whether the new figure should be visible. % Default: false. @@ -23,4 +24,6 @@ % 16/3/2012 Moved copyfig to its own function. Thanks to Bob Fratantonio % for pointing out that the function is also used in export_fig.m. +% 12/12/12 - Add support for isolating uipanels. Thanks to michael for +% suggesting it. function fh = isolate_axes(ah, vis) @@ -29,10 +32,10 @@ error('ah must be an array of handles'); end -% Check that the handles are all for axes, and are all in the same figure +% Check that the handles are all for axes or uipanels, and are all in the same figure fh = ancestor(ah(1), 'figure'); nAx = numel(ah); for a = 1:nAx - if ~strcmp(get(ah(a), 'Type'), 'axes') - error('All handles must be axes handles.'); + if ~ismember(get(ah(a), 'Type'), {'axes', 'uipanel'}) + error('All handles must be axes or uipanel handles.'); end if ~isequal(ancestor(ah(a), 'figure'), fh) @@ -40,5 +43,5 @@ end end -% Tag the axes so we can find them in the copy +% Tag the objects so we can find them in the copy old_tag = get(ah, 'Tag'); if nAx == 1 @@ -51,5 +54,5 @@ set(fh, 'Visible', 'off'); end -% Reset the axes tags +% Reset the object tags for a = 1:nAx set(ah(a), 'Tag', old_tag{a}); @@ -59,5 +62,5 @@ if numel(ah) ~= nAx close(fh); - error('Incorrect number of axes found.'); + error('Incorrect number of objects found.'); end % Set the axes tags to what they should be @@ -87,5 +90,5 @@ % Get all the objects in the figure axs = findall(fh); -% Delete everything except for the input axes and associated items +% Delete everything except for the input objects and associated items delete(axs(~ismember(axs, [ah; allchildren(ah); allancestors(ah)]))); return Index: /issm/trunk/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/trunk/externalpackages/export_fig/pdftops.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/pdftops.m (revision 14310) @@ -33,10 +33,10 @@ return -function path = xpdf_path +function path_ = xpdf_path % Return a valid path % Start with the currently set path -path = user_string('pdftops'); +path_ = user_string('pdftops'); % Check the path works -if check_xpdf_path(path) +if check_xpdf_path(path_) return end @@ -48,14 +48,14 @@ end if check_store_xpdf_path(bin) - path = bin; + path_ = bin; return end % Search the obvious places if ispc - path = 'C:\Program Files\xpdf\pdftops.exe'; + path_ = 'C:\Program Files\xpdf\pdftops.exe'; else - path = '/usr/local/bin/pdftops'; + path_ = '/usr/local/bin/pdftops'; end -if check_store_xpdf_path(path) +if check_store_xpdf_path(path_) return end @@ -75,10 +75,10 @@ bin_dir = {'', ['bin' filesep], ['lib' filesep]}; for a = 1:numel(bin_dir) - path = [base bin_dir{a} bin]; - if exist(path, 'file') == 2 + path_ = [base bin_dir{a} bin]; + if exist(path_, 'file') == 2 break; end end - if check_store_xpdf_path(path) + if check_store_xpdf_path(path_) return end @@ -86,12 +86,12 @@ error('pdftops executable not found.'); -function good = check_store_xpdf_path(path) +function good = check_store_xpdf_path(path_) % Check the path is valid -good = check_xpdf_path(path); +good = check_xpdf_path(path_); if ~good return end % Update the current default path to the path found -if ~user_string('pdftops', path) +if ~user_string('pdftops', path_) warning('Path to pdftops executable could not be saved. Enter it manually in pdftops.txt.'); return @@ -99,7 +99,7 @@ return -function good = check_xpdf_path(path) +function good = check_xpdf_path(path_) % Check the path is valid -[good message] = system(sprintf('"%s" -h', path)); +[good message] = system(sprintf('"%s" -h', path_)); % system returns good = 1 even when the command runs % Look for something distinct in the help text Index: /issm/trunk/externalpackages/export_fig/print2array.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2array.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/print2array.m (revision 14310) @@ -25,25 +25,24 @@ % bcol - 1x3 uint8 vector of the background color -% Copyright (C) Oliver Woodford 2008-2011 +% Copyright (C) Oliver Woodford 2008-2012 -% 5/9/2011 Set EraseModes to normal when using opengl or zbuffer renderers. -% Thanks to Pawel Kocieniewski for reporting the issue. +% 05/09/11: Set EraseModes to normal when using opengl or zbuffer +% renderers. Thanks to Pawel Kocieniewski for reporting the +% issue. +% 21/09/11: Bug fix: unit8 -> uint8! Thanks to Tobias Lamour for reporting +% the issue. +% 14/11/11: Bug fix: stop using hardcopy(), as it interfered with figure +% size and erasemode settings. Makes it a bit slower, but more +% reliable. Thanks to Phil Trinh and Meelis Lootus for reporting +% the issues. +% 09/12/11: Pass font path to ghostscript. +% 27/01/12: Bug fix affecting painters rendering tall figures. Thanks to +% Ken Campbell for reporting it. +% 03/04/12: Bug fix to median input. Thanks to Andy Matthews for reporting +% it. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. -% 21/9/2011 Bug fix: unit8 -> uint8! -% Thanks to Tobias Lamour for reporting the issue. - -% 14/11/2011 Bug fix: stop using hardcopy(), as it interfered with figure -% size and erasemode settings. Makes it a bit slower, but more reliable. -% Thanks to Phil Trinh and Meelis Lootus for reporting the issues. - -% 9/12/2011 Pass font path to ghostscript. - -% 27/1/2012 Bug fix affecting painters rendering tall figures. Thanks to -% Ken Campbell for reporting it. - -% 3/4/2012 Bug fix to median input. Thanks to Andy Matthews for reporting -% it. - -function [A bcol] = print2array(fig, res, renderer) +function [A, bcol] = print2array(fig, res, renderer) % Generate default input arguments, if needed if nargin < 2 @@ -85,8 +84,8 @@ % Execute the ghostscript command ghostscript(cmd_str); - catch + catch me % Delete the intermediate file delete(tmp_eps); - rethrow(lasterror); + rethrow(me); end % Delete the intermediate file @@ -134,6 +133,7 @@ err = false; % Set paper size - old_mode = get(fig, 'PaperPositionMode'); - set(fig, 'PaperPositionMode', 'auto'); + old_pos_mode = get(fig, 'PaperPositionMode'); + old_orientation = get(fig, 'PaperOrientation'); + set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); try % Print to tiff file @@ -147,5 +147,5 @@ end % Reset paper size - set(fig, 'PaperPositionMode', old_mode); + set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); % Throw any error that occurred if err Index: /issm/trunk/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2eps.m (revision 14309) +++ /issm/trunk/externalpackages/export_fig/print2eps.m (revision 14310) @@ -28,22 +28,24 @@ % fex id: 5743, but the implementation is mine :) -% 14/11/2011 Fix a MATLAB bug rendering black or white text incorrectly. -% Thanks to Mathieu Morlighem for reporting the issue and obtaining a fix -% from TMW. - -% 8/12/2011 Added ability to correct fonts. Several people have requested -% this at one time or another, and also pointed me to printeps (fex id: -% 7501), so thank you to them. My implementation (which was not inspired by -% printeps - I'd already had the idea for my approach) goes -% slightly further in that it allows multiple fonts to be swapped. - -% 14/12/2011 Fix bug affecting font names containing spaces. Many thanks to -% David Szwer for reporting the issue. - -% 25/1/2012 Add a font not to be swapped. Thanks to Anna Rafferty and Adam -% Jackson for reporting the issue. Also fix a bug whereby using a font -% alias can lead to another font being swapped in. - -% 10/4/2012 Make the font swapping case insensitive. +% 14/11/2011: Fix a MATLAB bug rendering black or white text incorrectly. +% Thanks to Mathieu Morlighem for reporting the issue and +% obtaining a fix from TMW. +% 08/12/11: Added ability to correct fonts. Several people have requested +% this at one time or another, and also pointed me to printeps +% (fex id: 7501), so thank you to them. My implementation (which +% was not inspired by printeps - I'd already had the idea for my +% approach) goes slightly further in that it allows multiple +% fonts to be swapped. +% 14/12/11: Fix bug affecting font names containing spaces. Thanks to David +% Szwer for reporting the issue. +% 25/01/12: Add a font not to be swapped. Thanks to Anna Rafferty and Adam +% Jackson for reporting the issue. Also fix a bug whereby using a +% font alias can lead to another font being swapped in. +% 10/04/12: Make the font swapping case insensitive. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. +% 26/10/12: Fix issue to do with swapping fonts changing other fonts and +% sizes we don't want, due to listeners. Thanks to Malcolm Hudson +% for reporting the issue. function print2eps(name, fig, varargin) @@ -59,5 +61,5 @@ end % Find all the used fonts in the figure -font_handles = findall(fig, '-property', 'FontName'); +font_handles = findobj(fig, '-property', 'FontName'); fonts = get(font_handles, 'FontName'); if ~iscell(fonts) @@ -86,19 +88,44 @@ require_swap = find(~ismember(fontslu, matlab_fontsl)); unused_fonts = find(~ismember(matlab_fontsl, fontslu)); -font_swap = cell(3, 0); -for a = 1:min(numel(require_swap), numel(unused_fonts)) - ind = find(strcmp(fontslu{require_swap(a)}, fontsl)); - n = numel(ind); - font_swap(1,end+1:end+n) = reshape(mat2cell(font_handles(ind), ones(n, 1)), 1, []); - font_swap(2,end-n+1:end) = matlab_fonts(unused_fonts(a)); - font_swap(3,end-n+1:end) = reshape(fonts(ind), 1, []); +font_swap = cell(3, min(numel(require_swap), numel(unused_fonts))); +fonts_new = fonts; +for a = 1:size(font_swap, 2) + font_swap{1,a} = find(strcmp(fontslu{require_swap(a)}, fontsl)); + font_swap{2,a} = matlab_fonts{unused_fonts(a)}; + font_swap{3,a} = fonts{font_swap{1,end}(1)}; + fonts_new(font_swap{1,a}) = {font_swap{2,a}}; end % Swap the fonts -for a = 1:size(font_swap, 2) - set(font_swap{1,a}, 'FontName', font_swap{2,a}); +if ~isempty(font_swap) + fonts_size = get(font_handles, 'FontSize'); + if iscell(fonts_size) + fonts_size = cell2mat(fonts_size); + end + M = false(size(font_handles)); + % Loop because some changes may not stick first time, due to listeners + c = 0; + update = zeros(1000, 1); + for b = 1:10 % Limit number of loops to avoid infinite loop case + for a = 1:numel(M) + M(a) = ~isequal(get(font_handles(a), 'FontName'), fonts_new{a}) || ~isequal(get(font_handles(a), 'FontSize'), fonts_size(a)); + if M(a) + set(font_handles(a), 'FontName', fonts_new{a}, 'FontSize', fonts_size(a)); + c = c + 1; + update(c) = a; + end + end + if ~any(M) + break; + end + end + % Compute the order to revert fonts later, without the need of a loop + [update, M] = unique(update(1:c)); + [M, M] = sort(M); + update = reshape(update(M), 1, []); end % Set paper size -old_mode = get(fig, 'PaperPositionMode'); -set(fig, 'PaperPositionMode', 'auto'); +old_pos_mode = get(fig, 'PaperPositionMode'); +old_orientation = get(fig, 'PaperOrientation'); +set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); % MATLAB bug fix - black and white text can come out inverted sometimes % Find the white and black text @@ -120,10 +147,10 @@ set(white_text_handles, 'Color', [1 1 1]); % Reset paper size -set(fig, 'PaperPositionMode', old_mode); +set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); % Correct the fonts if ~isempty(font_swap) % Reset the font names in the figure - for a = 1:size(font_swap, 2) - set(font_swap{1,a}, 'FontName', font_swap{3,a}); + for a = update + set(font_handles(a), 'FontName', fonts{a}, 'FontSize', fonts_size(a)); end % Replace the font names in the eps file Index: sm/trunk/externalpackages/gdal/GDALmake.opt.patch =================================================================== --- /issm/trunk/externalpackages/gdal/GDALmake.opt.patch (revision 14309) +++ (revision ) @@ -1,8 +1,0 @@ -31c31 -< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ ---- -> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ -225c225 -< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz ---- -> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: sm/trunk/externalpackages/gdal/GDALmake.opt.patch.astrid =================================================================== --- /issm/trunk/externalpackages/gdal/GDALmake.opt.patch.astrid (revision 14309) +++ (revision ) @@ -1,8 +1,0 @@ -31c31 -< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ ---- -> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ -225c225 -< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz ---- -> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.astrid =================================================================== --- /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.astrid (revision 14310) +++ /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.astrid (revision 14310) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.murdo =================================================================== --- /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 14310) +++ /issm/trunk/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 14310) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/trunk/externalpackages/gdal/install-1.6-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.6-linux64-astrid.sh (revision 14310) +++ /issm/trunk/externalpackages/gdal/install-1.6-linux64-astrid.sh (revision 14310) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no \ + --with-expat-lib=/usr/lib64/libexpat.so + +#Patch GDALmake.opt +patch GDALmake.opt ../configs/GDALmake.opt.patch.astrid + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-1.6-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 14310) +++ /issm/trunk/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 14310) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no + +#Patch GDALmake.opt +patch GDALmake.opt ../configs/GDALmake.opt.patch + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-1.6-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.6-macosx64.sh (revision 14310) +++ /issm/trunk/externalpackages/gdal/install-1.6-macosx64.sh (revision 14310) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no \ + --with-expat-lib=/usr/lib64/libexpat.so + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-1.9-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.9-linux64.sh (revision 14310) +++ /issm/trunk/externalpackages/gdal/install-1.9-linux64.sh (revision 14310) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#WARNING: you need to have python installed in externalpackages + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.9.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.9.2.tar.gz' 'gdal-1.9.2.tar.gz' + +#Untar +tar -zxvf gdal-1.9.2.tar.gz + +#Move gdal into src directory +mv gdal-1.9.2/* src +rm -rf gdal-1.9.2 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --with-python \ + --with-netcdf=no \ + --with-jasper=no \ + --without-hdf5 + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install-1.9-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-1.9-macosx64.sh (revision 14310) +++ /issm/trunk/externalpackages/gdal/install-1.9-macosx64.sh (revision 14310) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.9.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.9.2.tar.gz' 'gdal-1.9.2.tar.gz' + +#Untar +tar -zxvf gdal-1.9.2.tar.gz + +#Move gdal into src directory +mv gdal-1.9.2/* src +rm -rf gdal-1.9.2 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --with-python \ + --with-netcdf=no \ + --without-hdf5 + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/gdal/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-linux64-astrid.sh (revision 14309) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.6.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' - -#Untar -tar -zxvf gdal-1.6.0.tar.gz - -#Move gdal into src directory -mv gdal-1.6.0/* src -rm -rf gdal-1.6.0 - -#Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --without-python \ - --without-png \ - --with-netcdf=no \ - --with-jasper=no \ - --without-ld-shared \ - --with-unix-stdio-64=no \ - --with-expat-lib=/usr/lib64/libexpat.so - -#Patch GDALmake.opt -patch GDALmake.opt ../GDALmake.opt.patch.astrid - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gdal/install-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-linux64-murdo.sh (revision 14309) +++ (revision ) @@ -1,39 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.6.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' - -#Untar -tar -zxvf gdal-1.6.0.tar.gz - -#Move gdal into src directory -mv gdal-1.6.0/* src -rm -rf gdal-1.6.0 - -#Configure gdal -cd src -./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --without-python \ - --without-png \ - --with-netcdf=no \ - --with-jasper=no \ - --without-ld-shared \ - --with-unix-stdio-64=no - -#Patch GDALmake.opt -patch GDALmake.opt ../GDALmake.opt.patch - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk/externalpackages/gdal/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-macosx64.sh (revision 14309) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src -rm -rf install -rm -rf gdal-1.6.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' - -#Untar -tar -zxvf gdal-1.6.0.tar.gz - -#Move gdal into src directory -mv gdal-1.6.0/* src -rm -rf gdal-1.6.0 - -#Configure gdal -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/gdal/install" \ - --without-python \ - --without-png \ - --with-netcdf=no \ - --with-jasper=no \ - --without-ld-shared \ - --with-unix-stdio-64=no \ - --with-expat-lib=/usr/lib64/libexpat.so - -#Compile and install gdal -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/gsl/install-android.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-android.sh (revision 14309) +++ /issm/trunk/externalpackages/gsl/install-android.sh (revision 14310) @@ -28,11 +28,10 @@ patch Makefile.am < Makefile.am.patch - autoreconf -iv --force -I $ISSM_DIR/externalpackages/autotools/install/share/aclocal + autoreconf -i ./configure \ --build="i386-apple-darwin10.8.0" \ --host=$host_triplet \ - --prefix="$ISSM_DIR/externalpackages/gsl/install/" \ - --disable-static + --prefix="$ISSM_DIR/externalpackages/gsl/install" fi Index: /issm/trunk/externalpackages/gsl/install-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-greenplanet.sh (revision 14310) +++ /issm/trunk/externalpackages/gsl/install-greenplanet.sh (revision 14310) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/howatmask/enviread.m =================================================================== --- /issm/trunk/externalpackages/howatmask/enviread.m (revision 14310) +++ /issm/trunk/externalpackages/howatmask/enviread.m (revision 14310) @@ -0,0 +1,323 @@ +function I=enviread(varargin) +%enviread: Read binary image files using ENVI header information +% +%I=enviread('filename') where the header file is named filename.hdr +%and exists in the same directory. Otherwise use +% +%I=enviread('filename','hdrfilename') +% +%The output structure I contains fields I.x, I.y, I.z and I.info +%containing the x-coordinate vector, y-coordinate vector, +%images data and header info, respectively. I.z will be in whatever +%number format (double, int, etc.) as in the envi file. +% +%Original version by Ian Howat, Ohio State Universtiy, ihowat@gmail.com +%Thanks to Yushin Ahn and Ray Jung +% +%% Current version 3 - adding subsetting feature to read only parts of +%% files. + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; +if nargin==2 + if varargin{2}=='date' + [pathstr, name, ext, versn] = fileparts(file); + info.hdrname=hdrfile; + info.ipath=pathstr; + info.iname=name; + info.ipname=file; + info.year =name(1:4); + info.month=name(5:6); + info.day =name(7:8); + info.date =name(1:8); + info.sfname=name(1:14); + info.datenum=datenum(str2double(info.year),... + str2double(info.month),str2double(info.day)); + end +end + +% subset +if nargin == 3; + if strcmp(varargin{2},'pixel_subset'); + sub = varargin{3}; + elseif strcmp(varargin{2},'map_subset'); + sub = varargin{3}; + subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; + suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; + subx = round(subx); + suby = round(suby); + + subx(subx < 1) = 1; + suby(suby < 1) = 1; + subx(subx > info.samples) = info.samples; + suby(suby > info.lines) = info.lines; + + sub = [subx,suby]; + end +end + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + %I.x = xm + (subE(1):subE(2)-1).*info.map_info.dx; + %I.y = ym - (subE(3):subE(4)-1).*info.map_info.dy; +end + + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end +switch info.data_type + case {1} + format = 'uint8'; + case {2} + format= 'int16'; + case{3} + format= 'int32'; + case {4} + format= 'single'; + case {5} + format= 'double'; + case {6} + disp('>> Sorry, Complex (2x32 bits)data currently not supported'); + disp('>> Importing as double-precision instead'); + format= 'double'; + case {9} + error('Sorry, double-precision complex (2x64 bits) data currently not supported'); + case {12} + format= 'uint16'; + case {13} + format= 'uint32'; + case {14} + format= 'int64'; + case {15} + format= 'uint64'; + otherwise + error(['File type number: ',num2str(dtype),' not supported']); +end + +%% file read +% Version 2 code by Yushin Ahn - replaces resize calls with loops (except +% for BIP formats) to work on big arrays. + + %tmp=zeros(info.lines, info.samples,info.bands,format); + tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); + fid=fopen(file,'r'); + +switch lower(info.interleave) + + case {'bsq'} + % Format: + % [Band 1] + % R1: C1, C2, C3, ... + % R2: C1, C2, C3, ... + % ... + % RN: C1, C2, C3, ... + % + % [Band 2] + % ... + % [Band N] + +%% Old Script w/out subsetting +% for b=1:info.bands +% for i=1:info.lines +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + offset1=(sub(3)-1)*info.samples; + fseek(fid,offset1,'bof'); + for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + %if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + %end + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); + end + + case {'bil'} + % Format: + % [Row 1] + % B1: C1, C2, C3, ... + % B2: C1, C2, C3, ... + % + % ... + % [Row N] + +% for i=1:info.lines +% for b=1:info.bands +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + for i=1:sub(4) + for b=1:info.bands + t=fread(fid,info.samples,format); + if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + end + end + + + + case {'bip'} + + % Row 1 + % C1: B1 B2 B3, ... + % C2: B1 B2 B3, ... + % ... + % Row N + %This section authored by Ray Jung, APL-Johns Hopkins + Z = fread(fid,info.samples*info.lines*info.bands,format,0,machine); + Z = reshape(Z, [info.bands, info.samples, info.lines]); + + for k=1:info.bands + tmp(:,:,k) = squeeze(Z(k,:,:))'; + end +end +fclose(fid); + +% tmp2=zeros(subE(4)-subE(3)+1,subE(2)-subE(1)+1,info.bands,format); +% [a,b]=size(tmp); +% for i=1:info.bands +% tmp2(xoff+1:a,yoff+1:b,1)=tmp(1:a,1:b,1); +% end +I.z=tmp; +I.info =info; + + + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end Index: /issm/trunk/externalpackages/howatmask/subsetGimpIceMask.m =================================================================== --- /issm/trunk/externalpackages/howatmask/subsetGimpIceMask.m (revision 14310) +++ /issm/trunk/externalpackages/howatmask/subsetGimpIceMask.m (revision 14310) @@ -0,0 +1,282 @@ +function [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) +% subsetGimpIceMask samples mask tiles for a given coordinate range +% +% [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) returns the mask in array M +% with map vectors Mx and My within the bounding box specified by +% coordinate ranges x0 < x1 and y0 < y1. The function finds tiles +% overlappimg the box, samples the tiles and mosaics the samples into one +% array. +% +% Example: Specify the following coordinate range and map the result. +% >> x0 = 260000; x1 = 377900; y0 = -2609400; y1 = -2543000; +% >> [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1); +% >> imagesc(Mx,My,M); axis equal xy; colormap gray; +% +% Ian Howat, Ohio State University, ihowat@gmail.com +% The Greenland Ice Mapping Project is funded by NASA. +% $Revision: 0 $ $Date: 09-Nov-2011 14:48:24$ +% + +%make coordinate index +nt = 6; +ps = 15; +xn0 = -640000 ; %xn1 = 857550; +yn0 = -3313350; %yn1 = -665450; + +c = 16640; +r = 29420; + +x = xn0:ps:xn0 + c.*ps.*nt; +y = yn0:ps:yn0 + r.*ps.*nt; + +X = cell(1,nt); +Y = cell(nt,1); +i=1; +for i=1:nt; + + X{i} = [x((i-1)*c+1),x(i*c)]; + Y{i} = [y((i-1)*r+1),y(i*r)]; + +end + +X = repmat(X,[nt,1]); +Y = repmat(Y,[1,nt]); +N = cell(size(X)); + + +i=1; +for i=1:numel(X) + N{i} = [[X{i}(1),Y{i}(2)];... + [X{i}(2),Y{i}(2)];... + [X{i}(2),Y{i}(1)];... + [X{i}(1),Y{i}(1)]]; +end + + +%% find overlapping tiles +p = [[x0,y1];[x1,y1];[x1,y0];[x0,y0]]; + +n = zeros(size(N)); + +i=1; +for i=1:numel(N) + n(i) = any(inpolygon(p(:,1),p(:,2),N{i}(:,1),N{i}(:,2))); +end +i=1; +for i=1:size(n,1) + n(i,find(n(i,:),1,'first'):find(n(i,:),1,'last')) = 1; +end +i=1; +for i=1:size(n,2) + n(find(n(:,i),1,'first'):find(n(:,i),1,'last'),i) = 1; +end + +[i,j] = find(n); +row = (min(i):max(i))'; +col = min(j):max(j); +col = repmat(col,[length(row),1])-1; +row = repmat(row,[1,size(col,2)])-1; + +% make output cells +M = cell(size(row)); +Mx = M; +My = M; + +% read each overlapping file and populate output cell +j=1; +for j=1:size(col,2) + i=1; + for i=1:size(row,1); + m = enviread(['GimpIceMask_15m_tile',num2str(col(i,j)),'_',... + num2str(row(i,j))],'map_subset',[x0 x1 y0 y1]); + M{end-i+1,j} = m.z; + Mx{end-i+1,j} = m.x; + My{end-i+1,j} = m.y'; + + + end +end + +% put together cells +M = cell2mat(M); +Mx =cell2mat(Mx(1,:)); +My =cell2mat(My(:,1)); + + +function I=enviread(varargin) + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; + +sub = varargin{3}; +subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; +suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; +subx = round(subx); +suby = round(suby); + +subx(subx < 1) = 1; +suby(suby < 1) = 1; +subx(subx > info.samples) = info.samples; +suby(suby > info.lines) = info.lines; + +sub = [subx,suby]; + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + +end + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end + +format = 'uint8'; + +tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); +fid=fopen(file,'r'); + +offset1=(sub(3)-1)*info.samples; +fseek(fid,offset1,'bof'); +for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); +end + +fclose(fid); + +I.z=tmp; +I.info =info; + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end + + + + Index: /issm/trunk/externalpackages/metis/install-4.0-hoffman2.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-hoffman2.sh (revision 14310) +++ /issm/trunk/externalpackages/metis/install-4.0-hoffman2.sh (revision 14310) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/pleiades/Makefile.in.patch + +#Compile +make Index: /issm/trunk/externalpackages/petsc/install-3.2-hoffman2.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-hoffman2.sh (revision 14310) +++ /issm/trunk/externalpackages/petsc/install-3.2-hoffman2.sh (revision 14310) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi=1 \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 14309) +++ /issm/trunk/m4/issm_options.m4 (revision 14310) @@ -163,12 +163,4 @@ fi AC_MSG_RESULT($HAVE_TRIANGLE) - - AC_MSG_CHECKING(for triangle and parallel status) - if test $HAVE_TRIANGLE = no; then - if test "$SERIAL_VALUE" = "yes" ; then - AC_MSG_ERROR([--with-triangle-dir missing. Triangle is needed to run ISSM serially!]) - fi - fi - AC_MSG_RESULT(ok) dnl }}} dnl dakota{{{ @@ -182,15 +174,42 @@ dnl defaults HAVE_DAKOTA=yes + AC_MSG_RESULT($HAVE_DAKOTA) DAKOTAINCL=-I$DAKOTA_ROOT/include + AC_MSG_CHECKING(for dakota version) + DAKOTA_VERSION=`cat $DAKOTA_ROOT/include/dakota_config.h | grep "#define PACKAGE_VERSION" | sed 's/#define PACKAGE_VERSION//' | sed 's/ //g' | sed -e 's/\"//g' ` + AC_MSG_RESULT($DAKOTA_VERSION) + AC_DEFINE_UNQUOTED([DAKOTA_VERSION],"$DAKOTA_VERSION",[Dakota version number]) case "${host_os}" in *cygwin*) - DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + if test x$DAKOTA_VERSION = x4.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + else + AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]); + fi + fi ;; *linux*) - DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + if test x$DAKOTA_VERSION = x4.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + else + AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]); + fi + fi ;; *darwin*) - DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" - dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack" + if test x$DAKOTA_VERSION = x4.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack" + else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack" + else + AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]); + fi + fi ;; esac @@ -201,7 +220,7 @@ else HAVE_DAKOTA=no + AC_MSG_RESULT($HAVE_DAKOTA) fi AM_CONDITIONAL([DAKOTA], [test x$HAVE_DAKOTA = xyes]) - AC_MSG_RESULT($HAVE_DAKOTA) dnl }}} dnl boost{{{ @@ -1045,7 +1064,19 @@ dnl check that --with-fortran-lib may have been provided if test -n "$FORTRAN_LIB" ; then - FORTRANLIB="$FORTRAN_LIB" - AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src]) - AC_SUBST([FORTRANLIB]) + dnl check that library provided EXISTS! + FORTRAN_DIR=$(echo $FORTRAN_LIB | sed -e "s/-L//g" | awk '{print $[1]}') + if test -d "$FORTRAN_DIR" || test -f "$FORTRAN_DIR"; then + FORTRANLIB="$FORTRAN_LIB" + AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src]) + AC_SUBST([FORTRANLIB]) + else + if test "x$HAVE_MPI" = "xyes"; then + FORTRANLIB=$(mpif77 -print-file-name="libgfortran.a") + if test -f "$FORTRANLIB"; then + AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist, MPI suggests the following library: $FORTRANLIB]); + fi + fi + AC_MSG_ERROR([frtran library provided ($FORTRAN_LIB$) does not exist!]); + fi fi AC_MSG_RESULT(done) @@ -1059,10 +1090,20 @@ dnl check that --with-graphics-lib may have been provided + if test -n "$GRAPHICS_LIB" ; then - HAVE_GRAPHICS=yes - GRAPHICSLIB="$GRAPHICS_LIB" - - AC_DEFINE([_HAVE_GRAPHICS_],[1],[with GRAPHICS in ISSM src]) - AC_SUBST([GRAPHICSLIB]) + dnl check that library provided EXISTS! + GRAPHICS_DIR=$(echo $GRAPHICS_LIB | sed -e "s/-L//g" | awk '{print $[1]}') + if test -d "$GRAPHICS_DIR" || test -f "$GRAPHICS_DIR"; then + HAVE_GRAPHICS=yes + GRAPHICSLIB="$GRAPHICS_LIB" + AC_DEFINE([_HAVE_GRAPHICS_],[1],[with GRAPHICS in ISSM src]) + AC_SUBST([GRAPHICSLIB]) + else + if test -f "$PETSC_ROOT/conf/petscvariables"; then + GRAPHICSLIB=$(cat $PETSC_ROOT/conf/petscvariables | grep X_LIB) + AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB) does not exist, PETSc suggests the following library: $GRAPHICSLIB]); + fi + AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB$) does not exist!]); + fi fi AC_MSG_RESULT(done) @@ -1326,6 +1367,6 @@ dnl defaults HAVE_ANDROID=jni - AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability]) + AC_DEFINE([_HAVE_ANDROID_JNI_],[1],[with android jni]) elif test "x$ANDROID" = "xexe"; then dnl defaults @@ -1342,4 +1383,22 @@ AM_CONDITIONAL([ANDROIDEXE], [test x$HAVE_ANDROID = xexe]) AC_MSG_RESULT($HAVE_ANDROID) + dnl }}} + dnl with-android-ndk{{{ + AC_ARG_WITH([android-ndk], + AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]), + [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) + AC_MSG_CHECKING(with android ndk) + + if test -d "$ANDROID_NDK_ROOT"; then + dnl defaults + HAVE_ANDROID_NDK=yes + ANDROID_NDKINCL="-I$ANDROID_NDK_ROOT/arm-linux-android-install/sysroot/usr/include" + + AC_DEFINE([_HAVE_ANDROID_NDK_],[1],[with android ndk in ISSM src]) + AC_SUBST([ANDROID_NDKINCL]) + else + HAVE_ANDROID_NDK=no + fi + AC_MSG_RESULT($HAVE_ANDROID_NDK) dnl }}} dnl with-3d{{{ Index: /issm/trunk/scripts/DownloadExternalPackage.py =================================================================== --- /issm/trunk/scripts/DownloadExternalPackage.py (revision 14309) +++ /issm/trunk/scripts/DownloadExternalPackage.py (revision 14310) @@ -6,11 +6,11 @@ # +# imports {{{ import os,sys,re import urllib from HTMLParser import HTMLParser from urllib import FancyURLopener - -# Start class myHTMLParser -class MyHTMLParser(HTMLParser): +# }}} +class MyHTMLParser(HTMLParser): #{{{ def __init__(self, pattern): @@ -23,113 +23,117 @@ if "href" == i[0] and str(self.matcher.match(i[1])) != "None": self.targets.append(i[1]) -# End class myHTMLParser +#}}} +def main(argv=None): # {{{ + # Separates the URL into a directory and the file or pattern based on the + # last appearance of '/'. + if len(sys.argv) > 1: + pivot = sys.argv[1].rfind("/") + url = (sys.argv[1])[:pivot] + pivot += 1 + find = (sys.argv[1])[pivot:] + else: + print "******************************************************************************************************************************" + print "* Invalid input! *" + print "* *" + print "* Try: 'DownloadExternalPackage.py url [localFile]' *" + print "* *" + print "* Where 'URL' is the URL with an explicit package name or the URL followed by the truncated package name. And 'localFile' is *" + print "* the file name (including extension) that you would like to save as. *" + print "* *" + print "* Examples: *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' *" + print "* *" + print "* This is the old style and the safest way to download a package. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' 'libtool.tar.gz' *" + print "* *" + print "* This is the new style. For packages like 'Libtool', which we never expect to be using multiple versions, this will *" + print "* download the most recent version and save it as the generic 'libtool.tar.gz'. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' *" + print "* *" + print "* This is the new style. This is a demonstration of how this script can be used to disambiguate a package name if there *" + print "* are more than once package matching 'gsl-'. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' *" + print "* *" + print "* This is the new style. This will download a package with 'libtool' as a prefix and save it as its canonical name. *" + print "* *" + print "* *" + print "******************************************************************************************************************************" + + if len(sys.argv) > 2: + localFile=sys.argv[2] + print "Downloaded file will be saved as: " + localFile + else: + localFile = None + print "Downloaded file will saved with the same file name." + + + print "Looking for: " + find + + # As an extra precaution, if no extension is given for a particular package + # such as '.../libtool', then ensure that files found are of appropriate + # file extensions. + # + # WARNING: The external packages directory includes executable binaries with + # '.exe' extensions. As such, '.exe' is an acceptable suffix, but this is + # inherently dangerous since this script can be used to download from any + # valid website. Furthermore, if an individual attempts a "man-in-the-middle" + # attack, then the user would be capable of downloading executables from + # an untrusted source. + pattern = find + "[\w.-]*(\.tar\.gz|tar\.gz2|tgz|zip|exe)?" + parser = MyHTMLParser(pattern) + + # Creates a 'FancyURL' which allows the script to fail gracefully by catching + # HTTP error codes 30X and several 40X(where 'X' is a natural number). + urlObject = FancyURLopener() + obj = urlObject.open(url) + parser.feed(obj.read()) + + # If a file pattern was used to describe the file that should be downloaded, + # then there is the potential for multiple file matches. Currently, the script + # will detect this ambiguity and print out all the matches, while informing + # the user that he must refine his search. + # + # TODO: Prompt the user to select from a list his/her preferred target. + if len(parser.targets) > 1: + print "Could not resolve your download due to the number of hits." + print "Refine your search." + for i in parser.targets: + print i + + elif len(parser.targets) == 1: + print "Found: " + parser.targets[0] + url += "/" + parser.targets[0] + + if localFile is None: + if os.path.exists(parser.targets[0]): + print "File " + parser.targets[0] + " already exists and will not be downloaded..." + else: + urllib.urlretrieve(url, parser.targets[0]) + print "File saved as: " + parser.targets[0] + else: + if os.path.exists(localFile): + print "File "+ localFile +" already exists and will not be downloaded..." + else: + if parser.targets[0] == localFile: + print "File found and destination match." + elif parser.matcher.match(localFile) != "None": + print "File found matches destination pattern." + else: + print "WARNING: the file found \'" + parser.targets[0] + "\' does not match \'" + localFile + "\'" + print "Ensure the downloaded version is suitable." + + urllib.urlretrieve(url, localFile) + print "File saved as: " + localFile + + else: + print "No matches found!" + + obj.close() +# End 'main' function. }}} -# Separates the URL into a directory and the file or pattern based on the -# last appearance of '/'. -if len(sys.argv) > 1: - pivot = sys.argv[1].rfind("/") - url = (sys.argv[1])[:pivot] - pivot += 1 - find = (sys.argv[1])[pivot:] -else: - print "******************************************************************************************************************************" - print "* Invalid input! *" - print "* *" - print "* Try: 'DownloadExternalPackage.py url [localFile]' *" - print "* *" - print "* Where 'URL' is the URL with an explicit package name or the URL followed by the truncated package name. And 'localFile' is *" - print "* the file name (including extension) that you would like to save as. *" - print "* *" - print "* Examples: *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' *" - print "* *" - print "* This is the old style and the safest way to download a package. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' 'libtool.tar.gz' *" - print "* *" - print "* This is the new style. For packages like 'Libtool', which we never expect to be using multiple versions, this will *" - print "* download the most recent version and save it as the generic 'libtool.tar.gz'. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' *" - print "* *" - print "* This is the new style. This is a demonstration of how this script can be used to disambiguate a package name if there *" - print "* are more than once package matching 'gsl-'. *" - print "* *" - print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' *" - print "* *" - print "* This is the new style. This will download a package with 'libtool' as a prefix and save it as its canonical name. *" - print "* *" - print "* *" - print "******************************************************************************************************************************" - -if len(sys.argv) > 2: - localFile=sys.argv[2] - print "Downloaded file will saved as: " + localFile -else: - localFile = None - print "Downloaded file will saved with the same file name." - - -print "Looking for " + find - -# As an extra precaution, if no extension is given for a particular package -# such as '.../libtool', then ensure that files found are of appropriate -# file extensions. -# -# WARNING: The external packages directory includes executable binaries with -# '.exe' extensions. As such, '.exe' is an acceptable suffix, but this is -# inherently dangerous since this script can be used to download from any -# valid website. Furthermore, if an individual attempts a "man-in-the-middle" -# attack, then the user would be capable of downloading executables from -# an untrusted source. -pattern = find + "[\w.-]*(\.tar\.gz|tar\.gz2|tgz|zip|exe)?" -parser = MyHTMLParser(pattern) - -# Creates a 'FancyURL' which allows the script to fail gracefully by catching -# HTTP error codes 30X and several 40X(where 'X' is a natural number). -urlObject = FancyURLopener() -obj = urlObject.open(url) -parser.feed(obj.read()) - -# If a file pattern was used to describe the file that should be downloaded, -# then there is the potential for multiple file matches. Currently, the script -# will detect this ambiguity and print out all the matches, while informing -# the user that he must refine his search. -# -# TODO: Prompt the user to select from a list his/her preferred target. -if len(parser.targets) > 1: - print "Could not resolve your download due to the number of hits." - print "Refine your search." - for i in parser.targets: - print i - -elif len(parser.targets) == 1: - print "Found: " + parser.targets[0] - url += "/" + parser.targets[0] - - if localFile is None: - if os.path.exists(parser.targets[0]): - print "File " + parser.targets[0] + " already exists and will not be downloaded..." - else: - urllib.urlretrieve(url, parser.targets[0]) - print "File saved as: " + parser.targets[0] - else: - if os.path.exists(localFile): - print "File "+ localFile +" already exists and will not be downloaded..." - else: - if parser.targets[0] == localFile: - print "File found and destination match." - elif parser.matcher.match(localFile) != "None": - print "File found matches destination pattern." - else: - print "WARNING: the file found \'" + parser.targets[0] + "\' does not match \'" + localFile + "\'" - print "Ensure the downloaded version is suitable." - - urllib.urlretrieve(url, localFile) - print "File saved as: " + localFile - -else: - print "No matches found!" - -obj.close() +if __name__ == "__main__": + main() Index: /issm/trunk/src/CMakeLists.txt =================================================================== --- /issm/trunk/src/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +add_subdirectory(c) +#add_subdirectory(m) +#add_subdirectory(wrappers) +#Android Dir {{{ +# add_subdirectory(android) +#}}} +# }}} Index: /issm/trunk/src/android/ISSM/AndroidManifest.xml =================================================================== --- /issm/trunk/src/android/ISSM/AndroidManifest.xml (revision 14309) +++ /issm/trunk/src/android/ISSM/AndroidManifest.xml (revision 14310) @@ -2,6 +2,6 @@ package="com.example.issm" android:versionCode="1" - android:versionName="1.0" > - + android:versionName="1.0" + android:installLocation="preferExternal" > - @@ -20,4 +20,8 @@ + + Index: /issm/trunk/src/android/ISSM/Makefile.am =================================================================== --- /issm/trunk/src/android/ISSM/Makefile.am (revision 14309) +++ /issm/trunk/src/android/ISSM/Makefile.am (revision 14310) @@ -5,5 +5,5 @@ deps = else -deps = ../../c/libISSMCore.a +deps = $(ISSM_DIR)/src/c/libISSMCore.a ./jni/Main.cpp endif @@ -14,2 +14,5 @@ $(ANDROID_NDK_DIR)/ndk-build -C ./jni clean $(ANDROID_NDK_DIR)/ndk-build -C ./jni + +clean: + rm -rf libs obj Index: /issm/trunk/src/android/ISSM/assets/Map/antarctica.petsc =================================================================== --- /issm/trunk/src/android/ISSM/assets/Map/antarctica.petsc (revision 14310) +++ /issm/trunk/src/android/ISSM/assets/Map/antarctica.petsc (revision 14310) @@ -0,0 +1,19 @@ +%Petsc options file: SeaRISEgreenland.petsc written from Matlab solver array + ++NoneAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 + ++DiagnosticVertAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 Index: /issm/trunk/src/android/ISSM/assets/Map/greenland.petsc =================================================================== --- /issm/trunk/src/android/ISSM/assets/Map/greenland.petsc (revision 14310) +++ /issm/trunk/src/android/ISSM/assets/Map/greenland.petsc (revision 14310) @@ -0,0 +1,19 @@ +%Petsc options file: SeaRISEgreenland.petsc written from Matlab solver array + ++NoneAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 + ++DiagnosticVertAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 Index: /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml =================================================================== --- /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml (revision 14309) +++ /issm/trunk/src/android/ISSM/bin/AndroidManifest.xml (revision 14310) @@ -2,6 +2,6 @@ package="com.example.issm" android:versionCode="1" - android:versionName="1.0" > - + android:versionName="1.0" + android:installLocation="preferExternal" > - @@ -20,4 +20,8 @@ + + Index: /issm/trunk/src/android/ISSM/jni/Android.mk =================================================================== --- /issm/trunk/src/android/ISSM/jni/Android.mk (revision 14309) +++ /issm/trunk/src/android/ISSM/jni/Android.mk (revision 14310) @@ -2,7 +2,5 @@ my_LOCAL_PATH:=$(LOCAL_PATH) -#include $(LOCAL_PATH)/issmlib\Android.mk include $(call all-subdir-makefiles) - LOCAL_PATH := $(my_LOCAL_PATH) @@ -12,8 +10,7 @@ LOCAL_ALLOW_UNDEFINED_SYMBOLS := true LOCAL_CFLAGS := -Wno-psabi -DHAVE_CONFIG_H -LOCAL_LDLIBS := -llog -ldl +LOCAL_LDLIBS := -L$(SYSROOT)/usr/lib -llog -ldl -lm LOCAL_MODULE := IssmJni LOCAL_SRC_FILES := Main.cpp -LOCAL_STATIC_LIBRARIES := libISSMCore - +LOCAL_STATIC_LIBRARIES := libISSMCore libgsl libgslcblas include $(BUILD_SHARED_LIBRARY) Index: /issm/trunk/src/android/ISSM/jni/Application.mk =================================================================== --- /issm/trunk/src/android/ISSM/jni/Application.mk (revision 14309) +++ /issm/trunk/src/android/ISSM/jni/Application.mk (revision 14310) @@ -1,3 +1,4 @@ -APP_STL:=stlport_static +APP_STL:= gnustl_static APP_CPPFLAGS := -frtti APP_CPPFLAGS += -fexceptions +APP_ABI := armeabi Index: /issm/trunk/src/android/ISSM/jni/Main.cpp =================================================================== --- /issm/trunk/src/android/ISSM/jni/Main.cpp (revision 14309) +++ /issm/trunk/src/android/ISSM/jni/Main.cpp (revision 14310) @@ -1,58 +1,167 @@ #include -#include "../../../c/android/fac.h" +#include #include "../../../c/issm.h" #include #include -/////////////////////////////////////////////////////////////////////////////////////////// +#include + namespace com_example_issm { - fac* f; + /*Global variables{{{*/ FemModel *fm; -//------------------------------------------------------------------------------------ - jint initilize(JNIEnv *env, jclass clazz, jstring file) + double* xyz; /*keep vertices information here*/ + /*}}}*/ + jint Initialize(JNIEnv *env, jclass clazz, jstring jsolution_type, jstring jabsfile, jstring jrelfile) /*{{{*/ { - char *nativefile = (char*)env->GetStringUTFChars(file,0); + + /*arguments to constructor: */ + int argc; //arguments to constructor. + char** argv = NULL; + COMM communicator = 1; //fake communicator for constructor + const char* issmname = "issm.exe"; + char *solution_type = NULL; + char *absfile = NULL; + char *relfile = NULL; - f = new fac(); + /*log:*/ + __android_log_print(ANDROID_LOG_INFO, "Native","Initializing FemModel"); - //call Model constructor passing in infile as File Descriptor parameter. - fm = new FemModel(nativefile); + /*retrieve from java machine: */ + solution_type = (char*)env->GetStringUTFChars(jsolution_type,0); + absfile = (char*)env->GetStringUTFChars(jabsfile,0); + relfile = (char*)env->GetStringUTFChars(jrelfile,0); - env->ReleaseStringUTFChars(file, nativefile); //must realease the char* - //jint size = (jint) fm->bufferSize(); - //return size; + /*creat arguments to call constructor for FemModel: */ + argc=4; + argv=(char**)malloc(argc*sizeof(char*)); + argv[0]=(char*)issmname; + argv[1]=solution_type; + argv[2]=absfile; + argv[3]=relfile; + + /*call Model constructor passing in infile as File Descriptor parameter.*/ + fm = new FemModel(argc,argv,communicator); - return 0; //return 0 for now. + /*release strings: */ + env->ReleaseStringUTFChars(jsolution_type, solution_type); //must realease the char* + env->ReleaseStringUTFChars(jabsfile, absfile); //must realease the char* + env->ReleaseStringUTFChars(jrelfile, relfile); //must realease the char* + + /*figure out size of solution: */ + __android_log_print(ANDROID_LOG_INFO, "Native","Number of elements"); + jint size = (jint) fm->elements->NumberOfElements(); + + /*retrieve vertices x,y and z coordinates: */ + __android_log_print(ANDROID_LOG_INFO, "Native","Retrieving vertices"); + xyz=fm->vertices->ToXYZ(); + + /*log: */ + __android_log_print(ANDROID_LOG_INFO, "Native","Done Initializing FemModel"); + + return size; + } -//------------------------------------------------------------------------------------ - //fill out the first two slots, extract the same way in java using get(int position) - void solve(JNIEnv *env, jclass clazz , jint alpha, jobject buf) - { + /*}}}*/ + void Solve(JNIEnv *env, jclass clazz , jdouble alpha, jobject buf){ /*{{{*/ + + int i,count; + double x1,y1,z1,vel1; + double x2,y2,z2,vel2; + double x3,y3,z3,vel3; + int v1,v2,v3,eid; + Patch* patch=NULL; + + /*log:*/ + __android_log_print(ANDROID_LOG_INFO, "Native","Solving "); + + /*retrieve buffer: */ jdouble *dBuf = (jdouble *)env->GetDirectBufferAddress(buf); - //pass bBuff to fem model to allocate data - // fm -> solve(dBuf, alpha); + /*reset basal friction to what it was before: */ + __android_log_print(ANDROID_LOG_INFO, "Native","alpha %g ",alpha); + InputDuplicatex(fm->elements,fm->nodes,fm->vertices,fm->loads,fm->materials,fm->parameters,AndroidFrictionCoefficientEnum,FrictionCoefficientEnum); - } -//------------------------------------------------------------------------------------ - jlong factorial(JNIEnv *env, jclass clazz, jlong n) + /*now scale friction by alpha: */ + InputScalex(fm->elements,fm->nodes,fm->vertices,fm->loads,fm->materials,fm->parameters,FrictionCoefficientEnum,alpha/100); + + /*solve: */ + fm -> Solve(); + + /*retrieve results: */ + __android_log_print(ANDROID_LOG_INFO, "Native","Retrieving results "); + patch=fm->elements->ResultsToPatch(); + + /*sort out the velocities: */ + for(i=0;inumrows;i++){ + if ((patch->values[i*patch->numcols+0])==VelEnum){ + + /*Each row of the Patch object is made of the following information: + - the result enum_type, + - the step and time, + - the id of the element, + - the interpolation type, + - the vertices ids, + - and the values at the nodes (could be different from the vertices) + */ + eid=(int)patch->values[i*patch->numcols+3]-1; + v1=(int)patch->values[i*patch->numcols+5]; + x1=xyz[3*(v1-1)+0]; y1=xyz[3*(v1-1)+1]; z1=xyz[3*(v1-1)+2]; + + v2=(int)patch->values[i*patch->numcols+6]; + x2=xyz[3*(v2-1)+0]; y2=xyz[3*(v2-1)+1]; z2=xyz[3*(v2-1)+2]; + + v3=(int)patch->values[i*patch->numcols+7]; + x3=xyz[3*(v3-1)+0]; y3=xyz[3*(v3-1)+1]; z3=xyz[3*(v3-1)+2]; + + vel1=patch->values[i*patch->numcols+8]; + vel2=patch->values[i*patch->numcols+9]; + vel3=patch->values[i*patch->numcols+10]; + + /*plug into dBuf: */ + /*vertex 1: */ + dBuf[12*eid+0]=x1; + dBuf[12*eid+1]=y1; + dBuf[12*eid+2]=z1; + + /*vertex 2: */ + dBuf[12*eid+3]=x2; + dBuf[12*eid+4]=y2; + dBuf[12*eid+5]=z2; + + /*vertex 3: */ + dBuf[12*eid+6]=x3; + dBuf[12*eid+7]=y3; + dBuf[12*eid+8]=z3; + + /*values at 3 vertices: */ + dBuf[12*eid+9]=vel1; + dBuf[12*eid+10]=vel2; + dBuf[12*eid+11]=vel3; + + } + } + + /*for(i=0;i<148;i++){ + __android_log_print(ANDROID_LOG_INFO, "Native","%g %g %g | %g %g %g | %g %g %g | %g %g %g\n", + dBuf[12*i+0],dBuf[12*i+1],dBuf[12*i+2], + dBuf[12*i+3],dBuf[12*i+4],dBuf[12*i+5], + dBuf[12*i+6],dBuf[12*i+7],dBuf[12*i+8], + dBuf[12*i+9],dBuf[12*i+10],dBuf[12*i+11]); + }*/ + + /*delete temporary data:*/ + delete patch; + + }/*}}}*/ + static JNINativeMethod method_table[] = /*{{{*/ { - if( f != NULL) - return (jlong) (f->factorial(n)); - return 0; - } + {"createISSMModel" ,"(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)I" , (void *) Initialize}, + {"solveISSMModel", "(DLjava/nio/DoubleBuffer;)V", (void *) Solve} + }; + /*}}}*/ +} -//------------------------------------------------------------------------------------ - static JNINativeMethod method_table[] = - { - {"fac" , "(J)J" , (void *) factorial}, - {"createISSMModel" ,"(Ljava/lang/String;)I" , (void *) initilize}, - {"processBuffer", "(ILjava/nio/DoubleBuffer;)V", (void *) solve} - }; -} -//------------------------------------------------------------------------------------ using namespace com_example_issm; - -extern "C" jint JNI_OnLoad(JavaVM* vm, void* reserved) +extern "C" jint JNI_OnLoad(JavaVM* vm, void* reserved) /*{{{*/ { JNIEnv* env; @@ -72,3 +181,3 @@ } } -/////////////////////////////////////////////////////////////////////////////////////////// +/*}}}*/ Index: /issm/trunk/src/android/ISSM/jni/gsllib/Android.mk =================================================================== --- /issm/trunk/src/android/ISSM/jni/gsllib/Android.mk (revision 14310) +++ /issm/trunk/src/android/ISSM/jni/gsllib/Android.mk (revision 14310) @@ -0,0 +1,13 @@ +LOCAL_PATH:= $(call my-dir) +my_directory:= $(LOCAL_PATH) +include $(CLEAR_VARS) +LOCAL_MODULE := libgsl +LOCAL_SRC_FILES := ../../../../../externalpackages/gsl/install/lib/libgsl.a +LOCAL_EXPORT_C_INCLUDES := $(ISSM_DIR)/externalpackages/gsl/install/include/gsl/ +include $(PREBUILT_STATIC_LIBRARY) + +LOCAL_PATH=$(my_directory) +include $(CLEAR_VARS) +LOCAL_MODULE := libgslcblas +LOCAL_SRC_FILES := ../../../../../externalpackages/gsl/install/lib/libgslcblas.a +include $(PREBUILT_STATIC_LIBRARY) Index: /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk =================================================================== --- /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk (revision 14309) +++ /issm/trunk/src/android/ISSM/jni/issmlib/Android.mk (revision 14310) @@ -2,5 +2,7 @@ include $(CLEAR_VARS) LOCAL_MODULE := libISSMCore -LOCAL_SRC_FILES := libISSMCore.a +LOCAL_LDLIBS := -L$(SYSROOT)/usr/lib -llog +LOCAL_SRC_FILES := ../../../../../lib/libISSMCore.a LOCAL_EXPORT_C_INCLUDES := $(ISSM_DIR) include $(PREBUILT_STATIC_LIBRARY) + Index: /issm/trunk/src/android/ISSM/project.properties =================================================================== --- /issm/trunk/src/android/ISSM/project.properties (revision 14309) +++ /issm/trunk/src/android/ISSM/project.properties (revision 14310) @@ -12,3 +12,3 @@ # Project target. -target=android-15 +target=android-16 Index: /issm/trunk/src/android/ISSM/res/anim/alpha.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/anim/alpha.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/anim/alpha.xml (revision 14310) @@ -0,0 +1,6 @@ + + Index: /issm/trunk/src/android/ISSM/res/anim/translate.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/anim/translate.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/anim/translate.xml (revision 14310) @@ -0,0 +1,14 @@ + + + + + + Index: sm/trunk/src/android/ISSM/res/layout/activity_issm.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/layout/activity_issm.xml (revision 14309) +++ (revision ) @@ -1,33 +1,0 @@ - - - - - + Index: /issm/trunk/src/android/ISSM/res/layout/seekbar_progress.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/layout/seekbar_progress.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/layout/seekbar_progress.xml (revision 14310) @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + Index: /issm/trunk/src/android/ISSM/res/layout/seekbar_progress_bg.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/layout/seekbar_progress_bg.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/layout/seekbar_progress_bg.xml (revision 14310) @@ -0,0 +1,14 @@ + + + + + + + + Index: /issm/trunk/src/android/ISSM/res/layout/splashscreen.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/layout/splashscreen.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/layout/splashscreen.xml (revision 14310) @@ -0,0 +1,16 @@ + + + + + Index: /issm/trunk/src/android/ISSM/res/menu/issm_menu.xml =================================================================== --- /issm/trunk/src/android/ISSM/res/menu/issm_menu.xml (revision 14310) +++ /issm/trunk/src/android/ISSM/res/menu/issm_menu.xml (revision 14310) @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + Index: /issm/trunk/src/android/ISSM/src/com/example/issm/ColorBar.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/ColorBar.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/ColorBar.java (revision 14310) @@ -0,0 +1,94 @@ +package com.example.issm; + +import android.content.Context; +import android.graphics.Canvas; +import android.graphics.Color; +import android.graphics.Paint; +import android.view.MotionEvent; +import android.view.View; +///////////////////////////////////////////////////////////// +public class ColorBar extends View +{ + Paint paint = new Paint(); + Paint textpaint = new Paint(); + //coordinate of the colorbar + private int width = 30; + private int start_x = 10; + private int start_y = 30; + private int end_y = 0; + boolean touch; + final int MAX_SCALING =255; + double [][] colorBuffer; + public ColorBar(Context context) + { + super(context); + setWillNotDraw(false); + paint.setStrokeWidth(5); + textpaint.setColor(Color.WHITE); + textpaint.setTextSize(20); + touch = false; + } +//---------------------------------------------------------------- + //change the color map + public void setColorMap(ColorMap colorMap) + { + this.colorBuffer = colorMap.getColorBuffer(); + } +//---------------------------------------------------------------- + @Override + public void onDraw(Canvas canvas) + { + int r,g,b; + int y = start_y; + for(int i = 0; i < 64; i++ ) + { + r = Math.round((float)colorBuffer[i][0]*MAX_SCALING); + g = Math.round((float)colorBuffer[i][1]*MAX_SCALING); + b = Math.round((float)colorBuffer[i][2]*MAX_SCALING); + paint.setColor(Color.argb(MAX_SCALING, r, g, b)); + canvas.drawLine(start_x, y, start_x+width, y, paint); + + if(i == 60) canvas.drawText("_0.0", start_x+width, y, textpaint); + if(i == 48) canvas.drawText("_0.2", start_x+width, y, textpaint); + if(i == 36) canvas.drawText("_0.4", start_x+width, y, textpaint); + if(i == 24) canvas.drawText("_0.6", start_x+width, y, textpaint); + if(i == 12) canvas.drawText("_0.8", start_x+width, y, textpaint); + if(i == 0) canvas.drawText("_1.0", start_x+width, y, textpaint); + + y+=5; + } + + end_y = y; + } +//---------------------------------------------------------------- + //allow user to move color bar around + @Override + public boolean onTouchEvent (MotionEvent event) + { + + if (event.getAction() == MotionEvent.ACTION_DOWN) + { + int x = (int) event.getX(); + int y = (int) event.getY(); + if(x >= start_x && x <= start_x+width && y >= start_y && y <= end_y) + touch = true; + } + else if (event.getAction() == MotionEvent.ACTION_MOVE) + { + if(touch) + { + start_x = (int) event.getX(); + start_y = (int) event.getY(); + } + invalidate(); + + } + else if (event.getAction() == MotionEvent.ACTION_UP) + { + touch = false; + } + return true; + } +//---------------------------------------------------------------- +} +//////////////////////////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/ColorMap.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/ColorMap.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/ColorMap.java (revision 14310) @@ -0,0 +1,915 @@ +package com.example.issm; + +///////////////////////////////////////////////////////// +class ColorMap +{ + private double[][] d; + final int rowNumber = 64; +//------------------------------------------------------- + public ColorMap() + { + setDefault(); + } +//------------------------------------------------------- + public double[][] getColorBuffer() + { + return d; + } +//-------------------------------------------------------- + //set default color map => hsv {{{ + public void setDefault() + { + d = new double[][]{ + {1.0, 0.0, 0.0 }, + { 1.0, 0.0938, 0.0 }, + { 1.0, 0.1875, 0.0 }, + { 1.0, 0.2813, 0.0 }, + { 1.0, 0.375, 0.0 }, + { 1.0, 0.4688, 0.0 }, + { 1.0, 0.5625, 0.0 }, + { 1.0, 0.6563, 0.0 }, + { 1.0, 0.75, 0.0 }, + { 1.0, 0.8438, 0.0 }, + { 1.0, 0.9375, 0.0 }, + { 0.9688, 1.0, 0.0 }, + { 0.875, 1.0, 0.0 }, + { 0.7813, 1.0, 0.0 }, + { 0.6875, 1.0, 0.0 }, + { 0.5938, 1.0, 0.0 }, + { 0.5, 1.0, 0.0 }, + { 0.4063, 1.0, 0.0 }, + { 0.3125, 1.0, 0.0 }, + { 0.2188, 1.0, 0.0 }, + { 0.125, 1.0, 0.0 }, + { 0.0313, 1.0, 0.0 }, + { 0.0, 1.0, 0.0625 }, + { 0.0, 1.0, 0.1563 }, + { 0.0, 1.0, 0.25 }, + { 0.0, 1.0, 0.3438 }, + { 0.0, 1.0, 0.4375 }, + { 0.0, 1.0, 0.5313 }, + { 0.0, 1.0, 0.625 }, + { 0.0, 1.0, 0.7188 }, + { 0.0, 1.0, 0.8125 }, + { 0.0, 1.0, 0.9063 }, + { 0.0, 1.0, 1.0 }, + { 0.0, 0.9063, 1.0 }, + { 0.0, 0.8125, 1.0 }, + { 0.0, 0.7188, 1.0 }, + { 0.0, 0.625, 1.0 }, + { 0.0, 0.5313, 1.0 }, + { 0.0, 0.4375, 1.0 }, + { 0.0, 0.3438, 1.0 }, + { 0.0, 0.25, 1.0 }, + { 0.0, 0.1563, 1.0 }, + { 0.0, 0.0625, 1.0 }, + { 0.0313, 0.0, 1.0 }, + { 0.125, 0.0, 1.0 }, + { 0.2188, 0.0, 1.0 }, + { 0.3125, 0.0, 1.0 }, + { 0.4063, 0.0, 1.0 }, + { 0.5, 0.0, 1.0 }, + { 0.5938, 0.0, 1.0 }, + { 0.6875, 0.0, 1.0 }, + { 0.7813, 0.0, 1.0 }, + { 0.875, 0.0, 1.0 }, + { 0.9688, 0.0, 1.0 }, + { 1.0, 0.0, 0.9375 }, + { 1.0, 0.0, 0.8438 }, + { 1.0, 0.0, 0.75 }, + { 1.0, 0.0, 0.6563 }, + { 1.0, 0.0, 0.5625 }, + { 1.0, 0.0, 0.4688 }, + { 1.0, 0.0, 0.375 }, + { 1.0, 0.0, 0.2813 }, + { 1.0, 0.0, 0.1875 }, + { 1.0, 0.0, 0.0938 } + }; + } + //}}} +//------------------------------------------------------- + public void setAutumn() + { + d = new double[][]{ + { 1.0, 0.0, 0.0 }, + { 1.0, 0.0159, 0.0 }, + { 1.0, 0.0317, 0.0 }, + { 1.0, 0.0476, 0.0 }, + { 1.0, 0.0635, 0.0 }, + { 1.0, 0.0794, 0.0 }, + { 1.0, 0.0952, 0.0 }, + { 1.0, 0.1111, 0.0 }, + { 1.0, 0.127, 0.0 }, + { 1.0, 0.1429, 0.0 }, + { 1.0, 0.1587, 0.0 }, + { 1.0, 0.1746, 0.0 }, + { 1.0, 0.1905, 0.0 }, + { 1.0, 0.2063, 0.0 }, + { 1.0, 0.2222, 0.0 }, + { 1.0, 0.2381, 0.0 }, + { 1.0, 0.254, 0.0 }, + { 1.0, 0.2698, 0.0 }, + { 1.0, 0.2857, 0.0 }, + { 1.0, 0.3016, 0.0 }, + { 1.0, 0.3175, 0.0 }, + { 1.0, 0.3333, 0.0 }, + { 1.0, 0.3492, 0.0 }, + { 1.0, 0.3651, 0.0 }, + { 1.0, 0.381, 0.0 }, + { 1.0, 0.3968, 0.0 }, + { 1.0, 0.4127, 0.0 }, + { 1.0, 0.4286, 0.0 }, + { 1.0, 0.4444, 0.0 }, + { 1.0, 0.4603, 0.0 }, + { 1.0, 0.4762, 0.0 }, + { 1.0, 0.4921, 0.0 }, + { 1.0, 0.5079, 0.0 }, + { 1.0, 0.5238, 0.0 }, + { 1.0, 0.5397, 0.0 }, + { 1.0, 0.5556, 0.0 }, + { 1.0, 0.5714, 0.0 }, + { 1.0, 0.5873, 0.0 }, + { 1.0, 0.6032, 0.0 }, + { 1.0, 0.619, 0.0 }, + { 1.0, 0.6349, 0.0 }, + { 1.0, 0.6508, 0.0 }, + { 1.0, 0.6667, 0.0 }, + { 1.0, 0.6825, 0.0 }, + { 1.0, 0.6984, 0.0 }, + { 1.0, 0.7143, 0.0 }, + { 1.0, 0.7302, 0.0 }, + { 1.0, 0.746, 0.0 }, + { 1.0, 0.7619, 0.0 }, + { 1.0, 0.7778, 0.0 }, + { 1.0, 0.7937, 0.0 }, + { 1.0, 0.8095, 0.0 }, + { 1.0, 0.8254, 0.0 }, + { 1.0, 0.8413, 0.0 }, + { 1.0, 0.8571, 0.0 }, + { 1.0, 0.873, 0.0 }, + { 1.0, 0.8889, 0.0 }, + { 1.0, 0.9048, 0.0 }, + { 1.0, 0.9206, 0.0 }, + { 1.0, 0.9365, 0.0 }, + { 1.0, 0.9524, 0.0 }, + { 1.0, 0.9683, 0.0 }, + { 1.0, 0.9841, 0.0 }, + { 1.0, 1.0, 0.0 } + }; + } +//------------------------------------------------------- + public void setBone() + { + d = new double[][]{ + { 0.0, 0.0, 0.0052 }, + { 0.0139, 0.0139, 0.0243 }, + { 0.0278, 0.0278, 0.0434 }, + { 0.0417, 0.0417, 0.0625 }, + { 0.0556, 0.0556, 0.0816 }, + { 0.0694, 0.0694, 0.1007 }, + { 0.0833, 0.0833, 0.1198 }, + { 0.0972, 0.0972, 0.1389 }, + { 0.1111, 0.1111, 0.158 }, + { 0.125, 0.125, 0.1771 }, + { 0.1389, 0.1389, 0.1962 }, + { 0.1528, 0.1528, 0.2153 }, + { 0.1667, 0.1667, 0.2344 }, + { 0.1806, 0.1806, 0.2535 }, + { 0.1944, 0.1944, 0.2726 }, + { 0.2083, 0.2083, 0.2917 }, + { 0.2222, 0.2222, 0.3108 }, + { 0.2361, 0.2361, 0.3299 }, + { 0.25, 0.25, 0.349 }, + { 0.2639, 0.2639, 0.3681 }, + { 0.2778, 0.2778, 0.3872 }, + { 0.2917, 0.2917, 0.4062 }, + { 0.3056, 0.3056, 0.4253 }, + { 0.3194, 0.3194, 0.4444 }, + { 0.3333, 0.3385, 0.4583 }, + { 0.3472, 0.3576, 0.4722 }, + { 0.3611, 0.3767, 0.4861 }, + { 0.375, 0.3958, 0.5 }, + { 0.3889, 0.4149, 0.5139 }, + { 0.4028, 0.434, 0.5278 }, + { 0.4167, 0.4531, 0.5417 }, + { 0.4306, 0.4722, 0.5556 }, + { 0.4444, 0.4913, 0.5694 }, + { 0.4583, 0.5104, 0.5833 }, + { 0.4722, 0.5295, 0.5972 }, + { 0.4861, 0.5486, 0.6111 }, + { 0.5, 0.5677, 0.625 }, + { 0.5139, 0.5868, 0.6389 }, + { 0.5278, 0.6059, 0.6528 }, + { 0.5417, 0.625, 0.6667 }, + { 0.5556, 0.6441, 0.6806 }, + { 0.5694, 0.6632, 0.6944 }, + { 0.5833, 0.6823, 0.7083 }, + { 0.5972, 0.7014, 0.7222 }, + { 0.6111, 0.7205, 0.7361 }, + { 0.625, 0.7396, 0.75 }, + { 0.6389, 0.7587, 0.7639 }, + { 0.6528, 0.7778, 0.7778 }, + { 0.6745, 0.7917, 0.7917 }, + { 0.6962, 0.8056, 0.8056 }, + { 0.7179, 0.8194, 0.8194 }, + { 0.7396, 0.8333, 0.8333 }, + { 0.7613, 0.8472, 0.8472 }, + { 0.783, 0.8611, 0.8611 }, + { 0.8047, 0.875, 0.875 }, + { 0.8264, 0.8889, 0.8889 }, + { 0.8481, 0.9028, 0.9028 }, + { 0.8698, 0.9167, 0.9167 }, + { 0.8915, 0.9306, 0.9306 }, + { 0.9132, 0.9444, 0.9444 }, + { 0.9349, 0.9583, 0.9583 }, + { 0.9566, 0.9722, 0.9722 }, + { 0.9783, 0.9861, 0.9861 }, + { 1.0, 1.0, 1.0 } + }; + } +//------------------------------------------------------- + public void setCool() + { + d = new double[][]{ + { 0.0, 1.0, 1.0 }, + { 0.0159, 0.9841, 1.0 }, + { 0.0317, 0.9683, 1.0 }, + { 0.0476, 0.9524, 1.0 }, + { 0.0635, 0.9365, 1.0 }, + { 0.0794, 0.9206, 1.0 }, + { 0.0952, 0.9048, 1.0 }, + { 0.1111, 0.8889, 1.0 }, + { 0.127, 0.873, 1.0 }, + { 0.1429, 0.8571, 1.0 }, + { 0.1587, 0.8413, 1.0 }, + { 0.1746, 0.8254, 1.0 }, + { 0.1905, 0.8095, 1.0 }, + { 0.2063, 0.7937, 1.0 }, + { 0.2222, 0.7778, 1.0 }, + { 0.2381, 0.7619, 1.0 }, + { 0.254, 0.746, 1.0 }, + { 0.2698, 0.7302, 1.0 }, + { 0.2857, 0.7143, 1.0 }, + { 0.3016, 0.6984, 1.0 }, + { 0.3175, 0.6825, 1.0 }, + { 0.3333, 0.6667, 1.0 }, + { 0.3492, 0.6508, 1.0 }, + { 0.3651, 0.6349, 1.0 }, + { 0.381, 0.619, 1.0 }, + { 0.3968, 0.6032, 1.0 }, + { 0.4127, 0.5873, 1.0 }, + { 0.4286, 0.5714, 1.0 }, + { 0.4444, 0.5556, 1.0 }, + { 0.4603, 0.5397, 1.0 }, + { 0.4762, 0.5238, 1.0 }, + { 0.4921, 0.5079, 1.0 }, + { 0.5079, 0.4921, 1.0 }, + { 0.5238, 0.4762, 1.0 }, + { 0.5397, 0.4603, 1.0 }, + { 0.5556, 0.4444, 1.0 }, + { 0.5714, 0.4286, 1.0 }, + { 0.5873, 0.4127, 1.0 }, + { 0.6032, 0.3968, 1.0 }, + { 0.619, 0.381, 1.0 }, + { 0.6349, 0.3651, 1.0 }, + { 0.6508, 0.3492, 1.0 }, + { 0.6667, 0.3333, 1.0 }, + { 0.6825, 0.3175, 1.0 }, + { 0.6984, 0.3016, 1.0 }, + { 0.7143, 0.2857, 1.0 }, + { 0.7302, 0.2698, 1.0 }, + { 0.746, 0.254, 1.0 }, + { 0.7619, 0.2381, 1.0 }, + { 0.7778, 0.2222, 1.0 }, + { 0.7937, 0.2063, 1.0 }, + { 0.8095, 0.1905, 1.0 }, + { 0.8254, 0.1746, 1.0 }, + { 0.8413, 0.1587, 1.0 }, + { 0.8571, 0.1429, 1.0 }, + { 0.873, 0.127, 1.0 }, + { 0.8889, 0.1111, 1.0 }, + { 0.9048, 0.0952, 1.0 }, + { 0.9206, 0.0794, 1.0 }, + { 0.9365, 0.0635, 1.0 }, + { 0.9524, 0.0476, 1.0 }, + { 0.9683, 0.0317, 1.0 }, + { 0.9841, 0.0159, 1.0 }, + { 1.0, 0.0, 1.0 } + }; + } +//------------------------------------------------------- + public void setCopper() + { + d = new double[][]{ + { 0.0, 0.0, 0.0 }, + { 0.0198, 0.0124, 0.0079 }, + { 0.0397, 0.0248, 0.0158 }, + { 0.0595, 0.0372, 0.0237 }, + { 0.0794, 0.0496, 0.0316 }, + { 0.0992, 0.062, 0.0395 }, + { 0.119, 0.0744, 0.0474 }, + { 0.1389, 0.0868, 0.0553 }, + { 0.1587, 0.0992, 0.0632 }, + { 0.1786, 0.1116, 0.0711 }, + { 0.1984, 0.124, 0.079 }, + { 0.2183, 0.1364, 0.0869 }, + { 0.2381, 0.1488, 0.0948 }, + { 0.2579, 0.1612, 0.1027 }, + { 0.2778, 0.1736, 0.1106 }, + { 0.2976, 0.186, 0.1185 }, + { 0.3175, 0.1984, 0.1263 }, + { 0.3373, 0.2108, 0.1342 }, + { 0.3571, 0.2232, 0.1421 }, + { 0.377, 0.2356, 0.15 }, + { 0.3968, 0.248, 0.1579 }, + { 0.4167, 0.2604, 0.1658 }, + { 0.4365, 0.2728, 0.1737 }, + { 0.4563, 0.2852, 0.1816 }, + { 0.4762, 0.2976, 0.1895 }, + { 0.496, 0.31, 0.1974 }, + { 0.5159, 0.3224, 0.2053 }, + { 0.5357, 0.3348, 0.2132 }, + { 0.5556, 0.3472, 0.2211 }, + { 0.5754, 0.3596, 0.229 }, + { 0.5952, 0.372, 0.2369 }, + { 0.6151, 0.3844, 0.2448 }, + { 0.6349, 0.3968, 0.2527 }, + { 0.6548, 0.4092, 0.2606 }, + { 0.6746, 0.4216, 0.2685 }, + { 0.6944, 0.434, 0.2764 }, + { 0.7143, 0.4464, 0.2843 }, + { 0.7341, 0.4588, 0.2922 }, + { 0.754, 0.4712, 0.3001 }, + { 0.7738, 0.4836, 0.308 }, + { 0.7937, 0.496, 0.3159 }, + { 0.8135, 0.5084, 0.3238 }, + { 0.8333, 0.5208, 0.3317 }, + { 0.8532, 0.5332, 0.3396 }, + { 0.873, 0.5456, 0.3475 }, + { 0.8929, 0.558, 0.3554 }, + { 0.9127, 0.5704, 0.3633 }, + { 0.9325, 0.5828, 0.3712 }, + { 0.9524, 0.5952, 0.379 }, + { 0.9722, 0.6076, 0.3869 }, + { 0.9921, 0.62, 0.3948 }, + { 1.0, 0.6324, 0.4027 }, + { 1.0, 0.6448, 0.4106 }, + { 1.0, 0.6572, 0.4185 }, + { 1.0, 0.6696, 0.4264 }, + { 1.0, 0.682, 0.4343 }, + { 1.0, 0.6944, 0.4422 }, + { 1.0, 0.7068, 0.4501 }, + { 1.0, 0.7192, 0.458 }, + { 1.0, 0.7316, 0.4659 }, + { 1.0, 0.744, 0.4738 }, + { 1.0, 0.7564, 0.4817 }, + { 1.0, 0.7688, 0.4896 }, + { 1.0, 0.7812, 0.4975 }, + }; + } +//------------------------------------------------------- + public void setGray() + { + d = new double[][]{ + { 0.0, 0.0, 0.0 }, + { 0.0159, 0.0159, 0.0159 }, + { 0.0317, 0.0317, 0.0317 }, + { 0.0476, 0.0476, 0.0476 }, + { 0.0635, 0.0635, 0.0635 }, + { 0.0794, 0.0794, 0.0794 }, + { 0.0952, 0.0952, 0.0952 }, + { 0.1111, 0.1111, 0.1111 }, + { 0.127, 0.127, 0.127 }, + { 0.1429, 0.1429, 0.1429 }, + { 0.1587, 0.1587, 0.1587 }, + { 0.1746, 0.1746, 0.1746 }, + { 0.1905, 0.1905, 0.1905 }, + { 0.2063, 0.2063, 0.2063 }, + { 0.2222, 0.2222, 0.2222 }, + { 0.2381, 0.2381, 0.2381 }, + { 0.254, 0.254, 0.254 }, + { 0.2698, 0.2698, 0.2698 }, + { 0.2857, 0.2857, 0.2857 }, + { 0.3016, 0.3016, 0.3016 }, + { 0.3175, 0.3175, 0.3175 }, + { 0.3333, 0.3333, 0.3333 }, + { 0.3492, 0.3492, 0.3492 }, + { 0.3651, 0.3651, 0.3651 }, + { 0.381, 0.381, 0.381 }, + { 0.3968, 0.3968, 0.3968 }, + { 0.4127, 0.4127, 0.4127 }, + { 0.4286, 0.4286, 0.4286 }, + { 0.4444, 0.4444, 0.4444 }, + { 0.4603, 0.4603, 0.4603 }, + { 0.4762, 0.4762, 0.4762 }, + { 0.4921, 0.4921, 0.4921 }, + { 0.5079, 0.5079, 0.5079 }, + { 0.5238, 0.5238, 0.5238 }, + { 0.5397, 0.5397, 0.5397 }, + { 0.5556, 0.5556, 0.5556 }, + { 0.5714, 0.5714, 0.5714 }, + { 0.5873, 0.5873, 0.5873 }, + { 0.6032, 0.6032, 0.6032 }, + { 0.619, 0.619, 0.619 }, + { 0.6349, 0.6349, 0.6349 }, + { 0.6508, 0.6508, 0.6508 }, + { 0.6667, 0.6667, 0.6667 }, + { 0.6825, 0.6825, 0.6825 }, + { 0.6984, 0.6984, 0.6984 }, + { 0.7143, 0.7143, 0.7143 }, + { 0.7302, 0.7302, 0.7302 }, + { 0.746, 0.746, 0.746 }, + { 0.7619, 0.7619, 0.7619 }, + { 0.7778, 0.7778, 0.7778 }, + { 0.7937, 0.7937, 0.7937 }, + { 0.8095, 0.8095, 0.8095 }, + { 0.8254, 0.8254, 0.8254 }, + { 0.8413, 0.8413, 0.8413 }, + { 0.8571, 0.8571, 0.8571 }, + { 0.873, 0.873, 0.873 }, + { 0.8889, 0.8889, 0.8889 }, + { 0.9048, 0.9048, 0.9048 }, + { 0.9206, 0.9206, 0.9206 }, + { 0.9365, 0.9365, 0.9365 }, + { 0.9524, 0.9524, 0.9524 }, + { 0.9683, 0.9683, 0.9683 }, + { 0.9841, 0.9841, 0.9841 }, + { 1.0, 1.0, 1.0 } + }; + } +//------------------------------------------------------- + public void setHot() + { + d = new double[][]{ + { 0.0417, 0.0, 0.0 }, + { 0.0833, 0.0, 0.0 }, + { 0.125, 0.0, 0.0 }, + { 0.1667, 0.0, 0.0 }, + { 0.2083, 0.0, 0.0 }, + { 0.25, 0.0, 0.0 }, + { 0.2917, 0.0, 0.0 }, + { 0.3333, 0.0, 0.0 }, + { 0.375, 0.0, 0.0 }, + { 0.4167, 0.0, 0.0 }, + { 0.4583, 0.0, 0.0 }, + { 0.5, 0.0, 0.0 }, + { 0.5417, 0.0, 0.0 }, + { 0.5833, 0.0, 0.0 }, + { 0.625, 0.0, 0.0 }, + { 0.6667, 0.0, 0.0 }, + { 0.7083, 0.0, 0.0 }, + { 0.75, 0.0, 0.0 }, + { 0.7917, 0.0, 0.0 }, + { 0.8333, 0.0, 0.0 }, + { 0.875, 0.0, 0.0 }, + { 0.9167, 0.0, 0.0 }, + { 0.9583, 0.0, 0.0 }, + { 1.0, 0.0, 0.0 }, + { 1.0, 0.0417, 0.0 }, + { 1.0, 0.0833, 0.0 }, + { 1.0, 0.125, 0.0 }, + { 1.0, 0.1667, 0.0 }, + { 1.0, 0.2083, 0.0 }, + { 1.0, 0.25, 0.0 }, + { 1.0, 0.2917, 0.0 }, + { 1.0, 0.3333, 0.0 }, + { 1.0, 0.375, 0.0 }, + { 1.0, 0.4167, 0.0 }, + { 1.0, 0.4583, 0.0 }, + { 1.0, 0.5, 0.0 }, + { 1.0, 0.5417, 0.0 }, + { 1.0, 0.5833, 0.0 }, + { 1.0, 0.625, 0.0 }, + { 1.0, 0.6667, 0.0 }, + { 1.0, 0.7083, 0.0 }, + { 1.0, 0.75, 0.0 }, + { 1.0, 0.7917, 0.0 }, + { 1.0, 0.8333, 0.0 }, + { 1.0, 0.875, 0.0 }, + { 1.0, 0.9167, 0.0 }, + { 1.0, 0.9583, 0.0 }, + { 1.0, 1.0, 0.0 }, + { 1.0, 1.0, 0.0625 }, + { 1.0, 1.0, 0.125 }, + { 1.0, 1.0, 0.1875 }, + { 1.0, 1.0, 0.25 }, + { 1.0, 1.0, 0.3125 }, + { 1.0, 1.0, 0.375 }, + { 1.0, 1.0, 0.4375 }, + { 1.0, 1.0, 0.5 }, + { 1.0, 1.0, 0.5625 }, + { 1.0, 1.0, 0.625 }, + { 1.0, 1.0, 0.6875 }, + { 1.0, 1.0, 0.75 }, + { 1.0, 1.0, 0.8125 }, + { 1.0, 1.0, 0.875 }, + { 1.0, 1.0, 0.9375 }, + { 1.0, 1.0, 1.0 }, + }; + } +//------------------------------------------------------- + public void setJet() + { + d = new double[][]{ + { 0.0, 0.0, 0.5625 }, + { 0.0, 0.0, 0.625 }, + { 0.0, 0.0, 0.6875 }, + { 0.0, 0.0, 0.75 }, + { 0.0, 0.0, 0.8125 }, + { 0.0, 0.0, 0.875 }, + { 0.0, 0.0, 0.9375 }, + { 0.0, 0.0, 1.0 }, + { 0.0, 0.0625, 1.0 }, + { 0.0, 0.125, 1.0 }, + { 0.0, 0.1875, 1.0 }, + { 0.0, 0.25, 1.0 }, + { 0.0, 0.3125, 1.0 }, + { 0.0, 0.375, 1.0 }, + { 0.0, 0.4375, 1.0 }, + { 0.0, 0.5, 1.0 }, + { 0.0, 0.5625, 1.0 }, + { 0.0, 0.625, 1.0 }, + { 0.0, 0.6875, 1.0 }, + { 0.0, 0.75, 1.0 }, + { 0.0, 0.8125, 1.0 }, + { 0.0, 0.875, 1.0 }, + { 0.0, 0.9375, 1.0 }, + { 0.0, 1.0, 1.0 }, + { 0.0625, 1.0, 0.9375 }, + { 0.125, 1.0, 0.875 }, + { 0.1875, 1.0, 0.8125 }, + { 0.25, 1.0, 0.75 }, + { 0.3125, 1.0, 0.6875 }, + { 0.375, 1.0, 0.625 }, + { 0.4375, 1.0, 0.5625 }, + { 0.5, 1.0, 0.5 }, + { 0.5625, 1.0, 0.4375 }, + { 0.625, 1.0, 0.375 }, + { 0.6875, 1.0, 0.3125 }, + { 0.75, 1.0, 0.25 }, + { 0.8125, 1.0, 0.1875 }, + { 0.875, 1.0, 0.125 }, + { 0.9375, 1.0, 0.0625 }, + { 1.0, 1.0, 0.0 }, + { 1.0, 0.9375, 0.0 }, + { 1.0, 0.875, 0.0 }, + { 1.0, 0.8125, 0.0 }, + { 1.0, 0.75, 0.0 }, + { 1.0, 0.6875, 0.0 }, + { 1.0, 0.625, 0.0 }, + { 1.0, 0.5625, 0.0 }, + { 1.0, 0.5, 0.0 }, + { 1.0, 0.4375, 0.0 }, + { 1.0, 0.375, 0.0 }, + { 1.0, 0.3125, 0.0 }, + { 1.0, 0.25, 0.0 }, + { 1.0, 0.1875, 0.0 }, + { 1.0, 0.125, 0.0 }, + { 1.0, 0.0625, 0.0 }, + { 1.0, 0.0, 0.0 }, + { 0.9375, 0.0, 0.0 }, + { 0.875, 0.0, 0.0 }, + { 0.8125, 0.0, 0.0 }, + { 0.75, 0.0, 0.0 }, + { 0.6875, 0.0, 0.0 }, + { 0.625, 0.0, 0.0 }, + { 0.5625, 0.0, 0.0 }, + { 0.5, 0.0, 0.0 } + }; + } +//------------------------------------------------------- + public void setPink() + { + d = new double[][]{ + { 0.1179, 0.0, 0.0 }, + { 0.1959, 0.1029, 0.1029 }, + { 0.2507, 0.1455, 0.1455 }, + { 0.2955, 0.1782, 0.1782 }, + { 0.3343, 0.2057, 0.2057 }, + { 0.3691, 0.23, 0.23 }, + { 0.4009, 0.252, 0.252 }, + { 0.4303, 0.2722, 0.2722 }, + { 0.4579, 0.291, 0.291 }, + { 0.4839, 0.3086, 0.3086 }, + { 0.5085, 0.3253, 0.3253 }, + { 0.532, 0.3412, 0.3412 }, + { 0.5546, 0.3563, 0.3563 }, + { 0.5762, 0.3709, 0.3709 }, + { 0.5971, 0.3849, 0.3849 }, + { 0.6172, 0.3984, 0.3984 }, + { 0.6367, 0.4115, 0.4115 }, + { 0.6557, 0.4241, 0.4241 }, + { 0.6741, 0.4364, 0.4364 }, + { 0.692, 0.4484, 0.4484 }, + { 0.7094, 0.46, 0.46 }, + { 0.7265, 0.4714, 0.4714 }, + { 0.7431, 0.4825, 0.4825 }, + { 0.7594, 0.4933, 0.4933 }, + { 0.7664, 0.5175, 0.504 }, + { 0.7732, 0.5407, 0.5143 }, + { 0.78, 0.5628, 0.5245 }, + { 0.7868, 0.5842, 0.5345 }, + { 0.7935, 0.6048, 0.5443 }, + { 0.8001, 0.6247, 0.554 }, + { 0.8067, 0.644, 0.5634 }, + { 0.8133, 0.6627, 0.5727 }, + { 0.8197, 0.6809, 0.5819 }, + { 0.8262, 0.6986, 0.5909 }, + { 0.8325, 0.7159, 0.5998 }, + { 0.8389, 0.7328, 0.6086 }, + { 0.8452, 0.7493, 0.6172 }, + { 0.8514, 0.7655, 0.6257 }, + { 0.8576, 0.7813, 0.6341 }, + { 0.8637, 0.7968, 0.6424 }, + { 0.8698, 0.812, 0.6506 }, + { 0.8759, 0.827, 0.6587 }, + { 0.8819, 0.8416, 0.6667 }, + { 0.8879, 0.856, 0.6746 }, + { 0.8938, 0.8702, 0.6824 }, + { 0.8997, 0.8842, 0.6901 }, + { 0.9056, 0.8979, 0.6977 }, + { 0.9114, 0.9114, 0.7052 }, + { 0.9172, 0.9172, 0.7272 }, + { 0.923, 0.923, 0.7485 }, + { 0.9287, 0.9287, 0.7692 }, + { 0.9344, 0.9344, 0.7893 }, + { 0.94, 0.94, 0.809 }, + { 0.9456, 0.9456, 0.8282 }, + { 0.9512, 0.9512, 0.8469 }, + { 0.9567, 0.9567, 0.8653 }, + { 0.9623, 0.9623, 0.8832 }, + { 0.9677, 0.9677, 0.9008 }, + { 0.9732, 0.9732, 0.9181 }, + { 0.9786, 0.9786, 0.9351 }, + { 0.984, 0.984, 0.9517 }, + { 0.9894, 0.9894, 0.9681 }, + { 0.9947, 0.9947, 0.9842 }, + { 1.0, 1.0, 1.0 } + }; + } +//------------------------------------------------------- + public void setSpring() + { + d = new double[][]{ + { 1.0, 0.0, 1.0 }, + { 1.0, 0.0159, 0.9841 }, + { 1.0, 0.0317, 0.9683 }, + { 1.0, 0.0476, 0.9524 }, + { 1.0, 0.0635, 0.9365 }, + { 1.0, 0.0794, 0.9206 }, + { 1.0, 0.0952, 0.9048 }, + { 1.0, 0.1111, 0.8889 }, + { 1.0, 0.127, 0.873 }, + { 1.0, 0.1429, 0.8571 }, + { 1.0, 0.1587, 0.8413 }, + { 1.0, 0.1746, 0.8254 }, + { 1.0, 0.1905, 0.8095 }, + { 1.0, 0.2063, 0.7937 }, + { 1.0, 0.2222, 0.7778 }, + { 1.0, 0.2381, 0.7619 }, + { 1.0, 0.254, 0.746 }, + { 1.0, 0.2698, 0.7302 }, + { 1.0, 0.2857, 0.7143 }, + { 1.0, 0.3016, 0.6984 }, + { 1.0, 0.3175, 0.6825 }, + { 1.0, 0.3333, 0.6667 }, + { 1.0, 0.3492, 0.6508 }, + { 1.0, 0.3651, 0.6349 }, + { 1.0, 0.381, 0.619 }, + { 1.0, 0.3968, 0.6032 }, + { 1.0, 0.4127, 0.5873 }, + { 1.0, 0.4286, 0.5714 }, + { 1.0, 0.4444, 0.5556 }, + { 1.0, 0.4603, 0.5397 }, + { 1.0, 0.4762, 0.5238 }, + { 1.0, 0.4921, 0.5079 }, + { 1.0, 0.5079, 0.4921 }, + { 1.0, 0.5238, 0.4762 }, + { 1.0, 0.5397, 0.4603 }, + { 1.0, 0.5556, 0.4444 }, + { 1.0, 0.5714, 0.4286 }, + { 1.0, 0.5873, 0.4127 }, + { 1.0, 0.6032, 0.3968 }, + { 1.0, 0.619, 0.381 }, + { 1.0, 0.6349, 0.3651 }, + { 1.0, 0.6508, 0.3492 }, + { 1.0, 0.6667, 0.3333 }, + { 1.0, 0.6825, 0.3175 }, + { 1.0, 0.6984, 0.3016 }, + { 1.0, 0.7143, 0.2857 }, + { 1.0, 0.7302, 0.2698 }, + { 1.0, 0.746, 0.254 }, + { 1.0, 0.7619, 0.2381 }, + { 1.0, 0.7778, 0.2222 }, + { 1.0, 0.7937, 0.2063 }, + { 1.0, 0.8095, 0.1905 }, + { 1.0, 0.8254, 0.1746 }, + { 1.0, 0.8413, 0.1587 }, + { 1.0, 0.8571, 0.1429 }, + { 1.0, 0.873, 0.127 }, + { 1.0, 0.8889, 0.1111 }, + { 1.0, 0.9048, 0.0952 }, + { 1.0, 0.9206, 0.0794 }, + { 1.0, 0.9365, 0.0635 }, + { 1.0, 0.9524, 0.0476 }, + { 1.0, 0.9683, 0.0317 }, + { 1.0, 0.9841, 0.0159 }, + { 1.0, 1.0, 0.0 } + }; + } +//------------------------------------------------------- + public void setSummer() + { + d = new double[][]{ + { 0.0, 0.5, 0.4 }, + { 0.0159, 0.5079, 0.4 }, + { 0.0317, 0.5159, 0.4 }, + { 0.0476, 0.5238, 0.4 }, + { 0.0635, 0.5317, 0.4 }, + { 0.0794, 0.5397, 0.4 }, + { 0.0952, 0.5476, 0.4 }, + { 0.1111, 0.5556, 0.4 }, + { 0.127, 0.5635, 0.4 }, + { 0.1429, 0.5714, 0.4 }, + { 0.1587, 0.5794, 0.4 }, + { 0.1746, 0.5873, 0.4 }, + { 0.1905, 0.5952, 0.4 }, + { 0.2063, 0.6032, 0.4 }, + { 0.2222, 0.6111, 0.4 }, + { 0.2381, 0.619, 0.4 }, + { 0.254, 0.627, 0.4 }, + { 0.2698, 0.6349, 0.4 }, + { 0.2857, 0.6429, 0.4 }, + { 0.3016, 0.6508, 0.4 }, + { 0.3175, 0.6587, 0.4 }, + { 0.3333, 0.6667, 0.4 }, + { 0.3492, 0.6746, 0.4 }, + { 0.3651, 0.6825, 0.4 }, + { 0.381, 0.6905, 0.4 }, + { 0.3968, 0.6984, 0.4 }, + { 0.4127, 0.7063, 0.4 }, + { 0.4286, 0.7143, 0.4 }, + { 0.4444, 0.7222, 0.4 }, + { 0.4603, 0.7302, 0.4 }, + { 0.4762, 0.7381, 0.4 }, + { 0.4921, 0.746, 0.4 }, + { 0.5079, 0.754, 0.4 }, + { 0.5238, 0.7619, 0.4 }, + { 0.5397, 0.7698, 0.4 }, + { 0.5556, 0.7778, 0.4 }, + { 0.5714, 0.7857, 0.4 }, + { 0.5873, 0.7937, 0.4 }, + { 0.6032, 0.8016, 0.4 }, + { 0.619, 0.8095, 0.4 }, + { 0.6349, 0.8175, 0.4 }, + { 0.6508, 0.8254, 0.4 }, + { 0.6667, 0.8333, 0.4 }, + { 0.6825, 0.8413, 0.4 }, + { 0.6984, 0.8492, 0.4 }, + { 0.7143, 0.8571, 0.4 }, + { 0.7302, 0.8651, 0.4 }, + { 0.746, 0.873, 0.4 }, + { 0.7619, 0.881, 0.4 }, + { 0.7778, 0.8889, 0.4 }, + { 0.7937, 0.8968, 0.4 }, + { 0.8095, 0.9048, 0.4 }, + { 0.8254, 0.9127, 0.4 }, + { 0.8413, 0.9206, 0.4 }, + { 0.8571, 0.9286, 0.4 }, + { 0.873, 0.9365, 0.4 }, + { 0.8889, 0.9444, 0.4 }, + { 0.9048, 0.9524, 0.4 }, + { 0.9206, 0.9603, 0.4 }, + { 0.9365, 0.9683, 0.4 }, + { 0.9524, 0.9762, 0.4 }, + { 0.9683, 0.9841, 0.4 }, + { 0.9841, 0.9921, 0.4 }, + { 1.0, 1.0, 0.4 } + }; + } +//------------------------------------------------------- + public void setWinter() + { + d = new double[][]{ + { 0.0, 0.0, 1.0 }, + { 0.0, 0.0159, 0.9921 }, + { 0.0, 0.0317, 0.9841 }, + { 0.0, 0.0476, 0.9762 }, + { 0.0, 0.0635, 0.9683 }, + { 0.0, 0.0794, 0.9603 }, + { 0.0, 0.0952, 0.9524 }, + { 0.0, 0.1111, 0.9444 }, + { 0.0, 0.127, 0.9365 }, + { 0.0, 0.1429, 0.9286 }, + { 0.0, 0.1587, 0.9206 }, + { 0.0, 0.1746, 0.9127 }, + { 0.0, 0.1905, 0.9048 }, + { 0.0, 0.2063, 0.8968 }, + { 0.0, 0.2222, 0.8889 }, + { 0.0, 0.2381, 0.881 }, + { 0.0, 0.254, 0.873 }, + { 0.0, 0.2698, 0.8651 }, + { 0.0, 0.2857, 0.8571 }, + { 0.0, 0.3016, 0.8492 }, + { 0.0, 0.3175, 0.8413 }, + { 0.0, 0.3333, 0.8333 }, + { 0.0, 0.3492, 0.8254 }, + { 0.0, 0.3651, 0.8175 }, + { 0.0, 0.381, 0.8095 }, + { 0.0, 0.3968, 0.8016 }, + { 0.0, 0.4127, 0.7937 }, + { 0.0, 0.4286, 0.7857 }, + { 0.0, 0.4444, 0.7778 }, + { 0.0, 0.4603, 0.7698 }, + { 0.0, 0.4762, 0.7619 }, + { 0.0, 0.4921, 0.754 }, + { 0.0, 0.5079, 0.746 }, + { 0.0, 0.5238, 0.7381 }, + { 0.0, 0.5397, 0.7302 }, + { 0.0, 0.5556, 0.7222 }, + { 0.0, 0.5714, 0.7143 }, + { 0.0, 0.5873, 0.7063 }, + { 0.0, 0.6032, 0.6984 }, + { 0.0, 0.619, 0.6905 }, + { 0.0, 0.6349, 0.6825 }, + { 0.0, 0.6508, 0.6746 }, + { 0.0, 0.6667, 0.6667 }, + { 0.0, 0.6825, 0.6587 }, + { 0.0, 0.6984, 0.6508 }, + { 0.0, 0.7143, 0.6429 }, + { 0.0, 0.7302, 0.6349 }, + { 0.0, 0.746, 0.627 }, + { 0.0, 0.7619, 0.619 }, + { 0.0, 0.7778, 0.6111 }, + { 0.0, 0.7937, 0.6032 }, + { 0.0, 0.8095, 0.5952 }, + { 0.0, 0.8254, 0.5873 }, + { 0.0, 0.8413, 0.5794 }, + { 0.0, 0.8571, 0.5714 }, + { 0.0, 0.873, 0.5635 }, + { 0.0, 0.8889, 0.5556 }, + { 0.0, 0.9048, 0.5476 }, + { 0.0, 0.9206, 0.5397 }, + { 0.0, 0.9365, 0.5317 }, + { 0.0, 0.9524, 0.5238 }, + { 0.0, 0.9683, 0.5159 }, + { 0.0, 0.9841, 0.5079 }, + { 0.0, 1.0, 0.5 } + }; + } +//------------------------------------------------------- + public void getRGB(double alpha, RGB rgb) + { + + double d1,d2,d3; + double d1a,d2a,d3a; + double d1b,d2b,d3b; + int index1,index2; + + if (alpha==0){ + d1=d[0][0]; + d2=d[0][1]; + d3=d[0][2]; + } + else if (alpha==1){ + d1=d[rowNumber-1][0]; + d2=d[rowNumber-1][1]; + d3=d[rowNumber-1][2]; + } + else{ + index1=(int)(alpha*(rowNumber-1)); + index2=index1+1; + + d1a=d[index1][0]; + d2a=d[index1][1]; + d3a=d[index1][2]; + + d1b=d[index2][0]; + d2b=d[index2][1]; + d3b=d[index2][2]; + + d1=(d1a+d1b)/2; + d2=(d2a+d2b)/2; + d3=(d3a+d3b)/2; + } + + rgb.setR( (float) d1); + rgb.setG( (float) d2); + rgb.setB( (float) d3); + } +//------------------------------------------------------- +} // end class colorMap +///////////////////////////////////////////////////////// +class RGB +{ + private float R,G,B; +//------------------------------------------------------- + public void setR(float value) {this.R = value;} + public void setG(float value) {this.G = value;} + public void setB(float value) {this.B = value;} + public float getR() { return R;} + public float getG() { return G;} + public float getB() { return B;} +//------------------------------------------------------- +} //end class RGB +///////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/ISSM.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/ISSM.java (revision 14309) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/ISSM.java (revision 14310) @@ -1,26 +1,32 @@ package com.example.issm; -import java.io.IOException; -import java.io.InputStream; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.DoubleBuffer; - +import android.opengl.GLSurfaceView; +import android.os.AsyncTask; import android.os.Bundle; import android.app.Activity; -import android.content.res.AssetManager; -import android.text.TextUtils; +import android.app.ProgressDialog; import android.view.Menu; +import android.view.MenuInflater; +import android.view.MenuItem; import android.view.View; import android.view.View.OnClickListener; +import android.view.animation.AccelerateInterpolator; +import android.view.animation.Animation; +import android.view.animation.TranslateAnimation; import android.widget.Button; -import android.widget.EditText; +import android.widget.FrameLayout; +import android.widget.ImageButton; +import android.widget.SeekBar; +import android.widget.SeekBar.OnSeekBarChangeListener; import android.widget.TextView; - - -public class ISSM extends Activity implements OnClickListener +import android.widget.Toast; +import android.widget.ViewFlipper; + + +public class ISSM extends Activity implements OnClickListener { - private EditText input; - private TextView output; private DoubleBuffer buff; private IssmJni issmNative; @@ -28,62 +34,313 @@ private String issmFolder; private int size; + private GLSurfaceView mGLView; + private FrameLayout frame; + private VerticalSeekBar bar; + private TextView value; + private ColorMap colorMap; + private int alpha; + private final int MINIMUM = 90; + private final int OFFSET = 10; + private ViewFlipper viewflipper; + private ProgressDialog dialog; + private ColorBar colorBar; + //------------------------------------------------------------------------------------------------ @Override - //------------------------------------------------------------------------------------------------ - public void onCreate(Bundle savedInstanceState) { + public void onCreate(Bundle savedInstanceState) + { super.onCreate(savedInstanceState); - Bundle map = getIntent().getExtras(); + setContentView(R.layout.main_issm); + this.initialize(); + } + //---------------------------------------------------------------------------------------------- + private void initialize() + { + Bundle map = getIntent().getExtras(); { if(map!= null) { - mapName = map.getString("map"); issmFolder = map.getString("pathToFile"); } } - setContentView(R.layout.activity_issm); - this.input = (EditText) super.findViewById(R.id.input); - this.output = (TextView) super.findViewById(R.id.output); - Button button = (Button) super.findViewById(R.id.button1); - button.setOnClickListener(this); + alpha = MINIMUM + OFFSET; + frame = (FrameLayout)findViewById(R.id.frame); + viewflipper = (ViewFlipper) findViewById(R.id.flipper); + this.bar = (VerticalSeekBar) findViewById(R.id.seekbar); + this.value = (TextView) super.findViewById(R.id.value); + Button solve = (Button) super.findViewById(R.id.solve); + solve.setOnClickListener(this); + Button back = (Button) super.findViewById(R.id.back); + back.setOnClickListener(this); + ImageButton gl = (ImageButton) findViewById(R.id.greenland); + gl.setOnClickListener(this); + ImageButton art = (ImageButton) findViewById(R.id.antarctica); + art.setOnClickListener(this); + bar.setOnSeekBarChangeListener(new OnSeekBarChangeListener() + { + public void onProgressChanged(SeekBar seekBar, int progress,boolean fromUser) + { + + alpha = progress + OFFSET; + value.setText("" + alpha + "%"); + } + + @Override + public void onStartTrackingTouch(SeekBar seekBar) {} + + @Override + public void onStopTrackingTouch(SeekBar seekBar) {} + }); + + //load up the ISSM library and create double buffer in java + //which later on will be pass for native for allocation. + issmNative = new IssmJni(); - //load up the ISSM library and create double buffer in java - //which later on will be pass for native allocation. - issmNative = new IssmJni(); - buff = ByteBuffer.allocateDirect(15*8).order(ByteOrder.nativeOrder()).asDoubleBuffer(); - this.createModel(); + //set default color map to be HSV + this.colorMap = new ColorMap(); + //create colorBar + colorBar = new ColorBar(this); + colorBar.setColorMap(colorMap); } //------------------------------------------------------------------------------------------------ public void createModel() { + String solution_type="DiagnosticSolution"; String file = ""; if( mapName.equals("greenland")) { - file = "test102.petsc"; - } - else file = "test102.petsc"; - size = issmNative.createISSMModel(issmFolder + file); - } -//------------------------------------------------------------------------------------------------ - public void fillBuffer() - { - issmNative.processBuffer(5,buff); - } - //------------------------------------------------------------------------------------------------ + file = "greenland"; + } + else file = "antarctica"; + + size = issmNative.createISSMModel(solution_type,issmFolder,file); + buff = ByteBuffer.allocateDirect(size*12*8).order(ByteOrder.nativeOrder()).asDoubleBuffer(); + } +//------------------------------------------------------------------------------------------------ + public boolean onCreateOptionsMenu(Menu menu) + { + MenuInflater menuInflater = getMenuInflater(); + menuInflater.inflate(R.menu.issm_menu,menu); + + return true; + } +//------------------------------------------------------------------------------------------------ + //Option Menu that allow user to choose color. + public boolean onOptionsItemSelected(MenuItem item) + { + switch (item.getItemId()) + { + case R.id.menu_about: + Toast.makeText(ISSM.this, "ISSM Application", Toast.LENGTH_SHORT).show(); + return true; + + case R.id.cl_autumn: + colorMap.setAutumn(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_bone: + colorMap.setBone(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_cool: + colorMap.setCool(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_copper: + colorMap.setCopper(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_gray: + colorMap.setGray(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_hot: + colorMap.setGray(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_hsv: + colorMap.setDefault(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_jet: + colorMap.setJet(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_pink: + colorMap.setPink(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_spring: + colorMap.setSpring(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_summer: + colorMap.setSummer(); colorBar.setColorMap(colorMap); + drawFigure(); + return true; + + case R.id.cl_winter: + colorMap.setWinter();colorBar.setColorMap(colorMap); + drawFigure(); + return true; + default: + return super.onOptionsItemSelected(item); + } + + } +// + +//--------------------------------------------------------------------------------- public void onClick(View view) { - //factorial method - String input = this.input.getText().toString(); - if(TextUtils.isEmpty(input)) - { - return; - } - long resultfromFac = issmNative.fac(Long.parseLong(input)); - //example of how to fill buffer Native - this.fillBuffer(); + switch(view.getId()) + { + case R.id.greenland: + { + mapName= "greenland"; + viewflipper.setInAnimation(inFromRightAnimation()); + viewflipper.setOutAnimation(outToLeftAnimation()); + viewflipper.showNext(); + //create FemModel in native code and return the size of the model + this.createModel(); + break; + } + case R.id.antarctica: + { + mapName= "antarctica"; + viewflipper.setInAnimation(inFromRightAnimation()); + viewflipper.setOutAnimation(outToLeftAnimation()); + viewflipper.showNext(); + //create FemModel in native code and return the size of the model + this.createModel(); + break; + } + case R.id.back: + { + frame.removeView(mGLView); + viewflipper.setInAnimation(inFromLeftAnimation()); + viewflipper.setOutAnimation(outToRightAnimation()); + viewflipper.showPrevious(); + break; + } + case R.id.solve: + { + dialog = new ProgressDialog(view.getContext()); + dialog.setCancelable(true); + dialog.setMessage("Loading View. Please Wait ..."); + dialog.setProgressStyle(ProgressDialog.STYLE_HORIZONTAL); + dialog.setProgress(0); + dialog.setMax(100); + new CalculationTask().execute(alpha); + break; + } + } + } +//---------------------------------------------------------------------------------- + public void drawFigure() + { + frame.removeAllViews(); + mGLView = new MyGLSurfaceView(this, buff, size, colorMap); + frame.addView(mGLView); + //frame.addView(colorBar); + } +//------------------------------------------------------------------------------------ + //AsyncTask will allow to display while doing some task in the background + private class CalculationTask extends AsyncTask + { + @Override + protected Boolean doInBackground(Integer... target) + { + Thread thread = new Thread() + { + public void run() + { + for(int i = 0; i <= 100; i+=5) + { + try { + Thread.sleep(300); + } catch (InterruptedException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + publishProgress(i); + } + } + }; + thread.start(); + issmNative.solveISSMModel(target[0],buff); + return true; + } - //print result from fac and the first two slot of filled buffer. - this.output.setText("Result = " + resultfromFac + "\n" - + "First slot from buffer:\n" - + buff.get(0) + " size " + size); - - } + protected void onPreExecute() + { + super.onPostExecute(null); + dialog.show(); + } + protected void onProgressUpdate(Integer ... value) + { + super.onProgressUpdate(); + dialog.setProgress(value[0]); + } + protected void onPostExecute(Boolean result) + { + super.onPostExecute(result); + dialog.dismiss(); + if(result) drawFigure(); + } + + } +//----------------------------------------------------------------------------------- + + // Below are implementation for the animation between map selection and core computation + + private Animation inFromRightAnimation() { + + Animation inFromRight = new TranslateAnimation( + Animation.RELATIVE_TO_PARENT, +1.0f, Animation.RELATIVE_TO_PARENT, 0.0f, + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, 0.0f + ); + inFromRight.setDuration(500); + inFromRight.setInterpolator(new AccelerateInterpolator()); + return inFromRight; + } + private Animation outToLeftAnimation() { + Animation outtoLeft = new TranslateAnimation( + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, -1.0f, + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, 0.0f + ); + outtoLeft.setDuration(500); + outtoLeft.setInterpolator(new AccelerateInterpolator()); + return outtoLeft; + } + + private Animation inFromLeftAnimation() { + Animation inFromLeft = new TranslateAnimation( + Animation.RELATIVE_TO_PARENT, -1.0f, Animation.RELATIVE_TO_PARENT, 0.0f, + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, 0.0f + ); + inFromLeft.setDuration(500); + inFromLeft.setInterpolator(new AccelerateInterpolator()); + return inFromLeft; + } + private Animation outToRightAnimation() { + Animation outtoRight = new TranslateAnimation( + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, +1.0f, + Animation.RELATIVE_TO_PARENT, 0.0f, Animation.RELATIVE_TO_PARENT, 0.0f + ); + outtoRight.setDuration(500); + outtoRight.setInterpolator(new AccelerateInterpolator()); + return outtoRight; + } +//------------------------------------------------------------------------------------------- } +///////////////////////////////////////////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/IssmJni.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/IssmJni.java (revision 14309) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/IssmJni.java (revision 14310) @@ -4,7 +4,6 @@ class IssmJni { - public native long fac(long n); - public native void processBuffer(int alpha, DoubleBuffer buff); - public native int createISSMModel(String file); + public native void solveISSMModel(double alpha, DoubleBuffer buff); + public native int createISSMModel(String solution_type, String absfile, String relfile); static { Index: sm/trunk/src/android/ISSM/src/com/example/issm/MapSelection.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/MapSelection.java (revision 14309) +++ (revision ) @@ -1,143 +1,0 @@ -package com.example.issm; - -import java.io.File; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; - -import android.app.Activity; -import android.os.Bundle; -import android.os.Environment; -import android.text.TextUtils; -import android.util.Log; -import android.view.Menu; -import android.view.View; -import android.widget.Button; -import android.widget.Toast; -import android.content.Intent; -import android.content.SharedPreferences; -import android.content.res.AssetManager; -/////////////////////////////////////////////////////////////////////////// -public class MapSelection extends Activity -{ - ISSM issm = new ISSM(); - private static final String PREFERENCE_FIRST_RUN = null; - private String extStorageDirectory; - private String issmFolder; -//------------------------------------------------------------------------ - public void onCreate(Bundle icicle) - { - super.onCreate(icicle); - setContentView(R.layout.activity_mapselection); - - SharedPreferences settings = this.getSharedPreferences("ISSM", 0); - boolean firstrun = settings.getBoolean(PREFERENCE_FIRST_RUN, true); - extStorageDirectory = Environment.getExternalStorageDirectory().toString(); - - issmFolder = extStorageDirectory + "/ISSM/input_files/"; - if (firstrun) - { // Checks to see if we've ran the application b4 - SharedPreferences.Editor e = settings.edit(); - e.putBoolean(PREFERENCE_FIRST_RUN, false); - - e.commit(); - // If not, run these methods: - SetDirectory(issmFolder); - } - - - //this button represents greenland and pass signal to issm - Button gl = (Button) findViewById(R.id.button1); - gl.setOnClickListener(new View.OnClickListener() - { - public void onClick(View v) - { - Intent i = new Intent(MapSelection.this, ISSM.class); - i.putExtra("map", "greenland"); - i.putExtra("pathToFile", issmFolder); - startActivity(i); - } - }); - - //this button represents artarctica and pass signal to issm - Button art = (Button) findViewById(R.id.button2); - art.setOnClickListener(new View.OnClickListener() - { - public void onClick(View v) - { - Intent i = new Intent(MapSelection.this, ISSM.class); - i.putExtra("map", "antarctica"); - i.putExtra("pathToFile", issmFolder); - startActivity(i); - } - }); - } -//------------------------------------------------------------------------ - private void SetDirectory(String directory) - { - if (android.os.Environment.getExternalStorageState().equals(android.os.Environment.MEDIA_MOUNTED)) - { - System.out.println(issmFolder); - File txtDirectory = new File(issmFolder); - - // Check and create directory in SDcard - if(!txtDirectory.exists()) - { - txtDirectory.mkdirs(); - System.out.println("making directory"); - } - CopyAssets(); // Then run the method to copy the file. - - } - else if (android.os.Environment.getExternalStorageState().equals(android.os.Environment.MEDIA_MOUNTED_READ_ONLY)) - { - Toast toast = Toast.makeText(this.getApplicationContext(), "Memory is not mounted to device", Toast.LENGTH_LONG); - toast.show(); - } - - } -//---------------------------------------------------------------------------- - /** - * -- Copy the file from the assets folder to the sdCard - * =========================================================== - **/ - private void CopyAssets() - { - AssetManager assetManager = getAssets(); - String[] files = null; - try { - files = assetManager.list("Map"); - } catch (IOException e) { - Log.e("tag", e.getMessage()); - } - for (int i = 0; i < files.length; i++) { - InputStream in = null; - OutputStream out = null; - try { - in = assetManager.open("Map/"+files[i]); - out = new FileOutputStream(issmFolder + files[i]); - copyFile(in, out); - in.close(); - in = null; - out.flush(); - out.close(); - out = null; - } catch (Exception e) { - Log.e("tag", e.getMessage()); - } - } - System.out.println("Done"); - } -//---------------------------------------------------------------------------- - private void copyFile(InputStream in, OutputStream out) throws IOException - { - byte[] buffer = new byte[1024]; - int read; - while ((read = in.read(buffer)) != -1) { - out.write(buffer, 0, read); - } - } -//---------------------------------------------------------------------------- -} -/////////////////////////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/MenuPage.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/MenuPage.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/MenuPage.java (revision 14310) @@ -0,0 +1,88 @@ +package com.example.issm; + +import android.app.Activity; +import android.net.Uri; +import android.os.Bundle; +import android.view.Gravity; +import android.view.LayoutInflater; +import android.view.View; +import android.widget.Button; +import android.widget.ImageButton; +import android.widget.PopupWindow; +import android.content.Intent; +/////////////////////////////////////////////////////////////////////////// +public class MenuPage extends Activity +{ + ISSM issm = new ISSM(); + private String issmFolder; +//------------------------------------------------------------------------ + public void onCreate(Bundle icicle) + { + super.onCreate(icicle); + setContentView(R.layout.menupage); + Bundle map = getIntent().getExtras(); + { + if(map!= null) + { + issmFolder = map.getString("pathToFile"); + } + } + //start the core implementation of ISSM + ImageButton start = (ImageButton) findViewById(R.id.start); + start.setOnClickListener(new View.OnClickListener() + { + public void onClick(View v) + { + Intent i = new Intent(MenuPage.this, ISSM.class); + i.putExtra("pathToFile", issmFolder); + startActivity(i); + } + }); + // navigate to youtube video + ImageButton video = (ImageButton) findViewById(R.id.video); + video.setOnClickListener(new View.OnClickListener() + { + public void onClick(View v) + { + String url = "http://www.youtube.com/watch?v=KlDO0C8r_ws"; + Intent i = new Intent(Intent.ACTION_VIEW); + i.setData(Uri.parse(url)); + startActivity(i); + } + }); + // pop up a text box that contains information about ISSM + final ImageButton intro = (ImageButton) findViewById(R.id.intro); + intro.setOnClickListener(new View.OnClickListener() + { + public void onClick(View v) + { + LayoutInflater layoutInflater = (LayoutInflater)getBaseContext().getSystemService(LAYOUT_INFLATER_SERVICE); + View popupView = layoutInflater.inflate(R.layout.popuptext, null); + final PopupWindow popupWindow = new PopupWindow( popupView, 400,600, true); + popupWindow.showAtLocation(popupView, Gravity.CENTER, 0, 0); + Button dismiss = (Button)popupView.findViewById(R.id.dismiss); + dismiss.setOnClickListener(new Button.OnClickListener() + { + public void onClick(View v) + { + popupWindow.dismiss(); + } + }); + } + }); + //navigate to website + ImageButton visitus = (ImageButton) findViewById(R.id.visitus); + visitus.setOnClickListener(new View.OnClickListener() + { + public void onClick(View v) + { + String url = "http://issm.jpl.nasa.gov/"; + Intent i = new Intent(Intent.ACTION_VIEW); + i.setData(Uri.parse(url)); + startActivity(i); + } + }); + } +//------------------------------------------------------------------------------------- +} +///////////////////////////////////////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLRenderer.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLRenderer.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLRenderer.java (revision 14310) @@ -0,0 +1,349 @@ +/* + * Copyright (C) 2012 The Android Open Source Project + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package com.example.issm; +import java.nio.ByteBuffer; +import java.nio.ByteOrder; +import java.nio.FloatBuffer; + +import javax.microedition.khronos.egl.EGLConfig; +import javax.microedition.khronos.opengles.GL10; + +import android.opengl.GLES20; +import android.opengl.GLSurfaceView; +import android.opengl.Matrix; + +public class MyGLRenderer implements GLSurfaceView.Renderer +{ + public volatile float mAngle; + public volatile float mAngleX; /* NEW STUFF*/ + public volatile float mAngleY; + + + private FloatBuffer[] triangleVert; + + private float[][] mScaleMatrix; // scaling /* NEW STUFF*/ + private float[][] mRotXMatrix; // rotation x + private float[][] mRotYMatrix; // rotation x + + /** + * Store the model matrix. This matrix is used to move models from object space (where each model can be thought + * of being located at the center of the universe) to world space. + */ + private float[][] mModelMatrix; + + /** + * Store the view matrix. This can be thought of as our camera. This matrix transforms world space to eye space; + * it positions things relative to our eye. + */ + private float[][] mViewMatrix; + + /** Store the projection matrix. This is used to project the scene onto a 2D viewport. */ + private float[][] mProjectionMatrix; + + /** Allocate storage for the final combined matrix. This will be passed into the shader program. */ + private float[][] mMVPMatrix; + + /** This will be used to pass in the transformation matrix. */ + private int mMatrixHandle; + + private float[][] triangleData2DArr; + + private int mPositionHandle; + + private int mColorHandle; + + /** How many bytes per float. */ + private final int mBytesPerFloat = 4; + + /** How many elements per vertex. */ + private final int mStrideBytes = 7 * mBytesPerFloat; + + /** Offset of the position data. */ + private final int mPositionOffset = 0; + + /** Size of the position data in elements. */ + private final int mPositionDataSize = 3; + + /** Offset of the color data. */ + private final int mColorOffset = 3; + + /** Size of the color data in elements. */ + private final int mColorDataSize = 4; + + // scaling /* NEW STUFF*/ + float scaleX = 1.0f; + float scaleY = 1.0f; + float scaleZ = 1.0f; + + public float eyeX; + public float eyeY; + public float eyeZ; + + public MyGLRenderer(float[][] vertices) + { + triangleData2DArr = new float[vertices.length][21]; + + triangleVert = new FloatBuffer[vertices.length]; + mScaleMatrix = new float[triangleVert.length][16]; // scaling /* NEW STUFF*/ + mRotXMatrix = new float[triangleVert.length][16]; // rotation x + mRotYMatrix = new float[triangleVert.length][16]; // rotation x + + for (int i = 0; i < vertices.length; i++) + { + for (int j = 0; j < 21; j++) + triangleData2DArr[i][j] = vertices[i][j]; + } + + // initialize vertex byte buffer for shape coordinates + for (int i = 0; i < vertices.length; i++) + { + triangleVert[i] = ByteBuffer.allocateDirect(triangleData2DArr[i].length * mBytesPerFloat) + .order(ByteOrder.nativeOrder()).asFloatBuffer(); + triangleVert[i].put(triangleData2DArr[i]).position(0); + } + } + + public void changeScale(float scale) /* NEW STUFF*/ + { + if (scaleX * scale > 3.0f) return; + scaleX *= scale; scaleY *= scale; scaleZ *= scale; + + //scaleX += scale;scaleY += scale;scaleZ += scale; + //scaleX = scale;scaleY = scale;scaleZ = scale; + //scaleX /= 100;scaleY /= 100;scaleZ /= 100; + } + + public void defaultScale() + { + scaleX = 1f; + scaleY = 1f; + scaleZ = 1f; + } + + public void onSurfaceCreated(GL10 unused, EGLConfig config) + { + // Set the background frame color + GLES20.glClearColor(0.0f, 0.0f, 0.0f, 1.0f); + + // Position the eye behind the origin. + eyeX = 0.0f; + eyeY = 0.0f; + eyeZ = 1.5f; + + // We are looking toward the distance + final float lookX = 0.0f; + final float lookY = 0.0f; + final float lookZ = -5.0f; + + // Set our up vector. This is where our head would be pointing were we holding the camera. + final float upX = 0.0f; + final float upY = 1.0f; + final float upZ = 0.0f; + + // Set the view matrix. This matrix can be said to represent the camera position. + // NOTE: In OpenGL 1, a ModelView matrix is used, which is a combination of a model and + // view matrix. In OpenGL 2, we can keep track of these matrices separately if we choose. + mViewMatrix = new float[triangleVert.length][16]; + + + for (int i = 0; i < triangleVert.length; i++) + Matrix.setLookAtM(mViewMatrix[i], 0, eyeX, eyeY, eyeZ, lookX, lookY, lookZ, upX, upY, upZ); + //Matrix.setLookAtM(mVMatrix[i], 0, 0, 0, -5.0f, 0.0f, 0f, 0f, 0f, 1.0f, 0.0f); + + final String vertexShader = + "uniform mat4 u_MVPMatrix; \n" // A constant representing the combined model/view/projection matrix. + + "attribute vec4 a_Position; \n" // Per-vertex position information we will pass in. + + "attribute vec4 a_Color; \n" // Per-vertex color information we will pass in. + + "varying vec4 v_Color; \n" // This will be passed into the fragment shader. + + "void main() \n" // The entry point for our vertex shader. + + "{ \n" + + " v_Color = a_Color; \n" // Pass the color through to the fragment shader. + + // It will be interpolated across the triangle. + + " gl_Position = u_MVPMatrix \n" // gl_Position is a special variable used to store the final position. + + " * a_Position; \n" // Multiply the vertex by the matrix to get the final point in + + "} \n"; // normalized screen coordinates. + + final String fragmentShader = + "precision mediump float; \n" // Set the default precision to medium. We don't need as high of a // precision in the fragment shader. + + "varying vec4 v_Color; \n" // This is the color from the vertex shader interpolated across the + // triangle per fragment. + + "void main() \n" // The entry point for our fragment shader. + + "{ \n" + + " gl_FragColor = v_Color; \n" // Pass the color directly through the pipeline. + + "} \n"; + + + int vertexShaderHandle = GLES20.glCreateShader(GLES20.GL_VERTEX_SHADER); + // Pass in the shader source. + GLES20.glShaderSource(vertexShaderHandle, vertexShader); + + // Compile the shader. + GLES20.glCompileShader(vertexShaderHandle); + + // Get the compilation status. + final int[] compileStatus1 = new int[1]; + GLES20.glGetShaderiv(vertexShaderHandle, GLES20.GL_COMPILE_STATUS, compileStatus1, 0); + + // If the compilation failed, delete the shader. + if (compileStatus1[0] == 0) + { + GLES20.glDeleteShader(vertexShaderHandle); + vertexShaderHandle = 0; + } + + + int fragmentShaderHandle = GLES20.glCreateShader(GLES20.GL_FRAGMENT_SHADER); + // Pass in the shader source. + GLES20.glShaderSource(fragmentShaderHandle, fragmentShader); + + // Compile the shader. + GLES20.glCompileShader(fragmentShaderHandle); + + // Get the compilation status. + final int[] compileStatus2 = new int[1]; + GLES20.glGetShaderiv(fragmentShaderHandle, GLES20.GL_COMPILE_STATUS, compileStatus2, 0); + + // If the compilation failed, delete the shader. + if (compileStatus2[0] == 0) + { + GLES20.glDeleteShader(fragmentShaderHandle); + fragmentShaderHandle = 0; + } + + + int mProgram = GLES20.glCreateProgram(); + // Bind the vertex shader to the program. + GLES20.glAttachShader(mProgram, vertexShaderHandle); + + // Bind the fragment shader to the program. + GLES20.glAttachShader(mProgram, fragmentShaderHandle); + + // Bind attributes + GLES20.glBindAttribLocation(mProgram, 0, "a_Position"); + GLES20.glBindAttribLocation(mProgram, 1, "a_Color"); + + // Link the two shaders together into a program. + GLES20.glLinkProgram(mProgram); + + // Get the link status. + final int[] linkStatus = new int[1]; + GLES20.glGetProgramiv(mProgram, GLES20.GL_LINK_STATUS, linkStatus, 0); + + // If the link failed, delete the program. + if (linkStatus[0] == 0) + { + GLES20.glDeleteProgram(mProgram); + mProgram = 0; + } + + for (int i = 0; i < triangleVert.length; i++) + { + mMatrixHandle = GLES20.glGetUniformLocation(mProgram, "u_MVPMatrix"); + mPositionHandle = GLES20.glGetAttribLocation(mProgram, "a_Position"); + mColorHandle = GLES20.glGetAttribLocation(mProgram, "a_Color"); + } + + // Add program to OpenGL environment + GLES20.glUseProgram(mProgram); + } + public void onSurfaceChanged(GL10 unused, int width, int height) + { + // Adjust the viewport based on geometry changes, + // such as screen rotation + GLES20.glViewport(0, 0, width, height); + + // Create a new perspective projection matrix. The height will stay the same + // while the width will vary as per aspect ratio. + final float ratio = (float) width / height; + + mProjectionMatrix = new float[triangleVert.length][16]; + for (int i = 0; i < triangleVert.length; i++) + Matrix.frustumM(mProjectionMatrix[i], 0, -ratio*0.7f, ratio*1.0f, 0.0f, 1.0f, 1.0f, 14f); + } + + public void onDrawFrame(GL10 glUnused) + { + // Draw background color + GLES20.glClear(GLES20.GL_COLOR_BUFFER_BIT); + + mModelMatrix = new float[triangleVert.length][16]; + // Draw the triangle facing straight on. + for (int i = 0; i < triangleVert.length; i++) + { + //Matrix.setIdentityM(mModelMatrix[i], 0); /* NEW STUFF*/ + Matrix.setIdentityM(mScaleMatrix[i], 0); + Matrix.scaleM(mScaleMatrix[i], 0, scaleX, scaleY, scaleZ); + + // Rotation along x + Matrix.setRotateM(mRotXMatrix[i], 0, this.mAngleY, -1.0f, 0.0f, 0.0f); + Matrix.setRotateM(mRotYMatrix[i], 0, this.mAngleX, 0.0f, 1.0f, 0.0f); /* NEW STUFF*/ + + Matrix.setLookAtM(mViewMatrix[i], 0, eyeX, eyeY, eyeZ, 0.0f, 0.0f, -5.0f, 0.0f, 1.0f, 0.0f); + + } + + mMVPMatrix = new float[triangleVert.length][16]; + draw(triangleVert); + + } + + private void draw(final FloatBuffer[] aTriangleBuffer) + { + for (int i = 0; i < aTriangleBuffer.length; i++) + { + // Pass in the position information + aTriangleBuffer[i].position(mPositionOffset); + GLES20.glVertexAttribPointer(mPositionHandle, mPositionDataSize, GLES20.GL_FLOAT, false, + mStrideBytes, aTriangleBuffer[i]); + + GLES20.glEnableVertexAttribArray(mPositionHandle); + + + // Pass in the color information + aTriangleBuffer[i].position(mColorOffset); + GLES20.glVertexAttribPointer(mColorHandle, mColorDataSize, GLES20.GL_FLOAT, false, + mStrideBytes, aTriangleBuffer[i]); + + GLES20.glEnableVertexAttribArray(mColorHandle); + + Matrix.setRotateM(mRotXMatrix[i], 0, this.mAngleY, -1.0f, 0.0f, 0.0f); /* NEW STUFF*/ + Matrix.setRotateM(mRotYMatrix[i], 0, this.mAngleX, 0.0f, 1.0f, 0.0f); + + float tempMatrix[][] = new float[triangleVert.length][16]; /* NEW STUFF*/ + Matrix.multiplyMM(tempMatrix[i], 0, mRotYMatrix[i], 0, mRotXMatrix[i], 0); + Matrix.multiplyMM(mModelMatrix[i], 0, mScaleMatrix[i], 0, tempMatrix[i], 0); + + // This multiplies the view matrix by the model matrix, and stores the result in the MVP matrix + // (which currently contains model * view). + Matrix.multiplyMM(mMVPMatrix[i], 0, mViewMatrix[i], 0, mModelMatrix[i], 0); + + // This multiplies the modelview matrix by the projection matrix, and stores the result in the MVP matrix + // (which now contains model * view * projection). + Matrix.multiplyMM(mMVPMatrix[i], 0, mProjectionMatrix[i], 0, mMVPMatrix[i], 0); + + GLES20.glUniformMatrix4fv(mMatrixHandle, 1, false, mMVPMatrix[i], 0); + + // Draw the triangle + GLES20.glDrawArrays(GLES20.GL_TRIANGLES, 0, 3); + + // Disable vertex array + GLES20.glDisableVertexAttribArray(mPositionHandle); + } + } + +} Index: /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLSurfaceView.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLSurfaceView.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/MyGLSurfaceView.java (revision 14310) @@ -0,0 +1,229 @@ +package com.example.issm; + +import java.nio.DoubleBuffer; +import java.util.Random; + +import android.content.Context; +import android.opengl.GLSurfaceView; +import android.util.FloatMath; +import android.view.MotionEvent; + + +class MyGLSurfaceView extends GLSurfaceView +{ + private MyGLRenderer mRend; + private DoubleBuffer db; + private int size; + double vmax = 0, vmin=0; + final int firstVelocity = 9; + ColorMap colorMap; + + // pinch to zoom + float oldDist = 100.0f; + float newDist; + + int mode = 0; + public MyGLSurfaceView(Context context, DoubleBuffer db, int size, ColorMap colorMap) + { + super(context); + // Create an OpenGL ES 2.0 context. + setEGLContextClientVersion(2); + this.db = db; + this.size = size; + this.colorMap = colorMap; + vmin = db.get(firstVelocity); + findMinMaxVelocity(); + intialize(); + } + private void intialize() + { + final int MAX_VERTICES = 21; + float f[][] = new float[size][MAX_VERTICES]; + //indexes prefer to velocity at each vertices of triangles. + double alpha1, alpha2, alpha3; + float xmin,xmax,ymin,ymax; + final int XSCALE_FACTOR = 1; + final int YSCALE_FACTOR = 2; + RGB rgb = new RGB(); + + for (int i = 0; i < size; i++) { + f[i][0] = (float)db.get(12*i+0); + f[i][1] = (float)db.get(12*i+1); + f[i][2] = (float)db.get(12*i+2); + f[i][7] = (float)db.get(12*i+3); + f[i][8] = (float)db.get(12*i+4); + f[i][9] = (float)db.get(12*i+5); + f[i][14] = (float)db.get(12*i+6); + f[i][15] = (float)db.get(12*i+7); + f[i][16] = (float)db.get(12*i+8); + + f[i][6] = 1.0f; + f[i][13] = 1.0f; + f[i][20] = 1.0f; + + alpha1 = getAlphaColor(db.get(12*i+9)); + alpha2 = getAlphaColor(db.get(12*i+10)); + alpha3 = getAlphaColor(db.get(12*i+11)); + + colorMap.getRGB(alpha1, rgb); + float r1 = rgb.getR(); + float g1 = rgb.getG(); + float b1 = rgb.getB(); + + colorMap.getRGB(alpha2, rgb); + float r2 = rgb.getR(); + float g2 = rgb.getG(); + float b2 = rgb.getB(); + + colorMap.getRGB(alpha3, rgb); + float r3 = rgb.getR(); + float g3 = rgb.getG(); + float b3 = rgb.getB(); + + + f[i][3] = r1; + f[i][4] = g1; + f[i][5] = b1; + + f[i][10] = r2; + f[i][11] = g2; + f[i][12] = b2; + + f[i][17] = r3; + f[i][18] = g3; + f[i][19] = b3; + + } + + /*scale coordinates: */ + xmin=0; ymin=0; xmax=0; ymax=0; + + for (int i = 0; i < size; i++) { + if (f[i][0]xmax) xmax=f[i][0]; + + if (f[i][1]ymax) ymax=f[i][1]; + } + + for (int i = 0; i < size; i++) { + f[i][0] = (f[i][0]-xmin)/(xmax-xmin)*XSCALE_FACTOR; + f[i][1] = (f[i][1]-ymin)/(ymax-ymin)*YSCALE_FACTOR; + f[i][7] = (f[i][7]-xmin)/(xmax-xmin)*XSCALE_FACTOR; + f[i][8] = (f[i][8]-ymin)/(ymax-ymin)*YSCALE_FACTOR; + f[i][14] = (f[i][14]-xmin)/(xmax-xmin)*XSCALE_FACTOR; + f[i][15] = (f[i][15]-ymin)/(ymax-ymin)*YSCALE_FACTOR; + } + + //Random r = new Random(); + //float z1,z2,z3; + for(int i = 0 ; i = vmax) vmax = db.get(i); + } + else continue; + } + + } + private double getAlphaColor(double velocity) + { + return (velocity-vmin)/(vmax-vmin); + } + + private final float TOUCH_SCALE_FACTOR = 180.0f / 320; + private float mPreviousX; + + private float mPreviousY; + // touch events + private final int NONE = 0; + private final int DRAG = 0; + private final int ZOOM = 0; + @Override + public boolean onTouchEvent(MotionEvent e) /* NEW STUFF*/ + { + float x = e.getX(); + float y = e.getY(); + switch (e.getAction()) { + case MotionEvent.ACTION_DOWN: // one touch: drag + mode = DRAG; + //mRend.eyeX = e.getX(); + //mRend.eyeY = e.getY; + break; + + case MotionEvent.ACTION_POINTER_DOWN: // two touches: zoom + oldDist = spacing(e); + if (oldDist > 10.0f) + mode = ZOOM; // zoom + break; + + case MotionEvent.ACTION_UP: // no mode + mode = NONE; + oldDist = 100.0f; + break; + + case MotionEvent.ACTION_POINTER_UP: // no mode + mode = NONE; + oldDist = 100.0f; + break; + + case MotionEvent.ACTION_MOVE: // rotation + if (e.getPointerCount() > 1 && mode == ZOOM) + { + newDist = spacing(e); + if (newDist > 10.0f) { + float scale = newDist/oldDist; // scale + + // scale in the renderer + mRend.changeScale(scale); + oldDist = newDist; + } + } + else if (mode == DRAG) + { + float dx = x - mPreviousX; + float dy = y - mPreviousY; + + mRend.mAngleX += dx * TOUCH_SCALE_FACTOR; + mRend.mAngleY += dy * TOUCH_SCALE_FACTOR; + + requestRender(); + } + break; + } + mPreviousX = x; + mPreviousY = y; + return true; + } + + private float spacing(MotionEvent event) /* NEW STUFF*/ + { + float x = event.getX(0) - event.getX(1); + float y = event.getY(0) - event.getY(1); + return FloatMath.sqrt(x * x + y * y); + } +} + Index: /issm/trunk/src/android/ISSM/src/com/example/issm/SplashScreen.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/SplashScreen.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/SplashScreen.java (revision 14310) @@ -0,0 +1,156 @@ +package com.example.issm; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import android.app.Activity; +import android.os.AsyncTask; +import android.os.Bundle; +import android.os.Environment; +import android.util.Log; +import android.view.animation.Animation; +import android.view.animation.AnimationUtils; +import android.widget.ImageView; +import android.widget.LinearLayout; +import android.widget.Toast; +import android.content.Intent; +import android.content.SharedPreferences; +import android.content.res.AssetManager; +/////////////////////////////////////////////////////////////////////////// +public class SplashScreen extends Activity +{ + MenuPage mp = new MenuPage(); + private static final String PREFERENCE_FIRST_RUN = null; + private String extStorageDirectory; + private String issmFolder; + SharedPreferences settings; +//------------------------------------------------------------------------ + public void onCreate(Bundle icicle) + { + super.onCreate(icicle); + setContentView(R.layout.splashscreen); + settings = this.getSharedPreferences("MenuPage", 0); + boolean firstrun = settings.getBoolean(PREFERENCE_FIRST_RUN, true); + extStorageDirectory = Environment.getExternalStorageDirectory().toString(); + issmFolder = extStorageDirectory + "/ISSM/input_files/"; + + new CopyDataTask().execute(firstrun); + } +//------------------------------------------------------------------------------------------- + //Start the splashscreen at beginning while transferring + //data file from Assets folder to SDcard + private class CopyDataTask extends AsyncTask + { + @Override + protected Boolean doInBackground(Boolean... target) + { + StartAnimations(); + try { + Thread.sleep(3000); + } catch (InterruptedException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + if(target[0] = false) + { + SharedPreferences.Editor e = settings.edit(); + e.putBoolean(PREFERENCE_FIRST_RUN, false); + + e.commit(); + // If not, run these methods: + SetDirectory(issmFolder); + } + return true; + } + protected void onPostExecute(Boolean result) + { + Intent i = new Intent(SplashScreen.this, MenuPage.class); + i.putExtra("pathToFile", issmFolder); + startActivity(i); + } + } +//------------------------------------------------------------------------------------------- + private void SetDirectory(String directory) + { + if (android.os.Environment.getExternalStorageState().equals(android.os.Environment.MEDIA_MOUNTED)) + { + System.out.println(issmFolder); + File txtDirectory = new File(issmFolder); + + // Check and create directory in SDcard + if(!txtDirectory.exists()) + { + txtDirectory.mkdirs(); + System.out.println("making directory"); + } + CopyAssets(); // Then run the method to copy the file. + + } + else if (android.os.Environment.getExternalStorageState().equals(android.os.Environment.MEDIA_MOUNTED_READ_ONLY)) + { + Toast toast = Toast.makeText(this.getApplicationContext(), "Memory is not mounted to device", Toast.LENGTH_LONG); + toast.show(); + } + + } +//---------------------------------------------------------------------------- + /** + * -- Copy the file from the assets folder to the sdCard + * =========================================================== + **/ + private void CopyAssets() + { + AssetManager assetManager = getAssets(); + String[] files = null; + try { + files = assetManager.list("Map"); + } catch (IOException e) { + Log.e("tag", e.getMessage()); + } + for (int i = 0; i < files.length; i++) { + InputStream in = null; + OutputStream out = null; + try { + in = assetManager.open("Map/"+files[i]); + out = new FileOutputStream(issmFolder + files[i]); + copyFile(in, out); + in.close(); + in = null; + out.flush(); + out.close(); + out = null; + } catch (Exception e) { + Log.e("tag", e.getMessage()); + } + } + System.out.println("Done"); + } +//---------------------------------------------------------------------------- + private void copyFile(InputStream in, OutputStream out) throws IOException + { + byte[] buffer = new byte[1024]; + int read; + while ((read = in.read(buffer)) != -1) { + out.write(buffer, 0, read); + } + } +//---------------------------------------------------------------------------- + private void StartAnimations() + { + Animation anim = AnimationUtils.loadAnimation(this, R.anim.alpha); + anim.reset(); + LinearLayout l=(LinearLayout) findViewById(R.id.lin_lay); + l.clearAnimation(); + l.startAnimation(anim); + + anim = AnimationUtils.loadAnimation(this, R.anim.translate); + anim.reset(); + ImageView iv = (ImageView) findViewById(R.id.logo); + iv.clearAnimation(); + iv.startAnimation(anim); + } +//------------------------------------------------------------------------------- +} +////////////////////////////////////////////////////////////////////////////////// Index: /issm/trunk/src/android/ISSM/src/com/example/issm/VerticalSeekBar.java =================================================================== --- /issm/trunk/src/android/ISSM/src/com/example/issm/VerticalSeekBar.java (revision 14310) +++ /issm/trunk/src/android/ISSM/src/com/example/issm/VerticalSeekBar.java (revision 14310) @@ -0,0 +1,60 @@ +package com.example.issm; + +import android.content.Context; +import android.graphics.Canvas; +import android.util.AttributeSet; +import android.view.MotionEvent; +import android.widget.SeekBar; + +public class VerticalSeekBar extends SeekBar { + + private final int MAX_SIZE = 500; + public VerticalSeekBar(Context context) { + super(context); + } + + public VerticalSeekBar(Context context, AttributeSet attrs, int defStyle) { + super(context, attrs, defStyle); + } + + public VerticalSeekBar(Context context, AttributeSet attrs) { + super(context, attrs); + } + + protected void onSizeChanged(int w, int h, int oldw, int oldh) { + super.onSizeChanged(h, w, oldh, oldw); + } + + @Override + protected synchronized void onMeasure(int widthMeasureSpec, int heightMeasureSpec) { + super.onMeasure(heightMeasureSpec, widthMeasureSpec); + setMeasuredDimension(getMeasuredHeight(), getMeasuredWidth()); + } + + protected void onDraw(Canvas c) { + c.rotate(-90); + c.translate(-getHeight(),0); + super.onDraw(c); + } + + @Override + public boolean onTouchEvent(MotionEvent event) { + if (!isEnabled()) { + return false; + } + int i = 0; + switch (event.getAction()) { + case MotionEvent.ACTION_DOWN: + case MotionEvent.ACTION_MOVE: + case MotionEvent.ACTION_UP: + i = getMax() - (int) (getMax() * event.getY() / getHeight()); + setProgress(i); + onSizeChanged(getWidth(), getHeight(), 0, 0); + break; + + case MotionEvent.ACTION_CANCEL: + break; + } + return true; + } +} Index: /issm/trunk/src/android/ISSM_Visual/AndroidManifest.xml =================================================================== --- /issm/trunk/src/android/ISSM_Visual/AndroidManifest.xml (revision 14309) +++ /issm/trunk/src/android/ISSM_Visual/AndroidManifest.xml (revision 14310) @@ -1,4 +1,4 @@ Index: /issm/trunk/src/android/ISSM_Visual/bin/AndroidManifest.xml =================================================================== --- /issm/trunk/src/android/ISSM_Visual/bin/AndroidManifest.xml (revision 14309) +++ /issm/trunk/src/android/ISSM_Visual/bin/AndroidManifest.xml (revision 14310) @@ -1,4 +1,4 @@ Index: /issm/trunk/src/android/ISSM_Visual/res/layout/activity_issmvisual.xml =================================================================== --- /issm/trunk/src/android/ISSM_Visual/res/layout/activity_issmvisual.xml (revision 14309) +++ /issm/trunk/src/android/ISSM_Visual/res/layout/activity_issmvisual.xml (revision 14310) @@ -15,11 +15,11 @@ + android:layout_marginBottom="15dp" + android:text="alpha value = 0" /> + android:layout_marginBottom="12dp" > - + android:layout_above="@+id/seekBar" + android:layout_alignParentRight="true" + android:text="Reset" /> Index: /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/ISSMVisual.java =================================================================== --- /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/ISSMVisual.java (revision 14310) +++ /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/ISSMVisual.java (revision 14310) @@ -0,0 +1,95 @@ +package gov.nasa.jpl.issm.visual; + + +import android.app.Activity; +import android.content.DialogInterface.OnClickListener; +import android.opengl.GLSurfaceView; +import android.os.Bundle; +import android.view.Menu; +import android.view.View; +import android.widget.Button; +import android.widget.FrameLayout; +import android.widget.SeekBar; +import android.widget.SeekBar.OnSeekBarChangeListener; +import android.widget.TextView; + +public class ISSMVisual extends Activity implements OnSeekBarChangeListener +{ + private SeekBar bar; + private TextView /*txtStatus,*/ txtValue; + private GLSurfaceView mGLView; + private FrameLayout frame; + + @Override + public void onCreate(Bundle savedInstanceState) + { + super.onCreate(savedInstanceState); + setContentView(R.layout.activity_issmvisual); + + bar = (SeekBar)findViewById(R.id.seekBar); // make seekbar object + bar.setOnSeekBarChangeListener(this); // set seekbar listener + txtValue = (TextView)findViewById(R.id.value); + Button reset = (Button)findViewById(R.id.button1); + reset.setOnClickListener(new View.OnClickListener() + { + public void onClick(View v) + { + frame.removeView(mGLView); + mGLView = new MyGLSurfaceView(ISSMVisual.this); + frame.addView(mGLView); + } + }); + //txtStatus = (TextView)findViewById(R.id.status); + + mGLView = new MyGLSurfaceView(this); + frame = (FrameLayout)findViewById(R.id.frame); + frame.addView(mGLView); + } + public void onProgressChanged(SeekBar seekBar, int val, + boolean fromUser) + { + // change progress text label with current Seekbar value + txtValue.setText("alpha value = " + val); + //txtStatus.setText("Status: changing"); + } + + public void onStartTrackingTouch(SeekBar seekBar) {/*txtStatus.setText("Status: Starting to track touch");*/} + + public void onStopTrackingTouch(SeekBar seekBar) + { + seekBar.setSecondaryProgress(seekBar.getProgress()); // set the shade of the previous value. + + //txtStatus.setText("Status: Ended tracking touch"); + frame.removeView(mGLView); + mGLView = new MyGLSurfaceView(this); + frame.addView(mGLView); + } + + @Override + protected void onPause() + { + super.onPause(); + // The following call pauses the rendering thread. + // If your OpenGL application is memory intensive, + // you should consider de-allocating objects that + // consume significant memory here. + mGLView.onPause(); + } + + @Override + protected void onResume() + { + super.onResume(); + // The following call resumes a paused rendering thread. + // If you de-allocated graphic objects for onPause() + // this is a good place to re-allocate them. + mGLView.onResume(); + } + + @Override + public boolean onCreateOptionsMenu(Menu menu) + { + getMenuInflater().inflate(R.menu.activity_issmvisual, menu); + return true; + } +} Index: /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLRenderer.java =================================================================== --- /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLRenderer.java (revision 14310) +++ /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLRenderer.java (revision 14310) @@ -0,0 +1,294 @@ +/* + * Copyright (C) 2012 The Android Open Source Project + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package gov.nasa.jpl.issm.visual; +import java.nio.ByteBuffer; +import java.nio.ByteOrder; +import java.nio.FloatBuffer; + +import javax.microedition.khronos.egl.EGLConfig; +import javax.microedition.khronos.opengles.GL10; + +import android.opengl.GLES20; +import android.opengl.GLSurfaceView; +import android.opengl.Matrix; + +public class MyGLRenderer implements GLSurfaceView.Renderer +{ + public volatile float mAngle; + + /** + * Store the model matrix. This matrix is used to move models from object space (where each model can be thought + * of being located at the center of the universe) to world space. + */ + private float[][] mModelMatrix; + + /** + * Store the view matrix. This can be thought of as our camera. This matrix transforms world space to eye space; + * it positions things relative to our eye. + */ + private float[][] mViewMatrix; + + /** Store the projection matrix. This is used to project the scene onto a 2D viewport. */ + private float[][] mProjectionMatrix; + + /** Allocate storage for the final combined matrix. This will be passed into the shader program. */ + private float[][] mMVPMatrix; + + /** This will be used to pass in the transformation matrix. */ + private int mMatrixHandle; + + private FloatBuffer[] triangleVert; + + private float[][] triangleData2DArr; + + private int mPositionHandle; + + private int mColorHandle; + + /** How many bytes per float. */ + private final int mBytesPerFloat = 4; + + /** How many elements per vertex. */ + private final int mStrideBytes = 7 * mBytesPerFloat; + + /** Offset of the position data. */ + private final int mPositionOffset = 0; + + /** Size of the position data in elements. */ + private final int mPositionDataSize = 3; + + /** Offset of the color data. */ + private final int mColorOffset = 3; + + /** Size of the color data in elements. */ + private final int mColorDataSize = 4; + + public MyGLRenderer(float[][] vertices) + { + triangleData2DArr = new float[vertices.length][21]; + triangleVert = new FloatBuffer[vertices.length]; + + for (int i = 0; i < vertices.length; i++) + { + for (int j = 0; j < 21; j++) + triangleData2DArr[i][j] = vertices[i][j]; + } + + // initialize vertex byte buffer for shape coordinates + for (int i = 0; i < vertices.length; i++) + { + triangleVert[i] = ByteBuffer.allocateDirect(triangleData2DArr[i].length * mBytesPerFloat) + .order(ByteOrder.nativeOrder()).asFloatBuffer(); + triangleVert[i].put(triangleData2DArr[i]).position(0); + } + } + + public void onSurfaceCreated(GL10 unused, EGLConfig config) + { + // Set the background frame color + GLES20.glClearColor(0.0f, 0.0f, 0.0f, 1.0f); + + // Position the eye behind the origin. + final float eyeX = 0.0f; + final float eyeY = 0.0f; + final float eyeZ = 1.5f; + + // We are looking toward the distance + final float lookX = 0.0f; + final float lookY = 0.0f; + final float lookZ = -5.0f; + + // Set our up vector. This is where our head would be pointing were we holding the camera. + final float upX = 0.0f; + final float upY = 1.0f; + final float upZ = 0.0f; + + // Set the view matrix. This matrix can be said to represent the camera position. + // NOTE: In OpenGL 1, a ModelView matrix is used, which is a combination of a model and + // view matrix. In OpenGL 2, we can keep track of these matrices separately if we choose. + mViewMatrix = new float[triangleVert.length][16]; + + for (int i = 0; i < triangleVert.length; i++) + Matrix.setLookAtM(mViewMatrix[i], 0, eyeX, eyeY, eyeZ, lookX, lookY, lookZ, upX, upY, upZ); + + final String vertexShader = + "uniform mat4 u_MVPMatrix; \n" // A constant representing the combined model/view/projection matrix. + + "attribute vec4 a_Position; \n" // Per-vertex position information we will pass in. + + "attribute vec4 a_Color; \n" // Per-vertex color information we will pass in. + + "varying vec4 v_Color; \n" // This will be passed into the fragment shader. + + "void main() \n" // The entry point for our vertex shader. + + "{ \n" + + " v_Color = a_Color; \n" // Pass the color through to the fragment shader. + // It will be interpolated across the triangle. + + " gl_Position = u_MVPMatrix \n" // gl_Position is a special variable used to store the final position. + + " * a_Position; \n" // Multiply the vertex by the matrix to get the final point in + + "} \n"; // normalized screen coordinates. + + final String fragmentShader = + "precision mediump float; \n" // Set the default precision to medium. We don't need as high of a // precision in the fragment shader. + + "varying vec4 v_Color; \n" // This is the color from the vertex shader interpolated across the + // triangle per fragment. + + "void main() \n" // The entry point for our fragment shader. + + "{ \n" + + " gl_FragColor = v_Color; \n" // Pass the color directly through the pipeline. + + "} \n"; + + + int vertexShaderHandle = GLES20.glCreateShader(GLES20.GL_VERTEX_SHADER); + // Pass in the shader source. + GLES20.glShaderSource(vertexShaderHandle, vertexShader); + + // Compile the shader. + GLES20.glCompileShader(vertexShaderHandle); + + // Get the compilation status. + final int[] compileStatus1 = new int[1]; + GLES20.glGetShaderiv(vertexShaderHandle, GLES20.GL_COMPILE_STATUS, compileStatus1, 0); + + // If the compilation failed, delete the shader. + if (compileStatus1[0] == 0) + { + GLES20.glDeleteShader(vertexShaderHandle); + vertexShaderHandle = 0; + } + + + int fragmentShaderHandle = GLES20.glCreateShader(GLES20.GL_FRAGMENT_SHADER); + // Pass in the shader source. + GLES20.glShaderSource(fragmentShaderHandle, fragmentShader); + + // Compile the shader. + GLES20.glCompileShader(fragmentShaderHandle); + + // Get the compilation status. + final int[] compileStatus2 = new int[1]; + GLES20.glGetShaderiv(fragmentShaderHandle, GLES20.GL_COMPILE_STATUS, compileStatus2, 0); + + // If the compilation failed, delete the shader. + if (compileStatus2[0] == 0) + { + GLES20.glDeleteShader(fragmentShaderHandle); + fragmentShaderHandle = 0; + } + + + int mProgram = GLES20.glCreateProgram(); + // Bind the vertex shader to the program. + GLES20.glAttachShader(mProgram, vertexShaderHandle); + + // Bind the fragment shader to the program. + GLES20.glAttachShader(mProgram, fragmentShaderHandle); + + // Bind attributes + GLES20.glBindAttribLocation(mProgram, 0, "a_Position"); + GLES20.glBindAttribLocation(mProgram, 1, "a_Color"); + + // Link the two shaders together into a program. + GLES20.glLinkProgram(mProgram); + + // Get the link status. + final int[] linkStatus = new int[1]; + GLES20.glGetProgramiv(mProgram, GLES20.GL_LINK_STATUS, linkStatus, 0); + + // If the link failed, delete the program. + if (linkStatus[0] == 0) + { + GLES20.glDeleteProgram(mProgram); + mProgram = 0; + } + + for (int i = 0; i < triangleVert.length; i++) + { + mMatrixHandle = GLES20.glGetUniformLocation(mProgram, "u_MVPMatrix"); + mPositionHandle = GLES20.glGetAttribLocation(mProgram, "a_Position"); + mColorHandle = GLES20.glGetAttribLocation(mProgram, "a_Color"); + } + + // Add program to OpenGL environment + GLES20.glUseProgram(mProgram); + } + + public void onSurfaceChanged(GL10 unused, int width, int height) + { + // Adjust the viewport based on geometry changes, + // such as screen rotation + GLES20.glViewport(0, 0, width, height); + + // Create a new perspective projection matrix. The height will stay the same + // while the width will vary as per aspect ratio. + final float ratio = (float) width / height; + + mProjectionMatrix = new float[triangleVert.length][16]; + for (int i = 0; i < triangleVert.length; i++) + Matrix.frustumM(mProjectionMatrix[i], 0, -ratio*1.4f, ratio*1.4f, -1.4f, 1.4f, 1.4f, 14f); + } + + public void onDrawFrame(GL10 glUnused) + { + // Draw background color + GLES20.glClear(GLES20.GL_COLOR_BUFFER_BIT); + + mModelMatrix = new float[triangleVert.length][16]; + // Draw the triangle facing straight on. + for (int i = 0; i < triangleVert.length; i++) + Matrix.setIdentityM(mModelMatrix[i], 0); + + mMVPMatrix = new float[triangleVert.length][16]; + draw(triangleVert); + + } + + private void draw(final FloatBuffer[] aTriangleBuffer) + { + for (int i = 0; i < aTriangleBuffer.length; i++) + { + // Pass in the position information + aTriangleBuffer[i].position(mPositionOffset); + GLES20.glVertexAttribPointer(mPositionHandle, mPositionDataSize, GLES20.GL_FLOAT, false, + mStrideBytes, aTriangleBuffer[i]); + + GLES20.glEnableVertexAttribArray(mPositionHandle); + + + // Pass in the color information + aTriangleBuffer[i].position(mColorOffset); + GLES20.glVertexAttribPointer(mColorHandle, mColorDataSize, GLES20.GL_FLOAT, false, + mStrideBytes, aTriangleBuffer[i]); + + GLES20.glEnableVertexAttribArray(mColorHandle); + + Matrix.setRotateM(mModelMatrix[i], 0, mAngle, 0, 0, -1.0f); + + // This multiplies the view matrix by the model matrix, and stores the result in the MVP matrix + // (which currently contains model * view). + Matrix.multiplyMM(mMVPMatrix[i], 0, mViewMatrix[i], 0, mModelMatrix[i], 0); + + // This multiplies the modelview matrix by the projection matrix, and stores the result in the MVP matrix + // (which now contains model * view * projection). + Matrix.multiplyMM(mMVPMatrix[i], 0, mProjectionMatrix[i], 0, mMVPMatrix[i], 0); + + GLES20.glUniformMatrix4fv(mMatrixHandle, 1, false, mMVPMatrix[i], 0); + + // Draw the triangle + GLES20.glDrawArrays(GLES20.GL_TRIANGLES, 0, 3); + + // Disable vertex array + GLES20.glDisableVertexAttribArray(mPositionHandle); + } + } + +} Index: /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLSurfaceView.java =================================================================== --- /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLSurfaceView.java (revision 14310) +++ /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/MyGLSurfaceView.java (revision 14310) @@ -0,0 +1,82 @@ +package gov.nasa.jpl.issm.visual; + +import android.content.Context; +import android.opengl.GLSurfaceView; +import android.view.MotionEvent; + + +class MyGLSurfaceView extends GLSurfaceView +{ + private MyGLRenderer mRend; + public MyGLSurfaceView(Context context) + { + super(context); + + // Create an OpenGL ES 2.0 context. + setEGLContextClientVersion(2); + + final int NMAX_TRIANGLES = 2000; + final int MAX_VERTICES = 21; + + float f[][] = new float[NMAX_TRIANGLES][MAX_VERTICES]; + int n, random; + for (int i = 0; i < f.length; i++) + { + for (int j = 0; j < MAX_VERTICES; j++) + { + if (j == 6 || j == 13 || j == 20) continue; + n = 1; + random = (int)(Math.floor((Math.random()*10)+1)); + if (random <= 5) n = -1; + + f[i][j] = (float)(Math.random()*n); + } + } + + mRend = new MyGLRenderer(f); + + // Set the Renderer for drawing on the GLSurfaceView + setRenderer(mRend); + + // Render the view only when there is a change in the drawing data + setRenderMode(GLSurfaceView.RENDERMODE_WHEN_DIRTY); + } + + private final float TOUCH_SCALE_FACTOR = 180.0f / 320; + private float mPreviousX; + + private float mPreviousY; + @Override + public boolean onTouchEvent(MotionEvent e) { + // MotionEvent reports input details from the touch screen + // and other input controls. In this case, you are only + // interested in events where the touch position changed. + + float x = e.getX(); + float y = e.getY(); + + switch (e.getAction()) { + case MotionEvent.ACTION_MOVE: + + float dx = x - mPreviousX; + float dy = y - mPreviousY; + + // reverse direction of rotation above the mid-line + if (y > getHeight() / 2) { + dx = dx * -1 ; + } + + // reverse direction of rotation to left of the mid-line + if (x < getWidth() / 2) { + dy = dy * -1 ; + } + + mRend.mAngle += (dx + dy) * TOUCH_SCALE_FACTOR; // = 180.0f / 320 + requestRender(); + } + + mPreviousX = x; + mPreviousY = y; + return true; + } +} Index: /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/colormap.c =================================================================== --- /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/colormap.c (revision 14310) +++ /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/colormap.c (revision 14310) @@ -0,0 +1,83 @@ +int nrows=64; +double hsv[nrows,3]={ +1.0000 0 0 + 1.0000 0.0938 0 + 1.0000 0.1875 0 + 1.0000 0.2812 0 + 1.0000 0.3750 0 + 1.0000 0.4688 0 + 1.0000 0.5625 0 + 1.0000 0.6562 0 + 1.0000 0.7500 0 + 1.0000 0.8438 0 + 1.0000 0.9375 0 + 0.9688 1.0000 0 + 0.8750 1.0000 0 + 0.7812 1.0000 0 + 0.6875 1.0000 0 + 0.5938 1.0000 0 + 0.5000 1.0000 0 + 0.4062 1.0000 0 + 0.3125 1.0000 0 + 0.2188 1.0000 0 + 0.1250 1.0000 0 + 0.0312 1.0000 0 + 0 1.0000 0.0625 + 0 1.0000 0.1562 + 0 1.0000 0.2500 + 0 1.0000 0.3438 + 0 1.0000 0.4375 + 0 1.0000 0.5312 + 0 1.0000 0.6250 + 0 1.0000 0.7188 + 0 1.0000 0.8125 + 0 1.0000 0.9062 + 0 1.0000 1.0000 + 0 0.9062 1.0000 + 0 0.8125 1.0000 + 0 0.7188 1.0000 + 0 0.6250 1.0000 + 0 0.5312 1.0000 + 0 0.4375 1.0000 + 0 0.3438 1.0000 + 0 0.2500 1.0000 + 0 0.1562 1.0000 + 0 0.0625 1.0000 + 0.0312 0 1.0000 + 0.1250 0 1.0000 + 0.2188 0 1.0000 + 0.3125 0 1.0000 + 0.4062 0 1.0000 + 0.5000 0 1.0000 + 0.5938 0 1.0000 + 0.6875 0 1.0000 + 0.7812 0 1.0000 + 0.8750 0 1.0000 + 0.9688 0 1.0000 + 1.0000 0 0.9375 + 1.0000 0 0.8438 + 1.0000 0 0.7500 + 1.0000 0 0.6562 + 1.0000 0 0.5625 + 1.0000 0 0.4688 + 1.0000 0 0.3750 + 1.0000 0 0.2812 + 1.0000 0 0.1875 + 1.0000 0 0.0938 +} + + + +value v=5*10^-5; // (m/s) +value vmin,vmax; + + + +double alpha=(vmax-alpha)/(vmax-vmin); +int i=(int)(alpha*nrows); + +double r,g,b; + +r=hsv[i,1]; +g=hsv[i,2]; +b=hsv[i,3]; Index: /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/list_of_colormaps =================================================================== --- /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/list_of_colormaps (revision 14310) +++ /issm/trunk/src/android/ISSM_Visual/src/gov/nasa/jpl/issm/visual/colormap/list_of_colormaps (revision 14310) @@ -0,0 +1,23 @@ +hsv - Hue-saturation-value color map. +hot - Black-red-yellow-white color map. +gray - Linear gray-scale color map. +bone - Gray-scale with tinge of blue color map. +copper - Linear copper-tone color map. +pink - Pastel shades of pink color map. +white - All white color map. +flag - Alternating red, white, blue, and black color map. +lines - Color map with the line colors. +colorcube - Enhanced color-cube color map. +vga - Windows colormap for 16 colors. +jet - Variant of HSV. +prism - Prism color map. +cool - Shades of cyan and magenta color map. +autumn - Shades of red and yellow color map. +spring - Shades of magenta and yellow color map. +winter - Shades of blue and green color map. +summer + + + +a=colormap('hsv'); +a Index: /issm/trunk/src/c/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/CMakeLists.txt (revision 14310) @@ -0,0 +1,15 @@ +# Subdirectories {{{ +add_subdirectory(classes) +add_subdirectory(Container) +add_subdirectory(EnumDefinitions) +add_subdirectory(include) +add_subdirectory(io) +add_subdirectory(modules) +add_subdirectory(shared) +add_subdirectory(solutions) +add_subdirectory(solvers) +add_subdirectory(toolkits) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c) +# }}} Index: /issm/trunk/src/c/Container/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/Container/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/Container/CMakeLists.txt (revision 14310) @@ -0,0 +1,24 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/Container) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/Container/Constraints.cpp + $ENV{ISSM_DIR}/src/c/Container/DataSet.cpp + $ENV{ISSM_DIR}/src/c/Container/Elements.cpp + $ENV{ISSM_DIR}/src/c/Container/Inputs.cpp + $ENV{ISSM_DIR}/src/c/Container/Loads.cpp + $ENV{ISSM_DIR}/src/c/Container/Materials.cpp + $ENV{ISSM_DIR}/src/c/Container/Nodes.cpp + $ENV{ISSM_DIR}/src/c/Container/Options.cpp + $ENV{ISSM_DIR}/src/c/Container/Parameters.cpp + $ENV{ISSM_DIR}/src/c/Container/Results.cpp + $ENV{ISSM_DIR}/src/c/Container/Vertices.cpp PARENT_SCOPE) +# }}} +# KRIGING_SOURCES {{{ +set(KRIGING_SOURCES $ENV{ISSM_DIR}/src/c/Container/Observations.cpp PARENT_SCOPE) +# }}} +# PKRIGING_SOURCES {{{ +set(PKRIGING_SOURCES $ENV{ISSM_DIR}/src/c/Container/Observations.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/Container/DataSet.cpp =================================================================== --- /issm/trunk/src/c/Container/DataSet.cpp (revision 14309) +++ /issm/trunk/src/c/Container/DataSet.cpp (revision 14310) @@ -178,4 +178,5 @@ /*Check index in debugging mode*/ _assert_(this!=NULL); + _assert_(offset>=0); _assert_(offsetSize()); Index: /issm/trunk/src/c/Container/Observations.cpp =================================================================== --- /issm/trunk/src/c/Container/Observations.cpp (revision 14309) +++ /issm/trunk/src/c/Container/Observations.cpp (revision 14310) @@ -45,4 +45,7 @@ IssmPDouble offset,minlength,minspacing,mintrimming,maxtrimming; Observation *observation = NULL; + + /*Check that observations is not empty*/ + if(n==0) _error_("No observation found"); /*Get extrema*/ @@ -122,5 +125,5 @@ /*Output and Intermediaries*/ int nobs,i,index; - IssmPDouble h2,hmin2,radius2; + IssmPDouble hmin,h2,hmin2,radius2; int *indices = NULL; Observation *observation = NULL; @@ -128,4 +131,12 @@ /*If radius is not provided or is 0, return all observations*/ if(radius==0) radius=this->quadtree->root->length; + + /*First, find closest point in Quadtree (fast but might not be the true closest obs)*/ + this->quadtree->ClosestObs(&index,x_interp,y_interp); + if(index>=0){ + observation=dynamic_cast(this->GetObjectByOffset(index)); + hmin = sqrt((observation->x-x_interp)*(observation->x-x_interp) + (observation->y-y_interp)*(observation->y-y_interp)); + if(hmin(this->GetObjectByOffset(indices[i])); h2 = (observation->x-x_interp)*(observation->x-x_interp) + (observation->y-y_interp)*(observation->y-y_interp); - if(i==0){ hmin2 = h2; - index = i; + index = indices[i]; } else{ if(h2=0){ + observation=dynamic_cast(this->GetObjectByOffset(index)); + *px=observation->x; + *py=observation->y; + *pobs=observation->value; + } + else{ + *px=UNDEF; *py=UNDEF; *pobs=UNDEF; } - else{ - observation=dynamic_cast(this->GetObjectByOffset(indices[index])); - *px=observation->x; - *py=observation->y; - *pobs=observation->value; - } xDelete(indices); +}/*}}}*/ +/*FUNCTION Observations::Distances{{{*/ +void Observations::Distances(IssmPDouble* distances,IssmPDouble *x,IssmPDouble *y,int n,IssmPDouble radius){ + + IssmPDouble xi,yi,obs; + + for(int i=0;iClosestObservation(&xi,&yi,&obs,x[i],y[i],radius); + if(xi==UNDEF && yi==UNDEF) + distances[i]=UNDEF; + else + distances[i]=sqrt( (x[i]-xi)*(x[i]-xi) + (y[i]-yi)*(y[i]-yi) ); + } }/*}}}*/ /*FUNCTION Observations::ObservationList(IssmPDouble **px,IssmPDouble **py,IssmPDouble **pobs,int* pnobs,IssmPDouble x_interp,IssmPDouble y_interp,IssmPDouble radius,int maxdata){{{*/ Index: /issm/trunk/src/c/Container/Observations.h =================================================================== --- /issm/trunk/src/c/Container/Observations.h (revision 14309) +++ /issm/trunk/src/c/Container/Observations.h (revision 14310) @@ -27,4 +27,5 @@ /*Methods*/ void ClosestObservation(IssmDouble *px,IssmDouble *py,IssmDouble *pobs,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius); + void Distances(IssmPDouble* distances,IssmPDouble *x,IssmPDouble *y,int n,IssmPDouble radius); void InterpolationIDW(IssmDouble *pprediction,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius,int mindata,int maxdata,IssmDouble power); void InterpolationV4(IssmDouble *pprediction,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius,int mindata,int maxdata); Index: /issm/trunk/src/c/Container/Vertices.cpp =================================================================== --- /issm/trunk/src/c/Container/Vertices.cpp (revision 14309) +++ /issm/trunk/src/c/Container/Vertices.cpp (revision 14310) @@ -199,2 +199,45 @@ } /*}}}*/ +/*FUNCTION Vertices::ToXYZ{{{*/ +IssmDouble* Vertices::ToXYZ(void){ + + /*intermediary: */ + int i; + int my_rank; + int num_vertices; + + /*output: */ + Matrix* xyz = NULL; + IssmDouble* xyz_serial=NULL; + + /*recover my_rank:*/ + my_rank=IssmComm::GetRank(); + + /*First, figure out number of vertices: */ + num_vertices=this->NumberOfVertices(); + + /*Now, allocate matrix to hold all the vertices x,y and z values: */ + xyz= new Matrix(num_vertices,3); + + /*Go through vertices, and for each vertex, object, report it cpu: */ + for(i=0;iSize();i++){ + + /*let vertex fill matrix: */ + Vertex* vertex=dynamic_cast(this->GetObjectByOffset(i)); + vertex->ToXYZ(xyz); + } + + /*Assemble:*/ + xyz->Assemble(); + + /*gather on cpu 0: */ + xyz_serial=xyz->ToSerial(); + + /*free ressources: */ + delete xyz; + if(my_rank!=0)delete xyz_serial; + + /*return matrix: */ + return xyz_serial; +} +/*}}}*/ Index: /issm/trunk/src/c/Container/Vertices.h =================================================================== --- /issm/trunk/src/c/Container/Vertices.h (revision 14309) +++ /issm/trunk/src/c/Container/Vertices.h (revision 14310) @@ -28,4 +28,5 @@ int NumberOfVertices(void); void Ranks(int* ranks); + IssmDouble* ToXYZ(void); }; Index: /issm/trunk/src/c/EnumDefinitions/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/EnumDefinitions/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/EnumDefinitions/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/EnumDefinitions) +# }}} Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 14309) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 14310) @@ -196,12 +196,7 @@ SurfaceforcingsIssmbgradientsEnum, SurfaceforcingsMonthlytemperaturesEnum, - SurfaceforcingsHcEnum, SurfaceforcingsHrefEnum, SurfaceforcingsSmbrefEnum, - SurfaceforcingsSmbPosMaxEnum, - SurfaceforcingsSmbPosMinEnum, - SurfaceforcingsAPosEnum, SurfaceforcingsBPosEnum, - SurfaceforcingsANegEnum, SurfaceforcingsBNegEnum, ThermalMaxiterEnum, @@ -235,4 +230,6 @@ BalancethicknessAnalysisEnum, BalancethicknessSolutionEnum, + WeakBalancethicknessAnalysisEnum, + WeakBalancethicknessSolutionEnum, BedSlopeAnalysisEnum, BedSlopeSolutionEnum, @@ -355,4 +352,5 @@ AdjointyEnum, AdjointzEnum, + BalancethicknessMisfitEnum, BedSlopeXEnum, BedSlopeYEnum, @@ -382,4 +380,5 @@ QmuSurfaceEnum, QmuMeltingEnum, + AndroidFrictionCoefficientEnum, ResetPenaltiesEnum, SegmentOnIceShelfEnum, @@ -425,5 +424,4 @@ DragCoefficientAbsGradientEnum, TransientInputEnum, - OutputfilenameEnum, WaterfractionEnum, WatercolumnEnum, Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 14309) +++ /issm/trunk/src/c/Makefile.am (revision 14310) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ +AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ EXEEXT=$(ISSMEXT) @@ -475,5 +475,6 @@ ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ - ./solutions/balancethickness_core.cpp + ./solutions/balancethickness_core.cpp \ + ./solutions/dummy_core.cpp #}}} #Slope sources {{{ @@ -499,6 +500,5 @@ #}}} #Android sources {{{ -android_sources = ./android/fac.h\ - ./android/fac.cpp +android_sources = #}}} #3D sources {{{ @@ -627,4 +627,6 @@ ./modules/Kml2Expx/Kml2Expx.h\ ./modules/Kml2Expx/Kml2Expx.cpp\ + ./modules/Shp2Expx/Shp2Expx.h\ + ./modules/Shp2Expx/Shp2Expx.cpp\ ./modules/Shp2Kmlx/Shp2Kmlx.h\ ./modules/Shp2Kmlx/Shp2Kmlx.cpp\ @@ -739,5 +741,5 @@ ./shared/Exp/IsInPoly.cpp\ ./shared/Exp/IsInPolySerial.cpp\ - ./shared/Exp/DomainOutlineWrite.cpp\ + ./shared/Exp/ExpWrite.cpp\ ./shared/TriMesh/trimesh.h\ ./shared/TriMesh/AssociateSegmentToElement.cpp\ @@ -781,9 +783,4 @@ ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h\ - ./modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp\ - ./modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp\ - ./modules/MeshProfileIntersectionx/ElementSegment.cpp\ - ./modules/MeshProfileIntersectionx/SegmentIntersect.cpp\ - ./modules/MeshProfileIntersectionx/NodeInElement.cpp\ ./modules/ContourToMeshx/ContourToMeshx.cpp\ ./modules/ContourToMeshx/ContourToMeshxt.cpp\ Index: /issm/trunk/src/c/classes/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/CMakeLists.txt (revision 14310) @@ -0,0 +1,20 @@ +# Subdirectories {{{ +add_subdirectory(bamg) +add_subdirectory(dakota) +add_subdirectory(gauss) +add_subdirectory(kriging) +add_subdirectory(matrix) +add_subdirectory(objects) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/DofIndexing.cpp + $ENV{ISSM_DIR}/src/c/classes/FemModel.cpp + $ENV{ISSM_DIR}/src/c/classes/Hook.cpp + $ENV{ISSM_DIR}/src/c/classes/IoModel.cpp + $ENV{ISSM_DIR}/src/c/classes/IssmComm.cpp + $ENV{ISSM_DIR}/src/c/classes/Patch.cpp + $ENV{ISSM_DIR}/src/c/classes/RiftStruct.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/FemModel.cpp =================================================================== --- /issm/trunk/src/c/classes/FemModel.cpp (revision 14309) +++ /issm/trunk/src/c/classes/FemModel.cpp (revision 14310) @@ -20,9 +20,4 @@ /*Object constructors and destructor*/ -/*FUNCTION FemModel::FemModel(char* filename) {{{*/ -FemModel::FemModel(char* filename){ - -} -/*}}}*/ /*FUNCTION FemModel::FemModel(int argc,char** argv){{{*/ FemModel::FemModel(int argc,char** argv,COMM incomm){ @@ -707,4 +702,5 @@ case ThicknessAlongGradientEnum: ThicknessAlongGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; case ThicknessAcrossGradientEnum:ThicknessAcrossGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; + case BalancethicknessMisfitEnum:BalancethicknessMisfitx(responses,process_units,weight_index); break; case TotalSmbEnum: this->TotalSmbx(responses,process_units); break; case RheologyBbarAbsGradientEnum:RheologyBbarAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; @@ -1363,4 +1359,23 @@ #endif #ifdef _HAVE_CONTROL_ +void FemModel::BalancethicknessMisfitx(IssmDouble* presponse,bool process_units,int weight_index){/*{{{*/ + + IssmDouble J = 0; + IssmDouble J_sum; + + for(int i=0;ielements->Size();i++){ + Element* element=dynamic_cast(this->elements->GetObjectByOffset(i)); + J+=element->BalancethicknessMisfit(process_units,weight_index); + } + #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,IssmComm::GetComm() ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,IssmComm::GetComm()); + J=J_sum; + #endif + + /*Assign output pointers: */ + *presponse=J; + +}/*}}}*/ void FemModel::ThicknessAbsGradientx( IssmDouble* pJ, bool process_units, int weight_index){/*{{{*/ Index: /issm/trunk/src/c/classes/FemModel.h =================================================================== --- /issm/trunk/src/c/classes/FemModel.h (revision 14309) +++ /issm/trunk/src/c/classes/FemModel.h (revision 14310) @@ -47,5 +47,4 @@ /*constructors, destructors: */ - FemModel(char* filename); FemModel(int argc,char** argv,COMM comm_init); FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); @@ -81,4 +80,5 @@ void IceVolumex(IssmDouble* pV,bool process_units); void ElementResponsex(IssmDouble* presponse,int response_enum,bool process_units); + void BalancethicknessMisfitx(IssmDouble* pV,bool process_units,int weight_index); #endif #ifdef _HAVE_DAKOTA_ Index: /issm/trunk/src/c/classes/IssmComm.cpp =================================================================== --- /issm/trunk/src/c/classes/IssmComm.cpp (revision 14309) +++ /issm/trunk/src/c/classes/IssmComm.cpp (revision 14310) @@ -11,16 +11,32 @@ #include "./IssmComm.h" #include "../include/types.h" +#include "../include/macros.h" +#include "../shared/Exceptions/exceptions.h" void IssmComm::SetComm(COMM incomm){ /*{{{*/ - comm=incomm; + + /*A comm is provided, we are running in parallel (this is not a module)*/ + parallel = true; + comm = incomm; + +}/*}}}*/ +void IssmComm::SetComm(void){ /*{{{*/ + + /*no comm provided, This is a matlab/python module*/ + parallel = false; + + /*No need to initialise comm*/ + }/*}}}*/ COMM IssmComm::GetComm(){ /*{{{*/ + if(!parallel) _error_("Cannot return comm in serial mode"); return comm; }/*}}}*/ int IssmComm::GetRank(){ /*{{{*/ + int my_rank = 0; - - /*for matlab and python modules, comm == -1*/ - if((int)comm==-1) return my_rank; + + /*for matlab and python modules*/ + if(!parallel) return my_rank; #ifdef _HAVE_MPI_ @@ -35,6 +51,6 @@ int size = 1; - /*for matlab and python modules, comm == -1*/ - if((int)comm==-1) return size; + /*for matlab and python modules*/ + if(!parallel) return size; #ifdef _HAVE_MPI_ Index: /issm/trunk/src/c/classes/IssmComm.h =================================================================== --- /issm/trunk/src/c/classes/IssmComm.h (revision 14309) +++ /issm/trunk/src/c/classes/IssmComm.h (revision 14310) @@ -21,10 +21,12 @@ private: static COMM comm; + static bool parallel; public: static void SetComm(COMM incomm); - static COMM GetComm(); - static int GetRank(); - static int GetSize(); + static void SetComm(void); + static COMM GetComm(void); + static int GetRank(void); + static int GetSize(void); }; Index: /issm/trunk/src/c/classes/RiftStruct.cpp =================================================================== --- /issm/trunk/src/c/classes/RiftStruct.cpp (revision 14309) +++ /issm/trunk/src/c/classes/RiftStruct.cpp (revision 14310) @@ -22,5 +22,5 @@ }/*}}}*/ -RiftStruct::RiftStruct(int numrifts_in,int *riftsnumsegments_in,double **riftssegments_in,int *riftsnumpairs_in,double **riftspairs_in,int *riftsnumpenaltypairs_in,double **riftspenaltypairs_in,double* riftstips_in){/*{{{*/ +RiftStruct::RiftStruct(int numrifts_in,int *riftsnumsegments_in,int**riftssegments_in,int *riftsnumpairs_in,int**riftspairs_in,int *riftsnumpenaltypairs_in,double **riftspenaltypairs_in,int * riftstips_in){/*{{{*/ int i; @@ -37,8 +37,8 @@ /*riftssegments*/ _assert_(riftssegments_in); - this->riftssegments=xNew(numrifts_in); + this->riftssegments=xNew(numrifts_in); for(i=0;iriftssegments[i]=xNew(riftsnumsegments_in[i]*3); - xMemCpy(this->riftssegments[i],riftssegments_in[i],riftsnumsegments_in[i]*3); + this->riftssegments[i]=xNew(riftsnumsegments_in[i]*3); + xMemCpy(this->riftssegments[i],riftssegments_in[i],riftsnumsegments_in[i]*3); } @@ -50,8 +50,8 @@ /*riftspairs*/ _assert_(riftspairs_in); - this->riftspairs=xNew(numrifts_in); + this->riftspairs=xNew(numrifts_in); for(i=0;iriftspairs[i]=xNew(riftsnumpairs_in[i]*2); - xMemCpy(this->riftspairs[i],riftspairs_in[i],riftsnumpairs_in[i]*2); + this->riftspairs[i]=xNew(riftsnumpairs_in[i]*2); + xMemCpy(this->riftspairs[i],riftspairs_in[i],riftsnumpairs_in[i]*2); } @@ -71,6 +71,6 @@ /*riftstips*/ _assert_(riftstips_in); - this->riftstips=xNew(2*numrifts_in); - xMemCpy(this->riftstips,riftstips_in,2*numrifts_in); + this->riftstips=xNew(2*numrifts_in); + xMemCpy(this->riftstips,riftstips_in,2*numrifts_in); /*state*/ @@ -85,10 +85,10 @@ xDelete(this->riftsnumsegments); - xDelete(this->riftssegments); + xDelete(this->riftssegments); xDelete(this->riftsnumpairs); - xDelete(this->riftspairs); + xDelete(this->riftspairs); xDelete(this->riftsnumpenaltypairs); xDelete(this->riftspenaltypairs); - xDelete(this->riftstips); + xDelete(this->riftstips); xDelete(this->state); Index: /issm/trunk/src/c/classes/RiftStruct.h =================================================================== --- /issm/trunk/src/c/classes/RiftStruct.h (revision 14309) +++ /issm/trunk/src/c/classes/RiftStruct.h (revision 14310) @@ -10,15 +10,15 @@ public: int numrifts; - double **riftssegments; + int **riftssegments; int *riftsnumsegments; - double **riftspairs; + int **riftspairs; int *riftsnumpairs; double **riftspenaltypairs; int *riftsnumpenaltypairs; - double *riftstips; + int *riftstips; double **state; RiftStruct(); - RiftStruct(int numrifts_in,int *riftsnumsegments_in,double **riftssegments_in,int *riftsnumpairs_in,double **riftspairs_in,int *riftsnumpenaltypairs_in,double **riftspenaltypairs_in,double* riftstips_in); + RiftStruct(int numrifts_in,int *riftsnumsegments_in,int **riftssegments_in,int *riftsnumpairs_in,int **riftspairs_in,int *riftsnumpenaltypairs_in,double **riftspenaltypairs_in,int* riftstips_in); ~RiftStruct(); }; Index: /issm/trunk/src/c/classes/bamg/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/bamg/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/bamg/CMakeLists.txt (revision 14310) @@ -0,0 +1,31 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/bamg) +# }}} +# BAMG_SOURCES {{{ +set(BAMG_SOURCES $ENV{ISSM_DIR}/src/c/classes/bamg/AdjacentTriangle.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/BamgGeom.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/BamgMesh.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/BamgOpts.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/BamgQuadtree.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/BamgVertex.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/CrackedEdge.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Curve.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Direction.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Edge.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/EigenMetric.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/GeomEdge.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Geometry.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/GeomSubDomain.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/GeomVertex.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/ListofIntersectionTriangles.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Mesh.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Metric.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/SetOfE4.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/SubDomain.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/Triangle.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/VertexOnEdge.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/VertexOnGeom.cpp + $ENV{ISSM_DIR}/src/c/classes/bamg/VertexOnVertex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/bamg/Mesh.cpp =================================================================== --- /issm/trunk/src/c/classes/bamg/Mesh.cpp (revision 14309) +++ /issm/trunk/src/c/classes/bamg/Mesh.cpp (revision 14310) @@ -899,8 +899,9 @@ } //Build output + connectivitymax_2++;//add last column for size bamgmesh->NodalConnectivitySize[0]=nbv; bamgmesh->NodalConnectivitySize[1]=connectivitymax_2; bamgmesh->NodalConnectivity=xNew(connectivitymax_2*nbv); - for (i=0;iNodalConnectivity[i]=NAN; + for (i=0;iNodalConnectivity[i]=0; for (i=0;iNodalConnectivity[connectivitymax_2*(i+1)-1]=k; } Index: /issm/trunk/src/c/classes/dakota/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/dakota/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/dakota/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/dakota) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/classes/dakota/DakotaPlugin.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/gauss/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/gauss/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/gauss/CMakeLists.txt (revision 14310) @@ -0,0 +1,11 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/gauss) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/gauss/GaussTria.cpp PARENT_SCOPE) +# }}} +# THREED_SOURCES {{{ +set(THREED_SOURCES $ENV{ISSM_DIR}/src/c/classes/gauss/GaussPenta.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/kriging/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/kriging/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/kriging/CMakeLists.txt (revision 14310) @@ -0,0 +1,21 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/kriging) +# }}} +# KRIGING_SOURCES {{{ +set(KRIGING_SOURCES $ENV{ISSM_DIR}/src/c/classes/kriging/ExponentialVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/GaussianVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/Observation.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/PowerVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/Quadtree.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/SphericalVariogram.cpp PARENT_SCOPE) +# }}} +# PKRIGING_SOURCES {{{ +set(PKRIGING_SOURCES $ENV{ISSM_DIR}/src/c/classes/kriging/ExponentialVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/GaussianVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/Observation.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/PowerVariogram.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/Quadtree.cpp + $ENV{ISSM_DIR}/src/c/classes/kriging/SphericalVariogram.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/matrix/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/matrix/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/matrix/CMakeLists.txt (revision 14310) @@ -0,0 +1,9 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/matrix) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/matrix/ElementMatrix.cpp + $ENV{ISSM_DIR}/src/c/classes/matrix/ElementVector.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/CMakeLists.txt (revision 14310) @@ -0,0 +1,22 @@ +# Subdirectories {{{ +add_subdirectory(Constraints) +add_subdirectory(ElementResults) +add_subdirectory(Elements) +add_subdirectory(ExternalResults) +add_subdirectory(Inputs) +add_subdirectory(KML) +add_subdirectory(Loads) +add_subdirectory(Materials) +add_subdirectory(Options) +add_subdirectory(Params) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/DependentObject.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/IndependentObject.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Node.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Profiler.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Vertex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Constraints/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Constraints/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Constraints/CMakeLists.txt (revision 14310) @@ -0,0 +1,10 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Constraints) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Constraints/SpcDynamic.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Constraints/SpcStatic.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Constraints/SpcTransient.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/ElementResults/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/ElementResults/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/ElementResults/CMakeLists.txt (revision 14310) @@ -0,0 +1,13 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/ElementResults) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/ElementResults/BoolElementResult.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/ElementResults/DoubleElementResult.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp PARENT_SCOPE) +# }}} +# THREED_SOURCES {{{ +set(THREED_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Elements/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Elements/CMakeLists.txt (revision 14310) @@ -0,0 +1,15 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Elements) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Elements/Tria.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Elements/TriaHook.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Elements/TriaRef.cpp PARENT_SCOPE) +# }}} +# THREED_SOURCES {{{ +set(THREED_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Elements/Penta.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Elements/PentaHook.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Elements/PentaRef.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Elements/Element.h =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/Element.h (revision 14309) +++ /issm/trunk/src/c/classes/objects/Elements/Element.h (revision 14310) @@ -110,4 +110,5 @@ virtual IssmDouble ThicknessAlongGradient(bool process_units,int weight_index)=0; virtual IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index)=0; + virtual IssmDouble BalancethicknessMisfit(bool process_units,int weight_index)=0; virtual IssmDouble RheologyBbarAbsGradient(bool process_units,int weight_index)=0; virtual IssmDouble DragCoefficientAbsGradient(bool process_units,int weight_index)=0; Index: /issm/trunk/src/c/classes/objects/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/Penta.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/Elements/Penta.cpp (revision 14310) @@ -2727,12 +2727,7 @@ /*Recover SmbGradients*/ - GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum); GetInputListOnVertices(&Href[0],SurfaceforcingsHrefEnum); GetInputListOnVertices(&Smbref[0],SurfaceforcingsSmbrefEnum); - GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum); - GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum); - GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum); GetInputListOnVertices(&b_pos[0],SurfaceforcingsBPosEnum); - GetInputListOnVertices(&a_neg[0],SurfaceforcingsANegEnum); GetInputListOnVertices(&b_neg[0],SurfaceforcingsBNegEnum); @@ -2747,13 +2742,9 @@ // loop over all vertices for(i=0;iHc[i]){ - if(Href[i]>Hc[i]){smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]);} - if(Href[i]<=Hc[i]){smb[i]=a_pos[i]+b_pos[i]*s[i];} - if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} - if(smb[i]0){ + smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]); } else{ - if(Href[i]>Hc[i]){smb[i]=a_neg[i]+b_neg[i]*s[i];} - if(Href[i]<=Hc[i]){smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]);} + smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]); } smb[i]=smb[i]/rho_ice; // SMB in m/y ice Index: /issm/trunk/src/c/classes/objects/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/Penta.h (revision 14309) +++ /issm/trunk/src/c/classes/objects/Elements/Penta.h (revision 14310) @@ -166,4 +166,5 @@ IssmDouble ThicknessAlongGradient( bool process_units,int weight_index){_error_("not supported");}; IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index){_error_("not supported");}; + IssmDouble BalancethicknessMisfit(bool process_units,int weight_index){_error_("not supported");}; void InputControlUpdate(IssmDouble scalar,bool save_parameter); #endif Index: /issm/trunk/src/c/classes/objects/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/Tria.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/Elements/Tria.cpp (revision 14310) @@ -1550,4 +1550,12 @@ for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts; this->inputs->AddInput(new ControlInput(VyEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1)); + } + break; + case ThicknessEnum: + if (iomodel->Data(ThicknessEnum)){ + for(j=0;j<3;j++)nodeinputs[j]=iomodel->Data(ThicknessEnum)[tria_vertex_ids[j]-1]; + for(j=0;j<3;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]; + for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]; + this->inputs->AddInput(new ControlInput(ThicknessEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1)); } break; @@ -2317,13 +2325,8 @@ IssmDouble h[NUMVERTICES]; // ice thickness (m) IssmDouble s[NUMVERTICES]; // surface elevation (m) - IssmDouble a_pos[NUMVERTICES]; // Hs-SMB relation parameter IssmDouble b_pos[NUMVERTICES]; // Hs-SMB relation parameter - IssmDouble a_neg[NUMVERTICES]; // Hs-SMB relation parameter IssmDouble b_neg[NUMVERTICES]; // Hs-SMB relation paremeter - IssmDouble Hc[NUMVERTICES]; // elevation of transition between accumulation regime and ablation regime IssmDouble Href[NUMVERTICES]; // reference elevation from which deviations are used to calculate the SMB adjustment IssmDouble Smbref[NUMVERTICES]; // reference SMB to which deviations are added - IssmDouble smb_pos_max[NUMVERTICES]; // maximum SMB value in the accumulation regime - IssmDouble smb_pos_min[NUMVERTICES]; // minimum SMB value in the accumulation regime IssmDouble rho_water; // density of fresh water IssmDouble rho_ice; // density of ice @@ -2333,12 +2336,7 @@ /*Recover SmbGradients*/ - GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum); GetInputListOnVertices(&Href[0],SurfaceforcingsHrefEnum); GetInputListOnVertices(&Smbref[0],SurfaceforcingsSmbrefEnum); - GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum); - GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum); - GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum); GetInputListOnVertices(&b_pos[0],SurfaceforcingsBPosEnum); - GetInputListOnVertices(&a_neg[0],SurfaceforcingsANegEnum); GetInputListOnVertices(&b_neg[0],SurfaceforcingsBNegEnum); @@ -2353,22 +2351,11 @@ // loop over all vertices for(i=0;iHc[i]){ - if(Href[i]>Hc[i]){smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]);} - if(Href[i]<=Hc[i]){smb[i]=a_pos[i]+b_pos[i]*s[i];} - if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} - if(smb[i]0){ + smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]); } else{ - if(Href[i]>Hc[i]){smb[i]=a_neg[i]+b_neg[i]*s[i];} - if(Href[i]<=Hc[i]){smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]);} + smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]); } smb[i]=smb[i]/rho_ice; // SMB in m/y ice - /* printf("s %e \n",s[i]); - printf("Hsref %e \n",Href[i]); - printf("Hc %e \n",Hc[i]); - printf("Smbref %e \n",Smbref[i]); - printf("b_neg %e \n",b_neg[i]); - printf("smb %e \n",smb[i]); - _error_("stop-in-code"); */ } //end of the loop over the vertices /*Update inputs*/ @@ -3459,4 +3446,62 @@ #ifdef _HAVE_CONTROL_ +/*FUNCTION Tria::BalancethicknessMisfit{{{*/ +IssmDouble Tria::BalancethicknessMisfit(bool process_units,int weight_index){ + + /* Intermediaries */ + IssmDouble Jelem = 0; + IssmDouble weight; + IssmDouble Jdet,temp; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble dH[2]; + IssmDouble vx,vy,H; + IssmDouble dvx[2],dvy[2]; + IssmDouble dhdt,basal_melting,surface_mass_balance; + GaussTria *gauss = NULL; + + /*If on water, return 0: */ + if(IsOnWater()) return 0; + + /*Retrieve all inputs we will be needing: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + Input* weights_input = inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input); + Input* thickness_input = inputs->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* vx_input = inputs->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = inputs->GetInput(VyEnum); _assert_(vy_input); + Input* surface_mass_balance_input = inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input); + Input* basal_melting_input = inputs->GetInput(BasalforcingsMeltingRateEnum); _assert_(basal_melting_input); + Input* dhdt_input = inputs->GetInput(BalancethicknessThickeningRateEnum); _assert_(dhdt_input); + + /* Start looping on the number of gaussian points: */ + gauss=new GaussTria(2); + for(int ig=gauss->begin();igend();ig++){ + + gauss->GaussPoint(ig); + + /* Get Jacobian determinant: */ + GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss); + + /*Get all parameters at gaussian point*/ + weights_input->GetInputValue(&weight,gauss,weight_index); + thickness_input->GetInputValue(&H, gauss); + thickness_input->GetInputDerivativeValue(&dH[0],&xyz_list[0][0],gauss); + surface_mass_balance_input->GetInputValue(&surface_mass_balance,gauss); + basal_melting_input->GetInputValue(&basal_melting,gauss); + dhdt_input->GetInputValue(&dhdt,gauss); + vx_input->GetInputValue(&vx,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss); + + /*Weak balance thickness J = 1/2 (div(Hv)-a)^2*/ + temp = vx*dH[0]+vy*dH[1]+H*(dvx[0]+dvy[1]) - (surface_mass_balance-basal_melting-dhdt); + Jelem+=weight*1/2*temp*temp*Jdet*gauss->weight; + } + + /*Clean up and return*/ + delete gauss; + return Jelem; +} +/*}}}*/ /*FUNCTION Tria::InputControlUpdate{{{*/ void Tria::InputControlUpdate(IssmDouble scalar,bool save_parameter){ @@ -3580,4 +3625,7 @@ GradjVyBalancedthickness(gradient,control_index); break; + case ThicknessEnum: + GradjThicknessWeakBalancedthickness(gradient,control_index); + break; default: _error_("control type not supported yet: " << control_type); @@ -3597,4 +3645,5 @@ case ThicknessAlongGradientEnum: case ThicknessAcrossGradientEnum: + case BalancethicknessMisfitEnum: case SurfaceAbsVelMisfitEnum: case SurfaceRelVelMisfitEnum: @@ -4042,4 +4091,114 @@ /*Clean up and return*/ delete gauss; +} +/*}}}*/ +/*FUNCTION Tria::GradjThicknessWeakBalancedthickness{{{*/ +void Tria::GradjThicknessWeakBalancedthickness(Vector* gradient,int control_index){ + + /*Intermediaries */ + int i,resp; + int vertexpidlist[NUMVERTICES]; + IssmDouble Jdet; + IssmDouble thickness,thicknessobs,weight; + int num_responses; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble basis[3]; + IssmDouble dbasis[NDOF2][NUMVERTICES]; + IssmDouble dH[2]; + IssmDouble vx,vy,vel; + IssmDouble dvx[2],dvy[2]; + IssmDouble dhdt,basal_melting,surface_mass_balance; + GaussTria *gauss = NULL; + int *responses = NULL; + IssmDouble grade_g[NUMVERTICES] = {0.0}; + + /* Get node coordinates and dof list: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + GradientIndexing(&vertexpidlist[0],control_index); + + /*Retrieve all inputs and parameters*/ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); + this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum); + Input* thickness_input = inputs->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* thicknessobs_input = inputs->GetInput(InversionThicknessObsEnum); _assert_(thicknessobs_input); + Input* weights_input = inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input); + Input* vx_input = inputs->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = inputs->GetInput(VyEnum); _assert_(vy_input); + Input* surface_mass_balance_input = inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input); + Input* basal_melting_input = inputs->GetInput(BasalforcingsMeltingRateEnum); _assert_(basal_melting_input); + Input* dhdt_input = inputs->GetInput(BalancethicknessThickeningRateEnum); _assert_(dhdt_input); + + /* Start looping on the number of gaussian points: */ + gauss=new GaussTria(2); + for(int ig=gauss->begin();igend();ig++){ + + gauss->GaussPoint(ig); + + GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss); + GetNodalFunctions(basis, gauss); + GetNodalFunctionsDerivatives(&dbasis[0][0],&xyz_list[0][0],gauss); + + thickness_input->GetInputValue(&thickness, gauss); + thickness_input->GetInputDerivativeValue(&dH[0],&xyz_list[0][0],gauss); + thicknessobs_input->GetInputValue(&thicknessobs, gauss); + + /*Loop over all requested responses*/ + for(resp=0;respGetInputValue(&weight, gauss,resp); + for(i=0;iweight*basis[i]; + break; + case ThicknessAbsGradientEnum: + weights_input->GetInputValue(&weight, gauss,resp); + for(i=0;iweight; + for(i=0;iweight; + break; + case ThicknessAlongGradientEnum: + weights_input->GetInputValue(&weight, gauss,resp); + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + vel = sqrt(vx*vx+vy*vy); + vx = vx/(vel+1.e-9); + vy = vy/(vel+1.e-9); + for(i=0;iweight; + break; + case ThicknessAcrossGradientEnum: + weights_input->GetInputValue(&weight, gauss,resp); + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + vel = sqrt(vx*vx+vy*vy); + vx = vx/(vel+1.e-9); + vy = vy/(vel+1.e-9); + for(i=0;iweight; + break; + case BalancethicknessMisfitEnum: + weights_input->GetInputValue(&weight, gauss,resp); + surface_mass_balance_input->GetInputValue(&surface_mass_balance,gauss); + basal_melting_input->GetInputValue(&basal_melting,gauss); + dhdt_input->GetInputValue(&dhdt,gauss); + vx_input->GetInputValue(&vx,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss); + for(i=0;iweight*( + (vx*dH[0]+vy*dH[1] + thickness*(dvx[0]+dvy[1]))*(vx*dbasis[0][i]+ vy*dbasis[1][i] + basis[i]*(dvx[0]+dvy[1])) + -(surface_mass_balance-basal_melting-dhdt)*(vx*dbasis[0][i]+ vy*dbasis[1][i] + basis[i]*(dvx[0]+dvy[1])) + ); + } + break; + default: + _error_("response " << EnumToStringx(responses[resp]) << " not supported yet"); + } + } + + + gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; + xDelete(responses); } /*}}}*/ Index: /issm/trunk/src/c/classes/objects/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/classes/objects/Elements/Tria.h (revision 14309) +++ /issm/trunk/src/c/classes/objects/Elements/Tria.h (revision 14310) @@ -153,4 +153,5 @@ void GradjVxBalancedthickness(Vector* gradient,int control_index); void GradjVyBalancedthickness(Vector* gradient,int control_index); + void GradjThicknessWeakBalancedthickness(Vector* gradient,int control_index); void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data); void SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index); @@ -164,4 +165,5 @@ IssmDouble ThicknessAlongGradient( bool process_units,int weight_index); IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index); + IssmDouble BalancethicknessMisfit( bool process_units,int weight_index); IssmDouble SurfaceRelVelMisfit( bool process_units,int weight_index); IssmDouble SurfaceLogVelMisfit( bool process_units,int weight_index); Index: /issm/trunk/src/c/classes/objects/ExternalResults/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/ExternalResults/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/ExternalResults/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/ExternalResults) +# }}} Index: /issm/trunk/src/c/classes/objects/Inputs/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Inputs/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Inputs/CMakeLists.txt (revision 14310) @@ -0,0 +1,16 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Inputs) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/BoolInput.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/DatasetInput.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/DoubleInput.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/IntInput.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/TransientInput.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/TriaP1Input.cpp PARENT_SCOPE) +# }}} +# THREED_SOURCES {{{ +set(THREED_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Inputs/PentaP1Input.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/KML/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/KML/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/KML/CMakeLists.txt (revision 14310) @@ -0,0 +1,34 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/KML) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Attribute.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_ColorStyle.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Comment.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Container.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Document.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Feature.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_File.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Folder.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Geometry.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_GroundOverlay.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Icon.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_LatLonBox.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_LinearRing.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_LineString.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_LineStyle.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_MultiGeometry.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Object.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Overlay.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Placemark.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Point.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Polygon.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_PolyStyle.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Style.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_StyleSelector.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_SubStyle.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KML_Unknown.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/KML/KMLFileReadUtils.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp (revision 14310) @@ -197,5 +197,11 @@ x =xNew(ncoord); y =xNew(ncoord); - Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + if (sgn) { + Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + } + else { + memcpy(x,lon,ncoord*sizeof(IssmDouble)); + memcpy(y,lat,ncoord*sizeof(IssmDouble)); + } /* write header */ Index: /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp (revision 14310) @@ -186,5 +186,11 @@ x =xNew(ncoord); y =xNew(ncoord); - Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + if (sgn) { + Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + } + else { + memcpy(x,lon,ncoord*sizeof(IssmDouble)); + memcpy(y,lat,ncoord*sizeof(IssmDouble)); + } /* write header */ Index: /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp (revision 14310) @@ -166,5 +166,11 @@ /* convert latitude and longitude to x and y */ - Ll2xyx(&x,&y,&lat,&lon,1,sgn,cm,sp); + if (sgn) { + Ll2xyx(&x,&y,&lat,&lon,1,sgn,cm,sp); + } + else { + memcpy(&x,&lon,1*sizeof(IssmDouble)); + memcpy(&y,&lat,1*sizeof(IssmDouble)); + } /* write header */ Index: /issm/trunk/src/c/classes/objects/Loads/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Loads/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Loads/CMakeLists.txt (revision 14310) @@ -0,0 +1,15 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Loads) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Friction.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Icefront.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Numericalflux.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Pengrid.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Penpair.cpp PARENT_SCOPE) +# }}} +# RIFTS_SOURCES {{{ +set(RIFTS_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Loads/Riftfront.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Materials/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Materials/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Materials/CMakeLists.txt (revision 14310) @@ -0,0 +1,10 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Materials) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Materials/Matdamageice.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Materials/Matice.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Materials/Matpar.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Options/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Options/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Options/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Options) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Options/OptionUtilities.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Params/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/classes/objects/Params/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/classes/objects/Params/CMakeLists.txt (revision 14310) @@ -0,0 +1,23 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/classes/objects/Params) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/classes/objects/Params/BoolParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DataSetParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DoubleMatArrayParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DoubleMatParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DoubleParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DoubleTransientMatParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/DoubleVecParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/FileParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/IntMatParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/IntParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/IntVecParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/MatrixParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/StringArrayParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/StringParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/TransientParam.cpp + $ENV{ISSM_DIR}/src/c/classes/objects/Params/VectorParam.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/classes/objects/Vertex.cpp =================================================================== --- /issm/trunk/src/c/classes/objects/Vertex.cpp (revision 14309) +++ /issm/trunk/src/c/classes/objects/Vertex.cpp (revision 14310) @@ -194,2 +194,20 @@ } /*}}}*/ +/*FUNCTION Vertex::ToXYZ {{{*/ +void Vertex::ToXYZ(Matrix* matrix){ + + IssmDouble xyz[3]; + int indices[3]; + + if (this->clone==true) return; + + xyz[0]=x; + xyz[1]=y; + xyz[2]=z; + indices[0]=0; + indices[1]=1; + indices[2]=2; + + matrix->SetValues(1,&sid,3,&indices[0],&xyz[0],INS_VAL); +} +/*}}}*/ Index: /issm/trunk/src/c/classes/objects/Vertex.h =================================================================== --- /issm/trunk/src/c/classes/objects/Vertex.h (revision 14309) +++ /issm/trunk/src/c/classes/objects/Vertex.h (revision 14310) @@ -13,4 +13,5 @@ #include "../../include/include.h" template class Vector; +template class Matrix; class Parameters; class IoModel; @@ -53,4 +54,5 @@ void UpdateClonePids(int* allborderpids); void SetClone(int* minranks); + void ToXYZ(Matrix* matrix); }; #endif /* _VERTEX_H */ Index: /issm/trunk/src/c/include/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/include/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/include/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/include) +# }}} Index: /issm/trunk/src/c/include/globals.h =================================================================== --- /issm/trunk/src/c/include/globals.h (revision 14309) +++ /issm/trunk/src/c/include/globals.h (revision 14310) @@ -10,4 +10,5 @@ COMM IssmComm::comm; +bool IssmComm::parallel; #endif Index: /issm/trunk/src/c/io/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/io/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/io/CMakeLists.txt (revision 14310) @@ -0,0 +1,9 @@ +# Subdirectories {{{ +add_subdirectory(Disk) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/io) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/io/PrintfFunction.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/io/Disk/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/io/Disk/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/io/Disk/CMakeLists.txt (revision 14310) @@ -0,0 +1,10 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/io/Disk) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/io/Disk/pfclose.cpp + $ENV{ISSM_DIR}/src/c/io/Disk/pfopen.cpp + $ENV{ISSM_DIR}/src/c/io/Disk/WriteLockFile.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/io/PrintfFunction.cpp =================================================================== --- /issm/trunk/src/c/io/PrintfFunction.cpp (revision 14309) +++ /issm/trunk/src/c/io/PrintfFunction.cpp (revision 14310) @@ -8,4 +8,8 @@ #include "../shared/shared.h" #include "../include/include.h" + +#ifdef _HAVE_ANDROID_NDK_ +#include +#endif int PrintfFunction(const char* format,...){ @@ -58,5 +62,9 @@ if(my_rank==0){ + #ifdef _HAVE_ANDROID_JNI_ + __android_log_print(ANDROID_LOG_INFO, "Native",message.c_str()); + #else printf("%s\n",message.c_str()); + #endif } return 1; Index: /issm/trunk/src/c/modules/AverageFilterx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/AverageFilterx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/AverageFilterx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/AverageFilterx) +# }}} Index: /issm/trunk/src/c/modules/AverageOntoPartitionx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/AverageOntoPartitionx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/AverageOntoPartitionx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/AverageOntoPartitionx) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/BamgConvertMeshx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/BamgConvertMeshx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/BamgConvertMeshx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/BamgConvertMeshx) +# }}} +# BAMG_SOURCES {{{ +set(BAMG_SOURCES $ENV{ISSM_DIR}/src/c/modules/BamgConvertMeshx/BamgConvertMeshx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/BamgTriangulatex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/BamgTriangulatex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/BamgTriangulatex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/BamgTriangulatex) +# }}} +# BAMG_SOURCES {{{ +set(BAMG_SOURCES $ENV{ISSM_DIR}/src/c/modules/BamgTriangulatex/BamgTriangulatex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Bamgx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Bamgx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Bamgx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Bamgx) +# }}} +# BAMG_SOURCES {{{ +set(BAMG_SOURCES $ENV{ISSM_DIR}/src/c/modules/Bamgx/Bamgx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/CMakeLists.txt (revision 14310) @@ -0,0 +1,100 @@ +# Subdirectories {{{ +add_subdirectory(AverageFilterx) +add_subdirectory(AverageOntoPartitionx) +add_subdirectory(BamgConvertMeshx) +add_subdirectory(BamgTriangulatex) +add_subdirectory(Bamgx) +add_subdirectory(Chacox) +add_subdirectory(ComputeBasalStressx) +add_subdirectory(ComputeStrainRatex) +add_subdirectory(ConfigureObjectsx) +add_subdirectory(ConstraintsStatex) +add_subdirectory(ContourToMeshx) +add_subdirectory(ContourToNodesx) +add_subdirectory(ControlInputGetGradientx) +add_subdirectory(ControlInputScaleGradientx) +add_subdirectory(ControlInputSetGradientx) +add_subdirectory(CreateNodalConstraintsx) +add_subdirectory(Delta18oParameterizationx) +add_subdirectory(DragCoefficientAbsGradientx) +add_subdirectory(ElementConnectivityx) +add_subdirectory(EnumToStringx) +add_subdirectory(Exp2Kmlx) +add_subdirectory(GetSolutionFromInputsx) +add_subdirectory(GetVectorFromControlInputsx) +add_subdirectory(GetVectorFromInputsx) +add_subdirectory(Gradjx) +add_subdirectory(GroundinglineMigrationx) +add_subdirectory(HoleFillerx) +add_subdirectory(InputArtificialNoisex) +add_subdirectory(InputControlUpdatex) +add_subdirectory(InputConvergencex) +add_subdirectory(InputDuplicatex) +add_subdirectory(InputScalex) +add_subdirectory(InputToResultx) +add_subdirectory(InputUpdateFromConstantx) +add_subdirectory(InputUpdateFromDakotax) +add_subdirectory(InputUpdateFromMatrixDakotax) +add_subdirectory(InputUpdateFromSolutionx) +add_subdirectory(InputUpdateFromVectorDakotax) +add_subdirectory(InputUpdateFromVectorx) +add_subdirectory(InterpFromGridToMeshx) +add_subdirectory(InterpFromMesh2dx) +add_subdirectory(InterpFromMeshToGridx) +add_subdirectory(InterpFromMeshToMesh2dx) +add_subdirectory(InterpFromMeshToMesh3dx) +add_subdirectory(IoModelToConstraintsx) +add_subdirectory(Kml2Expx) +add_subdirectory(KMLFileReadx) +add_subdirectory(KMLMeshWritex) +add_subdirectory(KMLOverlayx) +add_subdirectory(Krigingx) +add_subdirectory(Ll2xyx) +add_subdirectory(Mergesolutionfromftogx) +add_subdirectory(MeshPartitionx) +add_subdirectory(MeshProfileIntersectionx) +add_subdirectory(ModelProcessorx) +add_subdirectory(NodalValuex) +add_subdirectory(NodeConnectivityx) +add_subdirectory(NodesDofx) +add_subdirectory(Orthx) +add_subdirectory(OutputResultsx) +add_subdirectory(OutputRiftsx) +add_subdirectory(ParsePetscOptionsx) +add_subdirectory(PointCloudFindNeighborsx) +add_subdirectory(PositiveDegreeDayx) +add_subdirectory(PropagateFlagsFromConnectivityx) +add_subdirectory(Reduceloadx) +add_subdirectory(Reducevectorgtofx) +add_subdirectory(Reducevectorgtosx) +add_subdirectory(ResetConstraintsx) +add_subdirectory(ResetCoordinateSystemx) +add_subdirectory(RheologyBbarAbsGradientx) +add_subdirectory(Scotchx) +add_subdirectory(SetControlInputsFromVectorx) +add_subdirectory(Shp2Expx) +add_subdirectory(Shp2Kmlx) +add_subdirectory(SmbGradientsx) +add_subdirectory(Solverx) +add_subdirectory(SpcNodesx) +add_subdirectory(StringToEnumx) +add_subdirectory(SurfaceAbsVelMisfitx) +add_subdirectory(SurfaceAreax) +add_subdirectory(SurfaceAverageVelMisfitx) +add_subdirectory(SurfaceLogVelMisfitx) +add_subdirectory(SurfaceLogVxVyMisfitx) +add_subdirectory(SurfaceRelVelMisfitx) +add_subdirectory(ThicknessAbsMisfitx) +add_subdirectory(ThicknessAcrossGradientx) +add_subdirectory(ThicknessAlongGradientx) +add_subdirectory(TriaSearchx) +add_subdirectory(TriMeshProcessRiftsx) +add_subdirectory(TriMeshx) +add_subdirectory(UpdateDynamicConstraintsx) +add_subdirectory(VecMergex) +add_subdirectory(VerticesDofx) +add_subdirectory(Xy2llx) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules) +# }}} Index: /issm/trunk/src/c/modules/Chacox/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Chacox/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Chacox/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Chacox) +# }}} Index: /issm/trunk/src/c/modules/ComputeBasalStressx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ComputeBasalStressx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ComputeBasalStressx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ComputeBasalStressx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ComputeStrainRatex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ComputeStrainRatex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ComputeStrainRatex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ComputeStrainRatex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ConfigureObjectsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ConfigureObjectsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ConfigureObjectsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ConfigureObjectsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ConstraintsStatex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ConstraintsStatex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ConstraintsStatex/CMakeLists.txt (revision 14310) @@ -0,0 +1,15 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ConstraintsStatex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp PARENT_SCOPE) +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp + $ENV{ISSM_DIR}/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp PARENT_SCOPE) +# }}} +# RIFTS_SOURCES {{{ +set(RIFTS_SOURCES $ENV{ISSM_DIR}/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ContourToMeshx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ContourToMeshx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ContourToMeshx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ContourToMeshx) +# }}} Index: /issm/trunk/src/c/modules/ContourToNodesx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ContourToNodesx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ContourToNodesx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ContourToNodesx) +# }}} Index: /issm/trunk/src/c/modules/ControlInputGetGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ControlInputGetGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ControlInputGetGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ControlInputGetGradientx) +# }}} Index: /issm/trunk/src/c/modules/ControlInputScaleGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ControlInputScaleGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ControlInputScaleGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ControlInputScaleGradientx) +# }}} Index: /issm/trunk/src/c/modules/ControlInputSetGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ControlInputSetGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ControlInputSetGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ControlInputSetGradientx) +# }}} Index: /issm/trunk/src/c/modules/CreateNodalConstraintsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/CreateNodalConstraintsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/CreateNodalConstraintsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/CreateNodalConstraintsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Delta18oParameterizationx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Delta18oParameterizationx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Delta18oParameterizationx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Delta18oParameterizationx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Delta18oParameterizationx/Delta18oParameterizationx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/DragCoefficientAbsGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/DragCoefficientAbsGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/DragCoefficientAbsGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/DragCoefficientAbsGradientx) +# }}} Index: /issm/trunk/src/c/modules/ElementConnectivityx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ElementConnectivityx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ElementConnectivityx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ElementConnectivityx) +# }}} Index: /issm/trunk/src/c/modules/EnumToStringx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/EnumToStringx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/EnumToStringx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/EnumToStringx/EnumToStringx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 14310) @@ -201,12 +201,7 @@ case SurfaceforcingsIssmbgradientsEnum : return "SurfaceforcingsIssmbgradients"; case SurfaceforcingsMonthlytemperaturesEnum : return "SurfaceforcingsMonthlytemperatures"; - case SurfaceforcingsHcEnum : return "SurfaceforcingsHc"; case SurfaceforcingsHrefEnum : return "SurfaceforcingsHref"; case SurfaceforcingsSmbrefEnum : return "SurfaceforcingsSmbref"; - case SurfaceforcingsSmbPosMaxEnum : return "SurfaceforcingsSmbPosMax"; - case SurfaceforcingsSmbPosMinEnum : return "SurfaceforcingsSmbPosMin"; - case SurfaceforcingsAPosEnum : return "SurfaceforcingsAPos"; case SurfaceforcingsBPosEnum : return "SurfaceforcingsBPos"; - case SurfaceforcingsANegEnum : return "SurfaceforcingsANeg"; case SurfaceforcingsBNegEnum : return "SurfaceforcingsBNeg"; case ThermalMaxiterEnum : return "ThermalMaxiter"; @@ -238,4 +233,6 @@ case BalancethicknessAnalysisEnum : return "BalancethicknessAnalysis"; case BalancethicknessSolutionEnum : return "BalancethicknessSolution"; + case WeakBalancethicknessAnalysisEnum : return "WeakBalancethicknessAnalysis"; + case WeakBalancethicknessSolutionEnum : return "WeakBalancethicknessSolution"; case BedSlopeAnalysisEnum : return "BedSlopeAnalysis"; case BedSlopeSolutionEnum : return "BedSlopeSolution"; @@ -346,4 +343,5 @@ case AdjointyEnum : return "Adjointy"; case AdjointzEnum : return "Adjointz"; + case BalancethicknessMisfitEnum : return "BalancethicknessMisfit"; case BedSlopeXEnum : return "BedSlopeX"; case BedSlopeYEnum : return "BedSlopeY"; @@ -373,4 +371,5 @@ case QmuSurfaceEnum : return "QmuSurface"; case QmuMeltingEnum : return "QmuMelting"; + case AndroidFrictionCoefficientEnum : return "AndroidFrictionCoefficient"; case ResetPenaltiesEnum : return "ResetPenalties"; case SegmentOnIceShelfEnum : return "SegmentOnIceShelf"; @@ -416,5 +415,4 @@ case DragCoefficientAbsGradientEnum : return "DragCoefficientAbsGradient"; case TransientInputEnum : return "TransientInput"; - case OutputfilenameEnum : return "Outputfilename"; case WaterfractionEnum : return "Waterfraction"; case WatercolumnEnum : return "Watercolumn"; Index: /issm/trunk/src/c/modules/Exp2Kmlx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Exp2Kmlx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Exp2Kmlx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Exp2Kmlx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/GetSolutionFromInputsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/GetSolutionFromInputsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/GetSolutionFromInputsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/GetSolutionFromInputsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/GetVectorFromControlInputsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/GetVectorFromControlInputsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/GetVectorFromControlInputsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/GetVectorFromControlInputsx) +# }}} Index: /issm/trunk/src/c/modules/GetVectorFromInputsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/GetVectorFromInputsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/GetVectorFromInputsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/GetVectorFromInputsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Gradjx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Gradjx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Gradjx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Gradjx) +# }}} Index: /issm/trunk/src/c/modules/GroundinglineMigrationx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/GroundinglineMigrationx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/GroundinglineMigrationx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/GroundinglineMigrationx) +# }}} Index: /issm/trunk/src/c/modules/HoleFillerx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/HoleFillerx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/HoleFillerx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/HoleFillerx) +# }}} Index: /issm/trunk/src/c/modules/InputArtificialNoisex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputArtificialNoisex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputArtificialNoisex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputArtificialNoisex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputArtificialNoisex/InputArtificialNoisex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputControlUpdatex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputControlUpdatex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputControlUpdatex/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputControlUpdatex) +# }}} Index: /issm/trunk/src/c/modules/InputConvergencex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputConvergencex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputConvergencex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputConvergencex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputConvergencex/InputConvergencex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputDuplicatex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputDuplicatex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputDuplicatex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputDuplicatex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputDuplicatex/InputDuplicatex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputScalex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputScalex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputScalex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputScalex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputScalex/InputScalex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputToResultx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputToResultx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputToResultx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputToResultx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputToResultx/InputToResultx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromConstantx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromConstantx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromConstantx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromConstantx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromConstantx/InputUpdateFromConstantx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromDakotax/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromDakotax/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromDakotax/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromDakotax) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromMatrixDakotax/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromMatrixDakotax/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromMatrixDakotax/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromMatrixDakotax) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromSolutionx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromSolutionx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromSolutionx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromSolutionx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromVectorDakotax/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromVectorDakotax/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromVectorDakotax/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromVectorDakotax) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InputUpdateFromVectorx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InputUpdateFromVectorx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InputUpdateFromVectorx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromVectorx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/InterpFromGridToMeshx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InterpFromGridToMeshx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InterpFromGridToMeshx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InterpFromGridToMeshx) +# }}} Index: /issm/trunk/src/c/modules/InterpFromMesh2dx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InterpFromMesh2dx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InterpFromMesh2dx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InterpFromMesh2dx) +# }}} Index: /issm/trunk/src/c/modules/InterpFromMeshToGridx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToGridx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InterpFromMeshToGridx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InterpFromMeshToGridx) +# }}} Index: /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InterpFromMeshToMesh2dx) +# }}} Index: /issm/trunk/src/c/modules/InterpFromMeshToMesh3dx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToMesh3dx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/InterpFromMeshToMesh3dx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/InterpFromMeshToMesh3dx) +# }}} Index: /issm/trunk/src/c/modules/IoModelToConstraintsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/IoModelToConstraintsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/IoModelToConstraintsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/IoModelToConstraintsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/KMLFileReadx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/KMLFileReadx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/KMLFileReadx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/KMLFileReadx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/KMLFileReadx/KMLFileReadx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/KMLMeshWritex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/KMLMeshWritex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/KMLMeshWritex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/KMLMeshWritex) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/KMLMeshWritex/KMLMeshWritex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/KMLOverlayx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/KMLOverlayx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/KMLOverlayx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/KMLOverlayx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/KMLOverlayx/KMLOverlayx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Kml2Expx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Kml2Expx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Kml2Expx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Kml2Expx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/Kml2Expx/Kml2Expx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Krigingx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Krigingx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Krigingx/CMakeLists.txt (revision 14310) @@ -0,0 +1,11 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Krigingx) +# }}} +# KRIGING_SOURCES {{{ +set(KRIGING_SOURCES $ENV{ISSM_DIR}/src/c/modules/Krigingx/Krigingx.cpp PARENT_SCOPE) +# }}} +# PKRIGING_SOURCES {{{ +set(PKRIGING_SOURCES $ENV{ISSM_DIR}/src/c/modules/Krigingx/pKrigingx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp =================================================================== --- /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp (revision 14310) @@ -57,4 +57,22 @@ else if(strcmp(output,"variomap")==0){ observations->Variomap(predictions,x_interp,n_interp); + } + else if(strcmp(output,"distance")==0){ + /*initialize thread parameters: */ + gate.n_interp = n_interp; + gate.x_interp = x_interp; + gate.y_interp = y_interp; + gate.radius = radius; + gate.mindata = mindata; + gate.maxdata = maxdata; + gate.variogram = variogram; + gate.observations = observations; + gate.predictions = predictions; + gate.error = error; + gate.numdone = xNewZeroInit(num); + + /*launch the thread manager with Krigingxt as a core: */ + LaunchThread(Distancest,(void*)&gate,num); + xDelete(gate.numdone); } else if(strcmp(output,"delaunay")==0){ @@ -360,4 +378,38 @@ return NULL; }/*}}}*/ +/*FUNCTION Distancest{{{*/ +void* Distancest(void* vpthread_handle){ + + /*gate variables :*/ + KrigingxThreadStruct *gate = NULL; + pthread_handle *handle = NULL; + int my_thread; + int num_threads; + int i0,i1; + + /*recover handle and gate: */ + handle = (pthread_handle*)vpthread_handle; + gate = (KrigingxThreadStruct*)handle->gate; + my_thread = handle->id; + num_threads = handle->num; + + /*recover parameters :*/ + int n_interp = gate->n_interp; + double *x_interp = gate->x_interp; + double *y_interp = gate->y_interp; + double radius = gate->radius; + int mindata = gate->mindata; + int maxdata = gate->maxdata; + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; + double *error = gate->error; + int *numdone = gate->numdone; + + /*partition loop across threads: */ + PartitionRange(&i0,&i1,n_interp,num_threads,my_thread); + observations->Distances(&predictions[i0],&x_interp[i0],&y_interp[i0],i1-i0,radius); + return NULL; +}/*}}}*/ void ProcessVariogram(Variogram **pvariogram,Options* options){/*{{{*/ Index: /issm/trunk/src/c/modules/Krigingx/Krigingx.h =================================================================== --- /issm/trunk/src/c/modules/Krigingx/Krigingx.h (revision 14309) +++ /issm/trunk/src/c/modules/Krigingx/Krigingx.h (revision 14310) @@ -36,3 +36,4 @@ void* idwt(void*); void* v4t(void*); +void* Distancest(void*); #endif /* _KRIGINGX_H */ Index: /issm/trunk/src/c/modules/Ll2xyx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Ll2xyx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Ll2xyx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Ll2xyx) +# }}} Index: /issm/trunk/src/c/modules/Mergesolutionfromftogx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Mergesolutionfromftogx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Mergesolutionfromftogx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Mergesolutionfromftogx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/MeshPartitionx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/MeshPartitionx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/MeshPartitionx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/MeshPartitionx) +# }}} Index: /issm/trunk/src/c/modules/MeshProfileIntersectionx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/MeshProfileIntersectionx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/MeshProfileIntersectionx) +# }}} Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/ElementSegment.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/ElementSegment.cpp (revision 14309) +++ (revision ) @@ -1,90 +1,0 @@ -/*! \file ElementSegment.cpp - */ - -#include "./MeshProfileIntersectionx.h" - -void ElementSegment(DataSet* segments_dataset,int el,double* xnodes,double* ynodes,double* xsegment,double* ysegment){ - - /*We have a tria element (xnodes,ynodes) and a segment (xsegment,ysegment). Find whether they intersect. - * If they do, create a Segment object with the intersection, and add to segments_dataset dataset: */ - - double alpha1,alpha2; - double beta1,beta2; - double gamma1,gamma2; - - int edge1,edge2,edge3; - - double xel[2],yel[2]; - double coord1,coord2; - double xfinal[2],yfinal[2]; - - /*edge 1: */ - xel[0]=xnodes[0]; yel[0]=ynodes[0]; xel[1]=xnodes[1]; yel[1]=ynodes[1]; - edge1=SegmentIntersect(&alpha1,&alpha2, xel,yel,xsegment,ysegment); //alpha1: segment coordinate of intersection. alpha2: same thing for second interesection if it exists (colinear edges) - - /*edge 2: */ - xel[0]=xnodes[1]; yel[0]=ynodes[1]; xel[1]=xnodes[2]; yel[1]=ynodes[2]; - edge2=SegmentIntersect(&beta1,&beta2, xel,yel,xsegment,ysegment); - - /*edge 3: */ - xel[0]=xnodes[2]; yel[0]=ynodes[2]; xel[1]=xnodes[0]; yel[1]=ynodes[0]; - edge3=SegmentIntersect(&gamma1,&gamma2, xel,yel,xsegment,ysegment); - - /*edge can be either IntersectEnum (one iand only one intersection between the edge and the segment), ColinearEnum (edge and segment are collinear) and SeparateEnum (no intersection): */ - - if( (edge1==IntersectEnum) && (edge2==IntersectEnum) && (edge3==IntersectEnum) ){ - /*This case is impossible: */ - _error_("error: a line cannot go through 3 different vertices!"); - } - else if( ((edge1==IntersectEnum) && (edge2==IntersectEnum)) || ((edge2==IntersectEnum) && (edge3==IntersectEnum)) || ((edge3==IntersectEnum) && (edge1==IntersectEnum)) ){ - - /*segment interscts 2 opposite edges of our triangle, at 2 segment coordinates, pick up the lowest (coord1) and highest (coord2): */ - if((edge1==IntersectEnum) && (edge2==IntersectEnum)) {coord1=min(alpha1,beta1); coord2=max(alpha1,beta1);} - if((edge2==IntersectEnum) && (edge3==IntersectEnum)) {coord1=min(beta1,gamma1); coord2=max(beta1,gamma1);} - if((edge3==IntersectEnum) && (edge1==IntersectEnum)) {coord1=min(gamma1,alpha1); coord2=max(gamma1,alpha1);} - - /*check this segment did not intersect at a vertex of the tria: */ - if(coord1!=coord2){ - - xfinal[0]=xsegment[0]+coord1*(xsegment[1]-xsegment[0]); - xfinal[1]=xsegment[0]+coord2*(xsegment[1]-xsegment[0]); - yfinal[0]=ysegment[0]+coord1*(ysegment[1]-ysegment[0]); - yfinal[1]=ysegment[0]+coord2*(ysegment[1]-ysegment[0]); - - segments_dataset->AddObject(new Segment(el+1,xfinal[0],yfinal[0],xfinal[1],yfinal[1])); - } - else{ - /*the segment intersected at the vertex, do not bother with this "0" length segment!:*/ - } - } - else if( (edge1==IntersectEnum) || (edge2==IntersectEnum) || (edge3==IntersectEnum) ){ - - /*segment intersect only 1 edge. Figure out where the first point in the segment is, inside or outside the element, - * this will decide the coordinate: */ - if (NodeInElement(xnodes,ynodes,xsegment[0],ysegment[0])){ - coord1=0; - if(edge1==IntersectEnum){coord2=alpha1;} - if(edge2==IntersectEnum){coord2=beta1;} - if(edge3==IntersectEnum){coord2=gamma1;} - } - else{ - if(edge1==IntersectEnum){coord1=alpha1;} - if(edge2==IntersectEnum){coord1=beta1;} - if(edge3==IntersectEnum){coord1=gamma1;} - coord2=1.0; - } - - xfinal[0]=xsegment[0]+coord1*(xsegment[1]-xsegment[0]); - xfinal[1]=xsegment[0]+coord2*(xsegment[1]-xsegment[0]); - yfinal[0]=ysegment[0]+coord1*(ysegment[1]-ysegment[0]); - yfinal[1]=ysegment[0]+coord2*(ysegment[1]-ysegment[0]); - - segments_dataset->AddObject(new Segment(el+1,xfinal[0],yfinal[0],xfinal[1],yfinal[1])); - } - else{ - /*No interesections, but the segment might be entirely inside this triangle!: */ - if ( (NodeInElement(xnodes,ynodes,xsegment[0],ysegment[0])) && (NodeInElement(xnodes,ynodes,xsegment[1],ysegment[1])) ){ - segments_dataset->AddObject(new Segment(el+1,xsegment[0],ysegment[0],xsegment[1],ysegment[1])); - } - } -} Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp (revision 14309) +++ (revision ) @@ -1,23 +1,0 @@ -/*! \file ElementSegmentsIntersection.cpp - */ - -#include "./MeshProfileIntersectionx.h" - -void ElementSegmentsIntersection(DataSet* segments_dataset,int el, double* xnodes,double* ynodes,double* xc,double* yc,int numnodes){ - - int i; - double xsegment[2]; - double ysegment[2]; - - /*Loop through contour: */ - for(i=0;i** contours,int numcontours){ +void MeshProfileIntersectionx(double** psegments, int* pnumsegs, int* index, double* x, double* y, int nel, int nods, Contour** contours,int numcontours){/*{{{*/ int i,j,k; @@ -20,8 +20,8 @@ /*intermediary: */ double** allsegments=NULL; - double* segmentsi=NULL; - int* allnumsegs=NULL; - int numsegsi; - int count; + double* segmentsi=NULL; + int* allnumsegs=NULL; + int numsegsi; + int count; /*Allocate: */ @@ -69,3 +69,278 @@ *psegments=segments; *pnumsegs=numsegs; -} +}/*}}}*/ +void MeshSegmentsIntersection(double** psegments, int* pnumsegs,int* index, double* x, double* y, int nel, int nods, double* xc, double* yc, int numnodes){/*{{{*/ + + int i,j; + + /*output: */ + double* segments=NULL; + Segment* segment=NULL; + int numsegs; + + /*intermediary: */ + DataSet* segments_dataset=NULL; + double xnodes[3]; + double ynodes[3]; + + /*We don't know how many segments we are going to get, so have a dynamic container: */ + segments_dataset=new DataSet(); + + /*Go through elements, and call ElementSegmentsIntersection routine: */ + for(i=0;iSize(); + segments=xNew(5*numsegs); + for(i=0;i* segment=(Segment*)segments_dataset->GetObjectByOffset(i); + + /*x1,y1,x2,y2 then element_id: */ + segments[5*i+0]=segment->x1; + segments[5*i+1]=segment->y1; + segments[5*i+2]=segment->x2; + segments[5*i+3]=segment->y2; + segments[5*i+4]=(double)segment->eid; + } + + /*Free ressources:*/ + delete segments_dataset; + + /*Assign output pointers:*/ + *psegments=segments; + *pnumsegs=numsegs; +}/*}}}*/ + +/*Utilities*/ +void ElementSegmentsIntersection(DataSet* segments_dataset,int el, double* xnodes,double* ynodes,double* xc,double* yc,int numnodes){/*{{{*/ + + double xsegment[2]; + double ysegment[2]; + + /*Loop through contour: */ + for(int i=0;iAddObject(new Segment(el+1,xfinal[0],yfinal[0],xfinal[1],yfinal[1])); + } + else{ + /*the segment intersected at the vertex, do not bother with this "0" length segment!:*/ + } + } + else if( (edge1==IntersectEnum) || (edge2==IntersectEnum) || (edge3==IntersectEnum) ){ + + /*segment intersect only 1 edge. Figure out where the first point in the segment is, inside or outside the element, + * this will decide the coordinate: */ + if (NodeInElement(xnodes,ynodes,xsegment[0],ysegment[0])){ + coord1=0; + if(edge1==IntersectEnum){coord2=alpha1;} + if(edge2==IntersectEnum){coord2=beta1;} + if(edge3==IntersectEnum){coord2=gamma1;} + } + else{ + if(edge1==IntersectEnum){coord1=alpha1;} + if(edge2==IntersectEnum){coord1=beta1;} + if(edge3==IntersectEnum){coord1=gamma1;} + coord2=1.0; + } + + xfinal[0]=xsegment[0]+coord1*(xsegment[1]-xsegment[0]); + xfinal[1]=xsegment[0]+coord2*(xsegment[1]-xsegment[0]); + yfinal[0]=ysegment[0]+coord1*(ysegment[1]-ysegment[0]); + yfinal[1]=ysegment[0]+coord2*(ysegment[1]-ysegment[0]); + + segments_dataset->AddObject(new Segment(el+1,xfinal[0],yfinal[0],xfinal[1],yfinal[1])); + } + else{ + /*No interesections, but the segment might be entirely inside this triangle!: */ + if ( (NodeInElement(xnodes,ynodes,xsegment[0],ysegment[0])) && (NodeInElement(xnodes,ynodes,xsegment[1],ysegment[1])) ){ + segments_dataset->AddObject(new Segment(el+1,xsegment[0],ysegment[0],xsegment[1],ysegment[1])); + } + } +}/*}}}*/ +bool NodeInElement(double* xnodes, double* ynodes, double x, double y){/*{{{*/ + + double x1,y1; + double x2,y2; + double x3,y3; + double lambda1,lambda2,lambda3; + double det; + + x1=xnodes[0]; + x2=xnodes[1]; + x3=xnodes[2]; + y1=ynodes[0]; + y2=ynodes[1]; + y3=ynodes[2]; + + /*compute determinant: */ + det=x1*y2-x1*y3-x3*y2-x2*y1+x2*y3+x3*y1; + + /*area coordinates: */ + lambda1=((y2-y3)*(x-x3)+(x3-x2)*(y-y3))/det; + lambda2=((y3-y1)*(x-x3)+(x1-x3)*(y-y3))/det; + lambda3=1-lambda1-lambda2; + + if( ((lambda1<=1) && (lambda1>=0)) && ((lambda2<=1) && (lambda2>=0)) && ((lambda3<=1) && (lambda3>=0)) )return true; + else return false; + +}/*}}}*/ +int SegmentIntersect(double* palpha, double* pbeta, double* x1, double* y1, double* x2, double* y2){/*{{{*/ + + /*See ISSM_DIR/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ + + /*output: */ + double alpha=-1; + double beta=-1; + + double xA,xB,xC,xD,yA,yB,yC,yD; + double O2A[2],O2B[2],O1C[2],O1D[2]; + double n1[2],n2[2]; + double test1, test2, test3, test4; + double det; + double O2O1[2]; + double pO1A,pO1B,pO1C,pO1D; + + xA=x1[0]; yA=y1[0]; + xB=x1[1]; yB=y1[1]; + xC=x2[0]; yC=y2[0]; + xD=x2[1]; yD=y2[1]; + + O2A[0]=xA -(xD/2+xC/2); O2A[1]=yA -(yD/2+yC/2); + O2B[0]=xB -(xD/2+xC/2); O2B[1]=yB -(yD/2+yC/2); + O1C[0]=xC -(xA/2+xB/2); O1C[1]=yC -(yA/2+yB/2); + O1D[0]=xD -(xA/2+xB/2); O1D[1]=yD -(yA/2+yB/2); + + n1[0]=yA-yB; n1[1]=xB-xA; //normal vector to segA + n2[0]=yC-yD; n2[1]=xD-xC; //normal vector to segB + + test1=n2[0]*O2A[0]+n2[1]*O2A[1]; + test2=n2[0]*O2B[0]+n2[1]*O2B[1]; + + if (test1*test2>0){ + return SeparateEnum; + } + + test3=n1[0]*O1C[0]+n1[1]*O1C[1]; + test4=n1[0]*O1D[0]+n1[1]*O1D[1]; + + if (test3*test4>0){ + return SeparateEnum; + } + + /*If colinear: */ + det=n1[0]*n2[1]-n2[0]*n1[1]; + + if(test1*test2==0 && test3*test4==0 && det==0){ + + //projection on the axis O1O2 + O2O1[0]=(xA/2+xB/2)-(xD/2+xC/2); + O2O1[1]=(yA/2+yB/2)-(yD/2+yC/2); + + pO1A=O2O1[0]*(O2A[0]-O2O1[0])+O2O1[1]*(O2A[1]-O2O1[1]); + pO1B=O2O1[0]*(O2B[0]-O2O1[0])+O2O1[1]*(O2B[1]-O2O1[1]); + pO1C=O2O1[0]*O1C[0]+O2O1[1]*O1C[1]; + pO1D=O2O1[0]*O1D[0]+O2O1[1]*O1D[1]; + + //test if one point is included in the other segment (->intersects=true) + if ((pO1C-pO1A)*(pO1D-pO1A)<0){ + alpha=0; beta=0; + *palpha=alpha;*pbeta=beta; + return ColinearEnum; + } + if ((pO1C-pO1B)*(pO1D-pO1B)<0){ + alpha=0; beta=0; + *palpha=alpha;*pbeta=beta; + return ColinearEnum; + } + if ((pO1A-pO1C)*(pO1B-pO1C)<0){ + alpha=0; beta=0; + *palpha=alpha;*pbeta=beta; + return ColinearEnum; + } + if ((pO1A-pO1D)*(pO1B-pO1D)<0){ + alpha=0; beta=0; + *palpha=alpha;*pbeta=beta; + return ColinearEnum; + } + + //test if the 2 segments have the same middle (->intersects=true) + if (O2O1==0){ + alpha=0; beta=0; + *palpha=alpha;*pbeta=beta; + return ColinearEnum; + } + + //if we are here, both segments are colinear, but do not interset: + alpha=-1; beta=-1; + *palpha=alpha;*pbeta=beta; + return SeparateEnum; + } + + /*if we are here, both segments intersect. Determine where in the segment coordinate + * system: */ + beta=-1; + alpha=-(xA*yB-xC*yB+yC*xB-yC*xA+xC*yA-yA*xB)/(-xD*yB+xD*yA+xC*yB-xC*yA-yD*xA+yD*xB+yC*xA-yC*xB); //from intersect.m in formal calculus + + *palpha=alpha;*pbeta=beta; + return IntersectEnum; +}/*}}}*/ Index: /issm/trunk/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h (revision 14309) +++ /issm/trunk/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h (revision 14310) @@ -10,5 +10,5 @@ /* local prototypes: */ -void MeshProfileIntersectionx( double** psegments, int* pnumseg, int* index, double* x, double* y, int nel, int nods, Contour** contours,int numcontours); +void MeshProfileIntersectionx(double** psegments, int* pnumseg, int* index, double* x, double* y, int nel, int nods, Contour** contours,int numcontours); void MeshSegmentsIntersection(double** psegments, int* pnumsegs,int* index, double* x, double* y, int nel, int nods, double* xc, double* yc, int numnodes); void ElementSegmentsIntersection(DataSet* segments_dataset,int el, double* xnodes,double* ynodes,double* xc,double* yc,int numnodes); Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp (revision 14309) +++ (revision ) @@ -1,52 +1,0 @@ -/*! \file MeshSegmentsIntersectionx.c - */ - -#include "./MeshProfileIntersectionx.h" - -void MeshSegmentsIntersection(double** psegments, int* pnumsegs,int* index, double* x, double* y, int nel, int nods, double* xc, double* yc, int numnodes){ - - int i,j; - - /*output: */ - double* segments=NULL; - Segment* segment=NULL; - int numsegs; - - /*intermediary: */ - DataSet* segments_dataset=NULL; - double xnodes[3]; - double ynodes[3]; - - /*We don't know how many segments we are going to get, so have a dynamic container: */ - segments_dataset=new DataSet(); - - /*Go through elements, and call ElementSegmentsIntersection routine: */ - for(i=0;iSize(); - segments=xNew(5*numsegs); - for(i=0;i* segment=(Segment*)segments_dataset->GetObjectByOffset(i); - - /*x1,y1,x2,y2 then element_id: */ - *(segments+5*i+0)=segment->x1; - *(segments+5*i+1)=segment->y1; - *(segments+5*i+2)=segment->x2; - *(segments+5*i+3)=segment->y2; - *(segments+5*i+4)=(double)segment->eid; - } - - /*Free ressources:*/ - delete segments_dataset; - - /*Assign output pointers:*/ - *psegments=segments; - *pnumsegs=numsegs; -} Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/NodeInElement.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/NodeInElement.cpp (revision 14309) +++ (revision ) @@ -1,32 +1,0 @@ -/*! \file NodeInElement.cpp -*/ - -#include "./MeshProfileIntersectionx.h" - -bool NodeInElement(double* xnodes, double* ynodes, double x, double y){ - - double x1,y1; - double x2,y2; - double x3,y3; - double lambda1,lambda2,lambda3; - double det; - - x1=xnodes[0]; - x2=xnodes[1]; - x3=xnodes[2]; - y1=ynodes[0]; - y2=ynodes[1]; - y3=ynodes[2]; - - /*compute determinant: */ - det=x1*y2-x1*y3-x3*y2-x2*y1+x2*y3+x3*y1; - - /*area coordinates: */ - lambda1=((y2-y3)*(x-x3)+(x3-x2)*(y-y3))/det; - lambda2=((y3-y1)*(x-x3)+(x1-x3)*(y-y3))/det; - lambda3=1-lambda1-lambda2; - - if( ((lambda1<=1) && (lambda1>=0)) && ((lambda2<=1) && (lambda2>=0)) && ((lambda3<=1) && (lambda3>=0)) )return true; - else return false; - -} Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 14309) +++ (revision ) @@ -1,105 +1,0 @@ -/*! \file SegmentIntersect.cpp -*/ - -#include "./MeshProfileIntersectionx.h" - -int SegmentIntersect(double* palpha, double* pbeta, double* x1, double* y1, double* x2, double* y2){ - - /*See ISSM_DIR/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ - - /*output: */ - double alpha=-1; - double beta=-1; - - double xA,xB,xC,xD,yA,yB,yC,yD; - double O2A[2],O2B[2],O1C[2],O1D[2]; - double n1[2],n2[2]; - double test1, test2, test3, test4; - double det; - double O2O1[2]; - double pO1A,pO1B,pO1C,pO1D; - - xA=x1[0]; yA=y1[0]; - xB=x1[1]; yB=y1[1]; - xC=x2[0]; yC=y2[0]; - xD=x2[1]; yD=y2[1]; - - O2A[0]=xA -(xD/2+xC/2); O2A[1]=yA -(yD/2+yC/2); - O2B[0]=xB -(xD/2+xC/2); O2B[1]=yB -(yD/2+yC/2); - O1C[0]=xC -(xA/2+xB/2); O1C[1]=yC -(yA/2+yB/2); - O1D[0]=xD -(xA/2+xB/2); O1D[1]=yD -(yA/2+yB/2); - - n1[0]=yA-yB; n1[1]=xB-xA; //normal vector to segA - n2[0]=yC-yD; n2[1]=xD-xC; //normal vector to segB - - test1=n2[0]*O2A[0]+n2[1]*O2A[1]; - test2=n2[0]*O2B[0]+n2[1]*O2B[1]; - - if (test1*test2>0){ - return SeparateEnum; - } - - test3=n1[0]*O1C[0]+n1[1]*O1C[1]; - test4=n1[0]*O1D[0]+n1[1]*O1D[1]; - - if (test3*test4>0){ - return SeparateEnum; - } - - /*If colinear: */ - det=n1[0]*n2[1]-n2[0]*n1[1]; - - if(test1*test2==0 && test3*test4==0 && det==0){ - - //projection on the axis O1O2 - O2O1[0]=(xA/2+xB/2)-(xD/2+xC/2); - O2O1[1]=(yA/2+yB/2)-(yD/2+yC/2); - - pO1A=O2O1[0]*(O2A[0]-O2O1[0])+O2O1[1]*(O2A[1]-O2O1[1]); - pO1B=O2O1[0]*(O2B[0]-O2O1[0])+O2O1[1]*(O2B[1]-O2O1[1]); - pO1C=O2O1[0]*O1C[0]+O2O1[1]*O1C[1]; - pO1D=O2O1[0]*O1D[0]+O2O1[1]*O1D[1]; - - //test if one point is included in the other segment (->intersects=true) - if ((pO1C-pO1A)*(pO1D-pO1A)<0){ - alpha=0; beta=0; - *palpha=alpha;*pbeta=beta; - return ColinearEnum; - } - if ((pO1C-pO1B)*(pO1D-pO1B)<0){ - alpha=0; beta=0; - *palpha=alpha;*pbeta=beta; - return ColinearEnum; - } - if ((pO1A-pO1C)*(pO1B-pO1C)<0){ - alpha=0; beta=0; - *palpha=alpha;*pbeta=beta; - return ColinearEnum; - } - if ((pO1A-pO1D)*(pO1B-pO1D)<0){ - alpha=0; beta=0; - *palpha=alpha;*pbeta=beta; - return ColinearEnum; - } - - //test if the 2 segments have the same middle (->intersects=true) - if (O2O1==0){ - alpha=0; beta=0; - *palpha=alpha;*pbeta=beta; - return ColinearEnum; - } - - //if we are here, both segments are colinear, but do not interset: - alpha=-1; beta=-1; - *palpha=alpha;*pbeta=beta; - return SeparateEnum; - } - - /*if we are here, both segments intersect. Determine where in the segment coordinate - * system: */ - beta=-1; - alpha=-(xA*yB-xC*yB+yC*xB-yC*xA+xC*yA-yA*xB)/(-xD*yB+xD*yA+xC*yB-xC*yA-yD*xA+yD*xB+yC*xA-yC*xB); //from intersect.m in formal calculus - - *palpha=alpha;*pbeta=beta; - return IntersectEnum; -} Index: sm/trunk/src/c/modules/MeshProfileIntersectionx/intersect.m =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/intersect.m (revision 14309) +++ (revision ) @@ -1,12 +1,0 @@ -syms xA yA xB yB xC yC xD yD alpha beta x y - -A=[xA;yA]; -B=[xB;yB]; -C=[xC;yC]; -D=[xD;yD]; - - -Eq=C+alpha*(D-C)-A+beta*(B-A); - -%from Eq, we specify the system to solve: -S=solve( xC+alpha*(xD-xC)-xA+beta*(xB-xA), yC+alpha*(yD-yC)-yA+beta*(yB-yA),alpha,beta); Index: /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# BALANCED_SOURCES {{{ +set(BALANCED_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# SLOPE_SOURCES {{{ +set(SLOPE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/BedSlope/CreateLoadsBedSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/CMakeLists.txt (revision 14310) @@ -0,0 +1,33 @@ +# Subdirectories {{{ +add_subdirectory(Autodiff) +add_subdirectory(Balancethickness) +add_subdirectory(BedSlope) +add_subdirectory(Control) +add_subdirectory(Dakota) +add_subdirectory(DiagnosticHoriz) +add_subdirectory(DiagnosticHutter) +add_subdirectory(DiagnosticVert) +add_subdirectory(Enthalpy) +add_subdirectory(Hydrology) +add_subdirectory(Melting) +add_subdirectory(Prognostic) +add_subdirectory(SurfaceSlope) +add_subdirectory(Thermal) +add_subdirectory(Transient) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/CreateDataSets.cpp +$ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp +$ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/CreateParameters.cpp +$ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DistributeNumDofs.cpp +$ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/ModelProcessorx.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/NodesPartitioning.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/SortDataSets.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/UpdateCounters.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Control/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Control/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Control/CMakeLists.txt (revision 14310) @@ -0,0 +1,2 @@ +# Subdirectories {{{ +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Control/CreateParametersControl.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Control/CreateParametersControl.cpp (revision 14309) +++ /issm/trunk/src/c/modules/ModelProcessorx/Control/CreateParametersControl.cpp (revision 14310) @@ -15,5 +15,5 @@ Parameters *parameters = NULL; - bool control_analysis; + bool control_analysis,tao_analysis; int nsteps; int num_control_type; @@ -30,4 +30,5 @@ /*retrieve some parameters: */ iomodel->Constant(&control_analysis,InversionIscontrolEnum); + iomodel->Constant(&tao_analysis,InversionTaoEnum); if(control_analysis){ @@ -37,7 +38,9 @@ parameters->AddObject(iomodel->CopyConstantObject(InversionNumCostFunctionsEnum)); parameters->AddObject(iomodel->CopyConstantObject(InversionNstepsEnum)); - parameters->AddObject(iomodel->CopyConstantObject(InversionCostFunctionThresholdEnum)); - parameters->AddObject(iomodel->CopyConstantObject(InversionGradientOnlyEnum)); parameters->AddObject(iomodel->CopyConstantObject(InversionIncompleteAdjointEnum)); + if(!tao_analysis){ + parameters->AddObject(iomodel->CopyConstantObject(InversionCostFunctionThresholdEnum)); + parameters->AddObject(iomodel->CopyConstantObject(InversionGradientOnlyEnum)); + } /*What solution type?*/ @@ -52,13 +55,21 @@ iomodel->FetchData(&control_type,NULL,&num_control_type,InversionControlParametersEnum); iomodel->FetchData(&cm_responses,&nsteps,&num_cm_responses,InversionCostFunctionsEnum); - iomodel->FetchData(&cm_jump,&nsteps,NULL,InversionStepThresholdEnum); - iomodel->FetchData(&optscal,NULL,NULL,InversionGradientScalingEnum); - iomodel->FetchData(&maxiter,NULL,NULL,InversionMaxiterPerStepEnum); + if(!tao_analysis){ + iomodel->FetchData(&cm_jump,&nsteps,NULL,InversionStepThresholdEnum); + iomodel->FetchData(&optscal,NULL,NULL,InversionGradientScalingEnum); + iomodel->FetchData(&maxiter,NULL,NULL,InversionMaxiterPerStepEnum); + } - parameters->AddObject(new IntVecParam(InversionControlParametersEnum,control_type,num_control_type)); - parameters->AddObject(new DoubleMatParam(InversionGradientScalingEnum,optscal,nsteps,num_control_type)); - parameters->AddObject(new DoubleMatParam(InversionCostFunctionsEnum,cm_responses,nsteps,num_cm_responses)); - parameters->AddObject(new DoubleVecParam(InversionStepThresholdEnum,cm_jump,nsteps)); - parameters->AddObject(new DoubleVecParam(InversionMaxiterPerStepEnum,maxiter,nsteps)); + if(tao_analysis){ + parameters->AddObject(new IntVecParam(InversionControlParametersEnum,control_type,num_control_type)); + parameters->AddObject(new DoubleVecParam(InversionCostFunctionsEnum,cm_responses,num_cm_responses)); + } + else{ + parameters->AddObject(new IntVecParam(InversionControlParametersEnum,control_type,num_control_type)); + parameters->AddObject(new DoubleMatParam(InversionGradientScalingEnum,optscal,nsteps,num_control_type)); + parameters->AddObject(new DoubleMatParam(InversionCostFunctionsEnum,cm_responses,nsteps,num_cm_responses)); + parameters->AddObject(new DoubleVecParam(InversionStepThresholdEnum,cm_jump,nsteps)); + parameters->AddObject(new DoubleVecParam(InversionMaxiterPerStepEnum,maxiter,nsteps)); + } xDelete(control_type); Index: /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 14309) +++ /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 14310) @@ -45,7 +45,8 @@ case VxEnum: iomodel->FetchData(1,VxEnum); break; case VyEnum: iomodel->FetchData(1,VyEnum); break; - case FrictionCoefficientEnum: iomodel->FetchData(1,FrictionCoefficientEnum); break; - case MaterialsRheologyBbarEnum: iomodel->FetchData(1,MaterialsRheologyBEnum); break; - case MaterialsRheologyZbarEnum: iomodel->FetchData(1,MaterialsRheologyZEnum); break; + case ThicknessEnum: iomodel->FetchData(1,ThicknessEnum); break; + case FrictionCoefficientEnum: iomodel->FetchData(1,FrictionCoefficientEnum); break; + case MaterialsRheologyBbarEnum: iomodel->FetchData(1,MaterialsRheologyBEnum); break; + case MaterialsRheologyZbarEnum: iomodel->FetchData(1,MaterialsRheologyZEnum); break; default: _error_("Control " << EnumToStringx(reCast(iomodel->Data(InversionControlParametersEnum)[i])) << " not implemented yet"); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Dakota/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Dakota/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Dakota/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 14309) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 14310) @@ -2,4 +2,9 @@ * UpdateElementsDiagnosticHoriz: */ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif #include "../../../Container/Container.h" @@ -85,4 +90,8 @@ elements->InputDuplicate(VxEnum,InversionVxObsEnum); if(dakota_analysis)elements->InputDuplicate(VxEnum,QmuVxEnum); + + #ifdef _HAVE_ANDROID_ + elements->InputDuplicate(FrictionCoefficientEnum,AndroidFrictionCoefficientEnum); + #endif elements->InputDuplicate(VyEnum,VyPicardEnum); Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Enthalpy/CreateConstraintsEnthalpy.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Enthalpy/CreateLoadsEnthalpy.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Enthalpy/CreateNodesEnthalpy.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Enthalpy/UpdateElementsEnthalpy.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# HYDROLOGY_SOURCES {{{ +set(HYDROLOGY_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Melting/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Melting/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Melting/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Melting/CreateConstraintsMelting.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Melting/CreateNodesMelting.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# PROGNOSTIC_SOURCES {{{ +set(PROGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 14309) +++ /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 14310) @@ -72,12 +72,7 @@ } if(issmbgradients){ - iomodel->FetchDataToInput(elements,SurfaceforcingsHcEnum); iomodel->FetchDataToInput(elements,SurfaceforcingsHrefEnum); iomodel->FetchDataToInput(elements,SurfaceforcingsSmbrefEnum); - iomodel->FetchDataToInput(elements,SurfaceforcingsSmbPosMaxEnum); - iomodel->FetchDataToInput(elements,SurfaceforcingsSmbPosMinEnum); - iomodel->FetchDataToInput(elements,SurfaceforcingsAPosEnum); iomodel->FetchDataToInput(elements,SurfaceforcingsBPosEnum); - iomodel->FetchDataToInput(elements,SurfaceforcingsANegEnum); iomodel->FetchDataToInput(elements,SurfaceforcingsBNegEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# SLOPE_SOURCES {{{ +set(SLOPE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp + $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ModelProcessorx/Transient/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Transient/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ModelProcessorx/Transient/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# TRANSIENT_SOURCES {{{ +set(TRANSIENT_SOURCES $ENV{ISSM_DIR}/src/c/modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/NodalValuex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/NodalValuex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/NodalValuex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/NodalValuex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/NodalValuex/NodalValuex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/NodeConnectivityx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/NodeConnectivityx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/NodeConnectivityx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/NodeConnectivityx) +# }}} Index: /issm/trunk/src/c/modules/NodeConnectivityx/NodeConnectivityx.cpp =================================================================== --- /issm/trunk/src/c/modules/NodeConnectivityx/NodeConnectivityx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/NodeConnectivityx/NodeConnectivityx.cpp (revision 14310) @@ -21,5 +21,5 @@ int i,j,n; - const int maxels=25; + const int maxels=50; const int width=maxels+1; Index: /issm/trunk/src/c/modules/NodesDofx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/NodesDofx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/NodesDofx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/NodesDofx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/NodesDofx/NodesDofx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Orthx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Orthx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Orthx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Orthx) +# }}} Index: /issm/trunk/src/c/modules/OutputResultsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/OutputResultsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/OutputResultsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/OutputResultsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/OutputResultsx/OutputResultsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp =================================================================== --- /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 14310) @@ -56,5 +56,5 @@ /*We don't have a file pointer. Retrieve the output file name and open it for writing:*/ - parameters->FindParam(&outputfilename,OutputfilenameEnum); + parameters->FindParam(&outputfilename,OutputFileNameEnum); /*What strategy? : */ Index: /issm/trunk/src/c/modules/OutputRiftsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/OutputRiftsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/OutputRiftsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/OutputRiftsx) +# }}} Index: /issm/trunk/src/c/modules/ParsePetscOptionsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ParsePetscOptionsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ParsePetscOptionsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ParsePetscOptionsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/PointCloudFindNeighborsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/PointCloudFindNeighborsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/PointCloudFindNeighborsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/PointCloudFindNeighborsx) +# }}} Index: /issm/trunk/src/c/modules/PositiveDegreeDayx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/PositiveDegreeDayx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/PositiveDegreeDayx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/PositiveDegreeDayx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/PropagateFlagsFromConnectivityx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/PropagateFlagsFromConnectivityx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/PropagateFlagsFromConnectivityx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/PropagateFlagsFromConnectivityx) +# }}} Index: /issm/trunk/src/c/modules/Reduceloadx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Reduceloadx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Reduceloadx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Reduceloadx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Reduceloadx/Reduceloadx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Reducevectorgtofx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Reducevectorgtofx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Reducevectorgtofx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Reducevectorgtofx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Reducevectorgtosx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Reducevectorgtosx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Reducevectorgtosx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Reducevectorgtosx) +# }}} Index: /issm/trunk/src/c/modules/ResetConstraintsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ResetConstraintsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ResetConstraintsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,11 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ResetConstraintsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ResetConstraintsx/ResetConstraintsx.cpp PARENT_SCOPE) +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/modules/ResetConstraintsx/ThermalConstraintsReset.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/ResetCoordinateSystemx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ResetCoordinateSystemx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ResetCoordinateSystemx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ResetCoordinateSystemx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/RheologyBbarAbsGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/RheologyBbarAbsGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/RheologyBbarAbsGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/RheologyBbarAbsGradientx) +# }}} Index: /issm/trunk/src/c/modules/Scotchx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Scotchx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Scotchx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Scotchx) +# }}} Index: /issm/trunk/src/c/modules/SetControlInputsFromVectorx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SetControlInputsFromVectorx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SetControlInputsFromVectorx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SetControlInputsFromVectorx) +# }}} Index: /issm/trunk/src/c/modules/Shp2Expx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Shp2Expx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Shp2Expx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Shp2Expx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/Shp2Expx/Shp2Expx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.cpp =================================================================== --- /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.cpp (revision 14310) +++ /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.cpp (revision 14310) @@ -0,0 +1,629 @@ +/*!\file Shp2Expx + * \brief shp to exp conversion routines. + */ + +#include "./Shp2Expx.h" +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "../../io/io.h" +#include "../../toolkits/toolkits.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../modules.h" + +int Shp2Expx(char* filshp,char* filexp){ + + #ifdef _HAVE_SHAPELIB_ //only works if Shapelib library has been compiled in. + + return(Shp2Expx(filshp,filexp, + 0)); + + #else //ifdef _HAVE_SHAPELIB_ + return 0; + #endif +} + +int Shp2Expx(char* filshp,char* filexp, + int sgn){ + + #ifdef _HAVE_SHAPELIB_ //only works if Shapelib library has been compiled in. + + double cm,sp; + + if (sgn) + Xy2lldef(&cm,&sp,sgn); + + return(Shp2Expx(filshp,filexp, + sgn,cm,sp)); + + #else //ifdef _HAVE_SHAPELIB_ + return 0; + #endif +} + +int Shp2Expx(char* filshp,char* filexp, + int sgn,double cm,double sp){ + + #ifdef _HAVE_SHAPELIB_ //only works if Shapelib library has been compiled in. + + int i,j,k,iret=0; + int lwidth=1; + double popac=0.50; + int nshape,ncoord; + double cpsum; + int *pstype = NULL, *pnpart=NULL,**ppstrt=NULL,**pptype=NULL,*pnvert=NULL; + double **pshapx = NULL,**pshapy=NULL,**pshapz=NULL,**pshapm=NULL; + double *lat = NULL, *lon=NULL; + + SHPHandle hSHP; + int nShapeType, nEntities, iPart, bValidate = 0,nInvalidCount=0; + const char *pszPlus; + double adfMinBound[4], adfMaxBound[4]; + + char indent[81]=""; + KML_File *kfile = NULL; + KML_Document *kdoc = NULL; + KML_Style *kstyle = NULL; + KML_LineStyle *klsty = NULL; + KML_PolyStyle *kpsty = NULL; + KML_Folder *kfold = NULL; + KML_Placemark *kplace = NULL; + KML_MultiGeometry *kmulti = NULL; + KML_Polygon *kpoly = NULL; + KML_LinearRing *kring = NULL; + KML_LineString *kline = NULL; + KML_Point *kpoint = NULL; + FILE *fid = NULL; + + clock_t clock0,clock1; + time_t time0, time1; + + clock0=clock(); + time0 =time(NULL); + _pprintString_("\nShp2Expx Module -- " << ctime(&time0)); + +/* note that much of the following code is taken from shpdump.c in shapelib. */ + +/* open shp/shx files */ + + hSHP = SHPOpen( filshp, "rb" ); + if (!hSHP) _error_("Error opening shp/shx files."); + +/* read header and print out file bounds */ + + SHPGetInfo( hSHP, &nEntities, &nShapeType, adfMinBound, adfMaxBound ); + + printf( "Shapefile Type: %s # of Shapes: %d\n\n", + SHPTypeName( nShapeType ), nEntities ); + + printf( "File Bounds: (%12.3f,%12.3f,%g,%g)\n" + " to (%12.3f,%12.3f,%g,%g)\n", + adfMinBound[0], + adfMinBound[1], + adfMinBound[2], + adfMinBound[3], + adfMaxBound[0], + adfMaxBound[1], + adfMaxBound[2], + adfMaxBound[3] ); + + nshape=nEntities; + pstype=xNew(nshape); + pnpart=xNew(nshape); + ppstrt=xNew(nshape); + pptype=xNew(nshape); + pnvert=xNew(nshape); + pshapx=xNew(nshape); + pshapy=xNew(nshape); + pshapz=xNew(nshape); + pshapm=xNew(nshape); + +/* loop over the list of shapes */ + + for( i = 0; i < nEntities; i++ ) + { +// int j; + SHPObject *psShape; + + psShape = SHPReadObject( hSHP, i ); + + printf( "\nShape:%d (%s) nVertices=%d, nParts=%d\n" + " Bounds:(%12.3f,%12.3f, %g, %g)\n" + " to (%12.3f,%12.3f, %g, %g)\n", + i, SHPTypeName(psShape->nSHPType), + psShape->nVertices, psShape->nParts, + psShape->dfXMin, psShape->dfYMin, + psShape->dfZMin, psShape->dfMMin, + psShape->dfXMax, psShape->dfYMax, + psShape->dfZMax, psShape->dfMMax ); + + pstype[i]=psShape->nSHPType; + pnpart[i]=psShape->nParts; + if (pnpart[i]) { + ppstrt[i]=xNew(pnpart[i]); + pptype[i]=xNew(pnpart[i]); + } + else { + ppstrt[i]=NULL; + pptype[i]=NULL; + } + pnvert[i]=psShape->nVertices; + if (pnvert[i]) { + pshapx[i]=xNew(pnvert[i]); + pshapy[i]=xNew(pnvert[i]); + pshapz[i]=xNew(pnvert[i]); + pshapm[i]=xNew(pnvert[i]); + } + else { + pshapx[i]=NULL; + pshapy[i]=NULL; + pshapz[i]=NULL; + pshapm[i]=NULL; + } + + for( j = 0, iPart = 1; j < psShape->nVertices; j++ ) + { + const char *pszPartType = ""; + + if( j == 0 && psShape->nParts > 0 ) + { + pszPartType = SHPPartTypeName( psShape->panPartType[0] ); + ppstrt[i][0]=psShape->panPartStart[0]; + pptype[i][0]=psShape->panPartType[0]; + } + + if( iPart < psShape->nParts + && psShape->panPartStart[iPart] == j ) + { + pszPartType = SHPPartTypeName( psShape->panPartType[iPart] ); + ppstrt[i][iPart]=psShape->panPartStart[iPart]; + pptype[i][iPart]=psShape->panPartType[iPart]; + iPart++; + pszPlus = "+"; + } + else + pszPlus = " "; + +// printf(" %s (%12.3f,%12.3f, %g, %g) %s \n", +// pszPlus, +// psShape->padfX[j], +// psShape->padfY[j], +// psShape->padfZ[j], +// psShape->padfM[j], +// pszPartType ); + + pshapx[i][j]=psShape->padfX[j]; + pshapy[i][j]=psShape->padfY[j]; + pshapz[i][j]=psShape->padfZ[j]; + pshapm[i][j]=psShape->padfM[j]; + } + + if( bValidate ) + { + int nAltered = SHPRewindObject( hSHP, psShape ); + + if( nAltered > 0 ) + { + printf( " %d rings wound in the wrong direction.\n", + nAltered ); + nInvalidCount++; + } + } + + SHPDestroyObject( psShape ); + } + +/* close shp/shx files */ + + SHPClose( hSHP ); + +/* construct kml file */ + + kfile =new KML_File(); + kfile->AddAttrib("xmlns","http://www.opengis.net/kml/2.2"); + +/* construct kml document */ + + kdoc =new KML_Document(); + sprintf(kdoc->name ,"Shp2Kmlx Module -- %s",ctime(&time0)); + kdoc->open =1; + +/* construct style templates for defaults */ + + klsty =new KML_LineStyle(); + sprintf(klsty->color ,"ff000000"); + sprintf(klsty->colormode ,"normal"); + klsty->width =lwidth; + kpsty =new KML_PolyStyle(); + sprintf(kpsty->color ,"%02xffffff",(int)floor(popac*255+0.5)); + sprintf(kpsty->colormode ,"random"); + kstyle=new KML_Style(); + kstyle->AddAttrib("id","BlackLineRandomPoly"); + kstyle->line =klsty; + kstyle->poly =kpsty; + (kdoc->style )->AddObject((Object*)kstyle); + + klsty =new KML_LineStyle(); + sprintf(klsty->color ,"ff000000"); + sprintf(klsty->colormode ,"normal"); + klsty->width ,lwidth; + kpsty =new KML_PolyStyle(); + sprintf(kpsty->color ,"00ffffff"); + sprintf(kpsty->colormode ,"random"); + kstyle=new KML_Style(); + kstyle->AddAttrib("id","BlackLineEmptyPoly"); + kstyle->line =klsty; + kstyle->poly =kpsty; + (kdoc->style )->AddObject((Object*)kstyle); + + klsty =new KML_LineStyle(); + sprintf(klsty->color ,"%02xffffff",(int)floor(popac*255+0.5)); + sprintf(klsty->colormode ,"random"); + klsty->width =lwidth*2; + kpsty =new KML_PolyStyle(); + sprintf(kpsty->color ,"00ffffff"); + sprintf(kpsty->colormode ,"random"); + kstyle=new KML_Style(); + kstyle->AddAttrib("id","RandomLineEmptyPoly"); + kstyle->line =klsty; + kstyle->poly =kpsty; + (kdoc->style )->AddObject((Object*)kstyle); + +/* construct kml folder for shapes */ + + kfold =new KML_Folder(); + sprintf(kfold->name ,"Shapefile: %s Type: %s nShapes: %d", + filshp, SHPTypeName( nShapeType ), nEntities ); + kfold->open =1; + +/* loop over the list of shapes */ + + for (i=0; iname ,"Shape:%d (%s) nVertices=%d, nParts=%d", + i,SHPTypeName(pstype[i]),pnvert[i],pnpart[i]); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#RandomLineEmptyPoly"); + + if (pnpart[i] > 0) + _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n", + i,SHPTypeName( pstype[i] ),pnpart[i]); + if (pnvert[i] > 1) + _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 1 vertices.\n", + i,SHPTypeName( pstype[i] ),pnvert[i]); + + kpoint=new KML_Point(); + + lat=xNew(pnvert[i]); + lon=xNew(pnvert[i]); + if (sgn) { + Xy2llx(lat,lon,pshapx[i],pshapy[i],pnvert[i],sgn,cm,sp); + } + else { + memcpy(lon,pshapx[i],pnvert[i]*sizeof(double)); + memcpy(lat,pshapy[i],pnvert[i]*sizeof(double)); + } + + kpoint->coords[0]=lon [0]; + kpoint->coords[1]=lat [0]; + kpoint->coords[2]=pshapz[i][0]; + + xDelete(lon); + xDelete(lat); + + (kplace->geometry )->AddObject((Object*)kpoint); + kpoint=NULL; + (kfold ->feature )->AddObject((Object*)kplace); + kplace=NULL; + } + +/* polyline types */ + + else if (pstype[i] == SHPT_ARC || + pstype[i] == SHPT_ARCZ || + pstype[i] == SHPT_ARCM) { + kplace=new KML_Placemark(); + + sprintf(kplace->name ,"Shape:%d (%s) nVertices=%d, nParts=%d", + i,SHPTypeName(pstype[i]),pnvert[i],pnpart[i]); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#RandomLineEmptyPoly"); + +/* create a multigeometry to hold all the lines */ + + kmulti=new KML_MultiGeometry(); + +/* convert to lat/lon, if necessary */ + + lat=xNew(pnvert[i]); + lon=xNew(pnvert[i]); + if (sgn) { + Xy2llx(lat,lon,pshapx[i],pshapy[i],pnvert[i],sgn,cm,sp); + } + else { + memcpy(lon,pshapx[i],pnvert[i]*sizeof(double)); + memcpy(lat,pshapy[i],pnvert[i]*sizeof(double)); + } + +/* loop over the lines */ + + for (j=0; jncoord =(jcoords =xNew(kline->ncoord*3); + for (k=0; kncoord; k++) { + kline->coords[3*k+0]=lon [ppstrt[i][j]+k]; + kline->coords[3*k+1]=lat [ppstrt[i][j]+k]; + kline->coords[3*k+2]=pshapz[i][ppstrt[i][j]+k]; + } + (kmulti->geometry )->AddObject((Object*)kline); + kline = NULL; + } + + xDelete(lon); + xDelete(lat); + + (kplace->geometry)->AddObject((Object*)kmulti); + kmulti=NULL; + (kfold ->feature )->AddObject((Object*)kplace); + kplace=NULL; + } + +/* polygon types */ + + else if (pstype[i] == SHPT_POLYGON || + pstype[i] == SHPT_POLYGONZ || + pstype[i] == SHPT_POLYGONM) { + +/* the shp format specifies that outer rings are cw, while inner rings are ccw. there + may be multiple outer rings and inner rings in any order. the kml format specifies + all rings are ccw (right-hand rule). there may be only one outer ring with multiple + inner rings, and rings are differentiated by keyword. + + at least for now, assume that each cw ring forms a new kml polygon, and each ccw + ring forms an inner ring for the most recent outer ring. a more elaborate solution + would be for each inner ring to search in which outer ring it occurs. */ + + kplace=new KML_Placemark(); + + sprintf(kplace->name ,"Shape:%d (%s) nVertices=%d, nParts=%d", + i,SHPTypeName(pstype[i]),pnvert[i],pnpart[i]); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#BlackLineRandomPoly"); + +/* create a multigeometry to hold all the polygons */ + + kmulti=new KML_MultiGeometry(); + +/* convert to lat/lon, if necessary */ + + lat=xNew(pnvert[i]); + lon=xNew(pnvert[i]); + if (sgn) { + Xy2llx(lat,lon,pshapx[i],pshapy[i],pnvert[i],sgn,cm,sp); + } + else { + memcpy(lon,pshapx[i],pnvert[i]*sizeof(double)); + memcpy(lat,pshapy[i],pnvert[i]*sizeof(double)); + } + +/* loop over the polygons */ + + for (j=0; jgeometry )->AddObject((Object*)kpoly); + kpoly =NULL; + } + +/* create a new polygon from the outer ring (reversing cw to ccw) */ + + kpoly =new KML_Polygon(); + kring =new KML_LinearRing(); + + kring->ncoord =(jcoords =xNew(kring->ncoord*3); + if (cpsum < 0) + for (k=0; kncoord; k++) { + kring->coords[3*(kring->ncoord-1-k)+0]=lon [ppstrt[i][j]+k]; + kring->coords[3*(kring->ncoord-1-k)+1]=lat [ppstrt[i][j]+k]; + kring->coords[3*(kring->ncoord-1-k)+2]=pshapz[i][ppstrt[i][j]+k]; + } + else + for (k=0; kncoord; k++) { + kring->coords[3*k+0]=lon [ppstrt[i][j]+k]; + kring->coords[3*k+1]=lat [ppstrt[i][j]+k]; + kring->coords[3*k+2]=pshapz[i][ppstrt[i][j]+k]; + } + + (kpoly ->outer )->AddObject((Object*)kring); + kring =NULL; + } + +/* inner ring (ccw) */ + + else { + if (!kpoly) { + _printf_(true,"Warning -- Shape %d of type \"%s\", part %d, expected to be outer loop (cw).\n", + i,SHPTypeName( pstype[i] ),j); + continue; + } + +/* add the inner ring to the current polygon */ + + kring =new KML_LinearRing(); + + kring->ncoord =(jcoords =xNew(kring->ncoord*3); + for (k=0; kncoord; k++) { + kring->coords[3*k+0]=lon [ppstrt[i][j]+k]; + kring->coords[3*k+1]=lat [ppstrt[i][j]+k]; + kring->coords[3*k+2]=pshapz[i][ppstrt[i][j]+k]; + } + + (kpoly ->inner )->AddObject((Object*)kring); + kring =NULL; + } + } + + if (kpoly) { + (kmulti->geometry )->AddObject((Object*)kpoly); + kpoly =NULL; + } + + xDelete(lon); + xDelete(lat); + + (kplace->geometry )->AddObject((Object*)kmulti); + kmulti=NULL; + (kfold ->feature )->AddObject((Object*)kplace); + kplace=NULL; + } + +/* multipoint types */ + + else if (pstype[i] == SHPT_MULTIPOINT || + pstype[i] == SHPT_MULTIPOINTZ || + pstype[i] == SHPT_MULTIPOINTM) { + kplace=new KML_Placemark(); + + sprintf(kplace->name ,"Shape:%d (%s) nVertices=%d, nParts=%d", + i,SHPTypeName(pstype[i]),pnvert[i],pnpart[i]); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#RandomLineEmptyPoly"); + + if (pnpart[i] > 0) + _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n", + i,SHPTypeName( pstype[i] ),pnpart[i]); + +/* create a multigeometry to hold all the points */ + + kmulti=new KML_MultiGeometry(); + +/* convert to lat/lon, if necessary */ + + lat=xNew(pnvert[i]); + lon=xNew(pnvert[i]); + if (sgn) { + Xy2llx(lat,lon,pshapx[i],pshapy[i],pnvert[i],sgn,cm,sp); + } + else { + memcpy(lon,pshapx[i],pnvert[i]*sizeof(double)); + memcpy(lat,pshapy[i],pnvert[i]*sizeof(double)); + } + +/* loop over the points */ + + for (j=0; jcoords[0]=lon [j]; + kpoint->coords[1]=lat [j]; + kpoint->coords[2]=pshapz[i][j]; + + (kmulti->geometry )->AddObject((Object*)kpoint); + kpoint=NULL; + } + + xDelete(lon); + xDelete(lat); + + (kplace->geometry )->AddObject((Object*)kmulti); + kmulti=NULL; + (kfold ->feature )->AddObject((Object*)kplace); + kplace=NULL; + } + +/* multipatch types */ + + else if (pstype[i] == SHPT_MULTIPATCH) { + _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n", + i,SHPTypeName( pstype[i] )); + continue; + } + +/* unknown type */ + + else { + _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n", + i,SHPTypeName( pstype[i] )); + } + } + +/* assemble the rest of the kml hierarchy */ + + (kdoc ->feature )->AddObject((Object*)kfold); + kfold=NULL; + (kfile->kmlobj )->AddObject((Object*)kdoc); + kdoc =NULL; + +/* open exp file */ + + _pprintLine_("Writing exp profiles to file."); + fid=fopen(filexp,"w"); + +/* write the polygons and linestrings */ + + kfile->WriteExp(fid,"",sgn,cm,sp); + +/* close exp file */ + + fclose(fid); + + delete kfile; + for (i=nshape-1; i>=0; i--) { + xDelete((pshapm[i])); + xDelete((pshapz[i])); + xDelete((pshapy[i])); + xDelete((pshapx[i])); + } + xDelete(pshapm); + xDelete(pshapz); + xDelete(pshapy); + xDelete(pshapx); + xDelete(pnvert); + for (i=nshape-1; i>=0; i--) { + xDelete((pptype[i])); + xDelete((ppstrt[i])); + } + xDelete(pptype); + xDelete(ppstrt); + xDelete(pnpart); + xDelete(pstype); + + clock1=clock(); + time1 =time(NULL); + _printf_(true,"Shp2Expx Module -- %f CPU seconds; %f elapsed seconds.\n\n", + ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0)); + + return(iret); + + #else //ifdef _HAVE_SHAPELIB_ + return 0; + #endif +} Index: /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.h =================================================================== --- /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.h (revision 14310) +++ /issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.h (revision 14310) @@ -0,0 +1,28 @@ +/*!\file: Shp2Expx.h + * \brief header file for shp to exp conversion routines. + */ + +#ifndef _SHP2EXPX_H +#define _SHP2EXPX_H + +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _HAVE_SHAPELIB_ //only works if Shapelib library has been compiled in. + +#include "shapefil.h" + +#endif + +#include "../../Container/Container.h" +#include "../../classes/objects/objects.h" + +/* local prototypes: */ +int Shp2Expx(char* filshp,char* filexp); +int Shp2Expx(char* filshp,char* filexp, int sgn); +int Shp2Expx(char* filshp,char* filexp, int sgn,double cm,double sp); + +#endif /* _SHP2EXPX_H */ Index: /issm/trunk/src/c/modules/Shp2Kmlx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Shp2Kmlx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Shp2Kmlx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Shp2Kmlx) +# }}} +# KML_SOURCES {{{ +set(KML_SOURCES $ENV{ISSM_DIR}/src/c/modules/Shp2Kmlx/Shp2Kmlx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/SmbGradientsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SmbGradientsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SmbGradientsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SmbGradientsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/SmbGradientsx/SmbGradientsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Solverx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Solverx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Solverx/CMakeLists.txt (revision 14310) @@ -0,0 +1,9 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Solverx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Solverx/Solverx.cpp + $ENV{ISSM_DIR}/src/c/modules/Solverx/SolverxSeq.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/SpcNodesx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SpcNodesx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SpcNodesx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SpcNodesx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/SpcNodesx/SpcNodesx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/StringToEnumx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/StringToEnumx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/StringToEnumx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/StringToEnumx/StringToEnumx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 14310) @@ -205,12 +205,7 @@ else if (strcmp(name,"SurfaceforcingsIssmbgradients")==0) return SurfaceforcingsIssmbgradientsEnum; else if (strcmp(name,"SurfaceforcingsMonthlytemperatures")==0) return SurfaceforcingsMonthlytemperaturesEnum; - else if (strcmp(name,"SurfaceforcingsHc")==0) return SurfaceforcingsHcEnum; else if (strcmp(name,"SurfaceforcingsHref")==0) return SurfaceforcingsHrefEnum; else if (strcmp(name,"SurfaceforcingsSmbref")==0) return SurfaceforcingsSmbrefEnum; - else if (strcmp(name,"SurfaceforcingsSmbPosMax")==0) return SurfaceforcingsSmbPosMaxEnum; - else if (strcmp(name,"SurfaceforcingsSmbPosMin")==0) return SurfaceforcingsSmbPosMinEnum; - else if (strcmp(name,"SurfaceforcingsAPos")==0) return SurfaceforcingsAPosEnum; else if (strcmp(name,"SurfaceforcingsBPos")==0) return SurfaceforcingsBPosEnum; - else if (strcmp(name,"SurfaceforcingsANeg")==0) return SurfaceforcingsANegEnum; else if (strcmp(name,"SurfaceforcingsBNeg")==0) return SurfaceforcingsBNegEnum; else if (strcmp(name,"ThermalMaxiter")==0) return ThermalMaxiterEnum; @@ -242,4 +237,6 @@ else if (strcmp(name,"BalancethicknessAnalysis")==0) return BalancethicknessAnalysisEnum; else if (strcmp(name,"BalancethicknessSolution")==0) return BalancethicknessSolutionEnum; + else if (strcmp(name,"WeakBalancethicknessAnalysis")==0) return WeakBalancethicknessAnalysisEnum; + else if (strcmp(name,"WeakBalancethicknessSolution")==0) return WeakBalancethicknessSolutionEnum; else if (strcmp(name,"BedSlopeAnalysis")==0) return BedSlopeAnalysisEnum; else if (strcmp(name,"BedSlopeSolution")==0) return BedSlopeSolutionEnum; @@ -261,11 +258,11 @@ else if (strcmp(name,"PrognosticSolution")==0) return PrognosticSolutionEnum; else if (strcmp(name,"SteadystateSolution")==0) return SteadystateSolutionEnum; + else if (strcmp(name,"SurfaceSlopeAnalysis")==0) return SurfaceSlopeAnalysisEnum; + else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; + else if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; else stage=3; } if(stage==3){ - if (strcmp(name,"SurfaceSlopeAnalysis")==0) return SurfaceSlopeAnalysisEnum; - else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; - else if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; - else if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; + if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; else if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; @@ -353,4 +350,5 @@ else if (strcmp(name,"Adjointy")==0) return AdjointyEnum; else if (strcmp(name,"Adjointz")==0) return AdjointzEnum; + else if (strcmp(name,"BalancethicknessMisfit")==0) return BalancethicknessMisfitEnum; else if (strcmp(name,"BedSlopeX")==0) return BedSlopeXEnum; else if (strcmp(name,"BedSlopeY")==0) return BedSlopeYEnum; @@ -380,13 +378,14 @@ else if (strcmp(name,"QmuSurface")==0) return QmuSurfaceEnum; else if (strcmp(name,"QmuMelting")==0) return QmuMeltingEnum; + else if (strcmp(name,"AndroidFrictionCoefficient")==0) return AndroidFrictionCoefficientEnum; else if (strcmp(name,"ResetPenalties")==0) return ResetPenaltiesEnum; else if (strcmp(name,"SegmentOnIceShelf")==0) return SegmentOnIceShelfEnum; else if (strcmp(name,"SurfaceAbsVelMisfit")==0) return SurfaceAbsVelMisfitEnum; else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; + else if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; else stage=4; } if(stage==4){ - if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; - else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; + if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; else if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; @@ -426,5 +425,4 @@ else if (strcmp(name,"DragCoefficientAbsGradient")==0) return DragCoefficientAbsGradientEnum; else if (strcmp(name,"TransientInput")==0) return TransientInputEnum; - else if (strcmp(name,"Outputfilename")==0) return OutputfilenameEnum; else if (strcmp(name,"Waterfraction")==0) return WaterfractionEnum; else if (strcmp(name,"Watercolumn")==0) return WatercolumnEnum; @@ -507,10 +505,10 @@ else if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; else if (strcmp(name,"Regular")==0) return RegularEnum; + else if (strcmp(name,"Scaled")==0) return ScaledEnum; + else if (strcmp(name,"Separate")==0) return SeparateEnum; else stage=5; } if(stage==5){ - if (strcmp(name,"Scaled")==0) return ScaledEnum; - else if (strcmp(name,"Separate")==0) return SeparateEnum; - else if (strcmp(name,"Sset")==0) return SsetEnum; + if (strcmp(name,"Sset")==0) return SsetEnum; else if (strcmp(name,"Verbose")==0) return VerboseEnum; else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; Index: /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceAbsVelMisfitx) +# }}} Index: /issm/trunk/src/c/modules/SurfaceAreax/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceAreax/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceAreax/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceAreax) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/SurfaceAreax/SurfaceAreax.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceAverageVelMisfitx) +# }}} Index: /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceLogVelMisfitx) +# }}} Index: /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceLogVxVyMisfitx) +# }}} Index: /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/SurfaceRelVelMisfitx) +# }}} Index: /issm/trunk/src/c/modules/ThicknessAbsMisfitx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ThicknessAbsMisfitx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ThicknessAbsMisfitx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ThicknessAbsMisfitx) +# }}} Index: /issm/trunk/src/c/modules/ThicknessAcrossGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ThicknessAcrossGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ThicknessAcrossGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ThicknessAcrossGradientx) +# }}} Index: /issm/trunk/src/c/modules/ThicknessAlongGradientx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/ThicknessAlongGradientx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/ThicknessAlongGradientx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/ThicknessAlongGradientx) +# }}} Index: /issm/trunk/src/c/modules/TriMeshProcessRiftsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/TriMeshProcessRiftsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/TriMeshProcessRiftsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/TriMeshProcessRiftsx) +# }}} Index: /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.cpp =================================================================== --- /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.cpp (revision 14310) @@ -9,13 +9,13 @@ #include "../../toolkits/toolkits.h" -void TriMeshProcessRiftsx(double** pindex, int* pnel,double** px,double** py,int* pnods,double** psegments,double** psegmentmarkers,int *pnum_seg,RiftStruct **priftstruct){ +void TriMeshProcessRiftsx(int** pindex, int* pnel,double** px,double** py,int* pnods,int** psegments,int** psegmentmarkers,int *pnum_seg,RiftStruct **priftstruct){ /*Output*/ int numrifts,numrifts0; int *riftsnumsegments = NULL; - double **riftssegments = NULL; + int **riftssegments = NULL; int *riftsnumpairs = NULL; - double **riftspairs = NULL; - double *riftstips = NULL; + int **riftspairs = NULL; + int *riftstips = NULL; double **riftspenaltypairs = NULL; int *riftsnumpenaltypairs = NULL; @@ -23,10 +23,10 @@ /*Recover initial mesh*/ int nel = *pnel; - double *index = *pindex; + int *index = *pindex; double *x = *px; double *y = *py; int nods = *pnods; - double *segments = *psegments; - double *segmentmarkers = *psegmentmarkers; + int *segments = *psegments; + int *segmentmarkers = *psegmentmarkers; int num_seg = *pnum_seg; Index: /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.h =================================================================== --- /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.h (revision 14309) +++ /issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.h (revision 14310) @@ -8,5 +8,5 @@ class RiftStruct; -void TriMeshProcessRiftsx(double** pindex, int* pnel,double** px,double** py,int* pnods,double** psegments,double** psegmentmarkers,int *pnum_seg,RiftStruct **priftstruct); +void TriMeshProcessRiftsx(int** pindex,int* pnel,double** px,double** py,int* pnods,int** psegments,int** psegmentmarkers,int *pnum_seg,RiftStruct **priftstruct); #endif /* _TRIMESHPROCESSRIFTX_H*/ Index: /issm/trunk/src/c/modules/TriMeshx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/TriMeshx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/TriMeshx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/TriMeshx) +# }}} Index: /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp =================================================================== --- /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp (revision 14309) +++ /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp (revision 14310) @@ -22,5 +22,5 @@ /*}}}*/ -void TriMeshx(SeqMat** pindex,SeqVec** px,SeqVec** py,SeqMat** psegments,SeqVec** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ +void TriMeshx(SeqMat** pindex,SeqVec** px,SeqVec** py,SeqMat** psegments,SeqVec** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ #if !defined(_HAVE_TRIANGLE_) @@ -31,11 +31,11 @@ /*output: */ - IssmPDouble *index = NULL; - SeqMat *index_matrix = NULL; - double *x = NULL; - double *y = NULL; - double *segments = NULL; - SeqMat *segments_matrix = NULL; - double *segmentmarkerlist = NULL; + int *index = NULL; + SeqMat *index_matrix = NULL; + double *x = NULL; + double *y = NULL; + int *segments = NULL; + SeqMat *segments_matrix = NULL; + int *segmentmarkerlist = NULL; /*intermediary: */ @@ -169,23 +169,23 @@ /*Allocate index, x and y: */ - index=xNew(3*out.numberoftriangles); + index=xNew(3*out.numberoftriangles); x=xNew(out.numberofpoints); y=xNew(out.numberofpoints); - segments=xNew(3*out.numberofsegments); - segmentmarkerlist=xNew(out.numberofsegments); + segments=xNew(3*out.numberofsegments); + segmentmarkerlist=xNew(out.numberofsegments); for (i = 0; i< out.numberoftriangles; i++) { for (j = 0; j < out.numberofcorners; j++) { - index[3*i+j]=(double)out.trianglelist[i*out.numberofcorners+j]+1; + index[3*i+j]=(int)out.trianglelist[i*out.numberofcorners+j]+1; } } for (i = 0; i< out.numberofpoints; i++){ - x[i]=out.pointlist[i*2+0]; - y[i]=out.pointlist[i*2+1]; + x[i]=(double)out.pointlist[i*2+0]; + y[i]=(double)out.pointlist[i*2+1]; } for (i = 0; i(index,out.numberoftriangles,3,1.0); + index_matrix=new SeqMat(index,out.numberoftriangles,3,1); *pindex=index_matrix; - segments_matrix=new SeqMat(segments,out.numberofsegments,3,1.0); + segments_matrix=new SeqMat(segments,out.numberofsegments,3,1); *psegments=segments_matrix; *px=new SeqVec(x,out.numberofpoints); *py=new SeqVec(y,out.numberofpoints); - *psegmentmarkerlist=new SeqVec(segmentmarkerlist,out.numberofsegments); + *psegmentmarkerlist=new SeqVec(segmentmarkerlist,out.numberofsegments); #endif } Index: /issm/trunk/src/c/modules/TriMeshx/TriMeshx.h =================================================================== --- /issm/trunk/src/c/modules/TriMeshx/TriMeshx.h (revision 14309) +++ /issm/trunk/src/c/modules/TriMeshx/TriMeshx.h (revision 14310) @@ -11,5 +11,5 @@ /* local prototypes: */ -void TriMeshx(SeqMat** pindex,SeqVec** px,SeqVec** py,SeqMat** psegments,SeqVec** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area); +void TriMeshx(SeqMat** pindex,SeqVec** px,SeqVec** py,SeqMat** psegments,SeqVec** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area); #endif /* _TRIMESHX_H */ Index: /issm/trunk/src/c/modules/TriaSearchx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/TriaSearchx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/TriaSearchx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/TriaSearchx) +# }}} Index: /issm/trunk/src/c/modules/UpdateDynamicConstraintsx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/UpdateDynamicConstraintsx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/UpdateDynamicConstraintsx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/UpdateDynamicConstraintsx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/VecMergex/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/VecMergex/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/VecMergex/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/VecMergex) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/VecMergex/VecMergex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/VerticesDofx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/VerticesDofx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/VerticesDofx/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/VerticesDofx) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/VerticesDofx/VerticesDofx.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/modules/Xy2llx/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/modules/Xy2llx/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/modules/Xy2llx/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/modules/Xy2llx) +# }}} Index: /issm/trunk/src/c/modules/modules.h =================================================================== --- /issm/trunk/src/c/modules/modules.h (revision 14309) +++ /issm/trunk/src/c/modules/modules.h (revision 14310) @@ -60,5 +60,4 @@ #include "./Kml2Expx/Kml2Expx.h" #include "./Krigingx/Krigingx.h" -#include "./Shp2Kmlx/Shp2Kmlx.h" #include "./Mergesolutionfromftogx/Mergesolutionfromftogx.h" #include "./MeshPartitionx/MeshPartitionx.h" @@ -87,4 +86,6 @@ #include "./RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h" #include "./Scotchx/Scotchx.h" +#include "./Shp2Expx/Shp2Expx.h" +#include "./Shp2Kmlx/Shp2Kmlx.h" #include "./SmbGradientsx/SmbGradientsx.h" #include "./Solverx/Solverx.h" Index: /issm/trunk/src/c/shared/Alloc/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Alloc/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Alloc/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Alloc) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/Alloc/alloc.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/Bamg/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Bamg/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Bamg/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Bamg) +# }}} +# BAMG_SOURCES {{{ +set(BAMG_SOURCES $ENV{ISSM_DIR}/src/c/shared/Bamg/BigPrimeNumber.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/CMakeLists.txt (revision 14310) @@ -0,0 +1,17 @@ +# Subdirectories {{{ +add_subdirectory(Alloc) +add_subdirectory(Bamg) +add_subdirectory(Elements) +add_subdirectory(Exceptions) +add_subdirectory(Exp) +add_subdirectory(Matrix) +add_subdirectory(MemOps) +add_subdirectory(Numerics) +add_subdirectory(Sorting) +add_subdirectory(String) +add_subdirectory(Threads) +add_subdirectory(TriMesh) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared) +# }}} Index: /issm/trunk/src/c/shared/Elements/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Elements/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Elements/CMakeLists.txt (revision 14310) @@ -0,0 +1,23 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Elements) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/Elements/Arrhenius.cpp +$ENV{ISSM_DIR}/src/c/shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/GetGlobalDofList.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/GetLocalDofList.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/GetNumberOfDofs.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/GetVerticesCoordinates.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/Paterson.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/PddSurfaceMassBalance.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/PrintArrays.cpp PARENT_SCOPE) +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/shared/Elements/CoordinateSystemTransform.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/TransformInvStiffnessMatrixCoord.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/TransformLoadVectorCoord.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/TransformSolutionCoord.cpp + $ENV{ISSM_DIR}/src/c/shared/Elements/TransformStiffnessMatrixCoord.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/Elements/PrintArrays.cpp =================================================================== --- /issm/trunk/src/c/shared/Elements/PrintArrays.cpp (revision 14309) +++ /issm/trunk/src/c/shared/Elements/PrintArrays.cpp (revision 14310) @@ -39,4 +39,13 @@ _printLine_(""); } +void printarray(bool* array,int lines,int cols){ + _printLine_(""); + for(int i=0;i -#include "../Alloc/alloc.h" -#include "../../include/include.h" -#include "../Exceptions/exceptions.h" - -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname){ - - /*Error management: */ - int noerr=1; - int i,counter; - - /*I/O: */ - FILE* fid=NULL; - - /*open domain outline file for writing: */ - if ((fid=fopen(domainname,"w"))==NULL){ - _error_("could not open domain file " << domainname); - noerr=0; goto cleanupandreturn; - } - - /*Start writing profiles: */ - for(counter=0;counter +#include "../Alloc/alloc.h" +#include "../../include/include.h" +#include "../Exceptions/exceptions.h" +#include "../../Container/DataSet.h" +#include "../../classes/objects/Contour.h" + +int ExpWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,char* domainname){/*{{{*/ + + /*I/O: */ + FILE* fid=NULL; + + /*open domain outline file for writing: */ + if((fid=fopen(domainname,"w"))==NULL) _error_("could not open domain file " << domainname); + + /*Start writing profiles: */ + for(int counter=0;counter* contour = NULL; + + /*open domain outline file for writing: */ + if((fid=fopen(domainname,"w"))==NULL) _error_("could not open domain file " << domainname); + + for(int counter=0;counterSize();counter++){ + contour=(Contour*)contours->GetObjectByOffset(counter); + + /*Write header: */ + fprintf(fid,"## Name:%s\n",domainname); + fprintf(fid,"## Icon:0\n"); + fprintf(fid,"# Points Count Value\n"); + fprintf(fid,"%u %s\n",contour->nods ,"1."); + fprintf(fid,"# X pos Y pos\n"); + + /*Write vertices: */ + for(int i=0;inods;i++){ + fprintf(fid,"%lf\t%lf\n",contour->x[i],contour->y[i]); + } + + /*Write blank line: */ + if(counterSize()-1) fprintf(fid,"\n"); + } + + /*close Exp file: */ + fclose(fid); + + return 1; +}/*}}}*/ Index: /issm/trunk/src/c/shared/Exp/exp.h =================================================================== --- /issm/trunk/src/c/shared/Exp/exp.h (revision 14309) +++ /issm/trunk/src/c/shared/Exp/exp.h (revision 14310) @@ -12,5 +12,6 @@ int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue); -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname); +int ExpWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,char* domainname); +int ExpWrite(DataSet* contours,char* domainname); int pnpoly(int npol, double *xp, double *yp, double x, double y, int edgevalue); Index: /issm/trunk/src/c/shared/Matrix/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Matrix/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Matrix/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Matrix) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/Matrix/MatrixUtils.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/MemOps/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/MemOps/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/MemOps/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/MemOps) +# }}} Index: /issm/trunk/src/c/shared/Numerics/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Numerics/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Numerics/CMakeLists.txt (revision 14310) @@ -0,0 +1,17 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Numerics) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/Numerics/cross.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/cubic.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/extrema.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/GaussPoints.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/IsInputConverged.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/isnan.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/OptionsFromAnalysis.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/UnitConversion.cpp + $ENV{ISSM_DIR}/src/c/shared/Numerics/Verbosity.cpp +$ENV{ISSM_DIR}/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/Numerics/UnitConversion.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/UnitConversion.cpp (revision 14309) +++ /issm/trunk/src/c/shared/Numerics/UnitConversion.cpp (revision 14310) @@ -65,9 +65,5 @@ case SurfaceforcingsPrecipitationEnum: scale=yts;break; //m/yr case SurfaceforcingsMassBalanceEnum: scale=yts;break; //m/yr - case SurfaceforcingsSmbPosMaxEnum: scale=yts;break; //m/yr - case SurfaceforcingsSmbPosMinEnum: scale=yts;break; //m/yr - case SurfaceforcingsAPosEnum: scale=yts;break; //m/yr case SurfaceforcingsBPosEnum: scale=yts;break; //m/yr - case SurfaceforcingsANegEnum: scale=yts;break; //m/yr case SurfaceforcingsBNegEnum: scale=yts;break; //m/yr case SurfaceforcingsSmbrefEnum: scale=yts;break; //m/yr Index: /issm/trunk/src/c/shared/Sorting/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Sorting/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Sorting/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Sorting) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/Sorting/binary_search.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/String/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/String/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/String/CMakeLists.txt (revision 14310) @@ -0,0 +1,8 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/String) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/shared/String/DescriptorIndex.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/shared/Threads/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/shared/Threads/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/shared/Threads/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/shared/Threads) +# }}} Index: /issm/trunk/src/c/shared/TriMesh/AssociateSegmentToElement.cpp =================================================================== --- /issm/trunk/src/c/shared/TriMesh/AssociateSegmentToElement.cpp (revision 14309) +++ /issm/trunk/src/c/shared/TriMesh/AssociateSegmentToElement.cpp (revision 14310) @@ -5,27 +5,20 @@ #include "./trimesh.h" -int AssociateSegmentToElement(double** psegments,int nseg, double* index,int nel){ - - /*Error management: */ - int i; - int noerr=1; - - /*Input: */ - double* segments=NULL; +int AssociateSegmentToElement(int** psegments,int nseg,int* index,int nel){ /*node indices: */ - double A,B; + int A,B; /*Recover segments: */ - segments=*psegments; + int* segments=*psegments; - for (i=0;i(riftsegments_uncompressed); @@ -185,5 +184,5 @@ }/*}}}*/ /*FUNCTION DetermineGridElementListOnOneSideOfRift{{{*/ -int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel){ +int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,int* index,int nel){ int noerr=1; @@ -249,5 +248,5 @@ }/*}}}*/ /*FUNCTION UpdateSegments{{{*/ -int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel){ +int UpdateSegments(int** psegments,int** psegmentmarkerlist, int* pnsegs,int* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel){ int noerr=1; @@ -255,7 +254,7 @@ int el1,el2; - double *segments = NULL; - double *segmentmarkerlist = NULL; - int nsegs; + int *segments = NULL; + int *segmentmarkerlist = NULL; + int nsegs; /*Recover input: */ @@ -265,6 +264,6 @@ /*Reallocate segments: */ - segments =xReNew(segments, nsegs*3,(nsegs+nriftsegs)*3); - segmentmarkerlist=xReNew(segmentmarkerlist,nsegs,(nsegs+nriftsegs)); + segments =xReNew(segments, nsegs*3,(nsegs+nriftsegs)*3); + segmentmarkerlist=xReNew(segmentmarkerlist,nsegs,(nsegs+nriftsegs)); /*First, update the existing segments to the new nodes :*/ @@ -278,5 +277,5 @@ *we can only rely on the position (x,y) of the rift nodes to create a segment:*/ for (k=0;k<3;k++){ - if ((x[(int)*(index+el1*3+k)-1]==x[(int)*(segments+3*j+0)-1]) && (y[(int)*(index+el1*3+k)-1]==y[(int)*(segments+3*j+0)-1])){ + if ((x[*(index+el1*3+k)-1]==x[*(segments+3*j+0)-1]) && (y[*(index+el1*3+k)-1]==y[*(segments+3*j+0)-1])){ *(segments+3*j+0)=*(index+el1*3+k); _assert_(segments[3*j+0](new_numsegs*3); - new_segmentmarkers=xNew(new_numsegs); + new_segments=xNew(new_numsegs*3); + new_segmentmarkers=xNew(new_numsegs); /*Copy new segments info : */ @@ -413,5 +411,5 @@ /*Now deal with rift segments: */ riftsnumsegs=xNew(numrifts); - riftssegments=xNew(numrifts); + riftssegments=xNew(numrifts); for (i=0;i(counter*3); + riftsegment=xNew(counter*3); /*Copy new segments info :*/ counter=0; @@ -436,5 +434,5 @@ /*Free ressources: */ - xDelete(segments); + xDelete(segments); /*Assign output pointers: */ @@ -448,5 +446,5 @@ }/*}}}*/ /*FUNCTION PairRiftElements{{{*/ -int PairRiftElements(int** priftsnumpairs, double*** priftspairs,int numrifts,int* riftsnumsegments, double** riftssegments,double* x,double* y){ +int PairRiftElements(int** priftsnumpairs,int*** priftspairs,int numrifts,int* riftsnumsegments,int** riftssegments,double* x,double* y){ int noerr=1; @@ -454,32 +452,32 @@ /*output: */ - int *riftsnumpairs = NULL; - double **riftspairs = NULL; + int *riftsnumpairs = NULL; + int **riftspairs = NULL; /*intermediary :*/ - int numsegs; - double* segments=NULL; - double* pairs=NULL; - int node1,node2,node3,node4; + int numsegs; + int* segments=NULL; + int* pairs=NULL; + int node1,node2,node3,node4; riftsnumpairs=xNew(numrifts); - riftspairs=xNew(numrifts); + riftspairs=xNew(numrifts); for (i=0;i(2*numsegs); + pairs=xNew(2*numsegs); for (j=0;j=2 indicates a certain rift: */ @@ -696,5 +686,5 @@ } } - if (numrifts)riftflag=1; + if(numrifts)riftflag=1; /*Assign output pointers:*/ @@ -704,5 +694,5 @@ }/*}}}*/ /*FUNCTION OrderRifts{{{*/ -int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y,int nods,int nels){ +int OrderRifts(int** priftstips,int** riftssegments,int** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y,int nods,int nels){ int noerr=1; @@ -710,34 +700,34 @@ /*intermediary: */ - double *riftsegments = NULL; - double *riftpairs = NULL; + int *riftsegments = NULL; + int *riftpairs = NULL; int numsegs; /*ordering and copy: */ - int *order = NULL; - double *riftsegments_copy = NULL; - double *riftpairs_copy = NULL; + int *order = NULL; + int *riftsegments_copy = NULL; + int *riftpairs_copy = NULL; /*node and element manipulation: */ - int node1,node2,node3,node4,temp_node,tip1,tip2,node; - double el2; - int already_ordered=0; + int node1,node2,node3,node4,temp_node,tip1,tip2,node; + int el2; + int already_ordered=0; /*output: */ - double* riftstips=NULL; + int* riftstips=NULL; /*Allocate byproduct of this routine, riftstips: */ - riftstips=xNew(numrifts*2); + riftstips=xNew(numrifts*2); /*Go through all rifts: */ for (i=0;i(numsegs*3); - riftpairs_copy=xNew(numsegs*2); + riftsegments_copy=xNew(numsegs*3); + riftpairs_copy=xNew(numsegs*2); order=xNew(numsegs); @@ -748,12 +738,12 @@ for (j=0;j(order); - xDelete(riftsegments_copy); - xDelete(riftpairs_copy); + xDelete(riftsegments_copy); + xDelete(riftpairs_copy); } @@ -859,6 +849,6 @@ }/*}}}*/ /*FUNCTION PenaltyPairs{{{*/ -int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, - int* riftsnumsegs,double** riftspairs,double* riftstips,double* x,double* y){ +int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,int** riftssegments, + int* riftsnumsegs,int** riftspairs,int* riftstips,double* x,double* y){ int noerr=1; @@ -875,6 +865,6 @@ /*intermediary: */ int numsegs; - double* riftsegments=NULL; - double* riftpairs=NULL; + int* riftsegments=NULL; + int* riftpairs=NULL; int counter; double normal[2]; @@ -980,5 +970,5 @@ /*Renormalize normals: */ for(j=0;j(index,nel*3,(nel+2*3)); + index=xReNew(index,nel*3,(nel+2*3)); /*First, reassign element el: */ *(index+3*el+0)=node1; @@ -1098,8 +1076,8 @@ /*we need to change the segment elements corresponding to el: */ for (k=0;k(numanalyses); + analyses[0]=BalancethicknessAnalysisEnum; + break; + case SurfaceSlopeSolutionEnum: numanalyses=1; Index: /issm/trunk/src/c/solutions/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/solutions/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/solutions/CMakeLists.txt (revision 14310) @@ -0,0 +1,61 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/solutions) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/solutions/ad_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/AnalysisConfiguration.cpp + $ENV{ISSM_DIR}/src/c/solutions/convergence.cpp +$ENV{ISSM_DIR}/src/c/solutions/CorePointerFromSolutionEnum.cpp + $ENV{ISSM_DIR}/src/c/solutions/EnvironmentFinalize.cpp + $ENV{ISSM_DIR}/src/c/solutions/EnvironmentInit.cpp + $ENV{ISSM_DIR}/src/c/solutions/ProcessArguments.cpp + $ENV{ISSM_DIR}/src/c/solutions/ResetBoundaryConditions.cpp +$ENV{ISSM_DIR}/src/c/solutions/WrapperCorePointerFromSolutionEnum.cpp PARENT_SCOPE) +# }}} +# DAKOTA_SOURCES {{{ +set(DAKOTA_SOURCES $ENV{ISSM_DIR}/src/c/solutions/dakota_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/DakotaSpawnCore.cpp PARENT_SCOPE) +# }}} +# TRANSIENT_SOURCES {{{ +set(TRANSIENT_SOURCES $ENV{ISSM_DIR}/src/c/solutions/transient_core.cpp PARENT_SCOPE) +# }}} +# STEADYSTATE_SOURCES {{{ +set(STEADYSTATE_SOURCES $ENV{ISSM_DIR}/src/c/solutions/steadystate_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/steadystateconvergence.cpp PARENT_SCOPE) +# }}} +# PROGNOSTIC_SOURCES {{{ +set(PROGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/solutions/prognostic_core.cpp PARENT_SCOPE) +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/solutions/enthalpy_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/thermal_core.cpp PARENT_SCOPE) +# }}} +# HYDROLOGY_SOURCES {{{ +set(HYDROLOGY_SOURCES $ENV{ISSM_DIR}/src/c/solutions/hydrology_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/hydrology_core_step.cpp PARENT_SCOPE) +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/solutions/diagnostic_core.cpp PARENT_SCOPE) +# }}} +# BALANCED_SOURCES {{{ +set(BALANCED_SOURCES $ENV{ISSM_DIR}/src/c/solutions/balancethickness_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/dummy_core.cpp PARENT_SCOPE) +# }}} +# SLOPE_SOURCES {{{ +set(SLOPE_SOURCES $ENV{ISSM_DIR}/src/c/solutions/bedslope_core.cpp + $ENV{ISSM_DIR}/src/c/solutions/surfaceslope_core.cpp PARENT_SCOPE) +# }}} +# LIBISSM_LA_SOURCES {{{ +set(LIBISSM_LA_SOURCES $ENV{ISSM_DIR}/src/c/solutions/issm.cpp PARENT_SCOPE) +# }}} +# ISSM_SOURCES {{{ +set(ISSM_SOURCES $ENV{ISSM_DIR}/src/c/solutions/issm.cpp PARENT_SCOPE) +# }}} +# KRIGING_SOURCES {{{ +set(KRIGING_SOURCES $ENV{ISSM_DIR}/src/c/solutions/kriging.cpp PARENT_SCOPE) +# }}} +# ISSMROSE_EXE_SOURCES {{{ +set(ISSMROSE_EXE_SOURCES $ENV{ISSM_DIR}/src/c/solutions/issm.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/solutions/CorePointerFromSolutionEnum.cpp =================================================================== --- /issm/trunk/src/c/solutions/CorePointerFromSolutionEnum.cpp (revision 14309) +++ /issm/trunk/src/c/solutions/CorePointerFromSolutionEnum.cpp (revision 14310) @@ -60,4 +60,11 @@ #endif break; + case WeakBalancethicknessSolutionEnum: + #ifdef _HAVE_BALANCED_ + solutioncore=&dummy_core; + #else + _error_("ISSM was not compiled with balanced capabilities. Exiting"); + #endif + break; case HydrologySolutionEnum: #ifdef _HAVE_HYDROLOGY_ Index: /issm/trunk/src/c/solutions/EnvironmentInit.cpp =================================================================== --- /issm/trunk/src/c/solutions/EnvironmentInit.cpp (revision 14309) +++ /issm/trunk/src/c/solutions/EnvironmentInit.cpp (revision 14310) @@ -31,5 +31,5 @@ if(!my_rank) printf("\n"); if(!my_rank) printf("Ice Sheet System Model (%s) version %s\n",PACKAGE_NAME,PACKAGE_VERSION); - if(!my_rank) printf("(website: %s contact: %s\n",PACKAGE_URL,PACKAGE_BUGREPORT); + if(!my_rank) printf("(website: %s contact: %s)\n",PACKAGE_URL,PACKAGE_BUGREPORT); if(!my_rank) printf("\n"); Index: /issm/trunk/src/c/solutions/controltao_core.cpp =================================================================== --- /issm/trunk/src/c/solutions/controltao_core.cpp (revision 14309) +++ /issm/trunk/src/c/solutions/controltao_core.cpp (revision 14310) @@ -49,7 +49,6 @@ femmodel->parameters->FindParam(&control_list,NULL,InversionControlParametersEnum); femmodel->parameters->FindParam(&nsteps,InversionNstepsEnum); - femmodel->parameters->FindParam(&dummy,NULL,NULL,InversionMaxiterPerStepEnum); femmodel->parameters->SetParam(false,SaveResultsEnum); - maxiter=nsteps*(int)dummy[0]; xDelete(dummy); + maxiter=nsteps*10; /*Initialize TAO*/ Index: /issm/trunk/src/c/solutions/convergence.cpp =================================================================== --- /issm/trunk/src/c/solutions/convergence.cpp (revision 14309) +++ /issm/trunk/src/c/solutions/convergence.cpp (revision 14310) @@ -65,4 +65,5 @@ //compute K[n]U[n-1]F = K[n]U[n-1] - F + _assert_(uf); _assert_(Kff); KUold=uf->Duplicate(); Kff->MatMult(old_uf,KUold); KUoldF=KUold->Duplicate();KUold->Copy(KUoldF); KUoldF->AYPX(pf,-1.0); Index: /issm/trunk/src/c/solutions/dummy_core.cpp =================================================================== --- /issm/trunk/src/c/solutions/dummy_core.cpp (revision 14310) +++ /issm/trunk/src/c/solutions/dummy_core.cpp (revision 14310) @@ -0,0 +1,19 @@ +/*!\file: dummy_core.cpp + * \brief: dummy core (nothing done) + */ + +#include "../toolkits/toolkits.h" +#include "../classes/objects/objects.h" +#include "../shared/shared.h" +#include "../io/io.h" +#include "../include/include.h" +#include "../EnumDefinitions/EnumDefinitions.h" +#include "./solutions.h" +#include "../modules/modules.h" +#include "../solvers/solvers.h" + +void dummy_core(FemModel* femmodel){ + + /*We do not do anything*/ + +} Index: /issm/trunk/src/c/solutions/objectivefunction.cpp =================================================================== --- /issm/trunk/src/c/solutions/objectivefunction.cpp (revision 14309) +++ /issm/trunk/src/c/solutions/objectivefunction.cpp (revision 14310) @@ -46,4 +46,7 @@ femmodel->SetCurrentConfiguration(BalancethicknessAnalysisEnum); } + else if (solution_type==WeakBalancethicknessSolutionEnum){ + femmodel->SetCurrentConfiguration(BalancethicknessAnalysisEnum); + } else{ _error_("Solution " << EnumToStringx(solution_type) << " not implemented yet"); @@ -63,4 +66,7 @@ solver_linear(femmodel); } + else if (solution_type==WeakBalancethicknessSolutionEnum){ + /*Don't do anything*/ + } else{ _error_("Solution " << EnumToStringx(solution_type) << " not implemented yet"); Index: /issm/trunk/src/c/solutions/solutions.h =================================================================== --- /issm/trunk/src/c/solutions/solutions.h (revision 14309) +++ /issm/trunk/src/c/solutions/solutions.h (revision 14310) @@ -33,4 +33,5 @@ void dakota_core(FemModel* femmodel); void ad_core(FemModel* femmodel); +void dummy_core(FemModel* femmodel); IssmDouble objectivefunction(IssmDouble search_scalar,OptArgs* optargs); Index: /issm/trunk/src/c/solvers/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/solvers/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/solvers/CMakeLists.txt (revision 14310) @@ -0,0 +1,16 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/solvers) +# }}} +# CORE_SOURCES {{{ +set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/solvers/solver_linear.cpp + $ENV{ISSM_DIR}/src/c/solvers/solver_newton.cpp + $ENV{ISSM_DIR}/src/c/solvers/solver_nonlinear.cpp PARENT_SCOPE) +# }}} +# THERMAL_SOURCES {{{ +set(THERMAL_SOURCES $ENV{ISSM_DIR}/src/c/solvers/solver_thermal_nonlinear.cpp PARENT_SCOPE) +# }}} +# DIAGNOSTIC_SOURCES {{{ +set(DIAGNOSTIC_SOURCES $ENV{ISSM_DIR}/src/c/solvers/solver_stokescoupling_nonlinear.cpp PARENT_SCOPE) +# }}} Index: /issm/trunk/src/c/solvers/solver_newton.cpp =================================================================== --- /issm/trunk/src/c/solvers/solver_newton.cpp (revision 14309) +++ /issm/trunk/src/c/solvers/solver_newton.cpp (revision 14310) @@ -56,10 +56,30 @@ /*Solver forward model*/ - femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + if(count==1){ + femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf,Kfs,ys);xdelete(&Kfs); + Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);xdelete(&df); + Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);xdelete(&ug); + xdelete(&old_ug);old_ug=ug; + xdelete(&old_uf);old_uf=uf; + } + uf=old_uf->Duplicate(); old_uf->Copy(uf); + + /*Prepare next iteration using Newton's method*/ + femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL);xdelete(&df); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf,Kfs,ys);xdelete(&Kfs); - Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);xdelete(&df); + Reduceloadx(pf,Kfs,ys); xdelete(&Kfs); + + pJf=pf->Duplicate(); + Kff->MatMult(uf,pJf);// xdelete(&Kff); + pJf->Scale(-1.0); pJf->AXPY(pf,+1.0); //xdelete(&pf); + + femmodel->CreateJacobianMatrixx(&Jff,kmax); + Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); xdelete(&Jff); xdelete(&pJf); + uf->AXPY(duf, 1.0); xdelete(&duf); Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); - InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);xdelete(&ug); + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug); /*Check convergence*/ @@ -82,18 +102,4 @@ } - /*Prepare next iteration using Newton's method*/ - femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); - CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf,Kfs,ys); xdelete(&Kfs); - - pJf=pf->Duplicate(); Kff->MatMult(uf,pJf); xdelete(&Kff); - pJf->Scale(-1.0); pJf->AXPY(pf,+1.0); xdelete(&pf); - - femmodel->CreateJacobianMatrixx(&Jff,kmax); - Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); xdelete(&Jff); xdelete(&pJf); - uf->AXPY(duf, 1.0); xdelete(&duf); - Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); - InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug); - count++; } Index: /issm/trunk/src/c/solvers/solver_thermal_nonlinear.cpp =================================================================== --- /issm/trunk/src/c/solvers/solver_thermal_nonlinear.cpp (revision 14309) +++ /issm/trunk/src/c/solvers/solver_thermal_nonlinear.cpp (revision 14310) @@ -33,10 +33,8 @@ /*parameters:*/ int kflag,pflag; - bool lowmem=0; int configuration_type; /*Recover parameters: */ kflag=1; pflag=1; - femmodel->parameters->FindParam(&lowmem,SettingsLowmemEnum); femmodel->parameters->FindParam(&thermal_penalty_threshold,ThermalPenaltyThresholdEnum); femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); Index: /issm/trunk/src/c/toolkits/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/CMakeLists.txt (revision 14310) @@ -0,0 +1,12 @@ +# Subdirectories {{{ +add_subdirectory(issm) +add_subdirectory(metis) +add_subdirectory(mpi) +add_subdirectory(petsc) +add_subdirectory(plapack) +add_subdirectory(scalapack) +add_subdirectory(triangle) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits) +# }}} Index: /issm/trunk/src/c/toolkits/issm/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/issm/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/issm/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/issm) +# }}} Index: /issm/trunk/src/c/toolkits/metis/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/metis/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/metis/CMakeLists.txt (revision 14310) @@ -0,0 +1,6 @@ +# Subdirectories {{{ +add_subdirectory(patches) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/metis) +# }}} Index: /issm/trunk/src/c/toolkits/metis/patches/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/metis/patches/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/metis/patches/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/metis/patches) +# }}} Index: /issm/trunk/src/c/toolkits/mpi/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/mpi/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/mpi/CMakeLists.txt (revision 14310) @@ -0,0 +1,6 @@ +# Subdirectories {{{ +add_subdirectory(patches) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/mpi) +# }}} Index: /issm/trunk/src/c/toolkits/mpi/patches/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/mpi/patches/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/mpi/patches/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/mpi/patches) +# }}} Index: /issm/trunk/src/c/toolkits/petsc/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/petsc/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/petsc/CMakeLists.txt (revision 14310) @@ -0,0 +1,7 @@ +# Subdirectories {{{ +add_subdirectory(objects) +add_subdirectory(patches) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/petsc) +# }}} Index: /issm/trunk/src/c/toolkits/petsc/objects/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/petsc/objects/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/petsc/objects/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/petsc/objects) +# }}} Index: /issm/trunk/src/c/toolkits/petsc/patches/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/petsc/patches/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/petsc/patches) +# }}} Index: /issm/trunk/src/c/toolkits/plapack/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/plapack/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/plapack/CMakeLists.txt (revision 14310) @@ -0,0 +1,6 @@ +# Subdirectories {{{ +add_subdirectory(patches) +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/plapack) +# }}} Index: /issm/trunk/src/c/toolkits/plapack/patches/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/plapack/patches/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/plapack/patches/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/plapack/patches) +# }}} Index: /issm/trunk/src/c/toolkits/scalapack/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/scalapack/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/scalapack/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/scalapack) +# }}} Index: /issm/trunk/src/c/toolkits/triangle/CMakeLists.txt =================================================================== --- /issm/trunk/src/c/toolkits/triangle/CMakeLists.txt (revision 14310) +++ /issm/trunk/src/c/toolkits/triangle/CMakeLists.txt (revision 14310) @@ -0,0 +1,5 @@ +# Subdirectories {{{ +# }}} +# Include Directory {{{ +include_directories(AFTER $ENV{ISSM_DIR}/src/c/toolkits/triangle) +# }}} Index: /issm/trunk/src/m/boundaryconditions/SetIceShelfBC.py =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetIceShelfBC.py (revision 14309) +++ /issm/trunk/src/m/boundaryconditions/SetIceShelfBC.py (revision 14310) @@ -25,5 +25,5 @@ if not os.path.exists(icefrontfile): raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) - [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) + [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) nodeonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)) else: Index: /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.py =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 14309) +++ /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 14310) @@ -27,5 +27,5 @@ if not os.path.exists(icefrontfile): raise IOError("SetMarineIceSheetBC error message: ice front file '%s' not found." % icefrontfile) - [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) + [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) vertexonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)) else: Index: /issm/trunk/src/m/classes/autodiff.m =================================================================== --- /issm/trunk/src/m/classes/autodiff.m (revision 14309) +++ /issm/trunk/src/m/classes/autodiff.m (revision 14310) @@ -43,5 +43,5 @@ end % }}} function disp(obj) % {{{ - disp(sprintf(' automatic differentiation parameters:')); + disp(sprintf(' automatic differentiation parameters:')); fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated'); fielddisplay(obj,'dependents','list of dependent variables'); Index: /issm/trunk/src/m/classes/balancethickness.py =================================================================== --- /issm/trunk/src/m/classes/balancethickness.py (revision 14309) +++ /issm/trunk/src/m/classes/balancethickness.py (revision 14310) @@ -29,5 +29,5 @@ string=' balance thickness solution parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)')) string="%s\n%s"%(string,fielddisplay(self,'stabilization',"0: None, 1: SU, 2: MacAyeal's artificial diffusivity, 3:DG")) Index: /issm/trunk/src/m/classes/basalforcings.py =================================================================== --- /issm/trunk/src/m/classes/basalforcings.py (revision 14309) +++ /issm/trunk/src/m/classes/basalforcings.py (revision 14310) @@ -28,5 +28,5 @@ string=" basal forcings parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,"melting_rate","basal melting rate (positive if melting)")) + string="%s\n%s"%(string,fielddisplay(self,"melting_rate","basal melting rate (positive if melting)")) string="%s\n%s"%(string,fielddisplay(self,"melting_rate_correction","additional melting applied when the grounding line retreats")) string="%s\n%s"%(string,fielddisplay(self,"geothermalflux","geothermal heat flux [W/m^2]")) Index: /issm/trunk/src/m/classes/constants.py =================================================================== --- /issm/trunk/src/m/classes/constants.py (revision 14309) +++ /issm/trunk/src/m/classes/constants.py (revision 14310) @@ -27,12 +27,11 @@ # {{{ Display string=" constants parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,"g","gravitational acceleration")) + + string="%s\n%s"%(string,fielddisplay(self,"g","gravitational acceleration")) string="%s\n%s"%(string,fielddisplay(self,"yts","number of seconds in a year")) string="%s\n%s"%(string,fielddisplay(self,"referencetemperature","reference temperature used in the enthalpy model")) - return string #}}} - def setdefaultparameters(self): # {{{setdefaultparameters Index: /issm/trunk/src/m/classes/debug.py =================================================================== --- /issm/trunk/src/m/classes/debug.py (revision 14309) +++ /issm/trunk/src/m/classes/debug.py (revision 14310) @@ -26,5 +26,5 @@ string=" debug parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,"valgrind","use Valgrind to debug (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(self,"valgrind","use Valgrind to debug (0 or 1)")) string="%s\n%s"%(string,fielddisplay(self,"gprof","use gnu-profiler to find out where the time is spent")) string="%s\n%s"%(string,fielddisplay(self,'profiling','enables profiling (memory, flops, time)')) Index: /issm/trunk/src/m/classes/diagnostic.py =================================================================== --- /issm/trunk/src/m/classes/diagnostic.py (revision 14309) +++ /issm/trunk/src/m/classes/diagnostic.py (revision 14310) @@ -45,6 +45,6 @@ # {{{ Display - string='\n Diagnostic solution parameters:' - string="%s\n\n%s"%(string,' Convergence criteria:') + string=' Diagnostic solution parameters:' + string="%s\n%s"%(string,' Convergence criteria:') string="%s\n%s"%(string,fielddisplay(self,'restol','mechanical equilibrium residual convergence criterion')) @@ -55,5 +55,5 @@ string="%s\n%s"%(string,fielddisplay(self,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)')) - string="%s\n%s"%(string,' boundary conditions:') + string="%s\n%s"%(string,'\n boundary conditions:') string="%s\n%s"%(string,fielddisplay(self,'spcvx','x-axis velocity constraint (NaN means no constraint)')) @@ -62,13 +62,13 @@ string="%s\n%s"%(string,fielddisplay(self,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice')) - string="%s\n%s"%(string,' Rift options:') + string="%s\n%s"%(string,'\n Rift options:') string="%s\n%s"%(string,fielddisplay(self,'rift_penalty_threshold','threshold for instability of mechanical constraints')) string="%s\n%s"%(string,fielddisplay(self,'rift_penalty_lock','number of iterations before rift penalties are locked')) - string="%s\n%s"%(string,' Penalty options:') + string="%s\n%s"%(string,'\n Penalty options:') string="%s\n%s"%(string,fielddisplay(self,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset')) string="%s\n%s"%(string,fielddisplay(self,'vertex_pairing','pairs of vertices that are penalized')) - string="%s\n%s"%(string,' Other:') + string="%s\n%s"%(string,'\n Other:') string="%s\n%s"%(string,fielddisplay(self,'shelf_dampening','use dampening for floating ice ? Only for Stokes model')) string="%s\n%s"%(string,fielddisplay(self,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model')) Index: /issm/trunk/src/m/classes/flowequation.py =================================================================== --- /issm/trunk/src/m/classes/flowequation.py (revision 14309) +++ /issm/trunk/src/m/classes/flowequation.py (revision 14310) @@ -37,5 +37,5 @@ string=' flow equation parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'ismacayealpattyn',"is the macayeal or pattyn approximation used ?")) + string="%s\n%s"%(string,fielddisplay(self,'ismacayealpattyn',"is the macayeal or pattyn approximation used ?")) string="%s\n%s"%(string,fielddisplay(self,'ishutter',"is the shallow ice approximation used ?")) string="%s\n%s"%(string,fielddisplay(self,'isl1l2',"are l1l2 equations used ?")) Index: /issm/trunk/src/m/classes/friction.py =================================================================== --- /issm/trunk/src/m/classes/friction.py (revision 14309) +++ /issm/trunk/src/m/classes/friction.py (revision 14310) @@ -27,5 +27,6 @@ # {{{ Display string="Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p" - string="%s\n\n%s"%(string,fielddisplay(self,"coefficient","friction coefficient [SI]")) + + string="%s\n%s"%(string,fielddisplay(self,"coefficient","friction coefficient [SI]")) string="%s\n%s"%(string,fielddisplay(self,"p","p exponent")) string="%s\n%s"%(string,fielddisplay(self,"q","q exponent")) Index: /issm/trunk/src/m/classes/geometry.py =================================================================== --- /issm/trunk/src/m/classes/geometry.py (revision 14309) +++ /issm/trunk/src/m/classes/geometry.py (revision 14310) @@ -31,5 +31,5 @@ string=" geometry parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,'surface','surface elevation')) + string="%s\n%s"%(string,fielddisplay(self,'surface','surface elevation')) string="%s\n%s"%(string,fielddisplay(self,'thickness','ice thickness')) string="%s\n%s"%(string,fielddisplay(self,'bed','bed elevation')) Index: /issm/trunk/src/m/classes/groundingline.py =================================================================== --- /issm/trunk/src/m/classes/groundingline.py (revision 14309) +++ /issm/trunk/src/m/classes/groundingline.py (revision 14310) @@ -30,5 +30,5 @@ string=' grounding line solution parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''')) + string="%s\n%s"%(string,fielddisplay(self,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''')) string="%s\n%s"%(string,fielddisplay(self,'melting_rate','melting rate applied when previously grounded parts start floating')) return string Index: /issm/trunk/src/m/classes/hydrology.py =================================================================== --- /issm/trunk/src/m/classes/hydrology.py (revision 14309) +++ /issm/trunk/src/m/classes/hydrology.py (revision 14310) @@ -32,5 +32,5 @@ string=' hydrology solution parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'spcwatercolumn','water thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(self,'spcwatercolumn','water thickness constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'n','Manning roughness coefficient')) string="%s\n%s"%(string,fielddisplay(self,'CR','tortuosity parameter')) Index: /issm/trunk/src/m/classes/initialization.py =================================================================== --- /issm/trunk/src/m/classes/initialization.py (revision 14309) +++ /issm/trunk/src/m/classes/initialization.py (revision 14310) @@ -90,6 +90,4 @@ WriteData(fid,'data',self.pressure,'format','DoubleMat','mattype',1,'enum',PressureEnum()) WriteData(fid,'data',self.temperature,'format','DoubleMat','mattype',1,'enum',TemperatureEnum()) - WriteData(fid,'data',self.surfacetemp,'format','DoubleMat','mattype',1,'enum',TemperatureSurfaceEnum()) - WriteData(fid,'data',self.basaltemp,'format','DoubleMat','mattype',1,'enum',TemperatureBasalEnum()) WriteData(fid,'data',self.watercolumn,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum()) WriteData(fid,'data',self.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum()) Index: /issm/trunk/src/m/classes/inversion.m =================================================================== --- /issm/trunk/src/m/classes/inversion.m (revision 14309) +++ /issm/trunk/src/m/classes/inversion.m (revision 14310) @@ -31,4 +31,28 @@ case 0 obj=setdefaultparameters(obj); + case 1 + if isa(varargin{1},'taoinversion'), + disp('converting taoinversion to inversion'); + in=varargin{1}; + obj.iscontrol = in.iscontrol; + obj.tao = 1; + obj.incomplete_adjoint = in.incomplete_adjoint; + obj.control_parameters = in.control_parameters; + obj.nsteps = in.nsteps; + obj.maxiter_per_step = 10*ones(in.nsteps,1); + obj.cost_functions = repmat(in.cost_functions,in.nsteps,1); + obj.cost_functions_coefficients = in.cost_functions_coefficients; + obj.gradient_scaling = 100*ones(in.nsteps,1); + obj.cost_function_threshold = NaN; + obj.min_parameters = in.min_parameters; + obj.max_parameters = in.max_parameters; + obj.step_threshold = .99*ones(in.nsteps,1); + obj.vx_obs = in.vx_obs; + obj.gradient_only = 0; + obj.vy_obs = in.vy_obs; + obj.vz_obs = in.vz_obs; + obj.vel_obs = in.vel_obs; + obj.thickness_obs = in.thickness_obs; + end otherwise error('constructor not supported'); @@ -86,9 +110,10 @@ md = checkfield(md,'inversion.tao','values',[0 1]); md = checkfield(md,'inversion.incomplete_adjoint','values',[0 1]); - md = checkfield(md,'inversion.control_parameters','cell',1,'values',{'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'MaterialsRheologyZbar' 'Vx' 'Vy'}); + md = checkfield(md,'inversion.control_parameters','cell',1,'values',... + {'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'MaterialsRheologyZbar' 'Vx' 'Vy' 'Thickness'}); md = checkfield(md,'inversion.nsteps','numel',1,'>=',1); md = checkfield(md,'inversion.maxiter_per_step','size',[md.inversion.nsteps 1],'>=',0); md = checkfield(md,'inversion.step_threshold','size',[md.inversion.nsteps 1]); - md = checkfield(md,'inversion.cost_functions','size',[md.inversion.nsteps num_costfunc],'values',[101:105 201 501:505]); + md = checkfield(md,'inversion.cost_functions','size',[md.inversion.nsteps num_costfunc],'values',[101:105 201 501:506]); md = checkfield(md,'inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0); md = checkfield(md,'inversion.gradient_only','values',[0 1]); @@ -99,4 +124,6 @@ if solution==BalancethicknessSolutionEnum() md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1); + elseif solution==WeakBalancethicknessSolutionEnum() + md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1); else md = checkfield(md,'inversion.vx_obs','size',[md.mesh.numberofvertices 1],'NaN',1); @@ -105,4 +132,5 @@ end % }}} function disp(obj) % {{{ + disp(sprintf(' inversion parameters:')); fielddisplay(obj,'iscontrol','is inversion activated?'); fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?'); @@ -176,4 +204,5 @@ pos=find(data==504); data(pos)=ThicknessAlongGradientEnum(); pos=find(data==505); data(pos)=ThicknessAcrossGradientEnum(); + pos=find(data==506); data(pos)=BalancethicknessMisfitEnum(); WriteData(fid,'data',data,'enum',InversionCostFunctionsEnum(),'format','DoubleMat','mattype',3); WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer'); Index: /issm/trunk/src/m/classes/inversion.py =================================================================== --- /issm/trunk/src/m/classes/inversion.py (revision 14309) +++ /issm/trunk/src/m/classes/inversion.py (revision 14310) @@ -45,5 +45,5 @@ def __repr__(self): # {{{ Display - string='\n Inversion parameters:' + string=' inversion parameters:' string="%s\n%s"%(string,fielddisplay(self,'iscontrol','is inversion activated?')) string="%s\n%s"%(string,fielddisplay(self,'incomplete_adjoint','do we assume linear viscosity?')) Index: /issm/trunk/src/m/classes/mask.m =================================================================== --- /issm/trunk/src/m/classes/mask.m (revision 14309) +++ /issm/trunk/src/m/classes/mask.m (revision 14310) @@ -12,4 +12,5 @@ vertexongroundedice = NaN; vertexonwater = NaN; + vertexonrock = NaN; end methods @@ -33,12 +34,16 @@ md = checkfield(md,'mask.vertexongroundedice','size',[md.mesh.numberofvertices 1],'values',[0 1]); md = checkfield(md,'mask.vertexonwater' ,'size',[md.mesh.numberofvertices 1],'values',[0 1]); + md = checkfield(md,'mask.vertexonrock' ,'size',[md.mesh.numberofvertices 1],'values',[0 1]); end % }}} function disp(obj) % {{{ + disp(sprintf(' masks:')); + fielddisplay(obj,'elementonfloatingice','element on floating ice flags list'); fielddisplay(obj,'vertexonfloatingice','vertex on floating ice flags list'); fielddisplay(obj,'elementongroundedice','element on grounded ice list'); fielddisplay(obj,'vertexongroundedice','vertex on grounded ice flags list'); - fielddisplay(obj,'elementonwater','element on water flags list'); + fielddisplay(obj,'elementonwater','element on rock flags list'); fielddisplay(obj,'vertexonwater','vertex on water flags list'); + fielddisplay(obj,'vertexonrock','vertex on rock flags list'); end % }}} function marshall(obj,fid) % {{{ Index: /issm/trunk/src/m/classes/mask.py =================================================================== --- /issm/trunk/src/m/classes/mask.py (revision 14309) +++ /issm/trunk/src/m/classes/mask.py (revision 14310) @@ -29,6 +29,6 @@ def __repr__(self): # {{{ Display + string=" masks:" - string=""; string="%s\n%s"%(string,fielddisplay(self,"elementonfloatingice","element on floating ice flags list")) string="%s\n%s"%(string,fielddisplay(self,"vertexonfloatingice","vertex on floating ice flags list")) Index: /issm/trunk/src/m/classes/matice.m =================================================================== --- /issm/trunk/src/m/classes/matice.m (revision 14309) +++ /issm/trunk/src/m/classes/matice.m (revision 14310) @@ -89,5 +89,5 @@ end % }}} function disp(obj) % {{{ - disp(sprintf(' Materials:\n')); + disp(sprintf(' Materials:')); fielddisplay(obj,'rho_ice','ice density [kg/m^3]'); Index: /issm/trunk/src/m/classes/matice.py =================================================================== --- /issm/trunk/src/m/classes/matice.py (revision 14309) +++ /issm/trunk/src/m/classes/matice.py (revision 14310) @@ -38,5 +38,5 @@ string=" Materials:" - string="%s\n\n%s"%(string,fielddisplay(self,"rho_ice","ice density [kg/m^3]")) + string="%s\n%s"%(string,fielddisplay(self,"rho_ice","ice density [kg/m^3]")) string="%s\n%s"%(string,fielddisplay(self,"rho_water","water density [kg/m^3]")) string="%s\n%s"%(string,fielddisplay(self,"rho_freshwater","fresh water density [kg/m^3]")) Index: /issm/trunk/src/m/classes/mesh.py =================================================================== --- /issm/trunk/src/m/classes/mesh.py (revision 14309) +++ /issm/trunk/src/m/classes/mesh.py (revision 14310) @@ -63,7 +63,9 @@ def __repr__(self): # {{{ Display + string=" Mesh:" + if self.dimension==3: - string="\n%s"%(" Elements and vertices of the original 2d mesh:") + string="%s\n%s"%(string,"\n Elements and vertices of the original 2d mesh:") string="%s\n%s"%(string,fielddisplay(self,"numberofelements2d","number of elements")) @@ -73,7 +75,7 @@ string="%s\n%s"%(string,fielddisplay(self,"y2d","vertices y coordinate")) - string="%s\n%s" %(string,"Elements and vertices of the extruded 3d mesh:") + string="%s\n%s"%(string,"\n\n Elements and vertices of the extruded 3d mesh:") else: - string="\n%s"%(" Elements and vertices:") + string="%s\n%s"%(string,"\n Elements and vertices:") string="%s\n%s"%(string,fielddisplay(self,"numberofelements","number of elements")) string="%s\n%s"%(string,fielddisplay(self,"numberofvertices","number of vertices")) @@ -85,5 +87,5 @@ string="%s\n%s"%(string,fielddisplay(self,"numberofedges","number of edges of the 2d mesh")) - string="%s%s"%(string,"\n Properties:") + string="%s%s"%(string,"\n\n Properties:") string="%s\n%s"%(string,fielddisplay(self,"dimension","mesh dimension (2d or 3d)")) string="%s\n%s"%(string,fielddisplay(self,"numberoflayers","number of extrusion layers")) @@ -103,9 +105,9 @@ string="%s\n%s"%(string,fielddisplay(self,"average_vertex_connectivity","average number of vertices connected to one vertex")) - string="%s%s"%(string,"\n Extracted model:") + string="%s%s"%(string,"\n\n Extracted model:") string="%s\n%s"%(string,fielddisplay(self,"extractedvertices","vertices extracted from the model")) string="%s\n%s"%(string,fielddisplay(self,"extractedelements","elements extracted from the model")) - string="%s%s"%(string,"\n Projection:") + string="%s%s"%(string,"\n\n Projection:") string="%s\n%s"%(string,fielddisplay(self,"lat","vertices latitude")) string="%s\n%s"%(string,fielddisplay(self,"long","vertices longitude")) Index: /issm/trunk/src/m/classes/miscellaneous.py =================================================================== --- /issm/trunk/src/m/classes/miscellaneous.py (revision 14309) +++ /issm/trunk/src/m/classes/miscellaneous.py (revision 14310) @@ -29,5 +29,5 @@ string=' miscellaneous parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'notes','notes in a cell of strings')) + string="%s\n%s"%(string,fielddisplay(self,'notes','notes in a cell of strings')) string="%s\n%s"%(string,fielddisplay(self,'name','model name')) string="%s\n%s"%(string,fielddisplay(self,'dummy','empty field to store some data')) Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 14309) +++ /issm/trunk/src/m/classes/model/model.m (revision 14310) @@ -212,4 +212,5 @@ md.mask.elementonwater=project2d(md,md.mask.elementonwater,1); md.mask.vertexonwater=project2d(md,md.mask.vertexonwater,1); + md.mask.vertexonrock=project2d(md,md.mask.vertexonrock,1); %lat long @@ -502,14 +503,25 @@ solutionfields=fields(md1.results); for i=1:length(solutionfields), - %get subfields - solutionsubfields=fields(md1.results.(solutionfields{i})); - for j=1:length(solutionsubfields), - field=md1.results.(solutionfields{i}).(solutionsubfields{j}); + if isstruct(md1.results.(solutionfields{i})) + %get subfields + solutionsubfields=fields(md1.results.(solutionfields{i})); + for j=1:length(solutionsubfields), + field=md1.results.(solutionfields{i}).(solutionsubfields{j}); + if length(field)==numberofvertices1, + md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node); + elseif length(field)==numberofelements1, + md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem); + else + md2.results.(solutionfields{i}).(solutionsubfields{j})=field; + end + end + else + field=md1.results.(solutionfields{i}); if length(field)==numberofvertices1, - md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node); + md2.results.(solutionfields{i})=field(pos_node); elseif length(field)==numberofelements1, - md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem); + md2.results.(solutionfields{i})=field(pos_elem); else - md2.results.(solutionfields{i}).(solutionsubfields{j})=field; + md2.results.(solutionfields{i})=field; end end @@ -744,4 +756,5 @@ md.mask.elementonwater=project3d(md,'vector',md.mask.elementonwater,'type','element'); md.mask.vertexonwater=project3d(md,'vector',md.mask.vertexonwater,'type','node'); + md.mask.vertexonrock=project3d(md,'vector',md.mask.vertexonrock,'type','node'); if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end; if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end; @@ -1120,4 +1133,20 @@ disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields')); end % }}} + function memory(obj) % {{{ + + disp(sprintf('\nMemory imprint: ')); + + objects=fields(obj); + memory=0; + + for i=1:length(objects), + field=objects{i}; + realobject=obj.(field); + s=whos('realobject'); + memory=memory+s.bytes/1e6; + disp(sprintf('%19s: %g Mb',field,s.bytes/1e6)); + end + disp(sprintf('Overall: %g Mb',memory)); + end % }}} end end Index: /issm/trunk/src/m/classes/model/model.py =================================================================== --- /issm/trunk/src/m/classes/model/model.py (revision 14309) +++ /issm/trunk/src/m/classes/model/model.py (revision 14310) @@ -45,4 +45,5 @@ from ElementConnectivity import * from contourenvelope import * +from PythonFuncs import * #}}} @@ -407,5 +408,5 @@ md2.diagnostic.icefront[:,2]=Pnode[md1.diagnostic.icefront[:,2].astype(int)-1] md2.diagnostic.icefront[:,3]=Pnode[md1.diagnostic.icefront[:,3].astype(int)-1] - md2.diagnostic.icefront=md2.diagnostic.icefront[numpy.nonzero(numpy.logical_and(numpy.logical_and(md2.diagnostic.icefront[:,0],md2.diagnostic.icefront[:,1]),md2.diagnostic.icefront[:,-1]))[0],:] + md2.diagnostic.icefront=md2.diagnostic.icefront[numpy.nonzero(logical_and_n(md2.diagnostic.icefront[:,0],md2.diagnostic.icefront[:,1],md2.diagnostic.icefront[:,-1]))[0],:] #Results fields Index: /issm/trunk/src/m/classes/organizer.m =================================================================== --- /issm/trunk/src/m/classes/organizer.m (revision 14309) +++ /issm/trunk/src/m/classes/organizer.m (revision 14310) @@ -13,5 +13,5 @@ % org = organizer('repository','Models/','prefix','AGU2015','steps',0); %build an empty organizer object with a given repository -classdef organizer +classdef organizer < handle properties (SetAccess=private) % {{{ @@ -112,4 +112,30 @@ end end%}}} + function md=loaddata(org,string),% {{{ + + %Get model path + if ~ischar(string), error('argument provided is not a string'); end + path=[org.repository '/' org.prefix string]; + + %figure out if the data is there, otherwise, we have to use the default path supplied by user. + if exist(path,'file') | exist([path '.mat'],'file'), + evalin('caller',['load -mat ' path]); + return; + end + + %If we are here, the data has not been found. Try trunk prefix if provided + if ~isempty(org.trunkprefix), + path2=[org.repository '/' org.trunkprefix string]; + if ~exist(path2,'file'), + error(['Could find neither ' path ', nor ' path2]); + else + disp(['--> Branching ' org.prefix ' from trunk ' org.trunkprefix]); + evalin('caller',['load -mat ' path2]); + return; + end + else + error(['Could not find ' path ]); + end + end%}}} function bool=perform(org,string) % {{{ @@ -142,7 +168,4 @@ end - %assign org back to calling workspace - assignin('caller',inputname(1),org); - end%}}} function savemodel(org,md) % {{{ @@ -162,4 +185,24 @@ save(name,'md','-v7.3'); end%}}} + function savedata(org,varargin) % {{{ + + %check + if (org.currentstep==0), error('Cannot save data because organizer (org) is empty! Make sure you did not skip any perform call'); end + if (org.currentstep>length(org.steps)), error('Cannot save data because organizer (org) is not up to date!'); end + + name=[org.repository '/' org.prefix org.steps(org.currentstep).string ]; + disp(['saving data in: ' name]); + + %check that md is a model + if (org.currentstep>length(org.steps)), error(['organizer error message: element with id ' num2str(org.currentstep) ' not found']); end + + %list of variable names: + variables=''; + for i=2:nargin, + variables=[variables ',' '''' inputname(i) '''']; + eval([inputname(i) '= varargin{' num2str(i-1) '};']); + end + eval(['save(''' name '''' variables ',''-v7.3'');']); + end%}}} end end Index: /issm/trunk/src/m/classes/pairoptions.m =================================================================== --- /issm/trunk/src/m/classes/pairoptions.m (revision 14309) +++ /issm/trunk/src/m/classes/pairoptions.m (revision 14310) @@ -5,8 +5,8 @@ % pairoptions=pairoptions('module',true,'solver',false); -classdef pairoptions +classdef pairoptions < handle properties (SetAccess = private,GetAccess = private) functionname = ''; - list = cell(0,2); + list = cell(0,3); end methods @@ -38,5 +38,5 @@ %Allocate memory - obj.list=cell(numoptions,2); + obj.list=cell(numoptions,3); %go through varargin and build list of obj @@ -45,4 +45,5 @@ obj.list{i,1}=varargin{2*i-1}; obj.list{i,2}=varargin{2*i}; + obj.list{i,3}=false; %used? else %option is not a string, ignore it @@ -57,4 +58,5 @@ obj.list{end+1,1} = field; obj.list{end,2} = value; + obj.list{end,3} = false; end end % }}} @@ -65,4 +67,5 @@ obj.list{end+1,1} = field; obj.list{end,2} = value; + obj.list{end,3} = true; %It is a default so user will not be notified if not used end end @@ -84,5 +87,5 @@ %CHANGEOPTIONVALUE - change the value of an option in an option list - %track occurance of field + %track occurrence of field lines=find(strcmpi(obj.list(:,1),field)); @@ -91,4 +94,5 @@ %add new field if not found obj=addfield(obj,field,newvalue); + obj.list{end,3}=true; % do not notify user if unused else for i=1:length(lines), @@ -100,5 +104,5 @@ %DELETEDUPLICATES - delete duplicates in an option list - %track the first occurance of each option + %track the first occurrence of each option [dummy lines]=unique(obj.list(:,1),'first'); clear dummy @@ -109,5 +113,5 @@ for i=1:numoptions, if ~ismember(i,lines), - disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurence will be kept']) + disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurrence will be kept']) end end @@ -116,4 +120,14 @@ %remove duplicates from the options list obj.list=obj.list(lines,:); + end % }}} + function displayunused(obj) % {{{ + %DISPLAYUNUSED - display unused options + + numoptions=size(obj.list,1); + for i=1:numoptions, + if ~obj.list{i,3}, + disp(['WARNING: option ' obj.list{i,1} ' was not used']) + end + end end % }}} function disp(obj) % {{{ @@ -137,5 +151,5 @@ end % }}} function bool = exist(obj,field) % {{{ - %EXIST - check if the option exist + %EXIST - check if the option exists %some argument checking: @@ -148,15 +162,21 @@ %Recover option - bool=any(strcmpi(field,obj.list(:,1))); - end % }}} - function num = fieldoccurences(obj,field), % {{{ - %FIELDOCCURENCES - get number of occurence of a field + pos=find(strcmpi(field,obj.list(:,1))); + if ~isempty(pos), + bool=true; + obj.list{pos,3} = true; %It is a default so user will not be notified if not used + else + bool=false; + end + end % }}} + function num = fieldoccurrences(obj,field), % {{{ + %FIELDOCCURRENCES - get number of occurrence of a field %check input if ~ischar(field), - error('fieldoccurences error message: field should be a string'); - end - - %get number of occurence + error('fieldoccurrences error message: field should be a string'); + end + + %get number of occurrence num=sum(strcmpi(field,obj.list(:,1))); end % }}} @@ -187,5 +207,6 @@ pos=find(strcmpi(obj.list(:,1),field)); if ~isempty(pos), - value=obj.list{pos(1),2}; %ignore extra entry + value=obj.list{pos(1),2}; % ignore extra entry + obj.list{pos(1),3}=true; % option used return; end @@ -204,5 +225,5 @@ % obj=removefield(obj,field,warn) % - % if warn==1 display an info message to wan user that + % if warn==1 display an info message to warn user that % some of his options have been removed. Index: /issm/trunk/src/m/classes/pairoptions.py =================================================================== --- /issm/trunk/src/m/classes/pairoptions.py (revision 14309) +++ /issm/trunk/src/m/classes/pairoptions.py (revision 14310) @@ -78,5 +78,5 @@ # %DELETEDUPLICATES - delete duplicates in an option list # -# %track the first occurance of each option +# %track the first occurrence of each option # [dummy lines]=unique(obj.list(:,1),'first'); # clear dummy @@ -87,5 +87,5 @@ # for i=1:numoptions, # if ~ismember(i,lines), -# disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurence will be kept']) +# disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurrence will be kept']) # end # end @@ -128,14 +128,14 @@ # }}} - #def fieldoccurences(self,field): #{{{ + #def fieldoccurrences(self,field): #{{{ # ''' - # FIELDOCCURENCES - get number of occurence of a field + # FIELDOCCURRENCES - get number of occurrence of a field # ''' # # #check input # if not isinstance(field,(str,unicode)): - # raise TypeError("fieldoccurences error message: field should be a string") - - # #get number of occurence + # raise TypeError("fieldoccurrences error message: field should be a string") + + # #get number of occurrence # # ?? # #return num Index: /issm/trunk/src/m/classes/plotoptions.m =================================================================== --- /issm/trunk/src/m/classes/plotoptions.m (revision 14309) +++ /issm/trunk/src/m/classes/plotoptions.m (revision 14310) @@ -68,5 +68,5 @@ %get number of data to be plotted - numberofplots=fieldoccurences(rawoptions,'data'); + numberofplots=fieldoccurrences(rawoptions,'data'); opt.numberofplots=numberofplots; @@ -112,5 +112,5 @@ continue; - %#all + %pound all elseif strcmpi(plotnum,'all'); for j=1:numberofplots, @@ -118,5 +118,5 @@ end - %#i-j + %pound i-j elseif ismember('-',plotnum) nums=strsplit(plotnum,'-'); @@ -129,5 +129,5 @@ end - %#i + %pound i else %assign to subplot Index: /issm/trunk/src/m/classes/prognostic.py =================================================================== --- /issm/trunk/src/m/classes/prognostic.py (revision 14309) +++ /issm/trunk/src/m/classes/prognostic.py (revision 14310) @@ -32,5 +32,5 @@ # {{{ Display string=' Prognostic solution parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'min_thickness','minimum ice thickness allowed')) string="%s\n%s"%(string,fielddisplay(self,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ')) Index: /issm/trunk/src/m/classes/qmu/@dakota_method/dakota_method.m =================================================================== --- /issm/trunk/src/m/classes/qmu/@dakota_method/dakota_method.m (revision 14309) +++ /issm/trunk/src/m/classes/qmu/@dakota_method/dakota_method.m (revision 14310) @@ -620,4 +620,5 @@ dm.params.seed=false; dm.params.fixed_seed=false; + dm.params.rng=false; dm.params.samples=false; dm.params.sample_type='lhs'; Index: /issm/trunk/src/m/classes/qmu/@dakota_method/dmeth_params_write.m =================================================================== --- /issm/trunk/src/m/classes/qmu/@dakota_method/dmeth_params_write.m (revision 14309) +++ /issm/trunk/src/m/classes/qmu/@dakota_method/dmeth_params_write.m (revision 14310) @@ -350,4 +350,7 @@ param_write(fid,sbeg,'seed',' = ','\n',dm.params); param_write(fid,sbeg,'fixed_seed','','\n',dm.params); + if (str2num(dakotaversion())>4.2) + param_write(fid,sbeg,'rng',' ','\n',dm.params); + end param_write(fid,sbeg,'samples',' = ','\n',dm.params); param_write(fid,sbeg,'sample_type',' ','\n',dm.params); Index: /issm/trunk/src/m/classes/radaroverlay.py =================================================================== --- /issm/trunk/src/m/classes/radaroverlay.py (revision 14309) +++ /issm/trunk/src/m/classes/radaroverlay.py (revision 14310) @@ -24,5 +24,5 @@ # {{{ Display string=' radaroverlay parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'pwr','radar power image (matrix)')) + string="%s\n%s"%(string,fielddisplay(self,'pwr','radar power image (matrix)')) string="%s\n%s"%(string,fielddisplay(self,'x','corresponding x coordinates')) string="%s\n%s"%(string,fielddisplay(self,'y','corresponding y coordinates')) Index: /issm/trunk/src/m/classes/rifts.py =================================================================== --- /issm/trunk/src/m/classes/rifts.py (revision 14309) +++ /issm/trunk/src/m/classes/rifts.py (revision 14310) @@ -29,5 +29,5 @@ string=' rifts parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'riftstruct','structure containing all rift information (vertices coordinates, segments, type of melange, ...)')) + string="%s\n%s"%(string,fielddisplay(self,'riftstruct','structure containing all rift information (vertices coordinates, segments, type of melange, ...)')) string="%s\n%s"%(string,fielddisplay(self,'riftproperties','')) return string Index: /issm/trunk/src/m/classes/settings.m =================================================================== --- /issm/trunk/src/m/classes/settings.m (revision 14309) +++ /issm/trunk/src/m/classes/settings.m (revision 14310) @@ -38,5 +38,5 @@ %onto the model after a parallel run by waiting for the lock file %N minutes that is generated once the solution has converged - %0 to desactivate + %0 to deactivate obj.waitonlock=Inf; end % }}} @@ -65,5 +65,9 @@ WriteData(fid,'object',obj,'fieldname','results_as_patches','format','Boolean'); WriteData(fid,'object',obj,'fieldname','output_frequency','format','Integer'); - WriteData(fid,'object',obj,'fieldname','waitonlock','format','Boolean'); + if obj.waitonlock>0, + WriteData(fid,'enum',SettingsWaitonlockEnum(),'data',true,'format','Boolean'); + else + WriteData(fid,'enum',SettingsWaitonlockEnum(),'data',false,'format','Boolean'); + end end % }}} end Index: /issm/trunk/src/m/classes/settings.py =================================================================== --- /issm/trunk/src/m/classes/settings.py (revision 14309) +++ /issm/trunk/src/m/classes/settings.py (revision 14310) @@ -56,6 +56,6 @@ #onto the model after a parallel run by waiting for the lock file #N minutes that is generated once the solution has converged - #0 to desactivate - self.waitonlock=float('Inf') + #0 to deactivate + self.waitonlock=2**31-1 return self @@ -77,5 +77,8 @@ WriteData(fid,'object',self,'fieldname','results_as_patches','format','Boolean') WriteData(fid,'object',self,'fieldname','output_frequency','format','Integer') - WriteData(fid,'object',self,'fieldname','waitonlock','format','Boolean') + if self.waitonlock>0: + WriteData(fid,'enum',SettingsWaitonlockEnum(),'data',True,'format','Boolean'); + else: + WriteData(fid,'enum',SettingsWaitonlockEnum(),'data',False,'format','Boolean'); # }}} Index: /issm/trunk/src/m/classes/solver.py =================================================================== --- /issm/trunk/src/m/classes/solver.py (revision 14309) +++ /issm/trunk/src/m/classes/solver.py (revision 14310) @@ -3,7 +3,8 @@ from iluasmoptions import * from EnumToString import EnumToString -from MatlabFuncs import * +from fielddisplay import fielddisplay from EnumDefinitions import * from checkfield import * +from MatlabFuncs import * class solver(object): @@ -48,6 +49,5 @@ s ="List of solver options per analysis:\n\n" for analysis in vars(self).iterkeys(): - s+="%s :\n" % analysis - s+="%s\n" % getattr(self,analysis) + s+="%s\n" % fielddisplay(self,analysis,'') return s Index: /issm/trunk/src/m/classes/surfaceforcings.m =================================================================== --- /issm/trunk/src/m/classes/surfaceforcings.m (revision 14309) +++ /issm/trunk/src/m/classes/surfaceforcings.m (revision 14310) @@ -11,12 +11,7 @@ issmbgradients = 0; isdelta18o = 0; - hc = NaN; href = NaN; smbref = NaN; - smb_pos_max = NaN; - smb_pos_min = NaN; - a_pos = NaN; b_pos = NaN; - a_neg = NaN; b_neg = NaN; monthlytemperatures = NaN; @@ -61,12 +56,7 @@ end elseif(obj.issmbgradients) - md = checkfield(md,'surfaceforcings.hc','forcing',1,'NaN',1); md = checkfield(md,'surfaceforcings.href','forcing',1,'NaN',1); md = checkfield(md,'surfaceforcings.smbref','forcing',1,'NaN',1); - md = checkfield(md,'surfaceforcings.smb_pos_max','forcing',1,'NaN',1); - md = checkfield(md,'surfaceforcings.smb_pos_min','forcing',1,'NaN',1); - md = checkfield(md,'surfaceforcings.a_pos','forcing',1,'NaN',1); md = checkfield(md,'surfaceforcings.b_pos','forcing',1,'NaN',1); - md = checkfield(md,'surfaceforcings.a_neg','forcing',1,'NaN',1); md = checkfield(md,'surfaceforcings.b_neg','forcing',1,'NaN',1); else @@ -92,12 +82,7 @@ fielddisplay(obj,'delta18o_surface','surface elevation of the delta18o site, required if pdd is activated and delta18o activated'); fielddisplay(obj,'issmbgradients','is smb gradients method activated (0 or 1, default is 0)'); - fielddisplay(obj,'hc',' elevation of intersection between accumulation and ablation regime required if smb gradients is activated'); fielddisplay(obj,'href',' reference elevation from which deviation is used to calculate SMB adjustment in smb gradients method'); fielddisplay(obj,'smbref',' reference smb from which deviation is calculated in smb gradients method'); - fielddisplay(obj,'smb_pos_max',' maximum value of positive smb required if smb gradients is activated'); - fielddisplay(obj,'smb_pos_min',' minimum value of positive smb required if smb gradients is activated'); - fielddisplay(obj,'a_pos',' intercept of hs - smb regression line for accumulation regime required if smb gradients is activated'); fielddisplay(obj,'b_pos',' slope of hs - smb regression line for accumulation regime required if smb gradients is activated'); - fielddisplay(obj,'a_neg',' intercept of hs - smb regression line for ablation regime required if smb gradients is activated'); fielddisplay(obj,'b_neg',' slope of hs - smb regression line for ablation regime required if smb gradients is activated'); @@ -122,12 +107,7 @@ WriteData(fid,'object',obj,'fieldname','issmbgradients','format','Boolean'); if obj.issmbgradients, - WriteData(fid,'object',obj,'fieldname','hc','format','DoubleMat','mattype',1); WriteData(fid,'object',obj,'fieldname','href','format','DoubleMat','mattype',1); WriteData(fid,'object',obj,'fieldname','smbref','format','DoubleMat','mattype',1); - WriteData(fid,'object',obj,'fieldname','smb_pos_max','format','DoubleMat','mattype',1); - WriteData(fid,'object',obj,'fieldname','smb_pos_min','format','DoubleMat','mattype',1); - WriteData(fid,'object',obj,'fieldname','a_pos','format','DoubleMat','mattype',1); WriteData(fid,'object',obj,'fieldname','b_pos','format','DoubleMat','mattype',1); - WriteData(fid,'object',obj,'fieldname','a_neg','format','DoubleMat','mattype',1); WriteData(fid,'object',obj,'fieldname','b_neg','format','DoubleMat','mattype',1); end Index: /issm/trunk/src/m/classes/surfaceforcings.py =================================================================== --- /issm/trunk/src/m/classes/surfaceforcings.py (revision 14309) +++ /issm/trunk/src/m/classes/surfaceforcings.py (revision 14310) @@ -21,12 +21,7 @@ self.issmbgradients = 0 self.isdelta18o = 0 - self.hc = float('NaN') self.href = float('NaN') self.smbref = float('NaN') - self.smb_pos_max = float('NaN') - self.smb_pos_min = float('NaN') - self.a_pos = float('NaN') self.b_pos = float('NaN') - self.a_neg = float('NaN') self.b_neg = float('NaN') self.monthlytemperatures = float('NaN') @@ -45,5 +40,5 @@ string=" surface forcings parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,'precipitation','surface precipitation [m/yr water eq]')) + string="%s\n%s"%(string,fielddisplay(self,'precipitation','surface precipitation [m/yr water eq]')) string="%s\n%s"%(string,fielddisplay(self,'mass_balance','surface mass balance [m/yr ice eq]')) string="%s\n%s"%(string,fielddisplay(self,'ispdd','is pdd activated (0 or 1, default is 0)')) @@ -57,17 +52,11 @@ string="%s\n%s"%(string,fielddisplay(self,'delta18o_surface','surface elevation of the delta18o site, required if pdd is activated and delta18o activated')) string="%s\n%s"%(string,fielddisplay(self,'issmbgradients','is smb gradients method activated (0 or 1, default is 0)')) - string="%s\n%s"%(string,fielddisplay(self,'hc',' elevation of intersection between accumulation and ablation regime required if smb gradients is activated')) string="%s\n%s"%(string,fielddisplay(self,'href',' reference elevation from which deviation is used to calculate SMB adjustment in smb gradients method')) string="%s\n%s"%(string,fielddisplay(self,'smbref',' reference smb from which deviation is calculated in smb gradients method')) - string="%s\n%s"%(string,fielddisplay(self,'smb_pos_max',' maximum value of positive smb required if smb gradients is activated')) - string="%s\n%s"%(string,fielddisplay(self,'smb_pos_min',' minimum value of positive smb required if smb gradients is activated')) - string="%s\n%s"%(string,fielddisplay(self,'a_pos',' intercept of hs - smb regression line for accumulation regime required if smb gradients is activated')) string="%s\n%s"%(string,fielddisplay(self,'b_pos',' slope of hs - smb regression line for accumulation regime required if smb gradients is activated')) - string="%s\n%s"%(string,fielddisplay(self,'a_neg',' intercept of hs - smb regression line for ablation regime required if smb gradients is activated')) string="%s\n%s"%(string,fielddisplay(self,'b_neg',' slope of hs - smb regression line for ablation regime required if smb gradients is activated')) return string #}}} - def setdefaultparameters(self): # {{{setdefaultparameters @@ -97,12 +86,7 @@ md = checkfield(md,'surfaceforcings.precipitations_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1) elif self.issmbgradients: - md = checkfield(md,'surfaceforcings.hc','forcing',1,'NaN',1) md = checkfield(md,'surfaceforcings.href','forcing',1,'NaN',1) md = checkfield(md,'surfaceforcings.smbref','forcing',1,'NaN',1) - md = checkfield(md,'surfaceforcings.smb_pos_max','forcing',1,'NaN',1) - md = checkfield(md,'surfaceforcings.smb_pos_min','forcing',1,'NaN',1) - md = checkfield(md,'surfaceforcings.a_pos','forcing',1,'NaN',1) md = checkfield(md,'surfaceforcings.b_pos','forcing',1,'NaN',1) - md = checkfield(md,'surfaceforcings.a_neg','forcing',1,'NaN',1) md = checkfield(md,'surfaceforcings.b_neg','forcing',1,'NaN',1) else: @@ -135,12 +119,7 @@ if self.issmbgradients: - WriteData(fid,'object',self,'fieldname','hc','format','DoubleMat','mattype',1) WriteData(fid,'object',self,'fieldname','href','format','DoubleMat','mattype',1) WriteData(fid,'object',self,'fieldname','smbref','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','smb_pos_max','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','smb_pos_min','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','a_pos','format','DoubleMat','mattype',1) WriteData(fid,'object',self,'fieldname','b_pos','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','a_neg','format','DoubleMat','mattype',1) WriteData(fid,'object',self,'fieldname','b_neg','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk/src/m/classes/taoinversion.m =================================================================== --- /issm/trunk/src/m/classes/taoinversion.m (revision 14310) +++ /issm/trunk/src/m/classes/taoinversion.m (revision 14310) @@ -0,0 +1,160 @@ +%INVERSION class definition +% +% Usage: +% taoinversion=taoinversion(); + +classdef taoinversion + properties (SetAccess=public) + iscontrol = 0 + incomplete_adjoint = 0 + control_parameters = NaN + nsteps = 0 + cost_functions = NaN + cost_functions_coefficients = NaN + min_parameters = NaN + max_parameters = NaN + vx_obs = NaN + vy_obs = NaN + vz_obs = NaN + vel_obs = NaN + thickness_obs = NaN + end + methods + function obj = taoinversion(varargin) % {{{ + switch nargin + case 0 + obj=setdefaultparameters(obj); + case 1 + if isa(varargin{1},'inversion'), + disp('converting inversion to taoinversion'); + in=varargin{1}; + obj.iscontrol = in.iscontrol; + obj.incomplete_adjoint = in.incomplete_adjoint; + obj.control_parameters = in.control_parameters; + obj.nsteps = in.nsteps; + obj.cost_functions = in.cost_functions(1,:); %Keep first line only + obj.cost_functions_coefficients = in.cost_functions_coefficients; + obj.min_parameters = in.min_parameters; + obj.max_parameters = in.max_parameters; + obj.vx_obs = in.vx_obs; + obj.vy_obs = in.vy_obs; + obj.vz_obs = in.vz_obs; + obj.vel_obs = in.vel_obs; + obj.thickness_obs = in.thickness_obs; + end + otherwise + error('constructor not supported'); + end + end % }}} + function obj = setdefaultparameters(obj) % {{{ + + %default is incomplete adjoint for now + obj.incomplete_adjoint=1; + + %parameter to be inferred by control methods (only + %drag and B are supported yet) + obj.control_parameters={'FrictionCoefficient'}; + + %number of steps in the control methods + obj.nsteps=20; + + %several responses can be used: + obj.cost_functions=101*ones(obj.nsteps,1); + + end % }}} + function md = checkconsistency(obj,md,solution,analyses) % {{{ + + %Early return + if ~obj.iscontrol, return; end + + num_controls=numel(md.inversion.control_parameters); + num_costfunc=size(md.inversion.cost_functions,2); + + md = checkfield(md,'inversion.iscontrol','values',[0 1]); + md = checkfield(md,'inversion.incomplete_adjoint','values',[0 1]); + md = checkfield(md,'inversion.control_parameters','cell',1,'values',... + {'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'MaterialsRheologyZbar' 'Vx' 'Vy' 'Thickness'}); + md = checkfield(md,'inversion.nsteps','numel',1,'>=',1); + md = checkfield(md,'inversion.cost_functions','size',[1 num_costfunc],'values',[101:105 201 501:506]); + md = checkfield(md,'inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0); + md = checkfield(md,'inversion.min_parameters','size',[md.mesh.numberofvertices num_controls]); + md = checkfield(md,'inversion.max_parameters','size',[md.mesh.numberofvertices num_controls]); + + if solution==BalancethicknessSolutionEnum() + md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1); + elseif solution==WeakBalancethicknessSolutionEnum() + md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1); + else + md = checkfield(md,'inversion.vx_obs','size',[md.mesh.numberofvertices 1],'NaN',1); + md = checkfield(md,'inversion.vy_obs','size',[md.mesh.numberofvertices 1],'NaN',1); + end + end % }}} + function disp(obj) % {{{ + disp(sprintf(' taoinversion parameters:')); + fielddisplay(obj,'iscontrol','is inversion activated?'); + fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?'); + fielddisplay(obj,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'); + fielddisplay(obj,'nsteps','number of optimization searches'); + fielddisplay(obj,'cost_functions','indicate the type of response for each optimization step'); + fielddisplay(obj,'cost_functions_coefficients','cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'); + fielddisplay(obj,'min_parameters','absolute minimum acceptable value of the inversed parameter on each vertex'); + fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex'); + fielddisplay(obj,'vx_obs','observed velocity x component [m/a]'); + fielddisplay(obj,'vy_obs','observed velocity y component [m/a]'); + fielddisplay(obj,'vel_obs','observed velocity magnitude [m/a]'); + fielddisplay(obj,'thickness_obs','observed thickness [m]'); + disp('Available cost functions:'); + disp(' 101: SurfaceAbsVelMisfit'); + disp(' 102: SurfaceRelVelMisfit'); + disp(' 103: SurfaceLogVelMisfit'); + disp(' 104: SurfaceLogVxVyMisfit'); + disp(' 105: SurfaceAverageVelMisfit'); + disp(' 201: ThicknessAbsMisfit'); + disp(' 501: DragCoefficientAbsGradient'); + disp(' 502: RheologyBbarAbsGradient'); + disp(' 503: ThicknessAbsGradient'); + end % }}} + function marshall(obj,fid) % {{{ + + WriteData(fid,'object',obj,'class','inversion','fieldname','iscontrol','format','Boolean'); + WriteData(fid,'enum',InversionTaoEnum(),'data',true,'format','Boolean'); + if ~obj.iscontrol, return; end + WriteData(fid,'object',obj,'class','inversion','fieldname','incomplete_adjoint','format','Boolean'); + WriteData(fid,'object',obj,'class','inversion','fieldname','nsteps','format','Integer'); + WriteData(fid,'object',obj,'class','inversion','fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'class','inversion','fieldname','min_parameters','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'class','inversion','fieldname','max_parameters','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'class','inversion','fieldname','vx_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'class','inversion','fieldname','vy_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'class','inversion','fieldname','vz_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'class','inversion','fieldname','thickness_obs','format','DoubleMat','mattype',1); + + %process control parameters + num_control_parameters=numel(obj.control_parameters); + data=zeros(1,num_control_parameters); + for i=1:num_control_parameters, + data(i)=StringToEnum(obj.control_parameters{i}); + end + WriteData(fid,'data',data,'enum',InversionControlParametersEnum(),'format','DoubleMat','mattype',3); + WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum(),'format','Integer'); + + %process cost functions + num_cost_functions=size(obj.cost_functions,2); + data=obj.cost_functions; + pos=find(data==101); data(pos)=SurfaceAbsVelMisfitEnum(); + pos=find(data==102); data(pos)=SurfaceRelVelMisfitEnum(); + pos=find(data==103); data(pos)=SurfaceLogVelMisfitEnum(); + pos=find(data==104); data(pos)=SurfaceLogVxVyMisfitEnum(); + pos=find(data==105); data(pos)=SurfaceAverageVelMisfitEnum(); + pos=find(data==201); data(pos)=ThicknessAbsMisfitEnum(); + pos=find(data==501); data(pos)=DragCoefficientAbsGradientEnum(); + pos=find(data==502); data(pos)=RheologyBbarAbsGradientEnum(); + pos=find(data==503); data(pos)=ThicknessAbsGradientEnum(); + pos=find(data==504); data(pos)=ThicknessAlongGradientEnum(); + pos=find(data==505); data(pos)=ThicknessAcrossGradientEnum(); + pos=find(data==506); data(pos)=BalancethicknessMisfitEnum(); + WriteData(fid,'data',data,'enum',InversionCostFunctionsEnum(),'format','DoubleMat','mattype',3); + WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer'); + end % }}} + end +end Index: /issm/trunk/src/m/classes/thermal.py =================================================================== --- /issm/trunk/src/m/classes/thermal.py (revision 14309) +++ /issm/trunk/src/m/classes/thermal.py (revision 14310) @@ -32,5 +32,5 @@ # {{{ Display string=' Thermal solution parameters:' - string="%s\n\n%s"%(string,fielddisplay(self,'spctemperature','temperature constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(self,'spctemperature','temperature constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'stabilization','0->no, 1->artificial_diffusivity, 2->SUPG')) string="%s\n%s"%(string,fielddisplay(self,'maxiter','maximum number of non linear iterations')) Index: /issm/trunk/src/m/classes/timestepping.m =================================================================== --- /issm/trunk/src/m/classes/timestepping.m (revision 14309) +++ /issm/trunk/src/m/classes/timestepping.m (revision 14310) @@ -6,9 +6,9 @@ classdef timestepping properties (SetAccess=public) - start_time = 0; - final_time = 0; - time_step = 0; + start_time = 0.; + final_time = 0.; + time_step = 0.; time_adapt = 0; - cfl_coefficient = 0; + cfl_coefficient = 0.; end methods @@ -24,12 +24,12 @@ %time between 2 time steps - obj.time_step=1/2; + obj.time_step=1./2.; %final time - obj.final_time=10*obj.time_step; + obj.final_time=10.*obj.time_step; %time adaptation? obj.time_adapt=0; - obj.cfl_coefficient=.5; + obj.cfl_coefficient=0.5; end % }}} function md = checkconsistency(obj,md,solution,analyses) % {{{ Index: /issm/trunk/src/m/classes/timestepping.py =================================================================== --- /issm/trunk/src/m/classes/timestepping.py (revision 14309) +++ /issm/trunk/src/m/classes/timestepping.py (revision 14310) @@ -16,9 +16,9 @@ def __init__(self): # {{{ Properties - self.start_time = 0 - self.final_time = 0 - self.time_step = 0 + self.start_time = 0. + self.final_time = 0. + self.time_step = 0. self.time_adapt = 0 - self.cfl_coefficient = 0 + self.cfl_coefficient = 0. #set defaults @@ -29,5 +29,5 @@ # {{{ Display string=" timestepping parameters:" - string="%s\n\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yrs]")) + string="%s\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yrs]")) string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yrs]")) string="%s\n%s"%(string,fielddisplay(self,"time_step","length of time steps [yrs]")) @@ -41,12 +41,12 @@ #time between 2 time steps - self.time_step=1/2 + self.time_step=1./2. #final time - self.final_time=10*self.time_step + self.final_time=10.*self.time_step #time adaptation? self.time_adapt=0 - self.cfl_coefficient=.5 + self.cfl_coefficient=0.5 return self Index: /issm/trunk/src/m/consistency/ismodelselfconsistent.m =================================================================== --- /issm/trunk/src/m/consistency/ismodelselfconsistent.m (revision 14309) +++ /issm/trunk/src/m/consistency/ismodelselfconsistent.m (revision 14310) @@ -69,4 +69,8 @@ analyses=[BalancethicknessAnalysisEnum()]; + case WeakBalancethicknessSolutionEnum(), + numanalyses=1; + analyses=[BalancethicknessAnalysisEnum()]; + case SurfaceSlopeSolutionEnum(), numanalyses=1; Index: /issm/trunk/src/m/contrib/bamg/YamsCall.m =================================================================== --- /issm/trunk/src/m/contrib/bamg/YamsCall.m (revision 14309) +++ /issm/trunk/src/m/contrib/bamg/YamsCall.m (revision 14310) @@ -16,5 +16,5 @@ %2d geometric parameter (do not change) -scale=2/9; +scale=2./9.; %Compute Hessian @@ -60,5 +60,5 @@ triangles=[]; for i=1:size(md.rifts.riftstruct,1), - triangles=[triangles md.rifts(i).segments(:,3)']; + triangles=[triangles md.rifts(i).riftstruct.segments(:,3)']; end @@ -76,5 +76,5 @@ %windows system(['yams2-win -O 1 -v -0 -ecp -hgrad ' num2str(gradation) ' carre0 carre1']); -elseif ismac +elseif ismac() %Macosx system(['yams2-osx -O 1 -v -0 -ecp -hgrad ' num2str(gradation) ' carre0 carre1']); Index: /issm/trunk/src/m/contrib/bamg/YamsCall.py =================================================================== --- /issm/trunk/src/m/contrib/bamg/YamsCall.py (revision 14310) +++ /issm/trunk/src/m/contrib/bamg/YamsCall.py (revision 14310) @@ -0,0 +1,128 @@ +import numpy +import time +import subprocess +import os +from ComputeHessian import * +from ComputeMetric import * +from MatlabFuncs import * + +def YamsCall(md,field,hmin,hmax,gradation,epsilon): + """ + YAMSCALL - call yams + + build a metric using the Hessian of the given field + call Yams and the output mesh is plugged onto the model + -hmin = minimum edge length (m) + -hmax = maximum edge length (m) + -gradation = maximum edge length gradation between 2 elements + -epsilon = average error on each element (m/yr) + + Usage: + md=YamsCall(md,field,hmin,hmax,gradation,epsilon); + + Example: + md=YamsCall(md,md.inversion.vel_obs,1500,10^8,1.3,0.9); + """ + + #2d geometric parameter (do not change) + scale=2./9. + + #Compute Hessian + t1=time.time() + print "%s" % ' computing Hessian...' + hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node') + t2=time.time() + print "%s%d%s\n" % (' done (',t2-t1,' seconds)') + + #Compute metric + t1=time.time() + print "%s" % ' computing metric...' + if numpy.size(md.mask.vertexonwater)==md.mesh.numberofvertices: + pos=numpy.nonzero(md.mask.vertexonwater)[0] + else: + pos=numpy.empty(0,int) + metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos) + t2=time.time() + print "%s%d%s\n" % (' done (',t2-t1,' seconds)') + + #write files + t1=time.time() + print "%s" % ' writing initial mesh files...' + numpy.savetxt('carre0.met',metric) + + f=open('carre0.mesh','w') + + #initialiation + f.write("\n%s\n%i\n" % ('MeshVersionFormatted',1)) + + #dimension + f.write("\n%s\n%i\n" % ('Dimension',2)) + + #Vertices + f.write("\n%s\n%i\n\n" % ('Vertices',md.mesh.numberofvertices)) + for i in xrange(0,md.mesh.numberofvertices): + f.write("%8g %8g %i\n" % (md.mesh.x[i],md.mesh.y[i],0)) + + #Triangles + f.write("\n\n%s\n%i\n\n" % ('Triangles',md.mesh.numberofelements)) + for i in xrange(0,md.mesh.numberofelements): + f.write("%i %i %i %i\n" % (md.mesh.elements[i,0],md.mesh.elements[i,1],md.mesh.elements[i,2],0)) + numberofelements1=md.mesh.numberofelements + + #Deal with rifts + if numpy.any(not numpy.isnan(md.rifts.riftstruct)): + + #we have the list of triangles that make up the rift. keep those triangles around during refinement. + triangles=numpy.empty(0,int) + for riftstruct in md.rifts.riftstruct: + triangles=numpy.concatenate((triangles,riftstruct.segments[:,2])) + + f.write("\n\n%s\n%i\n\n" % ('RequiredTriangles',numpy.size(triangles))) + for triangle in triangles: + f.write("%i\n" % triangle) + + #close + f.close() + t2=time.time() + print "%s%d%s\n" % (' done (',t2-t1,' seconds)') + + #call yams + print "%s\n" % ' call Yams...' + if ispc(): + #windows + subprocess.call('yams2-win -O 1 -v -0 -ecp -hgrad %g carre0 carre1' % gradation,shell=True) + elif ismac(): + #Macosx + subprocess.call('yams2-osx -O 1 -v -0 -ecp -hgrad %g carre0 carre1' % gradation,shell=True) + else: + #Linux + subprocess.call('yams2-linux -O 1 -v -0 -ecp -hgrad %g carre0 carre1' % gradation,shell=True) + + #plug new mesh + t1=time.time() + print "\n%s" % ' reading final mesh files...' + Tria=numpy.loadtxt('carre1.tria',int) + Coor=numpy.loadtxt('carre1.coor',float) + md.mesh.x=Coor[:,0] + md.mesh.y=Coor[:,1] + md.mesh.z=numpy.zeros((numpy.size(Coor,axis=0),1)) + md.mesh.elements=Tria + md.mesh.numberofvertices=numpy.size(Coor,axis=0) + md.mesh.numberofelements=numpy.size(Tria,axis=0) + numberofelements2=md.mesh.numberofelements + t2=time.time() + print "%s%d%s\n\n" % (' done (',t2-t1,' seconds)') + + #display number of elements + print "\n%s %i" % (' inital number of elements:',numberofelements1) + print "\n%s %i\n\n" % (' new number of elements:',numberofelements2) + + #clean up: + os.remove('carre0.mesh') + os.remove('carre0.met') + os.remove('carre1.tria') + os.remove('carre1.coor') + os.remove('carre1.meshb') + + return md + Index: /issm/trunk/src/m/enum/AndroidFrictionCoefficientEnum.m =================================================================== --- /issm/trunk/src/m/enum/AndroidFrictionCoefficientEnum.m (revision 14310) +++ /issm/trunk/src/m/enum/AndroidFrictionCoefficientEnum.m (revision 14310) @@ -0,0 +1,11 @@ +function macro=AndroidFrictionCoefficientEnum() +%ANDROIDFRICTIONCOEFFICIENTENUM - Enum of AndroidFrictionCoefficient +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=AndroidFrictionCoefficientEnum() + +macro=StringToEnum('AndroidFrictionCoefficient'); Index: /issm/trunk/src/m/enum/BalancethicknessMisfitEnum.m =================================================================== --- /issm/trunk/src/m/enum/BalancethicknessMisfitEnum.m (revision 14310) +++ /issm/trunk/src/m/enum/BalancethicknessMisfitEnum.m (revision 14310) @@ -0,0 +1,11 @@ +function macro=BalancethicknessMisfitEnum() +%BALANCETHICKNESSMISFITENUM - Enum of BalancethicknessMisfit +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=BalancethicknessMisfitEnum() + +macro=StringToEnum('BalancethicknessMisfit'); Index: /issm/trunk/src/m/enum/EnumDefinitions.py =================================================================== --- /issm/trunk/src/m/enum/EnumDefinitions.py (revision 14309) +++ /issm/trunk/src/m/enum/EnumDefinitions.py (revision 14310) @@ -1849,14 +1849,4 @@ return StringToEnum('SurfaceforcingsMonthlytemperatures')[0] -def SurfaceforcingsHcEnum(): - """ - SURFACEFORCINGSHCENUM - Enum of SurfaceforcingsHc - - Usage: - macro=SurfaceforcingsHcEnum() - """ - - return StringToEnum('SurfaceforcingsHc')[0] - def SurfaceforcingsHrefEnum(): """ @@ -1879,34 +1869,4 @@ return StringToEnum('SurfaceforcingsSmbref')[0] -def SurfaceforcingsSmbPosMaxEnum(): - """ - SURFACEFORCINGSSMBPOSMAXENUM - Enum of SurfaceforcingsSmbPosMax - - Usage: - macro=SurfaceforcingsSmbPosMaxEnum() - """ - - return StringToEnum('SurfaceforcingsSmbPosMax')[0] - -def SurfaceforcingsSmbPosMinEnum(): - """ - SURFACEFORCINGSSMBPOSMINENUM - Enum of SurfaceforcingsSmbPosMin - - Usage: - macro=SurfaceforcingsSmbPosMinEnum() - """ - - return StringToEnum('SurfaceforcingsSmbPosMin')[0] - -def SurfaceforcingsAPosEnum(): - """ - SURFACEFORCINGSAPOSENUM - Enum of SurfaceforcingsAPos - - Usage: - macro=SurfaceforcingsAPosEnum() - """ - - return StringToEnum('SurfaceforcingsAPos')[0] - def SurfaceforcingsBPosEnum(): """ @@ -1919,14 +1879,4 @@ return StringToEnum('SurfaceforcingsBPos')[0] -def SurfaceforcingsANegEnum(): - """ - SURFACEFORCINGSANEGENUM - Enum of SurfaceforcingsANeg - - Usage: - macro=SurfaceforcingsANegEnum() - """ - - return StringToEnum('SurfaceforcingsANeg')[0] - def SurfaceforcingsBNegEnum(): """ @@ -2219,4 +2169,24 @@ return StringToEnum('BalancethicknessSolution')[0] +def WeakBalancethicknessAnalysisEnum(): + """ + WEAKBALANCETHICKNESSANALYSISENUM - Enum of WeakBalancethicknessAnalysis + + Usage: + macro=WeakBalancethicknessAnalysisEnum() + """ + + return StringToEnum('WeakBalancethicknessAnalysis')[0] + +def WeakBalancethicknessSolutionEnum(): + """ + WEAKBALANCETHICKNESSSOLUTIONENUM - Enum of WeakBalancethicknessSolution + + Usage: + macro=WeakBalancethicknessSolutionEnum() + """ + + return StringToEnum('WeakBalancethicknessSolution')[0] + def BedSlopeAnalysisEnum(): """ @@ -3299,4 +3269,14 @@ return StringToEnum('Adjointz')[0] +def BalancethicknessMisfitEnum(): + """ + BALANCETHICKNESSMISFITENUM - Enum of BalancethicknessMisfit + + Usage: + macro=BalancethicknessMisfitEnum() + """ + + return StringToEnum('BalancethicknessMisfit')[0] + def BedSlopeXEnum(): """ @@ -3569,4 +3549,14 @@ return StringToEnum('QmuMelting')[0] +def AndroidFrictionCoefficientEnum(): + """ + ANDROIDFRICTIONCOEFFICIENTENUM - Enum of AndroidFrictionCoefficient + + Usage: + macro=AndroidFrictionCoefficientEnum() + """ + + return StringToEnum('AndroidFrictionCoefficient')[0] + def ResetPenaltiesEnum(): """ @@ -3999,14 +3989,4 @@ return StringToEnum('TransientInput')[0] -def OutputfilenameEnum(): - """ - OUTPUTFILENAMEENUM - Enum of Outputfilename - - Usage: - macro=OutputfilenameEnum() - """ - - return StringToEnum('Outputfilename')[0] - def WaterfractionEnum(): """ @@ -4997,4 +4977,4 @@ """ - return 498 - + return 496 + Index: /issm/trunk/src/m/enum/MaximumNumberOfEnums.m =================================================================== --- /issm/trunk/src/m/enum/MaximumNumberOfEnums.m (revision 14309) +++ /issm/trunk/src/m/enum/MaximumNumberOfEnums.m (revision 14310) @@ -9,3 +9,3 @@ % macro=MaximumNumberOfEnums() -macro=498; +macro=496; Index: /issm/trunk/src/m/enum/OutputFileNameEnum.m =================================================================== --- /issm/trunk/src/m/enum/OutputFileNameEnum.m (revision 14310) +++ /issm/trunk/src/m/enum/OutputFileNameEnum.m (revision 14310) @@ -0,0 +1,11 @@ +function macro=OutputFileNameEnum() +%OUTPUTFILENAMEENUM - Enum of OutputFileName +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=OutputFileNameEnum() + +macro=StringToEnum('OutputFileName'); Index: sm/trunk/src/m/enum/OutputfilenameEnum.m =================================================================== --- /issm/trunk/src/m/enum/OutputfilenameEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=OutputFileNameEnum() -%OUTPUTFILENAMEENUM - Enum of OutputFileName -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=OutputFileNameEnum() - -macro=StringToEnum('OutputFileName'); Index: sm/trunk/src/m/enum/SurfaceforcingsANegEnum.m =================================================================== --- /issm/trunk/src/m/enum/SurfaceforcingsANegEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SurfaceforcingsANegEnum() -%SURFACEFORCINGSANEGENUM - Enum of SurfaceforcingsANeg -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=SurfaceforcingsANegEnum() - -macro=StringToEnum('SurfaceforcingsANeg'); Index: sm/trunk/src/m/enum/SurfaceforcingsAPosEnum.m =================================================================== --- /issm/trunk/src/m/enum/SurfaceforcingsAPosEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SurfaceforcingsAPosEnum() -%SURFACEFORCINGSAPOSENUM - Enum of SurfaceforcingsAPos -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=SurfaceforcingsAPosEnum() - -macro=StringToEnum('SurfaceforcingsAPos'); Index: sm/trunk/src/m/enum/SurfaceforcingsHcEnum.m =================================================================== --- /issm/trunk/src/m/enum/SurfaceforcingsHcEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SurfaceforcingsHcEnum() -%SURFACEFORCINGSHCENUM - Enum of SurfaceforcingsHc -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=SurfaceforcingsHcEnum() - -macro=StringToEnum('SurfaceforcingsHc'); Index: sm/trunk/src/m/enum/SurfaceforcingsSmbPosMaxEnum.m =================================================================== --- /issm/trunk/src/m/enum/SurfaceforcingsSmbPosMaxEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SurfaceforcingsSmbPosMaxEnum() -%SURFACEFORCINGSSMBPOSMAXENUM - Enum of SurfaceforcingsSmbPosMax -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=SurfaceforcingsSmbPosMaxEnum() - -macro=StringToEnum('SurfaceforcingsSmbPosMax'); Index: sm/trunk/src/m/enum/SurfaceforcingsSmbPosMinEnum.m =================================================================== --- /issm/trunk/src/m/enum/SurfaceforcingsSmbPosMinEnum.m (revision 14309) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=SurfaceforcingsSmbPosMinEnum() -%SURFACEFORCINGSSMBPOSMINENUM - Enum of SurfaceforcingsSmbPosMin -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=SurfaceforcingsSmbPosMinEnum() - -macro=StringToEnum('SurfaceforcingsSmbPosMin'); Index: /issm/trunk/src/m/enum/WeakBalancethicknessAnalysisEnum.m =================================================================== --- /issm/trunk/src/m/enum/WeakBalancethicknessAnalysisEnum.m (revision 14310) +++ /issm/trunk/src/m/enum/WeakBalancethicknessAnalysisEnum.m (revision 14310) @@ -0,0 +1,11 @@ +function macro=WeakBalancethicknessAnalysisEnum() +%WEAKBALANCETHICKNESSANALYSISENUM - Enum of WeakBalancethicknessAnalysis +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=WeakBalancethicknessAnalysisEnum() + +macro=StringToEnum('WeakBalancethicknessAnalysis'); Index: /issm/trunk/src/m/enum/WeakBalancethicknessSolutionEnum.m =================================================================== --- /issm/trunk/src/m/enum/WeakBalancethicknessSolutionEnum.m (revision 14310) +++ /issm/trunk/src/m/enum/WeakBalancethicknessSolutionEnum.m (revision 14310) @@ -0,0 +1,11 @@ +function macro=WeakBalancethicknessSolutionEnum() +%WEAKBALANCETHICKNESSSOLUTIONENUM - Enum of WeakBalancethicknessSolution +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=WeakBalancethicknessSolutionEnum() + +macro=StringToEnum('WeakBalancethicknessSolution'); Index: /issm/trunk/src/m/exp/expwrite.m =================================================================== --- /issm/trunk/src/m/exp/expwrite.m (revision 14309) +++ /issm/trunk/src/m/exp/expwrite.m (revision 14310) @@ -15,4 +15,16 @@ % See also EXPDOC, EXPREAD, EXPWRITEASVERTICES +%check input variable +if ~isstruct(a), + error('first argument is not a structure'); +end + +%Add density if it's not there +if ~isfield(a,'density'), + for n=1:length(a), + a(n).density=1; + end +end + fid=fopen(filename,'w'); for n=1:length(a), @@ -22,11 +34,7 @@ if isfield(a,'name'), - if ~isempty(a(n).name), - fprintf(fid,'%s%s\n','## Name:',a(n).name); - else - fprintf(fid,'%s\n','## Name:'); - end + fprintf(fid,'%s%s\n','## Name:',a(n).name); else - fprintf(fid,'%s\n','## Name:'); + fprintf(fid,'%s%s\n','## Name:',filename); end @@ -35,5 +43,5 @@ fprintf(fid,'%i %f\n',[length(a(n).x) a(n).density]); fprintf(fid,'%s\n','# X pos Y pos'); - fprintf(fid,'%10.10f %10.10f\n',[a(n).x a(n).y]'); + fprintf(fid,'%10.10f %10.10f\n',[a(n).x(:) a(n).y(:)]'); fprintf(fid,'\n'); Index: /issm/trunk/src/m/exp/expwrite.py =================================================================== --- /issm/trunk/src/m/exp/expwrite.py (revision 14309) +++ /issm/trunk/src/m/exp/expwrite.py (revision 14310) @@ -25,11 +25,12 @@ if 'name' in contour: - if contour['name']: - fid.write("%s%s\n" % ('## Name:',contour['name'])) - else: - fid.write("%s\n" % '## Name:') + fid.write("%s%s\n" % ('## Name:',contour['name'])) else: - fid.write("%s\n" % '## Name:') + fid.write("%s%s\n" % ('## Name:',filename)) + #Add density if it's not there + if 'density' not in contour: + contour['density']=1 + fid.write("%s\n" % '## Icon:0') fid.write("%s\n" % '# Points Count Value') Index: /issm/trunk/src/m/exp/flowlines.m =================================================================== --- /issm/trunk/src/m/exp/flowlines.m (revision 14309) +++ /issm/trunk/src/m/exp/flowlines.m (revision 14310) @@ -38,5 +38,6 @@ %check seed points -tria=TriaSearch(index,x,y,x0,y0); +%tria=TriaSearch(index,x,y,x0,y0); +tria=tsearch(x,y,index,x0,y0); pos=find(isnan(tria)); x0(pos)=[]; @@ -69,5 +70,6 @@ %find current triangle queue=find(~done); - tria=TriaSearch(index,x,y,X(queue),Y(queue)); + %tria=TriaSearch(index,x,y,X(queue),Y(queue)); + tria=tsearch(x,y,index,X(queue),Y(queue)); %check that the point is actually inside a triangle of the mesh @@ -118,5 +120,6 @@ %find current triangle queue=find(~done); - tria=TriaSearch(index,x,y,X(queue),Y(queue)); + %tria=TriaSearch(index,x,y,X(queue),Y(queue)); + tria=tsearch(x,y,index,X(queue),Y(queue)); %check that the point is actually inside a triangle of the mesh Index: /issm/trunk/src/m/geometry/FlagElements.py =================================================================== --- /issm/trunk/src/m/geometry/FlagElements.py (revision 14309) +++ /issm/trunk/src/m/geometry/FlagElements.py (revision 14310) @@ -4,4 +4,5 @@ from ContourToMesh import * from MatlabFuncs import * +from PythonFuncs import * def FlagElements(md,region): @@ -43,9 +44,9 @@ raise RuntimeError("FlagElements.py calling basinzoom.py is not complete.") xlim,ylim=basinzoom('basin',region) - flag_nodes=numpy.logical_and(numpy.logical_and(md.mesh.xxlim[0]),numpy.logical_and(md.mesh.yylim[0])) + flag_nodes=logical_and_n(md.mesh.xxlim[0],md.mesh.yylim[0]) flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1).astype(bool) else: #ok, flag elements - [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3].copy(),md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) + [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3].copy(),md.mesh.x,md.mesh.y,region,'element',1) flag=flag.astype(bool) Index: /issm/trunk/src/m/io/getShapeTypeInfo.m =================================================================== --- /issm/trunk/src/m/io/getShapeTypeInfo.m (revision 14310) +++ /issm/trunk/src/m/io/getShapeTypeInfo.m (revision 14310) @@ -0,0 +1,181 @@ +function result = getShapeTypeInfo(shapeTypeCode,requestOrQuery) + +% CAUTION: This file contains experimental code that has had only +% minimal, informal testing. +% +%GETSHAPETYPEINFO Get information about a shape type. +% Returns a single value, based on the second argument: +% 'TypeString' -- Return a string +% 'IsValid' -- Return a scalar logical +% 'IsSupported' -- Return a scalar logical +% 'BoundingBoxSubscripts' -- Return a 1-by-n double array +% 'ShapeRecordReadFcn' -- Return a function handle +% 'ShapeDataFieldNames' -- Return a cell array of string. + +% Copyright 1996-2010 The MathWorks, Inc. +% $Revision$ $Date$ + +lutFields = { 'TypeCode',... + 'TypeString',... + 'IsValid',... + 'IsSupported',... + 'BoundingBoxSubscripts',... + 'ShapeRecordReadFcn',... + 'ShapeDataFieldNames' }; + +% Three kinds of bounding box subscripts +bbs2D = [1 2; 3 4]; +bbsZ = [1 2 5; 3 4 6]; % Ignore M for now, otherwise use [1 2 5 7; 3 4 6 8] +bbsM = [1 2 7; 3 4 8]; + +typeLUT = {... + -1, 'Not Valid', false, false, [], [], {''};... + 0, 'Null Shape', true, true, [], [], {''};... + 1, 'Point', true, true, bbs2D, @readPoint, {'Geometry','X','Y'};... + 3, 'PolyLine', true, true, bbs2D, @readPolyLine, {'Geometry','BoundingBox','X','Y'};... + 5, 'Polygon', true, true, bbs2D, @readPolygon, {'Geometry','BoundingBox','X','Y'};... + 8, 'MultiPoint', true, true, bbs2D, @readMultiPoint, {'Geometry','BoundingBox','X','Y'};... + 11, 'PointZ', true, false, bbsZ, [], {''};... + 13, 'PolyLineZ', true, true, bbsZ, @readPolyLineZ, {'Geometry','BoundingBox','X','Y','Z'};... + 15, 'PolygonZ', true, true, bbsZ, @readPolygonZ, {'Geometry','BoundingBox','X','Y','Z'};... + 18, 'MultiPointZ', true, false, bbsZ, [], {''};... + 21, 'PointM', true, false, bbsM, [], {''};... + 23, 'PolyLineM', true, false, bbsM, [], {''};... + 25, 'PolygonM', true, false, bbsM, [], {''};... + 28, 'MultiPointM', true, false, bbsM, [], {''};... + 31, 'MultiPatch', true, false, bbsZ, [], {''};... + }; +notValidRow = 1; +types = [typeLUT{:,1}]; + +% MAINTENANCE NOTE: To add support for additional types, add more rows +% to the type look up table (typeLUT), but be sure to keep 'Not Valid' +% in the first row. + +row = find(shapeTypeCode == types); +if length(row) ~= 1 + row = notValidRow; +end + +col = strmatch(lower(requestOrQuery),lower(lutFields)); +if length(col) ~= 1; + eid = sprintf('%s:%s:internalProblem',getcomp,mfilename); + error(eid,'Internal error: Invalid second argument in private function.'); +end + +result = typeLUT{row,col}; + +%--------------------------------------------------------------------------- +function shp = readPoint(fid) + +point = fread(fid,[2 1],'double','ieee-le'); +shp = {'Point', point(1), point(2)}; + +%--------------------------------------------------------------------------- +function shp = readMultiPoint(fid) + +boundingBox = fread(fid,4,'double','ieee-le'); +numPoints = fread(fid,1,'uint32','ieee-le'); +points = fread(fid,[2 numPoints],'double','ieee-le')'; +shp = {'MultiPoint', boundingBox([1 2; 3 4]), points(:,1)', points(:,2)'}; + +%--------------------------------------------------------------------------- +function shp = readPolyLine(fid) + +boundingBox = fread(fid,4,'double','ieee-le'); +numPartsPoints = fread(fid,2,'uint32','ieee-le'); +partOffsets = fread(fid,[1 numPartsPoints(1)],'uint32','ieee-le'); +points = fread(fid,[2 numPartsPoints(2)],'double','ieee-le')'; +[x,y] = organizeParts2D(partOffsets,points); +shp = {'Line', boundingBox([1 2; 3 4]), x, y}; + +%--------------------------------------------------------------------------- +function shp = readPolygon(fid) + +boundingBox = fread(fid,4,'double','ieee-le'); +numPartsPoints = fread(fid,2,'uint32','ieee-le'); +partOffsets = fread(fid,[1 numPartsPoints(1)],'uint32','ieee-le'); +points = fread(fid,[2 numPartsPoints(2)],'double','ieee-le')'; +[x,y] = organizeParts2D(partOffsets,points); +shp = {'Polygon', boundingBox([1 2; 3 4]), x, y}; + +%--------------------------------------------------------------------------- +function [x,y] = organizeParts2D(partOffsets,points) + +numParts = size(partOffsets,2); +numPoints = size(points,1); +% Initialize x and y to be row vectors of NaN +% with length numPoints * numParts +x = NaN + zeros(1, numPoints + numParts); +y = x; +if numParts == 1 + x(1, 1:numPoints) = points(:,1); + y(1, 1:numPoints) = points(:,2); +else + partStart = 1 + partOffsets; + partEnd = [partOffsets(2:end) numPoints]; + for k = 1:numParts + xyStart = partStart(k) + (k - 1); + xyEnd = partEnd(k) + (k - 1); + x(1, xyStart:xyEnd) = points(partStart(k):partEnd(k), 1); + y(1, xyStart:xyEnd) = points(partStart(k):partEnd(k), 2); + end +end + +%--------------------------------------------------------------------------- +function shp = readPolyLineZ(fid) + +boundingBox = fread(fid,4,'double','ieee-le'); +numPartsPoints = fread(fid,2,'uint32','ieee-le'); +partOffsets = fread(fid,[1 numPartsPoints(1)],'uint32','ieee-le'); +points = fread(fid,[2 numPartsPoints(2)],'double','ieee-le')'; +zRange = fread(fid,2,'double','ieee-le'); %#ok +zArray = fread(fid, numPartsPoints(2), 'double', 'ieee-le'); +[x,y,z] = organizeParts3D(partOffsets,points,zArray); +% shp = {'Line', [boundingBox([1 2; 3 4]) zRange], x, y, z}; +% Note: +% Keep bounding box 2-D for now for compatibility with +% mapshow and geoshow. +shp = {'Line', boundingBox([1 2; 3 4]), x, y, z}; + +%--------------------------------------------------------------------------- +function shp = readPolygonZ(fid) + +boundingBox = fread(fid,4,'double','ieee-le'); +numPartsPoints = fread(fid,2,'uint32','ieee-le'); +partOffsets = fread(fid,[1 numPartsPoints(1)],'uint32','ieee-le'); +points = fread(fid,[2 numPartsPoints(2)],'double','ieee-le')'; +zRange = fread(fid,2,'double','ieee-le'); %#ok +zArray = fread(fid, numPartsPoints(2), 'double', 'ieee-le'); +[x,y,z] = organizeParts3D(partOffsets,points,zArray); +% shp = {'Polygon', [boundingBox([1 2; 3 4]) zRange], x, y, z}; +% Note: +% Keep bounding box 2-D for now for compatibility with +% mapshow and geoshow. +shp = {'Polygon', boundingBox([1 2; 3 4]), x, y, z}; + +%--------------------------------------------------------------------------- +function [x,y,z] = organizeParts3D(partOffsets,points,zArray) + +numParts = size(partOffsets,2); +numPoints = size(points,1); +% Initialize x and y to be row vectors of NaN +% with length numPoints * numParts +x = NaN + zeros(1, numPoints + numParts); +y = x; +z = x; +if numParts == 1 + x(1, 1:numPoints) = points(:,1); + y(1, 1:numPoints) = points(:,2); + z(1, 1:numPoints) = zArray(:,1); +else + partStart = 1 + partOffsets; + partEnd = [partOffsets(2:end) numPoints]; + for k = 1:numParts + xyzStart = partStart(k) + (k - 1); + xyzEnd = partEnd(k) + (k - 1); + x(1, xyzStart:xyzEnd) = points(partStart(k):partEnd(k), 1); + y(1, xyzStart:xyzEnd) = points(partStart(k):partEnd(k), 2); + z(1, xyzStart:xyzEnd) = zArray(partStart(k):partEnd(k), 1); + end +end Index: sm/trunk/src/m/kml/exp2kml.m =================================================================== --- /issm/trunk/src/m/kml/exp2kml.m (revision 14309) +++ (revision ) @@ -1,17 +1,0 @@ -function exp2kml(input,output) -%EXP2KML: transform Argus exp file to kml -% -% Usage: exp2kml('temp.exp','temp2.kml') -% -% - -%First, read exp file -domain=expread(input); - -%then transform: -string=ge_plot(domain.x,domain.y,'name',domain.name); - -%open kml file for writing: -fid=fopen(output,'w'); -fprintf(fid,'%s',string); -fclose(fid); Index: /issm/trunk/src/m/mech/mechanicalproperties.m =================================================================== --- /issm/trunk/src/m/mech/mechanicalproperties.m (revision 14309) +++ /issm/trunk/src/m/mech/mechanicalproperties.m (revision 14310) @@ -119,10 +119,10 @@ strainrate=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]); -strainrate.xx=ux; -strainrate.yy=vy; -strainrate.xy=uyvx; -strainrate.principalvalue1=valuesstrain(:,1)*(365.25*24*3600); %strain rate in 1/a instead of 1/s +strainrate.xx=ux*md.constants.yts; %strain rate in 1/a instead of 1/s +strainrate.yy=vy*md.constants.yts; +strainrate.xy=uyvx*md.constants.yts; +strainrate.principalvalue1=valuesstrain(:,1)*md.constants.yts; strainrate.principalaxis1=directionsstrain(:,1:2); -strainrate.principalvalue2=valuesstrain(:,2)*(365.25*24*3600); %strain rate in 1/a instead of 1/s +strainrate.principalvalue2=valuesstrain(:,2)*md.constants.yts; strainrate.principalaxis2=directionsstrain(:,3:4); strainrate.effectivevalue=1/sqrt(2)*sqrt(strainrate.xx.^2+strainrate.yy.^2+2*strainrate.xy.^2); Index: /issm/trunk/src/m/mech/strainrateuncert.m =================================================================== --- /issm/trunk/src/m/mech/strainrateuncert.m (revision 14310) +++ /issm/trunk/src/m/mech/strainrateuncert.m (revision 14310) @@ -0,0 +1,71 @@ +function md=strainratuncert(md,vx,vy,dvx,dvy) +%STRAINRATEUNCERT - compute uncertainty in strain rate components +% +% this routine computes the uncertainties in the strain rate tensor +% components given the uncertainty in surface velocity data. +% The results are stored in md.results +% +% 'dvx' and 'dvy' are velocity errors in x and y components. These +% can either be scalars or arrays of length md.mesh.numberofvertices +% +% Usage: +% md=strainrateuncert(md,vx,vy,dv) +% +% Example: +% md=mechanicalproperties(md,md.initialization.vx,md.initialization.vy,5); +% md=mechanicalproperties(md,md.inversion.vx_obs,md.inversion.vy_obs,dv); + +%some checks +if length(vx)~=md.mesh.numberofvertices | length(vy)~=md.mesh.numberofvertices, + error(['the input velocity should be of size ' num2str(md.mesh.numberofvertices) '!']) +end +if length(dvx)==1, + dvx=dvx*ones(md.mesh.numberofelements,1); +end +if length(dvx)~=md.mesh.numberofelements, + error(['the velocity error dvx should be of size ' num2str(md.mesh.numberofelements) ' or 1!']) +end +if length(dvy)==1, + dvy=dvy*ones(md.mesh.numberofelements,1); +end +if length(dvy)~=md.mesh.numberofelements, + error(['the velocity error dvy should be of size ' num2str(md.mesh.numberofelements) ' or 1!']) +end +if ~(md.mesh.dimension==2) + error('only 2d model supported yet'); +end +if any(md.flowequation.element_equation~=2), + disp('Warning: the model has some non macayeal elements. These will be treated like MacAyeal''s elements'); +end + +%initialization +index=md.mesh.elements; +summation=[1;1;1]; + +%compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma +[alpha beta]=GetNodalFunctionsCoeff(index,md.mesh.x,md.mesh.y); + +strainrateuncert=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalvalue2',[],'effectivevalue',[]); + +strainrateuncert.xx=dvx.*sqrt(alpha.^2*summation); +strainrateuncert.yy=dvy.*sqrt(beta.^2*summation); +strainrateuncert.xy=0.5*sqrt(dvx.^2.*(beta.^2*summation)+dvy.^2.*(alpha.^2*summation)); + +exx=md.results.strainrate.xx; +eyy=md.results.strainrate.yy; +exy=md.results.strainrate.xy; +p1a=strainrateuncert.xx.*(0.5+0.25*(0.5*((exx-eyy)/2).^2+exy.^2).^(-1./2).*(exx-eyy)); +p2a=strainrateuncert.yy.*(0.5-0.25*(0.5*((exx-eyy)/2).^2+exy.^2).^(-1./2).*(exx-eyy)); +p3a=strainrateuncert.xy.*(((exx-eyy)/2).^(2)+exy.^2).^(-1./2).*exy; +p1b=strainrateuncert.xx.*(0.5-0.25*(0.5*((exx-eyy)/2).^2+exy.^2).^(-1./2).*(exx-eyy)); +p2b=strainrateuncert.yy.*(0.5+0.25*(0.5*((exx-eyy)/2).^2+exy.^2).^(-1./2).*(exx-eyy)); +p3b=strainrateuncert.xy.*(-(((exx-eyy)/2).^(2)+exy.^2).^(-1./2).*exy); +strainrateuncert.principalvalue1=sqrt(p1a.^2+p2a.^2+p3a.^2); +strainrateuncert.principalvalue2=sqrt(p1b.^2+p2b.^2+p3b.^2); + +effa=strainrateuncert.xx/sqrt(2).*(exx.^2+eyy.^2+2*exy.^2).^(-1./2).*exx; +effb=strainrateuncert.yy/sqrt(2).*(exx.^2+eyy.^2+2*exy.^2).^(-1./2).*eyy; +effc=2*strainrateuncert.xy/sqrt(2).*(exx.^2+eyy.^2+2*exy.^2).^(-1./2).*exy; +strainrateuncert.effectivevalue=sqrt(effa.^2+effb.^2+effc.^2); + +md.results.strainrateuncert=strainrateuncert; Index: /issm/trunk/src/m/mesh/ComputeMetric.m =================================================================== --- /issm/trunk/src/m/mesh/ComputeMetric.m (revision 14309) +++ /issm/trunk/src/m/mesh/ComputeMetric.m (revision 14310) @@ -13,7 +13,7 @@ lambda1=0.5*((a+d)+sqrt(4.*b.^2+(a-d).^2)); lambda2=0.5*((a+d)-sqrt(4.*b.^2+(a-d).^2)); -pos1=find(lambda1==0); -pos2=find(lambda2==0); -pos3=find(b==0 & lambda1==lambda2); +pos1=find(lambda1==0.); +pos2=find(lambda2==0.); +pos3=find(b==0. & lambda1==lambda2); %Modify the eigen values to control the shape of the elements Index: /issm/trunk/src/m/mesh/ComputeMetric.py =================================================================== --- /issm/trunk/src/m/mesh/ComputeMetric.py (revision 14309) +++ /issm/trunk/src/m/mesh/ComputeMetric.py (revision 14310) @@ -19,7 +19,7 @@ lambda1=0.5*((a+d)+numpy.sqrt(4.*b**2+(a-d)**2)) lambda2=0.5*((a+d)-numpy.sqrt(4.*b**2+(a-d)**2)) - pos1=numpy.nonzero(lambda1==0)[0] - pos2=numpy.nonzero(lambda2==0)[0] - pos3=numpy.nonzero(numpy.logical_and(b==0,lambda1==lambda2))[0] + pos1=numpy.nonzero(lambda1==0.)[0] + pos2=numpy.nonzero(lambda2==0.)[0] + pos3=numpy.nonzero(numpy.logical_and(b==0.,lambda1==lambda2))[0] #Modify the eigen values to control the shape of the elements @@ -54,5 +54,5 @@ #take care of NaNs if any (use Numpy eig in a loop) pos=numpy.nonzero(numpy.isnan(metric))[0] - if pos: + if numpy.size(pos): print(" %i NaN found in the metric. Use Numpy routine..." % numpy.size(pos)) for posi in pos: Index: /issm/trunk/src/m/mesh/ElementsFromEdge.py =================================================================== --- /issm/trunk/src/m/mesh/ElementsFromEdge.py (revision 14309) +++ /issm/trunk/src/m/mesh/ElementsFromEdge.py (revision 14310) @@ -1,3 +1,4 @@ import numpy +from PythonFuncs import * def ElementsFromEdge(elements,A,B): @@ -12,14 +13,10 @@ edgeelements=numpy.nonzero(\ - numpy.logical_or( \ - numpy.logical_or( \ - numpy.logical_or(numpy.logical_and(elements[:,0]==A,elements[:,1]==B), \ - numpy.logical_and(elements[:,0]==A,elements[:,2]==B)) \ - , \ - numpy.logical_or(numpy.logical_and(elements[:,1]==A,elements[:,2]==B), \ - numpy.logical_and(elements[:,1]==A,elements[:,0]==B)) \ - ), \ - numpy.logical_or(numpy.logical_and(elements[:,2]==A,elements[:,0]==B), \ - numpy.logical_and(elements[:,2]==A,elements[:,1]==B)) \ + logical_or_n(numpy.logical_and(elements[:,0]==A,elements[:,1]==B), \ + numpy.logical_and(elements[:,0]==A,elements[:,2]==B), \ + numpy.logical_and(elements[:,1]==A,elements[:,2]==B), \ + numpy.logical_and(elements[:,1]==A,elements[:,0]==B), \ + numpy.logical_and(elements[:,2]==A,elements[:,0]==B), \ + numpy.logical_and(elements[:,2]==A,elements[:,1]==B), \ ))[0]+1 Index: /issm/trunk/src/m/mesh/bamg.py =================================================================== --- /issm/trunk/src/m/mesh/bamg.py (revision 14309) +++ /issm/trunk/src/m/mesh/bamg.py (revision 14310) @@ -92,5 +92,5 @@ #Checks that all holes are INSIDE the principle domain outline if i: - flags=ContourToNodes(domaini['x'].reshape(-1,1),domaini['y'].reshape(-1,1),domainfile,0) + flags=ContourToNodes(domaini['x'],domaini['y'],domainfile,0) if numpy.any(numpy.logical_not(flags)): raise RuntimeError("bamg error message: All holes should be strictly inside the principal domain") @@ -118,5 +118,5 @@ #detect whether all points of the rift are inside the domain - flags=ContourToNodes(rifti['x'].reshape(-1,1),rifti['y'].reshape(-1,1),domain[0],0) + flags=ContourToNodes(rifti['x'],rifti['y'],domain[0],0) if numpy.all(numpy.logical_not(flags)): raise RuntimeError("one rift has all its points outside of the domain outline") Index: /issm/trunk/src/m/mesh/rifts/meshprocessoutsiderifts.py =================================================================== --- /issm/trunk/src/m/mesh/rifts/meshprocessoutsiderifts.py (revision 14309) +++ /issm/trunk/src/m/mesh/rifts/meshprocessoutsiderifts.py (revision 14310) @@ -16,5 +16,5 @@ #first, flag nodes that belong to the domain outline - flags=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),domainoutline,'node',0) + flags=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainoutline,'node',0) tips=rift.tips Index: /issm/trunk/src/m/mesh/rifts/meshprocessrifts.py =================================================================== --- /issm/trunk/src/m/mesh/rifts/meshprocessrifts.py (revision 14309) +++ /issm/trunk/src/m/mesh/rifts/meshprocessrifts.py (revision 14310) @@ -49,5 +49,5 @@ #In case we have rifts that open up the domain outline, we need to open them: - [flags,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),domainoutline,'node',0) + [flags,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainoutline,'node',0) found=0 for rift in md.rifts.riftstruct: Index: /issm/trunk/src/m/mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/mesh/squaremesh.m (revision 14309) +++ /issm/trunk/src/m/mesh/squaremesh.m (revision 14310) @@ -15,5 +15,4 @@ %initialization -segments=zeros(0,3); index=zeros(nel,3); x=zeros(nx*ny,1); @@ -23,6 +22,6 @@ for n=1:nx, for m=1:ny, - x((n-1)*ny+m)=(n-1); - y((n-1)*ny+m)=(m-1); + x((n-1)*ny+m)=(n-1.); + y((n-1)*ny+m)=(m-1.); end end Index: /issm/trunk/src/m/mesh/squaremesh.py =================================================================== --- /issm/trunk/src/m/mesh/squaremesh.py (revision 14310) +++ /issm/trunk/src/m/mesh/squaremesh.py (revision 14310) @@ -0,0 +1,83 @@ +import numpy +from NodeConnectivity import * +from ElementConnectivity import * + +def squaremesh(md,Lx,Ly,nx,ny): + """ + SQUAREMESH - create a structured square mesh + + This script will generate a structured square mesh + Lx and Ly are the dimension of the domain (in meters) + nx anx ny are the number of nodes in the x and y direction + The coordinates x and y returned are in meters. + + Usage: + [md]=squaremesh(md,Lx,Ly,nx,ny) + """ + + #get number of elements and number of nodes + nel=(nx-1)*(ny-1)*2 + nods=nx*ny + + #initialization + index=numpy.zeros((nel,3),int) + x=numpy.zeros((nx*ny)) + y=numpy.zeros((nx*ny)) + + #create coordinates + for n in xrange(0,nx): + for m in xrange(0,ny): + x[n*ny+m]=float(n) + y[n*ny+m]=float(m) + + #create index + for n in xrange(0,nx-1): + for m in xrange(0,ny-1): + A=n*ny+(m+1) + B=A+1 + C=(n+1)*ny+(m+1) + D=C+1 + index[n*(ny-1)*2+2*m,:]=[A,C,B] + index[n*(ny-1)*2+2*(m+1)-1,:]=[B,C,D] + + #Scale x and y + x=x/numpy.max(x)*Lx + y=y/numpy.max(y)*Ly + + #create segments + segments=numpy.zeros((2*(nx-1)+2*(ny-1),3),int) + #left edge: + segments[0:ny-1,:]=numpy.hstack((numpy.arange(2,ny+1).reshape(-1,1),numpy.arange(1,ny).reshape(-1,1),(2*numpy.arange(1,ny)-1).reshape(-1,1))) + #right edge: + segments[ny-1:2*(ny-1),:]=numpy.hstack((numpy.arange(ny*(nx-1)+1,nx*ny).reshape(-1,1),numpy.arange(ny*(nx-1)+2,nx*ny+1).reshape(-1,1),2*numpy.arange((ny-1)*(nx-2)+1,(nx-1)*(ny-1)+1).reshape(-1,1))) + #front edge: + segments[2*(ny-1):2*(ny-1)+(nx-1),:]=numpy.hstack((numpy.arange(2*ny,ny*nx+1,ny).reshape(-1,1),numpy.arange(ny,ny*(nx-1)+1,ny).reshape(-1,1),numpy.arange(2*(ny-1),2*(nx-1)*(ny-1)+1,2*(ny-1)).reshape(-1,1))) + #back edge + segments[2*(ny-1)+(nx-1):2*(nx-1)+2*(ny-1),:]=numpy.hstack((numpy.arange(1,(nx-2)*ny+2,ny).reshape(-1,1),numpy.arange(ny+1,ny*(nx-1)+2,ny).reshape(-1,1),numpy.arange(1,2*(nx-2)*(ny-1)+2,2*(ny-1)).reshape(-1,1))) + + #plug coordinates and nodes + md.mesh.x=x + md.mesh.y=y + md.mesh.z=numpy.zeros((nods)) + md.mesh.numberofvertices=nods + md.mesh.vertexonboundary=numpy.zeros((nods),bool) + md.mesh.vertexonboundary[segments[:,0:2]-1]=True + md.mesh.vertexonbed=numpy.ones((nods),bool) + md.mesh.vertexonsurface=numpy.ones((nods),bool) + + #plug elements + md.mesh.elements=index + md.mesh.segments=segments + md.mesh.numberofelements=nel + md.mesh.elementonbed=numpy.ones((nel),bool) + md.mesh.elementonsurface=numpy.ones((nel),bool) + + #Now, build the connectivity tables for this mesh. + [md.mesh.vertexconnectivity]=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices) + [md.mesh.elementconnectivity]=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity) + + #plug other field + md.mesh.dimension=2 + + return md + Index: /issm/trunk/src/m/miscellaneous/MatlabFuncs.py =================================================================== --- /issm/trunk/src/m/miscellaneous/MatlabFuncs.py (revision 14309) +++ /issm/trunk/src/m/miscellaneous/MatlabFuncs.py (revision 14310) @@ -8,4 +8,12 @@ if 'Windows' in platform.system(): + return True + else: + return False + +def ismac(): + import platform + + if 'Darwin' in platform.system(): return True else: @@ -89,2 +97,11 @@ return a +def heaviside(x): + import numpy + + y=numpy.zeros_like(x) + y[numpy.nonzero(x> 0.)]=1. + y[numpy.nonzero(x==0.)]=0.5 + + return y + Index: /issm/trunk/src/m/miscellaneous/PythonFuncs.py =================================================================== --- /issm/trunk/src/m/miscellaneous/PythonFuncs.py (revision 14310) +++ /issm/trunk/src/m/miscellaneous/PythonFuncs.py (revision 14310) @@ -0,0 +1,24 @@ +def logical_and_n(*arg): + from numpy import logical_and + + if len(arg): + result=arg[0] + for item in arg[1:]: + result=logical_and(result,item) + return result + + else: + return None + +def logical_or_n(*arg): + from numpy import logical_or + + if len(arg): + result=arg[0] + for item in arg[1:]: + result=logical_or(result,item) + return result + + else: + return None + Index: /issm/trunk/src/m/miscellaneous/normcdf_issm.m =================================================================== --- /issm/trunk/src/m/miscellaneous/normcdf_issm.m (revision 14310) +++ /issm/trunk/src/m/miscellaneous/normcdf_issm.m (revision 14310) @@ -0,0 +1,9 @@ +% +% wrapper for normcdf to avoid using the matlab statistics toolbox. +% +function [p]=normcdf_issm(x,mu,sigma) + + p=(1.+erf((x-mu)/(sigma*sqrt(2.))))/2.; + +end + Index: /issm/trunk/src/m/miscellaneous/normfit_issm.m =================================================================== --- /issm/trunk/src/m/miscellaneous/normfit_issm.m (revision 14310) +++ /issm/trunk/src/m/miscellaneous/normfit_issm.m (revision 14310) @@ -0,0 +1,36 @@ +% +% wrapper for normfit to avoid using the matlab statistics toolbox. +% +function [muhat,sigmahat,muci,sigmaci]=normfit_issm(x,alpha) + +% remove any NaN + + x=x(~isnan(x(:))); + n=length(x); + +% explicitly calculate the moments + + muhat =mean(x); + sigmahat=std(x); + + if (nargout>2) + if ~exist('alpha','var') + alpha=0.05; + end + prob=1.-alpha/2.; + + try + muci(1,1) =muhat-tinv(prob,n-1)*sigmahat/sqrt(n); + muci(2,1) =muhat+tinv(prob,n-1)*sigmahat/sqrt(n); + sigmaci(1,1)=sigmahat*sqrt((n-1)/chi2inv(prob ,n-1)); + sigmaci(2,1)=sigmahat*sqrt((n-1)/chi2inv(1.-prob,n-1)); + catch me + muci(1,1) =muhat; + muci(2,1) =muhat; + sigmaci(1,1)=sigmahat; + sigmaci(2,1)=sigmahat; + end + end + +end + Index: /issm/trunk/src/m/miscellaneous/norminv_issm.m =================================================================== --- /issm/trunk/src/m/miscellaneous/norminv_issm.m (revision 14310) +++ /issm/trunk/src/m/miscellaneous/norminv_issm.m (revision 14310) @@ -0,0 +1,9 @@ +% +% wrapper for norminv to avoid using the matlab statistics toolbox. +% +function [x]=norminv_issm(p,mu,sigma) + + x=mu+sigma*sqrt(2.)*erfinv(2.*p-1.); + +end + Index: /issm/trunk/src/m/miscellaneous/prctile_issm.m =================================================================== --- /issm/trunk/src/m/miscellaneous/prctile_issm.m (revision 14310) +++ /issm/trunk/src/m/miscellaneous/prctile_issm.m (revision 14310) @@ -0,0 +1,87 @@ +% +% wrapper for prctile to avoid using the matlab statistics toolbox. +% +function [y]=prctile_issm(x,p,dim) + + try + y=prctile(argin{:}); + + catch me + + if length(size(x)) > 2 + error('Number of dimensions %d not implemented.',length(size(x))); + end + if ~exist('dim','var') + dim=0; + for i=1:length(size(x)) + if ~dim && size(x,i)>1 + dim=i; + end + end + if ~dim + dim=1; + end + end + + psize=size(p); + if size(p,2)>1 + p=transp(p); + end + + xsize=size(x); + if dim==2 + x=transp(x); + end + +% check for any NaN in any columns + + if ~any(isnan(x)) + x=sort(x,1); + n=size(x,1); + +% branch based on number of elements + + if n>1 + +% set up percent values and interpolate + + xi=transp(100.*([1:n]-0.5)/n); + y=interp1q(xi,x,p); + +% fill in high and low values + + y(pxi(n),:)=repmat(x(n,:),nnz(p>xi(n)),1); + +% if one value, just copy it + + elseif n==1 + y=repmat(x(1,:),length(p),1); + +% if no values, use NaN + + else + y=repmat(NaN,size(p,1),size(x,2)); + end + + else + +% must loop over columns, since number of elements could be different + + y=zeros(size(p,1),size(x,2)); + for j=1:size(x,2) + +% remove any NaN and recursively call column + + y(:,j)=prctile_issm(x(~isnan(x(:,j)),j),p); + end + end + + if (min(xsize)==1 && xsize(dim)>1 && psize(2)>1) || ... + (min(xsize)> 1 && dim==2) + y=transp(y); + end + end + +end + Index: /issm/trunk/src/m/os/dakotaversion.m =================================================================== --- /issm/trunk/src/m/os/dakotaversion.m (revision 14310) +++ /issm/trunk/src/m/os/dakotaversion.m (revision 14310) @@ -0,0 +1,26 @@ +function DAKOTA_VERSION=dakotaversion() +%DAKOTAVERSION - recover dakota version number, inside config.h file +% +% Usage: +% DAKOTA_VERSION=dakotaversion(); + +%default +DAKOTA_VERSION=''; + +configfile=[issmdir() '/config.h']; +if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); +end + +%go through the file, and recover the line we want +fid=fopen(configfile,'r'); +if(fid==-1), error(['could not open file: ' configfile]); end + +while(true), + tline=fgets(fid); + if ~ischar(tline), break, end + if strncmp(tline,'#define DAKOTA_VERSION',22), + DAKOTA_VERSION=strtrim(strrep(tline(24:end),'"','')); + end +end +fclose(fid); Index: /issm/trunk/src/m/os/dakotaversion.py =================================================================== --- /issm/trunk/src/m/os/dakotaversion.py (revision 14310) +++ /issm/trunk/src/m/os/dakotaversion.py (revision 14310) @@ -0,0 +1,34 @@ +import os +from issmdir import * +from MatlabFuncs import * + +def dakotaversion(): + """ + DAKOTAVERSION - recover dakota version number, inside config.h file + + Usage: + DAKOTA_VERSION=dakotaversion(); + """ + + #default + DAKOTA_VERSION='' + + configfile=os.path.join(issmdir(),'config.h') + if not os.path.exists(configfile): + raise RuntimeError("File '%s' not found. ISSM has not been configured yet!" % configfile) + + #go through the file, and recover the line we want + try: + fid=open(configfile,'r') + except IOError as e: + raise IOerror("could not open file: '%s'" % configfile) + + for tline in fid: + if strncmp(tline,'#define DAKOTA_VERSION',22): + DAKOTA_VERSION=tline[23:].replace('"','').strip() + break + + fid.close() + + return DAKOTA_VERSION + Index: /issm/trunk/src/m/parameterization/contourenvelope.m =================================================================== --- /issm/trunk/src/m/parameterization/contourenvelope.m (revision 14309) +++ /issm/trunk/src/m/parameterization/contourenvelope.m (revision 14310) @@ -101,5 +101,5 @@ els2=mesh.elementconnectivity(el1,find(mesh.elementconnectivity(el1,:))); if length(els2)>1, - flag=intersect(mesh.elements(els2(1),:),mesh.elements(els2(2),:)); + flag=intersect(intersect(mesh.elements(els2(1),:),mesh.elements(els2(2),:)),mesh.elements(el1,:)); nods1=mesh.elements(el1,:); nods1(find(nods1==flag))=[]; Index: /issm/trunk/src/m/parameterization/contourenvelope.py =================================================================== --- /issm/trunk/src/m/parameterization/contourenvelope.py (revision 14309) +++ /issm/trunk/src/m/parameterization/contourenvelope.py (revision 14310) @@ -99,5 +99,5 @@ els2=mesh.elementconnectivity[el1,numpy.nonzero(mesh.elementconnectivity[el1,:])[0]]-1 if numpy.size(els2)>1: - flag=numpy.intersect1d(mesh.elements[els2[0],:],mesh.elements[els2[1],:]) + flag=numpy.intersect1d(numpy.intersect1d(mesh.elements[els2[0],:],mesh.elements[els2[1],:]),mesh.elements[el1,:]) nods1=mesh.elements[el1,:] nods1=numpy.delete(nods1,numpy.nonzero(nods1==flag)) Index: /issm/trunk/src/m/parameterization/setflowequation.py =================================================================== --- /issm/trunk/src/m/parameterization/setflowequation.py (revision 14309) +++ /issm/trunk/src/m/parameterization/setflowequation.py (revision 14310) @@ -3,4 +3,5 @@ from pairoptions import * from MatlabFuncs import * +from PythonFuncs import * from FlagElements import * @@ -50,9 +51,9 @@ #Flag the elements that have not been flagged as filltype if strcmpi(filltype,'hutter'): - hutterflag[numpy.nonzero(numpy.logical_not(numpy.logical_or(macayealflag,pattynflag)))]=True + hutterflag[numpy.nonzero(numpy.logical_not(logical_or_n(macayealflag,pattynflag)))]=True elif strcmpi(filltype,'macayeal'): - macayealflag[numpy.nonzero(numpy.logical_not(numpy.logical_or(hutterflag,numpy.logical_or(pattynflag,stokesflag))))]=True + macayealflag[numpy.nonzero(numpy.logical_not(logical_or_n(hutterflag,pattynflag,stokesflag)))]=True elif strcmpi(filltype,'pattyn'): - pattynflag[numpy.nonzero(numpy.logical_not(numpy.logical_or(hutterflag,numpy.logical_or(macayealflag,stokesflag))))]=True + pattynflag[numpy.nonzero(numpy.logical_not(logical_or_n(hutterflag,macayealflag,stokesflag)))]=True #check that each element has at least one flag @@ -69,5 +70,5 @@ #Check that no pattyn or stokes for 2d mesh if md.mesh.dimension==2: - if numpy.any(numpy.logical_or(l1l2flag,stokesflag,pattynflag)): + if numpy.any(logical_or_n(l1l2flag,stokesflag,pattynflag)): raise TypeError("stokes and pattyn elements not allowed in 2d mesh, extrude it first") Index: /issm/trunk/src/m/plot/applyoptions.m =================================================================== --- /issm/trunk/src/m/plot/applyoptions.m (revision 14309) +++ /issm/trunk/src/m/plot/applyoptions.m (revision 14310) @@ -331,50 +331,4 @@ end -%position of figure -if exist(options,'figposition'), - - figposition=getfieldvalue(options,'figposition'); - if ischar(figposition), - if strcmpi(figposition,'larour'), - set(gcf,'Position',[1604 4 1594 1177]); - elseif strcmpi(figposition,'larour2'), - set(gcf,'Position',[756 62 827 504]); - elseif strcmpi(figposition,'mathieu'), - set(gcf,'Position',[300 1 1580 1150]); - elseif strcmpi(figposition,'fullscreen'), - set(gcf,'Position',get(0,'ScreenSize')); - elseif strcmpi(figposition,'halfright'), - screen=get(0,'ScreenSize'); - left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; - set(gcf,'Position',fix([left+widt/2 bott widt/2 heig])); - elseif strcmpi(figposition,'halfleft'), - screen=get(0,'ScreenSize'); - left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; - set(gcf,'Position',fix([left bott widt/2 heig])); - elseif strcmpi(figposition,'square'), - screen=get(0,'ScreenSize'); - left=screen(1); bott=screen(2); widt=min(screen(3)-25,screen(4)-25); - set(gcf,'Position',fix([left+(screen(3)-widt) bott widt widt])); - elseif strcmpi(figposition,'portrait'), - %reformat with letter paper size (8.5" x 11") - screen=get(0,'ScreenSize'); - left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; - portrait=fix([left+widt-(heig*8.5/11) bott heig*8.5/11 heig]); - set(gcf,'Position',portrait) - elseif strcmpi(figposition,'landscape'), - %reformat with letter paper size (8.5" x 11") - screen=get(0,'ScreenSize'); - left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; - landscape=fix([left+widt-(heig*11/8.5) bott heig*11/8.5 heig]); - set(gcf,'Position',landscape) - else - disp('''figposition'' string not supported yet'); - end - else - set(gcf,'Position',figposition); - end - -end - %axes position if exist(options,'axesPosition') @@ -446,7 +400,4 @@ set(gca,'color',getfieldvalue(options,'backgroundcolor','none')); -%figurebackgrounbcolor -set(gcf,'color',getfieldvalue(options,'figurebackgroundcolor','w')); - %lighting if strcmpi(getfieldvalue(options,'light','off'),'on'), Index: /issm/trunk/src/m/plot/applyoptions.py =================================================================== --- /issm/trunk/src/m/plot/applyoptions.py (revision 14309) +++ /issm/trunk/src/m/plot/applyoptions.py (revision 14310) @@ -1,2 +1,3 @@ +from matplotlib.ticker import MaxNLocator try: @@ -107,4 +108,8 @@ #}}} + #ticklabel notation {{{ + p.gca().ticklabel_format(style='sci',scilimits=(0,0)) + #}}} + #ticklabelfontsize {{{ if options.exist('ticklabelfontsize'): @@ -116,4 +121,5 @@ label.set_fontsize(options.getfieldvalue('ticklabelfontsize')) #}}} + #view @@ -137,5 +143,12 @@ #ShowBasins - #Caxis + #clim {{{ + if options.exist('clim'): + lims=options.getfieldvalue('clim') + if len(lims)!=2: + print 'WARNING: clim should be passed as a list of length 2' + else: + p.clim(lims[0],lims[1]) + #}}} #shading @@ -152,6 +165,11 @@ #colorbar {{{ - if 'on' in options.getfieldvalue('colorbar','off'): - p.colorbar() + if options.getfieldvalue('colorbar','off')==1: + cb=p.colorbar() + cb.locator=MaxNLocator(nbins=5) # default 5 ticks + cb.update_ticks() + if options.exist('colorbarnumticks'): + cb.locator=MaxNLocator(nbins=options.getfieldvalue('colorbarnumticks',5)) + cb.update_ticks() #}}} Index: /issm/trunk/src/m/plot/checkplotoptions.m =================================================================== --- /issm/trunk/src/m/plot/checkplotoptions.m (revision 14309) +++ /issm/trunk/src/m/plot/checkplotoptions.m (revision 14310) @@ -81,4 +81,5 @@ end textweightvalues=repmat(textweightvalues,1,numtext); textweightvalues(numtext+1:end)=[]; + %3: textsize if exist(options,'textsize'), @@ -107,5 +108,5 @@ end textcolorvalues=repmat(textcolorvalues,1,numtext); textcolorvalues(numtext+1:end)=[]; - %4: textposition + %5: textposition if exist(options,'textposition'), textpositionvalues=getfieldvalue(options,'textposition'); @@ -191,5 +192,5 @@ if strcmpi(getfieldvalue(options,'scaleruler'),'on') %default values - Lx=max(md.mesh.y)-min(md.mesh.y); + Lx=max(md.mesh.x)-min(md.mesh.x); Ly=max(md.mesh.y)-min(md.mesh.y); %default values Index: /issm/trunk/src/m/plot/checkplotoptions.py =================================================================== --- /issm/trunk/src/m/plot/checkplotoptions.py (revision 14309) +++ /issm/trunk/src/m/plot/checkplotoptions.py (revision 14310) @@ -1,2 +1,4 @@ +import numpy as npy + def checkplotoptions(md,options): ''' @@ -11,5 +13,129 @@ ''' - print "WARNING: checkplotoptions not implemented: options returned as passed" + + #units + if options.exist('unit'): + if 'km' in options.getfieldvalue('unit','km'): + options.changefieldvalue('unit',10**-3) + if '100km' in options.getfieldvalue('unit','100km'): + options.changefieldvalue('unit',10**-5) + + #density + if options.exist('density'): + density=options.getfieldvalue('density') + options.changefieldvalue('density',abs(ceil(density))) + + #show section + if options.exist('showsection'): + if 'on' in options.getfieldvalue('showsection','on'): + options.changefieldvalue('showsection',4) + + #smooth values + if options.exist('smooth'): + if 'on' in options.getfieldvalue('smooth','on'): + options.changefieldvalue('smooth',0) + + #contouronly values + if options.exist('contouronly'): + if 'on' in options.getfieldvalue('contouronly','on'): + options.changefieldvalue('contouronly',1) + + #colorbar + if options.exist('colorbar'): + if 'on' in options.getfieldvalue('colorbar','on'): + options.changefieldvalue('colorbar',1) + elif 'off' in options.getfieldvalue('colorbar','off'): + options.changefieldvalue('colorbar',0) + + #text + if options.exist('text'): + #1: textvalue + textvalues=options.getfieldvalue('text') + numtext=len(textvalues) + + #2: textweight + if options.exist('textweight'): + textweightvalues=options.getfieldvalue('textweight') + else: + textweightvalues='n' + textweightvalues=npy.tile(textweightvalues,numtext) + + #3 textsize + if options.exist('textsize'): + textsizevalues=options.getfieldvalue('textsize') + else: + textsizevalues=14 + textsizevalues=npy.tile(textsizevalues,numtext) + + #4 textcolor + if options.exist('textcolor'): + textcolorvalues=options.getfieldvalue('textcolor') + else: + textcolorvalues='k' + textcolorvalues=npy.tile(textsizevalues,numtext) + + #5 textposition + if options.exist('textposition'): + options.getfieldvalue('textposition') + else: + raise Exception("plotmodel error message: 'textposition' option is missing") + + #6 textrotation + if options.exist('textrotation'): + textrotationvalues=options.getfieldvalue('textrotation') + else: + textrotationvalues=0 + textrotationvalues=npy.tile(textrotationvalues,numtext) + + options.changfieldvalue('text',textvalues) + options.changfieldvalue('textsize',textsizevalues) + options.changfieldvalue('textweight',textweightvalues) + options.changfieldvalue('textcolor',textcolorvalues) + options.changfieldvalue('textposition',textpositionvalues) + options.changfieldvalue('textrotation',textrotationvalues) + + #expdisp + expdispvaluesarray=[0,0] + expstylevaluesarray=[0,0] + expstylevalues=[0,0] + if options.exist('expstyle'): + expstylevalues=options.getfieldvalue('expstyle') + if options.exist('expdisp'): + expdispvalues=options.getfieldvalue('expdisp') + for i in npy.arange(len(expdispvalues)): + expdispvaluesarray.append(expdispvalues[i]) + if len(expstylevalues)>i+1: + expstylevaluesarray.append(expstylevalues[i]) + else: + expstylevaluesarray.append('-k') + + options.changefieldvalue('expstyle',expstylevaluesarray) + options.changefieldvalue('expdisp',expdispvaluesarray) + + #latlonnumbering + if options.exist('latlonclick'): + if 'on' in options.getfieldvalue('latlonclick','on'): + options.changefieldvalue('latlonclick',1) + + #northarrow + if options.exist('northarrow'): + if 'on' in options.getfieldvalue('northarrow','on'): + #default values + Lx=max(md.mesh.x)-min(md.mesh.x) + Ly=max(md.mesh.y)-min(md.mesh.y) + options.changefieldvalue('northarrow',[min(md.mesh.x)+1./6.*Lx, min(md.mesh.y)+5./6.*Ly, 1./15.*Ly, 0.25, 1./250.*Ly]) + + #scale ruler + if options.exist('scaleruler'): + if 'on' in options.exist('scaleruler','on'): + Lx=max(md.mesh.x)-min(md.mesh.x) + Ly=max(md.mesh.y)-min(md.mesh.y) + options.changefieldvalue('scaleruler',[min(md.mesh.x)+6./8.*Lx, min(md.mesh.y)+1./10.*Ly, 10**(ceil(log10(Lx)))/5, floor(Lx/100), 5]) + + #log scale + if options.exist('log'): + if options.exist('caxis'): + options.changefieldvalue('caxis',log(options.getfieldvalue('caxis'))/log(options.getfieldvalue('log'))) + options.changefieldvalue('cutoff',log(options.getfieldvalue('cutoff',1.5))/log(options.getfieldvalue('log'))) + return options - Index: /issm/trunk/src/m/plot/colormaps/demmap.m =================================================================== --- /issm/trunk/src/m/plot/colormaps/demmap.m (revision 14310) +++ /issm/trunk/src/m/plot/colormaps/demmap.m (revision 14310) @@ -0,0 +1,62 @@ +function cmap = demmap(ncolors,minZ,maxZ); +%DEMMAP - concatenate sea and land color depending on zmin and zmax +% +% Usage: +% cmap = demmap(n,zmin,zmax) + +if nargin<3, + help landseacolor + error('3 arguments necessary'); +end + +if minZ == maxZ; + maxZ = minZ+1; +end + +% determine appropriate number of sea and land colors +if minZ == maxZ; + maxZ = minZ+1; +end + +cmn = minZ; +cmx = maxZ; + +% determine appropriate number of sea and land colors +if minZ >= 0 + nsea = 0; + nland = ncolors; +elseif maxZ <= 0 + nland = 0; + nsea = ncolors; +else + % find optimal ratio of land to sea colors + maxminratio = maxZ/abs(minZ); + n1 = floor(ncolors/2); + n2 = ceil(ncolors/2); + if maxminratio>1 + sea = (1:n1)'; + land = (ncolors-1:-1:n2)'; + else + land = (1:n1)'; + sea = (ncolors-1:-1:n2)'; + end + ratio = land./sea; + errors = abs(ratio - maxminratio) / maxminratio; + indx = find(errors == min(min(errors))); + nsea = sea(indx); + nland = land(indx); + + % determine color limits + seaint = abs(minZ)/nsea; + landint = maxZ/nland; + if seaint >= landint + interval = seaint; + else + interval = landint; + end + cmn = -nsea*interval*(1 + 1e-9); % zero values treated as land + cmx = nland*interval; +end + +clim = [cmn cmx]; +cmap = [seacolor(nsea);landcolor(nland).^1.3]; Index: /issm/trunk/src/m/plot/colormaps/landcolor.m =================================================================== --- /issm/trunk/src/m/plot/colormaps/landcolor.m (revision 14310) +++ /issm/trunk/src/m/plot/colormaps/landcolor.m (revision 14310) @@ -0,0 +1,77 @@ +function y = landcolor(n) +%LANDCOLOR Land colormap +% +% Author: Francois Beauducel +% $Revision: 1.0.0 $ $Date: 2012/05/17 11:22:44 $ + +J = [ ... +0.095678 0.53427 0.21682 +0.15785 0.5979 0.23274 +0.21286 0.64673 0.2514 +0.26411 0.68789 0.27268 +0.32959 0.72416 0.31308 +0.39794 0.75695 0.36038 +0.46153 0.7871 0.40624 +0.52108 0.81516 0.45135 +0.57702 0.84152 0.49547 +0.62973 0.86645 0.53891 +0.67946 0.89016 0.58187 +0.72647 0.91282 0.62427 +0.77095 0.93455 0.66619 +0.81306 0.95546 0.70772 +0.85292 0.97563 0.7489 +0.89066 0.99514 0.78976 +0.88379 0.98595 0.77038 +0.86389 0.96758 0.73236 +0.84615 0.94972 0.69623 +0.8303 0.93233 0.66186 +0.81612 0.91536 0.6291 +0.80341 0.8988 0.59784 +0.79201 0.8826 0.56795 +0.78191 0.86676 0.53946 +0.7729 0.85123 0.51224 +0.76479 0.83602 0.48615 +0.75747 0.8211 0.46111 +0.75084 0.80645 0.43704 +0.74506 0.79206 0.41414 +0.73981 0.77792 0.39211 +0.73501 0.76401 0.37089 +0.73068 0.75033 0.35052 +0.72683 0.73685 0.33106 +0.72042 0.72074 0.31228 +0.71032 0.70085 0.29417 +0.69761 0.67821 0.27694 +0.68489 0.65558 0.26026 +0.67235 0.63313 0.24418 +0.65997 0.61082 0.22889 +0.64775 0.58874 0.21406 +0.63568 0.56689 0.19983 +0.62376 0.54527 0.18622 +0.61197 0.52391 0.17299 +0.60033 0.50283 0.16046 +0.58881 0.48203 0.14832 +0.57742 0.46151 0.13667 +0.56616 0.44133 0.12555 +0.55502 0.4214 0.11472 +0.54398 0.4019 0.10456 +0.53306 0.38266 0.094633 +0.52226 0.36382 0.085242 +0.51155 0.3453 0.076179 +0.50095 0.32714 0.067515 +0.49045 0.30938 0.059259 +0.48005 0.29193 0.051294 +0.46973 0.27495 0.043796 +0.45951 0.25823 0.0365 +0.44938 0.24206 0.029715 +0.43934 0.22609 0.023063 +0.42938 0.21074 0.016949 +0.41951 0.19556 0.010917 +0.40971 0.18105 0.0054326 +0.4 0.16667 0 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); Index: /issm/trunk/src/m/plot/colormaps/seacolor.m =================================================================== --- /issm/trunk/src/m/plot/colormaps/seacolor.m (revision 14310) +++ /issm/trunk/src/m/plot/colormaps/seacolor.m (revision 14310) @@ -0,0 +1,58 @@ +function y = seacolor(n) +%SEACOLOR Sea colormap adapted from NGDC ETOPO1 +% +% Author: Francois Beauducel + +J = [ ... + 0.0392 0 0.4745 + 0.1020 0 0.5373 + 0.1020 0 0.5373 + 0.1490 0 0.5961 + 0.1490 0 0.5961 + 0.1059 0.0118 0.6510 + 0.1059 0.0118 0.6510 + 0.0627 0.0235 0.7059 + 0.0627 0.0235 0.7059 + 0.0196 0.0353 0.7569 + 0.0196 0.0353 0.7569 + 0 0.0549 0.7961 + 0 0.0549 0.7961 + 0 0.0863 0.8235 + 0 0.0863 0.8235 + 0 0.1176 0.8471 + 0 0.1176 0.8471 + 0 0.1529 0.8745 + 0 0.1529 0.8745 + 0.0471 0.2667 0.9059 + 0.0471 0.2667 0.9059 + 0.1020 0.4000 0.9412 + 0.1020 0.4000 0.9412 + 0.0745 0.4588 0.9569 + 0.0745 0.4588 0.9569 + 0.0549 0.5216 0.9765 + 0.0549 0.5216 0.9765 + 0.0824 0.6196 0.9882 + 0.0824 0.6196 0.9882 + 0.1176 0.6980 1.0000 + 0.1176 0.6980 1.0000 + 0.1686 0.7294 1.0000 + 0.1686 0.7294 1.0000 + 0.2157 0.7569 1.0000 + 0.2157 0.7569 1.0000 + 0.2549 0.7843 1.0000 + 0.2549 0.7843 1.0000 + 0.3098 0.8235 1.0000 + 0.3098 0.8235 1.0000 + 0.3686 0.8745 1.0000 + 0.3686 0.8745 1.0000 + 0.5412 0.8902 1.0000 + 0.5412 0.8902 1.0000 + 0.7373 0.9020 1.0000 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/trunk/src/m/plot/kmlgridded.m =================================================================== --- /issm/trunk/src/m/plot/kmlgridded.m (revision 14310) +++ /issm/trunk/src/m/plot/kmlgridded.m (revision 14310) @@ -0,0 +1,145 @@ +function kmlgridded(md,data,varargin) + +%process options +options=pairoptions(varargin{:}); + +%process options +options=changefieldvalue(options,'coord','latlon'); + +%process mesh and data +[x y z elements is2d isplanet]=processmesh(md,[],options); +[data datatype]=processdata(md,data,options); + +%check is2d +if ~is2d, + error('buildgridded error message: gridded not supported for 3d meshes, project on a layer'); +end + +%Get xlim and ylim (used to extract radar image) +xlim=[min(x) max(x)]; +ylim=[min(y) max(y)]; +post=getfieldvalue(options,'posting',diff(xlim)/1000); +if(diff(xlim)/post>10000), + error(['posting too large']); +end + +%Interpolating data on grid +[x_m y_m data_grid]=InterpFromMeshToGrid(elements,x,y,data,xlim(1),ylim(2),post,post,round(diff(ylim)/post),round(diff(xlim)/post),NaN); +if size(data_grid,1)<3 | size(data_grid,2)<3, + error('data_grid size too small, check posting and units'); +end +pos=find(isinf(data_grid)); +if ~isempty(pos), + disp('Warning: removing Infs from vector (probably log(0)?)'); + data_grid(pos)=NaN; +end + +%Process data_grid: add white in NaN and correct caxis accordingly +data_nan=find(isnan(data_grid)); +data_min=min(data_grid(:)); +data_max=max(data_grid(:)); +if exist(options,'caxis'), + caxis_opt=getfieldvalue(options,'caxis'); + data_grid(find(data_gridcaxis_opt(2)))=caxis_opt(2); + data_min=caxis_opt(1); + data_max=caxis_opt(2); +end + +%Get colormap +colorm = getcolormap(options); +len = size(colorm,1); +ind = ceil((len-1)*(data_grid-data_min)/(data_max - data_min + eps) +1); +ind(find(ind>len))=len; +ind(find(ind<1) )=1; +ind(find(isnan(ind)))=1; +image_rgb=zeros(size(data_grid,1),size(data_grid,2),3); +r=colorm(:,1); image_rgb(:,:,1)=r(ind); clear r; +g=colorm(:,2); image_rgb(:,:,2)=g(ind); clear g; +b=colorm(:,3); image_rgb(:,:,3)=b(ind); clear b; + +%Deal with alpha +alpha=getfieldvalue(options,'alpha',.8); +alphaMatrix = alpha*ones(size(data_grid)); +alphaMatrix(data_nan) = 0; + +%write kml +kmlfilename=getfieldvalue(options,'kmlfilename','tempfile.kml'); +kmlroot=getfieldvalue(options,'kmlroot','./'); +kmlimagename=getfieldvalue(options,'kmlimagename','tempimage'); +kmlresolution=getfieldvalue(options,'kmlresolution',1); +kmlfolder=getfieldvalue(options,'kmlfolder','Ground Overlay'); +kmlfolderdescription=getfieldvalue(options,'kmlfolderdescription',''); +kmlgroundoverlayname=getfieldvalue(options,'kmlgroundoverlayname','ground overlay'); +kmlgroundoverlaydescription=getfieldvalue(options,'kmlgroundoverlaydescription','description'); + +%write png +imwrite(image_rgb,[kmlimagename '.png'],'png','alpha',alphaMatrix); +clear image_rgb alphaMatrix + +%prepare colorbar +iscolorbar=0; +if strcmpi(getfieldvalue(options,'colorbar','on'),'on'), + X = linspace(0,1,len)'; + Xlab = round(linspace(data_min,data_max,len+1)); + html = ['',10]; + + for k=len:-1:1 + f = (Xlab(k)-data_min)/(data_max-data_min); + if f<0, f=0; end + if f>1, f=1; end + polyColor(1,1) = interp1(X,colorm(:,1),f); + polyColor(1,2) = interp1(X,colorm(:,2),f); + polyColor(1,3) = interp1(X,colorm(:,3),f); + polyColorStr(1:2) = dec2hex(round(polyColor(1)*255),2); + polyColorStr(3:4) = dec2hex(round(polyColor(2)*255),2); + polyColorStr(5:6) = dec2hex(round(polyColor(3)*255),2); + html = [html,'','']; + end + html = [html,'',10]; + end + html = [html,'
 ']; + if k==1 + html=[html,'<= ',num2str(Xlab(k),'%g')]; + elseif k==len + html=[html,'>= ',num2str(Xlab(k),'%g')]; + else + html=[html,num2str(Xlab(k),'%g'),' to ',num2str(Xlab(k+1),'%g'),'
']; + iscolorbar = 1; +end + +%now write kml file +fid=fopen([kmlroot '/' kmlfilename],'w'); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s%s%s\n','',kmlfilename,''); +if iscolorbar, + fprintf(fid,'\n'); + fprintf(fid,'%s%s%s\n','','click the icon to see the colorbar',''); + fprintf(fid,'%s%s%s\n','','Ground overlay colorbar',''); + fprintf(fid,'1\n'); + fprintf(fid,['',10,'',10,'',10,'\n']); + fprintf(fid,['\n']); + fprintf(fid,'clampToGround\n'); + fprintf(fid,'1\n'); + fprintf(fid,'1\n'); + fprintf(fid,'%s%g,%g%s\n','',max(x),mean(y),''); + fprintf(fid,'\n'); + fprintf(fid,'\n'); +end +fprintf(fid,'%s\n',''); +fprintf(fid,'%s%s%s\n','',kmlgroundoverlayname,''); +fprintf(fid,'%s\n','',kmlgroundoverlaydescription,''); +fprintf(fid,'%s%s.%s%s\n','',kmlimagename,'png',''); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s%f%s\n','',max(y_m),''); +fprintf(fid,'%s%f%s\n','',min(y_m),''); +fprintf(fid,'%s%f%s\n','',max(x_m),''); +fprintf(fid,'%s%f%s\n','',min(x_m),''); +fprintf(fid,'%s\n','0'); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s\n',''); +fprintf(fid,'%s\n',''); +fclose(fid); Index: /issm/trunk/src/m/plot/kmlgroundoverlay.m =================================================================== --- /issm/trunk/src/m/plot/kmlgroundoverlay.m (revision 14309) +++ /issm/trunk/src/m/plot/kmlgroundoverlay.m (revision 14310) @@ -34,5 +34,6 @@ %print image at high resolution -printmodel([kmlroot '/' kmlimagename],kmlimagetype,'trim','on','resolution',kmlresolution,'margin','off','frame','off'); +export_fig([kmlroot '/' kmlimagename],'-transparent','-zbuffer'); %zbuffer to avoid "Bad data returned by HARDCOPY. Not calling IMWRITE" +%printmodel([kmlroot '/' kmlimagename],kmlimagetype,'trim','on','resolution',kmlresolution,'margin','off','frame','off'); %now write kml file Index: /issm/trunk/src/m/plot/latlonoverlay.m =================================================================== --- /issm/trunk/src/m/plot/latlonoverlay.m (revision 14309) +++ /issm/trunk/src/m/plot/latlonoverlay.m (revision 14310) @@ -87,6 +87,6 @@ if (xcorner>xlimits(1) & xcornerylimits(1) & ycornerxlimits(1) & xcornerylimits(1) & ycorner axisRatio + pos(1) = axisPos(1); + pos(3) = axisPos(3); + pos(4) = axisPos(3)/limDarRatio; + pos(2) = (axisPos(4) - pos(4))/2 + axisPos(2); + else + pos(2) = axisPos(2); + pos(4) = axisPos(4); + pos(3) = axisPos(4) * limDarRatio; + pos(1) = (axisPos(3) - pos(3))/2 + axisPos(1); + end + elseif pbarismanual + if pbarRatio > axisRatio + pos(1) = axisPos(1); + pos(3) = axisPos(3); + pos(4) = axisPos(3)/pbarRatio; + pos(2) = (axisPos(4) - pos(4))/2 + axisPos(2); + else + pos(2) = axisPos(2); + pos(4) = axisPos(4); + pos(3) = axisPos(4) * pbarRatio; + pos(1) = (axisPos(3) - pos(3))/2 + axisPos(1); + end + end +end + +% Convert plot box position to the units used by the axis + +temp = axes('Units', 'Pixels', 'Position', pos, 'Visible', 'off', 'parent', get(h, 'parent')); +set(temp, 'Units', currunit); +pos = get(temp, 'position'); +delete(temp); Index: /issm/trunk/src/m/plot/plotmodel.m =================================================================== --- /issm/trunk/src/m/plot/plotmodel.m (revision 14309) +++ /issm/trunk/src/m/plot/plotmodel.m (revision 14310) @@ -34,13 +34,54 @@ %Create figure + f=figure(figurenumber);clf; if strcmpi(getfieldvalue(options.list{1},'visible','on'),'off'), - F=figure(figurenumber);clf; - set(F,'Visible','Off'); - else - figure(figurenumber);clf; + set(f,'Visible','Off'); end - %Use zbuffer renderer (snoother colors) - set(gcf,'Renderer','zbuffer'); + if exist(options.list{1},'figposition'), % {{{ + figposition=getfieldvalue(options.list{1},'figposition'); + if ischar(figposition), + if strcmpi(figposition,'larour'), + set(gcf,'Position',[1604 4 1594 1177]); + elseif strcmpi(figposition,'larour2'), + set(gcf,'Position',[756 62 827 504]); + elseif strcmpi(figposition,'mathieu'), + set(gcf,'Position',[300 1 1580 1150]); + elseif strcmpi(figposition,'fullscreen'), + set(gcf,'Position',get(0,'ScreenSize')); + elseif strcmpi(figposition,'halfright'), + screen=get(0,'ScreenSize'); + left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; + set(gcf,'Position',fix([left+widt/2 bott widt/2 heig])); + elseif strcmpi(figposition,'halfleft'), + screen=get(0,'ScreenSize'); + left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; + set(gcf,'Position',fix([left bott widt/2 heig])); + elseif strcmpi(figposition,'square'), + screen=get(0,'ScreenSize'); + left=screen(1); bott=screen(2); widt=min(screen(3)-25,screen(4)-25); + set(gcf,'Position',fix([left+(screen(3)-widt) bott widt widt])); + elseif strcmpi(figposition,'portrait'), + %reformat with letter paper size (8.5" x 11") + screen=get(0,'ScreenSize'); + left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; + portrait=fix([left+widt-(heig*8.5/11) bott heig*8.5/11 heig]); + set(gcf,'Position',portrait) + elseif strcmpi(figposition,'landscape'), + %reformat with letter paper size (8.5" x 11") + screen=get(0,'ScreenSize'); + left=screen(1); bott=screen(2); widt=screen(3); heig=screen(4)-25; + landscape=fix([left+widt-(heig*11/8.5) bott heig*11/8.5 heig]); + set(gcf,'Position',landscape) + else + disp('''figposition'' string not supported yet'); + end + else + set(gcf,'Position',figposition); + end + end % }}} + + %Use zbuffer renderer (snoother colors) and white background + set(f,'Renderer','zbuffer','color',getfieldvalue(options.list{1},'figurebackgroundcolor','w')); %Go through all data plottable and close window if an error occurs @@ -48,4 +89,6 @@ for i=1:numberofplots, plot_manager(getfieldvalue(options.list{i},'model',md),options.list{i},subplotwidth,nlines,ncols,i); + %List all unused options + displayunused(options.list{i}) end catch me, Index: /issm/trunk/src/m/plot/plotmodel.py =================================================================== --- /issm/trunk/src/m/plot/plotmodel.py (revision 14309) +++ /issm/trunk/src/m/plot/plotmodel.py (revision 14310) @@ -1,2 +1,3 @@ +import numpy as npy try: @@ -21,4 +22,8 @@ subplotwidth=ceil(sqrt(options.numberofplots)) + #Get figure number and number of plots + figurenumber=options.figurenumber + numberofplots=options.numberofplots + #if nlines and ncols specified, then bypass if options.list[0].exist('nlines'): @@ -26,5 +31,5 @@ nl=True else: - nlines=subplotwidth + nlines=npy.ceil(numberofplots/subplotwidth) nl=False @@ -40,7 +45,4 @@ raise StandardError('error: nlines and ncols need to be specified together, or not at all') - #Get figure number and number of plots - figurenumber=options.figurenumber - numberofplots=options.numberofplots #Go through plots @@ -60,8 +62,7 @@ #try: for i in xrange(numberofplots): - plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i) + plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i+1) #except StandardError: # print 'error in plot_manager' else: raise StandardError('plotmodel error message: no output data found.') - Index: /issm/trunk/src/m/qmu/dakota_cdfs.m =================================================================== --- /issm/trunk/src/m/qmu/dakota_cdfs.m (revision 14309) +++ /issm/trunk/src/m/qmu/dakota_cdfs.m (revision 14310) @@ -247,5 +247,5 @@ irow=irow+1; cdf(irow,1)=resp(i); - cdf(irow,2)=normcdf(resp(i),mu,sigma); + cdf(irow,2)=normcdf_issm(resp(i),mu,sigma); cdf(irow,3)=(mu-resp(i))/sigma; cdf(irow,4)=(mu-resp(i))/sigma; @@ -256,8 +256,8 @@ for i=1:length(prob) irow=irow+1; - cdf(irow,1)=norminv(prob(i),mu,sigma); + cdf(irow,1)=norminv_issm(prob(i),mu,sigma); cdf(irow,2)=prob(i); - cdf(irow,3)=-norminv(prob(i),0,1); - cdf(irow,4)=-norminv(prob(i),0,1); + cdf(irow,3)=-norminv_issm(prob(i),0,1); + cdf(irow,4)=-norminv_issm(prob(i),0,1); end @@ -267,5 +267,5 @@ irow=irow+1; cdf(irow,1)=mu-sigma*rel(i); - cdf(irow,2)=normcdf(-rel(i),0,1); + cdf(irow,2)=normcdf_issm(-rel(i),0,1); cdf(irow,3)=rel(i); cdf(irow,4)=rel(i); @@ -277,5 +277,5 @@ irow=irow+1; cdf(irow,1)=mu-sigma*grel(i); - cdf(irow,2)=normcdf(-grel(i),0,1); + cdf(irow,2)=normcdf_issm(-grel(i),0,1); cdf(irow,3)=grel(i); cdf(irow,4)=grel(i); Index: /issm/trunk/src/m/qmu/dakota_moments.m =================================================================== --- /issm/trunk/src/m/qmu/dakota_moments.m (revision 14309) +++ /issm/trunk/src/m/qmu/dakota_moments.m (revision 14310) @@ -133,8 +133,15 @@ sigma=std(samp); - muci(1) =mu-tinv(prob,nsamp-1)*sigma/sqrt(nsamp); - muci(2) =mu+tinv(prob,nsamp-1)*sigma/sqrt(nsamp); - sigmaci(1)=sigma*sqrt((nsamp-1)/chi2inv(prob ,nsamp-1)); - sigmaci(2)=sigma*sqrt((nsamp-1)/chi2inv(1-prob,nsamp-1)); + try + muci(1,1) =mu-tinv(prob,nsamp-1)*sigma/sqrt(nsamp); + muci(2,1) =mu+tinv(prob,nsamp-1)*sigma/sqrt(nsamp); + sigmaci(1,1)=sigma*sqrt((nsamp-1)/chi2inv(prob ,nsamp-1)); + sigmaci(2,1)=sigma*sqrt((nsamp-1)/chi2inv(1-prob,nsamp-1)); + catch me + muci(1,1) =mu; + muci(2,1) =mu; + sigmaci(1,1)=sigma; + sigmaci(2,1)=sigma; + end end Index: /issm/trunk/src/m/qmu/dakota_out_parse.m =================================================================== --- /issm/trunk/src/m/qmu/dakota_out_parse.m (revision 14309) +++ /issm/trunk/src/m/qmu/dakota_out_parse.m (revision 14310) @@ -112,8 +112,13 @@ elseif strncmp(fline,'Moments for each response function',34) [dresp]=moments_read(fidi,dresp,fline); + elseif strncmp(fline,'Moment-based statistics for each response function',50) + [dresp]=mbstats_read(fidi,dresp,fline); elseif strncmp(fline,'95% confidence intervals for each response function',51) [dresp]=cis_read(fidi,dresp,fline); - elseif strncmp(fline,'Probabilities for each response function',40) + elseif strncmp(fline,'Probabilities for each response function',40) || ... + strncmp(fline,'Level mappings for each response function',41) [dresp]=cdfs_read(fidi,dresp,fline); + elseif strncmp(fline,'Probability Density Function (PDF) histograms for each response function',72) + [dresp]=pdfs_read(fidi,dresp,fline); elseif strncmp(fline,'Simple Correlation Matrix',25) [scm]=corrmat_read(fidi,'Simple Correlation Matrix',fline); @@ -137,5 +142,4 @@ else display(['Unexpected line: ' deblank(fline)]); - fline=fgetl(fidi); end fline=fgetl(fidi); @@ -198,5 +202,5 @@ %dstddev=std (data,0); [dmean,dstddev,dmeanci,dstddevci]=... - normfit(data,0.05); + normfit_issm(data,0.05); else dmean =zeros(1,size(data,2)); @@ -206,13 +210,13 @@ for i=1:size(data,2) [dmean(1,i),dstddev(1,i),dmeanci(:,i),dstddevci(:,i)]=... - normfit(data(:,i),0.05); - end -end - -dmin =min (data,[],1); -dquart1=prctile(data,25,1); -dmedian=median (data,1); -dquart3=prctile(data,75,1); -dmax =max (data,[],1); + normfit_issm(data(:,i),0.05); + end +end + +dmin =min (data,[],1); +dquart1=prctile_issm(data,25,1); +dmedian=median (data,1); +dquart3=prctile_issm(data,75,1); +dmax =max (data,[],1); % same as Dakota scm, Excel correl @@ -316,4 +320,43 @@ end +%% function to find and read the moment-based statistics + +function [dresp]=mbstats_read(fidi,dresp,fline) + +if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Moment-based statistics for each response function'); + if ~ischar(fline) + return + end +end + +display('Reading moment-based statistics for response functions:'); + +% skip column headings of moment-based statistics + + fline=fgetl(fidi); + +while 1 + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + +% add new response function and moment-based statistics + + dresp(end+1).descriptor=tokens{1}{ 1}; + display(sprintf(' %s',dresp(end).descriptor)); + dresp(end ).mean =tokens{1}{ 2}; + dresp(end ).stddev =tokens{1}{ 3}; + dresp(end ).skewness =tokens{1}{ 4}; + dresp(end ).kurtosis =tokens{1}{ 5}; +end + +display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end + %% function to find and read the confidence intervals @@ -336,4 +379,14 @@ end [ntokens,tokens]=fltokens(fline); + +% check for column headings in Dakota 5.2 + + if (ntokens == 4) + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + end % find response function associated with confidence intervals @@ -354,8 +407,15 @@ % add confidence intervals to response functions - dresp(i).meanci (1,1)=tokens{1}{ 5}; - dresp(i).meanci (2,1)=tokens{1}{ 6}; - dresp(i).stddevci(1,1)=tokens{1}{12}; - dresp(i).stddevci(2,1)=tokens{1}{13}; + if (ntokens == 14) + dresp(i).meanci (1,1)=tokens{1}{ 5}; + dresp(i).meanci (2,1)=tokens{1}{ 6}; + dresp(i).stddevci(1,1)=tokens{1}{12}; + dresp(i).stddevci(2,1)=tokens{1}{13}; + else + dresp(i).meanci (1,1)=tokens{1}{ 2}; + dresp(i).meanci (2,1)=tokens{1}{ 3}; + dresp(i).stddevci(1,1)=tokens{1}{ 4}; + dresp(i).stddevci(2,1)=tokens{1}{ 5}; + end end @@ -372,5 +432,8 @@ [fline]=findline(fidi,'Probabilities for each response function'); if ~ischar(fline) - return + [fline]=findline(fidi,'Level mappings for each response function'); + if ~ischar(fline) + return + end end end @@ -425,5 +488,71 @@ dresp(idresp).cdf(icdf,i)=tokens{1}{itoken}; end - end; + end + fline=fgetl(fidi); + end + end +end + +display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end + +%% function to find and read the pdf's + +function [dresp]=pdfs_read(fidi,dresp,fline) + +if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Probability Density Function (PDF) histograms for each response function'); + if ~ischar(fline) + return + end +end + +display('Reading PDF''s for response functions:'); + +while ischar(fline) && ~isempty(fline) + fline=fgetl(fidi); + if ~ischar(fline) + break; + end + +% process header line of pdf + + while ischar(fline) && ~isempty(fline) + [ntokens,tokens]=fltokens(fline); + +% find response function associated with pdf + + idresp=0; + for i=1:length(dresp) + if strcmpi(tokens{1}{ 3},dresp(i).descriptor) + idresp=i; + break; + end + end + if ~idresp + idresp=length(dresp)+1; + dresp(idresp).descriptor=tokens{1}{ 3}; + display(sprintf(' %s',dresp(idresp).descriptor)); + end + +% skip column headings of pdf + + fline=fgetl(fidi); + fline=fgetl(fidi); + +% read and add pdf table to response function + + fline=fgetl(fidi); + ipdf=0; + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'PDF for', 7) + [ntokens,tokens]=fltokens(fline); + ipdf=ipdf+1; + dresp(idresp).pdf(ipdf,1:3)=NaN; + for i=1:3 + dresp(idresp).pdf(ipdf,i)=tokens{1}{i}; + end fline=fgetl(fidi); end Index: /issm/trunk/src/m/qmu/plot/plot_cdf.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_cdf.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_cdf.m (revision 14310) @@ -139,7 +139,7 @@ if strncmpi(cplot,'p',1) && ... exist('ynorm','var') && strncmpi(ynorm,'y',1) - ydata(1:lcdfr(i),i)=norminv(dresp(i).cdf(:,iplot),0,1); + ydata(1:lcdfr(i),i)=norminv_issm(dresp(i).cdf(:,iplot),0,1); else - ydata(1:lcdfr(i),i)= dresp(i).cdf(:,iplot); + ydata(1:lcdfr(i),i)= dresp(i).cdf(:,iplot); end end @@ -237,5 +237,5 @@ end - tick = norminv(yprob,0,1); + tick = norminv_issm(yprob,0,1); set(ax1,'YTick',tick,'YTickLabel',label); ylim([tick(1) tick(end)]) Index: /issm/trunk/src/m/qmu/plot/plot_hist_norm.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_hist_norm.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_hist_norm.m (revision 14310) @@ -224,9 +224,9 @@ if exist('mu','var') && exist('sigma','var') for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),mu(i),sigma(i)); + dbelow(end+1)=normcdf_issm(edges( 1),mu(i),sigma(i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),mu(i),sigma(i))-... - normcdf(edges(1:end-1),mu(i),sigma(i)); - dabove(end+1)=norminv(edges(end),mu(i),sigma(i)); + normcdf_issm(edges(2:end ),mu(i),sigma(i))-... + normcdf_issm(edges(1:end-1),mu(i),sigma(i)); + dabove(end+1)=norminv_issm(edges(end),mu(i),sigma(i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm']}; Index: /issm/trunk/src/m/qmu/plot/plot_hist_norm_ci.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_hist_norm_ci.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_hist_norm_ci.m (revision 14310) @@ -129,5 +129,5 @@ % calculate 95% confidence intervals (same as dakota) [mu(i),sigma(i),muci(:,i),sigmaci(:,i)]=... - normfit(sampr(:,i),0.05); + normfit_issm(sampr(:,i),0.05); end display('Using calculated normal fits.') @@ -191,9 +191,9 @@ if exist('mu','var') && exist('sigma','var') for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),mu(i),sigma(i)); + dbelow(end+1)=normcdf_issm(edges( 1),mu(i),sigma(i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),mu(i),sigma(i))-... - normcdf(edges(1:end-1),mu(i),sigma(i)); - dabove(end+1)=norminv(edges(end),mu(i),sigma(i)); + normcdf_issm(edges(2:end ),mu(i),sigma(i))-... + normcdf_issm(edges(1:end-1),mu(i),sigma(i)); + dabove(end+1)=norminv_issm(edges(end),mu(i),sigma(i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm']}; @@ -204,9 +204,9 @@ if exist('muci','var') && exist('sigmaci','var') for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),muci(1,i),sigmaci(2,i)); + dbelow(end+1)=normcdf_issm(edges( 1),muci(1,i),sigmaci(2,i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),muci(1,i),sigmaci(2,i))-... - normcdf(edges(1:end-1),muci(1,i),sigmaci(2,i)); - dabove(end+1)=norminv(edges(end),muci(1,i),sigmaci(2,i)); + normcdf_issm(edges(2:end ),muci(1,i),sigmaci(2,i))-... + normcdf_issm(edges(1:end-1),muci(1,i),sigmaci(2,i)); + dabove(end+1)=norminv_issm(edges(end),muci(1,i),sigmaci(2,i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm-+']}; @@ -214,9 +214,9 @@ end for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),muci(1,i),sigmaci(1,i)); + dbelow(end+1)=normcdf_issm(edges( 1),muci(1,i),sigmaci(1,i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),muci(1,i),sigmaci(1,i))-... - normcdf(edges(1:end-1),muci(1,i),sigmaci(1,i)); - dabove(end+1)=norminv(edges(end),muci(1,i),sigmaci(1,i)); + normcdf_issm(edges(2:end ),muci(1,i),sigmaci(1,i))-... + normcdf_issm(edges(1:end-1),muci(1,i),sigmaci(1,i)); + dabove(end+1)=norminv_issm(edges(end),muci(1,i),sigmaci(1,i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm--']}; @@ -224,9 +224,9 @@ end for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),muci(2,i),sigmaci(1,i)); + dbelow(end+1)=normcdf_issm(edges( 1),muci(2,i),sigmaci(1,i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),muci(2,i),sigmaci(1,i))-... - normcdf(edges(1:end-1),muci(2,i),sigmaci(1,i)); - dabove(end+1)=norminv(edges(end),muci(2,i),sigmaci(1,i)); + normcdf_issm(edges(2:end ),muci(2,i),sigmaci(1,i))-... + normcdf_issm(edges(1:end-1),muci(2,i),sigmaci(1,i)); + dabove(end+1)=norminv_issm(edges(end),muci(2,i),sigmaci(1,i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm+-']}; @@ -234,9 +234,9 @@ end for i=1:ncol - dbelow(end+1)=normcdf(edges( 1),muci(2,i),sigmaci(2,i)); + dbelow(end+1)=normcdf_issm(edges( 1),muci(2,i),sigmaci(2,i)); dhistc(1:size(dhistc,1)-1,end+1)=... - normcdf(edges(2:end ),muci(2,i),sigmaci(2,i))-... - normcdf(edges(1:end-1),muci(2,i),sigmaci(2,i)); - dabove(end+1)=norminv(edges(end),muci(2,i),sigmaci(2,i)); + normcdf_issm(edges(2:end ),muci(2,i),sigmaci(2,i))-... + normcdf_issm(edges(1:end-1),muci(2,i),sigmaci(2,i)); + dabove(end+1)=norminv_issm(edges(end),muci(2,i),sigmaci(2,i)); if exist('descr','var') descr(end+1)={[descr{i} ' norm++']}; Index: /issm/trunk/src/m/qmu/plot/plot_normdist_bars.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_normdist_bars.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_normdist_bars.m (revision 14310) @@ -126,5 +126,5 @@ if ~isfield(dresp,'mean') || ~isfield(dresp,'stddev') for i=1:length(dresp) - [dresp(i).mean,dresp(i).stddev]=normfit(dresp(i).sample); + [dresp(i).mean,dresp(i).stddev]=normfit_issm(dresp(i).sample); end end @@ -141,5 +141,5 @@ for i=1:length(dresp) descr(i)=cellstr(dresp(i).descriptor); - data(i,:)=norminv(prob,dresp(i).mean,dresp(i).stddev); + data(i,:)=norminv_issm(prob,dresp(i).mean,dresp(i).stddev); end Index: /issm/trunk/src/m/qmu/plot/plot_rlev_bars_ci.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_rlev_bars_ci.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_rlev_bars_ci.m (revision 14310) @@ -133,5 +133,5 @@ [dresp(i).mean,dresp(i).stddev,... dresp(i).meanci,dresp(i).stddevci]=... - normfit(sampr(:,i),0.05); + normfit_issm(sampr(:,i),0.05); display('Using calculated normal fits from sample data.') end @@ -140,7 +140,7 @@ % use minus/plus integer standard deviations sdvect=[-4 -3 -2 -1 0 1 2 3 4]; - dresp(i).cdf(:,2)=normcdf(sdvect,0,1); - dresp(i).cdf(:,1)=norminv(dresp(i).cdf(:,2),... - dresp(i).mean,dresp(i).stddev); + dresp(i).cdf(:,2)=normcdf_issm(sdvect,0,1); + dresp(i).cdf(:,1)=norminv_issm(dresp(i).cdf(:,2),... + dresp(i).mean,dresp(i).stddev); display('Using integer standard deviations for percentages.') @@ -176,5 +176,5 @@ isfield(dresp(i),'stddev') && ~isempty(dresp(i).stddev) descr(end+1)=cellstr([dresp(i).descriptor ' norm']); - cdfr(end+1,:)=norminv(dresp(i).cdf(:,2),dresp(i).mean,dresp(i).stddev); + cdfr(end+1,:)=norminv_issm(dresp(i).cdf(:,2),dresp(i).mean,dresp(i).stddev); end if isfield(dresp(i),'meanci' ) && ~isempty(dresp(i).meanci ) && ... @@ -184,8 +184,8 @@ descr(end+1)=cellstr([dresp(i).descriptor ' norm+-']); descr(end+1)=cellstr([dresp(i).descriptor ' norm++']); - cdfr(end+1,:)=norminv(dresp(i).cdf(:,2),dresp(i).meanci(1),dresp(i).stddevci(2)); - cdfr(end+1,:)=norminv(dresp(i).cdf(:,2),dresp(i).meanci(1),dresp(i).stddevci(1)); - cdfr(end+1,:)=norminv(dresp(i).cdf(:,2),dresp(i).meanci(2),dresp(i).stddevci(1)); - cdfr(end+1,:)=norminv(dresp(i).cdf(:,2),dresp(i).meanci(2),dresp(i).stddevci(2)); + cdfr(end+1,:)=norminv_issm(dresp(i).cdf(:,2),dresp(i).meanci(1),dresp(i).stddevci(2)); + cdfr(end+1,:)=norminv_issm(dresp(i).cdf(:,2),dresp(i).meanci(1),dresp(i).stddevci(1)); + cdfr(end+1,:)=norminv_issm(dresp(i).cdf(:,2),dresp(i).meanci(2),dresp(i).stddevci(1)); + cdfr(end+1,:)=norminv_issm(dresp(i).cdf(:,2),dresp(i).meanci(2),dresp(i).stddevci(2)); end end Index: /issm/trunk/src/m/qmu/plot/plot_sampdist_bars.m =================================================================== --- /issm/trunk/src/m/qmu/plot/plot_sampdist_bars.m (revision 14309) +++ /issm/trunk/src/m/qmu/plot/plot_sampdist_bars.m (revision 14310) @@ -127,9 +127,9 @@ ~isfield(dresp,'max') for i=1:length(dresp) - dresp(i).min =min (dresp(i).sample); - dresp(i).quart1=prctile(dresp(i).sample,25); - dresp(i).median=median (dresp(i).sample); - dresp(i).quart3=prctile(dresp(i).sample,75); - dresp(i).max =max (dresp(i).sample); + dresp(i).min =min (dresp(i).sample); + dresp(i).quart1=prctile_issm(dresp(i).sample,25); + dresp(i).median=median (dresp(i).sample); + dresp(i).quart3=prctile_issm(dresp(i).sample,75); + dresp(i).max =max (dresp(i).sample); end end Index: /issm/trunk/src/m/solve/parseresultsfromdisk.py =================================================================== --- /issm/trunk/src/m/solve/parseresultsfromdisk.py (revision 14309) +++ /issm/trunk/src/m/solve/parseresultsfromdisk.py (revision 14310) @@ -43,8 +43,10 @@ result=ReadData(fid) while result: - if result['step'] > len(results): + if result['step'] > len(results): for i in xrange(len(results),result['step']-1): results.append(None) results.append(resultsclass.results()) + elif results[result['step']-1] is None: + results[result['step']-1]=resultsclass.results() #Get time and step setattr(results[result['step']-1],'step',result['step']) Index: /issm/trunk/src/m/solve/process_solve_options.m =================================================================== --- /issm/trunk/src/m/solve/process_solve_options.m (revision 14309) +++ /issm/trunk/src/m/solve/process_solve_options.m (revision 14310) @@ -11,5 +11,6 @@ if ~ismember(solution_type,[DiagnosticSolutionEnum(),PrognosticSolutionEnum(),ThermalSolutionEnum(),... SteadystateSolutionEnum(),TransientSolutionEnum(),EnthalpySolutionEnum(),... - BalancethicknessSolutionEnum(),BedSlopeSolutionEnum(),SurfaceSlopeSolutionEnum(),HydrologySolutionEnum(),FlaimSolutionEnum()]), + BalancethicknessSolutionEnum(),WeakBalancethicknessSolutionEnum(),BedSlopeSolutionEnum(),... + SurfaceSlopeSolutionEnum(),HydrologySolutionEnum(),FlaimSolutionEnum()]), error(['process_solve_options error message: solution_type ' EnumToString(solution_type) ' not supported yet!']); end Index: /issm/trunk/src/wrappers/Exp2Kml/Exp2Kml.h =================================================================== --- /issm/trunk/src/wrappers/Exp2Kml/Exp2Kml.h (revision 14309) +++ /issm/trunk/src/wrappers/Exp2Kml/Exp2Kml.h (revision 14310) @@ -51,3 +51,2 @@ #endif - Index: /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.cpp =================================================================== --- /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.cpp (revision 14310) +++ /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.cpp (revision 14310) @@ -0,0 +1,196 @@ +/*\file ExpSimplify.c + *\brief: exp to kml file conversion mex module. + */ +#include "./ExpSimplify.h" + +void ExpSimplifyUsage(void){/*{{{*/ + _pprintLine_("ExpSimplify - Simplify Exp contour"); + _pprintLine_(""); + _pprintLine_(" Recursive Douglas-Peucker Polygon Simplification"); + _pprintLine_(""); + _pprintLine_(" Usage:"); + _pprintLine_(" ExpSimplify(expfile,tol);"); + _pprintLine_(" - expfile: name of the exp file"); + _pprintLine_(" - tol: tolerance (maximal euclidean distance allowed between the new line and a vertex)"); + _pprintLine_(""); + _pprintLine_(" Example:"); + _pprintLine_(" ExpSimplify('file.exp',100);"); +}/*}}}*/ +void simplify(Contour* contour,bool* flags,int ind0,int ind1,double tolerance){/*{{{*/ + + bool closed = false; + double distance,beta,dx,dy; + double maxdistance; + int index; + double *x = contour->x; + double *y = contour->y; + + /*Some checks*/ + _assert_(ind0>=0 && ind0nods); + _assert_(ind1>=0 && ind1nods); + _assert_(ind1-ind0>=0); + + /*Check wether this portion is closed*/ + if(x[ind0]==x[ind1] && y[ind0]==y[ind1]) closed=true; + + if(closed){ + + /*calculate the shortest distance of all vertices between ind0 and ind1*/ + for(int i=ind0;imaxdistance){ + maxdistance=distance; + index = i; + } + } + } + else{ + /*calculate shortest distance of all points to the line from ind0 to ind1 + * subtract starting point from other locations + * + * d = || (x-x0) - beta (xend - x0) || + * = ||x-x0|| ||xend-x0|| cos(alpha) + * beta ||xend-x0|| = ||x-x0|| cos(alpha) + * + * So: beta = / */ + + for(int i=ind0+1;imaxdistance){ + maxdistance = distance; + index = i; + } + } + + } + + /*if the maximum distance is smaller than the tolerance remove vertices between ind0 and ind1*/ + if(maxdistance* contour = NULL; + Contour* newcontour = NULL; + int nods,newnods; + bool* flags = NULL; + double* x = NULL; + double* y = NULL; + double distance; + + /*Read old contours and allocate new contours*/ + oldcontours=DomainOutlineRead(expfile); + newcontours=new DataSet(0); + for(int counter=0;counterSize();counter++){ + + /*Get single contour*/ + contour = (Contour*)oldcontours->GetObjectByOffset(counter); + nods = contour->nods; + x = contour->x; + y = contour->y; + printf(" Initial number of vertices in contour #%i: %i\n",counter+1,nods); + + /*Allocate flags (1=keep, 0=remove)*/ + if(nods>0) flags = xNew(nods); + + if(nods==0){ + /*Don't do anything*/ + } + else if(nods==1){ + flags[0] = true; + } + else if(nods==2){ + /*check if the distance between both is less than the tolerance + * If so, return the center*/ + distance = sqrt((x[1]-x[0])*(x[1]-x[0]) + (y[1]-y[0])*(y[1]-y[0])); + if(distance<=tolerance){ + x[0]=(x[0]+x[1])/2.; + y[0]=(y[0]+y[1])/2.; + flags[0] = true; + flags[1] = false; + } + else{ + flags[0] = true; + flags[1] = true; + } + } + else{ + /*Start recursive call to simplify*/ + for(int i=0;i >(1); + newcontour->nods = newnods; + newcontour->x = xNew(newnods); + newcontour->y = xNew(newnods); + newnods = 0; + for(int i=0;ix[newnods] = contour->x[i]; + newcontour->y[newnods] = contour->y[i]; + newnods++; + } + } + _assert_(newnods==newcontour->nods); + + /*Add to main dataset*/ + newcontours->AddObject(newcontour); + } + + /*cleanup*/ + xDelete(flags); + } + + /*Write data: */ + ExpWrite(newcontours,expfile); + + /*Clean-up*/ + xDelete(expfile); + + /*end module: */ + MODULEEND(); +} Index: /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.h =================================================================== --- /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.h (revision 14310) +++ /issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.h (revision 14310) @@ -0,0 +1,47 @@ +/*!\file ExpSimplify.h + * \brief: prototype for exp to kml file conversion mex module. + */ + +#ifndef _EXPSIMPLIFY_H +#define _EXPSIMPLIFY_H + +#ifdef HAVE_CONFIG_H + #include +#else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*For python modules: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../bindings.h" + +#undef __FUNCT__ +#define __FUNCT__ "ExpSimplify" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define EXPFILE prhs[0] +#define TOLERANCE prhs[1] +/* serial output macros: */ +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define EXPFILE PyTuple_GetItem(args,0) +#define TOLERANCE PyTuple_GetItem(args,1) +#endif + +/* serial arg counts: */ +#undef NRHS +#define NRHS 2 +#undef NLHS +#define NLHS 0 + +#endif Index: /issm/trunk/src/wrappers/InternalFront/InternalFront.cpp =================================================================== --- /issm/trunk/src/wrappers/InternalFront/InternalFront.cpp (revision 14309) +++ /issm/trunk/src/wrappers/InternalFront/InternalFront.cpp (revision 14310) @@ -14,5 +14,4 @@ bool* elementonwater=NULL; int* elements=NULL; - int* connectivity=NULL; int* elementconnectivity=NULL; int* front=NULL; @@ -20,22 +19,17 @@ bool found; int numberofelements,numberofsegments; - int N,M; int i,j,ii,jj,id; + int dummy; /*Boot module: */ MODULEBOOT(); - /*checks on arguments on the matlab side: */ - CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InternalFrontUsage); + /*checks on arguments: */ + CHECKARGUMENTS(NLHS,NRHS,&InternalFrontUsage); - /*Fetch required fields*/ - FetchData(&numberofelements,mxGetAssignedField(MODEL,0,"numberofelements")); - if(numberofelements<=0) _error_("No elements found in the model"); - FetchData(&elements,&M,&N,mxGetAssignedField(MODEL,0,"elements")); - if(M!=numberofelements || N!=3) _error_("Field 'elements' should be of size [md.numberofelements 3]"); - FetchData(&elementonwater,&M,&N,mxGetAssignedField(MODEL,0,"elementonwater")); - if(M!=numberofelements || N!=1) _error_("Field 'elementonwater' should be of size [md.numberofelements 1]"); - FetchData(&elementconnectivity,&M,&N,mxGetAssignedField(MODEL,0,"elementconnectivity")); - if(M!=numberofelements || N!=3) _error_("Field 'elementconnectivity' should be of size [md.numberofelements 3]"); + /*Fetch inputs: */ + FetchData(&elements,&numberofelements,&dummy,ELEMENTS); + FetchData(&elementonwater,&dummy,&dummy,ELEMENTONWATER); + FetchData(&elementconnectivity,&dummy,&dummy,ELEMENTCONNECTIVITY); /*Allocate and initialize all variables*/ Index: /issm/trunk/src/wrappers/InternalFront/InternalFront.h =================================================================== --- /issm/trunk/src/wrappers/InternalFront/InternalFront.h (revision 14309) +++ /issm/trunk/src/wrappers/InternalFront/InternalFront.h (revision 14310) @@ -27,5 +27,7 @@ #ifdef _HAVE_MATLAB_MODULES_ /* serial input macros: */ -#define MODEL prhs[0] +#define ELEMENTS prhs[0] +#define ELEMENTONWATER prhs[1] +#define ELEMENTCONNECTIVITY prhs[2] /* serial output macros: */ #define FRONT (mxArray**)&plhs[0] @@ -34,5 +36,7 @@ #ifdef _HAVE_PYTHON_MODULES_ /* serial input macros: */ -#define MODEL PyTuple_GetItem(args,0) +#define ELEMENTS PyTuple_GetItem(args,0) +#define ELEMENTONWATER PyTuple_GetItem(args,1) +#define ELEMENTCONNECTIVITY PyTuple_GetItem(args,2) /* serial output macros: */ #define FRONT output,0] @@ -43,5 +47,5 @@ #define NLHS 1 #undef NRHS -#define NRHS 1 +#define NRHS 3 #endif Index: /issm/trunk/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp =================================================================== --- /issm/trunk/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 14309) +++ /issm/trunk/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 14310) @@ -45,8 +45,8 @@ //contours - DataSet *domain = NULL; - Contour** contours=NULL; - int numcontours; - Contour* contouri=NULL; + DataSet *domain = NULL; + Contour **contours=NULL; + int numcontours; + Contour *contouri=NULL; /* output: */ @@ -82,15 +82,4 @@ *(contours+i)=(Contour*)domain->GetObjectByOffset(i); - /* Debugging of contours :{{{1*/ - /*for(i=0;inods); - for (j=0;jnods;j++){ - _printLine_(" " << *(contouri->x+j) << "f " << *(contouri->y+j) << "f"); - } - }*/ - /*}}}*/ - /*Run interpolation routine: */ MeshProfileIntersectionx(&segments,&numsegs,index,x,y,nel,nods,contours,numcontours); Index: /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.cpp =================================================================== --- /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.cpp (revision 14310) +++ /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.cpp (revision 14310) @@ -0,0 +1,71 @@ +/*\file Shp2Exp.c + *\brief: shp to exp file conversion mex module. + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./Shp2Exp.h" + +void Shp2ExpUsage(void){/*{{{*/ + _pprintLine_("Shp2Exp - shp to exp file conversion module:"); + _pprintLine_(""); + _pprintLine_(" This module converts a file from shp to exp format."); + _pprintLine_(""); + _pprintLine_(" Usage:"); + _pprintLine_(" [ret]=Shp2Exp(filshp,filexp,sgn,'param name',param,...);"); + _pprintLine_(""); + _pprintLine_(" filshp file name of shp file to be read (char, extension optional)"); + _pprintLine_(" filexp file name of exp file to be written (char)"); + _pprintLine_(""); + _pprintLine_(" ret return code (non-zero for warning)"); + _pprintLine_(""); + _pprintLine_(" Examples:"); + _pprintLine_(" [ret]=Shp2Exp('file.shp','file.exp');"); + _pprintLine_(""); +}/*}}}*/ +WRAPPER(Shp2Exp){ + + int i,verbose=1; + + /*input: */ + char *filshp=NULL,*filexp=NULL; + + /* output: */ + int iret=0; + + #ifndef _HAVE_SHAPELIB_ //only works if shapelib library has been compiled in. + _error_("Shapelib not available! Cannot carry out shp file translation!"); + #endif + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + Shp2ExpUsage(); _error_("Shp2Exp usage error"); + } + if (nrhs < NRHS) { + Shp2ExpUsage(); _error_("Shp2Exp usage error"); + } + + /*Input datasets: */ + FetchData(&filshp,SHP_IN); + FetchData(&filexp,EXP_IN); + + /* Run core computations: */ + iret=Shp2Expx(filshp,filexp); + + /*Write data: */ + WriteData(RET_OUT,iret); + + /*Clean-up*/ + xDelete(filexp); + xDelete(filshp); + + /*end module: */ + MODULEEND(); +} Index: /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.h =================================================================== --- /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.h (revision 14310) +++ /issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.h (revision 14310) @@ -0,0 +1,51 @@ +/*!\file Shp2Exp.h + * \brief: prototype for shp to exp file conversion mex module. + */ + +#ifndef _SHP2EXP_H +#define _SHP2EXP_H + +#ifdef HAVE_CONFIG_H + #include +#else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*For python modules: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../bindings.h" + +#undef __FUNCT__ +#define __FUNCT__ "Shp2Exp" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define SHP_IN prhs[0] +#define EXP_IN prhs[1] +/* serial output macros: */ +#define RET_OUT (mxArray**)&plhs[0] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define SHP_IN PyTuple_GetItem(args,0) +#define EXP_IN PyTuple_GetItem(args,1) +/* serial output macros: */ +#define RET_OUT output,0 +#endif + +/* serial arg counts: */ +#undef NRHS +#define NRHS 2 +#undef NLHS +#define NLHS 1 + +#endif + Index: /issm/trunk/src/wrappers/TriMesh/TriMesh.cpp =================================================================== --- /issm/trunk/src/wrappers/TriMesh/TriMesh.cpp (revision 14309) +++ /issm/trunk/src/wrappers/TriMesh/TriMesh.cpp (revision 14310) @@ -22,9 +22,9 @@ /* output: */ - SeqMat *index = NULL; + SeqMat *index = NULL; SeqVec *x = NULL; SeqVec *y = NULL; - SeqMat *segments = NULL; - SeqVec *segmentmarkerlist = NULL; + SeqMat *segments = NULL; + SeqVec *segmentmarkerlist = NULL; /*Boot module: */ Index: /issm/trunk/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.cpp =================================================================== --- /issm/trunk/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 14309) +++ /issm/trunk/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 14310) @@ -18,9 +18,9 @@ /* input: */ int nel,nods; - double *index = NULL; + int *index = NULL; double *x = NULL; double *y = NULL; - double *segments = NULL; - double *segmentmarkers = NULL; + int *segments = NULL; + int *segmentmarkers = NULL; int num_seg; Index: /issm/trunk/src/wrappers/matlab/Makefile.am =================================================================== --- /issm/trunk/src/wrappers/matlab/Makefile.am (revision 14309) +++ /issm/trunk/src/wrappers/matlab/Makefile.am (revision 14310) @@ -48,4 +48,5 @@ ElementConnectivity.la\ EnumToString.la\ + ExpSimplify.la\ HoleFiller.la\ InternalFront.la\ @@ -76,7 +77,8 @@ KMLMeshWrite.la\ KMLOverlay.la\ - Shp2Kml.la\ Exp2Kml.la\ - Kml2Exp.la + Kml2Exp.la\ + Shp2Exp.la\ + Shp2Kml.la endif endif @@ -210,4 +212,8 @@ Ll2xy_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) +ExpSimplify_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp\ + ../ExpSimplify/ExpSimplify.h +ExpSimplify_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) + Exp2Kml_la_SOURCES = ../Exp2Kml/Exp2Kml.cpp\ ../Exp2Kml/Exp2Kml.h @@ -246,4 +252,8 @@ Scotch_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB) +Shp2Exp_la_SOURCES = ../Shp2Exp/Shp2Exp.cpp\ + ../Shp2Exp/Shp2Exp.h +Shp2Exp_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) + Shp2Kml_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp\ ../Shp2Kml/Shp2Kml.h Index: /issm/trunk/src/wrappers/matlab/include/wrapper_macros.h =================================================================== --- /issm/trunk/src/wrappers/matlab/include/wrapper_macros.h (revision 14309) +++ /issm/trunk/src/wrappers/matlab/include/wrapper_macros.h (revision 14310) @@ -19,5 +19,5 @@ * will be trapped*/ #define MODULEBOOT(); try{ \ - IssmComm::SetComm(-1); + IssmComm::SetComm(); #define MODULEEND(); }\ Index: /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp =================================================================== --- /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 14309) +++ /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 14310) @@ -290,4 +290,73 @@ } /*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,SeqMat* matrix){{{*/ +void WriteData(mxArray** pdataref,SeqMat* matrix){ + + int i,j; + int rows,cols; + mxArray *dataref = NULL; + int *matrix_ptr = NULL; + double *tmatrix_ptr = NULL; + + if(matrix){ + + matrix_ptr=matrix->ToSerial(); + matrix->GetSize(&rows,&cols); + + /*Now transpose the matrix and allocate with Matlab's memory manager: */ + tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); + for(i=0;i(matrix_ptr); + } + else{ + dataref = mxCreateDoubleMatrix(0,0,mxREAL); + } + + *pdataref=dataref; +} +/*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,SeqVec* vector){{{*/ +void WriteData(mxArray** pdataref,SeqVec* vector){ + + mxArray* dataref=NULL; + int* vector_ptr=NULL; + double* vector_matlab=NULL; + int rows; + + if(vector){ + /*call toolkit routine: */ + vector_ptr=vector->ToMPISerial(); + vector->GetSize(&rows); + + /*now create the matlab vector with Matlab's memory manager */ + vector_matlab=(double*)mxMalloc(rows*sizeof(double)); + for(int i=0;i(vector_ptr); + *pdataref=dataref; +} +/*}}}*/ /*FUNCTION WriteData(mxArray** pdataref,RiftStruct* riftstruct){{{*/ void WriteData(mxArray** pdataref,RiftStruct* riftstruct){ @@ -363,4 +432,16 @@ } /*}}}*/ +/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,int* fieldpointer){{{*/ +void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,int* fieldpointer){ + + mxArray* field = NULL; + + /*Convert field*/ + WriteData(&field,fieldpointer,M,N); + + /*Assign to structure*/ + mxSetField(dataref,i,fieldname,field); +} +/*}}}*/ /*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field){{{*/ void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldin){ Index: /issm/trunk/src/wrappers/matlab/io/matlabio.h =================================================================== --- /issm/trunk/src/wrappers/matlab/io/matlabio.h (revision 14309) +++ /issm/trunk/src/wrappers/matlab/io/matlabio.h (revision 14310) @@ -17,7 +17,9 @@ #include "../../c/include/include.h" +void WriteData(mxArray** pdataref,SeqMat* matrix); void WriteData(mxArray** pdataref,SeqMat* matrix); void WriteData(mxArray** pdataref,double* matrix, int M,int N); void WriteData(mxArray** pdataref,int* matrix, int M,int N); +void WriteData(mxArray** pdataref,SeqVec* vector); void WriteData(mxArray** pdataref,SeqVec* vector); void WriteData(mxArray** pdataref,double* vector, int M); @@ -64,4 +66,5 @@ void SetStructureField(mxArray* dataref,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldrows,int fieldcols,int* fieldpointer); void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field); void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field); Index: /issm/trunk/src/wrappers/python/include/wrapper_macros.h =================================================================== --- /issm/trunk/src/wrappers/python/include/wrapper_macros.h (revision 14309) +++ /issm/trunk/src/wrappers/python/include/wrapper_macros.h (revision 14310) @@ -23,5 +23,5 @@ if(!output) return NULL;\ try{ \ - IssmComm::SetComm(-1); + IssmComm::SetComm(); #define MODULEEND(); }\ Index: /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp =================================================================== --- /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp (revision 14309) +++ /issm/trunk/src/wrappers/python/io/FetchPythonData.cpp (revision 14310) @@ -20,39 +20,72 @@ void FetchData(double* pscalar,PyObject* py_float){ - double scalar; + double dscalar; /*return internal value: */ - scalar=PyFloat_AsDouble(py_float); - - /*output: */ - *pscalar=scalar; -} -/*}}}*/ -/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{*/ -void FetchData(int* pinteger, PyObject* py_long){ - - int integer; + if (PyFloat_Check(py_float)) + dscalar=PyFloat_AsDouble(py_float); + else if (PyInt_Check(py_float)) + dscalar=(double)PyInt_AsLong(py_float); + else if (PyLong_Check(py_float)) + dscalar=PyLong_AsDouble(py_float); + else if (PyBool_Check(py_float)) + dscalar=(double)PyLong_AsLong(py_float); + else if (PyTuple_Check(py_float) && (int)PyTuple_Size(py_float)==1) + FetchData(&dscalar,PyTuple_GetItem(py_float,(Py_ssize_t)0)); + else if (PyList_Check(py_float) && (int)PyList_Size(py_float)==1) + FetchData(&dscalar,PyList_GetItem(py_float,(Py_ssize_t)0)); + else + _error_("unrecognized float type in input!"); + + /*output: */ + *pscalar=dscalar; +} +/*}}}*/ +/*FUNCTION FetchData(int* pscalar,PyObject* py_long){{{*/ +void FetchData(int* pscalar, PyObject* py_long){ + + int iscalar; /*return internal value: */ - integer=(int)PyLong_AsLong(py_long); - - /*output: */ - *pinteger=integer; -} -/*}}}*/ -/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{*/ -void FetchData(bool* pboolean,PyObject* py_boolean){ - - bool boolean; - - /*check this is indeed a subtype of long type: */ - if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!"); - - /*extract boolean: */ - boolean=(bool)PyLong_AsLong(py_boolean); - - /*simple copy: */ - *pboolean=boolean; - + if (PyInt_Check(py_long)) + iscalar=(int)PyInt_AsLong(py_long); + else if (PyLong_Check(py_long)) + iscalar=(int)PyLong_AsLong(py_long); + else if (PyFloat_Check(py_long)) + iscalar=(int)PyFloat_AsDouble(py_long); + else if (PyBool_Check(py_long)) + iscalar=(int)PyLong_AsLong(py_long); + else if (PyTuple_Check(py_long) && (int)PyTuple_Size(py_long)==1) + FetchData(&iscalar,PyTuple_GetItem(py_long,(Py_ssize_t)0)); + else if (PyList_Check(py_long) && (int)PyList_Size(py_long)==1) + FetchData(&iscalar,PyList_GetItem(py_long,(Py_ssize_t)0)); + else + _error_("unrecognized long type in input!"); + + /*output: */ + *pscalar=iscalar; +} +/*}}}*/ +/*FUNCTION FetchData(bool* pscalar,PyObject* py_boolean){{{*/ +void FetchData(bool* pscalar,PyObject* py_boolean){ + + bool bscalar; + + /*return internal value: */ + if (PyBool_Check(py_boolean)) + bscalar=(bool)PyLong_AsLong(py_boolean); + else if (PyInt_Check(py_boolean)) + bscalar=(bool)PyInt_AsLong(py_boolean); + else if (PyLong_Check(py_boolean)) + bscalar=(bool)PyLong_AsLong(py_boolean); + else if (PyTuple_Check(py_boolean) && (int)PyTuple_Size(py_boolean)==1) + FetchData(&bscalar,PyTuple_GetItem(py_boolean,(Py_ssize_t)0)); + else if (PyList_Check(py_boolean) && (int)PyList_Size(py_boolean)==1) + FetchData(&bscalar,PyList_GetItem(py_boolean,(Py_ssize_t)0)); + else + _error_("unrecognized boolean type in input!"); + + /*output: */ + *pscalar=bscalar; } /*}}}*/ @@ -72,43 +105,59 @@ int i; - /*retrieve dimensions: */ - ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); - if(ndim!=2)_error_("expecting an MxN matrix in input!"); - dims=PyArray_DIMS((PyArrayObject*)py_matrix); - M=dims[0]; N=dims[1]; - - if (M && N) { - if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) { - /*retrieve internal value: */ - dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); - - /*copy matrix: */ - matrix=xNew(M*N); - memcpy(matrix,dmatrix,(M*N)*sizeof(double)); - } - - else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_INT64) { - /*retrieve internal value: */ - lmatrix=(long*)PyArray_DATA((PyArrayObject*)py_matrix); - - /*transform into double matrix: */ - matrix=xNew(M*N); - for(i=0;i(M*N); - for(i=0;i(M*N); + memcpy(matrix,dmatrix,(M*N)*sizeof(double)); + } + + else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_INT64) { + /*retrieve internal value: */ + lmatrix=(long*)PyArray_DATA((PyArrayObject*)py_matrix); + + /*transform into double matrix: */ + matrix=xNew(M*N); + for(i=0;i(M*N); + for(i=0;i(M*N); + FetchData(&(matrix[0]),py_matrix); + } /*output: */ @@ -133,43 +182,136 @@ int i; - /*retrieve dimensions: */ - ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); - if(ndim!=2)_error_("expecting an MxN matrix in input!"); - dims=PyArray_DIMS((PyArrayObject*)py_matrix); - M=dims[0]; N=dims[1]; - - if (M && N) { - if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) { - /*retrieve internal value: */ - dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); - - /*transform into integer matrix: */ - matrix=xNew(M*N); - for(i=0;i(M*N); - for(i=0;i(M*N); - for(i=0;i(M*N); + for(i=0;i(M*N); + for(i=0;i(M*N); + for(i=0;i(M*N); + FetchData(&(matrix[0]),py_matrix); + } + + /*output: */ + if(pM)*pM=M; + if(pN)*pN=N; + if(pmatrix)*pmatrix=matrix; +} +/*}}}*/ +/*FUNCTION FetchData(bool** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{*/ +void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_matrix){ + + /*output: */ + bool* bmatrix=NULL; + bool* matrix=NULL; + int M,N; + int ndim; + npy_intp* dims=NULL; + + /*intermediary:*/ + double* dmatrix=NULL; + long* lmatrix=NULL; + int i; + + if (PyArray_Check((PyArrayObject*)py_matrix)) { + /*retrieve dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); + if (ndim==2) { + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=dims[1]; + } + else if (ndim==1) { + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=1; + } + else + _error_("expecting an MxN matrix or M vector in input!"); + + if (M && N) { + if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) { + /*retrieve internal value: */ + dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); + + /*transform into bool matrix: */ + matrix=xNew(M*N); + for(i=0;i(M*N); + for(i=0;i(M*N); + memcpy(matrix,bmatrix,(M*N)*sizeof(bool)); + } + + else + _error_("unrecognized bool pyarray type in input!"); + } + else + matrix=NULL; + } + + else { + M=1; + N=1; + matrix=xNew(M*N); + FetchData(&(matrix[0]),py_matrix); + } /*output: */ @@ -194,43 +336,217 @@ int i; - /*retrieve dimensions: */ - ndim=PyArray_NDIM((const PyArrayObject*)py_vector); - if(ndim!=1)_error_("expecting an Mx1 vector in input!"); - dims=PyArray_DIMS((PyArrayObject*)py_vector); - M=dims[0]; - - if (M) { - if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) { - /*retrieve internal value: */ - dvector=(double*)PyArray_DATA((PyArrayObject*)py_vector); - - /*copy vector: */ - vector=xNew(M); - memcpy(vector,dvector,(M)*sizeof(double)); - } - - else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_INT64) { - /*retrieve internal value: */ - lvector=(long*)PyArray_DATA((PyArrayObject*)py_vector); - - /*transform into double vector: */ - vector=xNew(M); - for(i=0;i(M); - for(i=0;i(M); + memcpy(vector,dvector,(M)*sizeof(double)); + } + + else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_INT64) { + /*retrieve internal value: */ + lvector=(long*)PyArray_DATA((PyArrayObject*)py_vector); + + /*transform into double vector: */ + vector=xNew(M); + for(i=0;i(M); + for(i=0;i(M); + FetchData(&(vector[0]),py_vector); + } + + /*output: */ + if(pM)*pM=M; + if(pvector)*pvector=vector; +} +/*}}}*/ +/*FUNCTION FetchData(int** pvector,int* pM, PyObject* py_vector){{{*/ +void FetchData(int** pvector,int* pM,PyObject* py_vector){ + + /*output: */ + int* vector=NULL; + int M; + int ndim; + npy_intp* dims=NULL; + + /*intermediary:*/ + long* lvector=NULL; + bool* bvector=NULL; + double* dvector=NULL; + int i; + + if (PyArray_Check((PyArrayObject*)py_vector)) { + /*retrieve dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_vector); + if (ndim==1) { + dims=PyArray_DIMS((PyArrayObject*)py_vector); + M=dims[0]; + } + else if (ndim==2) { + dims=PyArray_DIMS((PyArrayObject*)py_vector); + if (dims[1]==1) + M=dims[0]; + else + _error_("expecting an Mx1 matrix or M vector in input!"); + } + else + _error_("expecting an Mx1 matrix or M vector in input!"); + + if (M) { + if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) { + /*retrieve internal value: */ + dvector=(double*)PyArray_DATA((PyArrayObject*)py_vector); + + /*transform into int vector: */ + vector=xNew(M); + for(i=0;i(M); + for(i=0;i(M); + for(i=0;i(M); + FetchData(&(vector[0]),py_vector); + } + + /*output: */ + if(pM)*pM=M; + if(pvector)*pvector=vector; +} +/*}}}*/ +/*FUNCTION FetchData(bool** pvector,int* pM, PyObject* py_vector){{{*/ +void FetchData(bool** pvector,int* pM,PyObject* py_vector){ + + /*output: */ + bool* bvector=NULL; + bool* vector=NULL; + int M; + int ndim; + npy_intp* dims=NULL; + + /*intermediary:*/ + double* dvector=NULL; + long* lvector=NULL; + int i; + + if (PyArray_Check((PyArrayObject*)py_vector)) { + /*retrieve dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_vector); + if (ndim==1) { + dims=PyArray_DIMS((PyArrayObject*)py_vector); + M=dims[0]; + } + else if (ndim==2) { + dims=PyArray_DIMS((PyArrayObject*)py_vector); + if (dims[1]==1) + M=dims[0]; + else + _error_("expecting an Mx1 matrix or M vector in input!"); + } + else + _error_("expecting an Mx1 matrix or M vector in input!"); + + if (M) { + if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) { + /*retrieve internal value: */ + dvector=(double*)PyArray_DATA((PyArrayObject*)py_vector); + + /*transform into bool vector: */ + vector=xNew(M); + for(i=0;i(M); + for(i=0;i(M); + memcpy(vector,bvector,(M)*sizeof(bool)); + } + + else + _error_("unrecognized bool pyarray type in input!"); + } + else + vector=NULL; + } + + else { + M=1; + vector=xNew(M); + FetchData(&(vector[0]),py_vector); + } /*output: */ Index: /issm/trunk/src/wrappers/python/io/WritePythonData.cpp =================================================================== --- /issm/trunk/src/wrappers/python/io/WritePythonData.cpp (revision 14309) +++ /issm/trunk/src/wrappers/python/io/WritePythonData.cpp (revision 14310) @@ -137,6 +137,7 @@ PyObject* array=NULL; + matrix->GetSize(&M,&N); buffer=matrix->ToSerial(); - matrix->GetSize(&M,&N); + dims[0]=(npy_intp)M; dims[1]=(npy_intp)N; @@ -154,8 +155,89 @@ PyObject* array=NULL; + vector->GetSize(&M); buffer=vector->ToMPISerial(); - vector->GetSize(&M); + dim=(npy_intp)M; array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer); + + PyTuple_SetItem(py_tuple, index, array); +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat* matrix){{{*/ +void WriteData(PyObject* py_tuple,int index,SeqMat* matrix){ + + int M,N; + int* ibuffer=NULL; + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + matrix->GetSize(&M,&N); + ibuffer=matrix->ToSerial(); + + /*convert to long*/ + long* lbuffer=xNew(M*N); + for(int i=0;i(ibuffer); + + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_INT64,lbuffer); + + PyTuple_SetItem(py_tuple, index, array); + +}/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec* vector){{{*/ +void WriteData(PyObject* py_tuple,int index,SeqVec* vector){ + + int M; + int* ibuffer=NULL; + npy_intp dim=10; + PyObject* array=NULL; + + vector->GetSize(&M); + ibuffer=vector->ToMPISerial(); + + /*convert to long*/ + long* lbuffer=xNew(M); + for(int i=0;i(ibuffer); + + dim=(npy_intp)M; + array=PyArray_SimpleNewFromData(1,&dim,NPY_INT64,lbuffer); + + PyTuple_SetItem(py_tuple, index, array); +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat* matrix){{{*/ +void WriteData(PyObject* py_tuple,int index,SeqMat* matrix){ + + int M,N; + bool* buffer=NULL; + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + matrix->GetSize(&M,&N); + buffer=matrix->ToSerial(); + + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_BOOL,buffer); + + PyTuple_SetItem(py_tuple, index, array); + +}/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec* vector){{{*/ +void WriteData(PyObject* py_tuple,int index,SeqVec* vector){ + + int M; + bool* buffer=NULL; + npy_intp dim=10; + PyObject* array=NULL; + + vector->GetSize(&M); + buffer=vector->ToMPISerial(); + + dim=(npy_intp)M; + array=PyArray_SimpleNewFromData(1,&dim,NPY_BOOL,buffer); PyTuple_SetItem(py_tuple, index, array); @@ -225,2 +307,34 @@ } /*}}}*/ +/*FUNCTION PyArrayFromCopiedData(int dimi,int dimj,int* data){{{*/ +PyObject* PyArrayFromCopiedData(int dimi,int dimj,int* data){ + + long* pydata; + npy_intp pydims[2]={0,0}; + + /* note that PyArray_SimpleNewFromData does not copy the data, so that when the original + object (e.g. bamggeom,bamgmesh) is deleted, the data is gone. */ + + pydims[0]=(npy_intp)dimi; + pydims[1]=(npy_intp)dimj; + pydata=xNew(dimi*dimj); + for(int i=0;i(dimi*dimj); + memcpy(pydata,data,dimi*dimj*sizeof(bool)); + return PyArray_SimpleNewFromData(2,pydims,NPY_BOOL,pydata); +} +/*}}}*/ Index: /issm/trunk/src/wrappers/python/io/pythonio.h =================================================================== --- /issm/trunk/src/wrappers/python/io/pythonio.h (revision 14309) +++ /issm/trunk/src/wrappers/python/io/pythonio.h (revision 14310) @@ -25,14 +25,21 @@ void WriteData(PyObject* py_tuple,int index, SeqMat* matrix); void WriteData(PyObject* py_tuple,int index, SeqVec* vector); +void WriteData(PyObject* py_tuple,int index, SeqMat* matrix); +void WriteData(PyObject* py_tuple,int index, SeqVec* vector); +void WriteData(PyObject* py_tuple,int index, SeqMat* matrix); +void WriteData(PyObject* py_tuple,int index, SeqVec* vector); void WriteData(PyObject* py_tuple,int index, BamgGeom* bamggeom); void WriteData(PyObject* py_tuple,int index, BamgMesh* bamgmesh); void WriteData(PyObject* py_tuple,int index, RiftStruct* riftstruct); -void FetchData(double** pvector,int* pM,PyObject* py_ref); void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array); void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_matrix); +void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_matrix); +void FetchData(double** pvector,int* pM,PyObject* py_ref); +void FetchData(int** pvector,int* pM,PyObject* py_ref); +void FetchData(bool** pvector,int* pM,PyObject* py_ref); void FetchData(char** pstring,PyObject* py_unicode); void FetchData(double* pscalar,PyObject* py_float); -void FetchData(int* pinteger,PyObject* py_long); +void FetchData(int* pscalar,PyObject* py_long); void FetchData(bool* pbool,PyObject* py_boolean); void FetchData(BamgGeom** bamggeom,PyObject* py_dict); @@ -47,4 +54,6 @@ PyObject* PyArrayFromCopiedData(int dims[2],double* data); PyObject* PyArrayFromCopiedData(int dimi,int dimj,double* data); +PyObject* PyArrayFromCopiedData(int dimi,int dimj,int* data); +PyObject* PyArrayFromCopiedData(int dimi,int dimj,bool* data); #endif /* _IO_H_ */ Index: /issm/trunk/startup.m =================================================================== --- /issm/trunk/startup.m (revision 14309) +++ /issm/trunk/startup.m (revision 14310) @@ -36,5 +36,7 @@ addpath(recursivepath([ISSM_DIR '/externalpackages/export_fig'])); addpath(recursivepath([ISSM_DIR '/externalpackages/googleearthtoolbox'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/howatmask'])); addpath(recursivepath([ISSM_DIR '/externalpackages/cm_and_cb_utilities'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/dem'])); clear ISSM_DIR; Index: /issm/trunk/test/NightlyRun/android.m =================================================================== --- /issm/trunk/test/NightlyRun/android.m (revision 14310) +++ /issm/trunk/test/NightlyRun/android.m (revision 14310) @@ -0,0 +1,32 @@ +md=triangle(model(),'../Exp/Square.exp',100000.); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareShelfConstrained.par'); +md=setflowequation(md,'macayeal','all'); +md.cluster=generic('name',oshostname(),'np',3); +md.verbose=verbose('mprocessor',true,'module',true,'solution',true,'solver',true,'convergence',true,'control',true,'qmu',true,'autodiff',true); +md.diagnostic.requested_outputs=StressTensorEnum(); +md=solve(md,DiagnosticSolutionEnum()); + + +index=md.mesh.elements; +nel=length(index); +x=md.mesh.x; +y=md.mesh.y; +z=md.mesh.z; +vel=md.results.DiagnosticSolution.Vel; + +patch=zeros(nel,12); +for i=1:nel, + patch(i,1)=x(index(i,1)); + patch(i,2)=y(index(i,1)); + patch(i,3)=z(index(i,1)); + patch(i,4)=x(index(i,2)); + patch(i,5)=y(index(i,2)); + patch(i,6)=z(index(i,2)); + patch(i,7)=x(index(i,3)); + patch(i,8)=y(index(i,3)); + patch(i,9)=z(index(i,3)); + patch(i,10)=vel(index(i,1)); + patch(i,11)=vel(index(i,2)); + patch(i,12)=vel(index(i,3)); +end Index: /issm/trunk/test/NightlyRun/python_skipped_tests.txt =================================================================== --- /issm/trunk/test/NightlyRun/python_skipped_tests.txt (revision 14309) +++ /issm/trunk/test/NightlyRun/python_skipped_tests.txt (revision 14310) @@ -11,2 +11,12 @@ test418 needs Dakota test420 needs Dakota + +test1401,test1402 +Roundoff error in ComputeHessian and ComputeMetric causes different meshes +from matlab, specifically in the handling of 0/0=nan, eps/0=inf, etc. Since +the mesh is of a different size, NR fails. (Note Matlab test1402 currently +fails.) + +test1109,test1110 +Ugly crashes in solver, but same behavior as Matlab. + Index: /issm/trunk/test/NightlyRun/runme.m =================================================================== --- /issm/trunk/test/NightlyRun/runme.m (revision 14309) +++ /issm/trunk/test/NightlyRun/runme.m (revision 14310) @@ -79,5 +79,10 @@ strncmp(fliplr(flist(i).name),fliplr('.m'),2)&... %File name must end by '.m' ~strcmp(flist(i).name,'test.m')) %File name must be different than 'test.m' - list_ids(end+1)=eval(flist(i).name(5:end-2)); %Keep test id only (skip 'test' and '.m') + id=str2num(flist(i).name(5:end-2)); + if isempty(id), + disp(['WARNING: ignore file ' flist(i).name ]); + else + list_ids(end+1)=eval(flist(i).name(5:end-2)); %Keep test id only (skip 'test' and '.m') + end end end Index: /issm/trunk/test/NightlyRun/test1101.m =================================================================== --- /issm/trunk/test/NightlyRun/test1101.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1101.m (revision 14310) @@ -1,7 +1,7 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 printingflag=false; -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; minvx=[]; @@ -26,13 +26,13 @@ pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times - posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; @@ -55,5 +55,5 @@ set(gcf,'Color','w') printmodel(['ismipapattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') @@ -61,5 +61,5 @@ set(gcf,'Color','w') printmodel(['ismipapattynvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') @@ -67,23 +67,23 @@ set(gcf,'Color','w') printmodel(['ismipapattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end - if(L==5000), + if(L==5000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 18],'xlim',[0 5000],'title','','xlabel','') - elseif(L==10000), + elseif(L==10000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 30],'xlim',[0 10000],'title','','xlabel','') - elseif(L==20000), + elseif(L==20000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 50],'xlim',[0 20000],'title','','xlabel','') - elseif(L==40000), + elseif(L==40000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 80],'xlim',[0 40000],'title','','xlabel','') - elseif(L==80000), + elseif(L==80000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 100],'xlim',[0 80000],'title','','xlabel','') - elseif(L==160000), + elseif(L==160000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') @@ -92,5 +92,5 @@ set(gcf,'Color','w') printmodel(['ismipapattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end end @@ -101,5 +101,5 @@ set(gcf,'Color','w') printmodel('ismipapattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) @@ -107,8 +107,9 @@ set(gcf,'Color','w') printmodel('ismipapattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipapattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipapattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end + %Fields and tolerances to track changes -field_names ={ ... +field_names ={... 'Vx5km','Vy5km','Vz5km',... 'Vx10km','Vy10km','Vz10km',... Index: /issm/trunk/test/NightlyRun/test1101.py =================================================================== --- /issm/trunk/test/NightlyRun/test1101.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1101.py (revision 14310) @@ -0,0 +1,153 @@ +import numpy +import shutil +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +printingflag=False + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] +minvx=[] +maxvx=[] + +for L in L_list: + nx=20 #numberof nodes in x direction + ny=20 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPA.py') + md.extrude(9,1.) + + md=setflowequation(md,'pattyn','all') + + #Create dirichlet on the bed only + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + + #Create MPCs to have periodic boundary conditions + posx=numpy.nonzero(md.mesh.x==0.)[0] + posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + + #Now plot vx, vy, vz and vx on a cross section +# plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipapattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipapattynvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +# plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipapattynvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipapattynvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +# plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipapattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipapattynvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + + if (L==5000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 18],'xlim',[0 5000],'title','','xlabel','') + elif (L==10000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 30],'xlim',[0 10000],'title','','xlabel','') + elif (L==20000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 50],'xlim',[0 20000],'title','','xlabel','') + elif (L==40000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 80],'xlim',[0 40000],'title','','xlabel','') + elif (L==80000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 100],'xlim',[0 80000],'title','','xlabel','') + elif (L==160000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipapattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipapattynvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + +#Now plot the min and max values of vx for each size of the square +#plot([5 10 20 40 80 160],minvx);ylim([0 18]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipapattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipapattynminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +#plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipapattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipapattynmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-09,1e-09,1e-09,\ + 1e-10,1e-10,1e-09,\ + 1e-09,1e-09,1e-09,\ + 1e-09,1e-08,1e-09,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-07,1e-08,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1102.m =================================================================== --- /issm/trunk/test/NightlyRun/test1102.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1102.m (revision 14310) @@ -1,7 +1,7 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 printingflag=false; -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; minvx=[]; @@ -17,5 +17,5 @@ % %Find elements at the corner and extract model -% posnodes=find((md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); +% posnodes=find((md.mesh.x==0. | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0. | md.mesh.y==max(md.mesh.y))); % [a,b]=find(ismember(md.mesh.elements,posnodes)); % elements=ones(md.mesh.numberofelements,1); @@ -29,23 +29,23 @@ %Create dirichlet on the bed only pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + md.diagnostic.spcvz(pos)=0.; - %Create MPCs to have periodic boundary conditions - %posx=find(md.mesh.x==0); - %posx2=find(md.mesh.x==max(md.mesh.x)); - %posx=find(md.mesh.x==0 & md.mesh.y~=0 & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); - %posx2=find(md.mesh.x==max(md.mesh.x) & md.mesh.y~=0 & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); +% %Create MPCs to have periodic boundary conditions +% posx=find(md.mesh.x==0.); +% posx2=find(md.mesh.x==max(md.mesh.x)); +% posx=find(md.mesh.x==0. & md.mesh.y~=0. & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); +% posx2=find(md.mesh.x==max(md.mesh.x) & md.mesh.y~=0. & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); - %posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); %Don't take the same nodes two times - %posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); +% posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); %Don't take the same nodes two times +% posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); - %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; +% md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; %Compute the diagnostic md.diagnostic.abstol=NaN; md.diagnostic.reltol=NaN; - md.diagnostic.restol=1; + md.diagnostic.restol=1.; md.cluster=generic('name',oshostname(),'np',8); md=solve(md,DiagnosticSolutionEnum()); @@ -62,45 +62,45 @@ %Now plot vx, vy, vz and vx on a cross section plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipastokesvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipastokesvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipastokesvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end - if(L==5000), + if(L==5000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 18],'xlim',[0 5000],'title','','xlabel','') - elseif(L==10000), + elseif(L==10000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 30],'xlim',[0 10000],'title','','xlabel','') - elseif(L==20000), + elseif(L==20000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 50],'xlim',[0 20000],'title','','xlabel','') - elseif(L==40000), + elseif(L==40000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 80],'xlim',[0 40000],'title','','xlabel','') - elseif(L==80000), + elseif(L==80000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 100],'xlim',[0 80000],'title','','xlabel','') - elseif(L==160000), + elseif(L==160000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') end - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipastokesvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end end @@ -108,15 +108,16 @@ %Now plot the min and max values of vx for each size of the square plot([5 10 20 40 80 160],minvx);ylim([0 18]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipastokesminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end plot([5 10 20 40 80 160],maxvx);ylim([0 120]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipastokesmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipastokesmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA ']); + system(['mv ismipastokesmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestA']); end + %Fields and tolerances to track changes field_names ={... @@ -127,5 +128,5 @@ 'Vx80km','Vy80km','Vz80km',... 'Vx160km','Vy160km','Vz160km' -} +}; field_tolerances={... 1e-12,1e-12,1e-12,... Index: /issm/trunk/test/NightlyRun/test1102.py =================================================================== --- /issm/trunk/test/NightlyRun/test1102.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1102.py (revision 14310) @@ -0,0 +1,163 @@ +import numpy +import shutil +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +printingflag=False + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] +minvx=[] +maxvx=[] + +for L in L_list: + nx=20 #numberof nodes in x direction + ny=20 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + +# #Find elements at the corner and extract model +# posnodes=numpy.nonzero(numpy.logical_and(numpy.logical_or(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y)))) +# a=numpy.nonzero(ismember(md.mesh.elements,posnodes))[0] +# elements=numpy.ones((md.mesh.numberofelements),int) +# elements[a]=0 +# md.modelextract(elements) + + md=parameterize(md,'../Par/ISMIPA.py') + md.extrude(10,1.) + md=setflowequation(md,'stokes','all') + + #Create dirichlet on the bed only + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + md.diagnostic.spcvz[pos]=0. + +# #Create MPCs to have periodic boundary conditions +# posx=numpy.nonzero(md.mesh.x==0.)[0] +# posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] +# posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,md.mesh.y!=0.,md.mesh.y!=numpy.max(md.mesh.y),numpy.logical_not(md.mesh.vertexonbed)))[0] +# posx2=numpy.nonzero(logical_and_n(md.mesh.x==numpy.max(md.mesh.x),md.mesh.y!=0.,md.mesh.y!=numpy.max(md.mesh.y),numpy.logical_not(md.mesh.vertexonbed)))[0] + +# posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x),numpy.logical_not(md.mesh.vertexonbed)))[0] #Don't take the same nodes two times +# posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x),numpy.logical_not(md.mesh.vertexonbed)))[0] + +# md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Compute the diagnostic + md.diagnostic.abstol=float('NaN') + md.diagnostic.reltol=float('NaN') + md.diagnostic.restol=1. + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + pressure=md.results.DiagnosticSolution.Pressure + results.append(md.results.DiagnosticSolution) + minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + + #Now plot vx, vy, vz and vx on a cross section +# plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipastokesvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipastokesvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +# plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipastokesvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipastokesvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +# plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipastokesvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipastokesvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + + if (L==5000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 18],'xlim',[0 5000],'title','','xlabel','') + elif (L==10000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 30],'xlim',[0 10000],'title','','xlabel','') + elif (L==20000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 50],'xlim',[0 20000],'title','','xlabel','') + elif (L==40000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 80],'xlim',[0 40000],'title','','xlabel','') + elif (L==80000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 100],'xlim',[0 80000],'title','','xlabel','') + elif (L==160000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipastokesvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipastokesvxsec.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + +#Now plot the min and max values of vx for each size of the square +#plot([5 10 20 40 80 160],minvx);ylim([0 18]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipastokesminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipastokesminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') +#plot([5 10 20 40 80 160],maxvx);ylim([0 120]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipastokesmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipastokesmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-11,1e-12,\ + 1e-12,1e-11,1e-12,\ + 1e-12,1e-11,1e-12,\ + 1e-12,1e-11,1e-12,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1103.m =================================================================== --- /issm/trunk/test/NightlyRun/test1103.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1103.m (revision 14310) @@ -1,8 +1,10 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 printingflag=false; -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; +minvx=[]; +maxvx=[]; for i=1:length(L_list), @@ -23,13 +25,13 @@ md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times - posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; @@ -49,39 +51,39 @@ %Now plot vx, vy, vz and vx on a cross section plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipbpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipbpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB ']); + system(['mv ismipbpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB']); end plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipbpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipbpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB ']); + system(['mv ismipbpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB']); end - if(L==5000), + if(L==5000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[6 16],'xlim',[0 5000],'title','','xlabel','') - elseif(L==10000), + elseif(L==10000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 40],'xlim',[0 10000],'title','','xlabel','') - elseif(L==20000), + elseif(L==20000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 60],'xlim',[0 20000],'title','','xlabel','') - elseif(L==40000), + elseif(L==40000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 100],'xlim',[0 40000],'title','','xlabel','') - elseif(L==80000), + elseif(L==80000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 120],'xlim',[0 80000],'title','','xlabel','') - elseif(L==160000), + elseif(L==160000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') end - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipbpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipbpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB ']); + system(['mv ismipbpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB']); end end @@ -89,15 +91,16 @@ %Now plot the min and max values of vx for each size of the square plot([5 10 20 40 80 160],minvx);ylim([0 14]);xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipbpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipbpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB ']); + system(['mv ismipbpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB']); end plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipbpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipbpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB ']); + system(['mv ismipbpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestB']); end + %Fields and tolerances to track changes field_names ={... Index: /issm/trunk/test/NightlyRun/test1103.py =================================================================== --- /issm/trunk/test/NightlyRun/test1103.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1103.py (revision 14310) @@ -0,0 +1,146 @@ +import numpy +import shutil +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +printingflag=False + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] +minvx=[] +maxvx=[] + +for L in L_list: + nx=20 #numberof nodes in x direction + ny=20 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPB.py') + md.extrude(10,1.) + + md=setflowequation(md,'pattyn','all') + + #Create dirichlet on the bed only + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + + #Create MPCs to have periodic boundary conditions + posx=numpy.nonzero(md.mesh.x==0.)[0] + posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + minvx.append(numpy.min(vx[md.mesh.numberofvertices2d:])) + maxvx.append(numpy.max(vx[md.mesh.numberofvertices2d:])) + + #Now plot vx, vy, vz and vx on a cross section +# plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipbpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipbpattynvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') +# plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipbpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipbpattynvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') + + if (L==5000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[6 16],'xlim',[0 5000],'title','','xlabel','') + elif (L==10000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 40],'xlim',[0 10000],'title','','xlabel','') + elif (L==20000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 60],'xlim',[0 20000],'title','','xlabel','') + elif (L==40000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 100],'xlim',[0 40000],'title','','xlabel','') + elif (L==80000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 120],'xlim',[0 80000],'title','','xlabel','') + elif (L==160000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 120],'xlim',[0 160000],'title','','xlabel','') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipbpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipbpattynvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') + +#Now plot the min and max values of vx for each size of the square +#plot([5 10 20 40 80 160],minvx);ylim([0 14]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipbpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipbpattynminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') +#plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipbpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipbpattynmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-09,1e-09,1e-09,\ + 1e-09,1e-09,1e-09,\ + 1e-09,1e-09,1e-09,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-07,1e-07,\ + 1e-07,1e-06,1e-07,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1104.m =================================================================== --- /issm/trunk/test/NightlyRun/test1104.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1104.m (revision 14310) @@ -1,6 +1,6 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; @@ -22,13 +22,13 @@ pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times - posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; @@ -38,5 +38,5 @@ md.cluster=generic('name',oshostname(),'np',8); md=solve(md,DiagnosticSolutionEnum()); - pos=find(md.mesh.x==0 | md.mesh.y==0 | md.mesh.x==max(md.mesh.x) | md.mesh.y==max(md.mesh.y)); + pos=find(md.mesh.x==0. | md.mesh.y==0. | md.mesh.x==max(md.mesh.x) | md.mesh.y==max(md.mesh.y)); md.diagnostic.spcvx(pos)=md.results.DiagnosticSolution.Vx(pos); md.diagnostic.spcvy(pos)=md.results.DiagnosticSolution.Vy(pos); Index: /issm/trunk/test/NightlyRun/test1104.py =================================================================== --- /issm/trunk/test/NightlyRun/test1104.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1104.py (revision 14310) @@ -0,0 +1,90 @@ +import numpy +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] + +for L in L_list: + nx=20 #numberof nodes in x direction + ny=20 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPB.py') + md.extrude(10,1.) + md=setflowequation(md,'pattyn','all') + + #Create dirichlet on the bed only + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + + #Create MPCs to have periodic boundary conditions + posx=numpy.nonzero(md.mesh.x==0.)[0] + posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Compute the diagnostic + md.diagnostic.abstol=float('NaN') + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + pos=numpy.nonzero(logical_or_n(md.mesh.x==0.,md.mesh.y==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==numpy.max(md.mesh.y))) + md.diagnostic.spcvx[pos]=md.results.DiagnosticSolution.Vx[pos] + md.diagnostic.spcvy[pos]=md.results.DiagnosticSolution.Vy[pos] + md.diagnostic.vertex_pairing=numpy.empty((0,2),int) + md=setflowequation(md,'stokes','all') + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + +# plotmodel(md,'data',vx,'data',vy,'data',vz,'layer#all',md.mesh.numberoflayers) + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-07,1e-08,\ + 1e-07,1e-07,1e-07,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1105.m =================================================================== --- /issm/trunk/test/NightlyRun/test1105.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1105.m (revision 14310) @@ -1,7 +1,7 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 printingflag=false; -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; minvx=[]; @@ -9,5 +9,5 @@ for i=1:length(L_list), - L=L_list{i}; %in m (3 times the desired lenght for BC problems) + L=L_list{i}; %in m (3 times the desired length for BC problems) nx=30; %number of nodes in x direction ny=30; @@ -18,5 +18,5 @@ md=extrude(md,10,1.); - md=setflowequation(md,'pattyn','all'); + md=setflowequation(md,'pattyn','all'); %Create MPCs to have periodic boundary conditions @@ -25,32 +25,32 @@ md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - posx=find(md.mesh.x==0 & md.mesh.y~=0 & md.mesh.y~=L); - posx2=find(md.mesh.x==L & md.mesh.y~=0 & md.mesh.y~=L); + posx=find(md.mesh.x==0. & md.mesh.y~=0. & md.mesh.y~=L); + posx2=find(md.mesh.x==L & md.mesh.y~=0. & md.mesh.y~=L); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=L); %Don't take the same nodes two times - posy2=find(md.mesh.y==L & md.mesh.x~=0 & md.mesh.x~=L); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=L); %Don't take the same nodes two times + posy2=find(md.mesh.y==L & md.mesh.x~=0. & md.mesh.x~=L); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; %Add spc on the corners - pos=find((md.mesh.x==0 | md.mesh.x==L) & (md.mesh.y==0 | md.mesh.y==L) & md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - if(L==5000), + pos=find((md.mesh.x==0. | md.mesh.x==L) & (md.mesh.y==0. | md.mesh.y==L) & md.mesh.vertexonbed); + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + if(L==5000.), md.diagnostic.spcvx(pos)=15.66; md.diagnostic.spcvy(pos)=-0.1967; - elseif(L==10000), + elseif(L==10000.), md.diagnostic.spcvx(pos)=16.04; md.diagnostic.spcvy(pos)=-0.1977; - elseif(L==20000), + elseif(L==20000.), md.diagnostic.spcvx(pos)=16.53; md.diagnostic.spcvy(pos)=-1.27; - elseif(L==40000), + elseif(L==40000.), md.diagnostic.spcvx(pos)=17.23; md.diagnostic.spcvy(pos)=-3.17; - elseif(L==80000), + elseif(L==80000.), md.diagnostic.spcvx(pos)=16.68; md.diagnostic.spcvy(pos)=-2.69; - elseif(L==160000), + elseif(L==160000.), md.diagnostic.spcvx(pos)=16.03; md.diagnostic.spcvy(pos)=-1.27; @@ -59,5 +59,5 @@ %Spc the bed at zero for vz pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvz(pos)=0; + md.diagnostic.spcvz(pos)=0.; %Compute the diagnostic @@ -75,45 +75,45 @@ %Now plot vx, vy, vz and vx on a cross section plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipcpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipcpattynvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynvy' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipcpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end - if(L==5000), + if(L==5000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 20],'xlim',[0 5000],'title','','xlabel','','figure',5) - elseif(L==10000), + elseif(L==10000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[13 18],'xlim',[0 10000],'title','','xlabel','') - elseif(L==20000), + elseif(L==20000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[14 22],'xlim',[0 20000],'title','','xlabel','') - elseif(L==40000), + elseif(L==40000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 40],'xlim',[0 40000],'title','','xlabel','') - elseif(L==80000), + elseif(L==80000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 80],'xlim',[0 80000],'title','','xlabel','') - elseif(L==160000), + elseif(L==160000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 200],'xlim',[0 160000],'title','','xlabel','') end - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipcpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end end @@ -121,15 +121,16 @@ %Now plot the min and max values of vx for each size of the square plot([5 10 20 40 80 160],minvx);ylim([4 18]);xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipcpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end plot([5 10 20 40 80 160],maxvx);ylim([0 200]); xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipcpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipcpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC ']); + system(['mv ismipcpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestC']); end + %Fields and tolerances to track changes field_names ={... Index: /issm/trunk/test/NightlyRun/test1105.py =================================================================== --- /issm/trunk/test/NightlyRun/test1105.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1105.py (revision 14310) @@ -0,0 +1,175 @@ +import numpy +import shutil +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +printingflag=False + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] +minvx=[] +maxvx=[] + +for L in L_list: #in m (3 times the desired length for BC problems) + nx=30 #number of nodes in x direction + ny=30 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPC.py') + md.extrude(10,1.) + + md=setflowequation(md,'pattyn','all') + + #Create MPCs to have periodic boundary conditions + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,md.mesh.y!=0.,md.mesh.y!=L))[0] + posx2=numpy.nonzero(logical_and_n(md.mesh.x==L,md.mesh.y!=0.,md.mesh.y!=L))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=L))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==L,md.mesh.x!=0.,md.mesh.x!=L))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Add spc on the corners + pos=numpy.nonzero(logical_and_n(numpy.logical_or(md.mesh.x==0.,md.mesh.x==L),numpy.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbed)) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + if (L==5000.): + md.diagnostic.spcvx[pos]=15.66 + md.diagnostic.spcvy[pos]=-0.1967 + elif (L==10000.): + md.diagnostic.spcvx[pos]=16.04 + md.diagnostic.spcvy[pos]=-0.1977 + elif (L==20000.): + md.diagnostic.spcvx[pos]=16.53 + md.diagnostic.spcvy[pos]=-1.27 + elif (L==40000.): + md.diagnostic.spcvx[pos]=17.23 + md.diagnostic.spcvy[pos]=-3.17 + elif (L==80000.): + md.diagnostic.spcvx[pos]=16.68 + md.diagnostic.spcvy[pos]=-2.69 + elif (L==160000.): + md.diagnostic.spcvx[pos]=16.03 + md.diagnostic.spcvy[pos]=-1.27 + + #Spc the bed at zero for vz + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvz[pos]=0. + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + + #Now plot vx, vy, vz and vx on a cross section +# plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipcpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipcpattynvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') +# plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipcpattynvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipcpattynvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') +# plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipcpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipcpattynvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') + + if (L==5000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 20],'xlim',[0 5000],'title','','xlabel','','figure',5) + elif (L==10000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[13 18],'xlim',[0 10000],'title','','xlabel','') + elif (L==20000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[14 22],'xlim',[0 20000],'title','','xlabel','') + elif (L==40000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 40],'xlim',[0 40000],'title','','xlabel','') + elif (L==80000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 80],'xlim',[0 80000],'title','','xlabel','') + elif (L==160000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 200],'xlim',[0 160000],'title','','xlabel','') + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipcpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipcpattynvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') + +#Now plot the min and max values of vx for each size of the square +#plot([5 10 20 40 80 160],minvx);ylim([4 18]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipcpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipcpattynminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') +#plot([5 10 20 40 80 160],maxvx);ylim([0 200]); xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipcpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipcpattynmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-08,1e-07,1e-07,\ + 1e-09,1e-07,1e-07,\ + 1e-09,1e-09,1e-07,\ + 1e-09,1e-09,1e-08,\ + 1e-09,1e-08,1e-08,\ + 1e-09,1e-08,1e-08,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1106.m =================================================================== --- /issm/trunk/test/NightlyRun/test1106.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1106.m (revision 14310) @@ -1,6 +1,6 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; @@ -10,32 +10,32 @@ md=setmask(md,'',''); %ice sheet test md=parameterize(md,'../Par/ISMIPC.par'); - md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/L).*sin(md.mesh.y*2*pi/L))); + md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/L).*sin(md.mesh.y*2.*pi/L))); md=extrude(md,10,1.); %Add spc on the borders - pos=find((md.mesh.x==0 | md.mesh.x==max(md.mesh.x) | md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - if(L==5000), + pos=find(md.mesh.x==0. | md.mesh.x==max(md.mesh.x) | md.mesh.y==0. | md.mesh.y==max(md.mesh.y)); + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + if(L==5000.), md.diagnostic.spcvx(pos)=15.66; md.diagnostic.spcvy(pos)=-0.1967; - elseif(L==10000), + elseif(L==10000.), md.diagnostic.spcvx(pos)=16.04; md.diagnostic.spcvy(pos)=-0.1977; - elseif(L==20000), + elseif(L==20000.), md.diagnostic.spcvx(pos)=16.53; md.diagnostic.spcvy(pos)=-1.27; - elseif(L==40000), + elseif(L==40000.), md.diagnostic.spcvx(pos)=17.23; md.diagnostic.spcvy(pos)=-3.17; - elseif(L==80000), + elseif(L==80000.), md.diagnostic.spcvx(pos)=16.68; md.diagnostic.spcvy(pos)=-2.69; - elseif(L==160000), + elseif(L==160000.), md.diagnostic.spcvx(pos)=16.03; md.diagnostic.spcvy(pos)=-1.27; end - md=setflowequation(md,'stokes','all'); + md=setflowequation(md,'stokes','all'); %Compute the diagnostic Index: /issm/trunk/test/NightlyRun/test1106.py =================================================================== --- /issm/trunk/test/NightlyRun/test1106.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1106.py (revision 14310) @@ -0,0 +1,87 @@ +import numpy +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] + +for L in L_list: + md=triangle(model(),"../Exp/Square_%d.exp" % L,L/10.) #size 3*L + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPC.py') + md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/L)*numpy.sin(md.mesh.y.reshape(-1,1)*2.*numpy.pi/L))) + md.extrude(10,1.) + + #Add spc on the borders + pos=numpy.nonzero(logical_or_n(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y))) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + if (L==5000.): + md.diagnostic.spcvx[pos]=15.66 + md.diagnostic.spcvy[pos]=-0.1967 + elif (L==10000.): + md.diagnostic.spcvx[pos]=16.04 + md.diagnostic.spcvy[pos]=-0.1977 + elif (L==20000.): + md.diagnostic.spcvx[pos]=16.53 + md.diagnostic.spcvy[pos]=-1.27 + elif (L==40000.): + md.diagnostic.spcvx[pos]=17.23 + md.diagnostic.spcvy[pos]=-3.17 + elif (L==80000.): + md.diagnostic.spcvx[pos]=16.68 + md.diagnostic.spcvy[pos]=-2.69 + elif (L==160000.): + md.diagnostic.spcvx[pos]=16.03 + md.diagnostic.spcvy[pos]=-1.27 + + md=setflowequation(md,'stokes','all') + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + +# plotmodel(md,'data',vx,'data',vy,'data',vz,'layer#all',md.mesh.numberoflayers) + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-12,1e-12,1e-11,\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-12,1e-12,\ + 1e-12,1e-11,1e-12,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1107.m =================================================================== --- /issm/trunk/test/NightlyRun/test1107.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1107.m (revision 14310) @@ -1,7 +1,7 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 printingflag=false; -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; minvx=[]; @@ -26,27 +26,27 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0 & ~(md.mesh.y==0 & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); - posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0 & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); + posx=find(md.mesh.x==0. & ~(md.mesh.y==0. & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); + posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0. & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times - posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; %Add spc on the corners - pos=find((md.mesh.x==0 | md.mesh.x==L) & (md.mesh.y==0 | md.mesh.y==L) & md.mesh.vertexonbed); - md.diagnostic.spcvy(:)=0; - md.diagnostic.spcvx(pos)=0; - if(L==5000), + pos=find((md.mesh.x==0. | md.mesh.x==L) & (md.mesh.y==0. | md.mesh.y==L) & md.mesh.vertexonbed); + md.diagnostic.spcvy(:)=0.; + md.diagnostic.spcvx(pos)=0.; + if(L==5000.), md.diagnostic.spcvx(pos)=16.0912; - elseif(L==10000), + elseif(L==10000.), md.diagnostic.spcvx(pos)=16.52; - elseif(L==20000), + elseif(L==20000.), md.diagnostic.spcvx(pos)=17.77; - elseif(L==40000), + elseif(L==40000.), md.diagnostic.spcvx(pos)=19.88; - elseif(L==80000), + elseif(L==80000.), md.diagnostic.spcvx(pos)=18.65; - elseif(L==160000), + elseif(L==160000.), md.diagnostic.spcvx(pos)=16.91; end @@ -54,5 +54,5 @@ %Spc the bed at zero for vz pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvz(pos)=0; + md.diagnostic.spcvz(pos)=0.; %Compute the diagnostic @@ -70,39 +70,39 @@ %Now plot vx, vy, vz and vx on a cross section plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipdpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipdpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD ']); + system(['mv ismipdpattynvx' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD']); end plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipdpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipdpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD ']); + system(['mv ismipdpattynvz' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD']); end - if(L==5000), + if(L==5000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 20],'xlim',[0 5000],'title','','xlabel','','figure',4) - elseif(L==10000), + elseif(L==10000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 20],'xlim',[0 10000],'title','','xlabel','','figure',4) - elseif(L==20000), + elseif(L==20000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 30],'xlim',[0 20000],'title','','xlabel','','figure',4) - elseif(L==40000), + elseif(L==40000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[10 60],'xlim',[0 40000],'title','','xlabel','','figure',4) - elseif(L==80000), + elseif(L==80000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 200],'xlim',[0 80000],'title','','xlabel','','figure',4) - elseif(L==160000), + elseif(L==160000.), plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... 'resolution',[10 10],'ylim',[0 400],'xlim',[0 160000],'title','','xlabel','','figure',4) end - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel(['ismipdpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipdpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD ']); + system(['mv ismipdpattynvxsec' num2str(L) '.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD']); end end @@ -110,15 +110,16 @@ %Now plot the min and max values of vx for each size of the square plot([5 10 20 40 80 160],minvx);ylim([2 18]);xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipdpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipdpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD ']); + system(['mv ismipdpattynminvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD']); end plot([5 10 20 40 80 160],maxvx);ylim([0 300]);xlim([0 160]) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('ismipdpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipdpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD ']); + system(['mv ismipdpattynmaxvx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestD']); end + %Fields and tolerances to track changes field_names ={... Index: /issm/trunk/test/NightlyRun/test1107.py =================================================================== --- /issm/trunk/test/NightlyRun/test1107.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1107.py (revision 14310) @@ -0,0 +1,166 @@ +import numpy +import shutil +from model import * +from squaremesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +printingflag=False + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] +minvx=[] +maxvx=[] + +for L in L_list: + nx=30 #numberof nodes in x direction + ny=30 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPD.py') + md.extrude(10,1.) + + md=setflowequation(md,'pattyn','all') + + #We need one grd on dirichlet: the 4 corners are set to zero + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + #Create MPCs to have periodic boundary conditions +# posx=find(md.mesh.x==0. & ~(md.mesh.y==0. & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); + posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,numpy.logical_not(numpy.logical_and(md.mesh.y==0.,md.mesh.vertexonbed)),numpy.logical_not(numpy.logical_and(md.mesh.y==L,md.mesh.vertexonbed))))[0] +# posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0. & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); + posx2=numpy.nonzero(logical_and_n(md.mesh.x==numpy.max(md.mesh.x),numpy.logical_not(numpy.logical_and(md.mesh.y==0.,md.mesh.vertexonbed)),numpy.logical_not(numpy.logical_and(md.mesh.y==L,md.mesh.vertexonbed))))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Add spc on the corners + pos=numpy.nonzero(logical_and_n(numpy.logical_or(md.mesh.x==0.,md.mesh.x==L),numpy.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbed)) + md.diagnostic.spcvy[:]=0. + md.diagnostic.spcvx[pos]=0. + if (L==5000.): + md.diagnostic.spcvx[pos]=16.0912 + elif (L==10000.): + md.diagnostic.spcvx[pos]=16.52 + elif (L==20000.): + md.diagnostic.spcvx[pos]=17.77 + elif (L==40000.): + md.diagnostic.spcvx[pos]=19.88 + elif (L==80000.): + md.diagnostic.spcvx[pos]=18.65 + elif (L==160000.): + md.diagnostic.spcvx[pos]=16.91 + + #Spc the bed at zero for vz + pos=numpy.nonzero(md.mesh.vertexonbed) + md.diagnostic.spcvz[pos]=0. + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + + #Now plot vx, vy, vz and vx on a cross section +# plotmodel(md,'data',vx,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',2) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipdpattynvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipdpattynvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') +# plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipdpattynvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipdpattynvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') + + if (L==5000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP5000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 20],'xlim',[0 5000],'title','','xlabel','','figure',4) + elif (L==10000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP10000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 20],'xlim',[0 10000],'title','','xlabel','','figure',4) + elif (L==20000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP20000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 30],'xlim',[0 20000],'title','','xlabel','','figure',4) + elif (L==40000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP40000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[10 60],'xlim',[0 40000],'title','','xlabel','','figure',4) + elif (L==80000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP80000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 200],'xlim',[0 80000],'title','','xlabel','','figure',4) + elif (L==160000.): + pass +# plotmodel(md,'data',vx,'sectionvalue','../Exp/ISMIP160000.exp','layer',md.mesh.numberoflayers,... +# 'resolution',[10 10],'ylim',[0 400],'xlim',[0 160000],'title','','xlabel','','figure',4) + if printingflag: + pass +# set(gcf,'Color','w') +# printmodel(['ismipdpattynvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move("ismipdpattynvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') + +#Now plot the min and max values of vx for each size of the square +#plot([5 10 20 40 80 160],minvx);ylim([2 18]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipdpattynminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipdpattynminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') +#plot([5 10 20 40 80 160],maxvx);ylim([0 300]);xlim([0 160]) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('ismipdpattynmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# shutil.move('ismipdpattynmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-07,1e-08,1e-06,\ + 1e-08,1e-08,1e-06,\ + 1e-08,1e-08,1e-07,\ + 1e-08,1e-08,1e-07,\ + 1e-08,1e-08,1e-07,\ + 1e-07,1e-08,1e-06,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1108.m =================================================================== --- /issm/trunk/test/NightlyRun/test1108.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1108.m (revision 14310) @@ -1,6 +1,6 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %Pattyn and Payne 2006 -L_list={5000,10000,20000,40000,80000,160000}; +L_list={5000.,10000.,20000.,40000.,80000.,160000.}; results={}; @@ -17,20 +17,20 @@ md=setflowequation(md,'pattyn','all'); - %We need one grd on dirichlet: the 4 corners are set to zero + %We need one grid on dirichlet: the 4 corners are set to zero md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - pos=find(md.mesh.vertexonbed & (md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; + pos=find(md.mesh.vertexonbed & (md.mesh.x==0. | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0. | md.mesh.y==max(md.mesh.y))); + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + md.diagnostic.spcvz(pos)=0.; %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times - posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); + posy=find(md.mesh.y==0. & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0. & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; @@ -47,5 +47,5 @@ md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - pos=find(md.mesh.y==0 | md.mesh.x==0 | md.mesh.x==max(md.mesh.x) | md.mesh.y==max(md.mesh.y)); %Don't take the same nodes two times + pos=find(md.mesh.y==0. | md.mesh.x==0. | md.mesh.x==max(md.mesh.x) | md.mesh.y==max(md.mesh.y)); %Don't take the same nodes two times md.diagnostic.spcvx(pos)=md.results.DiagnosticSolution.Vx(pos); md.diagnostic.spcvy(pos)=md.results.DiagnosticSolution.Vy(pos); Index: /issm/trunk/test/NightlyRun/test1108.py =================================================================== --- /issm/trunk/test/NightlyRun/test1108.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1108.py (revision 14310) @@ -0,0 +1,98 @@ +import numpy +from model import * +from bamg import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * +from PythonFuncs import * + +""" +This test is a test from the ISMP-HOM Intercomparison project. +Pattyn and Payne 2006 +""" + +L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +results=[] + +for L in L_list: + nx=30 #numberof nodes in x direction + ny=30 + md=model() + md=squaremesh(md,L,L,nx,ny) + md=setmask(md,'','') #ice sheet test + md=parameterize(md,'../Par/ISMIPD.py') + md.extrude(10,1.) + + md=setflowequation(md,'pattyn','all') + + #We need one grd on dirichlet: the 4 corners are set to zero + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + pos=numpy.nonzero(logical_and_n(md.mesh.vertexonbed,numpy.logical_or(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y)))) + md.diagnostic.spcvx[pos]=0. + md.diagnostic.spcvy[pos]=0. + md.diagnostic.spcvz[pos]=0. + + #Create MPCs to have periodic boundary conditions + posx=numpy.nonzero(md.mesh.x==0.)[0] + posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + + posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + + md.diagnostic.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + + #Compute the diagnostic + md.cluster=generic('name',oshostname(),'np',8) + md.verbose=verbose('convergence',True) + md=solve(md,DiagnosticSolutionEnum()) + md.diagnostic.reltol=float('NaN') + md.diagnostic.abstol=float('NaN') + md.diagnostic.vertex_pairing=numpy.empty((0,2)) + #We need one grid on dirichlet: the 4 corners are set to zero + md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + pos=numpy.nonzero(logical_or_n(md.mesh.y==0.,md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==numpy.max(md.mesh.y))) #Don't take the same nodes two times + md.diagnostic.spcvx[pos]=md.results.DiagnosticSolution.Vx[pos] + md.diagnostic.spcvy[pos]=md.results.DiagnosticSolution.Vy[pos] + md=setflowequation(md,'stokes','all') + md=solve(md,DiagnosticSolutionEnum()) + + #Plot the results and save them + vx=md.results.DiagnosticSolution.Vx + vy=md.results.DiagnosticSolution.Vy + vz=md.results.DiagnosticSolution.Vz + results.append(md.results.DiagnosticSolution) + +# plotmodel(md,'data',vx,'data',vy,'data',vz,'layer#all',md.mesh.numberoflayers) + +#Fields and tolerances to track changes +field_names =[\ + 'Vx5km','Vy5km','Vz5km',\ + 'Vx10km','Vy10km','Vz10km',\ + 'Vx20km','Vy20km','Vz20km',\ + 'Vx40km','Vy40km','Vz40km',\ + 'Vx80km','Vy80km','Vz80km',\ + 'Vx160km','Vy160km','Vz160km' +] +field_tolerances=[\ + 1e-07,1e-07,1e-07,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-07,1e-07,\ + 1e-08,1e-08,1e-08,\ + 1e-08,1e-07,1e-07,\ + 1e-07,1e-06,1e-07,\ +] +field_values=[] +for result in results: + field_values=field_values+[\ + result.Vx,\ + result.Vy,\ + result.Vz,\ + ] Index: /issm/trunk/test/NightlyRun/test1109.m =================================================================== --- /issm/trunk/test/NightlyRun/test1109.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1109.m (revision 14310) @@ -1,3 +1,3 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %TestE %Four tests to run: - Pattyn frozen @@ -9,6 +9,6 @@ for i=1:4, - Lx=10; %in m - Ly=5000; %in m + Lx=10.; %in m + Ly=5000.; %in m nx=3; %number of nodes in x direction ny=51; @@ -26,5 +26,5 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2]; @@ -35,7 +35,7 @@ md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + md.diagnostic.spcvz(pos)=0.; %Remove the spc where there is some sliding (case 3 and 4): @@ -58,34 +58,35 @@ if i==1, plotmodel(md,'data',vy,'ylim',[-10 80],'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIPE.exp','resolution',[10 10],'title','','xlabel','') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel('ismipepattynvxfrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipepattynvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE ']); + system(['mv ismipepattynvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE']); end elseif i==2, plotmodel(md,'data',vy,'ylim',[-10 80],'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIPE.exp','resolution',[10 10],'title','','xlabel','') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel('ismipestokesvxfrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipestokesvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE ']); + system(['mv ismipestokesvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE']); end elseif i==3, plotmodel(md,'data',vy,'ylim',[-50 200],'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIPE.exp','resolution',[10 10],'title','','xlabel','') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel('ismipepattynvxsliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipepattynvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE ']); + system(['mv ismipepattynvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE']); end elseif i==4, plotmodel(md,'data',vy,'ylim',[-50 200],'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIPE.exp','resolution',[10 10],'title','','xlabel','') - if printingflag, + if printingflag, set(gcf,'Color','w') printmodel('ismipestokesvxsliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipestokesvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE ']); + system(['mv ismipestokesvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestE']); end end end + %Fields and tolerances to track changes -field_names ={ ... +field_names ={... 'VyPattynSliding','VzPattynSliding',... 'VxStokesSliding','VyStokesSliding','VzStokesSliding',... Index: /issm/trunk/test/NightlyRun/test1110.m =================================================================== --- /issm/trunk/test/NightlyRun/test1110.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1110.m (revision 14310) @@ -1,13 +1,14 @@ -%This test is a test from the ISMP-HOM Intercomparison project +%This test is a test from the ISMP-HOM Intercomparison project. %TestF printingflag=false; +results={}; for i=1:4, - L=100000; %in m + L=100000.; %in m nx=30; %numberof nodes in x direction ny=30; md=model(); md=squaremesh(md,L,L,nx,ny); - %md=triangle(md,'../Exp/SquareISMIP.exp',5500.); +% md=triangle(md,'../Exp/SquareISMIP.exp',5500.); md=setmask(md,'',''); %ice sheet test md=parameterize(md,'../Par/ISMIPF.par'); @@ -26,21 +27,21 @@ %Create dirichlet on the bed if no slip pos=find(md.mesh.vertexonbed); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; + md.diagnostic.spcvx(pos)=0.; + md.diagnostic.spcvy(pos)=0.; + md.diagnostic.spcvz(pos)=0.; else - pos=find(md.mesh.vertexonbed & (md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); - md.diagnostic.spcvx(pos)=100; %because we need a dirichlet somewhere - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; + pos=find(md.mesh.vertexonbed & (md.mesh.x==0. | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0. | md.mesh.y==max(md.mesh.y))); + md.diagnostic.spcvx(pos)=100.; %because we need a dirichlet somewhere + md.diagnostic.spcvy(pos)=0.; + md.diagnostic.spcvz(pos)=0.; end pos=find(~md.mesh.vertexonbed); - md.thermal.spctemperature(pos)=255; + md.thermal.spctemperature(pos)=255.; %Create MPCs to have periodic boundary conditions - posx=find(md.mesh.x==0); + posx=find(md.mesh.x==0.); posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.mesh.y==0); + posy=find(md.mesh.y==0.); posy2=find(md.mesh.y==max(md.mesh.y)); @@ -48,6 +49,6 @@ md.prognostic.vertex_pairing=[posx,posx2;posy,posy2]; - md.timestepping.time_step=3; - md.timestepping.final_time=300; + md.timestepping.time_step=3.; + md.timestepping.final_time=300.; md.settings.output_frequency=50; md.prognostic.stabilization=1; @@ -68,36 +69,36 @@ plotmodel(md,'data',(md.results.TransientSolution(end).Vx),'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIP100000.exp','title','','xlabel','','ylabel','Velocity (m/yr)','linewidth',3,'grid','on','unit','km','ylim',[185 200]) end - if printingflag, + if printingflag, set(gcf,'Color','w') if i==1, printmodel('ismipfpattynvxfrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfpattynvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfpattynvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==2, printmodel('ismipfpattynvxsliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfpattynvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfpattynvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==3, printmodel('ismipfstokesvxfrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfstokesvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfstokesvxfrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==4, printmodel('ismipfstokesvxsliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfstokesvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfstokesvxsliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); end end plotmodel(md,'data',(md.results.TransientSolution(end).Surface)-md.geometry.surface,'layer',md.mesh.numberoflayers,'sectionvalue','../Exp/ISMIP100000.exp','title','','xlabel','','ylabel','Surface (m)','linewidth',3,'grid','on','unit','km','ylim',[-30 50]) - if printingflag, + if printingflag, set(gcf,'Color','w') if i==1, printmodel('ismipfpattyndeltasurfacefrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfpattyndeltasurfacefrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfpattyndeltasurfacefrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==2, printmodel('ismipfpattyndeltasurfacesliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfpattyndeltasurfacesliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfpattyndeltasurfacesliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==3, printmodel('ismipfstokesdeltasurfacefrozen','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfstokesdeltasurfacefrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfstokesdeltasurfacefrozen.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); elseif i==4, printmodel('ismipfstokesdeltasurfacesliding','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); - system(['mv ismipfstokesdeltasurfacesliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF ']); + system(['mv ismipfstokesdeltasurfacesliding.png ' ISSM_DIR '/website/doc_pdf/validation/Images/ISMIP/TestF']); end end @@ -105,5 +106,5 @@ %Fields and tolerances to track changes -field_names ={ ... +field_names ={... 'VxPattynFrozen','VyPattynFrozen','VzPattynFrozen','SurfacePattynFrozen',... 'VxPattynSliding','VyPattynSliding','VzPattynSliding','SurfacePattynSliding',... Index: /issm/trunk/test/NightlyRun/test1201.m =================================================================== --- /issm/trunk/test/NightlyRun/test1201.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1201.m (revision 14310) @@ -1,3 +1,3 @@ -%This test is a test from the EISMINT for Ice shelves Vincent Rommelaere 1996 +%This test is a test from the EISMINT for Ice shelves Vincent Rommelaere 1996. printingflag=false; @@ -6,8 +6,8 @@ for stabilization=1:3; %The goal is to test the prognostic model - md=bamg(model(),'domain','../Exp/SquareEISMINT.exp','hmax',3000); + md=bamg(model(),'domain','../Exp/SquareEISMINT.exp','hmax',3000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareEISMINT.par'); - md.surfaceforcings.mass_balance(:)=0; + md.surfaceforcings.mass_balance(:)=0.; md=setflowequation(md,'macayeal','all'); md.cluster=generic('name',oshostname(),'np',8); @@ -15,5 +15,5 @@ disp(' initial velocity'); md.initialization.vx=zeros(md.mesh.numberofvertices,1); - md.initialization.vy=-400*ones(md.mesh.numberofvertices,1); + md.initialization.vy=-400.*ones(md.mesh.numberofvertices,1); %Stabilization @@ -29,7 +29,7 @@ md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices+1,length(times)); md.prognostic.spcthickness(end,:)=times; - md.prognostic.spcthickness(pos,:)=repmat(500+100*sin(2*pi*times/200),length(pos),1); + md.prognostic.spcthickness(pos,:)=repmat(500.+100.*sin(2.*pi*times/200.),length(pos),1); if stabilization==3, - pos=find(isnan(md.prognostic.spcthickness)); md.prognostic.spcthickness(pos)=500; %No NaN for DG + pos=find(isnan(md.prognostic.spcthickness)); md.prognostic.spcthickness(pos)=500.; %No NaN for DG end @@ -43,11 +43,11 @@ %plot results -[elements,x,y,z,s,h1]=SectionValues(md,results{1},'../Exp/CrossLineEISMINT.exp',100); -[elements,x,y,z,s,h2]=SectionValues(md,results{2},'../Exp/CrossLineEISMINT.exp',100); -[elements,x,y,z,s,h3]=SectionValues(md,results{3},'../Exp/CrossLineEISMINT.exp',100); -[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100); +[elements,x,y,z,s,h1]=SectionValues(md,results{1},'../Exp/CrossLineEISMINT.exp',100.); +[elements,x,y,z,s,h2]=SectionValues(md,results{2},'../Exp/CrossLineEISMINT.exp',100.); +[elements,x,y,z,s,h3]=SectionValues(md,results{3},'../Exp/CrossLineEISMINT.exp',100.); +[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100.); plot(s,h1,'r',s,h2,'b',s,h3,'g',s,hth,'k') legend('Art. diff.','No Art. diff.','D.G.','Theoretical') -if printingflag, +if printingflag, set(gcf,'Color','w') export_fig([issmdir() '/website/doc_pdf/validation/Images/EISMINT/IceShelf/eismintmasscthickness.pdf']); @@ -56,5 +56,5 @@ %Fields and tolerances to track changes field_names ={ ... - 'ThicknessArtDigg','ThicknessNoArtDiff','ThicknessDG' ... + 'ThicknessArtDiff','ThicknessNoArtDiff','ThicknessDG' ... }; field_tolerances={... Index: /issm/trunk/test/NightlyRun/test1201.py =================================================================== --- /issm/trunk/test/NightlyRun/test1201.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1201.py (revision 14310) @@ -0,0 +1,78 @@ +import numpy +from model import * +from bamg import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +This test is a test from the EISMINT for Ice shelves Vincent Rommelaere 1996. +""" + +printingflag=False + +results=[] + +for stabilization in xrange(1,4): + #The goal is to test the prognostic model + md=bamg(model(),'domain','../Exp/SquareEISMINT.exp','hmax',3000.) + md=setmask(md,'all','') + md=parameterize(md,'../Par/SquareEISMINT.py') + md.surfaceforcings.mass_balance[:]=0. + md=setflowequation(md,'macayeal','all') + md.cluster=generic('name',oshostname(),'np',8) + + print " initial velocity" + md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) + md.initialization.vy=-400.*numpy.ones((md.mesh.numberofvertices,1)) + + #Stabilization + if stabilization==2: + md.prognostic.stabilization=0 + else: + md.prognostic.stabilization=stabilization + + #spc thickness + pos=numpy.nonzero(md.mesh.y>199999.9)[0] + times=numpy.arange(0,501) + md.prognostic.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices+1,numpy.size(times))) + md.prognostic.spcthickness[-1,:]=times + md.prognostic.spcthickness[pos,:]=numpy.tile(500.+100.*numpy.sin(2.*numpy.pi*times/200.),(numpy.size(pos),1)) + if stabilization==3: + pos=numpy.nonzero(numpy.isnan(md.prognostic.spcthickness)) + md.prognostic.spcthickness[pos]=500. #No NaN for DG + + #solve + md.transient.isdiagnostic=False + md.settings.output_frequency=500 #keep only last step + md.verbose=verbose() + md=solve(md,TransientSolutionEnum()) + results.append(md.results.TransientSolution[-1].Thickness) + +#plot results +#[elements,x,y,z,s,h1]=SectionValues(md,results[0],'../Exp/CrossLineEISMINT.exp',100.); +#[elements,x,y,z,s,h2]=SectionValues(md,results[1],'../Exp/CrossLineEISMINT.exp',100.); +#[elements,x,y,z,s,h3]=SectionValues(md,results[2],'../Exp/CrossLineEISMINT.exp',100.); +#[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100.); +#plot(s,h1,'r',s,h2,'b',s,h3,'g',s,hth,'k') +#legend('Art. diff.','No Art. diff.','D.G.','Theoretical') +if printingflag: + pass +# set(gcf,'Color','w') +# export_fig([issmdir() '/website/doc_pdf/validation/Images/EISMINT/IceShelf/eismintmasscthickness.pdf']); + +#Fields and tolerances to track changes +field_names =[ \ + 'ThicknessArtDiff','ThicknessNoArtDiff','ThicknessDG' \ +] +field_tolerances=[\ + 1e-13, 1e-13, 1e-13\ +] +field_values=[ + results[0], \ + results[1], \ + results[2], \ +] Index: /issm/trunk/test/NightlyRun/test1202.m =================================================================== --- /issm/trunk/test/NightlyRun/test1202.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1202.m (revision 14310) @@ -1,3 +1,3 @@ -%Test on the diagnostic model and the prognostic in 2d +%Test on the diagnostic model and the prognostic in 2d. printingflag=false; @@ -19,5 +19,5 @@ plotmodel(md,'data',vx,'contourlevels',{0,20,40,60,60,100,120,140,160,180,-20,-40,-60,-80,-100,-120,-140,-160,-180}, ... 'contourcolor','k') -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eismintdiag1vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); @@ -27,5 +27,5 @@ plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... 'contourcolor','k') -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eismintdiag1vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1202.py =================================================================== --- /issm/trunk/test/NightlyRun/test1202.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1202.py (revision 14310) @@ -0,0 +1,54 @@ +import numpy +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +Test on the diagnostic model and the prognostic in 2d +""" + +printingflag=False + +#tests 3 and 4: using Glen's flow law +md=model() +md=triangle(md,'../Exp/SquareEISMINT.exp',3550.) +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareEISMINT.py') +md=setflowequation(md,'macayeal','all') #MacAyeal's model and 2d + +#Compute solution for MacAyeal's model +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +#plot results +vx=md.results.DiagnosticSolution.Vx +vy=md.results.DiagnosticSolution.Vy + +#plotmodel(md,'data',vx,'contourlevels',{0,20,40,60,60,100,120,140,160,180,-20,-40,-60,-80,-100,-120,-140,-160,-180}, ... +# 'contourcolor','k') +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eismintdiag1vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eismintdiag1vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... +# 'contourcolor','k') +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eismintdiag1vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eismintdiag1vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#Fields and tolerances to track changes +field_names =['Vx','Vy'] +field_tolerances=[1e-13,1e-13] +field_values=[\ + vx, \ + vy, \ + ] Index: /issm/trunk/test/NightlyRun/test1203.m =================================================================== --- /issm/trunk/test/NightlyRun/test1203.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1203.m (revision 14310) @@ -2,5 +2,5 @@ printingflag=false; -%test 5 and 6 : +%test 5 and 6: md=model(); md=triangle(md,'../Exp/SquareEISMINT.exp',5100.); %test3 @@ -11,5 +11,5 @@ %Impose a non zero velocity on the upper boundary condition (y=max(y)) pos=find(md.mesh.y==max(md.mesh.y)); -md.diagnostic.spcvy(pos)=400*(((md.mesh.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000)/25000).^2); +md.diagnostic.spcvy(pos)=400.*(((md.mesh.x(pos)-100000.)/25000.).^2-ones(size(pos,1),1)).*heaviside((1.+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000.)/25000.).^2); %Compute solution for MacAyeal's model @@ -23,5 +23,5 @@ plotmodel(md,'data',vx,'contourlevels',{0,20,40,60,80,100,-20,-40,-60,-80,-100},... 'contourcolor','k') -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eismintdiag2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); @@ -30,5 +30,5 @@ plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... 'contourcolor','k') -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eismintdiag2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1203.py =================================================================== --- /issm/trunk/test/NightlyRun/test1203.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1203.py (revision 14310) @@ -0,0 +1,58 @@ +import numpy +import sys +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +Test on the diagnostic model and the prognostic in 2d +""" + +printingflag=False + +#test 5 and 6: +md=model() +md=triangle(md,'../Exp/SquareEISMINT.exp',5100.) #test3 +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareEISMINT.py') +md=setflowequation(md,'macayeal','all') #MacAyeal's model and 2d + +#Impose a non zero velocity on the upper boundary condition (y=max(y)) +pos=numpy.nonzero(md.mesh.y==numpy.max(md.mesh.y)) +md.diagnostic.spcvy[pos]=400.*(((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2-numpy.ones((numpy.size(pos),1)))*heaviside((1.+sys.float_info.epsilon)*numpy.ones((numpy.size(pos),1))-((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2) + +#Compute solution for MacAyeal's model +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +vx=md.results.DiagnosticSolution.Vx +vy=md.results.DiagnosticSolution.Vy + +#plot results +#plotmodel(md,'data',vx,'contourlevels',{0,20,40,60,80,100,-20,-40,-60,-80,-100},... +# 'contourcolor','k') +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eismintdiag2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eismintdiag2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +#plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... +# 'contourcolor','k') +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eismintdiag2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eismintdiag2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#Fields and tolerances to track changes +field_names =['Vx','Vy'] +field_tolerances=[1e-13,1e-13] +field_values=[\ + vx, \ + vy, \ + ] Index: /issm/trunk/test/NightlyRun/test1204.m =================================================================== --- /issm/trunk/test/NightlyRun/test1204.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1204.m (revision 14310) @@ -11,5 +11,5 @@ %Impose a non zero velocity on the upper boundary condition (y=max(y)) pos=find(md.mesh.y==max(md.mesh.y)); -md.diagnostic.spcvy(pos)=400*(((md.mesh.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000)/25000).^2); +md.diagnostic.spcvy(pos)=400.*(((md.mesh.x(pos)-100000.)/25000.).^2-ones(size(pos,1),1)).*heaviside((1.+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000.)/25000.).^2); %Compute solution for MacAyeal's model @@ -21,11 +21,11 @@ md.initialization.vy=(md.results.DiagnosticSolution.Vy); -md.timestepping.time_step=1; -md.timestepping.final_time=5000; +md.timestepping.time_step=1.; +md.timestepping.final_time=5000.; md.prognostic.stabilization=1; md=solve(md,TransientSolutionEnum()); plotmodel(md,'data',(md.results.TransientSolution(end).Vx)) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eisminttrans2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); @@ -34,5 +34,5 @@ plotmodel(md,'data',(md.results.TransientSolution(end).Vy)) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eisminttrans2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); @@ -41,5 +41,5 @@ plotmodel(md,'data',(md.results.TransientSolution(end).Thickness)) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('eisminttrans2thickness','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1204.py =================================================================== --- /issm/trunk/test/NightlyRun/test1204.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1204.py (revision 14310) @@ -0,0 +1,70 @@ +import numpy +import sys +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +Test on the diagnostic model and the prognostic in 2d +""" + +printingflag=False + +#tests 3 and 4: using Glen's flow law +md=model() +md=triangle(md,'../Exp/SquareEISMINT.exp',3550.) +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareEISMINT.py') +md=setflowequation(md,'macayeal','all') #MacAyeal's model and 2d + +#Impose a non zero velocity on the upper boundary condition (y=max(y)) +pos=numpy.nonzero(md.mesh.y==max(md.mesh.y)) +md.diagnostic.spcvy[pos]=400.*(((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2-numpy.ones((numpy.size(pos),1)))*heaviside((1.+sys.float_info.epsilon)*numpy.ones((numpy.size(pos),1))-((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2) + +#Compute solution for MacAyeal's model +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +#plot results +md.initialization.vx=md.results.DiagnosticSolution.Vx +md.initialization.vy=md.results.DiagnosticSolution.Vy + +md.timestepping.time_step=1. +md.timestepping.final_time=5000. +md.prognostic.stabilization=1 +md=solve(md,TransientSolutionEnum()) + +#plotmodel(md,'data',(md.results.TransientSolution(end).Vx)) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eisminttrans2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eisminttrans2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#plotmodel(md,'data',(md.results.TransientSolution(end).Vy)) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eisminttrans2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eisminttrans2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#plotmodel(md,'data',(md.results.TransientSolution(end).Thickness)) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('eisminttrans2thickness','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); +# system(['mv eisminttrans2thickness.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); + +#Fields and tolerances to track changes +field_names =['Vx','Vy','Thickness'] +field_tolerances=[1e-13,1e-13,1e-13] +field_values=[\ + md.results.TransientSolution[-1].Vx, \ + md.results.TransientSolution[-1].Vy, \ + md.results.TransientSolution[-1].Thickness, \ + ] Index: /issm/trunk/test/NightlyRun/test1205.m =================================================================== --- /issm/trunk/test/NightlyRun/test1205.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1205.m (revision 14310) @@ -1,11 +1,11 @@ -%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling +%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. printingflag=false; numlayers=10; -resolution=30000; +resolution=30000.; %To begin with the numerical model md=model(); -md=roundmesh(md,750000,resolution); +md=roundmesh(md,750000.,resolution); md=setmask(md,'',''); %We can not test iceshelves nor ice rises with this analytical solution md=parameterize(md,'../Par/RoundSheetStaticEISMINT.par'); @@ -13,7 +13,7 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; -vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); +vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); %We extrude the model to have a 3d model @@ -23,7 +23,7 @@ %Spc the nodes on the bed pos=find(md.mesh.vertexonbed); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; %Now we can solve the problem @@ -36,13 +36,12 @@ vel=zeros(md.mesh.numberofvertices2d,1); -node_vel=0; for i=1:md.mesh.numberofvertices2d - for j=1:(md.mesh.numberoflayers-1) - node_vel=node_vel+1/(2*(md.mesh.numberoflayers-1))*(sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+... - vy(i+j*md.mesh.numberofvertices2d,1).^2)+... + node_vel=0.; + for j=1:md.mesh.numberoflayers-1 + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*... + (sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+vy(i+j*md.mesh.numberofvertices2d,1).^2)+... sqrt(vx(i+(j-1)*md.mesh.numberofvertices2d,1).^2+vy(i+(j-1)*md.mesh.numberofvertices2d,1).^2)); end vel(i,1)=node_vel; - node_vel=0; end @@ -82,5 +81,5 @@ caxis([0 100]); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('hutterstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); @@ -92,8 +91,8 @@ 'Vx','Vy','Vel', ... }; -field_tolerances={... +field_tolerances={ ... 1e-13,1e-13,1e-13, ... }; -field_values={ +field_values={ ... vx,vy,vel, ... }; Index: /issm/trunk/test/NightlyRun/test1205.py =================================================================== --- /issm/trunk/test/NightlyRun/test1205.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1205.py (revision 14310) @@ -0,0 +1,109 @@ +import numpy +from model import * +from roundmesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. +""" + +printingflag=False + +numlayers=10 +resolution=30000. + +#To begin with the numerical model +md=model() +md=roundmesh(md,750000.,resolution) +md=setmask(md,'','') #We can not test iceshelves nor ice rises with this analytical solution +md=parameterize(md,'../Par/RoundSheetStaticEISMINT.py') + +#Calculation of the analytical 2d velocity field +constant=0.3 +vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 +vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 +vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) + +#We extrude the model to have a 3d model +md.extrude(numlayers,1.); +md=setflowequation(md,'hutter','all') + +#Spc the nodes on the bed +pos=numpy.nonzero(md.mesh.vertexonbed) +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. + +#Now we can solve the problem +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +#Calculate the depth averaged velocity field (2d): +vx=md.results.DiagnosticSolution.Vx +vy=md.results.DiagnosticSolution.Vy +vel=numpy.zeros((md.mesh.numberofvertices2d,1)) + +for i in xrange(0,md.mesh.numberofvertices2d): + node_vel=0. + for j in xrange(0,md.mesh.numberoflayers-1): + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ + (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ + numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i,0]=node_vel + +#Plot of the velocity from the exact and calculated solutions +#figure(1) +#set(gcf,'Position',[1 1 1580 1150]) +#subplot(2,2,1) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel,'FaceColor','interp','EdgeColor','none'); +#title('Modelled velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,2) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel_obs,'FaceColor','interp','EdgeColor','none'); +#title('Analytical velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,3) +#hold on; +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); +#legend('calculated velocity','exact velocity'); +#axis([0 750000 0 200]); +#hold off; + +#subplot(2,2,4) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#title('Relative misfit [%]','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 100]); + +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('hutterstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv hutterstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); + +#Fields and tolerances to track changes +field_names =[ \ + 'Vx','Vy','Vel', \ +] +field_tolerances=[ \ + 1e-13,1e-13,1e-13, \ +] +field_values=[ \ + vx,vy,vel, \ +] Index: /issm/trunk/test/NightlyRun/test1206.m =================================================================== --- /issm/trunk/test/NightlyRun/test1206.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1206.m (revision 14310) @@ -1,11 +1,11 @@ -%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling +%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. printingflag=false; numlayers=10; -resolution=30000; +resolution=30000.; %To begin with the numerical model md=model(); -md=roundmesh(md,750000,resolution); +md=roundmesh(md,750000.,resolution); md=setmask(md,'',''); %We can not test iceshelves nor ice rises with this analytical solution md=parameterize(md,'../Par/RoundSheetStaticEISMINT.par'); @@ -13,7 +13,7 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; -vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); +vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); %We extrude the model to have a 3d model @@ -23,7 +23,7 @@ %Spc the nodes on the bed pos=find(md.mesh.vertexonbed); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; %Now we can solve the problem @@ -36,13 +36,12 @@ vel=zeros(md.mesh.numberofvertices2d,1); -node_vel=0; for i=1:md.mesh.numberofvertices2d - for j=1:(md.mesh.numberoflayers-1) - node_vel=node_vel+1/(2*(md.mesh.numberoflayers-1))*(sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+... - vy(i+j*md.mesh.numberofvertices2d,1).^2)+... + node_vel=0.; + for j=1:md.mesh.numberoflayers-1 + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*... + (sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+vy(i+j*md.mesh.numberofvertices2d,1).^2)+... sqrt(vx(i+(j-1)*md.mesh.numberofvertices2d,1).^2+vy(i+(j-1)*md.mesh.numberofvertices2d,1).^2)); end vel(i,1)=node_vel; - node_vel=0; end @@ -81,5 +80,5 @@ caxis([0 100]); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('pattynstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); @@ -91,8 +90,8 @@ 'Vx','Vy','Vel', ... }; -field_tolerances={... +field_tolerances={ ... 1e-12,1e-12,1e-12, ... }; -field_values={ +field_values={ ... vx,vy,vel, ... }; Index: /issm/trunk/test/NightlyRun/test1206.py =================================================================== --- /issm/trunk/test/NightlyRun/test1206.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1206.py (revision 14310) @@ -0,0 +1,108 @@ +import numpy +from model import * +from roundmesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. +""" + +printingflag=False + +numlayers=10 +resolution=30000. + +#To begin with the numerical model +md=model() +md=roundmesh(md,750000.,resolution) +md=setmask(md,'','') #We can not test iceshelves nor ice rises with this analytical solution +md=parameterize(md,'../Par/RoundSheetStaticEISMINT.py') + +#Calculation of the analytical 2d velocity field +constant=0.3 +vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 +vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) + +#We extrude the model to have a 3d model +md.extrude(numlayers,1.) +md=setflowequation(md,'pattyn','all') + +#Spc the nodes on the bed +pos=numpy.nonzero(md.mesh.vertexonbed) +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. + +#Now we can solve the problem +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +#Calculate the depth averaged velocity field (2d): +vx=md.results.DiagnosticSolution.Vx +vy=md.results.DiagnosticSolution.Vy +vel=numpy.zeros((md.mesh.numberofvertices2d,1)) + +for i in xrange(0,md.mesh.numberofvertices2d): + node_vel=0. + for j in xrange(0,md.mesh.numberoflayers-1): + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ + (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ + numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i,0]=node_vel + +#Plot of the velocity from the exact and calculated solutions +#figure(1) +#subplot(2,2,1) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel,'FaceColor','interp','EdgeColor','none'); +#title('Modelled velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,2) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel_obs,'FaceColor','interp','EdgeColor','none'); +#title('Analytical velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,3) +#hold on; +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); +#legend('calculated velocity','exact velocity'); +#axis([0 750000 0 200]); +#hold off; + +#subplot(2,2,4) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#title('Relative misfit [%]','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 100]); + +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('pattynstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv pattynstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); + +#Fields and tolerances to track changes +field_names =[ \ + 'Vx','Vy','Vel', \ +] +field_tolerances=[ \ + 1e-12,1e-12,1e-12, \ +] +field_values=[ \ + vx,vy,vel, \ +] Index: /issm/trunk/test/NightlyRun/test1207.m =================================================================== --- /issm/trunk/test/NightlyRun/test1207.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1207.m (revision 14310) @@ -1,11 +1,11 @@ -%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling +%The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. printingflag=false; numlayers=10; -resolution=30000; +resolution=30000.; %To begin with the numerical model md=model(); -md=roundmesh(md,750000,resolution); +md=roundmesh(md,750000.,resolution); md=setmask(md,'',''); %We can not test iceshelves nor ice rises with this analytical solution md=parameterize(md,'../Par/RoundSheetStaticEISMINT.par'); @@ -13,7 +13,7 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; -vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); +vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); %We extrude the model to have a 3d model @@ -23,7 +23,7 @@ %Spc the nodes on the bed pos=find(md.mesh.vertexonbed); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; %Now we can solve the problem @@ -36,13 +36,12 @@ vel=zeros(md.mesh.numberofvertices2d,1); -node_vel=0; for i=1:md.mesh.numberofvertices2d - for j=1:(md.mesh.numberoflayers-1) - node_vel=node_vel+1/(2*(md.mesh.numberoflayers-1))*(sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+... - vy(i+j*md.mesh.numberofvertices2d,1).^2)+... + node_vel=0.; + for j=1:md.mesh.numberoflayers-1 + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*... + (sqrt(vx(i+j*md.mesh.numberofvertices2d,1).^2+vy(i+j*md.mesh.numberofvertices2d,1).^2)+... sqrt(vx(i+(j-1)*md.mesh.numberofvertices2d,1).^2+vy(i+(j-1)*md.mesh.numberofvertices2d,1).^2)); end vel(i,1)=node_vel; - node_vel=0; end @@ -81,5 +80,5 @@ caxis([0 100]); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('stokesstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); @@ -91,8 +90,8 @@ 'Vx','Vy','Vel', ... }; -field_tolerances={... +field_tolerances={ ... 1e-12,1e-12,1e-12, ... }; -field_values={ +field_values={ ... vx,vy,vel, ... }; Index: /issm/trunk/test/NightlyRun/test1207.py =================================================================== --- /issm/trunk/test/NightlyRun/test1207.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1207.py (revision 14310) @@ -0,0 +1,108 @@ +import numpy +from model import * +from roundmesh import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +The aim of this program is to compare a model with an analytical solution given in MacAyeal EISMINT : Lessons in Ice-Sheet Modeling. +""" + +printingflag=False + +numlayers=10 +resolution=30000. + +#To begin with the numerical model +md=model() +md=roundmesh(md,750000.,resolution) +md=setmask(md,'','') #We can not test iceshelves nor ice rises with this analytical solution +md=parameterize(md,'../Par/RoundSheetStaticEISMINT.py') + +#Calculation of the analytical 2d velocity field +constant=0.3 +vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 +vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) + +#We extrude the model to have a 3d model +md.extrude(numlayers,1.) +md=setflowequation(md,'stokes','all') + +#Spc the nodes on the bed +pos=numpy.nonzero(md.mesh.vertexonbed) +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. + +#Now we can solve the problem +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,DiagnosticSolutionEnum()) + +#Calculate the depth averaged velocity field (2d): +vx=md.results.DiagnosticSolution.Vx +vy=md.results.DiagnosticSolution.Vy +vel=numpy.zeros((md.mesh.numberofvertices2d,1)) + +for i in xrange(0,md.mesh.numberofvertices2d): + node_vel=0. + for j in xrange(0,md.mesh.numberoflayers-1): + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ + (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ + numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i,0]=node_vel + +#Plot of the velocity from the exact and calculated solutions +#figure(1) +#subplot(2,2,1) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel,'FaceColor','interp','EdgeColor','none'); +#title('Modelled velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,2) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#vel_obs,'FaceColor','interp','EdgeColor','none'); +#title('Analytical velocity','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 200]); + +#subplot(2,2,3) +#hold on; +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); +#legend('calculated velocity','exact velocity'); +#axis([0 750000 0 200]); +#hold off; + +#subplot(2,2,4) +#p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#title('Relative misfit [%]','FontSize',14,'FontWeight','bold') +#colorbar; +#caxis([0 100]); + +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('stokesstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv stokesstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); + +#Fields and tolerances to track changes +field_names =[ \ + 'Vx','Vy','Vel', \ +] +field_tolerances=[ \ + 1e-12,1e-12,1e-12, \ +] +field_values=[ \ + vx,vy,vel, \ +] Index: /issm/trunk/test/NightlyRun/test1208.m =================================================================== --- /issm/trunk/test/NightlyRun/test1208.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1208.m (revision 14310) @@ -1,5 +1,5 @@ %EISMINT benchmark experiment A numlayers=8; -resolution=50000; +resolution=50000.; %To begin with the numerical model @@ -14,12 +14,12 @@ %Spc the nodes on the bed pos=find(md.mesh.vertexonbed); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; %Adapt the time steps to the resolution -md.timestepping.time_step=15; +md.timestepping.time_step=15.; md.settings.output_frequency=500; -md.timestepping.final_time=30000; +md.timestepping.final_time=30000.; md.prognostic.stabilization=1; md.thermal.stabilization=1; Index: /issm/trunk/test/NightlyRun/test1208.py =================================================================== --- /issm/trunk/test/NightlyRun/test1208.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1208.py (revision 14310) @@ -0,0 +1,58 @@ +import numpy +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +EISMINT benchmark experiment A +""" + +numlayers=8 +resolution=50000. + +#To begin with the numerical model +md=triangle(model(),'../Exp/SquareEISMINT750000.exp',resolution) +md=setmask(md,'','') +md=parameterize(md,'../Par/RoundSheetEISMINT.py') + +#We extrude the model to have a 3d model +md.extrude(numlayers,1.) +md=setflowequation(md,'hutter','all') + +#Spc the nodes on the bed +pos=numpy.nonzero(md.mesh.vertexonbed) +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. + +#Adapt the time steps to the resolution +md.timestepping.time_step=15. +md.settings.output_frequency=500 +md.timestepping.final_time=30000. +md.prognostic.stabilization=1 +md.thermal.stabilization=1 + +#Now we can solve the problem +md.cluster=generic('name',oshostname(),'np',8) +md=solve(md,TransientSolutionEnum()) + +#Fields and tolerances to track changes +field_names =['Vx','Vy','Vz','Vel','Pressure','Thickness','Bed','Surface','Temperature','BasalforcingsMeltingRate'] +field_tolerances=[1e-08,1e-08,1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-07,1e-07] +field_values=[\ + md.results.TransientSolution[-1].Vx,\ + md.results.TransientSolution[-1].Vy,\ + md.results.TransientSolution[-1].Vz,\ + md.results.TransientSolution[-1].Vel,\ + md.results.TransientSolution[-1].Pressure,\ + md.results.TransientSolution[-1].Thickness,\ + md.results.TransientSolution[-1].Bed,\ + md.results.TransientSolution[-1].Surface,\ + md.results.TransientSolution[-1].Temperature,\ + md.results.TransientSolution[-1].BasalforcingsMeltingRate,\ + ] Index: /issm/trunk/test/NightlyRun/test1301.m =================================================================== --- /issm/trunk/test/NightlyRun/test1301.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1301.m (revision 14310) @@ -10,5 +10,5 @@ md=parameterize(md,'../Par/SquareThermal.par'); md=extrude(md,3,2.); -md=setflowequation(md,'Pattyn','all'); +md=setflowequation(md,'pattyn','all'); %Some conditions specific to melting test @@ -24,5 +24,5 @@ melting=md.basalforcings.geothermalflux/(md.materials.rho_ice*md.materials.latentheat)*md.constants.yts; -%modeled results +%modeled results md.cluster=generic('name',oshostname(),'np',2); md=solve(md,ThermalSolutionEnum()); @@ -30,10 +30,10 @@ %plot results comp_melting=md.results.ThermalSolution.BasalforcingsMeltingRate; -relative=abs((comp_melting-melting)./melting)*100; -relative(find(comp_melting==melting))=0; +relative=abs((comp_melting-melting)./melting)*100.; +relative(find(comp_melting==melting))=0.; plotmodel(md,'data',comp_melting,'title','Modeled melting','data',melting,'title','Analytical melting',... 'data',comp_melting-melting,'title','Absolute error','data',relative,'title','Relative error [%]',... 'layer#all',1,'caxis#2',[1.02964 1.02966]*10^-4,'FontSize#all',20,'figposition','mathieu') -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('thermalmelting','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); @@ -41,5 +41,4 @@ end - %Fields and tolerances to track changes field_names ={'BasalMelting'}; Index: /issm/trunk/test/NightlyRun/test1301.py =================================================================== --- /issm/trunk/test/NightlyRun/test1301.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1301.py (revision 14310) @@ -0,0 +1,60 @@ +import numpy +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from paterson import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +This file can be run to check that the melting in simple conduction is correctly modeled. +There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature +at upper surface and an impose flux at its base. The result must be a linear temperature from the upper to the lower +surface with an imposed slope (Geothermal flux). if it is not the case, something is thermal modeling has been changed... +""" + +printingflag=False + +md=model() +md=triangle(md,'../Exp/Square.exp',100000.) +md=setmask(md,'','') +md=parameterize(md,'../Par/SquareThermal.py') +md.extrude(3,2.) +md=setflowequation(md,'pattyn','all') + +#Some conditions specific to melting test +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) +md.initialization.temperature=273.15*numpy.ones((md.mesh.numberofvertices,1)) +pos=numpy.nonzero(md.mesh.vertexonsurface)[0] +md.thermal.spctemperature[pos]=md.initialization.temperature[pos] +md.materials.rheology_B=paterson(md.initialization.temperature) + +#analytical results +#melting heat = geothermal flux +#Mb*L*rho=G => Mb=G/L*rho +melting=md.basalforcings.geothermalflux/(md.materials.rho_ice*md.materials.latentheat)*md.constants.yts + +#modeled results +md.cluster=generic('name',oshostname(),'np',2) +md=solve(md,ThermalSolutionEnum()) + +#plot results +comp_melting=md.results.ThermalSolution.BasalforcingsMeltingRate +relative=numpy.abs((comp_melting-melting)/melting)*100. +relative[numpy.nonzero(comp_melting==melting)[0]]=0. +#plotmodel(md,'data',comp_melting,'title','Modeled melting','data',melting,'title','Analytical melting',... +# 'data',comp_melting-melting,'title','Absolute error','data',relative,'title','Relative error [%]',... +# 'layer#all',1,'caxis#2',[1.02964 1.02966]*10^-4,'FontSize#all',20,'figposition','mathieu') +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('thermalmelting','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv thermalmelting.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); + +#Fields and tolerances to track changes +field_names =['BasalMelting'] +field_tolerances=[1e-08] +field_values =[comp_melting] Index: /issm/trunk/test/NightlyRun/test1302.m =================================================================== --- /issm/trunk/test/NightlyRun/test1302.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1302.m (revision 14310) @@ -9,9 +9,9 @@ md=parameterize(md,'../Par/SquareThermal.par'); md=extrude(md,30,1.); %NB: the more one extrudes, the better (10-> relative~0.35%, 20->0.1%, 30->0.05%) -md=setflowequation(md,'Pattyn','all'); +md=setflowequation(md,'pattyn','all'); %Thermal boundary conditions -pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10; -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; +pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10.; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0.; md.initialization.vz=0.1*ones(md.mesh.numberofvertices,1); md.initialization.vel=sqrt( md.initialization.vx.^2+ md.initialization.vy.^2+ md.initialization.vz.^2); @@ -22,9 +22,9 @@ %d2T/dz2-w*rho_ice*c/k*dT/dz=0 T(surface)=0 T(bed)=10 => T=A exp(alpha z)+B alpha=0.1/md.constants.yts*md.materials.rho_ice*md.materials.heatcapacity/md.materials.thermalconductivity; %alpha=w rho_ice c /k and w=0.1m/an -A=10/(exp(alpha*(-1000))-1); %A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 +A=10./(exp(alpha*(-1000.))-1.); %A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 B=-A; md.initialization.temperature=A*exp(alpha*md.mesh.z)+B; -%modeled results +%modeled results md.cluster=generic('name',oshostname(),'np',2); md=solve(md,ThermalSolutionEnum()); @@ -32,11 +32,11 @@ %plot results comp_temp=md.results.ThermalSolution.Temperature; -relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100; -relative(find(comp_temp==md.initialization.temperature))=0; +relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100.; +relative(find(comp_temp==md.initialization.temperature))=0.; plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... 'figposition','mathieu','FontSize#all',20) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('thermaladvection','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1302.py =================================================================== --- /issm/trunk/test/NightlyRun/test1302.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1302.py (revision 14310) @@ -0,0 +1,65 @@ +import numpy +import sys +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +This file can be run to check that the advection-diffusion is correctly modeled. +There is u=v=0 and w=cst everywhere the only thermal boundary conditions are an imposed temperature +at upper surface and an impose flux at its base. +""" + +printingflag=False + +md=model() +md=triangle(md,'../Exp/Square.exp',100000.) +md=setmask(md,'','') +md=parameterize(md,'../Par/SquareThermal.py') +md.extrude(30,1.) #NB: the more one extrudes, the better (10-> relative~0.35%, 20->0.1%, 30->0.05%) +md=setflowequation(md,'pattyn','all') + +#Thermal boundary conditions +pos1=numpy.nonzero(md.mesh.elementonbed)[0] +md.thermal.spctemperature[md.mesh.elements[pos1,0:3]-1]=10. +pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. +md.initialization.vz=0.1*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.vel=numpy.sqrt( md.initialization.vx**2+ md.initialization.vy**2+ md.initialization.vz**2) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) + +md.thermal.stabilization=2 +#analytical results +#d2T/dz2-w*rho_ice*c/k*dT/dz=0 T(surface)=0 T(bed)=10 => T=A exp(alpha z)+B +alpha=0.1/md.constants.yts*md.materials.rho_ice*md.materials.heatcapacity/md.materials.thermalconductivity #alpha=w rho_ice c /k and w=0.1m/an +A=10./(numpy.exp(alpha*(-1000.))-1.) #A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 +B=-A +md.initialization.temperature=A*numpy.exp(alpha*md.mesh.z)+B + +#modeled results +md.cluster=generic('name',oshostname(),'np',2) +md=solve(md,ThermalSolutionEnum()) + +#plot results +comp_temp=md.results.ThermalSolution.Temperature +relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +#plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... +# 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... +# 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... +# 'figposition','mathieu','FontSize#all',20) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('thermaladvection','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv thermaladvection.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT ']); + +#Fields and tolerances to track changes +field_names =['AdvectionTemperature'] +field_tolerances=[1e-13] +field_values =[comp_temp] Index: /issm/trunk/test/NightlyRun/test1303.m =================================================================== --- /issm/trunk/test/NightlyRun/test1303.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1303.m (revision 14310) @@ -10,7 +10,8 @@ md=parameterize(md,'../Par/SquareThermal.par'); md=extrude(md,11,2.); -md=setflowequation(md,'Pattyn','all'); -pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10; -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; +md=setflowequation(md,'pattyn','all'); + +pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10.; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0.; md.initialization.pressure=zeros(md.mesh.numberofvertices,1); @@ -18,7 +19,7 @@ %d2T/dz2=0 T(bed)=10 T(surface)=0 => T=0*(z-bed)/thickness+10*(surface-z)/thickness %each layer of the 3d mesh must have a constant value -md.initialization.temperature=10*(md.geometry.surface-md.mesh.z)./md.geometry.thickness; +md.initialization.temperature=10.*(md.geometry.surface-md.mesh.z)./md.geometry.thickness; -%modeled results +%modeled results md.cluster=generic('name',oshostname(),'np',2); md=solve(md,ThermalSolutionEnum()); @@ -26,11 +27,11 @@ %plot results comp_temp=md.results.ThermalSolution.Temperature; -relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100; -relative(find(comp_temp==md.initialization.temperature))=0; +relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100.; +relative(find(comp_temp==md.initialization.temperature))=0.; plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... 'figposition','mathieu','FontSize#all',20) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('thermalconduction','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1303.py =================================================================== --- /issm/trunk/test/NightlyRun/test1303.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1303.py (revision 14310) @@ -0,0 +1,60 @@ +import numpy +import sys +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +This file can be run to check that the conduction is correctly modeled. +There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature +at the lower and upper surface. The result must be a linear temperature from the upper to the lower +surface. if it is not the case, something is thermal modeling has been changed... +""" + +printingflag=False + +md=model() +md=triangle(md,'../Exp/Square.exp',100000.) +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareThermal.py') +md.extrude(11,2.) +md=setflowequation(md,'pattyn','all') + +pos1=numpy.nonzero(md.mesh.elementonbed)[0] +md.thermal.spctemperature[md.mesh.elements[pos1,0:3]-1]=10. +pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) + +#analytical results +#d2T/dz2=0 T(bed)=10 T(surface)=0 => T=0*(z-bed)/thickness+10*(surface-z)/thickness +#each layer of the 3d mesh must have a constant value +md.initialization.temperature=10.*(md.geometry.surface-md.mesh.z)/md.geometry.thickness + +#modeled results +md.cluster=generic('name',oshostname(),'np',2) +md=solve(md,ThermalSolutionEnum()) + +#plot results +comp_temp=md.results.ThermalSolution.Temperature +relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +#plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... +# 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... +# 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... +# 'figposition','mathieu','FontSize#all',20) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('thermalconduction','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv thermalconduction.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); + +#Fields and tolerances to track changes +field_names =['ConductionTemperature'] +field_tolerances=[1e-13] +field_values =[comp_temp] Index: /issm/trunk/test/NightlyRun/test1304.m =================================================================== --- /issm/trunk/test/NightlyRun/test1304.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1304.m (revision 14310) @@ -10,7 +10,7 @@ md=parameterize(md,'../Par/SquareThermal.par'); md=extrude(md,11,1.); -md=setflowequation(md,'Pattyn','all'); +md=setflowequation(md,'pattyn','all'); -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0.; md.initialization.pressure=zeros(md.mesh.numberofvertices,1); md.basalforcings.geothermalflux(:)=0.1; %100mW/m^2 @@ -21,5 +21,5 @@ md.initialization.temperature=-0.1/md.materials.thermalconductivity*(md.mesh.z-md.geometry.surface); %G=0.1 W/m2 -%modeled results +%modeled results md.cluster=generic('name',oshostname(),'np',2); md=solve(md,ThermalSolutionEnum()); @@ -27,11 +27,11 @@ %plot results comp_temp=md.results.ThermalSolution.Temperature; -relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100; -relative(find(comp_temp==md.initialization.temperature))=0; +relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100.; +relative(find(comp_temp==md.initialization.temperature))=0.; plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... 'title','Analytical temperature','view',3,'data',comp_temp-md.initialization.temperature,... 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... 'figposition','mathieu','FontSize#all',20) -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('thermalgeothermalflux','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1304.py =================================================================== --- /issm/trunk/test/NightlyRun/test1304.py (revision 14310) +++ /issm/trunk/test/NightlyRun/test1304.py (revision 14310) @@ -0,0 +1,59 @@ +import numpy +import sys +from model import * +from triangle import * +from setmask import * +from parameterize import * +from setflowequation import * +from EnumDefinitions import * +from solve import * +from MatlabFuncs import * + +""" +This file can be run to check that the geothermal flux in simple conduction is correctly modeled. +There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature +at upper surface and an impose flux at its base. The result must be a linear temperature from the upper to the lower +surface with an imposed slope (Geothermal flux). if it is not the case, something is thermal modeling has been changed... +""" + +printingflag=False + +md=model() +md=triangle(md,'../Exp/Square.exp',100000.) +md=setmask(md,'','') +md=parameterize(md,'../Par/SquareThermal.py') +md.extrude(11,1.) +md=setflowequation(md,'pattyn','all') + +pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) +md.basalforcings.geothermalflux[:]=0.1 #100mW/m^2 + +#analytical results +#the result is linear with depth and is equal to 0 on the upper surface (See BC) +#d2T/dz2=0 -k*dT/dz(bed)=G T(surface)=0 => T=-G/k*(z-surface) +md.initialization.temperature=-0.1/md.materials.thermalconductivity*(md.mesh.z-md.geometry.surface) #G=0.1 W/m2 + +#modeled results +md.cluster=generic('name',oshostname(),'np',2) +md=solve(md,ThermalSolutionEnum()) + +#plot results +comp_temp=md.results.ThermalSolution.Temperature +relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +#plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... +# 'title','Analytical temperature','view',3,'data',comp_temp-md.initialization.temperature,... +# 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,... +# 'figposition','mathieu','FontSize#all',20) +if printingflag: + pass +# set(gcf,'Color','w') +# printmodel('thermalgeothermalflux','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); +# system(['mv thermalgeothermalflux.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); + +#Fields and tolerances to track changes +field_names =['GeothermalFluxTemperature'] +field_tolerances=[1e-13] +field_values =[comp_temp] Index: /issm/trunk/test/NightlyRun/test1401.m =================================================================== --- /issm/trunk/test/NightlyRun/test1401.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1401.m (revision 14310) @@ -1,8 +1,8 @@ %test the anisotropic mesh adaptation -%function to capture = exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +%function to capture = exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; printingflag=false; %create square mesh -L=1; %in m +L=1.; %in m nx=70; %numberof nodes in x direction ny=70; @@ -11,7 +11,7 @@ %mesh adaptation loop YAMS md=squaremesh(md,L,L,nx,ny); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_yams1','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -19,8 +19,8 @@ end -md=YamsCall(md,md.inversion.vel_obs,0.001,0.3,1.3,10^-4); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md=YamsCall(md,md.inversion.vel_obs,0.001,0.3,1.3,10.^-4); +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_yams2','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -29,7 +29,7 @@ md=YamsCall(md,md.inversion.vel_obs,0.001,0.3,2.5,0.008); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_yams3','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -41,7 +41,7 @@ %mesh adaptation loop BAMG md=squaremesh(md,L,L,nx,ny); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_bamg1','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -50,8 +50,8 @@ md.private.bamg=NaN; -md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.001,'hmax',0.3,'gradation',1.3,'err',10^-4); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.001,'hmax',0.3,'gradation',1.3,'err',10.^-4); +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_bamg2','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -61,7 +61,7 @@ md.private.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.001,'hmax',0.3,'gradation',2.5,'err',0.008); -md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10.^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2.; plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh1_bamg3','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test1402.m =================================================================== --- /issm/trunk/test/NightlyRun/test1402.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test1402.m (revision 14310) @@ -3,5 +3,5 @@ %create square mesh -L=1; %in m +L=1.; %in m nx=30; %numberof nodes in x direction ny=30; @@ -10,10 +10,10 @@ %mesh adaptation loop YAMS md=squaremesh(md,L,L,nx,ny); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_yams1','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -21,11 +21,11 @@ end -md=YamsCall(md,md.inversion.vel_obs,0.005,0.3,2.3,10^-2); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +md=YamsCall(md,md.inversion.vel_obs,0.005,0.3,2.3,10.^-2); +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_yams2','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -34,10 +34,10 @@ md=YamsCall(md,md.inversion.vel_obs,0.005,0.3,3,0.005); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_yams3','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -49,10 +49,10 @@ %mesh adaptation loop BAMG md=squaremesh(md,L,L,nx,ny); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_bamg1','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -61,11 +61,11 @@ md.private.bamg=NaN; -md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',2.3,'err',10^-2); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',2.3,'err',10.^-2); +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_bamg2','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -75,10 +75,10 @@ md.private.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',3,'err',0.005); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_bamg3','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); @@ -88,10 +88,10 @@ md.private.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',1.5,'err',0.003,'anisomax',1); -u=4*md.mesh.x-2; v=4*md.mesh.y-2; -md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... - +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... - +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; +u=4.*md.mesh.x-2.; v=4.*md.mesh.y-2.; +md.inversion.vel_obs=tanh(30.*(u.^2+v.^2-0.25)) ... + +tanh(30.*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30.*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30.*((u+0.75).^2+(v+0.75).^2-0.25)); plotmodel(md,'data',md.inversion.vel_obs,'data',md.inversion.vel_obs,'nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); -if printingflag, +if printingflag, set(gcf,'Color','w') printmodel('mesh2_bamgiso','png','margin','on','marginsize',25,'frame','off','resolution',1,'hardcopy','off'); Index: /issm/trunk/test/NightlyRun/test234.m =================================================================== --- /issm/trunk/test/NightlyRun/test234.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test234.m (revision 14310) @@ -42,4 +42,7 @@ md.qmu.method=dakota_method('nond_samp'); md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs'); +if (str2num(dakotaversion())>4.2) + md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'rng','rnum2') +end %parameters @@ -59,14 +62,14 @@ %Fields and tolerances to track changes -md.results.dakota.importancefactors=[]; +md.results.dakota.moments=[]; for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; + md.results.dakota.moments=[md.results.dakota.moments md.results.dakota.dresp_out(i).mean]; end for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; + md.results.dakota.moments=[md.results.dakota.moments md.results.dakota.dresp_out(i).stddev]; end -field_names ={'importancefactors'}; +field_names ={'moments'}; field_tolerances={1e-11}; field_values={... - md.results.dakota.importancefactors,... + md.results.dakota.moments,... }; Index: /issm/trunk/test/NightlyRun/test235.m =================================================================== --- /issm/trunk/test/NightlyRun/test235.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test235.m (revision 14310) @@ -59,14 +59,14 @@ %Fields and tolerances to track changes -md.results.dakota.importancefactors=[]; +md.results.dakota.moments=[]; for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; + md.results.dakota.moments=[md.results.dakota.moments md.results.dakota.dresp_out(i).mean]; end for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; + md.results.dakota.moments=[md.results.dakota.moments md.results.dakota.dresp_out(i).stddev]; end -field_names ={'importancefactors'}; +field_names ={'moments'}; field_tolerances={1e-11}; field_values={... - md.results.dakota.importancefactors,... + md.results.dakota.moments,... }; Index: /issm/trunk/test/NightlyRun/test328.m =================================================================== --- /issm/trunk/test/NightlyRun/test328.m (revision 14309) +++ /issm/trunk/test/NightlyRun/test328.m (revision 14310) @@ -4,21 +4,9 @@ md=setflowequation(md,'macayeal','all'); md.surfaceforcings.issmbgradients=1; -md.surfaceforcings.smb_pos_max=5000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; -md.surfaceforcings.smb_pos_min=1250. + 0.00005*md.mesh.x -0.0001*md.mesh.y; -md.surfaceforcings.a_pos=15000. - 0.000051*md.mesh.x + 0.00011*md.mesh.y; md.surfaceforcings.b_pos=-100. + 0.00005*md.mesh.x - 0.0001*md.mesh.y; -md.surfaceforcings.a_neg=-20000. - 0.00005*md.mesh.x + 0.0001*md.mesh.y; md.surfaceforcings.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y; -md.surfaceforcings.hc=(md.surfaceforcings.a_pos-md.surfaceforcings.a_neg)./(md.surfaceforcings.b_neg-md.surfaceforcings.b_pos); +md.surfaceforcings.href=md.geometry.surface; +md.surfaceforcings.smbref= 1000. - 0.001*md.mesh.x - 0.005*md.mesh.y; md.transient.requested_outputs=TotalSmbEnum(); -md.surfaceforcings.href=md.geometry.surface; -for i=1:size(md.surfaceforcings.hc), - if md.geometry.surface(i)0 -md.geometry.bed=md.geometry.surface-1000; +md.geometry.surface=2000.-md.mesh.x*tan(0.1*pi/180.); %to have z>0 +md.geometry.bed=md.geometry.surface-1000.; md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -%md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x/2)).*sin(md.mesh.y*2*pi/max(md.mesh.x/2)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); -md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x)).*sin(md.mesh.y*2*pi/max(md.mesh.x)))); +%md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/max(md.mesh.x/2.)).*sin(md.mesh.y*2.*pi/max(md.mesh.x/2.)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); +md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/max(md.mesh.x)).*sin(md.mesh.y*2.*pi/max(md.mesh.x)))); %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.mesh.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=zeros(md.mesh.numberofelements,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=6.8067*10^7*ones(md.mesh.numberofvertices,1); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); -disp(' boundary conditions for diagnostic model: '); -%Create node on boundary fist (because wi can not use mesh) +disp(' boundary conditions for diagnostic model:'); +%Create node on boundary first (because we can not use mesh) md=SetIceSheetBC(md); Index: /issm/trunk/test/Par/ISMIPC.py =================================================================== --- /issm/trunk/test/Par/ISMIPC.py (revision 14310) +++ /issm/trunk/test/Par/ISMIPC.py (revision 14310) @@ -0,0 +1,26 @@ +import numpy +from SetIceSheetBC import * + +#Ok, start defining model parameters here + +print " creating thickness" +md.geometry.surface=2000.-md.mesh.x.reshape(-1,1)*numpy.tan(0.1*numpy.pi/180.) #to have z>0 +md.geometry.bed=md.geometry.surface-1000. +md.geometry.thickness=md.geometry.surface-md.geometry.bed + +print " creating drag" +#md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/max(md.mesh.x/2.)).*sin(md.mesh.y*2.*pi/max(md.mesh.x/2.)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); +md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x))*numpy.sin(md.mesh.y.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)))) +#Take care of iceshelves: no basal drag +pos=numpy.nonzero(md.mask.elementonfloatingice)[0] +md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) + +print " creating flow law parameter" +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " boundary conditions for diagnostic model:" +#Create node on boundary first (because we can not use mesh) +md=SetIceSheetBC(md) Index: /issm/trunk/test/Par/ISMIPD.par =================================================================== --- /issm/trunk/test/Par/ISMIPD.par (revision 14309) +++ /issm/trunk/test/Par/ISMIPD.par (revision 14310) @@ -2,21 +2,21 @@ disp(' creating thickness'); -md.geometry.surface=2000-md.mesh.x*tan(0.1*pi/180); %to have z>0 -md.geometry.bed=md.geometry.surface-1000; +md.geometry.surface=2000.-md.mesh.x*tan(0.1*pi/180.); %to have z>0 +md.geometry.bed=md.geometry.surface-1000.; md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x)))); +md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/max(md.mesh.x)))); %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.mesh.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=zeros(md.mesh.numberofelements,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=6.8067*10^7*ones(md.mesh.numberofvertices,1); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); -disp(' boundary conditions for diagnostic model: '); -%Create node on boundary fist (because wi can not use mesh) +disp(' boundary conditions for diagnostic model:'); +%Create node on boundary first (because we can not use mesh) md=SetIceSheetBC(md); Index: /issm/trunk/test/Par/ISMIPD.py =================================================================== --- /issm/trunk/test/Par/ISMIPD.py (revision 14310) +++ /issm/trunk/test/Par/ISMIPD.py (revision 14310) @@ -0,0 +1,25 @@ +import numpy +from SetIceSheetBC import * + +#Ok, start defining model parameters here + +print " creating thickness" +md.geometry.surface=2000.-md.mesh.x.reshape(-1,1)*numpy.tan(0.1*numpy.pi/180.) #to have z>0 +md.geometry.bed=md.geometry.surface-1000. +md.geometry.thickness=md.geometry.surface-md.geometry.bed + +print " creating drag" +md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)))) +#Take care of iceshelves: no basal drag +pos=numpy.nonzero(md.mask.elementonfloatingice)[0] +md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) + +print " creating flow law parameter" +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " boundary conditions for diagnostic model:" +#Create node on boundary first (because we can not use mesh) +md=SetIceSheetBC(md) Index: /issm/trunk/test/Par/ISMIPE.par =================================================================== --- /issm/trunk/test/Par/ISMIPE.par (revision 14309) +++ /issm/trunk/test/Par/ISMIPE.par (revision 14310) @@ -7,9 +7,9 @@ for i=1:md.mesh.numberofvertices y=md.mesh.y(i); - point1=floor(y/100)+1; + point1=floor(y/100.)+1; point2=min(point1+1,51); - coeff=(y-(point1-1)*100)/100; - md.geometry.bed(i)=(1-coeff)*data(point1,2)+coeff*data(point2,2); - md.geometry.surface(i)=(1-coeff)*data(point1,3)+coeff*data(point2,3); + coeff=(y-(point1-1.)*100.)/100.; + md.geometry.bed(i)=(1.-coeff)*data(point1,2)+coeff*data(point2,2); + md.geometry.surface(i)=(1.-coeff)*data(point1,3)+coeff*data(point2,3); end md.geometry.thickness=md.geometry.surface-md.geometry.bed; @@ -22,9 +22,9 @@ md.friction.q=ones(md.mesh.numberofelements,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=6.8067*10^7*ones(md.mesh.numberofvertices,1); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); -disp(' boundary conditions for diagnostic model: '); -%Create node on boundary fist (because wi can not use mesh) +disp(' boundary conditions for diagnostic model:'); +%Create node on boundary first (because we can not use mesh) md=SetIceSheetBC(md); Index: /issm/trunk/test/Par/ISMIPE.py =================================================================== --- /issm/trunk/test/Par/ISMIPE.py (revision 14310) +++ /issm/trunk/test/Par/ISMIPE.py (revision 14310) @@ -0,0 +1,35 @@ +import numpy +import netCDF4 +from SetIceSheetBC import * + +#Ok, start defining model parameters here + +print " creating thickness" +f = netCDF4.Dataset('../Data/ISMIPE.nc','r') +data = f.variables['data'][:] +f.close() +md.geometry.surface=numpy.zeros((md.mesh.numberofvertices,1)) +md.geometry.bed=numpy.zeros((md.mesh.numberofvertices,1)) +for i in xrange(0,md.mesh.numberofvertices): + y=md.mesh.y[i] + point1=numpy.floor(y/100.) + point2=numpy.minimum(point1+1,50) + coeff=(y-(point1-1.)*100.)/100. + md.geometry.bed[i]=(1.-coeff)*data[point1,1]+coeff*data[point2,1] + md.geometry.surface[i]=(1.-coeff)*data[point1,2]+coeff*data[point2,2] +md.geometry.thickness=md.geometry.surface-md.geometry.bed +md.geometry.thickness[numpy.nonzero(numpy.logical_not(md.geometry.thickness))]=0.01 +md.geometry.bed=md.geometry.surface-md.geometry.thickness + +print " creating drag" +md.friction.coefficient=numpy.zeros((md.mesh.numberofvertices,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.ones((md.mesh.numberofelements,1)) + +print " creating flow law parameter" +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " boundary conditions for diagnostic model:" +#Create node on boundary first (because we can not use mesh) +md=SetIceSheetBC(md) Index: /issm/trunk/test/Par/ISMIPF.par =================================================================== --- /issm/trunk/test/Par/ISMIPF.par (revision 14309) +++ /issm/trunk/test/Par/ISMIPF.par (revision 14310) @@ -3,23 +3,23 @@ disp(' creating thickness'); -md.geometry.surface=-md.mesh.x*tan(3*pi/180); -%md.geometry.bed=md.geometry.surface-1000; -md.geometry.bed=md.geometry.surface-1000+100*exp(-((md.mesh.x-max(md.mesh.x)/2).^2+(md.mesh.y-max(md.mesh.y)/2).^2)/(10000^2)); +md.geometry.surface=-md.mesh.x*tan(3.*pi/180.); +%md.geometry.bed=md.geometry.surface-1000.; +md.geometry.bed=md.geometry.surface-1000.+100.*exp(-((md.mesh.x-max(md.mesh.x)/2.).^2+(md.mesh.y-max(md.mesh.y)/2.).^2)/(10000.^2)); md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -md.friction.coefficient=sqrt(md.constants.yts/(2.140373*10^-7*1000))*ones(md.mesh.numberofvertices,1); +md.friction.coefficient=sqrt(md.constants.yts/(2.140373*10^-7*1000.))*ones(md.mesh.numberofvertices,1); md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=zeros(md.mesh.numberofelements,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=1.4734*10^14*ones(md.mesh.numberofvertices,1); -md.materials.rheology_n=1*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=1.*ones(md.mesh.numberofelements,1); md.materials.rheology_law='None'; disp(' boundary conditions for diagnostic model'); -%Create node on boundary fist (because we cannot use mesh) +%Create node on boundary first (because we cannot use mesh) md=SetIceSheetBC(md); -md.diagnostic.spcvx=100*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvx=100.*ones(md.mesh.numberofvertices,1); md.initialization.vx=zeros(md.mesh.numberofvertices,1); md.initialization.vy=zeros(md.mesh.numberofvertices,1); @@ -27,5 +27,5 @@ md.initialization.vel=zeros(md.mesh.numberofvertices,1); md.initialization.pressure=zeros(md.mesh.numberofvertices,1); -md.initialization.temperature=255*ones(md.mesh.numberofvertices,1); +md.initialization.temperature=255.*ones(md.mesh.numberofvertices,1); pos=find(md.mesh.x==min(md.mesh.x) | md.mesh.x==max(md.mesh.x) | md.mesh.y==min(md.mesh.y) | md.mesh.y==max(md.mesh.y)); md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); @@ -33,5 +33,5 @@ md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); md.prognostic.spcthickness(pos)=md.geometry.thickness(pos); -md.thermal.spctemperature=255*ones(md.mesh.numberofvertices,1); +md.thermal.spctemperature=255.*ones(md.mesh.numberofvertices,1); md.basalforcings.geothermalflux=0.4*ones(md.mesh.numberofvertices,1); @@ -40,6 +40,6 @@ %Transient options -md.timestepping.time_step=1; -md.timestepping.final_time=10; +md.timestepping.time_step=1.; +md.timestepping.final_time=10.; md.prognostic.stabilization=1; md.thermal.stabilization=1; Index: /issm/trunk/test/Par/ISMIPF.py =================================================================== --- /issm/trunk/test/Par/ISMIPF.py (revision 14310) +++ /issm/trunk/test/Par/ISMIPF.py (revision 14310) @@ -0,0 +1,49 @@ +import numpy +from SetIceSheetBC import * + +#Ok, start defining model parameters here +md.verbose=2 + +print " creating thickness" +md.geometry.surface=-md.mesh.x.reshape(-1,1)*numpy.tan(3.*numpy.pi/180.) +#md.geometry.bed=md.geometry.surface-1000. +md.geometry.bed=md.geometry.surface-1000.+100.*numpy.exp(-((md.mesh.x.reshape(-1,1)-numpy.max(md.mesh.x)/2.)**2+(md.mesh.y.reshape(-1,1)-numpy.max(md.mesh.y)/2.)**2)/(10000.**2)) +md.geometry.thickness=md.geometry.surface-md.geometry.bed + +print " creating drag" +md.friction.coefficient=numpy.sqrt(md.constants.yts/(2.140373*10**-7*1000.))*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) + +print " creating flow law parameter" +md.materials.rheology_B=1.4734*10**14*numpy.ones((md.mesh.numberofvertices,1)) +md.materials.rheology_n=1.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_law='None' + +print " boundary conditions for diagnostic model" +#Create node on boundary first (because we cannot use mesh) +md=SetIceSheetBC(md) +md.diagnostic.spcvx=100.*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vel=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.temperature=255.*numpy.ones((md.mesh.numberofvertices,1)) +pos=numpy.nonzero(numpy.logical_or(numpy.logical_or(md.mesh.x==numpy.min(md.mesh.x),md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==numpy.min(md.mesh.y),md.mesh.y==numpy.max(md.mesh.y)))) +md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.balancethickness.spcthickness[pos]=md.geometry.thickness[pos] +md.prognostic.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.prognostic.spcthickness[pos]=md.geometry.thickness[pos] +md.thermal.spctemperature=255.*numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.geothermalflux=0.4*numpy.ones((md.mesh.numberofvertices,1)) + +#Parallel options +md.mesh.average_vertex_connectivity=200 + +#Transient options +md.timestepping.time_step=1. +md.timestepping.final_time=10. +md.prognostic.stabilization=1 +md.thermal.stabilization=1 +md.thermal.penalty_threshold=10**5 Index: /issm/trunk/test/Par/Pig.py =================================================================== --- /issm/trunk/test/Par/Pig.py (revision 14309) +++ /issm/trunk/test/Par/Pig.py (revision 14310) @@ -48,5 +48,5 @@ md.prognostic.stabilization=1. md.verbose=verbose(0) -md.settings.waitonlock=30. +md.settings.waitonlock=30 md.timestepping.time_step=1. md.timestepping.final_time=2. Index: /issm/trunk/test/Par/RoundSheetEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 14309) +++ /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 14310) @@ -1,10 +1,10 @@ %Ok, start defining model parameters here disp(' creating thickness'); -md.geometry.thickness=10*ones(md.mesh.numberofvertices,1); +md.geometry.thickness=10.*ones(md.mesh.numberofvertices,1); md.geometry.bed=zeros(md.mesh.numberofvertices,1); md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); -md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); %q=1. %no drag is specified in the analytical solution +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); %q=1. no drag is specified in the analytical solution md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); @@ -12,23 +12,23 @@ disp(' creating temperatures'); tmin=238.15; %K -st=1.67*10^-2/1000; %k/m; +st=1.67*10^-2/1000.; %k/m radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); md.initialization.temperature=(tmin+st*radius); md.basalforcings.geothermalflux=4.2*10^-2*ones(md.mesh.numberofvertices,1); -disp(' creating flow law paramter'); -md.materials.rheology_B=6.81*10^(7)*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +disp(' creating flow law parameter'); +md.materials.rheology_B=6.81*10^7*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); disp(' creating surface mass balance'); smb_max=0.5; %m/yr -sb=10^-2/1000; %m/yr/m -rel=450*1000; %m +sb=10^-2/1000.; %m/yr/m +rel=450.*1000.; %m md.surfaceforcings.mass_balance=min(smb_max,sb*(rel-radius)); disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; -md.inversion.vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; +md.inversion.vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); md.initialization.vx=zeros(md.mesh.numberofvertices,1); @@ -38,22 +38,22 @@ %Deal with boundary conditions: -disp(' boundary conditions for diagnostic model: '); +disp(' boundary conditions for diagnostic model:'); md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp'); -radius=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); pos=find(radius==min(radius)); -md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center +md.mesh.x(pos)=0.; md.mesh.y(pos)=0.; %the closest node to the center is changed to be exactly at the center -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; %parallel options -md.timestepping.final_time=50000; +md.timestepping.final_time=50000.; %Constants -md.materials.rho_ice=910; +md.materials.rho_ice=910.; md.materials.thermalconductivity=2.1; md.materials.latentheat=3.35*10^5; md.materials.beta=8.66*10^-4/(md.materials.rho_ice*md.constants.g); %conversion from K/m to K/Pa -md.constants.yts=31556926; +md.constants.yts=31556926.; Index: /issm/trunk/test/Par/RoundSheetEISMINT.py =================================================================== --- /issm/trunk/test/Par/RoundSheetEISMINT.py (revision 14310) +++ /issm/trunk/test/Par/RoundSheetEISMINT.py (revision 14310) @@ -0,0 +1,63 @@ +import numpy +from SetMarineIceSheetBC import * + +#Ok, start defining model parameters here +print " creating thickness" +md.geometry.thickness=10.*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.bed=numpy.zeros((md.mesh.numberofvertices,1)) +md.geometry.surface=md.geometry.bed+md.geometry.thickness + +print " creating drag" +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) #q=1. no drag is specified in the analytical solution +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.ones((md.mesh.numberofelements,1)) + +print " creating temperatures" +tmin=238.15 #K +st=1.67*10**-2/1000. #k/m +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2).reshape(-1,1) +md.initialization.temperature=tmin+st*radius +md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices,1)) + +print " creating flow law parameter" +md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices,1)) #to have the same B as the analytical solution +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " creating surface mass balance" +smb_max=0.5 #m/yr +sb=10**-2/1000. #m/yr/m +rel=450.*1000. #m +md.surfaceforcings.mass_balance=numpy.minimum(smb_max*numpy.ones_like(radius),sb*(rel-radius)) + +print " creating velocities" +constant=0.3 +md.inversion.vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) + +#Deal with boundary conditions: +print " boundary conditions for diagnostic model:" +md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp') + +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2) +pos=numpy.nonzero(radius==numpy.min(radius))[0] +md.mesh.x[pos]=0. +md.mesh.y[pos]=0. #the closest node to the center is changed to be exactly at the center + +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. + +#parallel options +md.timestepping.final_time=50000. + +#Constants +md.materials.rho_ice=910. +md.materials.thermalconductivity=2.1 +md.materials.latentheat=3.35*10**5 +md.materials.beta=8.66*10**-4/(md.materials.rho_ice*md.constants.g) #conversion from K/m to K/Pa +md.constants.yts=31556926. Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 14309) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 14310) @@ -2,15 +2,16 @@ hmin=0.01; hmax=2756.7; -radius=(sqrt((md.mesh.x).^2+(md.mesh.y).^2)); +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); radiusmax=max(radius); -md.geometry.thickness=hmin*ones(size(md.mesh.x,1),1)+hmax*(4*((1/2)^(4/3)*ones(size(md.mesh.x,1),1)-((radius)./(2*radiusmax)).^(4/3))).^(3/8); -md.geometry.bed=0*md.geometry.thickness; +radius(find(radius>(1.-10^-9)*radiusmax))=radiusmax; %eliminate roundoff issues in next statement +md.geometry.thickness=hmin*ones(size(md.mesh.x,1),1)+hmax*(4.*((1./2.)^(4./3.)*ones(size(md.mesh.x,1),1)-((radius)./(2.*radiusmax)).^(4./3.))).^(3./8.); +md.geometry.bed=0.*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); -md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); %q=1. %no drag is specified in the analytical solution +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); %q=1. no drag is specified in the analytical solution %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.mesh.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); @@ -18,23 +19,23 @@ disp(' creating temperatures'); tmin=238.15; %K -st=1.67*10^-2/1000; %k/m; -md.initialization.temperature=(tmin+st*radius); +st=1.67*10^-2/1000.; %k/m +md.initialization.temperature=tmin+st*radius; md.basalforcings.geothermalflux=4.2*10^-2*ones(md.mesh.numberofvertices,1); -disp(' creating flow law paramter'); -md.materials.rheology_B=6.81*10^(7)*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +disp(' creating flow law parameter'); +md.materials.rheology_B=6.81*10^7*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); disp(' creating surface mass balance'); smb_max=0.5; %m/yr -sb=10^-2/1000; %m/yr/m -rel=450*1000; %m +sb=10^-2/1000.; %m/yr/m +rel=450.*1000.; %m md.surfaceforcings.mass_balance=min(smb_max,sb*(rel-radius)); disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; -md.inversion.vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; -md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); +md.inversion.vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +md.inversion.vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); md.initialization.vx=zeros(md.mesh.numberofvertices,1); md.initialization.vy=zeros(md.mesh.numberofvertices,1); @@ -43,12 +44,12 @@ %Deal with boundary conditions: -disp(' boundary conditions for diagnostic model: '); +disp(' boundary conditions for diagnostic model:'); md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp'); -radius=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); pos=find(radius==min(radius)); -md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center +md.mesh.x(pos)=0.; md.mesh.y(pos)=0.; %the closest node to the center is changed to be exactly at the center -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; -md.diagnostic.spcvz(pos)=0; +md.diagnostic.spcvx(pos)=0.; +md.diagnostic.spcvy(pos)=0.; +md.diagnostic.spcvz(pos)=0.; Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.py =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.py (revision 14310) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.py (revision 14310) @@ -0,0 +1,59 @@ +import numpy +from SetMarineIceSheetBC import * + +print " creating thickness" +hmin=0.01 +hmax=2756.7 +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2).reshape(-1,1) +radiusmax=numpy.max(radius) +radius[numpy.nonzero(radius>(1.-10**-9)*radiusmax)]=radiusmax #eliminate roundoff issues in next statement +md.geometry.thickness=hmin*numpy.ones((numpy.size(md.mesh.x),1))+hmax*(4.*((1./2.)**(4./3.)*numpy.ones((numpy.size(md.mesh.x),1))-((radius)/(2.*radiusmax))**(4./3.)))**(3./8.) +md.geometry.bed=0.*md.geometry.thickness +md.geometry.surface=md.geometry.bed+md.geometry.thickness + +print " creating drag" +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) #q=1. no drag is specified in the analytical solution +#Take care of iceshelves: no basal drag +pos=numpy.nonzero(md.mask.elementonfloatingice)[0] +md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.ones((md.mesh.numberofelements,1)) + +print " creating temperatures" +tmin=238.15 #K +st=1.67*10**-2/1000. #k/m +md.initialization.temperature=tmin+st*radius +md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices,1)) + +print " creating flow law parameter" +md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices,1)) #to have the same B as the analytical solution +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " creating surface mass balance" +smb_max=0.5 #m/yr +sb=10**-2/1000. #m/yr/m +rel=450.*1000. #m +md.surfaceforcings.mass_balance=numpy.minimum(smb_max*numpy.ones_like(radius),sb*(rel-radius)) + +print " creating velocities" +constant=0.3 +md.inversion.vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) + +#Deal with boundary conditions: +print " boundary conditions for diagnostic model:" +md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp') + +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2) +pos=numpy.nonzero(radius==numpy.min(radius))[0] +md.mesh.x[pos]=0. +md.mesh.y[pos]=0. #the closest node to the center is changed to be exactly at the center + +md.diagnostic.spcvx[pos]=0. +md.diagnostic.spcvy[pos]=0. +md.diagnostic.spcvz[pos]=0. Index: /issm/trunk/test/Par/SquareEISMINT.par =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.par (revision 14309) +++ /issm/trunk/test/Par/SquareEISMINT.par (revision 14310) @@ -4,18 +4,18 @@ ymin=min(md.mesh.y); ymax=max(md.mesh.y); -md.geometry.thickness=500*ones(md.mesh.numberofvertices,1); +md.geometry.thickness=500.*ones(md.mesh.numberofvertices,1); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); -md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); %q=1. +md.friction.coefficient=200.*ones(md.mesh.numberofvertices,1); %q=1. %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.mesh.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); disp(' creating initial values'); -md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); md.initialization.vx=zeros(md.mesh.numberofvertices,1); md.initialization.vy=zeros(md.mesh.numberofvertices,1); @@ -24,23 +24,23 @@ md.initialization.pressure=zeros(md.mesh.numberofvertices,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=1.7687*10^8*ones(md.mesh.numberofvertices,1); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); disp(' creating surface mass balance'); md.surfaceforcings.mass_balance=0.2*ones(md.mesh.numberofvertices,1); %0m/a -md.basalforcings.melting_rate=0*ones(md.mesh.numberofvertices,1); %0m/a +md.basalforcings.melting_rate=0.*ones(md.mesh.numberofvertices,1); %0m/a -disp(' boundary conditions '); +disp(' boundary conditions'); md=SetMarineIceSheetBC(md,'../Exp/SquareFrontEISMINT.exp'); %Evolution of the ice shelf -pos=find(md.mesh.y==200000); %nodes on the upper boundary condition +pos=find(md.mesh.y==200000.); %nodes on the upper boundary condition md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); -md.balancethickness.spcthickness(pos)=500; +md.balancethickness.spcthickness(pos)=500.; md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); -md.prognostic.spcthickness(pos)=500; +md.prognostic.spcthickness(pos)=500.; md.prognostic.stabilization=0; %Better result with no artificial diffusivity -md.thermal.stabilization=0; -md.timestepping.final_time=500; +md.thermal.stabilization=0; +md.timestepping.final_time=500.; md.timestepping.time_step=1; Index: /issm/trunk/test/Par/SquareEISMINT.py =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.py (revision 14310) +++ /issm/trunk/test/Par/SquareEISMINT.py (revision 14310) @@ -0,0 +1,49 @@ +import numpy +from SetMarineIceSheetBC import * + +#Ok, start defining model parameters here + +print " creating thickness" +ymin=numpy.min(md.mesh.y) +ymax=numpy.max(md.mesh.y) +md.geometry.thickness=500.*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness +md.geometry.surface=md.geometry.bed+md.geometry.thickness + +print " creating drag" +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) #q=1. +#Take care of iceshelves: no basal drag +pos=numpy.nonzero(md.mask.elementonfloatingice)[0] +md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.ones((md.mesh.numberofelements,1)) + +print " creating initial values" +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vel=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) + +print " creating flow law parameter" +md.materials.rheology_B=1.7687*10**8*numpy.ones((md.mesh.numberofvertices,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " creating surface mass balance" +md.surfaceforcings.mass_balance=0.2*numpy.ones((md.mesh.numberofvertices,1)) #0m/a +md.basalforcings.melting_rate=0.*numpy.ones((md.mesh.numberofvertices,1)) #0m/a + +print " boundary conditions" +md=SetMarineIceSheetBC(md,'../Exp/SquareFrontEISMINT.exp') + +#Evolution of the ice shelf +pos=numpy.nonzero(md.mesh.y==200000.) #nodes on the upper boundary condition +md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.balancethickness.spcthickness[pos]=500. +md.prognostic.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.prognostic.spcthickness[pos]=500. +md.prognostic.stabilization=0 #Better result with no artificial diffusivity +md.thermal.stabilization=0 +md.timestepping.final_time=500. +md.timestepping.time_step=1 Index: /issm/trunk/test/Par/SquareSheetConstrained.py =================================================================== --- /issm/trunk/test/Par/SquareSheetConstrained.py (revision 14309) +++ /issm/trunk/test/Par/SquareSheetConstrained.py (revision 14310) @@ -51,5 +51,5 @@ md.thermal.stabilization=1. md.verbose=verbose(0) -md.settings.waitonlock=30. +md.settings.waitonlock=30 md.diagnostic.restol=0.05 md.steadystate.reltol=0.05 Index: /issm/trunk/test/Par/SquareSheetShelf.py =================================================================== --- /issm/trunk/test/Par/SquareSheetShelf.py (revision 14309) +++ /issm/trunk/test/Par/SquareSheetShelf.py (revision 14310) @@ -57,5 +57,5 @@ md.thermal.stabilization=1 md.verbose=verbose(0) -md.settings.waitonlock=30. +md.settings.waitonlock=30 md.diagnostic.restol=0.05 md.steadystate.reltol=0.05 Index: /issm/trunk/test/Par/SquareShelf.py =================================================================== --- /issm/trunk/test/Par/SquareShelf.py (revision 14309) +++ /issm/trunk/test/Par/SquareShelf.py (revision 14310) @@ -70,5 +70,5 @@ md.prognostic.stabilization = 1. md.thermal.stabilization = 1. -md.settings.waitonlock = 30. +md.settings.waitonlock = 30 md.verbose=verbose() md.diagnostic.restol = 0.10 Index: /issm/trunk/test/Par/SquareShelfConstrained.py =================================================================== --- /issm/trunk/test/Par/SquareShelfConstrained.py (revision 14309) +++ /issm/trunk/test/Par/SquareShelfConstrained.py (revision 14310) @@ -55,5 +55,5 @@ md.thermal.stabilization=1. md.verbose = verbose(0) -md.settings.waitonlock=30. +md.settings.waitonlock=30 md.diagnostic.restol=0.05 md.diagnostic.reltol=0.05 Index: /issm/trunk/test/Par/SquareThermal.par =================================================================== --- /issm/trunk/test/Par/SquareThermal.par (revision 14309) +++ /issm/trunk/test/Par/SquareThermal.par (revision 14310) @@ -4,7 +4,7 @@ disp(' creating thickness'); -h=1000; +h=1000.; md.geometry.thickness=h*ones(md.mesh.numberofvertices,1); -md.geometry.bed=-1000*ones(md.mesh.numberofvertices,1); +md.geometry.bed=-1000.*ones(md.mesh.numberofvertices,1); md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -15,21 +15,21 @@ disp(' creating drag'); -md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); %q=1. +md.friction.coefficient=200.*ones(md.mesh.numberofvertices,1); %q=1. %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.mesh.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0.; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); disp(' creating temperatures'); -md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); -disp(' creating flow law paramter'); +disp(' creating flow law parameter'); md.materials.rheology_B=paterson(md.initialization.temperature); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); disp(' creating surface mass balance'); md.surfaceforcings.mass_balance=ones(md.mesh.numberofvertices,1)/md.constants.yts; %1m/a -md.basalforcings.melting_rate=0*ones(md.mesh.numberofvertices,1)/md.constants.yts; %1m/a +md.basalforcings.melting_rate=0.*ones(md.mesh.numberofvertices,1)/md.constants.yts; %1m/a %Deal with boundary conditions: @@ -41,3 +41,3 @@ md.thermal.spctemperature(:)=md.initialization.temperature; md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); -pos=find(md.mask.elementongroundedice);md.basalforcings.geothermalflux(md.mesh.elements(pos,:))=1*10^-3; %1 mW/m^2 +pos=find(md.mask.elementongroundedice);md.basalforcings.geothermalflux(md.mesh.elements(pos,:))=1.*10^-3; %1 mW/m^2 Index: /issm/trunk/test/Par/SquareThermal.py =================================================================== --- /issm/trunk/test/Par/SquareThermal.py (revision 14310) +++ /issm/trunk/test/Par/SquareThermal.py (revision 14310) @@ -0,0 +1,48 @@ +import numpy +from paterson import * +from SetMarineIceSheetBC import * + +#Ok, start defining model parameters here + +md.timestepping.time_step=0 + +print " creating thickness" +h=1000. +md.geometry.thickness=h*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.bed=-1000.*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.surface=md.geometry.bed+md.geometry.thickness; + +print " creating velocities" +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) + +print " creating drag" +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) #q=1. +#Take care of iceshelves: no basal drag +pos=numpy.nonzero(md.mask.elementonfloatingice)[0] +md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. +md.friction.p=numpy.ones((md.mesh.numberofelements,1)) +md.friction.q=numpy.ones((md.mesh.numberofelements,1)) + +print " creating temperatures" +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) + +print " creating flow law parameter" +md.materials.rheology_B=paterson(md.initialization.temperature) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) + +print " creating surface mass balance" +md.surfaceforcings.mass_balance=numpy.ones((md.mesh.numberofvertices,1))/md.constants.yts #1m/a +md.basalforcings.melting_rate=0.*numpy.ones((md.mesh.numberofvertices,1))/md.constants.yts #1m/a + +#Deal with boundary conditions: + +print " boundary conditions for diagnostic model" +md=SetMarineIceSheetBC(md,'../Exp/SquareFront.exp') + +print " boundary conditions for thermal model" +md.thermal.spctemperature[:]=md.initialization.temperature +md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) +pos=numpy.nonzero(md.mask.elementongroundedice)[0] +md.basalforcings.geothermalflux[md.mesh.elements[pos,:]-1]=1.*10**-3 #1 mW/m^2