Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 13529) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 13530) @@ -67,4 +67,5 @@ ./classes/objects/Vertex.h\ ./classes/objects/Vertex.cpp\ + ./classes/objects/AdolcEdf.h\ ./classes/Hook.h\ ./classes/Hook.cpp\ @@ -188,5 +189,4 @@ ./shared/Matrix/matrix.h\ ./shared/Matrix/MatrixUtils.cpp\ - ./shared/Numerics/adolc_edf.h\ ./shared/Numerics/numerics.h\ ./shared/Numerics/Verbosity.h\ @@ -350,4 +350,5 @@ ./solutions/AnalysisConfiguration.cpp\ ./solutions/CorePointerFromSolutionEnum.cpp\ + ./solutions/EnvironmentInit.cpp\ ./solvers/solver_linear.cpp\ ./solvers/solver_nonlinear.cpp\ Index: /issm/trunk-jpl/src/c/classes/AdolcEdf.h =================================================================== --- /issm/trunk-jpl/src/c/classes/AdolcEdf.h (revision 13530) +++ /issm/trunk-jpl/src/c/classes/AdolcEdf.h (revision 13530) @@ -0,0 +1,26 @@ +/* + * adolc_edf.h + * + * Created on: Jun 26, 2012 + * Author: utke + */ + +#ifndef _ADOLC_EDF_H_ +#define _ADOLC_EDF_H_ + +#ifdef _HAVE_ADOLC_ + +struct Adolc_edf { + ext_diff_fct *myEDF_for_solverx_p; + Adolc_edf() : myEDF_for_solverx_p(0) {} + inline friend std::ostream& operator << ( ostream&, const Adolc_edf& ); +}; + +std::ostream& operator << ( std::ostream& out, const Adolc_edf& a) { + out << a.myEDF_for_solverx_p; + return out; +} + +#endif + +#endif Index: /issm/trunk-jpl/src/c/classes/bamg/BamgGeom.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/BamgGeom.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/BamgGeom.cpp (revision 13530) @@ -1,4 +1,4 @@ #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../io/io.h" #include "../../shared/shared.h" Index: /issm/trunk-jpl/src/c/classes/bamg/BamgMesh.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/BamgMesh.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/BamgMesh.cpp (revision 13530) @@ -1,4 +1,4 @@ #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../io/io.h" #include "../../shared/shared.h" Index: /issm/trunk-jpl/src/c/classes/bamg/BamgOpts.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/BamgOpts.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/BamgOpts.cpp (revision 13530) @@ -2,5 +2,5 @@ #include "../../shared/shared.h" #include "../../include/include.h" -#include "../objects.h" +#include "../objects/objects.h" #include "../../io/io.h" Index: /issm/trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp (revision 13530) @@ -3,5 +3,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" namespace bamg { Index: /issm/trunk-jpl/src/c/classes/bamg/BamgVertex.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/BamgVertex.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/BamgVertex.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" namespace bamg { Index: /issm/trunk-jpl/src/c/classes/bamg/Geometry.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/Geometry.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/Geometry.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../include/include.h" #include "../../shared/Exceptions/exceptions.h" Index: /issm/trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" namespace bamg { Index: /issm/trunk-jpl/src/c/classes/bamg/Mesh.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/Mesh.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/Mesh.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" namespace bamg { Index: /issm/trunk-jpl/src/c/classes/bamg/SetOfE4.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/SetOfE4.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/SetOfE4.cpp (revision 13530) @@ -1,3 +1,3 @@ -#include "../objects.h" +#include "../objects/objects.h" using namespace std; Index: /issm/trunk-jpl/src/c/classes/bamg/Triangle.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/bamg/Triangle.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/bamg/Triangle.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" namespace bamg { Index: /issm/trunk-jpl/src/c/classes/classes.h =================================================================== --- /issm/trunk-jpl/src/c/classes/classes.h (revision 13529) +++ /issm/trunk-jpl/src/c/classes/classes.h (revision 13530) @@ -30,4 +30,5 @@ #include "./OptArgs.h" #include "./OptPars.h" +#include "./AdolcEdf.h" #endif Index: /issm/trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp (revision 13530) @@ -11,5 +11,5 @@ #include #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../EnumDefinitions/EnumDefinitions.h" #include "../../shared/shared.h" Index: /issm/trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp (revision 13530) @@ -11,5 +11,5 @@ #include #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../EnumDefinitions/EnumDefinitions.h" #include "../../shared/shared.h" Index: /issm/trunk-jpl/src/c/classes/kriging/Observation.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/Observation.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/Observation.cpp (revision 13530) @@ -4,5 +4,5 @@ #include -#include "../objects.h" +#include "../objects/objects.h" /*Observation constructors and destructor*/ Index: /issm/trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp (revision 13530) @@ -11,5 +11,5 @@ #include #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../EnumDefinitions/EnumDefinitions.h" #include "../../shared/shared.h" Index: /issm/trunk-jpl/src/c/classes/kriging/Quadtree.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/Quadtree.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/Quadtree.cpp (revision 13530) @@ -1,3 +1,3 @@ -#include "../objects.h" +#include "../objects/objects.h" /*DOCUMENTATION What is a Quadtree? {{{ Index: /issm/trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp (revision 13530) @@ -11,5 +11,5 @@ #include #include -#include "../objects.h" +#include "../objects/objects.h" #include "../../EnumDefinitions/EnumDefinitions.h" #include "../../shared/shared.h" Index: sm/trunk-jpl/src/c/classes/objects.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects.h (revision 13529) +++ (revision ) @@ -1,68 +1,0 @@ -/* \file objects.h - * \brief: prototype header for all objects. - */ - -#ifndef ALL_OBJECTS_H_ -#define ALL_OBJECTS_H_ - -/*Abstract classes: */ -#include "./objects/objects.h" - -/*Objects: */ -#include "./Hook.h" -#include "./DofIndexing.h" -#include "./IoModel.h" -#include "./Patch.h" -#include "./Update.h" - -/*Gauss*/ -#include "./gauss/GaussTria.h" -#include "./gauss/GaussPenta.h" - -/*Numerics:*/ -#include "./matrix/ElementMatrix.h" -#include "./matrix/ElementVector.h" -#include "./matrix/Vector.h" -#include "./matrix/Matrix.h" - -/*C objects: */ -#include "./FemModel.h" -#include "./OptArgs.h" -#include "./OptPars.h" - -/*Bamg: */ -#include "./bamg/BamgOpts.h" -#include "./bamg/BamgGeom.h" -#include "./bamg/BamgMesh.h" -#include "./bamg/Metric.h" -#include "./bamg/DoubleAndInt.h" -#include "./bamg/Direction.h" -#include "./bamg/BamgVertex.h" -#include "./bamg/AdjacentTriangle.h" -#include "./bamg/Edge.h" -#include "./bamg/GeomVertex.h" -#include "./bamg/GeomEdge.h" -#include "./bamg/Curve.h" -#include "./bamg/Triangle.h" -#include "./bamg/ListofIntersectionTriangles.h" -#include "./bamg/GeomSubDomain.h" -#include "./bamg/SubDomain.h" -#include "./bamg/VertexOnGeom.h" -#include "./bamg/VertexOnVertex.h" -#include "./bamg/VertexOnEdge.h" -#include "./bamg/CrackedEdge.h" -#include "./bamg/Mesh.h" -#include "./bamg/Geometry.h" -#include "./bamg/BamgQuadtree.h" -#include "./bamg/SetOfE4.h" - -/*Kriging*/ -#include "./kriging/Variogram.h" -#include "./kriging/GaussianVariogram.h" -#include "./kriging/ExponentialVariogram.h" -#include "./kriging/SphericalVariogram.h" -#include "./kriging/PowerVariogram.h" -#include "./kriging/Quadtree.h" -#include "./kriging/Observation.h" - -#endif Index: /issm/trunk-jpl/src/c/include/macros.h =================================================================== --- /issm/trunk-jpl/src/c/include/macros.h (revision 13529) +++ /issm/trunk-jpl/src/c/include/macros.h (revision 13530) @@ -71,14 +71,14 @@ #endif /*}}}*/ -/* ISSMBOOT/ISSMEND {{{*/ +/* IssmBoot/IssmEnd {{{*/ /*The following macros hide the error exception handling in a matlab module. Just put - * ISSMBOOT(); and ISSMEND(); at the beginning and end of a module, and c++ exceptions + * IssmBoot(); and IssmEnd(); at the beginning and end of a module, and c++ exceptions * will be trapped. Really nifty!*/ -#define ISSMBOOT(); \ +#define IssmBoot(); \ try{ -#define ISSMEND(); }\ +#define IssmEnd(); }\ catch(ErrorException &exception){\ exception.Report(); \ Index: /issm/trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13530) @@ -8,5 +8,4 @@ #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" -#include "../../shared/Numerics/adolc_edf.h" Index: /issm/trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13530) @@ -12,4 +12,5 @@ #include "./Solverx.h" #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../include/include.h" #include "../../io/io.h" @@ -17,8 +18,4 @@ #ifdef _HAVE_GSL_ #include -#endif - -#ifdef _HAVE_ADOLC_ -#include "../../shared/Numerics/adolc_edf.h" #endif Index: sm/trunk-jpl/src/c/shared/Numerics/adolc_edf.h =================================================================== --- /issm/trunk-jpl/src/c/shared/Numerics/adolc_edf.h (revision 13529) +++ (revision ) @@ -1,28 +1,0 @@ -/* - * adolc_edf.h - * - * Created on: Jun 26, 2012 - * Author: utke - */ - -#ifndef _ADOLC_EDF_H_ -#define _ADOLC_EDF_H_ - -#include "../../include/include.h" - -#ifdef _HAVE_ADOLC_ - -struct Adolc_edf { - ext_diff_fct *myEDF_for_solverx_p; - Adolc_edf() : myEDF_for_solverx_p(0) {} - inline friend std::ostream& operator << ( ostream&, const Adolc_edf& ); -}; - -std::ostream& operator << ( std::ostream& out, const Adolc_edf& a) { - out << a.myEDF_for_solverx_p; - return out; -} - -#endif - -#endif Index: /issm/trunk-jpl/src/c/solutions/EnvironmentInit.cpp =================================================================== --- /issm/trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13530) +++ /issm/trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13530) @@ -0,0 +1,22 @@ +/*!\file: EnvironmentInit.cpp + * \brief: initialize Petsc, MPI, you name it + */ + +void EnvironmentInit(int argc,char** argv){ + + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ + ierr=PetscInitialize(&argc,&argv,(char*)0,""); + if(ierr) _error_("Could not initialize Petsc"); + #else + #ifdef _HAVE_MPI_ + MPI_Init(&argc,&argv); + #endif + #endif + + /*Size and rank: */ + #ifdef _HAVE_MPI_ + MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); + MPI_Comm_size(MPI_COMM_WORLD,&num_procs); + #endif +} Index: /issm/trunk-jpl/src/c/solutions/issm.cpp =================================================================== --- /issm/trunk-jpl/src/c/solutions/issm.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/solutions/issm.cpp (revision 13530) @@ -5,6 +5,5 @@ #include "../issm.h" #include "../include/globals.h" -#include "../shared/Numerics/adolc_edf.h" - + int main(int argc,char **argv){ @@ -46,18 +45,9 @@ IssmPDouble Solution_time, Memory_use, Current_flops; - ISSMBOOT(); - - - /*Initialize environments: Petsc, MPI, etc...: */ - #ifdef _HAVE_PETSC_ - ierr=PetscInitialize(&argc,&argv,(char*)0,""); - if(ierr) _error_("Could not initialize Petsc"); - #else - #ifdef _HAVE_MPI_ - MPI_Init(&argc,&argv); - #endif - #endif - - #ifdef _HAVE_MPI_ + IssmBoot(); + + EnvironmentInit(argc,argv); + + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); #else @@ -65,10 +55,5 @@ #endif - /*Size and rank: */ - #ifdef _HAVE_MPI_ - MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); - MPI_Comm_size(MPI_COMM_WORLD,&num_procs); - #endif - + /*First process inputs*/ _pprintLine_(""); @@ -115,5 +100,5 @@ #endif - /*If running AD, then initialize the tape: */ + /*If running AD, then initialize a placeholder with which to work: */ #ifdef _HAVE_ADOLC_ GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); @@ -249,7 +234,6 @@ #endif - /*end module: */ - ISSMEND(); + IssmEnd(); return 0; //unix success return; Index: /issm/trunk-jpl/src/c/solutions/kriging.cpp =================================================================== --- /issm/trunk-jpl/src/c/solutions/kriging.cpp (revision 13529) +++ /issm/trunk-jpl/src/c/solutions/kriging.cpp (revision 13530) @@ -36,21 +36,7 @@ IssmDouble *error = NULL; - ISSMBOOT(); + IssmBoot(); - /*Initialize environments: Petsc, MPI, etc...: */ -#ifdef _HAVE_PETSC_ - int ierr=PetscInitialize(&argc,&argv,(char*)0,""); - if(ierr) _error_("Could not initialize Petsc"); -#else -#ifdef _HAVE_MPI_ - MPI_Init(&argc,&argv); -#endif -#endif - - /*Size and rank: */ -#ifdef _HAVE_MPI_ - MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); - MPI_Comm_size(MPI_COMM_WORLD,&num_procs); -#endif + EnvironmentInit(argc,argv); /*First process inputs*/ @@ -112,5 +98,5 @@ /*end module: */ - ISSMEND(); + IssmEnd(); return 0; //unix success return; Index: /issm/trunk-jpl/src/c/solutions/solutions.h =================================================================== --- /issm/trunk-jpl/src/c/solutions/solutions.h (revision 13529) +++ /issm/trunk-jpl/src/c/solutions/solutions.h (revision 13530) @@ -45,4 +45,5 @@ void controlrestart(FemModel* femmodel,IssmDouble* J); void ResetBoundaryConditions(FemModel* femmodel, int analysis_type); +void EnvironmentInit(int argc,char** argv); //solution configuration