Index: /issm/oecreview/Archive/18296-19100/Date.tex
===================================================================
--- /issm/oecreview/Archive/18296-19100/Date.tex (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/Date.tex (revision 19102)
@@ -0,0 +1,1 @@
+Feb-12-2015
Index: /issm/oecreview/Archive/18296-19100/ISSM-18297-18298.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18297-18298.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18297-18298.diff (revision 19102)
@@ -0,0 +1,12183 @@
+Index: ../trunk-jpl/src/java/Changelog_1.0.0.txt
+===================================================================
+--- ../trunk-jpl/src/java/Changelog_1.0.0.txt (revision 18297)
++++ ../trunk-jpl/src/java/Changelog_1.0.0.txt (revision 18298)
+@@ -1,29 +0,0 @@
+-This is the changelog for Inishell release 1.0.0
+- *editing existing ini file:
+- +populate the GUI according to the values in an existing ini file
+- +show progress bar while loading
+- +Comments are preserved, nested template parameters properly handled, unknown keys are preserved
+-
+- *usability improvements:
+- +the file dialogs remember the last path they pointed to
+- +add ".ini" extension when saving to a config file if necessary
+- +new icons, hoping to make their meaning clearer
+- +reset button on the GUI to revert to defaults
+-
+- *layout improvements:
+- +fixed help text horizontal alignements issues
+- +the help text is now verticaly aligned with the top of the widget
+- +Notion of hierarchy for an easier handling of layout issues
+- +layout now consistent between Linux and Windows, still some small spacing differences with osX
+- +possibility to group parameters in a frame with a frame title
+-
+- *bug fixes:
+- +default value in comboBox is honored
+- +mandatory comboBox properly handled on osX
+- +better help text handling
+-
+- *others:
+- +keys are printed in the order they appear on the GUI
+- +code cleanup and optimizations
+- +add version information in MANIFEST and title bar
+- +clean up and reorganization in build.xml, add help and pack targets
+Index: ../trunk-jpl/src/java/dist/inishell.jar
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/doc/examples/min_example.xml
+===================================================================
+--- ../trunk-jpl/src/java/doc/examples/min_example.xml (revision 18297)
++++ ../trunk-jpl/src/java/doc/examples/min_example.xml (revision 18298)
+@@ -1,40 +0,0 @@
+-
+-
+-
+-
+-
+- This is a parameter that asks for a string value and that is present in
+- both the section "section1" and "section2".
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- This parameter belongs to section1.
+- When the "null" option is selected, the dropdown menu appears
+- red because this parameter is non-optional.
+- When the value "ONE" is selected a nested parameter "SOME_INTEGER" appears.
+-
+-
+-
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/doc/examples/io.ini
+===================================================================
+--- ../trunk-jpl/src/java/doc/examples/io.ini (revision 18297)
++++ ../trunk-jpl/src/java/doc/examples/io.ini (revision 18298)
+@@ -1,180 +0,0 @@
+-[General]
+-PLUGINPATH = ../../lib/plugins ;super
+-BUFF_CHUNK_SIZE = 30
+-BUFF_BEFORE = 1.5
+-
+-[Input]
+-COORDSYS = CH1903
+-TIME_ZONE = 1
+-; COORDSYS = PROJ4
+-; COORDPARAM = 21781
+-
+-#reading ARC dem
+-DEM = ARC
+-DEMFILE = ./input/surface-grids/Switzerland_1000m.asc
+-
+-#reading ARPS dem
+-; DEM = ARPS
+-; DEMFILE = ./wgrt10r2_vw4.asc
+-; ARPS_X = 653400
+-; ARPS_Y = 112204
+-
+-#reading PGM image as dem
+-; DEM = PGM
+-; DEMFILE = ./Switzerland.pgm
+-; PGM_XCOORD = 479500.
+-; PGM_YCOORD = 73500.
+-; PGM_CELLSIZE = 1000.
+-; PGM_MIN = 193.
+-; PGM_MAX = 4204.
+-
+-; LANDUSE = ARC
+-; LANDUSEFILE = ch_as97.asc
+-
+-#Alpine3D traditional inputs -> A3D plugin
+-; METEO = A3D
+-; METEOPATH = ./input/meteo
+-
+-#Borma
+-; METEO = BORMA
+-; METEOPATH = ./input/xml
+-; NROFSTATIONS = 1
+-; STATION1 = 00.00.00.2
+-
+-#Snowpack input
+-; METEO = SNOWPACK
+-; METEOPATH = input
+-; METAFILE = IMIS_Extracted_Info.txt ;metadata for all stations
+-; STATION1 = MST96_RR.inp
+-
+-#SMET meteorological file format
+-METEO = SMET
+-METEOPATH = ./input/meteo
+-STATION1 = FLU2.smet
+-STATION2 = FIR2.smet
+-STATION3 = FRA2.smet
+-STATION4 = GLA2.smet
+-STATION5 = ILI2.smet
+-STATION6 = OTT2.smet
+-STATION7 = TUJ3.smet
+-
+-#IMIS network database input -> IMIS plugin
+-; METEO = IMIS
+-; DBNAME = sdbo
+-; DBUSER = XXX
+-; DBPASS = XXX
+-; NROFSTATIONS = 4
+-; STATION1 = MORN2
+-; STATION2 = DAV3
+-; STATION3 = KLO2
+-; STATION4 = *SAM0
+-
+-#GEOtop traditional inputs -> GEOTOP plugin
+-; METEO = GEOTOP
+-; METEOPATH = meteo/
+-; METEOPREFIX = _meteo
+-
+-#GSN direct input -> GSN plugin
+-; METEO = GSN
+-; ENDPOINT = http://montblanc.slf.ch:22001/services/A3DWebService
+-; STATION1 = wan_sen14_2008
+-; STATION2 = wan2
+-
+-[Output]
+-COORDSYS = CH1903
+-TIME_ZONE = 1
+-
+-GRID2D = ARC
+-GRID2DPATH = ./
+-
+-; GRID2D = PNG
+-; GRID2DPATH = ./
+-; PNG_MIN_SIZE = 800x600
+-; PNG_WORLD_FILE = true
+-; PNG_AUTOSCALE = false
+-; PNG_SCALING = nearest
+-
+-METEO = SMET
+-METEOPATH = ./
+-
+-[Filters]
+-TA::filter1 = min_max
+-TA::arg1 = 240 320
+-
+-RH::filter1 = min_max
+-RH::arg1 = 0.01 1.2
+-RH::filter2 = min_max
+-RH::arg2 = soft 0.05 1.0
+-
+-HNW::filter1 = min
+-HNW::arg1 = -0.1
+-HNW::filter2 = min
+-HNW::arg2 = soft 0.
+-
+-ISWR::filter1 = min_max
+-ISWR::arg1 = -10. 1500.
+-ISWR::filter2 = min
+-ISWR::arg2 = soft 0.
+-
+-RSWR::filter1 = min_max
+-RSWR::arg1 = -10 1500
+-RSWR::filter2 = min
+-RSWR::arg2 = soft 0
+-
+-#for TA between 240 and 320 K
+-ILWR::filter1 = min_max
+-ILWR::arg1 = 188 600
+-ILWR::filter2 = min_max
+-ILWR::arg2 = soft 200 400
+-
+-#we need to consider time with no snow -> TSS>0
+-#min(TSS) in db since 1998: -50C
+-TSS::filter1 = min_max
+-TSS::arg1 = 200 320
+-
+-#idem
+-TSG::filter1 = min_max
+-TSG::arg1 = 200 320
+-
+-HS::filter1 = min
+-HS::arg1 = soft 0.0
+-HS::filter2 = rate
+-HS::arg2 = 5.55e-5 ;0.20 m/h
+-
+-VW::filter1 = min_max
+-VW::arg1 = -2 70
+-VW::filter2 = min_max
+-VW::arg2 = soft 0.2 50.0
+-
+-[Interpolations1D]
+-WINDOW_SIZE = 86400
+-
+-TA::resample = linear
+-
+-RH::resample = linear
+-
+-HS::resample = linear
+-
+-VW::resample = nearest_neighbour
+-VW::args = extrapolate
+-
+-HNW::resample = linear
+-
+-[Interpolations2D]
+-TA::algorithms = IDW_LAPSE CST_LAPSE
+-TA::cst_lapse = -0.008
+-TA::idw_lapse = -0.008 soft
+-
+-RH::algorithms = RH IDW_LAPSE CST
+-
+-HNW::algorithms = IDW_LAPSE CST_LAPSE CST
+-HNW::cst_lapse = 0.0005 frac
+-
+-VW::algorithms = IDW_LAPSE CST
+-
+-P::algorithms = STD_PRESS
+-
+-ILWR::algorithms = CST_LAPSE
+-ILWR::cst_lapse = -0.03125
+-
+-RSWR::algorithms = IDW CST
+Index: ../trunk-jpl/src/java/doc/examples/meteoio_config.xml
+===================================================================
+--- ../trunk-jpl/src/java/doc/examples/meteoio_config.xml (revision 18297)
++++ ../trunk-jpl/src/java/doc/examples/meteoio_config.xml (revision 18298)
+@@ -1,919 +0,0 @@
+-
+-
+-
+-
+-
+- Size in days of a chunk of data to read at once.
+-
+-
+-
+-
+- Alternate way of buffer centering: When rebuffering, the new date will be located BUFF_BEFORE days from the
+- beginning of the buffer (therefore, it takes a value in days).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- coordinate system
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for METEO data
+-
+-
+-
+-
+-
+- The name of the parameter to copy (e.g. TA, RH, VW, ISWR, etc)
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for Digital Elevation Model data
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for land cover data
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for 2D gridded data
+-
+-
+-
+-
+-
+- filename for station number #
+-
+-
+-
+-
+- station id for the given station number #
+-
+-
+-
+-
+- Coordinates are given as "lat lon" or "xcoord ycoord epsg_code"
+-
+-
+-
+-
+-
+-
+- string containing the path to the xml files
+-
+-
+-
+-
+-
+-
+- database name, as provided by your database administrator
+-
+-
+- database user name
+-
+-
+- database password associated with the user name
+-
+-
+-
+-
+- OPTIONAL: use ANETZ stations to provide precipitations for normal IMIS stations.
+- Each IMIS station is associated with one or two ANETZ stations and does a weighted
+- average to get what should be its local precipitations
+-
+-
+-
+-
+- OPTIONAL: if set to false (default), all IMIS precipitation will be deleted (since IMIS stations don't have heated rain gauges, their precipitation measurements are not good in winter conditions). If set to true, it is strongly advised to use a FilterHNWMelt filter to detect snow melting in the rain gauge and perform winter conditions detection in the application.
+-
+-
+-
+-
+- if set to true, the SNOWPACK simulated Snow Water Equivalent from the database will be used to compute HNW. Data gaps greater than 3 hours on SWE will lead to unchanged hnw while all data that can properly be computed will overwrite hnw. (default=false)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the grib files
+-
+-
+- grib file extension, or none for no file extension (default: .grb)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the data files
+-
+-
+- absolute filename of the geotop.inpts file
+-
+-
+- prefix to append when generating a file name for reading
+-
+-
+-
+-
+-
+- string containing the path to the data files
+-
+-
+- specifiy in which order the columns should be printed out
+-
+-
+-
+-
+-
+- webserver running GSN with its port number and full path. For example:
+- http://montblanc.slf.ch:22001/services/A3DWebService
+-
+-
+- Should the connection go through a proxy? This is useful for servers
+- filtering on domains but usually not necessary.
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the smet files
+-
+-
+-
+-
+-
+-
+- string representing path where SMET files should be saved
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the SNOWPACK files
+-
+-
+- filename of the meta data file (in METEOPATH)
+-
+-
+-
+- the number of measured snow temperatures provided
+-
+-
+-
+- the number of solutes for which input data are provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- OPTIONAL: wind velocity to use for blowing and drifting snow is provided
+-
+-
+-
+-
+- OPTIONAL: measured new snow density is provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- generate names compatible with Alpine3D's grid viewer?
+-
+-
+- grid file extension, or none for no file extension (default: .asc)
+-
+-
+-
+-
+-
+- x coordinate of the lower left corner of the grids
+-
+-
+- y coordinate of the lower left corner of the grids
+-
+-
+- grid file extension, or none for no file extension (default: .asc)
+-
+-
+-
+-
+-
+- prefix to append when generating a file name for reading (ie: something like "laf" for Cosmo-Analysis-full domain)
+-
+-
+- grib file extension, or none for no file extension (default: .grb)
+-
+-
+-
+-
+-
+-
+-
+- generate a world file for each output file? This file contains the geolocalization information
+-
+-
+-
+-
+- generate a legend?
+-
+-
+-
+-
+- autoscale color scale?
+-
+-
+-
+-
+- scaling algorithm (default=bilinear)
+-
+-
+- minimum dimensions of the PNG, like 640x480
+-
+-
+- maximum dimensions of the PNG, like 1024x768
+-
+-
+-
+-
+- generate a color indexed file (default=true)
+-
+-
+-
+-
+- optimize for speed (default=false)
+-
+-
+- number of colors in the palette (default=30)
+-
+-
+-
+-
+-
+- lower left x coordinate
+-
+-
+- lower left y coordinate
+-
+-
+- cellsize in meters
+-
+-
+- minimum value in real world coordinates to match with the minimum value read out of the PGM file (such minimum being greater than 0 because 0 is NODATA)
+-
+-
+- maximum value in real world coordinates to match with the maximum value read out of the PGM file
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Mean average processing. The mean average filter returns the mean value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median average processing. The median average filter returns the median value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Standard deviation filter. Values outside of mean ± 2 std_dev are rejected.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median Absolute Deviation. Values outside of median ± 3 σ_MAD are rejected. <br>
+- See http://en.wikipedia.org/wiki/Median_absolute_deviation for more information.
+-
+-
+-
+-
+-
+-
+- The keyword "soft" maybe added, if the window position is allowed to be adjusted to the data present.
+- The two arguments may be preceded by the keywords "left", "center" or "right", indicating the window position.
+-
+-
+- Tukey 53H method A smooth time sequence is generated from the median, substracted from the original signal and
+- compared with the standard deviation. see "Despiking Acoustic Doppler Velocimeter Data", Derek G. Goring and Vladimir
+- L. Nikora, Journal of Hydraulic Engineering, 128, 1, 2002 The deviation factor coeffecient is currently hard-coded as k=1.5.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Wind vector averaging. This calculates the vector average over a user given time period. Each wind vector
+- within this period is added and the final sum is normalized by the number of vectors that have been added.
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Alpha needs to be provided as last argument. Please note that the standard filter works with a left window!
+-
+-
+- Exponential smooting processing, exponential moving average s_0 = x_0 s_n = alpha*x_(t-1) + (1-alpha)*s_t-1
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Please note that the standard filter works with a left window!
+-
+-
+- Weighted moving average smoothing such as: WMA = (1*X1 + 2*X2 + ... + n*Xn) / sum_of_weights
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- This implements the standard methods for precipitation correction as described in "WMO Solid Precipitation Measurement Intercomparison", B. Goodison, P. Louie and D. Yang, 872, 1998 as well as the overview given by "Literature Study on the Correction of Precipitation Measurements", Annette Wagner, 2009. The correction parameters for the shielded Hellmann gauge (German version) are from "Wind-induced Precipitation Undercatch of the Hellmann Gauges", Daqing Yang et al, Nordic Hydrology, 30, 1999, pp 57-80.
+-
+-
+-
+-
+-
+-
+- This applies a constant correction factor to the precipitation, one for pure snow and one for mixed precipitation. The following thresholds are used: pure snow below -2 C; mixed precipitation between -2 and +2 C; pure rain above 2 C. These threshold can be changed (see online documentation).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Affects resampling: expresses (in seconds) how far a valid point can be
+- searched for when re-interpolating a missing value
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Detrend the measured data, fill the grid with the average over all the stations, reapply the elevation trend
+-
+-
+-
+-
+- Detrend the measured data, apply Inverse Distance Weighted average, reapply elevation trend
+-
+-
+-
+- Same as IDW_LAPSE, but only considering a given number of neighboring stations
+-
+-
+-
+-
+-
+- Base algorithm (do not forget to add the options for the base algorithm)
+-
+- Distribute precipitation with a base algorithm (IDW_LAPSE by default), then reduce/remove precipitation on
+- steep slopes and correct with the local curvature. This is to simulate snow redistribution processes.
+-
+-
+-
+- Variogram model
+-
+- Ordinary kriging (EXPERIMENTAL)
+-
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/doc/examples/snowpack_config.xml
+===================================================================
+--- ../trunk-jpl/src/java/doc/examples/snowpack_config.xml (revision 18297)
++++ ../trunk-jpl/src/java/doc/examples/snowpack_config.xml (revision 18298)
+@@ -1,1084 +0,0 @@
+-
+-
+-
+-
+-
+-
+- Size in days of a chunk of data to read at once.
+-
+-
+-
+-
+- Alternate way of buffer centering: When rebuffering, the new date will be located BUFF_BEFORE days from the
+- beginning of the buffer (therefore, it takes a value in days).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- coordinate system
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for METEO data
+-
+-
+-
+-
+- The name of the parameter to copy (e.g. TA, RH, VW, ISWR, etc)
+-
+- Copy a meteo parameter into a new one (you should not need this)
+-
+-
+-
+-
+-
+-
+-
+-
+- Path to the land surface and snow input parameters
+-
+-
+-
+-
+-
+- Plugin to use for reading SNO data
+-
+-
+-
+- file name for the initial profile for station number #
+-
+-
+-
+-
+-
+-
+-
+- Path to the outputs (this path MUST exist, it won't be created)
+-
+-
+-
+- Option to give an additional simulation specific output name to the run in addition to "STATION_NAME")
+-
+-
+-
+-
+-
+-
+-
+- Write meteo data out?
+-
+-
+-
+- When to start writing meteo data out (offset, in days)
+-
+-
+-
+- How often to write meteo data out (in days: 3 hours=.125, 1 hour=4.1666e-2)
+-
+-
+-
+-
+-
+- If AVGSUM_TIME_SERIES is set, mean fluxes and cumulated masses since last dump are written, else current energy fluxes, cumulated masses over last COMPUTATION_STEP_LENGTH (recommended setting in operational mode).
+-
+-
+-
+-
+-
+- If CUMSUM_MASS is set, current value of cumulated masses since begin of run are dumped. Precipitations (rain and snow, rain) are always dumped as rates (kg m-2 h-1).
+-
+-
+-
+-
+-
+- Write precipitation as rates (kg m-2 h-1, default) or as sums over the output time step. Please note that the units label in the output file and in SN_GUI <b>will remain kg m-2 h-1</b> and will therefore not match sums.
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- How to write the profiles (default: ASCII)
+-
+-
+-
+-
+-
+- Write profile data out?
+-
+-
+-
+- When to start writing profile data out (offset, in days)
+-
+-
+-
+- How often to write profile data out (in days: 3 hours=.125, 1 hour=4.1666e-2)
+-
+-
+-
+-
+-
+- Write the hand hardness in newtons (default) or as index
+-
+-
+-
+-
+-
+- Classify the profile (default=false)? This is according to Schweizer, J. and M. Luetschg, <i>Characteristics of human-triggered avalanches</i>, 2001, Cold Reg. Sci. Technol. <b>33</b>(2-3)
+-
+-
+-
+-
+-
+-
+-
+-
+- Plugin to use for reading SNO data
+-
+-
+-
+- Dump snow files every BACKUP_DAYS_BETWEEN days
+-
+-
+-
+- First dump of sno files happens at end of run or after FIRST_BACKUP days, whichever happens first
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Write canopy data out? To be set to TRUE only if CANOPY=TRUE
+-
+-
+-
+-
+-
+- Write hazard data out? This must be FALSE for Alpine3D
+-
+-
+-
+-
+-
+- Write turbulent fluxes out?
+-
+-
+-
+-
+-
+- Write snow/soil temperatures out?
+-
+-
+-
+-
+-
+-
+- Write long wave radiation out?
+-
+-
+-
+-
+-
+- Write short wave radiation out?
+-
+-
+-
+-
+-
+- Write mass balance terms out?
+-
+-
+-
+-
+-
+- Write meteo parameters out?
+-
+-
+-
+-
+-
+- Write stability parameters out?
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Internal time step (in minutes) used for model simulation. Please note that this MUST be the same as HNW::accumulate (the latter being in seconds) if re-acumulating precipitation, otherwise it would lead to wrong results.
+-
+-
+-
+- Aerodynamic roughness length as a parameter for the Monin-Obukhov bulk formulation; A typical value for complex terrain is 0.01 m and for snow covered flat sites 0.001 m.
+-
+-
+-
+- The instrument height (or model layer height) for meteorological input data except for wind, which may be at a different height; note that height is above ground for a standard SNOWPACK application but above surface (snow or ground) for Alpine3D applications.
+-
+-
+-
+- The instrument height (or model layer height) for wind input data; note that height is above ground for a standard SNOWPACK application but above surface (snow or ground) for Alpine3D applications
+-
+-
+-
+-
+-
+-
+-
+-
+- Input mode by which a measurement of snow depth is used to drive the snow cover mass balance
+-
+-
+-
+- Define the shortwave radiation input: <ol> <li value="0">Incoming shortwave radiation is measured and albedo estimated by the model;</li> <li>Reflected shortwave radiation is available as input and albedo is estimated by the model (IMIS standard);</li> <li>Incoming and reflected shortwave radiation are both measured and the albedo is estimated from both measurements subject to plausibility checks.</li> </ol>
+-
+-
+-
+- Select the atmospheric stability correction model:<ol> <li value="-1"> use a simplified Richardson number stability correction;</li> <li>assume standard Monin-Obukhov bulk formulation for surface exchange iteration with Paulson, Stearns and Weidner (can be used with BC_CHANGE=0); </li> <li> force Monin-Obukhov formulation to assume neutral conditions regardless of the actual stratification; it has been shown to work well in complex terrain settings. It should be used with BC_CHANGE=1, i.e., Dirichlet bc but also is recommended with Neumann b.c., i.e., BC_CHANGE=0.</li> </ol>
+-
+-
+-
+-
+-
+- Switch to tell the model that canopy is present (note that Canopy parameters should then be provided in the *.sno file)
+-
+-
+-
+-
+-
+- A measured surface temperature is available and can be reliably used for various consistency tests (it needs to be set to true if enabling CHANGE_BC).
+-
+-
+-
+-
+-
+- Use measured surface temperature as Dirichlet temperature BC for sub-freezing snowpacks and switch to Neumann only for melting snowpacks. If set to false, assumes Neumann boundary conditions.
+-
+-
+-
+- Threshold value (small number below freezing), which switches from Dirichlet to Neumann BCs if CHANGE_BC is selected
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Based on meteorological input from a (flat field) automatic station or numerical weather model, up to 8 expositions can be calculated in addition to the flat field if the corresponding *.sno files are provided. For example, if you provide a flat field *.snow file (mandatory), which is named KLO3.sno and you want 4 slopes to be calculated the corresponding slope files should be named KLO21.sno, …,KLO24.sno
+-
+-
+-
+-
+-
+- Use the provided incoming long wave on the virtual slopes?
+-
+-
+-
+-
+-
+- Specifies if redistribution of snow is allowed from (upwind) expositions to lee slopes. In case just the flat field is calculated, snow erosion is enabled but only for "ENFORCE_MEASURED_SNOW_HEIGHTS".
+-
+-
+-
+-
+-
+-
+-
+-
+- Soil layers as defined by the *.sno files are included in the simulation
+-
+-
+-
+-
+-
+- Assume that the lower temperature boundary condition is given by GEO_HEAT (Neumann) and not by a measured temperature
+-
+-
+-
+- Constant geothermal heat flux at great) depth W m-2): Lower flux boundary condition for temperature equation if BC is Neumann
+-
+-
+-
+-
+-
+-
+-
+-
+- <font color="FF0000">The keys in this section deeply affect the operation of the SNOWPACK model. This could lead to unexpected behavior or surprising results. If you are not an experienced Snowpack user, please do NOT change any keys below!</font>
+-
+-
+-
+-
+-
+-
+-
+- variant selection (includes a choice of specific models)
+-
+-
+-
+-
+-
+-
+-
+- perp_to_slope
+-
+-
+-
+-
+-
+- Shifts the origin of the wind rose for snow redistribution and slope simulations: e.g. choose 45° to have NE/SE/SW/NW
+-
+-
+-
+- Scaling factor to apply to wind values in case of drifting snow
+-
+-
+-
+-
+-
+-
+-
+-
+- Tell the model that relative humidity values are with respect to water regardless of the temperature
+-
+-
+-
+- Temperature threshold for rain/snow transition
+-
+-
+-
+- If ENFORCE_MEASURED_SNOW_HEIGHTS, relative humidity threshold for precipitation to occur
+-
+-
+-
+- If ENFORCE_MEASURED_SNOW_HEIGHTS, (TA-TSS) threshold for precipitation to occur
+-
+-
+-
+-
+-
+-
+- Relative humidity threshold above which no surface hoar is allowed to form (because at very high humidity, typically no hoar crystals can form)
+-
+-
+-
+- Wind speed threshold above which no surface hoar is allowed to form (because it will drift away)
+-
+-
+-
+- Define the initial density for surface hoar at the time it gets buried by new snow
+-
+-
+-
+- Define a threshold below which any traces of surface hoar will not be given a separate hoar layer when buried.
+-
+-
+-
+- Assumed density of surface hoar while exposed at the surface and not buried
+-
+-
+-
+-
+-
+-
+- positions of temperatur sensors in snow or soil: positive values refer to heigths measured from the ground surface (snow only), negative values refer to depths measured from either the ground surface or the snow surface in case no soil layers are present. A sensor must at least be covered by MIN_DEPTH_SUBSURF (m) snow for its temperature to be output.
+-
+-
+-
+-
+- Minimum snow depth above a temperature sensor to accept the measurement
+-
+-
+-
+- If you go to Antarctica or the tropics you may expect different reasonable temperatures
+-
+-
+-
+- If you go to Antarctica or the tropics you may expect different reasonable temperatures
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Choice of new snow density model (diverse statistical models)
+-
+-
+-
+- Fixed value to be used as new snow density if a constant density model is chosen, otherwise the choices are "PARAMETERIZED" "EVENT" "MEASURED"
+-
+-
+-
+-
+-
+- metamorphism_model
+-
+-
+-
+- new_snow_grain_rad
+-
+-
+-
+-
+-
+- strength_model
+-
+-
+-
+-
+-
+- viscosity_model
+-
+-
+-
+-
+-
+-
+- hardness_model
+-
+-
+-
+-
+-
+- Choose the Doorschot saltation model over the simple Sorenson parameterization
+-
+-
+-
+-
+-
+- Select a multi stream model for shortwave radiation penetration into the snow cover
+-
+-
+-
+-
+-
+- Force the model to work with a fixed albedo
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Identify grass growing under the snow height sensor. This usually works well but might sometimes lead to problems
+-
+-
+-
+-
+-
+- Switch to tell the model that a impermeable layer should be simulated on top of some snow or ice: this requires that the *.sno file contains this layer, which is characterized via the soil parameters; the option has successfully been used to simulate snow and ice protection using geo-textiles and saw dust.
+-
+-
+-
+-
+-
+- If switched on, you can also simulate ponding on impermeable ice surfaces below the snow cover
+-
+-
+-
+-
+-
+- Assuming an impermeable surface such as on a road or on geo-textiles (e.g. for snow farming), a liquid water layer is allowed to form on this surface
+-
+-
+-
+-
+-
+-
+- Standard size of a new element added to the stack of elements (layers) during snowfall events
+-
+-
+-
+- Threshold value for enforcing the layer to be merged with the layer above or below
+-
+-
+-
+-
+-
+- Combine neighboring elements based on a set of similarity conditions which are hard-coded
+-
+-
+-
+-
+-
+-
+- filename for station number #
+-
+-
+-
+-
+- station id for the given station number #
+-
+-
+-
+-
+- Coordinates are given as "lat lon" or "xcoord ycoord epsg_code"
+-
+-
+-
+-
+-
+-
+- string containing the path to the xml files
+-
+-
+-
+-
+-
+-
+- database name, as provided by your database administrator
+-
+-
+- database user name
+-
+-
+- database password associated with the user name
+-
+-
+-
+-
+- OPTIONAL: use ANETZ stations to provide precipitations for normal IMIS stations.
+- Each IMIS station is associated with one or two ANETZ stations and does a weighted
+- average to get what should be its local precipitations
+-
+-
+-
+-
+- OPTIONAL: if set to false (default), all IMIS precipitation will be deleted (since IMIS stations don't have heated rain gauges, their precipitation measurements are not good in winter conditions). If set to true, it is strongly advised to use a FilterHNWMelt filter to detect snow melting in the rain gauge and perform winter conditions detection in the application.
+-
+-
+-
+-
+- if set to true, the SNOWPACK simulated Snow Water Equivalent from the database will be used to compute HNW. Data gaps greater than 3 hours on SWE will lead to unchanged hnw while all data that can properly be computed will overwrite hnw. (default=false)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the grib files
+-
+-
+- grib file extension, or none for no file extension (default: .grb)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the data files
+-
+-
+- absolute filename of the geotop.inpts file
+-
+-
+- prefix to append when generating a file name for reading
+-
+-
+-
+-
+-
+- webserver running GSN with its port number and full path. For example:
+- http://montblanc.slf.ch:22001/services/A3DWebService
+-
+-
+- Should the connection go through a proxy? This is useful for servers
+- filtering on domains but usually not necessary.
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the smet files
+-
+-
+-
+-
+-
+-
+- string containing the path to the SNOWPACK files
+-
+-
+- filename of the meta data file (in METEOPATH)
+-
+-
+- the number of measured snow temperatures that are provided
+-
+-
+- the number of solutes for which input data are provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- OPTIONAL: wind velocity to use for blowing and drifting snow is provided
+-
+-
+-
+-
+- OPTIONAL: measured new snow density is provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Mean average processing. The mean average filter returns the mean value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median average processing. The median average filter returns the median value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Standard deviation filter. Values outside of mean ± 2 std_dev are rejected.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median Absolute Deviation. Values outside of median ± 3 σ_MAD are rejected. <br>
+- See http://en.wikipedia.org/wiki/Median_absolute_deviation for more information.
+-
+-
+-
+-
+-
+-
+- The keyword "soft" maybe added, if the window position is allowed to be adjusted to the data present.
+- The two arguments may be preceded by the keywords "left", "center" or "right", indicating the window position.
+-
+-
+- Tukey 53H method A smooth time sequence is generated from the median, substracted from the original signal and
+- compared with the standard deviation. see "Despiking Acoustic Doppler Velocimeter Data", Derek G. Goring and Vladimir
+- L. Nikora, Journal of Hydraulic Engineering, 128, 1, 2002 The deviation factor coeffecient is currently hard-coded as k=1.5.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Wind vector averaging. This calculates the vector average over a user given time period. Each wind vector
+- within this period is added and the final sum is normalized by the number of vectors that have been added.
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Alpha needs to be provided as last argument. Please note that the standard filter works with a left window!
+-
+-
+- Exponential smooting processing, exponential moving average s_0 = x_0 s_n = alpha*x_(t-1) + (1-alpha)*s_t-1
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Please note that the standard filter works with a left window!
+-
+-
+- Weighted moving average smoothing such as: WMA = (1*X1 + 2*X2 + ... + n*Xn) / sum_of_weights
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- This implements the standard methods for precipitation correction as described in "WMO Solid Precipitation Measurement Intercomparison", B. Goodison, P. Louie and D. Yang, 872, 1998 as well as the overview given by "Literature Study on the Correction of Precipitation Measurements", Annette Wagner, 2009. The correction parameters for the shielded Hellmann gauge (German version) are from "Wind-induced Precipitation Undercatch of the Hellmann Gauges", Daqing Yang et al, Nordic Hydrology, 30, 1999, pp 57-80.
+-
+-
+-
+-
+-
+-
+- This applies a constant correction factor to the precipitation, one for pure snow and one for mixed precipitation. The following thresholds are used: pure snow below -2 C; mixed precipitation between -2 and +2 C; pure rain above 2 C. These threshold can be changed (see online documentation).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Affects resampling: expresses (in seconds) how far a valid point can be
+- searched for when re-interpolating a missing value
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/doc/examples/issm.xml
+===================================================================
+--- ../trunk-jpl/src/java/doc/examples/issm.xml (revision 18297)
++++ ../trunk-jpl/src/java/doc/examples/issm.xml (revision 18298)
+@@ -1,1284 +0,0 @@
+-
+-
+-
+-
+-
+-
+-
+- select a mesh dimension 0(default) or 3
+-
+-
+-
+-
+-
+- number of elements
+-
+-
+-
+- number of verticies
+-
+-
+-
+- vertex indices of the mesh elements
+-
+-
+-
+- vertices x coordinate [m]
+-
+-
+-
+- vertices y coordinate [m]
+-
+-
+-
+- vertices z coordinate [m]
+-
+-
+-
+- edges of the 2d mesh (vertex1 vertex2 element1 element2)
+-
+-
+-
+- number of edges of the 2d mesh
+-
+-
+-
+-
+-
+-
+- mesh dimension
+-
+-
+-
+- number of extrusion layers
+-
+-
+-
+- lower vertices flags list
+-
+-
+-
+- lower elements flags list
+-
+-
+-
+- upper vertices flags list
+-
+-
+-
+- upper element flag list
+-
+-
+-
+- upper vertex list (NaN for vertex on the upper surface)
+-
+-
+-
+- upper element list (NaN for element on the upper layer)
+-
+-
+-
+- lower vertex list (NaN for vertex on the lower surface)
+-
+-
+-
+- lower element list (NaN for element on the lower layer
+-
+-
+-
+- vertices on the boundary of the domain flag list
+-
+-
+-
+- edges on domain boundary (vertex1 vertex2 element)
+-
+-
+-
+- number associated to each segment
+-
+-
+-
+- list of vertices connected to vertex_i
+-
+-
+-
+- list of vertices connected to element_i
+-
+-
+-
+- average number of vertices connected to one vertex
+-
+-
+-
+-
+-
+-
+- vertices extracted from the model
+-
+-
+-
+- elements extracted from the model
+-
+-
+-
+-
+-
+-
+- vertices latitude [degrees]
+-
+-
+-
+- verticies longitude [degrees]
+-
+-
+-
+- Indicate hemisphere 'n' or 's'
+-
+-
+-
+-
+-
+-
+- is ice grounded ? grounded ice if > 0, grounding line position if = 0, floating ice if < 0
+-
+-
+-
+- presence of ice if > 0, icefront position if = 0, no ice if < 0
+-
+-
+-
+-
+-
+-
+-
+- surface elevation [m]
+-
+-
+-
+- ice thickness [m]
+-
+-
+-
+- bed elevation [m]
+-
+-
+-
+- bathymetry elevation [m]
+-
+-
+-
+- coefficient for ice shelves; thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro
+-
+-
+-
+-
+-
+-
+- gravitational acceleration [m/s^2]
+-
+-
+-
+- number of seconds in a year [s/yr]
+-
+-
+-
+- reference temperature used in the enthalpy model [K]
+-
+-
+-
+-
+-
+- surface mass balance [m/yr ice eq]
+-
+-
+-
+-
+-
+- basal melting rate (positive if melting) [m/yr]
+-
+-
+-
+- additional melting applied to compensate for dh/dt [m/yr]
+-
+-
+-
+- geothermal heat flux [W/m^2]
+-
+-
+-
+-
+-
+- ice density [kg/m^3]
+-
+-
+-
+- ocean water density [kg/m^3]
+-
+-
+-
+- fresh water density [kg/m^3]
+-
+-
+-
+- water viscosity [N s/m^2]
+-
+-
+-
+- heat capacity [J/kg/K]
+-
+-
+-
+- latent heat of fusion [J/kg]
+-
+-
+-
+- ice thermal conductivity [W/m/K]
+-
+-
+-
+- temperate ice thermal conductivity [W/m/K]
+-
+-
+-
+- melting point of ice at 1atm in K
+-
+-
+-
+- rate of change of melting point with pressure [K/Pa]
+-
+-
+-
+- mixed layer capacity [W/kg/K]
+-
+-
+-
+- thermal exchange velocity [m/s]
+-
+-
+-
+- flow law parameter [Pa/s^(1/n)]
+-
+-
+-
+- Glens flow law exponent
+-
+-
+-
+- law for the temperature dependance of the rheology: "None", "Paterson", "Arrhenius" or "LliboutryDuval"
+-
+-
+-
+- Lithosphere shear modulus [Pa]
+-
+-
+-
+- Lithosphere density [g/cm^-3]
+-
+-
+-
+- Mantle shear modulus [Pa]
+-
+-
+-
+- Mantle density [g/cm^-3]
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- damage law (string) from {"undamaged","pralong"}
+-
+-
+-
+- damage tensor (scalar)
+-
+-
+-
+- damage law (string) from {"undamaged","pralong"}
+-
+-
+-
+- damage constraints (NaN means no constraint)
+-
+-
+-
+- maximum possible damage (0<=max_damage<1)
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: SUPG
+-
+-
+-
+- maximum number of non linear iterations
+-
+-
+-
+- stabilize unstable damage constraints that keep zigzagging after n iteration (default is 0, no stabilization)
+-
+-
+-
+- threshold to declare convergence of damage evolution solution (default is 0)
+-
+-
+-
+- scaling exponent (default is 3)
+-
+-
+-
+-
+-
+-
+-
+-
+- friction coefficient [SI]
+-
+-
+-
+- p exponent
+-
+-
+-
+- q exponent
+-
+-
+-
+-
+-
+-
+-
+-
+- is the Shallow Ice Approximation (SIA) used ?
+-
+-
+-
+- is the Shelfy-Stream Approximation (SSA) used ?
+-
+-
+-
+- is the L1L2 approximation used ?
+-
+-
+-
+- is the Higher-Order (HO) approximation used ?
+-
+-
+-
+- are the Full-FS (FS) equations used ?
+-
+-
+-
+- Finite Element for SSA "P1", "P1bubble" "P1bubblecondensed" "P2"
+-
+-
+-
+- Finite Element for HO "P1" "P1bubble" "P1bubblecondensed" "P1xP2" "P2xP1" "P2"
+-
+-
+-
+- Finite Element for FS "P1P1" (debugging only) "P1P1GLS" "MINIcondensed" "MINI" "TaylorHood"
+-
+-
+-
+- flow equation for each vertex
+-
+-
+-
+- flow equation for each element
+-
+-
+-
+- vertices on SSAs border (for tiling)
+-
+-
+-
+- vertices on HOs border (for tiling)
+-
+-
+-
+- vertices on FS border (for tiling)
+-
+-
+-
+-
+-
+-
+- simulation starting time [yr]
+-
+-
+-
+- final time to stop the simulation [yr]
+-
+-
+-
+- length of time steps [yr]
+-
+-
+-
+- use cfl condition to define time step ? (0 or 1)
+-
+-
+-
+- coefficient applied to cfl condition
+-
+-
+-
+-
+-
+-
+-
+-
+- x component of velocity [m/yr]
+-
+-
+-
+- y component of velocity [m/yr]
+-
+-
+-
+- z component of velocity [m/yr]
+-
+-
+-
+- velocity norm [m/yr]
+-
+-
+-
+- pressure field [Pa]
+-
+-
+-
+- fraction of water in the ice
+-
+-
+-
+- ice thickness [m]
+-
+-
+-
+- sediment water head of subglacial system [m]
+-
+-
+-
+- epl water head of subglacial system [m]
+-
+-
+-
+- thickness of subglacial water [m]
+-
+-
+-
+-
+-
+-
+- structure containing all rift information (vertices coordinates, segments, type of melange, ...)
+-
+-
+-
+- N/A
+-
+-
+-
+-
+-
+-
+-
+- use Valgrind to debug (0 or 1)
+-
+-
+-
+-
+- use gnu-profiler to find out where the time is spent
+-
+-
+-
+-
+- enables profiling (memory, flops, time)
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- results are output for all the nodes of each element
+-
+-
+-
+- I/O gathering strategy for result outputs (default 1)
+-
+-
+-
+- is the memory limited ? (0 or 1)
+-
+-
+-
+- frequency at which results are saved in all solutions with multiple time_steps
+-
+-
+-
+- maximum number of minutes to wait for batch results (NaN to deactivate)
+-
+-
+-
+- server hostname where model should be uploaded
+-
+-
+-
+- path on server where model should be uploaded
+-
+-
+-
+- server login
+-
+-
+-
+- port login (default is 0)
+-
+-
+-
+- unique id generated when uploading the file to server
+-
+-
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+-
+-
+- thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- ice thickening rate used in the mass conservation (dh/dt) [m/yr]
+-
+-
+-
+- 0: None, 1: SU, 2: SSAs artificial diffusivity, 3:DG
+-
+-
+-
+-
+-
+-
+-
+- mechanical equilibrium residual convergence criterion
+-
+-
+-
+- velocity relative convergence criterion, NaN: not applied
+-
+-
+-
+- velocity absolute convergence criterion, NaN: not applied
+-
+-
+-
+- 0: Picards fixed point, 1: Newtons method, 2: hybrid
+-
+-
+-
+- maximum number of nonlinear iterations
+-
+-
+-
+- over-shooting constant new=new+C*(new-old)
+-
+-
+-
+-
+-
+-
+- x-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+- y-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+- z-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+-
+-
+-
+- threshold for instability of mechanical constraints
+-
+-
+-
+- number of iterations before rift penalties are locked
+-
+-
+-
+-
+-
+-
+- use dampening for floating ice ? Only for FS model
+-
+-
+-
+- multiplier for incompressibility equation. Only for FS model
+-
+-
+-
+- local referential
+-
+-
+-
+- loading force applied on each point [N/m^3]
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- type of grounding line migration: "SoftMigration","AgressiveMigration" or "None"
+-
+-
+-
+- melting rate applied when previously grounded parts start floating [m/yr]
+-
+-
+-
+-
+-
+-
+-
+-
+- water thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- Manning roughness coefficient
+-
+-
+-
+- tortuosity parameter
+-
+-
+-
+- dimensionless exponent in Manning velocity formula
+-
+-
+-
+- dimensionless exponent in Manning velocity formula
+-
+-
+-
+- parameter in effective pressure formula
+-
+-
+-
+- artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.
+-
+-
+-
+-
+-
+-
+-
+- thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- calving rate at given location [m/a]
+-
+-
+-
+- do we use free surfaces (FS only) are mass conservation
+-
+-
+-
+- minimum ice thickness allowed [m]
+-
+-
+-
+- adjustment of ice shelves surface and bed elevations: 'Incremental' or 'Absolute'
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin
+-
+-
+-
+-
+-
+-
+- offset used by penalties: penalty = Kmax*10^offset
+-
+-
+-
+- pairs of vertices that are penalized
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- temperature constraints (NaN means no constraint) [K]
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: SUPG
+-
+-
+-
+- maximum number of non linear iterations
+-
+-
+-
+- stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)
+-
+-
+-
+- threshold to declare convergence of thermal solution (default is 0)
+-
+-
+-
+- scaling exponent (default is 3)
+-
+-
+-
+- use an enthalpy formulation to include temperate ice (default is 0)
+-
+-
+-
+- enable dynamic setting of basal forcing. required for enthalpy formulation (default is 0)
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- relative tolerance criterion [K]
+-
+-
+-
+- maximum number of iterations
+-
+-
+-
+- additional requested outputs
+-
+-
+-
+-
+-
+-
+-
+- indicates whether a masstransport solution is used in the transient
+-
+-
+-
+- indicates whether a stressbalance solution is used in the transient
+-
+-
+-
+- indicates whether a thermal solution is used in the transient
+-
+-
+-
+- indicates whether a groundingline migration is used in the transient
+-
+-
+-
+- indicates whether a postglacial rebound model is used in the transient
+-
+-
+-
+- indicates whether damage evolution is used in the transient
+-
+-
+-
+- LEVEL SET DESCRIPTION...
+-
+-
+-
+- list of additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- mantle viscosity[Pa s]
+-
+-
+-
+- lithosphere thickness (km)
+-
+-
+-
+- 1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore
+-
+-
+-
+-
+-
+-
+-
+-
+- indicates if the automatic differentiation is activated
+-
+-
+-
+- list of dependent variables
+-
+-
+-
+- list of independent variables
+-
+-
+-
+- ADOLC driver ('fos_forward' or 'fov_forward')
+-
+-
+-
+- Number of operations per buffer (==OBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of locations per buffer (==LBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of values per buffer (==CBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of taylors per buffer (<=TBUFSIZE in usrparms.h)
+-
+-
+-
+- free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio
+-
+-
+-
+- free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize
+-
+-
+-
+-
+-
+-
+-
+- name of kml output targets file
+-
+-
+-
+- name of kml input tracks file
+-
+-
+-
+- structure of kml flight requirements (not used yet)
+-
+-
+-
+- element or nodal criterion for flight path evaluation (metric)
+-
+-
+-
+-
+-
+-
+- number of grids at equator (determines resolution)
+-
+-
+-
+-
+- flag to consider target values for flight path evaluation
+-
+-
+-
+-
+- flag to split polygons on the antimeridian
+-
+-
+-
+-
+-
+-
+-
+- optimize? (default false)
+-
+-
+-
+- number of directions to test when moving a point. If this value = 1, a random direction is tested. A value > 1 results in directions equally spaced from [0, 2*PI] being tested. For example, 4 would result in directions [0, PI/2, PI, 3PI/2]
+-
+-
+-
+- specifies the distance in km (default 25) to move a randomly selected path point on each iteration
+-
+-
+-
+- number of iterations (default 30,000) to run for flightplan optimization, i.e. the number of times to randomly select a point and move it.
+-
+-
+-
+-
+-
+-
+- name of kml solution file
+-
+-
+-
+- quality of kml solution
+-
+-
+-
+-
+-
+-
+-
+- is inversion activated?
+-
+-
+-
+- 1: linear viscosity, 0: non-linear viscosity
+-
+-
+-
+- ex: {'FrictionCoefficient'}, or {'MaterialsRheologyBbar'}
+-
+-
+-
+- number of optimization searches
+-
+-
+-
+- indicate the type of response for each optimization step
+-
+-
+-
+- cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter
+-
+-
+-
+- misfit convergence criterion. Default is 1%, NaN if not applied
+-
+-
+-
+- maximum iterations during each optimization step
+-
+-
+-
+- scaling factor on gradient direction during optimization, for each optimization step
+-
+-
+-
+- decrease threshold for misfit, default is 30%
+-
+-
+-
+- absolute minimum acceptable value of the inversed parameter on each vertex
+-
+-
+-
+- absolute maximum acceptable value of the inversed parameter on each vertex
+-
+-
+-
+- observed velocity x component [m/yr]
+-
+-
+-
+- observed velocity y component [m/yr]
+-
+-
+-
+- observed velocity magnitude [m/yr]
+-
+-
+-
+- observed thickness [m])
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- is qmu analysis activated?
+-
+-
+-
+- (arrays of each variable class)
+-
+-
+-
+- (arrays of each response class)
+-
+-
+-
+- number of responses
+-
+-
+-
+- (array of method-independent parameters)
+-
+-
+-
+- (information from dakota files)
+-
+-
+-
+- user provided mesh partitioning, defaults to metis if not specified
+-
+-
+-
+- number of partitions for semi-discrete qmu
+-
+-
+-
+-
+-
+-
+-
+- use an enthalpy formulation to include temperate ice (default is 0)
+-
+-
+-
+- array of dakota_method class
+-
+-
+-
+- directory for mass flux profiles
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+- weight applied to each mesh vertex
+-
+-
+-
+-
+-
+-
+-
+- list of potential outputs that can be requested, but which need additional data to be defined
+-
+-
+-
+-
+-
+-
+-
+- notes in a cell of strings
+-
+-
+-
+- model name
+-
+-
+-
+- empty field to store some data
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/lib/miglayout-4.0.jar
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/MANIFEST.MF
+===================================================================
+--- ../trunk-jpl/src/java/MANIFEST.MF (revision 18297)
++++ ../trunk-jpl/src/java/MANIFEST.MF (revision 18298)
+@@ -1,14 +0,0 @@
+-Manifest-Version: 1.0
+-Ant-Version: Apache Ant 1.8.4
+-Created-By: 1.6.0_51-b11-457-11M4509 (Apple Inc.)
+-Built-By: larour
+-Built-On: 2014-04-14
+-Built-At: 14:27:23
+-Main-Class: main/GUIBuilder
+-Specification-Title: INI file generator
+-Specification-Version: 1.0.0-20140414
+-Specification-Vendor: SLF, www.slf.ch
+-Implementation-Title: INIshell ini creator
+-Implementation-Version: 1.0.0
+-Implementation-Vendor: SLF, www.slf.ch
+-
+Index: ../trunk-jpl/src/java/src/gui_elements/OptionPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/OptionPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/OptionPanel.java (revision 18298)
+@@ -1,144 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ItemEvent;
+-import java.awt.event.ItemListener;
+-import java.util.LinkedList;
+-import java.util.HashMap;
+-import javax.swing.event.EventListenerList;
+-
+-import main.GUIBuilder;
+-import main.XMLHelper;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-
+-/**
+- * A ControlledPanel that maintains a group of choices and invokes panel
+- * creation according to the current choices.
+- *
+- * @author korhammer et egger
+- *
+- */
+-public abstract class OptionPanel extends ControlledPanel implements ItemListener {
+-
+- private static final long serialVersionUID = 88L;
+-
+- protected LinkedList defaultTrues;
+- protected EventListenerList listenerList;
+-
+- protected String[] values;
+- protected String[] labels;
+- protected String[] helptexts;
+-
+- /**
+- * The constructor for an OptionPanel.
+- *
+- * @param element
+- * : The xml element which the OptionPanel is created for.
+- * @throws GUIBuildException
+- */
+- public OptionPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- this(element, parent, true);
+- }
+-
+- public OptionPanel(Element element, ControlledPanel parent, boolean doLayout) throws GUIBuildException {
+- super(element, parent, doLayout);
+-
+- String elementdefault = "";
+-
+- if (element.hasAttribute("default"))
+- elementdefault = element.getAttribute("default");
+-
+- listenerList = new EventListenerList();
+-
+- final Element[] options = XMLHelper.getElementArray(element, "option");
+- defaultTrues = new LinkedList();
+-
+- values = new String[options.length];
+- labels = new String[options.length];
+- helptexts = new String[options.length];
+-
+- for (int i=0;i.
+-*
+-*/
+-
+-package gui_elements;
+-
+-import main.GUI;
+-
+-import java.awt.*;
+-import java.awt.event.*;
+-import java.util.HashMap;
+-
+-import javax.swing.JTextField;
+-import javax.swing.JOptionPane;
+-
+-import org.w3c.dom.Element;
+-
+-/**
+- * A panel that contains a textfield.
+- *
+- * @author korhammer et egger
+- *
+- */
+-public class TextfieldPanel extends ControlledPanel implements KeyListener {
+-
+- private static final long serialVersionUID = 1L;
+- private String defaultText;
+-
+- protected JTextField textfield;
+-
+- /**
+- * The constructor for a TextfieldPanel.
+- *
+- * @param element
+- */
+- public TextfieldPanel(Element element, ControlledPanel parent) {
+- super(element, parent);
+- textfield = new JTextField(10);
+- textfield.setVisible(true);
+- this.add(textfield, "width 250:100:400, cell 1 0, growx, ay top, gaptop 3");
+- textfield.addKeyListener(this);
+-
+- defaultText = "";
+- if (element.hasAttribute("default")) {
+- defaultText = element.getAttribute("default");
+- }
+- textfield.setText(defaultText);
+-
+- if (!optional)
+- textfield.setBackground(GUI.WARNING_BACKGROUND_COLOR);
+-
+- this.checkBgColor();
+- textfield.invalidate();
+- }
+-
+-
+-
+- @Override
+- public void close() {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void set(HashMap hm, String key, String value) {
+- //System.out.println("\tI'm changing the label of the TextField with key '" + this.getKey() + "'");
+- String val = (String)hm.get(hashKey);
+- if (val != null) textfield.setText(val);
+- this.checkBgColor();
+- }
+-
+- @Override
+- public String getValue() {
+- String thetext = textfield.getText();
+-
+- if (!isOptional() && thetext.equals("")) {
+- JOptionPane.showMessageDialog(null, "No value was entered for "
+- + getKey() + " (section '" + getSection().toUpperCase() + "')"
+- + ".\nA value is required. Your .ini-file is probably incorrect.",
+- "Problem when building .ini file",
+- JOptionPane.WARNING_MESSAGE);
+- }
+-
+- if (thetext.equals(""))
+- return null;
+-
+- return thetext;
+- }
+-
+- /** Handle the key typed event from the text field. */
+- public void keyTyped(KeyEvent e) {}
+-
+- /** Handle the key-pressed event from the text field. */
+- public void keyPressed(KeyEvent e) {}
+-
+- /** Handle the key-released event from the text field. */
+- public void keyReleased(KeyEvent e) {
+- checkBgColor();
+- }
+-
+- public void checkBgColor() {
+- String text = textfield.getText();
+-
+- if (!optional) {
+- if (text.length() > 0) {
+- textfield.setBackground(GUI.NORMAL_BACKGROUND_COLOR);
+- } else {
+- textfield.setBackground(GUI.WARNING_BACKGROUND_COLOR);
+- }
+- textfield.invalidate();
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/FramePanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/FramePanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/FramePanel.java (revision 18298)
+@@ -1,71 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import main.GUIBuilder;
+-import main.XMLHelper;
+-
+-import java.util.HashMap;
+-import javax.swing.JPanel;
+-import javax.swing.border.*;
+-import javax.swing.BorderFactory;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-import org.w3c.dom.NodeList;
+-import net.miginfocom.swing.MigLayout;
+-
+-public class FramePanel extends ControlledPanel {
+-
+- private static final long serialVersionUID = 1987664773406118295L;
+- protected String title = "";
+-
+- /**
+- *
+- *
+- * @param element
+- * @throws GUIBuildException
+- */
+- public FramePanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent, false);
+- this.setLayout(new MigLayout("wrap 8, top, ins n 5 n n", "[200!][100!][100!][100!][100!][100!][300:400:400]", ""));
+-
+- if (parent == null) hierarchy = 1;
+-
+- title = element.getAttribute("label");
+-
+- Border mytitledborder = BorderFactory.createTitledBorder(title);
+- //Border loweredetched = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+- this.setBorder(mytitledborder);
+-
+- this.invalidate();
+- }
+-
+- @Override
+- public String getValue() {
+- return null;
+- }
+-
+- @Override
+- public void close() {
+-
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/PathPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/PathPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/PathPanel.java (revision 18298)
+@@ -1,118 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ActionEvent;
+-import java.awt.event.ActionListener;
+-import java.util.HashMap;
+-
+-import javax.swing.JButton;
+-import javax.swing.JFileChooser;
+-import javax.swing.JPanel;
+-
+-import org.w3c.dom.Element;
+-
+-public class PathPanel extends TextfieldPanel implements ActionListener {
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = 1486664773406118295L;
+-
+- JButton select_button;
+-
+- /**
+- * Creates a panel with a text field and a file / path chooser button.
+- *
+- * @param element
+- * @throws GUIBuildException
+- */
+- public PathPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent);
+-
+- if (element.getAttribute("type").equals("path")) {
+- select_button = new JButton("Select Path");
+- } else if (element.getAttribute("type").equals("file")) {
+- select_button = new JButton("Select File");
+- } else {
+- throw new GUIBuildException("PathPanel is not applicable for parameter types other than 'file' and 'path'.");
+- }
+-
+- this.remove(textfield);
+- this.add(textfield, "cell 1 0, growx, span2");
+-
+- select_button.addActionListener(this);
+- select_button.setActionCommand("open chooser");
+- select_button.setVisible(true);
+- this.add(select_button, "cell 3 0, growx, wrap");
+-
+- }
+-
+- @Override
+- public void actionPerformed(ActionEvent event) {
+- if (event.getActionCommand().equals("open chooser") && event.getSource() == this.select_button) {
+- try {
+- chooseFile();
+- } catch (final GUIBuildException e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- }
+- }
+-
+- @Override
+- public void set(HashMap hm, String key, String value) {
+- String val = (String)hm.get(hashKey);
+- if (val != null) textfield.setText(val);
+- this.checkBgColor();
+- }
+-
+- /**
+- * Opens the file chooser dialog and writes the path / filepath into the
+- * texfield.
+- *
+- * @throws GUIBuildException
+- */
+- public void chooseFile() throws GUIBuildException {
+- final JFileChooser filechooser = new JFileChooser(System.getProperty("user.dir"));
+-
+- if (element.getAttribute("type").equals("path")) {
+- filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+- } else if (element.getAttribute("type").equals("file")) {
+- filechooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+- } else {
+- throw new GUIBuildException("PathPanel is not applicable for parameter types other than 'file' and 'path'.");
+- }
+-
+- final int returnVal = filechooser.showOpenDialog(new JPanel());
+-
+- if (returnVal == JFileChooser.APPROVE_OPTION) {
+- if (element.getAttribute("type").equals("path")) {
+- textfield.setText(filechooser.getSelectedFile().getAbsolutePath());
+- } else {
+- textfield.setText(filechooser.getSelectedFile().getName());
+- }
+-
+- checkBgColor();
+- }
+- }
+-
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/IntegerPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/IntegerPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/IntegerPanel.java (revision 18298)
+@@ -1,246 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.*;
+-import java.util.HashMap;
+-
+-import javax.swing.JButton;
+-import javax.swing.JOptionPane;
+-import javax.swing.SwingConstants;
+-
+-import org.w3c.dom.Element;
+-
+-/**
+- * A panel that maintains a number in an editable textfield,
+- * optionally with a maximum and minimum value.
+- * @author korhammer
+- *
+- */
+-/**
+- * @author korhammer
+- *
+- */
+-public class IntegerPanel extends TextfieldPanel implements ActionListener, FocusListener {
+- /**
+- *
+- */
+- private static final long serialVersionUID = -8959578535487185306L;
+-
+- private int defaultvalue;
+- private int maximumvalue;
+- private int minimumvalue;
+-
+- private boolean printPlus;
+-
+- private final JButton down;
+- private final JButton up;
+-
+- /**
+- * Constructor for a NumberPanel.
+- *
+- * @param element
+- * @throws GUIBuildException
+- */
+- public IntegerPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent);
+-
+- setDefaultvalue(0);
+- minimumvalue = Integer.MIN_VALUE;
+- maximumvalue = Integer.MAX_VALUE;
+- printPlus = false;
+-
+- if (element.getAttribute("type").equals("integer+")) {
+- setPrintplus(true);
+- } else {
+- setPrintplus(false);
+- }
+-
+- if (element.hasAttribute("default")) {
+- setDefaultvalue(element.getAttribute("default"));
+- }
+- if (element.hasAttribute("maximum")) {
+- setMaximumvalue(element.getAttribute("maximum"));
+- }
+- if (element.hasAttribute("minimum")) {
+- setMinimumvalue(element.getAttribute("minimum"));
+- }
+-
+- textfield.setColumns(4);
+- textfield.invalidate();
+- textfield.setHorizontalAlignment(SwingConstants.RIGHT);
+-
+- up = new JButton("+");
+- up.addActionListener(this);
+- down = new JButton("-");
+- down.addActionListener(this);
+- this.add(up, "split 2, growx, ay top");
+- this.add(down, "growx, ay top");
+- textfield.addActionListener(this);
+- textfield.addFocusListener(this);
+-
+- }
+-
+- /**
+- * Parses a String to an integer. Different from the standard methods as it
+- * handles the + sign e.g. in time zones.
+- *
+- * @param text
+- * @return the parsed number
+- * @throws NumberFormatException
+- */
+- private static int parse(String text) throws NumberFormatException {
+-
+- final char first = text.charAt(0);
+-
+- if (first == '+')
+- return Integer.parseInt(text.substring(1));
+- if (first == '-')
+- return Integer.parseInt(text);
+- return Integer.parseInt(text);
+- }
+-
+- /*
+- * (non-Javadoc)
+- *
+- * @see
+- * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+- */
+- @Override
+- public void actionPerformed(ActionEvent e) {
+- if (e.getSource() == up) {
+- manipulateNumber(1);
+- } else if (e.getSource() == down) {
+- manipulateNumber(-1);
+- } else if (e.getSource() == textfield) {
+- parseTextfield();
+- }
+- }
+-
+- @Override
+- public void set(HashMap hm, String key, String value) {
+- String val = (String)hm.get(hashKey);
+- if (val != null) {
+- try {
+- Integer.parseInt(val);
+- textfield.setText(val);
+- } catch (Exception e) {} //Do nothing if conversion fails
+- }
+- }
+-
+- @Override
+- public void focusGained(FocusEvent arg0) {
+-
+- }
+-
+- @Override
+- public void focusLost(FocusEvent arg0) {
+- parseTextfield();
+- }
+-
+- /**
+- * Manipulates the number in the text field by parsing it, adding the
+- * increment and writing it back into the textfield.
+- *
+- * @param increment
+- */
+- public void manipulateNumber(int increment) {
+- int number;
+-
+- try {
+- number = parseTextfield();
+- } catch (final NumberFormatException nfe) {
+- return;
+- }
+-
+- if (number + increment <= maximumvalue
+- && number + increment >= minimumvalue) {
+- number += increment;
+- } else if (number + increment < minimumvalue) {
+- number = minimumvalue;
+- } else if (number + increment > maximumvalue) {
+- number = maximumvalue;
+- }
+-
+- printToTextfield(number);
+- }
+-
+- /**
+- * Calls the parse method on the textfield.
+- *
+- * @return
+- * @throws NumberFormatException
+- */
+- public int parseTextfield() throws NumberFormatException {
+- try {
+- return parse(textfield.getText());
+- } catch (final NumberFormatException nfe) {
+- JOptionPane.showMessageDialog(null, "The textfield " + getKey()
+- + " does not contain a number.");
+- throw nfe;
+- }
+- }
+-
+- /**
+- * Prints a number to the text field optionally with a plus sign.
+- *
+- * @param number
+- */
+- public void printToTextfield(int number) {
+- if (this.printPlus && number > 0) {
+- textfield.setText("+" + number);
+- } else {
+- textfield.setText("" + number);
+- }
+- checkBgColor();
+- }
+-
+- public void setDefaultvalue(int defaultvalue) {
+- this.defaultvalue = defaultvalue;
+- this.printToTextfield(defaultvalue);
+- }
+-
+- public void setDefaultvalue(String defaultvalue) {
+- this.defaultvalue = parse(defaultvalue);
+- this.printToTextfield(this.defaultvalue);
+- }
+-
+- public void setMaximumvalue(int maximumvalue) {
+- this.maximumvalue = maximumvalue;
+- }
+-
+- public void setMaximumvalue(String maximumvalue) {
+- this.maximumvalue = parse(maximumvalue);
+- }
+-
+- public void setMinimumvalue(int minimumvalue) {
+- this.minimumvalue = minimumvalue;
+- }
+-
+- public void setMinimumvalue(String minimumvalue) {
+- this.minimumvalue = parse(minimumvalue);
+- }
+-
+- public void setPrintplus(boolean printPlus) {
+- this.printPlus = printPlus;
+- printToTextfield(parse(textfield.getText()));
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/AlternativePanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/AlternativePanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/AlternativePanel.java (revision 18298)
+@@ -1,177 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ItemEvent;
+-
+-import javax.swing.JComboBox;
+-import javax.swing.JOptionPane;
+-import java.util.HashMap;
+-import javax.swing.*;
+-import java.awt.*;
+-
+-import main.GUI;
+-
+-import org.w3c.dom.Element;
+-
+-/**
+- * The AlternativePanel contains a dropdown list with alternatives to choose from.
+- *
+- * @author Thomas Egger
+- *
+- */
+-public class AlternativePanel extends OptionPanel {
+-
+- private static final long serialVersionUID = 4468480774697888798L;
+- private final JComboBox box;
+-
+- private String setKey = null, setValue = null;
+- private boolean doSet = false;
+- private HashMap setMap;
+-
+- /**
+- * Constructor for the AlternativePanel
+- *
+- * @param element the element for which the panel is created.
+- * @throws GUIBuildException
+- */
+- public AlternativePanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent);
+-
+- box = new JComboBox(labels);
+- box.insertItemAt("", 0); //Add an empty label
+- box.setVisible(true);
+- box.setSelectedIndex(0);
+- box.addItemListener(this);
+-
+- //Issue 263: On OSX the box.setBackground method does not function without this tweak:
+- if (System.getProperty("os.name").equals("Mac OS X"))
+- box.setRenderer(new ColorCellRenderer(box.getPreferredSize().width));
+-
+- if (!optional) box.setBackground(GUI.WARNING_BACKGROUND_COLOR);
+-
+- if (defaultTrues.size() > 1) {
+- throw new GUIBuildException("Element " + getHashKey() + " has multiple default values");
+- } else if (defaultTrues.size() == 1) {
+- box.setSelectedItem(defaultTrues.getFirst());
+- }
+-
+- this.add(box, "cell 1 0, growx, ay top, wrap");
+- }
+-
+- @Override
+- public void close() {
+- this.box.setSelectedIndex(0);
+- }
+-
+- @Override
+- public String getValue() {
+-
+- if (box.getSelectedIndex() != 0) {
+- //String selectedString = (String) box.getSelectedItem();
+- int index = box.getSelectedIndex() - 1;
+- if (index < 0)
+- return "";
+-
+- return values[index];
+- }
+-
+- if (!isOptional()) {
+- JOptionPane.showMessageDialog(null, "No option was selected for "
+- + getKey() + " (section '" + getSection().toUpperCase() + "')"
+- + ".\nA value is required. Your .ini-file is probably incorrect.",
+- "Problem when building .ini file",
+- JOptionPane.WARNING_MESSAGE);
+- }
+-
+- return null;
+- }
+-
+- @Override
+- public synchronized void set(HashMap hm, String key, String value) {
+- doSet = true;
+- setKey = key;
+- setValue = value;
+- setMap = hm;
+-
+- if (!hm.containsKey(hashKey)) return;
+- String val = ((String)hm.get(hashKey)).toUpperCase();
+-
+- //System.out.println("\tAP: Setting AlternativePanel: " + hashKey + " = " + val);
+-
+- for (int ii=0; ii 0) && (helptexts[box.getSelectedIndex()-1] != null)) {
+- help.setText("" + helptexts[box.getSelectedIndex()-1] + "");
+- } else {
+- if (helptext != null)
+- help.setText("" + helptext + "");
+- }
+-
+- //handle selected Item
+- final String selectedOption = (String) arg0.getItem();
+- if (selectedOption == "") {
+- if (!optional) {
+- box.setBackground(GUI.WARNING_BACKGROUND_COLOR);
+- }
+- } else {
+- if (!optional) {
+- box.setBackground(GUI.NORMAL_BACKGROUND_COLOR);
+- }
+- //System.out.println("\tDOSET of AlternativePanel: " + doSet);
+- super.handleItemEvent(arg0, selectedOption, doSet, setMap, setKey, setValue);
+- doSet = false;
+- setKey = null;
+- setMap = null;
+- setValue = null;
+- }
+- }
+-}
+-
+-class ColorCellRenderer implements ListCellRenderer {
+- protected DefaultListCellRenderer defaultRenderer = new DefaultListCellRenderer();
+- private Dimension preferredSize = new Dimension(0, 18);
+-
+- public ColorCellRenderer(int width) {
+- width -= 50;
+-
+- if (width < 100) width = 100; //Default size on OSX
+-
+- preferredSize = new Dimension(width, 18);
+- }
+-
+- public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
+- JLabel renderer = (JLabel) defaultRenderer.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+- renderer.setPreferredSize(preferredSize);
+- return renderer;
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/DecimalPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/DecimalPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/DecimalPanel.java (revision 18298)
+@@ -1,133 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ActionEvent;
+-import java.awt.event.ActionListener;
+-import java.awt.event.FocusEvent;
+-import java.awt.event.FocusListener;
+-import java.util.HashMap;
+-
+-import java.text.DecimalFormat;
+-import java.text.ParseException;
+-import java.text.DecimalFormatSymbols;
+-import javax.swing.JFormattedTextField;
+-
+-import org.w3c.dom.Element;
+-
+-public class DecimalPanel extends TextfieldPanel implements ActionListener, FocusListener{
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = 1555742510677354674L;
+- double defaultvalue;
+- double maximumvalue;
+- double minimumvalue;
+-
+- JFormattedTextField textfield;
+-
+- public DecimalPanel(Element element, ControlledPanel parent) {
+- super(element, parent);
+- this.remove(super.textfield);
+-
+- DecimalFormat format = (DecimalFormat)DecimalFormat.getInstance();
+- DecimalFormatSymbols custom = new DecimalFormatSymbols();
+- custom.setDecimalSeparator('.');
+- format.setDecimalFormatSymbols(custom);
+- format.setGroupingUsed(false);
+-
+- textfield = new JFormattedTextField(format);
+- textfield.addActionListener(this);
+- textfield.addFocusListener(this);
+- this.add(textfield,"cell 1 0, growx, ay top, gaptop 3");
+- textfield.setVisible(true);
+- this.invalidate();
+- defaultvalue = 0.0;
+- maximumvalue = Double.MAX_VALUE;
+- minimumvalue = Double.MIN_VALUE;
+-
+-
+- if(element.hasAttribute("minimum")){
+- minimumvalue = Double.parseDouble(element.getAttribute("minimum"));
+- }
+- if(element.hasAttribute("maximum")){
+- maximumvalue = Double.parseDouble(element.getAttribute("maximum"));
+- }
+- if(element.hasAttribute("default")){
+- defaultvalue = Double.parseDouble(element.getAttribute("default"));
+- }
+- setToDefaultValue();
+- }
+-
+- private void setToDefaultValue() {
+- textfield.setValue(new Double(defaultvalue));
+- this.invalidate();
+- }
+-
+- private void checkValue(){
+- try {
+- textfield.commitEdit();
+- } catch (ParseException e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- double currentvalue = ((Number)textfield.getValue()).doubleValue();
+- if(currentvalue > maximumvalue){
+- textfield.setValue(new Double(maximumvalue));
+- }
+- else if(currentvalue.
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ItemEvent;
+-import java.text.NumberFormat;
+-import java.util.*;
+-import java.text.DecimalFormat;
+-import java.text.DecimalFormatSymbols;
+-
+-import javax.swing.JCheckBox;
+-import javax.swing.JComponent;
+-import javax.swing.JFormattedTextField;
+-import javax.swing.JTextField;
+-import javax.swing.JLabel;
+-import javax.swing.JComboBox;
+-
+-import main.XMLHelper;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-import org.w3c.dom.NodeList;
+-import net.miginfocom.swing.MigLayout;
+-
+-/**
+- * @brief The CombinedPanel may contain other panels, such as check and drop down boxes and text fields
+- *
+- * @author Thomas Egger
+- */
+-public class CombinedPanel extends OptionPanel {
+- enum Type { CHOICE, INTEGER, DECIMAL, STRING, DROPDOWN }
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = -6751282938445852408L;;
+-
+- private final LinkedList valueComponents;
+-
+- /**
+- * Constructor for a panel that can hold text, numbers and check boxes. It
+- * corresponds to the parameter type "combination" in the configuration file
+- * and its subcomponents correspond to the option values.
+- *
+- * @param element
+- * @throws GUIBuildException
+- */
+- public CombinedPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent, false); //doing layout by itself
+-
+- //System.out.println("Hierarchy: Parent: " + parent.getKey() + ": "+ parent.getHierarchy() + " own: " + getHierarchy());
+-
+- int column1 = 200;
+- column1 -= getHierarchy() * 5;
+- this.setLayout(new MigLayout("gapx 6, wrap 8, ins n 5 n n", "["+column1+"!][78!][78!][78!][78!][78!][78!][20!][200:400:400]", ""));
+-
+- this.add(jlabel, "gapleft " + getHierarchy() * 5);
+- this.add(help, "cell 8 0, wrap");
+-
+- valueComponents = new LinkedList();
+-
+- final Element[] optionElements = XMLHelper.getElementArray(element, "option");
+-
+- byte lblcounter = 0;
+-
+- DecimalFormat format = (DecimalFormat)DecimalFormat.getInstance();
+- DecimalFormatSymbols custom = new DecimalFormatSymbols();
+- custom.setDecimalSeparator('.');
+- format.setDecimalFormatSymbols(custom);
+- format.setGroupingUsed(false);
+-
+- DecimalFormat integerFormat = (DecimalFormat)DecimalFormat.getIntegerInstance();
+- integerFormat.setGroupingUsed(false);
+-
+- int row = 0;
+- int column = 1;
+-
+- for (int i=0;i 12) width = 2; //for oversize labels
+-
+- if (column+width >= 7) {
+- column = 1;
+- row++;
+- }
+- lblcomponent = new JLabel(label);
+- valueComponents.add(lblcomponent);
+-
+- //System.out.println("component: " + component.getClass() + ");
+- //System.out.println("component: " + lblcomponent.getClass() + " size: " + lblcomponent.getWidth() + " col: " + column + " row: " + row);
+- this.add(lblcomponent, "cell " + column + " " + row + " " + width + " 1");
+- column += width;
+- width = 1;
+- lblcomponent.setVisible(true);
+- }
+-
+- if (column >= 7) {
+- column = 1;
+- row++;
+- }
+- //System.out.println("component: " + component.getClass() + " size: " + component.getWidth() + " col: " + column + " row: " + row);
+- this.add(component, "cell " + column + " " + row + " " + width + " 1");
+- column++;
+-
+- valueComponents.add(component);
+- component.setVisible(true);
+- }
+-
+- //System.out.println("\t-->Instantiated one Combined Panel with " + optionElements.length + " components");
+- }
+-
+- @Override
+- public void close() {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void set(HashMap hm, String inkey, String invalue) {
+- if (!hm.containsKey(hashKey)) return;
+- String val = (String)hm.get(hashKey);
+-
+- //System.out.println("\tSetting CombinedPanel: " + hashKey + " = " + val);
+- //System.out.println("\tThis CombinedPanel has the key: " + this.getKey() + " should be: " + inkey + " val: " + invalue);
+-
+- //Now loop through valueComponents and see if the value string can be matched
+- if (val == null) return;
+-
+- String[] tokens = val.split("\\s+");
+- int counter = 0;
+-
+- //System.out.println("\t\tLooking at VAL param: " + val);
+- for (final JComponent comp : valueComponents) {
+- boolean digested = false;
+- if (tokens.length <= counter) break;
+- //System.out.println("\t\tLooking at USER param: " + tokens[counter]);
+-
+- if (comp.getClass() == JCheckBox.class) {
+- String cbString = ((JCheckBox) comp).getText();
+- if (tokens[counter].equals(cbString)) {
+- ((JCheckBox) comp).setSelected(true);
+- digested = true;
+- }
+- } else if (comp.getClass() == JComboBox.class) {
+- JComboBox box = (JComboBox) comp;
+-
+- for (int ii=0; ii 0)
+- value += " ";
+- }
+-
+- if (value.equals("")) return null;
+- else return value;
+- }
+-
+- @Override
+- public void itemStateChanged(ItemEvent arg0) {
+- String selectedOption = null;
+-
+- if (arg0.getItemSelectable().getClass() == JCheckBox.class) {
+- selectedOption = ((JCheckBox) arg0.getItemSelectable()).getText();
+- super.handleItemEvent(arg0, selectedOption);
+- } else if (arg0.getItemSelectable().getClass() == JComboBox.class) {
+- selectedOption = ((String)((JComboBox)arg0.getItemSelectable()).getSelectedItem());
+- //HACK: should call super...
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/SelectorPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/SelectorPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/SelectorPanel.java (revision 18298)
+@@ -1,233 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+- *
+- * INIshell is free software: you can redistribute it and/or modify
+- * it under the terms of the GNU General Public License as published by
+- * the Free Software Foundation, either version 3 of the License, or
+- * (at your option) any later version.
+- *
+- * INIshell is distributed in the hope that it will be useful,
+- * but WITHOUT ANY WARRANTY; without even the implied warranty of
+- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+- * GNU General Public License for more details.
+- *
+- * You should have received a copy of the GNU General Public License
+- * along with INIshell. If not, see .
+- *
+- */
+-
+-package gui_elements;
+-
+-import java.awt.event.ActionEvent;
+-import java.awt.event.ActionListener;
+-
+-import javax.swing.JButton;
+-import javax.swing.JOptionPane;
+-
+-
+-import main.GUIBuilder;
+-import main.XMLHelper;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-import org.w3c.dom.NodeList;
+-
+-import java.util.List;
+-import java.util.ArrayList;
+-import java.util.HashMap;
+-
+-/**
+- * This class introduces more flexibility into the inishell interface:
+- * The SelectorPanel offers the user to add a specific parameter to
+- * the interface.
+- *
+- * @author Thomas Egger
+- */
+-public class SelectorPanel extends ControlledPanel implements ActionListener {
+-
+- private static final long serialVersionUID = 8610877538909126920L;
+-
+- String[] parameters;
+-
+- JButton addButton;
+- JButton removeButton;
+- Element template;
+- String templateKey;
+- HashMap mapOfParameters;
+- ControlledPanel cp = null;
+-
+- public SelectorPanel(Element element, ControlledPanel parent) {
+- super(element, parent);
+- templateKey = ""; //will store the pattern of the key
+-
+- addButton = new JButton("+");
+- this.add(addButton, "cell 1 0, split 2, grow");
+- addButton.addActionListener(this);
+-
+- removeButton = new JButton("-");
+- this.add(removeButton, "cell 1 0, grow, wrap");
+- removeButton.addActionListener(this);
+-
+- //The following lines try to extract the template key (e.g. %::filters#, %::resample, COPY::%)
+- final NodeList nodelist = element.getChildNodes();
+- for (int ii = 0; ii < nodelist.getLength(); ii++) {
+- if (nodelist.item(ii).getNodeType() == Node.ELEMENT_NODE) {
+- Element currentElement = (Element)nodelist.item(ii);
+- if (currentElement.getAttribute("template").equals("true")){
+- template = (Element)currentElement.cloneNode(true);
+- templateKey = template.getAttribute("key");
+- template.setAttribute("template", "false");
+- }
+- }
+- }
+-
+- final Element[] options = XMLHelper.getElementArray(element, "option");
+- parameters = new String[options.length + 1];
+- for (int ii=0; ii < options.length; ii++) {
+- parameters[ii] = options[ii].getAttribute("value");
+- }
+- parameters[options.length] = "Other...";
+-
+- key = templateKey; //IMPORTANT: this changes the key only, not the label!
+- hashKey = this.getSection().toUpperCase() + "::" + this.getKey().toUpperCase();
+- mapOfParameters = new HashMap();
+- }
+-
+- @Override
+- public void actionPerformed(ActionEvent arg0) {
+- if (arg0.getSource() == addButton) {
+- add();
+- } else if (arg0.getSource() == removeButton) {
+- remove();
+- }
+- }
+-
+- @Override
+- public void set(HashMap hm, String key, String value) {
+- //HACK
+- //System.out.println("\tKEY: " + key + " VAL: " + value);
+-
+- String myKey = this.section.toUpperCase() + "::" + templateKey.toUpperCase().replace("%","([a-zA-Z0-9_]+)");
+- myKey = myKey.replace("#","[1-9]+[0-9]*"); //all integer numbers from 1 to infinity
+- //System.out.println("PATTERN: " + myKey);
+- String myKey2 = key.replaceAll(myKey, "$1");
+- String myKey3 = key.replaceAll(myKey, "$0");
+-
+- //System.out.println("HUHUI: " + templateKey + " --- " + myKey2 + " -- " + myKey3);
+-
+- boolean toAdd = true;
+- if (mapOfParameters.get(myKey2) != null) toAdd = false; //Parameter already exists
+-
+- if (toAdd) {
+- ControlledPanel child = add(myKey2, true, hm, key, value);
+- cp = child;
+- if (child != null) child.set(hm, key, value);
+- } else {
+- if (cp != null) cp.set(hm, key, value);
+- }
+- }
+-
+- public void add() {
+- String param = "";
+- String choice = "Other...";
+-
+- if (parameters.length > 1)
+- choice = (String)JOptionPane.showInputDialog(this, "Add a parameter", "Add", JOptionPane.QUESTION_MESSAGE, null, parameters, null);
+-
+- if (choice == null) return;
+-
+- if (choice.equals("Other...")) {
+- param = JOptionPane.showInputDialog(this, "Enter the name of a meteo parameter\n(e.g. VW_AVG, P2");
+- } else {
+- param = choice;
+- }
+-
+- add(param, false, null, null, null);
+- }
+-
+- public ControlledPanel add(String param, boolean doSet, HashMap hm, String key, String value) {
+- //System.out.println("Trying to add SelectorPanel: " + key + " ... " + value);
+-
+- if ((param == null) || (param.length() == 0)) return null;
+- param = param.toUpperCase();
+-
+- if (mapOfParameters.get(param) != null) return null; //Parameter already exists
+-
+- Element child = (Element)template.cloneNode(true);
+- recursiveKeyReplace(child, param);
+- element.appendChild(child);
+-
+- ControlledPanel childPanel = null;
+- try {
+- childPanel = ControlledPanel.createSingleParameterPanel(child, this);
+- childPanel.setKey(childPanel.getKey());
+- GUIBuilder.gui.addToTab(childPanel, section, this);
+- childPanel.hold();
+- GUIBuilder.control(childPanel);
+- GUIBuilder.recursiveBuild(child, this, doSet, hm, key, value);
+-
+- mapOfParameters.put(param, childPanel);
+- } catch (final GUIBuildException e1) {
+- e1.printStackTrace();
+- }
+-
+- this.invalidate();
+-
+- return childPanel;
+- }
+-
+- @Override
+- public void close() {
+-
+- }
+-
+- @Override
+- public String getValue() {
+- return null;
+- }
+-
+- public void remove() {
+- if (mapOfParameters.size() == 0) return;
+-
+- String choice = (String)JOptionPane.showInputDialog(this, "Remove a parameter", "Remove", JOptionPane.QUESTION_MESSAGE, null, mapOfParameters.keySet().toArray(), null);
+-
+- if (choice == null) return; //nothing to do
+-
+- String childKey = templateKey.replaceAll("%", choice);
+- final Element child = XMLHelper.getCertainChildElement(element, "parameter", "key", childKey);
+-
+- if (child == null) return;
+-
+- try { //this makes sure that all child nodes are destroyed
+- GUIBuilder.recursiveDestruct(child, this);
+- element.removeChild(child);
+- final ControlledPanel childPanel = GUIBuilder.panelControl.get(section, childKey);
+-
+- childPanel.release();
+- childPanel.close();
+-
+- if (!childPanel.isNeeded())
+- GUIBuilder.gui.removeFromTab(childPanel, section, this);
+-
+- mapOfParameters.remove(choice);
+- } catch (final GUIBuildException e) {
+- e.printStackTrace();
+- }
+-
+- this.invalidate();
+- }
+-
+- private void recursiveKeyReplace(Element element, String string) {
+- if (element.hasAttribute("key"))
+- element.setAttribute("key", element.getAttribute("key").replaceAll("%", string));
+-
+- final NodeList nodelist = element.getChildNodes();
+- for (int i = 0; i < nodelist.getLength(); i++) {
+- if (nodelist.item(i).getNodeType() == Node.ELEMENT_NODE) {
+- recursiveKeyReplace(((Element) nodelist.item(i)), string);
+- }
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/GUIBuildException.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/GUIBuildException.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/GUIBuildException.java (revision 18298)
+@@ -1,33 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-public class GUIBuildException extends Exception {
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = 1L;
+-
+- public GUIBuildException(String message) {
+- super(message);
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/ControlledPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/ControlledPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/ControlledPanel.java (revision 18298)
+@@ -1,285 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.Color;
+-import java.awt.Component;
+-import java.awt.Font;
+-
+-import javax.swing.JEditorPane;
+-import javax.swing.JLabel;
+-import javax.swing.JPanel;
+-import javax.swing.JSeparator;
+-import javax.swing.*;
+-import java.util.HashMap;
+-import javax.swing.border.*;
+-
+-import main.GUI;
+-import main.GUIBuilder;
+-import main.XMLHelper;
+-import net.miginfocom.swing.MigLayout;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-
+-/**
+- * Abstract class for JPanels that are maintained with their key and designated
+- * section and can return their current value.
+- */
+-public abstract class ControlledPanel extends JPanel {
+-
+- private static final long serialVersionUID = 1L;
+-
+- private int dependencies;
+-
+- protected JLabel jlabel;
+-
+- protected String section;
+- protected String key;
+- protected String label;
+- protected String hashKey;
+-
+- protected Element element;
+-
+- protected boolean optional;
+- protected String replace;
+-
+- protected int hierarchy;
+- protected String helptext;
+- protected JEditorPane help;
+-
+- /**
+- * Constructor for a controlled panel.
+- *
+- * @param element
+- */
+- public ControlledPanel(Element element, ControlledPanel parent) {
+- this(element, parent, true);
+- }
+-
+- public ControlledPanel(Element element, ControlledPanel parent, boolean doLayout) {
+- super();
+- initialize(element, parent);
+-
+- if (doLayout) {
+- int column1 = 200;
+- column1 -= getHierarchy() * 5; //Indentation for the label, 5px per hierarchy level
+-
+- setLayout(new MigLayout("gapx 6, wrap 8, top, ins n 5 n n", "["+ column1 + "!][100!][100!][100!][100!][100!][300:400:400]", ""));
+- add(jlabel, "growx, ay top, gaptop 5, gapleft " + getHierarchy() * 5);
+- add(help, "cell 6 0, wrap");
+- }
+- }
+-
+- private void initialize(Element element, ControlledPanel parent) {
+- dependencies = 0;
+-
+- this.element = element;
+- this.key = element.getAttribute("key");
+- this.label = this.key;
+-
+- this.section = element.getAttribute("section");
+- this.hashKey = this.section.toUpperCase() + "::" + this.key.toUpperCase();
+- this.optional = element.getAttribute("optional").equals("true");
+-
+- jlabel = new JLabel(this.label + ": ");
+- jlabel.setForeground(GUI.LABEL_COLOR);
+-
+- this.setBackground(Color.white);
+- this.setVisible(true);
+-
+- /* Add help to the right side of the panel. */
+- helptext = XMLHelper.getChildElementContent(element, "help");
+- help = ControlledPanel.createHelpPane(""+helptext+"");
+- if (helptext != null) help.setText(helptext);
+-
+- if (parent != null) {
+- setHierarchy(parent.getHierarchy() + 1);
+- } else {
+- setHierarchy(0);
+- }
+- }
+-
+- /**
+- * Creates a ControlledPanel for a parameter that matches its type. (i.e.
+- * radio buttons for an option parameter, ...
+- *
+- * @param element
+- * @return the Controlled Panel
+- * @throws GUIBuildException
+- */
+- public static ControlledPanel createSingleParameterPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- ControlledPanel panel;
+-
+- //System.out.println("IN create: " + XMLHelper.getString((Node)element));
+-
+- if (element.hasAttribute("counter")) {
+- panel = new DuplicatorPanel(element, parent);
+- } else if (element.getTagName().equals("frame")) {
+- panel = new FramePanel(element, parent);
+- } else if (element.getAttribute("type").equals("path") || element.getAttribute("type").equals("file")) {
+- panel = new PathPanel(element, parent);
+- } else if (element.getAttribute("type").equals("alternative") || element.getAttribute("type").equals("logical")) {
+- panel = new AlternativePanel(element, parent);
+- } else if (element.getAttribute("type").equals("choice")) {
+- panel = new CheckBoxPanel(element, parent);
+- } else if (element.getAttribute("type").equals("integer") || element.getAttribute("type").equals("integer+")){
+- panel = new IntegerPanel(element, parent);
+- } else if (element.getAttribute("type").equals("decimal")) {
+- panel = new DecimalPanel(element, parent);
+- } else if (element.getAttribute("type").equals("double")) {
+- panel = new TextfieldPanel(element, parent);
+- } else if (element.getAttribute("type").equals("string") || element.getAttribute("type").equals("char") || element.getAttribute("type").equals("cell")){
+- panel = new TextfieldPanel(element, parent);
+- } else if (element.getAttribute("type").equals("combination")) {
+- panel = new CombinedPanel(element, parent);
+- } else if (element.getAttribute("type").equals("selector")) {
+- panel = new SelectorPanel(element, parent);
+- } else {
+- throw new GUIBuildException("Cannot create a GUI panel for a parameter of type " + element.getAttribute("type"));
+- }
+-
+- return panel;
+- }
+-
+- public static JEditorPane createHelpPane(String helptext){
+- JEditorPane help = new JEditorPane();
+- help.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
+- help.setFont(new Font(Font.SANS_SERIF, Font.PLAIN, 12));
+- help.setEditable(false);
+- help.setContentType("text/html");
+- help.setForeground(Color.GRAY);
+- help.addHyperlinkListener(GUIBuilder.gui);
+-
+- if (helptext!=null) {
+- help.setText(""+helptext+"");
+- } else {
+- help.setText("");
+- }
+-
+- return help;
+- }
+-
+- public void setHierarchy(int val) {
+- hierarchy = val;
+- }
+-
+- public int getHierarchy() {
+- return hierarchy;
+- }
+-
+- /**
+- * This method should be called when the panel is removed.
+- */
+- public abstract void close();
+-
+- /**
+- * @return the GUI component.
+- */
+- public Component getComponent() {
+- return this;
+- }
+-
+- /**
+- * @return the number of dependencies on the panel.
+- */
+- public int getDependencies() {
+- return dependencies;
+- }
+-
+- /**
+- * @return the key of the corresponding key / value set
+- */
+- public String getKey() {
+- return key;
+- }
+-
+- /**
+- * @return the current value of the key / value set null if the key value
+- * set should not be printed
+- */
+- public abstract String getValue();
+-
+- /**
+- * This method should be called when another panel depends needs this panel
+- * to exist.
+- */
+- public synchronized void hold() {
+- this.dependencies++;
+- }
+-
+- /**
+- * @return true if dependencies on this panel exist
+- * @throws GUIBuildException
+- */
+- public synchronized boolean isNeeded() throws GUIBuildException {
+- if (dependencies == 0) {
+- return false;
+- } else if (dependencies > 0) {
+- return true;
+- } else {
+- throw new GUIBuildException("Inplausible number of dependencies on panel");
+- }
+- }
+-
+- /**
+- * @return true if a value for the underlying parameter is optional
+- */
+- public boolean isOptional() {
+- return optional;
+- }
+-
+- /**
+- * This method should be called when a panel no longer needs this panel to
+- * exist. The panel will be removed if no dependency exists.
+- */
+- public synchronized void release() {
+- this.dependencies--;
+- }
+-
+- public void set(HashMap hm, String key, String value) {
+- System.out.println("Set not implemented for ControlledPanel: " + serialVersionUID);
+- }
+-
+- public String getHashKey() {
+- return hashKey;
+- }
+-
+- /**
+- * This method sets a new key for a panel and changes its label.
+- *
+- * @param key
+- * the new key
+- */
+- public void setKey(String key) {
+- this.key = key;
+- element.setAttribute("key", key);
+- jlabel.setText(this.label + ": ");
+- }
+-
+- /**
+- * Getter method for the section.
+- * @return the section
+- */
+- public String getSection() {
+- return section;
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/CheckBoxPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/CheckBoxPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/CheckBoxPanel.java (revision 18298)
+@@ -1,139 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import main.*;
+-
+-import java.awt.Color;
+-import java.awt.event.ItemEvent;
+-import java.util.HashMap;
+-
+-import javax.swing.JCheckBox;
+-import javax.swing.JOptionPane;
+-import javax.swing.JLabel;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-
+-public class CheckBoxPanel extends OptionPanel {
+-
+- private static final long serialVersionUID = 552186457208697362L;
+- private final JCheckBox[] boxes;
+- String concat;
+- private String setKey = null, setValue = null;
+- private boolean doSet = false;
+- private HashMap setMap;
+-
+-
+- /**
+- * Constructor for a panel that can hold a number of checkboxes to compose
+- * the value for a key/value set.
+- *
+- * @param element
+- * @throws GUIBuildException
+- */
+- public CheckBoxPanel(Element element, ControlledPanel parent) throws GUIBuildException {
+- super(element, parent);
+-
+- concat = "";
+- boxes = new JCheckBox[values.length];
+- for (int i = 0; i < values.length; i++) {
+- boxes[i] = new JCheckBox(values[i]);
+-
+- this.add(boxes[i], "cell 1 " + i + ", wrap, ay top");
+-
+- String extra = "";
+- if (i > 0)
+- extra = ", gapleft 12";
+-
+- this.add(ControlledPanel.createHelpPane(this.helptexts[i]), "cell 6 "+ i +", width 200:400:400, wrap" + extra);
+-
+- boxes[i].setBackground(Color.white);
+- boxes[i].setVisible(true);
+- boxes[i].addItemListener(this);
+- if (defaultTrues.contains(values[i])) {
+- boxes[i].setSelected(true);
+- concat += values[i] + " ";
+- }
+- }
+- }
+-
+- @Override
+- public void close() {
+- for (final JCheckBox box : boxes)
+- box.setSelected(false);
+- }
+-
+- @Override
+- public String getValue() {
+- if (!isOptional() && concat.equals("")) {
+- JOptionPane.showMessageDialog(null, "No option was selected for "
+- + getKey() + " (section '" + getSection().toUpperCase() + "')"
+- + ".\nA value is required. Your .ini-file is probably incorrect.",
+- "Problem when building .ini file",
+- JOptionPane.WARNING_MESSAGE);
+- }
+-
+- if (concat.equals("")) return null;
+- else return concat.trim();
+- }
+-
+- public synchronized void set(HashMap hm, String key, String value) {
+- String val = ((String)hm.get(hashKey)).toUpperCase();
+- //System.out.println("\tABOUT TO CHANGE CHECKBOXPANEL KEY: " + key + " VAL: " + val);
+-
+- String[] tokens = val.split("\\s+");
+- for (final JCheckBox box : boxes) {
+- box.setSelected(false);
+-
+- for (final String token : tokens) {
+- if (token.equals(box.getText())) {
+- //System.out.println("\t\tSelecting Checkbox: " + token);
+- doSet = true;
+- setKey = key;
+- setValue = value;
+- setMap = hm;
+- box.setSelected(true);
+- }
+- }
+- }
+- }
+-
+-
+- @Override
+- public synchronized void itemStateChanged(ItemEvent arg0) {
+- final String selectedOption = ((JCheckBox) arg0.getItemSelectable()).getText();
+-
+- if (arg0.getStateChange() == ItemEvent.SELECTED) {
+- concat += selectedOption + " ";
+- } else {
+- concat = concat.replaceAll(new String(" " + selectedOption + " "), " ");
+- concat = concat.replaceFirst(new String("^" + selectedOption + " "), ""); //at the beginning of the concat
+- }
+-
+- //super.handleItemEvent(arg0, selectedOption);
+- super.handleItemEvent(arg0, selectedOption, doSet, setMap, setKey, setValue);
+- doSet = false;
+- setKey = null;
+- setMap = null;
+- setValue = null;
+- }
+-}
+Index: ../trunk-jpl/src/java/src/gui_elements/DuplicatorPanel.java
+===================================================================
+--- ../trunk-jpl/src/java/src/gui_elements/DuplicatorPanel.java (revision 18297)
++++ ../trunk-jpl/src/java/src/gui_elements/DuplicatorPanel.java (revision 18298)
+@@ -1,175 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package gui_elements;
+-
+-import java.awt.event.ActionEvent;
+-import java.awt.event.ActionListener;
+-import java.util.*;
+-
+-import javax.swing.JButton;
+-
+-import main.GUIBuilder;
+-import main.XMLHelper;
+-
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-import org.w3c.dom.NodeList;
+-
+-public class DuplicatorPanel extends ControlledPanel implements ActionListener {
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = 6801877538909126920L;
+- JButton addButton;
+- Element clone;
+-
+- JButton removeButton;
+-
+- public DuplicatorPanel(Element element, ControlledPanel parent) {
+- super(element, parent);
+-
+- addButton = new JButton("+");
+- this.add(addButton, "cell 1 0, split 2, grow");
+- addButton.addActionListener(this);
+-
+- removeButton = new JButton("-");
+- this.add(removeButton, "cell 1 0, grow, wrap");
+- removeButton.addActionListener(this);
+-
+- clone = (Element) element.cloneNode(true);
+- clone.removeAttribute("counter");
+- clone.setAttribute("counted", "true");
+- }
+-
+- @Override
+- public void actionPerformed(ActionEvent arg0) {
+- if (arg0.getSource() == addButton) {
+- add();
+- } else if (arg0.getSource() == removeButton) {
+- remove();
+- }
+- }
+-
+- @Override
+- public void set(HashMap hm, String key, String value) {
+- //System.out.println("Trying to add DUPLICATOR Panel: " + key + " ... " + value + " HashKey: " + this.getHashKey());
+-
+- if (key.indexOf('#') == -1) {
+- ControlledPanel child = add(true, hm, key, value);
+- child.set(hm, key, value);
+- }
+- }
+-
+- public ControlledPanel add() {
+- return add(false, null, null, null);
+- }
+-
+- public ControlledPanel add(boolean doSet, HashMap hm, String key, String value) {
+-
+- final Element child = (Element) this.clone.cloneNode(true);
+- final int counter = Integer.parseInt(element.getAttribute("counter"));
+- element.setAttribute("counter", (counter + 1) + "");
+-
+- // child.setAttribute("key",element.getAttribute("key").replaceAll("#",counter+""));
+-
+- //System.out.println("\t-->Adding a child panel to DUPLICATOR with key: " + key + " val: " + value + " HASH: " + this.getHashKey() + " hier: " + this.getHierarchy());
+-
+- recursiveKeyReplace(child, counter + "");
+- element.appendChild(child);
+-
+- ControlledPanel childPanel = null;
+- try {
+- childPanel = ControlledPanel.createSingleParameterPanel(child, this);
+- childPanel.setKey(childPanel.getKey());
+- GUIBuilder.gui.addToTab(childPanel, section, this);
+- childPanel.hold();
+- GUIBuilder.control(childPanel);
+- GUIBuilder.recursiveBuild(child, this, doSet, hm, key, value);
+-
+- } catch (final GUIBuildException e1) {
+- // TODO Auto-generated catch block
+- e1.printStackTrace();
+- }
+-
+- this.invalidate();
+-
+- return childPanel;
+- }
+-
+- @Override
+- public void close() {
+- boolean doRemove = true;
+-
+- do {
+- doRemove = remove();
+- } while (doRemove);
+- }
+-
+- @Override
+- public String getValue() {
+- return null;
+- }
+-
+- public boolean remove() {
+- final int counter = Integer.parseInt(element.getAttribute("counter")) - 1;
+- final String childKey = element.getAttribute("key").replace("#", counter + "");
+- final Element child = XMLHelper.getCertainChildElement(element, "parameter", "key", childKey);
+-
+- if (child == null) return false;
+-
+- element.removeChild(child);
+- element.setAttribute("counter", (counter) + "");
+-
+- final ControlledPanel childPanel = GUIBuilder.panelControl.get(section, childKey);
+-
+- if (childPanel != null) {
+- childPanel.release();
+- childPanel.close();
+-
+- try {
+- if (!childPanel.isNeeded()) {
+- GUIBuilder.gui.removeFromTab(childPanel, section, this);
+- }
+- } catch (final GUIBuildException e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- }
+-
+- this.invalidate();
+-
+- return true;
+- }
+-
+- private void recursiveKeyReplace(Element element, String string) {
+- if (element.hasAttribute("key")) {
+- element.setAttribute("key", element.getAttribute("key").replaceAll("#", string));
+- }
+- final NodeList nodelist = element.getChildNodes();
+- for (int i = 0; i < nodelist.getLength(); i++) {
+- if (nodelist.item(i).getNodeType() == Node.ELEMENT_NODE) {
+- recursiveKeyReplace(((Element) nodelist.item(i)), string);
+- }
+- }
+- }
+-
+-}
+Index: ../trunk-jpl/src/java/src/main/GUIBuilder.java
+===================================================================
+--- ../trunk-jpl/src/java/src/main/GUIBuilder.java (revision 18297)
++++ ../trunk-jpl/src/java/src/main/GUIBuilder.java (revision 18298)
+@@ -1,391 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package main;
+-
+-import gui_elements.ControlledPanel;
+-import gui_elements.GUIBuildException;
+-
+-import java.io.IOException;
+-
+-import javax.swing.ProgressMonitor;
+-import javax.swing.JFileChooser;
+-import javax.swing.JOptionPane;
+-import javax.swing.JPanel;
+-import javax.swing.filechooser.FileNameExtensionFilter;
+-
+-import java.util.*;
+-
+-import org.w3c.dom.Document;
+-import org.w3c.dom.Element;
+-
+-/**
+- * The main class to build the .ini file creator. Upon construction it reads an
+- * XML file and creates the corresponding GUI. Maintains an ElementControl
+- * object.
+- *
+- * @author korhammer et egger
+- *
+- */
+-public class GUIBuilder {
+- public static ProgressMonitor monitor;
+-
+- public static final String xsd = GUIBuilder.class.getClassLoader().getResource("resources/config_schema-0.1.1.xsd").toString();
+- public static String res_filepath = GUIBuilder.class.getClassLoader().getResource("resources/default_config.xml").toString(); //the default config to start with
+- public static Document doc;
+-
+- public static GUI gui;
+- public static PanelControl panelControl;
+-
+- public static String application;
+- public static String currentConfigFile;
+-
+- public static String saveFilePath = System.getProperty("user.dir");
+-
+-
+- private static String getFileExtension(final String file_and_path) {
+- final String file_sep = System.getProperty("file.separator");
+-
+- // get filename without path
+- final int fileSepIndex = file_and_path.lastIndexOf(file_sep);
+- if (fileSepIndex == -1) {
+- return "";
+- }
+- final String filename = file_and_path.substring(fileSepIndex+1); //remove path
+-
+- // get the extension from the filename
+- final int extIndex = filename.lastIndexOf(".");
+- if (extIndex == -1)
+- return "";
+-
+- return filename.substring(extIndex+1);
+- }
+-
+- /**
+- * The main method. Opens the GUI Builder with a menu bar on the side.
+- * If an XML filepath is handed over as an argument,
+- * the XML file is opened.
+- *
+- * @param args
+- * @throws GUIBuildException
+- */
+- public static void main(String args[]) throws GUIBuildException {
+-
+- new GUIBuilder();
+-
+- if ((args.length != 0) && (args[0].length() > 0))
+- res_filepath = args[0]; //User may provice xml file as first argument
+-
+- buildGUI(res_filepath);
+- //gui.hideOpenButton();
+- }
+-
+- /**
+- * Builds a GUI from the XML-file specified with validation through
+- * the specified schema.
+- *
+- * @param filepath
+- * @param schemapath
+- * @throws GUIBuildException
+- */
+- public GUIBuilder() throws GUIBuildException {
+- if (System.getProperty("mrj.version") != null) { //detect if running on mac
+- System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Inishell");
+- System.setProperty("apple.awt.brushMetalLook", "true");
+- }
+- gui = new GUI();
+- }
+-
+- public static void setComments(HashMap added_comments, HashMap comments) {
+- panelControl.setComments(added_comments, comments);
+- }
+-
+- /**
+- * Builds the gui for a filepath that can either be handed over as an argument
+- * on application start or chosen by using the open button.
+- *
+- * @param filepath
+- * @throws GUIBuildException
+- */
+- public static void buildGUI(String filepath) throws GUIBuildException{
+- currentConfigFile = filepath;
+-
+- doc = XMLHelper.readXML(filepath, xsd);
+- doc = XMLHelper.resolveReferences(doc);
+-
+- application = doc.getDocumentElement().getAttribute("application");
+-
+- gui.setApplicationForTitle(application);
+-
+- panelControl = new PanelControl();
+-
+- final Element root = doc.getDocumentElement();
+- recursiveBuild(root, null, false);
+- }
+-
+-
+- public static void setValues(final HashMap hm, final HashMap added_comments, final HashMap comments) {
+- if (hm == null) return;
+-
+- monitor = new ProgressMonitor(gui, "Loading INI file", "0 out of " + panelControl.order.size() + " sections loaded", 0, panelControl.order.size());
+- monitor.setMillisToPopup(0);
+-
+- Thread myrunner = new Thread() {
+- public void run() {
+- int progress_counter = 0; //Effectively counts the sections already parsed into the GUI
+- try {
+- final int returnval = GUIBuilder.closeFile();
+- if (returnval == JOptionPane.CANCEL_OPTION) return;
+- monitor.setProgress(progress_counter);
+-
+- GUIBuilder.buildGUI(currentConfigFile);
+- } catch (GUIBuildException e) {
+- e.printStackTrace();
+- }
+-
+- gui.setEnabled(false); //Disable user interaction while the ProgressMonitor is on
+-
+- HashSet usedKeys = new HashSet(); //save all keys that were used from the HashMap
+- HashSet unusedKeys = new HashSet(); //save all keys that were used from the HashMap
+-
+- Iterator>> sectionIterator = panelControl.panels.entrySet().iterator();
+- while (sectionIterator.hasNext()) {
+- progress_counter++;
+- monitor.setProgress(progress_counter);
+- monitor.setNote(progress_counter + " out of " + panelControl.order.size() + " sections loaded");
+-
+- if (monitor.isCanceled()) { //user cancelled loading
+- monitor.close();
+- gui.setEnabled(true);
+- break; //HACK, should reset the whole environment before breaking
+- }
+-
+- Map.Entry> entry = sectionIterator.next();
+- TreeMap value = entry.getValue();
+-
+- List sectionKeys = new ArrayList(hm.keySet()); //all keys as defined in the existing ini
+- String sectionKey = entry.getKey().toUpperCase() + "::"; //The section string
+- filterList(sectionKey, sectionKeys); //filter keys for current section only (optimization)
+-
+- LinkedList todos = new LinkedList();
+- LinkedList keys = new LinkedList();
+- LinkedList values = new LinkedList();
+-
+- do {
+- todos.clear();
+- keys.clear();
+- values.clear();
+-
+- Iterator> keyIterator = value.entrySet().iterator();
+- while(keyIterator.hasNext()) { //go through all keys of current section
+- final ControlledPanel mypanel = keyIterator.next().getValue();
+- //System.out.println("\t" + mypanel.getKey());
+-
+- String pattern = mypanel.getHashKey();
+- pattern = pattern.replace("%","[a-zA-Z0-9_]+");
+- pattern = pattern.replace("#","[1-9]+[0-9]*"); //all integer numbers from 1 to infinity
+- //System.out.println("Current pattern: " + pattern);
+-
+- //Loop through all defined keys of this section and compare them with pattern
+- Iterator keyit = sectionKeys.iterator();
+- while (keyit.hasNext()) {
+- final String currkey = keyit.next();
+- //System.out.println("sectionKeys contains: " + currkey);
+-
+- if ((!usedKeys.contains(currkey)) && currkey.matches(pattern)) {
+- //Add mypanel to list of todos
+- //System.out.println("Adding panel for " + currkey);
+- todos.add(mypanel);
+- keys.add(currkey);
+- values.add(hm.get(currkey));
+-
+- usedKeys.add(currkey);
+- }
+- }
+- }
+-
+- for (int jj = 0; jj < todos.size(); jj++) {
+- //System.out.println("--> SETTING " + keys.get(jj) + " = " +values.get(jj));
+- todos.get(jj).set(hm, keys.get(jj), values.get(jj));
+- }
+- } while (todos.size() != 0);
+-
+- if (progress_counter == panelControl.order.size()) gui.setEnabled(true);
+- }
+-
+- //Now find out all keys that were not used in the hashmap
+- for (String key : hm.keySet()) {
+- if (!usedKeys.contains(key)) {
+- //System.out.println("Unknown key = " + key);
+- unusedKeys.add(key);
+- panelControl.setUnusedKeys(key, hm.get(key));
+- }
+- }
+-
+- setComments(added_comments, comments);
+- }
+- };//thread
+- myrunner.start();
+- }
+-
+- private static void filterList(String filter, List list) {
+- for (Iterator it=list.iterator(); it.hasNext();) {
+- final String next = it.next();
+- if (!next.startsWith(filter)) {
+- it.remove();
+- }
+- }
+- }
+-
+- public static int closeFile(){
+- final int returnval = JOptionPane.showConfirmDialog(new JPanel(),
+- "You will lose all changes made to the current ini-file. " +
+- "Do you want this?", "Inishell is already open for " + application, JOptionPane.OK_CANCEL_OPTION);
+-
+-
+-
+- if (returnval == JOptionPane.OK_OPTION) {
+- gui.closeAllTabs();
+- gui.rootNode = new PanelNode("");
+- application = null;
+- doc = null;
+- panelControl = null;
+- }
+-
+- return returnval;
+- }
+-
+-
+- /**
+- * Puts the specified panel into the panel control.
+- * @param panel
+- */
+- public static void control(ControlledPanel panel) {
+- final String section = panel.getSection();
+- panelControl.put(section, panel);
+- }
+-
+-
+- /**
+- * Recursively traverses all children of the specified element
+- * and builds the corresponding panels.
+- *
+- * @param parentElement
+- * @param parentPanel
+- * @throws GUIBuildException
+- */
+- public static void recursiveBuild(Element parentElement, ControlledPanel parentPanel, boolean doSet) throws GUIBuildException {
+- recursiveBuild(parentElement, parentPanel, doSet, null, null, null);
+- }
+-
+-
+- public static void recursiveBuild(Element parentElement, ControlledPanel parentPanel, boolean doSet, HashMap hm, String key, String value) throws GUIBuildException {
+-
+- /* get all child elements for the root */
+- final String[] tags = {"parameter", "frame"};
+- final Element[] parameterElements = XMLHelper.getElementArray(parentElement, tags);
+-
+- for (final Element element : parameterElements) {
+- final String section = element.getAttribute("section");
+- ControlledPanel parameterPanel;
+-
+- if (!panelControl.contains(section, element.getAttribute("key"))) {
+- //System.out.println("Adding through recursiveBuild: " + element.getAttribute("key"));
+- parameterPanel = ControlledPanel.createSingleParameterPanel(element, parentPanel);
+- parameterPanel.setKey(parameterPanel.getKey());
+-
+- if (!element.getAttribute("template").equals("true")) {
+- //if (doSet) System.out.println("\tSETTING component key: " + key + " value: " + value);
+- if (doSet) parameterPanel.set(hm, parameterPanel.getKey(), value);
+-
+- gui.addToTab(parameterPanel, section, parentPanel);
+- control(parameterPanel);
+- }
+- } else {
+- parameterPanel = panelControl.get(section, element.getAttribute("key"));
+- }
+-
+- parameterPanel.hold();
+- recursiveBuild(element, parameterPanel, doSet);
+- }
+-
+- gui.validate();
+- }
+-
+- /**
+- * Recursively destructs child elements of the specified root.
+- *
+- * @param rootElement
+- * @param rootPanel
+- * @throws GUIBuildException
+- */
+- public static void recursiveDestruct(Element rootElement, ControlledPanel rootPanel)
+- throws GUIBuildException {
+-
+- /* get all child elements for the root */
+- final Element[] parameterElements = XMLHelper.getElementArray(rootElement, "parameter");
+-
+- for (final Element element : parameterElements) {
+- final String section = element.getAttribute("section");
+- final ControlledPanel parameterPanel = panelControl.get(section, element.getAttribute("key"));
+- recursiveDestruct(element, parameterPanel);
+-
+- parameterPanel.release();
+- parameterPanel.close();
+-
+- if (!parameterPanel.isNeeded()) {
+- gui.removeFromTab(parameterPanel, section, rootPanel);
+- }
+-
+- }
+-
+- gui.validate();
+- }
+-
+-
+- /**
+- * Opens a prompt for the path to save the ini file to. Then prints the ini
+- * to the path specified.
+- *
+- * @throws IOException
+- * @throws GUIBuildException
+- */
+- public static void printIOFile() throws IOException, GUIBuildException {
+- final FileNameExtensionFilter inifilter = new FileNameExtensionFilter(".ini files", "ini");
+-
+- final JFileChooser filechooser = new JFileChooser(saveFilePath);
+- filechooser.setFileFilter(inifilter);
+-
+- final int returnval = filechooser.showSaveDialog(new JPanel());
+-
+- if (returnval == JFileChooser.APPROVE_OPTION) {
+- String path = filechooser.getSelectedFile().getAbsolutePath();
+- final String ext = getFileExtension(path).toLowerCase();
+- if(!ext.equals("ini")) {
+- path += ".ini";
+- }
+-
+- if (filechooser.getSelectedFile().isDirectory()) return;
+- saveFilePath = filechooser.getSelectedFile().getParent();
+-
+- panelControl.printToFile(path);
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/main/PanelControl.java
+===================================================================
+--- ../trunk-jpl/src/java/src/main/PanelControl.java (revision 18297)
++++ ../trunk-jpl/src/java/src/main/PanelControl.java (revision 18298)
+@@ -1,248 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package main;
+-
+-import gui_elements.ControlledPanel;
+-
+-import java.io.File;
+-import java.io.FileWriter;
+-import java.io.IOException;
+-import java.util.HashMap;
+-import java.util.LinkedList;
+-import java.util.Set;
+-import java.util.TreeMap;
+-import java.util.Iterator;
+-
+-/**
+- * Class that maintains all ControlledPanels so that values can be retrieved
+- * from panels, ini-files can be written. And a panel is not multiply created.
+- *
+- * @author korhammer
+- *
+- */
+-public class PanelControl {
+-
+- LinkedList order;
+- HashMap> panels;
+- HashMap comments = null;
+- HashMap added_comments = null;
+- HashMap> unusedKeys = null;
+- PanelNode rootNode = null;
+-
+- /**
+- * Constructor for the panel control.
+- */
+- public PanelControl() {
+- panels = new HashMap>();
+- order = new LinkedList();
+-
+- unusedKeys = new HashMap>();
+- }
+-
+- public PanelControl(PanelControl p) {
+- panels = new HashMap>(p.panels);
+- order = new LinkedList(p.order);
+- if (added_comments != null)
+- added_comments = new HashMap(p.added_comments);
+-
+- if (comments != null)
+- comments = new HashMap(p.comments);
+- }
+-
+- public void setUnusedKeys(String key, String value) {
+- //Parse key
+- int offset = key.indexOf("::");
+- String section = key.substring(0, offset);
+- String sectionkey = key.substring(offset + 2);
+-
+- HashMap hm = unusedKeys.get(section);
+- if (hm == null) unusedKeys.put(section, new HashMap());
+-
+- unusedKeys.get(section).put(sectionkey, value);
+- }
+-
+- public void setComments(HashMap inaddedcomments, HashMap incomments) {
+- this.added_comments = new HashMap(inaddedcomments);
+- this.comments = new HashMap(incomments);
+- }
+-
+- /**
+- * @param section
+- * @param key
+- * @return true if a panel with such key is maintained in the specified
+- * section
+- */
+- public boolean contains(String section, String key) {
+- if (!panels.containsKey(section))
+- return false;
+-
+- return panels.get(section).containsKey(key);
+- }
+-
+- /**
+- *
+- * @param section
+- * @param key
+- * @return the panel with the specified section / key pair
+- */
+- public ControlledPanel get(String section, String key) {
+- return panels.get(section).get(key);
+- }
+-
+- /**
+- * Prints the ini-file at the specified path.
+- *
+- * @param path
+- */
+- public void printToFile(String path) {
+- /* create file */
+- final File file = new File(path);
+-
+- try {
+- final FileWriter writer = new FileWriter(file);
+-
+- writer.write(this.toString());
+- writer.close();
+- } catch (final IOException e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- }
+-
+- /**
+- * Adds the panel to the specified section.
+- *
+- * @param section
+- * @param panel
+- */
+- public void put(String section, ControlledPanel panel) {
+- final String key = panel.getKey();
+- if (!panels.containsKey(section)) {
+- order.add(section);
+- panels.put(section, new TreeMap());
+- }
+- panels.get(section).put(key, panel);
+- }
+-
+- /**
+- * Removes the panel with the specified section and key.
+- *
+- * @param section
+- * @param key
+- * @return the panel
+- */
+- public ControlledPanel remove(String section, String key) {
+- return panels.get(section).remove(key);
+- }
+-
+- /**
+- * Prints the maintained panels to a string.
+- *
+- * @return an ini-file-like structure
+- */
+- public void setRootNode(PanelNode inrootNode) {
+- rootNode = inrootNode;
+- }
+-
+- public String extractKey(String instring) {
+- int offset = instring.indexOf("::");
+- if (offset == -1) return null;
+-
+- return instring.substring(offset+2);
+- }
+-
+- @Override
+- public String toString() {
+- String out = "";
+-
+- for (final String section : order) {
+- /* create section */
+- final String sectionstring = "[" + section.toUpperCase() + "]\n";
+- String keyvaluestring = "";
+-
+- /* print section */
+- LinkedList keys = new LinkedList();
+- PanelNode sectionNode = rootNode.get(section.toUpperCase());
+- if (sectionNode != null) sectionNode.getKeyList(keys);
+-
+- //final Set keys = panels.get(section).keySet();
+- for (final String hashKey : keys) {
+- String key = extractKey(hashKey);
+- if (key == null) continue;
+-
+- final String value = panels.get(section).get(key).getValue();
+- if (value != null) {
+- if ((comments != null) && comments.containsKey(hashKey.toUpperCase())) {
+- String precomments = comments.get(hashKey.toUpperCase());
+- if (!precomments.equals(""))
+- keyvaluestring += precomments;
+- }
+-
+- keyvaluestring += key + "\t=\t" + value;
+-
+- if ((added_comments != null) && added_comments.containsKey(hashKey.toUpperCase()))
+- keyvaluestring += "\t" + added_comments.get(hashKey.toUpperCase());
+-
+- keyvaluestring += "\n";
+- }
+- }
+-
+- //Add unused keys
+- HashMap extra = unusedKeys.get(section.toUpperCase());
+- if (extra != null) {
+- if (!keyvaluestring.equals("")) keyvaluestring += "\n";
+-
+- for (String extrakey : extra.keySet()) {
+- String hashKey = section.toUpperCase() + "::" + extrakey.toUpperCase();
+- if ((comments != null) && comments.containsKey(hashKey)) {
+- String precomments = comments.get(hashKey);
+- if (!precomments.equals(""))
+- keyvaluestring += precomments;
+- }
+-
+- keyvaluestring += extrakey + "\t=\t" + extra.get(extrakey);
+-
+- if ((added_comments != null) && added_comments.containsKey(hashKey))
+- keyvaluestring += "\t" + added_comments.get(hashKey);
+-
+- keyvaluestring += "\n";
+- }
+- }
+-
+- //check if there aren't any comments in that section
+- String hashKey = section.toUpperCase() + "::";
+- if ((comments != null) && comments.containsKey(hashKey)) {
+- String precomments = comments.get(hashKey);
+- if (!precomments.equals("")) {
+- if (precomments.indexOf("\n") == -1) precomments += "\n";
+- keyvaluestring = precomments + keyvaluestring + "\n";
+- }
+- }
+-
+- /* add section only if keys / values are printed */
+- if (!keyvaluestring.equals("")) {
+- out += sectionstring + keyvaluestring + "\n";
+- }
+- }
+-
+- return out;
+- }
+-}
+Index: ../trunk-jpl/src/java/src/main/XMLHelper.java
+===================================================================
+--- ../trunk-jpl/src/java/src/main/XMLHelper.java (revision 18297)
++++ ../trunk-jpl/src/java/src/main/XMLHelper.java (revision 18298)
+@@ -1,525 +0,0 @@
+-/***********************************************************************************/
+-/* Copyright 2012 WSL Institute for Snow and Avalanche Research SLF-DAVOS */
+-/***********************************************************************************/
+-/* This file is part of INIshell.
+-*
+-* INIshell is free software: you can redistribute it and/or modify
+-* it under the terms of the GNU General Public License as published by
+-* the Free Software Foundation, either version 3 of the License, or
+-* (at your option) any later version.
+-*
+-* INIshell is distributed in the hope that it will be useful,
+-* but WITHOUT ANY WARRANTY; without even the implied warranty of
+-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-* GNU General Public License for more details.
+-*
+-* You should have received a copy of the GNU General Public License
+-* along with INIshell. If not, see .
+-*
+-*/
+-
+-package main;
+-
+-import gui_elements.GUIBuildException;
+-
+-import java.io.IOException;
+-import java.util.LinkedList;
+-
+-import javax.xml.parsers.DocumentBuilder;
+-import javax.xml.parsers.DocumentBuilderFactory;
+-import javax.xml.parsers.ParserConfigurationException;
+-import javax.xml.transform.TransformerConfigurationException;
+-import javax.xml.transform.TransformerException;
+-import javax.xml.transform.TransformerFactory;
+-
+-import org.w3c.dom.Document;
+-import org.w3c.dom.Element;
+-import org.w3c.dom.Node;
+-import org.w3c.dom.NodeList;
+-import org.xml.sax.SAXException;
+-
+-//for the XML printing
+-import javax.xml.transform.stream.StreamResult;
+-import javax.xml.transform.*;
+-import javax.xml.transform.dom.*;
+-import java.io.StringWriter;
+-
+-public class XMLHelper {
+-
+- /**
+- * Find the parameter values for which the element should be cloned
+- * e.g. for section tags.
+- *
+- * @param element
+- * @param tagName
+- * @param attributeName
+- * @param parentArgument
+- * @return the
+- */
+- public static String[] findApplicableValues(Element element,
+- String tagName, String attributeName, String parentArgument) {
+-
+- final String[] argumentsFromElement = getAttributesFromChildren(
+- element, tagName, attributeName);
+-
+- /*
+- * If no such arguments are specified for the current element but there
+- * are for the parent element, take that of the parent.
+- */
+- if (argumentsFromElement.length == 0 && parentArgument != null)
+- return new String[] { parentArgument };
+- else if ((argumentsFromElement.length > 0 && parentArgument != null)) {
+- if (getCertainChildElement(element, tagName, attributeName,
+- parentArgument) != null)
+- return new String[] { parentArgument };
+- else
+- /*
+- * The empty intersection is an empty array so that his case can
+- * be handled differently from the null case below.
+- */
+- return new String[0];
+- }
+-
+- /*
+- * If no arguments are specified for the parent use all element
+- * arguments.
+- */
+- else if (argumentsFromElement.length > 0 && parentArgument == null)
+- return argumentsFromElement;
+- else if (argumentsFromElement.length == 0 && parentArgument == null)
+- return null;
+- return null;
+- }
+-
+- /**
+- * Get all children of an element that have a certain element tag and
+- * extract the values for a certain attribute.
+- *
+- * @param parent
+- * the parent element
+- * @param tag
+- * the element tag
+- * @param attribute
+- * the attribute name
+- *
+- * @return a String array with the attribute values
+- */
+- public static String[] getAttributesFromChildren(Element parent, String tag, String attribute) {
+- final Element[] elements = getElementArray(parent, tag);
+-
+- final String[] attributes = new String[elements.length];
+- for (int i = 0; i < elements.length; i++) {
+- attributes[i] = elements[i].getAttribute(attribute);
+- }
+- return attributes;
+- }
+-
+- /**
+- * Returns the first child element that has the specified element tag and
+- * the value for the specified attribute.
+- *
+- * @param parent
+- * @param tag
+- * @param attribute
+- * @param value
+- * @return the first child element that meets the criteria
+- */
+- public static Element getCertainChildElement(Element parent, String tag,
+- String attribute, String value) {
+- final Element[] allElements = getElementArray(parent, tag);
+- for (final Element element : allElements) {
+- if (element.hasAttribute(attribute)) {
+- if (element.getAttribute(attribute).equals(value))
+- return element;
+- }
+- }
+- return null;
+- }
+-
+- /**
+- * For the specified element gets the text that is contained in the first
+- * child that has a certain element name.
+- *
+- *
+- * @param parent
+- * the parent element
+- * @param tag
+- * the element tag for the child
+- * @return the text content
+- */
+- public static String getChildElementContent(Element parent, String tag) {
+- final Element[] elements = getElementArray(parent, tag);
+- if (elements.length == 0)
+- return null;
+-
+- return elements[0].getTextContent();
+- }
+-
+-
+-
+- /**
+- * @param parent
+- * @param tag
+- * @return all child elements of the parent with the specified tag
+- */
+- public static Element[] getElementArray(Element parent, String tag) {
+- if (!parent.hasChildNodes())
+- return new Element[0];
+-
+- final NodeList nodeList = parent.getChildNodes();
+- final LinkedList elementlist = new LinkedList();
+- for (int i = 0; i < nodeList.getLength(); i++) {
+-
+- final Node element = nodeList.item(i);
+- if (element.getNodeType() == Node.ELEMENT_NODE && ((Element) element).getTagName().equals(tag)) {
+- elementlist.add((Element) element);
+- }
+- }
+- final Element[] elements = new Element[elementlist.size()];
+-
+- return elementlist.toArray(elements);
+- }
+-
+- public static Element[] getElementArray(Element parent, String[] tags) {
+- if (!parent.hasChildNodes())
+- return new Element[0];
+-
+- final NodeList nodeList = parent.getChildNodes();
+- final LinkedList elementlist = new LinkedList();
+- for (int ii = 0; ii < nodeList.getLength(); ii++) {
+-
+- final Node element = nodeList.item(ii);
+- if (element.getNodeType() == Node.ELEMENT_NODE) {
+- //Loop through all possible tags
+- for (int jj=0; jj.
+-*
+-*/
+-
+-package main;
+-
+-import gui_elements.ControlledPanel;
+-import gui_elements.GUIBuildException;
+-
+-import java.awt.BorderLayout;
+-import java.awt.Color;
+-import java.awt.Component;
+-import java.awt.Container;
+-import java.awt.Desktop;
+-import java.awt.*;
+-import java.awt.event.ActionEvent;
+-import java.awt.event.ActionListener;
+-import java.awt.event.WindowEvent;
+-import java.awt.event.WindowListener;
+-import java.io.IOException;
+-import java.net.URISyntaxException;
+-import java.util.HashMap;
+-import java.util.LinkedList;
+-
+-import javax.swing.BoxLayout;
+-import javax.swing.ImageIcon;
+-import javax.swing.JButton;
+-import javax.swing.JEditorPane;
+-import javax.swing.JFileChooser;
+-import javax.swing.JFrame;
+-import javax.swing.JOptionPane;
+-import javax.swing.JPanel;
+-import javax.swing.JScrollPane;
+-import javax.swing.JTabbedPane;
+-import javax.swing.JToolBar;
+-import javax.swing.event.HyperlinkEvent;
+-import javax.swing.event.HyperlinkListener;
+-import javax.swing.filechooser.FileNameExtensionFilter;
+-import java.io.*;
+-import javax.swing.*;
+-import java.awt.*;
+-import java.awt.event.*;
+-
+-import net.miginfocom.swing.MigLayout;
+-
+-/**
+- * The GUI created by the author.
+- *
+- * @author korhammer et egger
+- *
+- */
+-public class GUI extends JFrame implements WindowListener, ActionListener, HyperlinkListener {
+-
+- /**
+- *
+- */
+- private static final long serialVersionUID = -2428732881181670225L;
+- public static PanelNode rootNode = null;
+-
+- private static String title = GUI.class.getPackage().getImplementationTitle() + " " + GUI.class.getPackage().getImplementationVersion();
+-
+- public static final Color LABEL_COLOR = Color.decode("#000080");
+- public static Color NORMAL_BACKGROUND_COLOR = Color.decode("#EEEEEE");
+- public static Color WARNING_BACKGROUND_COLOR = Color.decode("#FF0011");
+-
+- public static ImageIcon openicon = new ImageIcon(GUI.class.getClassLoader().getResource("resources/icons/xml_open.png"));
+- public static ImageIcon openiniicon = new ImageIcon(GUI.class.getClassLoader().getResource("resources/icons/fileopen.png"));
+- public static ImageIcon exporticon = new ImageIcon(GUI.class.getClassLoader().getResource("resources/icons/filesave.png"));
+- public static ImageIcon previewicon = new ImageIcon(GUI.class.getClassLoader().getResource("resources/icons/kghostview.png"));
+- public static ImageIcon reseticon = new ImageIcon(GUI.class.getClassLoader().getResource("resources/icons/reset.png"));
+-
+- private final JButton createbutton;
+- private final JButton previewButton;
+- private final JButton openbutton;
+- private final JButton openinibutton;
+- private final JButton resetbutton;
+-
+- private final JTabbedPane tabpane;
+- private final JToolBar toolbar;
+- private HashMap tabpanels;
+-
+- private String configFilePath, iniFilePath;
+-
+- /*
+- * Creates a window with the static components of the GUI, i.e. components
+- * that do not depend on the configuration file.
+- */
+- public GUI() throws GUIBuildException {
+- super(title);
+-
+- configFilePath = System.getProperty("user.dir");
+- iniFilePath = System.getProperty("user.dir");
+-
+- tabpanels = new HashMap();
+-
+- Dimension screenDim = new Dimension(1280, 800);
+- Dimension maxDim = null;
+-
+- if (this.getMaximizedBounds() == null) {
+- Toolkit tk = Toolkit.getDefaultToolkit();
+- maxDim = tk.getScreenSize();
+- this.setMaximizedBounds(new Rectangle(0, 0, (int)maxDim.getWidth(), (int)maxDim.getHeight()));
+- } else {
+- maxDim = this.getMaximizedBounds().getSize();
+- }
+-
+- if (maxDim.height < screenDim.height) {
+- screenDim.height = maxDim.height;
+- if (screenDim.height > 100)
+- screenDim.height -= 25;
+- }
+-
+- if (maxDim.width < screenDim.width) {
+- screenDim.width = maxDim.width;
+- if (screenDim.width > 100)
+- screenDim.width -= 25;
+- }
+-
+- this.setSize(screenDim);
+- //this.setExtendedState(MAXIMIZED_BOTH);
+- this.setVisible(true);
+- this.setLayout(new BorderLayout());
+-
+- this.toolbar = new JToolBar();
+- toolbar.setLayout(new BoxLayout(toolbar, 1));
+- toolbar.setFloatable(false);
+- this.setVisible(true);
+- this.add(toolbar, BorderLayout.WEST);
+-
+- this.tabpane = new JTabbedPane();
+- this.add(tabpane);
+- tabpane.setVisible(true);
+-
+- this.openbutton = new JButton(openicon);
+- this.openbutton.setActionCommand("open config");
+- this.openbutton.setToolTipText("Open XML-configuration");
+- openbutton.addActionListener(this);
+- toolbar.add(this.openbutton);
+-
+- this.openinibutton = new JButton(openiniicon);
+- this.openinibutton.setActionCommand("open ini");
+- this.openinibutton.setToolTipText("Open existing INI file");
+- openinibutton.addActionListener(this);
+- toolbar.add(this.openinibutton);
+-
+- this.resetbutton = new JButton(reseticon);
+- this.resetbutton.setActionCommand("reset");
+- this.resetbutton.setToolTipText("Reset Interface");
+- resetbutton.addActionListener(this);
+- toolbar.add(this.resetbutton);
+-
+- this.createbutton = new JButton(exporticon);
+- this.createbutton.setActionCommand("write config");
+- this.createbutton.setToolTipText("Write to INI-file");
+- createbutton.addActionListener(this);
+- toolbar.add(this.createbutton);
+-
+- this.previewButton = new JButton(previewicon);
+- this.previewButton.setActionCommand("preview");
+- this.previewButton.setToolTipText("Preview INI-file");
+- previewButton.addActionListener(this);
+- toolbar.add(previewButton);
+-
+- this.addWindowListener(this);
+-
+- rootNode = new PanelNode("");
+- }
+-
+- /**
+- * Writes the application name into the GUI window title bar.
+- *
+- * @param application
+- */
+- public void setApplicationForTitle(String application){
+- if(application.equals("")){
+- this.setTitle(title);
+- }
+- else{
+- this.setTitle(title + " for "+application);
+- }
+- }
+-
+- public void hideOpenButton(){
+- openbutton.setVisible(false);
+- }
+-
+- /**
+- * Closes all tabs.
+- */
+- public void closeAllTabs(){
+- tabpane.removeAll();
+- }
+-
+- /**
+- * Adds a component to the tab specified and creates the tab if it does not
+- * already exist.
+- *
+- * @param comp
+- * @param tabName
+- * @throws GUIBuildException
+- */
+- public void addToTab(ControlledPanel comp, String tabName, ControlledPanel parentPanel) throws GUIBuildException {
+- tabName = Character.toUpperCase(tabName.charAt(0)) + tabName.substring(1).toLowerCase();
+-
+- String section = ((ControlledPanel)comp).getSection().toUpperCase();
+- String key = section + "::" + ((ControlledPanel)comp).getKey();//((ControlledPanel)comp).getHashKey();
+- //System.out.println("\tPanel: " + ((ControlledPanel)comp).getHashKey() + " Section: " + ((ControlledPanel)comp).getSection());
+-
+- PanelNode sectionNode = rootNode.getChild(section);
+- if (sectionNode == null) {
+- PanelNode tmp = new PanelNode(section);
+- //System.out.println("\t--Adding section '" + section + "' to tree");
+- sectionNode = rootNode.add(tmp);
+- }
+-
+- if (parentPanel != null) {
+- //System.out.println("\tLooking for node: " + parentPanel.getHashKey());
+- sectionNode = sectionNode.get(parentPanel.getSection().toUpperCase() + "::" + parentPanel.getKey());
+- }
+-
+- if (sectionNode != null) {
+- PanelNode keyNode = sectionNode.get(key);
+- if (keyNode == null) {
+- PanelNode tmp = new PanelNode(key);
+- keyNode = sectionNode.add(tmp);
+- //System.out.println("\t--Adding key '" + key + "' to tree as leaf to " + sectionNode.getData());
+- }
+- }
+-
+- JPanel tab;
+- if (tabpane.indexOfTab(tabName) == -1) {
+-
+- tab = new JPanel();
+- tab.setBackground(Color.white);
+- tab.setVisible(true);
+- tab.setLayout(new MigLayout("wrap 1"));
+-
+- JScrollPane scrollpane = new JScrollPane(tab);
+- tabpane.add(tabName, scrollpane);
+- tabpanels.put(tabName, tab);
+-
+- } else {
+- tab = tabpanels.get(tabName);
+- }
+-
+- if (parentPanel != null && containsPanel(tab, parentPanel)) {
+- parentPanel.add(comp, "span");
+- } else {
+- tab.add(comp);
+- }
+-
+- //JViewport jv = ((JScrollPane)tabpane.getComponentAt(tabpane.indexOfTab(tabName))).getViewport();
+- //jv.setViewPosition(new Point(0,0));
+-
+- this.validate();
+- }
+-
+- public void removeFromTab(ControlledPanel parameterPanel, String section, ControlledPanel parentPanel) {
+- final String tabTitle = section.substring(0, 1).toUpperCase() + section.substring(1).toLowerCase();
+- final int index = tabpane.indexOfTab(tabTitle);
+-
+- final Container container = (Container) tabpane.getComponentAt(index);
+-
+- //System.out.println("Removing Panel: " + parameterPanel.getHashKey());
+- PanelNode tmp = rootNode.get(parameterPanel.getSection().toUpperCase() + "::" + parameterPanel.getKey());
+- tmp.getParent().remove(tmp);
+-
+- if (parentPanel != null && containsPanel(container, parentPanel)) {
+- parentPanel.remove(parameterPanel);
+- } else {
+- container.remove(parameterPanel);
+- }
+-
+- GUIBuilder.panelControl.remove(section, parameterPanel.getKey());
+-
+- container.repaint();
+- this.validate();
+- }
+-
+- public boolean containsPanel(Container container, JPanel panel) {
+-
+- for (final Component component : container.getComponents()) {
+- if (component == panel)
+- return true;
+- if (containsPanel((Container) component, panel))
+- return true;
+- }
+- return false;
+- }
+-
+- @Override
+- public void actionPerformed(ActionEvent e) {
+- if (e.getActionCommand().equals("write config") && GUIBuilder.application!=null ) {
+- GUIBuilder.panelControl.setRootNode(rootNode);
+-
+- try {
+- GUIBuilder.printIOFile();
+- } catch (final IOException e1) {
+- // TODO Auto-generated catch block
+- e1.printStackTrace();
+- } catch (final GUIBuildException e2) {
+- // TODO Auto-generated catch block
+- e2.printStackTrace();
+- }
+- } else if (e.getActionCommand().equals("preview") && GUIBuilder.application!=null) {
+- GUIBuilder.panelControl.setRootNode(rootNode);
+- previewINIFile();
+- } else if (e.getActionCommand().equals("reset") && GUIBuilder.application!=null) {
+- resetGUI();
+- } else if( (e.getActionCommand().equals("open config"))) {
+- openFile();
+- } else if( (e.getActionCommand().equals("open ini"))) {
+- openINIFile();
+- }
+- }
+-
+- public void resetGUI() {
+- try {
+- int returnval = GUIBuilder.closeFile();
+- if (returnval == JOptionPane.CANCEL_OPTION) return;
+- GUIBuilder.buildGUI(GUIBuilder.currentConfigFile);
+- } catch (GUIBuildException e) {
+- e.printStackTrace();
+- }
+- }
+-
+- public void previewINIFile(){
+- JFrame frame = new JFrame();
+- frame.setSize(600,800);
+- frame.setVisible(true);
+- //frame.setLayout(new BorderLayout());
+-
+- JEditorPane pane = new JEditorPane();
+-
+- pane.setText(GUIBuilder.panelControl.toString());
+- pane.setVisible(true);
+- pane.setEditable(false);
+-
+- JScrollPane scrollPane = new JScrollPane(pane);
+- scrollPane.setVisible(true);
+- frame.add(scrollPane);
+-
+- frame.validate();
+- frame.repaint();
+- }
+-
+- public void openINIFile(){
+- final FileNameExtensionFilter inifilter = new FileNameExtensionFilter(".ini files", "ini");
+- final JFileChooser filechooser = new JFileChooser(iniFilePath);
+- filechooser.setFileFilter(inifilter);
+- final int returnval = filechooser.showOpenDialog(new JPanel());
+-
+- HashMap hm = new HashMap();
+- HashMap comments = new HashMap();
+- HashMap added_comments = new HashMap();
+-
+- if (returnval == JFileChooser.APPROVE_OPTION) {
+- final String path = filechooser.getSelectedFile().toString();
+- if (filechooser.getSelectedFile().isDirectory()) return;
+-
+- iniFilePath = filechooser.getSelectedFile().getParent();
+-
+- System.out.println("Opening INI file: " + path);
+-
+- try {
+- BufferedReader br = new BufferedReader(new FileReader(path));
+- String line;
+-
+- String section = "GENERAL::";
+- String clines = "";
+-
+- while((line = br.readLine()) != null) {
+- int offset = line.indexOf(";");
+- int offset2 = line.indexOf("#");
+-
+- if ((offset2 != -1) && (offset != -1)) {
+- if (offset2 < offset) offset = offset2;
+- } else if ((offset2 != -1) && (offset == -1)) {
+- offset = offset2;
+- }
+-
+- String comment = null;
+- //System.out.println("CLINES" + clines);
+- if (offset != -1) {
+- //System.out.println("COMMENT: " + line.substring(offset));
+- comment = line.substring(offset);
+- } else {
+- //System.out.println("COMMENTLESS");
+- }
+-
+- if (-1 != offset) line = line.substring(0, offset);
+-
+- offset = line.indexOf("#");
+- if (-1 != offset) line = line.substring(0, offset);
+-
+- line = line.trim(); //take away ws
+-
+- if (line.length()>1) {
+-
+- if (line.charAt(0) == '[') {
+- offset = line.indexOf("]");
+- if ((offset == -1) || (offset <= 1)) continue;
+-
+- if (!clines.equals("")) {
+- int lbr = clines.indexOf("\n");
+- clines = clines.substring(0, lbr);
+- //System.out.println("Adding the precomment: " + clines);
+- comments.put(section, clines);
+- clines = "";
+- }
+-
+- section = line.substring(1, offset).toUpperCase() + "::";
+- //System.out.println("New Section: " + section);
+-
+- } else {
+- String[] tokens = line.split("=");
+- if (tokens.length == 2) {
+- String key = tokens[0].trim();
+- String value = tokens[1].trim();
+- if (key.length() > 0) {
+- hm.put(section + key.toUpperCase(), value);
+- if (comment != null) added_comments.put(section + key.toUpperCase(), comment);
+- if (!clines.equals("")) {
+- //System.out.println("Adding the precomment: " + clines);
+- comments.put(section + key.toUpperCase(), clines);
+- clines = "";
+- }
+- }
+- }
+- }
+-
+- //System.out.println(line);
+- } else {
+- //it was a comment line only, associate it with the next key
+- if (comment != null) clines += comment;
+- clines += "\n";
+- }
+- }
+- br.close();
+-
+- GUIBuilder.setValues(hm, added_comments, comments);
+- } catch (Exception e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- }
+- }
+-
+- public void openFile(){
+- /* If a configuration is already open, ask for close. */
+- final FileNameExtensionFilter xmlfilter = new FileNameExtensionFilter(".xml files", "xml");
+- final JFileChooser filechooser = new JFileChooser(configFilePath);
+- filechooser.setFileFilter(xmlfilter);
+- final int returnval = filechooser.showOpenDialog(new JPanel());
+- if (returnval == JFileChooser.APPROVE_OPTION) {
+- if(GUIBuilder.application != null){
+- final int returnval2 = GUIBuilder.closeFile();
+- if (returnval2 == JOptionPane.CANCEL_OPTION) return;
+- }
+-
+- final String path = filechooser.getSelectedFile().toString();
+- if (filechooser.getSelectedFile().isDirectory()) return;
+-
+- configFilePath = filechooser.getSelectedFile().getParent();
+-
+- try {
+- GUIBuilder.buildGUI(path);
+- } catch (GUIBuildException e) {
+- // TODO Auto-generated catch block
+- e.printStackTrace();
+- }
+- }
+- }
+-
+- @Override
+- public void windowActivated(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void windowClosed(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void windowClosing(WindowEvent e) {
+- System.exit(NORMAL);
+-
+- }
+-
+- @Override
+- public void windowDeactivated(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void windowDeiconified(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void windowIconified(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void windowOpened(WindowEvent e) {
+- // TODO Auto-generated method stub
+-
+- }
+-
+- @Override
+- public void hyperlinkUpdate(HyperlinkEvent e) {
+-
+- if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+- try {
+- Desktop.getDesktop().browse(e.getURL().toURI());
+- } catch (IOException e1) {
+- // TODO Auto-generated catch block
+- e1.printStackTrace();
+- } catch (URISyntaxException e1) {
+- // TODO Auto-generated catch block
+- e1.printStackTrace();
+- }
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/main/PanelNode.java
+===================================================================
+--- ../trunk-jpl/src/java/src/main/PanelNode.java (revision 18297)
++++ ../trunk-jpl/src/java/src/main/PanelNode.java (revision 18298)
+@@ -1,69 +0,0 @@
+-package main;
+-
+-import java.util.List;
+-import java.util.LinkedList;
+-
+-public class PanelNode {
+- private String data;
+- private PanelNode parent;
+- private LinkedList children = new LinkedList();
+-
+- public PanelNode(String indata) {
+- data = indata;
+- parent = null;
+- }
+-
+- public PanelNode(PanelNode p) {
+- data = p.data;
+- parent = p.parent;
+- children = new LinkedList(p.children);
+- }
+-
+- public String getData() {
+- return data;
+- }
+-
+- public PanelNode getChild(String data) {
+- for (PanelNode child : children) {
+- if (child.data.equals(data))
+- return child;
+- }
+-
+- return null;
+- }
+-
+- public PanelNode add(PanelNode c) {
+- c.parent = this;
+- children.add(c);
+-
+- return children.getLast();
+- }
+-
+- public PanelNode get(String searchstring) {
+- if (data.equals(searchstring)) return this;
+-
+- for (PanelNode child : children) {
+- PanelNode tmp = child.get(searchstring);
+- if (tmp != null) return tmp;
+- }
+-
+- return null; //Nothing found in subtree
+- }
+-
+- public boolean remove(PanelNode tmp) {
+- return children.remove(tmp);
+- }
+-
+- public PanelNode getParent() {
+- return parent;
+- }
+-
+- public void getKeyList(LinkedList keyList) {
+- if ((data.indexOf('#') == -1) && (data.indexOf('%') == -1))
+- keyList.add(data);
+-
+- for (PanelNode child : children) {
+- child.getKeyList(keyList);
+- }
+- }
+-}
+Index: ../trunk-jpl/src/java/src/resources/icons/mydocuments.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/readme.txt
+===================================================================
+--- ../trunk-jpl/src/java/src/resources/icons/readme.txt (revision 18297)
++++ ../trunk-jpl/src/java/src/resources/icons/readme.txt (revision 18298)
+@@ -1,10 +0,0 @@
+-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+-This copyright and license notice covers the images in this directory.
+-************************************************************************
+-
+-TITLE: Crystal Project Icons
+-AUTHOR: Everaldo Coelho
+-SITE: http://www.everaldo.com
+-CONTACT: everaldo@everaldo.com
+-
+-Copyright (c) 2006-2007 Everaldo Coelho.
+Index: ../trunk-jpl/src/java/src/resources/icons/kghostview.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/file_ops.xcf
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/filesave.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/viewmag.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/ini_open.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/fileopen.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/xml_open.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/filesaveas.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/opensettings.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/reset.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/icons/advancedsettings.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/config_schema-0.1.1.xsd
+===================================================================
+--- ../trunk-jpl/src/java/src/resources/config_schema-0.1.1.xsd (revision 18297)
++++ ../trunk-jpl/src/java/src/resources/config_schema-0.1.1.xsd (revision 18298)
+@@ -1,154 +0,0 @@
+-
+-
+-
+-
+-
+-
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+-
+Index: ../trunk-jpl/src/java/src/resources/document-open-2.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/document-preview.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/document-export-4.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/src/resources/config_schema.xsd
+===================================================================
+--- ../trunk-jpl/src/java/src/resources/config_schema.xsd (revision 18297)
++++ ../trunk-jpl/src/java/src/resources/config_schema.xsd (revision 18298)
+@@ -1,141 +0,0 @@
+-
+-
+-
+-
+-
+-
+-
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+-
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+-
+Index: ../trunk-jpl/src/java/src/resources/default_config.xml
+===================================================================
+--- ../trunk-jpl/src/java/src/resources/default_config.xml (revision 18297)
++++ ../trunk-jpl/src/java/src/resources/default_config.xml (revision 18298)
+@@ -1,919 +0,0 @@
+-
+-
+-
+-
+-
+- Size in days of a chunk of data to read at once.
+-
+-
+-
+-
+- Alternate way of buffer centering: When rebuffering, the new date will be located BUFF_BEFORE days from the
+- beginning of the buffer (therefore, it takes a value in days).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- coordinate system
+-
+-
+-
+-
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+-
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+-
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+-
+-
+-
+-
+-
+-
+- plugin for METEO data
+-
+-
+-
+-
+-
+- The name of the parameter to copy (e.g. TA, RH, VW, ISWR, etc)
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for Digital Elevation Model data
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for land cover data
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- plugin for 2D gridded data
+-
+-
+-
+-
+-
+- filename for station number #
+-
+-
+-
+-
+- station id for the given station number #
+-
+-
+-
+-
+- Coordinates are given as "lat lon" or "xcoord ycoord epsg_code"
+-
+-
+-
+-
+-
+-
+- string containing the path to the xml files
+-
+-
+-
+-
+-
+-
+- database name, as provided by your database administrator
+-
+-
+- database user name
+-
+-
+- database password associated with the user name
+-
+-
+-
+-
+- OPTIONAL: use ANETZ stations to provide precipitations for normal IMIS stations.
+- Each IMIS station is associated with one or two ANETZ stations and does a weighted
+- average to get what should be its local precipitations
+-
+-
+-
+-
+- OPTIONAL: if set to false (default), all IMIS precipitation will be deleted (since IMIS stations don't have heated rain gauges, their precipitation measurements are not good in winter conditions). If set to true, it is strongly advised to use a FilterHNWMelt filter to detect snow melting in the rain gauge and perform winter conditions detection in the application.
+-
+-
+-
+-
+- if set to true, the SNOWPACK simulated Snow Water Equivalent from the database will be used to compute HNW. Data gaps greater than 3 hours on SWE will lead to unchanged hnw while all data that can properly be computed will overwrite hnw. (default=false)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the grib files
+-
+-
+- grib file extension, or none for no file extension (default: .grb)
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the data files
+-
+-
+- absolute filename of the geotop.inpts file
+-
+-
+- prefix to append when generating a file name for reading
+-
+-
+-
+-
+-
+- string containing the path to the data files
+-
+-
+- specifiy in which order the columns should be printed out
+-
+-
+-
+-
+-
+- webserver running GSN with its port number and full path. For example:
+- http://montblanc.slf.ch:22001/services/A3DWebService
+-
+-
+- Should the connection go through a proxy? This is useful for servers
+- filtering on domains but usually not necessary.
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the smet files
+-
+-
+-
+-
+-
+-
+- string representing path where SMET files should be saved
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- string containing the path to the SNOWPACK files
+-
+-
+- filename of the meta data file (in METEOPATH)
+-
+-
+-
+- the number of measured snow temperatures provided
+-
+-
+-
+- the number of solutes for which input data are provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- OPTIONAL: wind velocity to use for blowing and drifting snow is provided
+-
+-
+-
+-
+- OPTIONAL: measured new snow density is provided
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- generate names compatible with Alpine3D's grid viewer?
+-
+-
+- grid file extension, or none for no file extension (default: .asc)
+-
+-
+-
+-
+-
+- x coordinate of the lower left corner of the grids
+-
+-
+- y coordinate of the lower left corner of the grids
+-
+-
+- grid file extension, or none for no file extension (default: .asc)
+-
+-
+-
+-
+-
+- prefix to append when generating a file name for reading (ie: something like "laf" for Cosmo-Analysis-full domain)
+-
+-
+- grib file extension, or none for no file extension (default: .grb)
+-
+-
+-
+-
+-
+-
+-
+- generate a world file for each output file? This file contains the geolocalization information
+-
+-
+-
+-
+- generate a legend?
+-
+-
+-
+-
+- autoscale color scale?
+-
+-
+-
+-
+- scaling algorithm (default=bilinear)
+-
+-
+- minimum dimensions of the PNG, like 640x480
+-
+-
+- maximum dimensions of the PNG, like 1024x768
+-
+-
+-
+-
+- generate a color indexed file (default=true)
+-
+-
+-
+-
+- optimize for speed (default=false)
+-
+-
+- number of colors in the palette (default=30)
+-
+-
+-
+-
+-
+- lower left x coordinate
+-
+-
+- lower left y coordinate
+-
+-
+- cellsize in meters
+-
+-
+- minimum value in real world coordinates to match with the minimum value read out of the PGM file (such minimum being greater than 0 because 0 is NODATA)
+-
+-
+- maximum value in real world coordinates to match with the maximum value read out of the PGM file
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Mean average processing. The mean average filter returns the mean value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median average processing. The median average filter returns the median value of all values within a user given time window.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Standard deviation filter. Values outside of mean ± 2 std_dev are rejected.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Median Absolute Deviation. Values outside of median ± 3 σ_MAD are rejected. <br>
+- See http://en.wikipedia.org/wiki/Median_absolute_deviation for more information.
+-
+-
+-
+-
+-
+-
+- The keyword "soft" maybe added, if the window position is allowed to be adjusted to the data present.
+- The two arguments may be preceded by the keywords "left", "center" or "right", indicating the window position.
+-
+-
+- Tukey 53H method A smooth time sequence is generated from the median, substracted from the original signal and
+- compared with the standard deviation. see "Despiking Acoustic Doppler Velocimeter Data", Derek G. Goring and Vladimir
+- L. Nikora, Journal of Hydraulic Engineering, 128, 1, 2002 The deviation factor coeffecient is currently hard-coded as k=1.5.
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+-
+-
+- Wind vector averaging. This calculates the vector average over a user given time period. Each wind vector
+- within this period is added and the final sum is normalized by the number of vectors that have been added.
+-
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Alpha needs to be provided as last argument. Please note that the standard filter works with a left window!
+-
+-
+- Exponential smooting processing, exponential moving average s_0 = x_0 s_n = alpha*x_(t-1) + (1-alpha)*s_t-1
+-
+-
+-
+-
+-
+-
+- Activate "soft" if the window position is allowed to be adjusted, window position maybe left, center or right.
+- Minimal number of points in window and minimal time interval spanning the window (seconds) are required.
+- Please note that the standard filter works with a left window!
+-
+-
+- Weighted moving average smoothing such as: WMA = (1*X1 + 2*X2 + ... + n*Xn) / sum_of_weights
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- This implements the standard methods for precipitation correction as described in "WMO Solid Precipitation Measurement Intercomparison", B. Goodison, P. Louie and D. Yang, 872, 1998 as well as the overview given by "Literature Study on the Correction of Precipitation Measurements", Annette Wagner, 2009. The correction parameters for the shielded Hellmann gauge (German version) are from "Wind-induced Precipitation Undercatch of the Hellmann Gauges", Daqing Yang et al, Nordic Hydrology, 30, 1999, pp 57-80.
+-
+-
+-
+-
+-
+-
+- This applies a constant correction factor to the precipitation, one for pure snow and one for mixed precipitation. The following thresholds are used: pure snow below -2 C; mixed precipitation between -2 and +2 C; pure rain above 2 C. These threshold can be changed (see online documentation).
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Affects resampling: expresses (in seconds) how far a valid point can be
+- searched for when re-interpolating a missing value
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- Detrend the measured data, fill the grid with the average over all the stations, reapply the elevation trend
+-
+-
+-
+-
+- Detrend the measured data, apply Inverse Distance Weighted average, reapply elevation trend
+-
+-
+-
+- Same as IDW_LAPSE, but only considering a given number of neighboring stations
+-
+-
+-
+-
+-
+- Base algorithm (do not forget to add the options for the base algorithm)
+-
+- Distribute precipitation with a base algorithm (IDW_LAPSE by default), then reduce/remove precipitation on
+- steep slopes and correct with the local curvature. This is to simulate snow redistribution processes.
+-
+-
+-
+- Variogram model
+-
+- Ordinary kriging (EXPERIMENTAL)
+-
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/COPYING
+===================================================================
+--- ../trunk-jpl/src/java/COPYING (revision 18297)
++++ ../trunk-jpl/src/java/COPYING (revision 18298)
+@@ -1,674 +0,0 @@
+- GNU GENERAL PUBLIC LICENSE
+- Version 3, 29 June 2007
+-
+- Copyright (C) 2007 Free Software Foundation, Inc.
+- Everyone is permitted to copy and distribute verbatim copies
+- of this license document, but changing it is not allowed.
+-
+- Preamble
+-
+- The GNU General Public License is a free, copyleft license for
+-software and other kinds of works.
+-
+- The licenses for most software and other practical works are designed
+-to take away your freedom to share and change the works. By contrast,
+-the GNU General Public License is intended to guarantee your freedom to
+-share and change all versions of a program--to make sure it remains free
+-software for all its users. We, the Free Software Foundation, use the
+-GNU General Public License for most of our software; it applies also to
+-any other work released this way by its authors. You can apply it to
+-your programs, too.
+-
+- When we speak of free software, we are referring to freedom, not
+-price. Our General Public Licenses are designed to make sure that you
+-have the freedom to distribute copies of free software (and charge for
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+-
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+-these rights or asking you to surrender the rights. Therefore, you have
+-certain responsibilities if you distribute copies of the software, or if
+-you modify it: responsibilities to respect the freedom of others.
+-
+- For example, if you distribute copies of such a program, whether
+-gratis or for a fee, you must pass on to the recipients the same
+-freedoms that you received. You must make sure that they, too, receive
+-or can get the source code. And you must show them these terms so they
+-know their rights.
+-
+- Developers that use the GNU GPL protect your rights with two steps:
+-(1) assert copyright on the software, and (2) offer you this License
+-giving you legal permission to copy, distribute and/or modify it.
+-
+- For the developers' and authors' protection, the GPL clearly explains
+-that there is no warranty for this free software. For both users' and
+-authors' sake, the GPL requires that modified versions be marked as
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+-authors of previous versions.
+-
+- Some devices are designed to deny users access to install or run
+-modified versions of the software inside them, although the manufacturer
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+-pattern of such abuse occurs in the area of products for individuals to
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+- The precise terms and conditions for copying, distribution and
+-modification follow.
+-
+- TERMS AND CONDITIONS
+-
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+- "This License" refers to version 3 of the GNU General Public License.
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+-
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+-to the extent that it includes a convenient and prominently visible
+-feature that (1) displays an appropriate copyright notice, and (2)
+-tells the user that there is no warranty for the work (except to the
+-extent that warranties are provided), that licensees may convey the
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+- author attributions in that material or in the Appropriate Legal
+- Notices displayed by works containing it; or
+-
+- c) Prohibiting misrepresentation of the origin of that material, or
+- requiring that modified versions of such material be marked in
+- reasonable ways as different from the original version; or
+-
+- d) Limiting the use for publicity purposes of names of licensors or
+- authors of the material; or
+-
+- e) Declining to grant rights under trademark law for use of some
+- trade names, trademarks, or service marks; or
+-
+- f) Requiring indemnification of licensors and authors of that
+- material by anyone who conveys the material (or modified versions of
+- it) with contractual assumptions of liability to the recipient, for
+- any liability that these contractual assumptions directly impose on
+- those licensors and authors.
+-
+- All other non-permissive additional terms are considered "further
+-restrictions" within the meaning of section 10. If the Program as you
+-received it, or any part of it, contains a notice stating that it is
+-governed by this License along with a term that is a further
+-restriction, you may remove that term. If a license document contains
+-a further restriction but permits relicensing or conveying under this
+-License, you may add to a covered work material governed by the terms
+-of that license document, provided that the further restriction does
+-not survive such relicensing or conveying.
+-
+- If you add terms to a covered work in accord with this section, you
+-must place, in the relevant source files, a statement of the
+-additional terms that apply to those files, or a notice indicating
+-where to find the applicable terms.
+-
+- Additional terms, permissive or non-permissive, may be stated in the
+-form of a separately written license, or stated as exceptions;
+-the above requirements apply either way.
+-
+- 8. Termination.
+-
+- You may not propagate or modify a covered work except as expressly
+-provided under this License. Any attempt otherwise to propagate or
+-modify it is void, and will automatically terminate your rights under
+-this License (including any patent licenses granted under the third
+-paragraph of section 11).
+-
+- However, if you cease all violation of this License, then your
+-license from a particular copyright holder is reinstated (a)
+-provisionally, unless and until the copyright holder explicitly and
+-finally terminates your license, and (b) permanently, if the copyright
+-holder fails to notify you of the violation by some reasonable means
+-prior to 60 days after the cessation.
+-
+- Moreover, your license from a particular copyright holder is
+-reinstated permanently if the copyright holder notifies you of the
+-violation by some reasonable means, this is the first time you have
+-received notice of violation of this License (for any work) from that
+-copyright holder, and you cure the violation prior to 30 days after
+-your receipt of the notice.
+-
+- Termination of your rights under this section does not terminate the
+-licenses of parties who have received copies or rights from you under
+-this License. If your rights have been terminated and not permanently
+-reinstated, you do not qualify to receive new licenses for the same
+-material under section 10.
+-
+- 9. Acceptance Not Required for Having Copies.
+-
+- You are not required to accept this License in order to receive or
+-run a copy of the Program. Ancillary propagation of a covered work
+-occurring solely as a consequence of using peer-to-peer transmission
+-to receive a copy likewise does not require acceptance. However,
+-nothing other than this License grants you permission to propagate or
+-modify any covered work. These actions infringe copyright if you do
+-not accept this License. Therefore, by modifying or propagating a
+-covered work, you indicate your acceptance of this License to do so.
+-
+- 10. Automatic Licensing of Downstream Recipients.
+-
+- Each time you convey a covered work, the recipient automatically
+-receives a license from the original licensors, to run, modify and
+-propagate that work, subject to this License. You are not responsible
+-for enforcing compliance by third parties with this License.
+-
+- An "entity transaction" is a transaction transferring control of an
+-organization, or substantially all assets of one, or subdividing an
+-organization, or merging organizations. If propagation of a covered
+-work results from an entity transaction, each party to that
+-transaction who receives a copy of the work also receives whatever
+-licenses to the work the party's predecessor in interest had or could
+-give under the previous paragraph, plus a right to possession of the
+-Corresponding Source of the work from the predecessor in interest, if
+-the predecessor has it or can get it with reasonable efforts.
+-
+- You may not impose any further restrictions on the exercise of the
+-rights granted or affirmed under this License. For example, you may
+-not impose a license fee, royalty, or other charge for exercise of
+-rights granted under this License, and you may not initiate litigation
+-(including a cross-claim or counterclaim in a lawsuit) alleging that
+-any patent claim is infringed by making, using, selling, offering for
+-sale, or importing the Program or any portion of it.
+-
+- 11. Patents.
+-
+- A "contributor" is a copyright holder who authorizes use under this
+-License of the Program or a work on which the Program is based. The
+-work thus licensed is called the contributor's "contributor version".
+-
+- A contributor's "essential patent claims" are all patent claims
+-owned or controlled by the contributor, whether already acquired or
+-hereafter acquired, that would be infringed by some manner, permitted
+-by this License, of making, using, or selling its contributor version,
+-but do not include claims that would be infringed only as a
+-consequence of further modification of the contributor version. For
+-purposes of this definition, "control" includes the right to grant
+-patent sublicenses in a manner consistent with the requirements of
+-this License.
+-
+- Each contributor grants you a non-exclusive, worldwide, royalty-free
+-patent license under the contributor's essential patent claims, to
+-make, use, sell, offer for sale, import and otherwise run, modify and
+-propagate the contents of its contributor version.
+-
+- In the following three paragraphs, a "patent license" is any express
+-agreement or commitment, however denominated, not to enforce a patent
+-(such as an express permission to practice a patent or covenant not to
+-sue for patent infringement). To "grant" such a patent license to a
+-party means to make such an agreement or commitment not to enforce a
+-patent against the party.
+-
+- If you convey a covered work, knowingly relying on a patent license,
+-and the Corresponding Source of the work is not available for anyone
+-to copy, free of charge and under the terms of this License, through a
+-publicly available network server or other readily accessible means,
+-then you must either (1) cause the Corresponding Source to be so
+-available, or (2) arrange to deprive yourself of the benefit of the
+-patent license for this particular work, or (3) arrange, in a manner
+-consistent with the requirements of this License, to extend the patent
+-license to downstream recipients. "Knowingly relying" means you have
+-actual knowledge that, but for the patent license, your conveying the
+-covered work in a country, or your recipient's use of the covered work
+-in a country, would infringe one or more identifiable patents in that
+-country that you have reason to believe are valid.
+-
+- If, pursuant to or in connection with a single transaction or
+-arrangement, you convey, or propagate by procuring conveyance of, a
+-covered work, and grant a patent license to some of the parties
+-receiving the covered work authorizing them to use, propagate, modify
+-or convey a specific copy of the covered work, then the patent license
+-you grant is automatically extended to all recipients of the covered
+-work and works based on it.
+-
+- A patent license is "discriminatory" if it does not include within
+-the scope of its coverage, prohibits the exercise of, or is
+-conditioned on the non-exercise of one or more of the rights that are
+-specifically granted under this License. You may not convey a covered
+-work if you are a party to an arrangement with a third party that is
+-in the business of distributing software, under which you make payment
+-to the third party based on the extent of your activity of conveying
+-the work, and under which the third party grants, to any of the
+-parties who would receive the covered work from you, a discriminatory
+-patent license (a) in connection with copies of the covered work
+-conveyed by you (or copies made from those copies), or (b) primarily
+-for and in connection with specific products or compilations that
+-contain the covered work, unless you entered into that arrangement,
+-or that patent license was granted, prior to 28 March 2007.
+-
+- Nothing in this License shall be construed as excluding or limiting
+-any implied license or other defenses to infringement that may
+-otherwise be available to you under applicable patent law.
+-
+- 12. No Surrender of Others' Freedom.
+-
+- If conditions are imposed on you (whether by court order, agreement or
+-otherwise) that contradict the conditions of this License, they do not
+-excuse you from the conditions of this License. If you cannot convey a
+-covered work so as to satisfy simultaneously your obligations under this
+-License and any other pertinent obligations, then as a consequence you may
+-not convey it at all. For example, if you agree to terms that obligate you
+-to collect a royalty for further conveying from those to whom you convey
+-the Program, the only way you could satisfy both those terms and this
+-License would be to refrain entirely from conveying the Program.
+-
+- 13. Use with the GNU Affero General Public License.
+-
+- Notwithstanding any other provision of this License, you have
+-permission to link or combine any covered work with a work licensed
+-under version 3 of the GNU Affero General Public License into a single
+-combined work, and to convey the resulting work. The terms of this
+-License will continue to apply to the part which is the covered work,
+-but the special requirements of the GNU Affero General Public License,
+-section 13, concerning interaction through a network will apply to the
+-combination as such.
+-
+- 14. Revised Versions of this License.
+-
+- The Free Software Foundation may publish revised and/or new versions of
+-the GNU General Public License from time to time. Such new versions will
+-be similar in spirit to the present version, but may differ in detail to
+-address new problems or concerns.
+-
+- Each version is given a distinguishing version number. If the
+-Program specifies that a certain numbered version of the GNU General
+-Public License "or any later version" applies to it, you have the
+-option of following the terms and conditions either of that numbered
+-version or of any later version published by the Free Software
+-Foundation. If the Program does not specify a version number of the
+-GNU General Public License, you may choose any version ever published
+-by the Free Software Foundation.
+-
+- If the Program specifies that a proxy can decide which future
+-versions of the GNU General Public License can be used, that proxy's
+-public statement of acceptance of a version permanently authorizes you
+-to choose that version for the Program.
+-
+- Later license versions may give you additional or different
+-permissions. However, no additional obligations are imposed on any
+-author or copyright holder as a result of your choosing to follow a
+-later version.
+-
+- 15. Disclaimer of Warranty.
+-
+- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+-
+- 16. Limitation of Liability.
+-
+- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+-SUCH DAMAGES.
+-
+- 17. Interpretation of Sections 15 and 16.
+-
+- If the disclaimer of warranty and limitation of liability provided
+-above cannot be given local legal effect according to their terms,
+-reviewing courts shall apply local law that most closely approximates
+-an absolute waiver of all civil liability in connection with the
+-Program, unless a warranty or assumption of liability accompanies a
+-copy of the Program in return for a fee.
+-
+- END OF TERMS AND CONDITIONS
+-
+- How to Apply These Terms to Your New Programs
+-
+- If you develop a new program, and you want it to be of the greatest
+-possible use to the public, the best way to achieve this is to make it
+-free software which everyone can redistribute and change under these terms.
+-
+- To do so, attach the following notices to the program. It is safest
+-to attach them to the start of each source file to most effectively
+-state the exclusion of warranty; and each file should have at least
+-the "copyright" line and a pointer to where the full notice is found.
+-
+-
+- Copyright (C)
+-
+- This program is free software: you can redistribute it and/or modify
+- it under the terms of the GNU General Public License as published by
+- the Free Software Foundation, either version 3 of the License, or
+- (at your option) any later version.
+-
+- This program is distributed in the hope that it will be useful,
+- but WITHOUT ANY WARRANTY; without even the implied warranty of
+- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+- GNU General Public License for more details.
+-
+- You should have received a copy of the GNU General Public License
+- along with this program. If not, see .
+-
+-Also add information on how to contact you by electronic and paper mail.
+-
+- If the program does terminal interaction, make it output a short
+-notice like this when it starts in an interactive mode:
+-
+- Copyright (C)
+- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+- This is free software, and you are welcome to redistribute it
+- under certain conditions; type `show c' for details.
+-
+-The hypothetical commands `show w' and `show c' should show the appropriate
+-parts of the General Public License. Of course, your program's commands
+-might be different; for a GUI interface, you would use an "about box".
+-
+- You should also get your employer (if you work as a programmer) or school,
+-if any, to sign a "copyright disclaimer" for the program, if necessary.
+-For more information on this, and how to apply and follow the GNU GPL, see
+-.
+-
+- The GNU General Public License does not permit incorporating your program
+-into proprietary programs. If your program is a subroutine library, you
+-may consider it more useful to permit linking proprietary applications with
+-the library. If this is what you want to do, use the GNU Lesser General
+-Public License instead of this License. But first, please read
+-.
+Index: ../trunk-jpl/src/java/build.xml
+===================================================================
+--- ../trunk-jpl/src/java/build.xml (revision 18297)
++++ ../trunk-jpl/src/java/build.xml (revision 18298)
+@@ -1,126 +0,0 @@
+-
+-
+- Build and run the inishell Application from the command line.
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- You can use the following targets:
+-
+- help : (default) Prints this message
+- init : create necessary directories
+- clean : Deletes work directories
+- compile : Compiles into class files
+- dist : pack all necessary files into a JAR file
+- issm : create inishell GUI using issm.xml
+- snowpack : dist tailored for snowpack
+- meteoio : dist tailored for meteoio
+- run : run the previously compiled version
+- pack : pack all in a zip file for a release
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
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+-
+-
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+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+Index: ../trunk-jpl/src/java/build/resources/document-open-2.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/document-preview.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/document-export-4.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/config_schema.xsd
+===================================================================
+--- ../trunk-jpl/src/java/build/resources/config_schema.xsd (revision 18297)
++++ ../trunk-jpl/src/java/build/resources/config_schema.xsd (revision 18298)
+@@ -1,141 +0,0 @@
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
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+-
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+-
+-
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+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+Index: ../trunk-jpl/src/java/build/resources/default_config.xml
+===================================================================
+--- ../trunk-jpl/src/java/build/resources/default_config.xml (revision 18297)
++++ ../trunk-jpl/src/java/build/resources/default_config.xml (revision 18298)
+@@ -1,1284 +0,0 @@
+-
+-
+-
+-
+-
+-
+-
+- select a mesh dimension 0(default) or 3
+-
+-
+-
+-
+-
+- number of elements
+-
+-
+-
+- number of verticies
+-
+-
+-
+- vertex indices of the mesh elements
+-
+-
+-
+- vertices x coordinate [m]
+-
+-
+-
+- vertices y coordinate [m]
+-
+-
+-
+- vertices z coordinate [m]
+-
+-
+-
+- edges of the 2d mesh (vertex1 vertex2 element1 element2)
+-
+-
+-
+- number of edges of the 2d mesh
+-
+-
+-
+-
+-
+-
+- mesh dimension
+-
+-
+-
+- number of extrusion layers
+-
+-
+-
+- lower vertices flags list
+-
+-
+-
+- lower elements flags list
+-
+-
+-
+- upper vertices flags list
+-
+-
+-
+- upper element flag list
+-
+-
+-
+- upper vertex list (NaN for vertex on the upper surface)
+-
+-
+-
+- upper element list (NaN for element on the upper layer)
+-
+-
+-
+- lower vertex list (NaN for vertex on the lower surface)
+-
+-
+-
+- lower element list (NaN for element on the lower layer
+-
+-
+-
+- vertices on the boundary of the domain flag list
+-
+-
+-
+- edges on domain boundary (vertex1 vertex2 element)
+-
+-
+-
+- number associated to each segment
+-
+-
+-
+- list of vertices connected to vertex_i
+-
+-
+-
+- list of vertices connected to element_i
+-
+-
+-
+- average number of vertices connected to one vertex
+-
+-
+-
+-
+-
+-
+- vertices extracted from the model
+-
+-
+-
+- elements extracted from the model
+-
+-
+-
+-
+-
+-
+- vertices latitude [degrees]
+-
+-
+-
+- verticies longitude [degrees]
+-
+-
+-
+- Indicate hemisphere 'n' or 's'
+-
+-
+-
+-
+-
+-
+- is ice grounded ? grounded ice if > 0, grounding line position if = 0, floating ice if < 0
+-
+-
+-
+- presence of ice if > 0, icefront position if = 0, no ice if < 0
+-
+-
+-
+-
+-
+-
+-
+- surface elevation [m]
+-
+-
+-
+- ice thickness [m]
+-
+-
+-
+- bed elevation [m]
+-
+-
+-
+- bathymetry elevation [m]
+-
+-
+-
+- coefficient for ice shelves; thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro
+-
+-
+-
+-
+-
+-
+- gravitational acceleration [m/s^2]
+-
+-
+-
+- number of seconds in a year [s/yr]
+-
+-
+-
+- reference temperature used in the enthalpy model [K]
+-
+-
+-
+-
+-
+- surface mass balance [m/yr ice eq]
+-
+-
+-
+-
+-
+- basal melting rate (positive if melting) [m/yr]
+-
+-
+-
+- additional melting applied to compensate for dh/dt [m/yr]
+-
+-
+-
+- geothermal heat flux [W/m^2]
+-
+-
+-
+-
+-
+- ice density [kg/m^3]
+-
+-
+-
+- ocean water density [kg/m^3]
+-
+-
+-
+- fresh water density [kg/m^3]
+-
+-
+-
+- water viscosity [N s/m^2]
+-
+-
+-
+- heat capacity [J/kg/K]
+-
+-
+-
+- latent heat of fusion [J/kg]
+-
+-
+-
+- ice thermal conductivity [W/m/K]
+-
+-
+-
+- temperate ice thermal conductivity [W/m/K]
+-
+-
+-
+- melting point of ice at 1atm in K
+-
+-
+-
+- rate of change of melting point with pressure [K/Pa]
+-
+-
+-
+- mixed layer capacity [W/kg/K]
+-
+-
+-
+- thermal exchange velocity [m/s]
+-
+-
+-
+- flow law parameter [Pa/s^(1/n)]
+-
+-
+-
+- Glens flow law exponent
+-
+-
+-
+- law for the temperature dependance of the rheology: "None", "Paterson", "Arrhenius" or "LliboutryDuval"
+-
+-
+-
+- Lithosphere shear modulus [Pa]
+-
+-
+-
+- Lithosphere density [g/cm^-3]
+-
+-
+-
+- Mantle shear modulus [Pa]
+-
+-
+-
+- Mantle density [g/cm^-3]
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- damage law (string) from {"undamaged","pralong"}
+-
+-
+-
+- damage tensor (scalar)
+-
+-
+-
+- damage law (string) from {"undamaged","pralong"}
+-
+-
+-
+- damage constraints (NaN means no constraint)
+-
+-
+-
+- maximum possible damage (0<=max_damage<1)
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: SUPG
+-
+-
+-
+- maximum number of non linear iterations
+-
+-
+-
+- stabilize unstable damage constraints that keep zigzagging after n iteration (default is 0, no stabilization)
+-
+-
+-
+- threshold to declare convergence of damage evolution solution (default is 0)
+-
+-
+-
+- scaling exponent (default is 3)
+-
+-
+-
+-
+-
+-
+-
+-
+- friction coefficient [SI]
+-
+-
+-
+- p exponent
+-
+-
+-
+- q exponent
+-
+-
+-
+-
+-
+-
+-
+-
+- is the Shallow Ice Approximation (SIA) used ?
+-
+-
+-
+- is the Shelfy-Stream Approximation (SSA) used ?
+-
+-
+-
+- is the L1L2 approximation used ?
+-
+-
+-
+- is the Higher-Order (HO) approximation used ?
+-
+-
+-
+- are the Full-FS (FS) equations used ?
+-
+-
+-
+- Finite Element for SSA "P1", "P1bubble" "P1bubblecondensed" "P2"
+-
+-
+-
+- Finite Element for HO "P1" "P1bubble" "P1bubblecondensed" "P1xP2" "P2xP1" "P2"
+-
+-
+-
+- Finite Element for FS "P1P1" (debugging only) "P1P1GLS" "MINIcondensed" "MINI" "TaylorHood"
+-
+-
+-
+- flow equation for each vertex
+-
+-
+-
+- flow equation for each element
+-
+-
+-
+- vertices on SSAs border (for tiling)
+-
+-
+-
+- vertices on HOs border (for tiling)
+-
+-
+-
+- vertices on FS border (for tiling)
+-
+-
+-
+-
+-
+-
+- simulation starting time [yr]
+-
+-
+-
+- final time to stop the simulation [yr]
+-
+-
+-
+- length of time steps [yr]
+-
+-
+-
+- use cfl condition to define time step ? (0 or 1)
+-
+-
+-
+- coefficient applied to cfl condition
+-
+-
+-
+-
+-
+-
+-
+-
+- x component of velocity [m/yr]
+-
+-
+-
+- y component of velocity [m/yr]
+-
+-
+-
+- z component of velocity [m/yr]
+-
+-
+-
+- velocity norm [m/yr]
+-
+-
+-
+- pressure field [Pa]
+-
+-
+-
+- fraction of water in the ice
+-
+-
+-
+- ice thickness [m]
+-
+-
+-
+- sediment water head of subglacial system [m]
+-
+-
+-
+- epl water head of subglacial system [m]
+-
+-
+-
+- thickness of subglacial water [m]
+-
+-
+-
+-
+-
+-
+- structure containing all rift information (vertices coordinates, segments, type of melange, ...)
+-
+-
+-
+- N/A
+-
+-
+-
+-
+-
+-
+-
+- use Valgrind to debug (0 or 1)
+-
+-
+-
+-
+- use gnu-profiler to find out where the time is spent
+-
+-
+-
+-
+- enables profiling (memory, flops, time)
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- results are output for all the nodes of each element
+-
+-
+-
+- I/O gathering strategy for result outputs (default 1)
+-
+-
+-
+- is the memory limited ? (0 or 1)
+-
+-
+-
+- frequency at which results are saved in all solutions with multiple time_steps
+-
+-
+-
+- maximum number of minutes to wait for batch results (NaN to deactivate)
+-
+-
+-
+- server hostname where model should be uploaded
+-
+-
+-
+- path on server where model should be uploaded
+-
+-
+-
+- server login
+-
+-
+-
+- port login (default is 0)
+-
+-
+-
+- unique id generated when uploading the file to server
+-
+-
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+- N/A
+-
+-
+-
+-
+-
+- thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- ice thickening rate used in the mass conservation (dh/dt) [m/yr]
+-
+-
+-
+- 0: None, 1: SU, 2: SSAs artificial diffusivity, 3:DG
+-
+-
+-
+-
+-
+-
+-
+- mechanical equilibrium residual convergence criterion
+-
+-
+-
+- velocity relative convergence criterion, NaN: not applied
+-
+-
+-
+- velocity absolute convergence criterion, NaN: not applied
+-
+-
+-
+- 0: Picards fixed point, 1: Newtons method, 2: hybrid
+-
+-
+-
+- maximum number of nonlinear iterations
+-
+-
+-
+- over-shooting constant new=new+C*(new-old)
+-
+-
+-
+-
+-
+-
+- x-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+- y-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+- z-axis velocity constraint (NaN means no constraint) [m/yr]
+-
+-
+-
+-
+-
+-
+- threshold for instability of mechanical constraints
+-
+-
+-
+- number of iterations before rift penalties are locked
+-
+-
+-
+-
+-
+-
+- use dampening for floating ice ? Only for FS model
+-
+-
+-
+- multiplier for incompressibility equation. Only for FS model
+-
+-
+-
+- local referential
+-
+-
+-
+- loading force applied on each point [N/m^3]
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- type of grounding line migration: "SoftMigration","AgressiveMigration" or "None"
+-
+-
+-
+- melting rate applied when previously grounded parts start floating [m/yr]
+-
+-
+-
+-
+-
+-
+-
+-
+- water thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- Manning roughness coefficient
+-
+-
+-
+- tortuosity parameter
+-
+-
+-
+- dimensionless exponent in Manning velocity formula
+-
+-
+-
+- dimensionless exponent in Manning velocity formula
+-
+-
+-
+- parameter in effective pressure formula
+-
+-
+-
+- artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.
+-
+-
+-
+-
+-
+-
+-
+- thickness constraints (NaN means no constraint) [m]
+-
+-
+-
+- calving rate at given location [m/a]
+-
+-
+-
+- do we use free surfaces (FS only) are mass conservation
+-
+-
+-
+- minimum ice thickness allowed [m]
+-
+-
+-
+- adjustment of ice shelves surface and bed elevations: 'Incremental' or 'Absolute'
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin
+-
+-
+-
+-
+-
+-
+- offset used by penalties: penalty = Kmax*10^offset
+-
+-
+-
+- pairs of vertices that are penalized
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- temperature constraints (NaN means no constraint) [K]
+-
+-
+-
+- 0: no, 1: artificial_diffusivity, 2: SUPG
+-
+-
+-
+- maximum number of non linear iterations
+-
+-
+-
+- stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)
+-
+-
+-
+- threshold to declare convergence of thermal solution (default is 0)
+-
+-
+-
+- scaling exponent (default is 3)
+-
+-
+-
+- use an enthalpy formulation to include temperate ice (default is 0)
+-
+-
+-
+- enable dynamic setting of basal forcing. required for enthalpy formulation (default is 0)
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- relative tolerance criterion [K]
+-
+-
+-
+- maximum number of iterations
+-
+-
+-
+- additional requested outputs
+-
+-
+-
+-
+-
+-
+-
+- indicates whether a masstransport solution is used in the transient
+-
+-
+-
+- indicates whether a stressbalance solution is used in the transient
+-
+-
+-
+- indicates whether a thermal solution is used in the transient
+-
+-
+-
+- indicates whether a groundingline migration is used in the transient
+-
+-
+-
+- indicates whether a postglacial rebound model is used in the transient
+-
+-
+-
+- indicates whether damage evolution is used in the transient
+-
+-
+-
+- LEVEL SET DESCRIPTION...
+-
+-
+-
+- list of additional outputs requested
+-
+-
+-
+-
+-
+-
+-
+- mantle viscosity[Pa s]
+-
+-
+-
+- lithosphere thickness (km)
+-
+-
+-
+- 1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore
+-
+-
+-
+-
+-
+-
+-
+-
+- indicates if the automatic differentiation is activated
+-
+-
+-
+- list of dependent variables
+-
+-
+-
+- list of independent variables
+-
+-
+-
+- ADOLC driver ('fos_forward' or 'fov_forward')
+-
+-
+-
+- Number of operations per buffer (==OBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of locations per buffer (==LBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of values per buffer (==CBUFSIZE in usrparms.h)
+-
+-
+-
+- Number of taylors per buffer (<=TBUFSIZE in usrparms.h)
+-
+-
+-
+- free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio
+-
+-
+-
+- free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize
+-
+-
+-
+-
+-
+-
+-
+- name of kml output targets file
+-
+-
+-
+- name of kml input tracks file
+-
+-
+-
+- structure of kml flight requirements (not used yet)
+-
+-
+-
+- element or nodal criterion for flight path evaluation (metric)
+-
+-
+-
+-
+-
+-
+- number of grids at equator (determines resolution)
+-
+-
+-
+-
+- flag to consider target values for flight path evaluation
+-
+-
+-
+-
+- flag to split polygons on the antimeridian
+-
+-
+-
+-
+-
+-
+-
+- optimize? (default false)
+-
+-
+-
+- number of directions to test when moving a point. If this value = 1, a random direction is tested. A value > 1 results in directions equally spaced from [0, 2*PI] being tested. For example, 4 would result in directions [0, PI/2, PI, 3PI/2]
+-
+-
+-
+- specifies the distance in km (default 25) to move a randomly selected path point on each iteration
+-
+-
+-
+- number of iterations (default 30,000) to run for flightplan optimization, i.e. the number of times to randomly select a point and move it.
+-
+-
+-
+-
+-
+-
+- name of kml solution file
+-
+-
+-
+- quality of kml solution
+-
+-
+-
+-
+-
+-
+-
+- is inversion activated?
+-
+-
+-
+- 1: linear viscosity, 0: non-linear viscosity
+-
+-
+-
+- ex: {'FrictionCoefficient'}, or {'MaterialsRheologyBbar'}
+-
+-
+-
+- number of optimization searches
+-
+-
+-
+- indicate the type of response for each optimization step
+-
+-
+-
+- cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter
+-
+-
+-
+- misfit convergence criterion. Default is 1%, NaN if not applied
+-
+-
+-
+- maximum iterations during each optimization step
+-
+-
+-
+- scaling factor on gradient direction during optimization, for each optimization step
+-
+-
+-
+- decrease threshold for misfit, default is 30%
+-
+-
+-
+- absolute minimum acceptable value of the inversed parameter on each vertex
+-
+-
+-
+- absolute maximum acceptable value of the inversed parameter on each vertex
+-
+-
+-
+- observed velocity x component [m/yr]
+-
+-
+-
+- observed velocity y component [m/yr]
+-
+-
+-
+- observed velocity magnitude [m/yr]
+-
+-
+-
+- observed thickness [m])
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- is qmu analysis activated?
+-
+-
+-
+- (arrays of each variable class)
+-
+-
+-
+- (arrays of each response class)
+-
+-
+-
+- number of responses
+-
+-
+-
+- (array of method-independent parameters)
+-
+-
+-
+- (information from dakota files)
+-
+-
+-
+- user provided mesh partitioning, defaults to metis if not specified
+-
+-
+-
+- number of partitions for semi-discrete qmu
+-
+-
+-
+-
+-
+-
+-
+- use an enthalpy formulation to include temperate ice (default is 0)
+-
+-
+-
+- array of dakota_method class
+-
+-
+-
+- directory for mass flux profiles
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+- additional outputs requested
+-
+-
+-
+- weight applied to each mesh vertex
+-
+-
+-
+-
+-
+-
+-
+- list of potential outputs that can be requested, but which need additional data to be defined
+-
+-
+-
+-
+-
+-
+-
+- notes in a cell of strings
+-
+-
+-
+- model name
+-
+-
+-
+- empty field to store some data
+-
+-
+-
+-
+-
+\ No newline at end of file
+Index: ../trunk-jpl/src/java/build/resources/icons/kghostview.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/file_ops.xcf
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/filesave.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/viewmag.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/ini_open.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/fileopen.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/xml_open.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/filesaveas.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/opensettings.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/reset.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/advancedsettings.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/mydocuments.png
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/resources/icons/readme.txt
+===================================================================
+--- ../trunk-jpl/src/java/build/resources/icons/readme.txt (revision 18297)
++++ ../trunk-jpl/src/java/build/resources/icons/readme.txt (revision 18298)
+@@ -1,10 +0,0 @@
+-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+-This copyright and license notice covers the images in this directory.
+-************************************************************************
+-
+-TITLE: Crystal Project Icons
+-AUTHOR: Everaldo Coelho
+-SITE: http://www.everaldo.com
+-CONTACT: everaldo@everaldo.com
+-
+-Copyright (c) 2006-2007 Everaldo Coelho.
+Index: ../trunk-jpl/src/java/build/resources/config_schema-0.1.1.xsd
+===================================================================
+--- ../trunk-jpl/src/java/build/resources/config_schema-0.1.1.xsd (revision 18297)
++++ ../trunk-jpl/src/java/build/resources/config_schema-0.1.1.xsd (revision 18298)
+@@ -1,154 +0,0 @@
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+Index: ../trunk-jpl/src/java/build/gui_elements/CheckBoxPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/CombinedPanel$Type.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/TextfieldPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/FramePanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/PathPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/IntegerPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/DecimalPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/GUIBuildException.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/CombinedPanel$1.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/ControlledPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/DuplicatorPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/OptionPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/AlternativePanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/CombinedPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/SelectorPanel.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/gui_elements/ColorCellRenderer.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/GUIBuilder$1.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/PanelControl.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/XMLHelper.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/GUI.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/PanelNode.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/build/main/GUIBuilder.class
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/src/java/License.txt
+===================================================================
+--- ../trunk-jpl/src/java/License.txt (revision 18297)
++++ ../trunk-jpl/src/java/License.txt (revision 18298)
+@@ -1,674 +0,0 @@
+- GNU GENERAL PUBLIC LICENSE
+- Version 3, 29 June 2007
+-
+- Copyright (C) 2007 Free Software Foundation, Inc.
+- Everyone is permitted to copy and distribute verbatim copies
+- of this license document, but changing it is not allowed.
+-
+- Preamble
+-
+- The GNU General Public License is a free, copyleft license for
+-software and other kinds of works.
+-
+- The licenses for most software and other practical works are designed
+-to take away your freedom to share and change the works. By contrast,
+-the GNU General Public License is intended to guarantee your freedom to
+-share and change all versions of a program--to make sure it remains free
+-software for all its users. We, the Free Software Foundation, use the
+-GNU General Public License for most of our software; it applies also to
+-any other work released this way by its authors. You can apply it to
+-your programs, too.
+-
+- When we speak of free software, we are referring to freedom, not
+-price. Our General Public Licenses are designed to make sure that you
+-have the freedom to distribute copies of free software (and charge for
+-them if you wish), that you receive source code or can get it if you
+-want it, that you can change the software or use pieces of it in new
+-free programs, and that you know you can do these things.
+-
+- To protect your rights, we need to prevent others from denying you
+-these rights or asking you to surrender the rights. Therefore, you have
+-certain responsibilities if you distribute copies of the software, or if
+-you modify it: responsibilities to respect the freedom of others.
+-
+- For example, if you distribute copies of such a program, whether
+-gratis or for a fee, you must pass on to the recipients the same
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+-
+- Developers that use the GNU GPL protect your rights with two steps:
+-(1) assert copyright on the software, and (2) offer you this License
+-giving you legal permission to copy, distribute and/or modify it.
+-
+- For the developers' and authors' protection, the GPL clearly explains
+-that there is no warranty for this free software. For both users' and
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+-
+- Some devices are designed to deny users access to install or run
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+- Finally, every program is threatened constantly by software patents.
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+-
+- TERMS AND CONDITIONS
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+- "This License" refers to version 3 of the GNU General Public License.
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+- "Copyright" also means copyright-like laws that apply to other kinds of
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+- (at your option) any later version.
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+- The GNU General Public License does not permit incorporating your program
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+-Public License instead of this License. But first, please read
+-.
+Index: ../trunk-jpl/src/java/inishell.sh
+===================================================================
+--- ../trunk-jpl/src/java/inishell.sh (revision 18297)
++++ ../trunk-jpl/src/java/inishell.sh (revision 18298)
+@@ -1,8 +0,0 @@
+-#/bin/bash
+-#This is just the necessary command line to run a jar file
+-
+-#recover file name:
+-xmlfilename=$1
+-
+-#call inishell
+-java -jar dist/inishell.jar $xmlfilename
Index: /issm/oecreview/Archive/18296-19100/ISSM-18302-18303.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18302-18303.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18302-18303.diff (revision 19102)
@@ -0,0 +1,33 @@
+Index: ../trunk-jpl/src/m/classes/groundingline.py
+===================================================================
+--- ../trunk-jpl/src/m/classes/groundingline.py (revision 18302)
++++ ../trunk-jpl/src/m/classes/groundingline.py (revision 18303)
+@@ -43,9 +43,9 @@
+ md.checkmessage("requesting grounding line migration, but bathymetry is absent!")
+ pos=numpy.nonzero(md.mask.groundedice_levelset>0.)[0]
+ if any(numpy.abs(md.geometry.base[pos]-md.geometry.bed[pos])>10**-10):
+- md.checkmessage("bathymetry not equal to bed on grounded ice!")
++ md.checkmessage("base not equal to bed on grounded ice!")
+ if any(md.geometry.bed - md.geometry.base > 10**-9):
+- md.checkmessage("bathymetry superior to bed on floating ice!")
++ md.checkmessage("bed superior to base on floating ice!")
+
+ return md
+ # }}}
+Index: ../trunk-jpl/src/m/classes/groundingline.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/groundingline.m (revision 18302)
++++ ../trunk-jpl/src/m/classes/groundingline.m (revision 18303)
+@@ -47,10 +47,10 @@
+ end
+ pos=find(md.mask.groundedice_levelset>0.);
+ if any(abs(md.geometry.base(pos)-md.geometry.bed(pos))>10^-10),
+- md = checkmessage(md,['bathymetry not equal to bed on grounded ice!']);
++ md = checkmessage(md,['baase not equal to bed on grounded ice!']);
+ end
+ if any(md.geometry.bed - md.geometry.base > 10^-9),
+- md = checkmessage(md,['bathymetry superior to bed on floating ice!']);
++ md = checkmessage(md,['bed superior to base on floating ice!']);
+ end
+ end
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18303-18304.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18303-18304.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18303-18304.diff (revision 19102)
@@ -0,0 +1,72 @@
+Index: ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 18303)
++++ ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 18304)
+@@ -22,8 +22,9 @@
+ export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
+ export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
+ cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
+-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
++patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.mac.patch
+ patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
++patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch
+
+ #Apply patches
+ patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch
+@@ -32,9 +33,20 @@
+ patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
+ patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
+
++export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
++
+ #Configure dakota
++# Set your local gcc compiler here
+ cd $DAK_BUILD
+-cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++cmake -DBoost_NO_BOOST_CMAKE=TRUE \
++ -DBoost_NO_SYSTEM_PATHS=TRUE \
++ -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \
++ -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \
++ -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CC_COMPILER=gcc \
++ -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++
++#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran
++
+ cd ..
+
+ #Compile and install dakota
+Index: ../trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 0)
++++ ../trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 18304)
+@@ -0,0 +1,14 @@
++64,65c64,65
++< #set( DAKOTA_HAVE MPI ON
++< # CACHE BOOL "Build with MPI enabled" FORCE)
++---
++> set( DAKOTA_HAVE MPI OFF
++> CACHE BOOL "Build with MPI disabled" FORCE)
++91,93c91,93
++< #set( CMAKE_INSTALL_PREFIX
++< # "/path/to/Dakota/installation"
++< # CACHE PATH "Path to Dakota installation" )
++---
++> set( CMAKE_INSTALL_PREFIX
++> "$ENV{ISSM_DIR}/externalpackages/dakota/install"
++> CACHE PATH "Path to Dakota installation" )
+
+Property changes on: ../trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 0)
++++ ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 18304)
+@@ -0,0 +1,4 @@
++47a48,50
++> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE)
++> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE)
++>
Index: /issm/oecreview/Archive/18296-19100/ISSM-18304-18305.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18304-18305.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18304-18305.diff (revision 19102)
@@ -0,0 +1,42 @@
+Index: ../trunk-jpl/src/m/classes/groundingline.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/groundingline.m (revision 18304)
++++ ../trunk-jpl/src/m/classes/groundingline.m (revision 18305)
+@@ -47,7 +47,7 @@
+ end
+ pos=find(md.mask.groundedice_levelset>0.);
+ if any(abs(md.geometry.base(pos)-md.geometry.bed(pos))>10^-10),
+- md = checkmessage(md,['baase not equal to bed on grounded ice!']);
++ md = checkmessage(md,['base not equal to bed on grounded ice!']);
+ end
+ if any(md.geometry.bed - md.geometry.base > 10^-9),
+ md = checkmessage(md,['bed superior to base on floating ice!']);
+Index: ../trunk-jpl/src/m/classes/clusters/greenplanet.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/clusters/greenplanet.m (revision 18304)
++++ ../trunk-jpl/src/m/classes/clusters/greenplanet.m (revision 18305)
+@@ -86,7 +86,9 @@
+ fprintf(fid,'#PBS -M mmorligh@uci.edu\n');
+ fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+ fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+- %fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
++ fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
++ fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME
++ fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
+ fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+ if ~io_gather, %concatenate the output files:
+ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+Index: ../trunk-jpl/src/m/classes/clusters/pfe.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 18304)
++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 18305)
+@@ -128,7 +128,8 @@
+ fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+ fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+ fprintf(fid,'. /usr/share/modules/init/bash\n\n');
+- fprintf(fid,'module load comp-intel/2013.1.117\n');
++ fprintf(fid,'module load comp-intel/11.1.046\n');
++ fprintf(fid,'module load math/intel_mkl_64_10.0.011\n');
+ fprintf(fid,'module load mpi-sgi/mpt.2.06rp16\n');
+ fprintf(fid,'export PATH="$PATH:."\n\n');
+ fprintf(fid,'export MPI_GROUP_MAX=64\n\n');
Index: /issm/oecreview/Archive/18296-19100/ISSM-18305-18306.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18305-18306.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18305-18306.diff (revision 19102)
@@ -0,0 +1,69 @@
+Index: ../trunk-jpl/externalpackages/boost/install-1.55-macosx-mavericks.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 18305)
++++ ../trunk-jpl/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 18306)
+@@ -21,20 +21,25 @@
+ mv boost_1_55_0/* src
+ rm -rf boost_1_55_0
+
+-patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
+-patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
++#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
++#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
++patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
++patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
++patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
+
+ #Configure and compile
+ cd src
+ ./bootstrap.sh \
+ --prefix="$ISSM_DIR/externalpackages/boost/install" \
+- --with-python=python3.2 \
++ --with-python=python2.7 \
+ --with-python-root="$ISSM_DIR/externalpackages/python/install"
+
+ #Compile boost
+-./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi install
+-#./bjam install
++# Need gcc with iconv installed in a location that has been added to your path
++./bjam toolset=darwin-std0x link=static install
+
++#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal
++
+ #put bjam into install also:
+ mkdir ../install/bin
+ cp bjam ../install/bin
+Index: ../trunk-jpl/externalpackages/boost/configs/1.55/user-config.jam.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 0)
++++ ../trunk-jpl/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 18306)
+@@ -0,0 +1,4 @@
++42c42
++< # using gcc ;
++---
++> using darwin : std0x : "/usr/local/gfortran/bin/x86_64-apple-darwin10-g++" : -std=gnu++0x;
+Index: ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.jam.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 0)
++++ ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 18306)
+@@ -0,0 +1,4 @@
++587c587
++< "$(.LIBTOOL)" -static -o "$(<:T)" $(ARFLAGS) "$(>:T)"
++---
++> /usr/bin/libtool -static -o "$(<:T)" $(ARFLAGS) "$(>:T)"
+
+Property changes on: ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.jam.patch
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.py.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.py.patch (revision 0)
++++ ../trunk-jpl/externalpackages/boost/configs/1.55/darwin.py.patch (revision 18306)
+@@ -0,0 +1,4 @@
++40c40
++< toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double', '-no-cpp-precomp'])
++---
++> toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double'])
Index: /issm/oecreview/Archive/18296-19100/ISSM-18308-18309.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18308-18309.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18308-18309.diff (revision 19102)
@@ -0,0 +1,147 @@
+Index: ../trunk-jpl/src/m/classes/flowequation.py
+===================================================================
+--- ../trunk-jpl/src/m/classes/flowequation.py (revision 18308)
++++ ../trunk-jpl/src/m/classes/flowequation.py (revision 18309)
+@@ -72,34 +72,37 @@
+ #}}}
+ def checkconsistency(self,md,solution,analyses): # {{{
+
+- if StressbalanceAnalysisEnum() in analyses:
+- md = checkfield(md,'fieldname','flowequation.isSIA','numel',[1],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.fe_SSA','values',['P1','P1bubble','P1bubblecondensed','P2','P2bubble'])
+- md = checkfield(md,'fieldname','flowequation.fe_HO' ,'values',['P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4'])
+- md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',['P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart'])
+- md = checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.borderFS','size',[md.mesh.numberofvertices],'values',[0,1])
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_r','numel',[1],'>',0.)
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rhop','numel',[1],'>',0.)
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rlambda','numel',[1],'>',0.)
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rholambda','numel',[1],'>',0.)
+- md = checkfield(md,'fieldname','flowequation.XTH_theta','numel',[1],'>=',0.,'<',.5)
+- if m.strcmp(md.mesh.domaintype(),'2Dhorizontal'):
+- md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',[1,2])
+- md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',[1,2])
+- elif m.strcmp(md.mesh.domaintype(),'3D'):
+- md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',numpy.arange(0,8+1))
+- md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',numpy.arange(0,8+1))
+- else:
+- raise RuntimeError('mesh type not supported yet')
+- if not (self.isSIA or self.isSSA or self.isL1L2 or self.isHO or self.isFS):
+- md.checkmessage("no element types set for this model")
++ #Early return
++ if (StressbalanceAnalysisEnum() not in analyses and StressbalanceSIAAnalysisEnum() not in analyses) or (solution==TransientSolutionEnum() and not md.transient.isstressbalance):
++ return md
+
++ md = checkfield(md,'fieldname','flowequation.isSIA','numel',[1],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.fe_SSA','values',['P1','P1bubble','P1bubblecondensed','P2','P2bubble'])
++ md = checkfield(md,'fieldname','flowequation.fe_HO' ,'values',['P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4'])
++ md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',['P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart'])
++ md = checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.borderFS','size',[md.mesh.numberofvertices],'values',[0,1])
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_r','numel',[1],'>',0.)
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rhop','numel',[1],'>',0.)
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rlambda','numel',[1],'>',0.)
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rholambda','numel',[1],'>',0.)
++ md = checkfield(md,'fieldname','flowequation.XTH_theta','numel',[1],'>=',0.,'<',.5)
++ if m.strcmp(md.mesh.domaintype(),'2Dhorizontal'):
++ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',[1,2])
++ md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',[1,2])
++ elif m.strcmp(md.mesh.domaintype(),'3D'):
++ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',numpy.arange(0,8+1))
++ md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',numpy.arange(0,8+1))
++ else:
++ raise RuntimeError('mesh type not supported yet')
++ if not (self.isSIA or self.isSSA or self.isL1L2 or self.isHO or self.isFS):
++ md.checkmessage("no element types set for this model")
++
+ if StressbalanceSIAAnalysisEnum() in analyses:
+ if any(self.element_equation==1):
+ if numpy.any(numpy.logical_and(self.vertex_equation,md.mask.groundedice_levelset)):
+Index: ../trunk-jpl/src/m/classes/flowequation.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/flowequation.m (revision 18308)
++++ ../trunk-jpl/src/m/classes/flowequation.m (revision 18309)
+@@ -127,40 +127,41 @@
+ end % }}}
+ function md = checkconsistency(obj,md,solution,analyses) % {{{
+
+- if ismember(StressbalanceAnalysisEnum(),analyses),
+
+- md = checkfield(md,'fieldname','flowequation.isSIA','numel',[1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.fe_SSA','values',{'P1','P1bubble','P1bubblecondensed','P2','P2bubble'});
+- md = checkfield(md,'fieldname','flowequation.fe_HO' ,'values',{'P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4'});
+- md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',{'P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','LATaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart'});
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_r','numel',[1],'>',0.);
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rlambda','numel',[1],'>',0.);
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rhop','numel',[1],'>',0.);
+- md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rholambda','numel',[1],'>',0.);
+- md = checkfield(md,'fieldname','flowequation.XTH_theta','numel',[1],'>=',0.,'<',0.5);
+- md = checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices 1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices 1],'values',[0 1]);
+- md = checkfield(md,'fieldname','flowequation.borderFS','size',[md.mesh.numberofvertices 1],'values',[0 1]);
+- if strcmp(domaintype(md.mesh),'2Dhorizontal')
+- md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[1:2]);
+- md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[1:2]);
+- elseif strcmp(domaintype(md.mesh),'2Dvertical')
+- md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[2,4,5]);
+- md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[2,4,5]);
+- elseif strcmp(domaintype(md.mesh),'3D'),
+- md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[0:8]);
+- md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[0:8]);
+- else
+- error('Case not supported yet');
+- end
+- if ~(obj.isSIA || obj.isSSA || obj.isL1L2 || obj.isHO || obj.isFS),
+- md = checkmessage(md,['no element types set for this model']);
+- end
++ %Early return
++ if (~ismember(StressbalanceAnalysisEnum(),analyses) & ~ismember(StressbalanceSIAAnalysisEnum(),analyses)) | (solution==TransientSolutionEnum() & md.transient.isstressbalance==0), return; end
++
++ md = checkfield(md,'fieldname','flowequation.isSIA','numel',[1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.fe_SSA','values',{'P1','P1bubble','P1bubblecondensed','P2','P2bubble'});
++ md = checkfield(md,'fieldname','flowequation.fe_HO' ,'values',{'P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4'});
++ md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',{'P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','LATaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart'});
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_r','numel',[1],'>',0.);
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rlambda','numel',[1],'>',0.);
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rhop','numel',[1],'>',0.);
++ md = checkfield(md,'fieldname','flowequation.augmented_lagrangian_rholambda','numel',[1],'>',0.);
++ md = checkfield(md,'fieldname','flowequation.XTH_theta','numel',[1],'>=',0.,'<',0.5);
++ md = checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices 1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices 1],'values',[0 1]);
++ md = checkfield(md,'fieldname','flowequation.borderFS','size',[md.mesh.numberofvertices 1],'values',[0 1]);
++ if strcmp(domaintype(md.mesh),'2Dhorizontal')
++ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[1:2]);
++ md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[1:2]);
++ elseif strcmp(domaintype(md.mesh),'2Dvertical')
++ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[2,4,5]);
++ md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[2,4,5]);
++ elseif strcmp(domaintype(md.mesh),'3D'),
++ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices 1],'values',[0:8]);
++ md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements 1],'values',[0:8]);
++ else
++ error('Case not supported yet');
+ end
++ if ~(obj.isSIA || obj.isSSA || obj.isL1L2 || obj.isHO || obj.isFS),
++ md = checkmessage(md,['no element types set for this model']);
++ end
+ if ismember(StressbalanceSIAAnalysisEnum(),analyses),
+ if any(obj.element_equation==1),
+ if(obj.vertex_equation & md.mask.groundedice_levelset<0.),
Index: /issm/oecreview/Archive/18296-19100/ISSM-18309-18310.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18309-18310.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18309-18310.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/m/classes/taoinversion.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/taoinversion.m (revision 18309)
++++ ../trunk-jpl/src/m/classes/taoinversion.m (revision 18310)
+@@ -87,7 +87,7 @@
+ md = checkfield(md,'fieldname','inversion.gatol','numel',1,'>=',0);
+ md = checkfield(md,'fieldname','inversion.grtol','numel',1,'>=',0);
+ md = checkfield(md,'fieldname','inversion.gttol','numel',1,'>=',0);
+- md = checkfield(md,'fieldname','inversion.algorithm','values',{'tao_blmvm','tao_cg','tao_lmvm'});
++ md = checkfield(md,'fieldname','inversion.algorithm','values',{'tao_blmvm','tao_cg','tao_lmvm','blmvm','cg','lmvm'});
+ md = checkfield(md,'fieldname','inversion.cost_functions','size',[1 num_costfunc],'values',[101:105 201 501:506]);
+ md = checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0);
+ md = checkfield(md,'fieldname','inversion.min_parameters','size',[md.mesh.numberofvertices num_controls]);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18310-18311.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18310-18311.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18310-18311.diff (revision 19102)
@@ -0,0 +1,36 @@
+Index: ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp (revision 18310)
++++ ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp (revision 18311)
+@@ -39,7 +39,6 @@
+ iomodel->FetchDataToInput(elements,MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(elements,MeshVertexonsurfaceEnum);
+ }
+- iomodel->FetchDataToInput(elements,FlowequationElementEquationEnum);
+ iomodel->FetchDataToInput(elements,MaterialsRheologyBEnum);
+ iomodel->FetchDataToInput(elements,MaterialsRheologyNEnum);
+ iomodel->FetchDataToInput(elements,BasalforcingsGroundediceMeltingRateEnum);
+Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 18310)
++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 18311)
+@@ -60,7 +60,6 @@
+ iomodel->FetchDataToInput(elements,MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(elements,MeshVertexonsurfaceEnum);
+ }
+- iomodel->FetchDataToInput(elements,FlowequationElementEquationEnum);
+ iomodel->FetchDataToInput(elements,MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(elements,MeshVertexonsurfaceEnum);
+ iomodel->FetchDataToInput(elements,MaterialsRheologyBEnum);
+Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 18310)
++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 18311)
+@@ -61,7 +61,6 @@
+ iomodel->FetchDataToInput(elements,MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(elements,MeshVertexonsurfaceEnum);
+ }
+- iomodel->FetchDataToInput(elements,FlowequationElementEquationEnum);
+ iomodel->FetchDataToInput(elements,MaterialsRheologyBEnum);
+ iomodel->FetchDataToInput(elements,MaterialsRheologyNEnum);
+ iomodel->FetchDataToInput(elements,PressureEnum);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18313-18314.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18313-18314.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18313-18314.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18313)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18314)
+@@ -864,7 +864,7 @@
+ libISSMModules_la_SOURCES += $(kml_sources)
+ endif
+ libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS)
+-libISSMModules_la_LIBADD = ./libISSMCore.la
++libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB)
+ endif
+
+ if VERSION
Index: /issm/oecreview/Archive/18296-19100/ISSM-18314-18315.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18314-18315.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18314-18315.diff (revision 19102)
@@ -0,0 +1,16 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18314)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18315)
+@@ -713,9 +713,9 @@
+ ./classes/kriging/Observation.h\
+ ./classes/kriging/Observation.cpp\
+ ./modules/Krigingx/Krigingx.cpp\
+- ./modules/Krigingx/Krigingx.h
++ ./modules/Krigingx/Krigingx.h\
++ ./modules/Krigingx/pKrigingx.cpp
+ issm_sources +=$(kriging_sources)
+-#issm_sources +=./modules/Krigingx/pKrigingx.cpp
+ endif
+ #}}}
+ #Kml sources {{{
Index: /issm/oecreview/Archive/18296-19100/ISSM-18315-18316.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18315-18316.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18315-18316.diff (revision 19102)
@@ -0,0 +1,15 @@
+Index: ../trunk-jpl/src/wrappers/matlab/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 18315)
++++ ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 18316)
+@@ -97,6 +97,10 @@
+ deps += $(ADOLCLIB)
+ endif
+
++if FORTRAN
++deps += $(FLIBS) $(FORTRANLIB)
++endif
++
+ #MEXLIB needs to be the last (undefined references on larsen)
+ deps += ${MEXLIB}
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18316-18317.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18316-18317.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18316-18317.diff (revision 19102)
@@ -0,0 +1,26 @@
+Index: ../trunk-jpl/test/NightlyRun/test513.py
+===================================================================
+--- ../trunk-jpl/test/NightlyRun/test513.py (revision 18316)
++++ ../trunk-jpl/test/NightlyRun/test513.py (revision 18317)
+@@ -35,7 +35,7 @@
+
+ # Fields and tolerances to track changes
+ field_names =['Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsGroundediceMeltingRate']
+-field_tolerances=[1e-09,2e-10,1e-10,1e-10,3e-6,3e-6,3e-6,3e-6,2e-6,2e-06]
++field_tolerances=[5e-08,2e-10,1e-10,1e-10,3e-6,3e-6,3e-6,3e-6,2e-6,2e-06]
+ field_values=[\
+ md.results.SteadystateSolution.Gradient1,\
+ md.results.SteadystateSolution.J,\
+Index: ../trunk-jpl/test/NightlyRun/test513.m
+===================================================================
+--- ../trunk-jpl/test/NightlyRun/test513.m (revision 18316)
++++ ../trunk-jpl/test/NightlyRun/test513.m (revision 18317)
+@@ -24,7 +24,7 @@
+
+ %Fields and tolerances to track changes
+ field_names ={'Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsGroundediceMeltingRate'};
+-field_tolerances={1e-09,2e-10,1e-10,1e-10,3e-6,3e-6,3e-6,3e-6,2e-6,2e-06};
++field_tolerances={5e-08,2e-10,1e-10,1e-10,3e-6,3e-6,3e-6,3e-6,2e-6,2e-06};
+ field_values={...
+ (md.results.SteadystateSolution.Gradient1),...
+ md.results.SteadystateSolution.J,...
Index: /issm/oecreview/Archive/18296-19100/ISSM-18317-18318.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18317-18318.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18317-18318.diff (revision 19102)
@@ -0,0 +1,236 @@
+Index: ../trunk-jpl/m4/issm_options.m4
+===================================================================
+--- ../trunk-jpl/m4/issm_options.m4 (revision 18317)
++++ ../trunk-jpl/m4/issm_options.m4 (revision 18318)
+@@ -1622,6 +1622,20 @@
+ dnl }}}
+
+ dnl Capabilities
++ dnl with-bamg{{{
++ AC_ARG_WITH([bamg],
++ AS_HELP_STRING([--with-bamg = YES],[compile with bamg capabilities (default is yes)]),
++ [BAMG=$withval],[BAMG=yes])
++ AC_MSG_CHECKING(for bamg capability compilation)
++
++ HAVE_BAMG=no
++ if test "x$BAMG" = "xyes"; then
++ HAVE_BAMG=yes
++ AC_DEFINE([_HAVE_BAMG_],[1],[with bamg meshing capability])
++ fi
++ AM_CONDITIONAL([BAMG], [test x$HAVE_BAMG = xyes])
++ AC_MSG_RESULT($HAVE_BAMG)
++ dnl }}}
+ dnl with-kml{{{
+ AC_ARG_WITH([kml],
+ AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is yes)]),
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18317)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18318)
+@@ -458,6 +458,75 @@
+ ./cores/DakotaSpawnCore.cpp
+ endif
+ #}}}
++#BAMG sources {{{
++if BAMG
++issm_sources += ./bamg/bamgobjects.h\
++ ./bamg/BamgGeom.h\
++ ./bamg/BamgGeom.cpp\
++ ./bamg/BamgMesh.h\
++ ./bamg/BamgMesh.cpp\
++ ./bamg/BamgOpts.h\
++ ./bamg/BamgOpts.cpp\
++ ./bamg/CrackedEdge.h\
++ ./bamg/CrackedEdge.cpp\
++ ./bamg/Curve.h\
++ ./bamg/Curve.cpp\
++ ./bamg/Direction.h\
++ ./bamg/Direction.cpp\
++ ./bamg/DoubleAndInt.h\
++ ./bamg/Edge.h\
++ ./bamg/Edge.cpp\
++ ./bamg/GeomEdge.h\
++ ./bamg/GeomEdge.cpp\
++ ./bamg/GeomSubDomain.h\
++ ./bamg/GeomSubDomain.cpp\
++ ./bamg/GeomVertex.h\
++ ./bamg/GeomVertex.cpp\
++ ./bamg/Geometry.cpp\
++ ./bamg/Geometry.h\
++ ./bamg/ListofIntersectionTriangles.cpp\
++ ./bamg/ListofIntersectionTriangles.h\
++ ./bamg/EigenMetric.cpp\
++ ./bamg/Metric.cpp\
++ ./bamg/Metric.h\
++ ./bamg/BamgQuadtree.cpp\
++ ./bamg/BamgQuadtree.h\
++ ./bamg/R2.h\
++ ./bamg/SetOfE4.cpp\
++ ./bamg/SetOfE4.h\
++ ./bamg/SubDomain.h\
++ ./bamg/SubDomain.cpp\
++ ./bamg/AdjacentTriangle.h\
++ ./bamg/AdjacentTriangle.cpp\
++ ./bamg/Triangle.cpp\
++ ./bamg/det.h \
++ ./bamg/Triangle.h\
++ ./bamg/BamgVertex.cpp\
++ ./bamg/BamgVertex.h\
++ ./bamg/VertexOnEdge.h\
++ ./bamg/VertexOnEdge.cpp\
++ ./bamg/VertexOnGeom.h\
++ ./bamg/VertexOnGeom.cpp\
++ ./bamg/VertexOnVertex.h\
++ ./bamg/VertexOnVertex.cpp\
++ ./bamg/Mesh.cpp\
++ ./bamg/Mesh.h\
++ ./shared/Bamg/Abs.h \
++ ./shared/Bamg/BigPrimeNumber.h\
++ ./shared/Bamg/BigPrimeNumber.cpp\
++ ./shared/Bamg/BinaryRand.h \
++ ./shared/Bamg/Exchange.h \
++ ./shared/Bamg/extrema.h \
++ ./shared/Bamg/HeapSort.h \
++ ./shared/Bamg/OppositeAngle.h \
++ ./modules/Bamgx/Bamgx.cpp\
++ ./modules/Bamgx/Bamgx.h\
++ ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\
++ ./modules/BamgConvertMeshx/BamgConvertMeshx.h\
++ ./modules/BamgTriangulatex/BamgTriangulatex.cpp\
++ ./modules/BamgTriangulatex/BamgTriangulatex.h
++endif
++#}}}
+ #Petsc sources {{{
+ if PETSC
+ issm_sources += ./toolkits/petsc\
+@@ -629,95 +698,8 @@
+
+ #Wrapper sources
+ #Bamg sources {{{
+-bamg_sources = ./bamg/bamgobjects.h\
+- ./bamg/BamgGeom.h\
+- ./bamg/BamgGeom.cpp\
+- ./bamg/BamgMesh.h\
+- ./bamg/BamgMesh.cpp\
+- ./bamg/BamgOpts.h\
+- ./bamg/BamgOpts.cpp\
+- ./bamg/CrackedEdge.h\
+- ./bamg/CrackedEdge.cpp\
+- ./bamg/Curve.h\
+- ./bamg/Curve.cpp\
+- ./bamg/Direction.h\
+- ./bamg/Direction.cpp\
+- ./bamg/DoubleAndInt.h\
+- ./bamg/Edge.h\
+- ./bamg/Edge.cpp\
+- ./bamg/GeomEdge.h\
+- ./bamg/GeomEdge.cpp\
+- ./bamg/GeomSubDomain.h\
+- ./bamg/GeomSubDomain.cpp\
+- ./bamg/GeomVertex.h\
+- ./bamg/GeomVertex.cpp\
+- ./bamg/Geometry.cpp\
+- ./bamg/Geometry.h\
+- ./bamg/ListofIntersectionTriangles.cpp\
+- ./bamg/ListofIntersectionTriangles.h\
+- ./bamg/EigenMetric.cpp\
+- ./bamg/Metric.cpp\
+- ./bamg/Metric.h\
+- ./bamg/BamgQuadtree.cpp\
+- ./bamg/BamgQuadtree.h\
+- ./bamg/R2.h\
+- ./bamg/SetOfE4.cpp\
+- ./bamg/SetOfE4.h\
+- ./bamg/SubDomain.h\
+- ./bamg/SubDomain.cpp\
+- ./bamg/AdjacentTriangle.h\
+- ./bamg/AdjacentTriangle.cpp\
+- ./bamg/Triangle.cpp\
+- ./bamg/det.h \
+- ./bamg/Triangle.h\
+- ./bamg/BamgVertex.cpp\
+- ./bamg/BamgVertex.h\
+- ./bamg/VertexOnEdge.h\
+- ./bamg/VertexOnEdge.cpp\
+- ./bamg/VertexOnGeom.h\
+- ./bamg/VertexOnGeom.cpp\
+- ./bamg/VertexOnVertex.h\
+- ./bamg/VertexOnVertex.cpp\
+- ./bamg/Mesh.cpp\
+- ./bamg/Mesh.h\
+- ./shared/Bamg/Abs.h \
+- ./shared/Bamg/BigPrimeNumber.h\
+- ./shared/Bamg/BigPrimeNumber.cpp\
+- ./shared/Bamg/BinaryRand.h \
+- ./shared/Bamg/Exchange.h \
+- ./shared/Bamg/extrema.h \
+- ./shared/Bamg/HeapSort.h \
+- ./shared/Bamg/OppositeAngle.h \
+- ./modules/Bamgx/Bamgx.cpp\
+- ./modules/Bamgx/Bamgx.h\
+- ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\
+- ./modules/BamgConvertMeshx/BamgConvertMeshx.h\
+- ./modules/BamgTriangulatex/BamgTriangulatex.cpp\
+- ./modules/BamgTriangulatex/BamgTriangulatex.h
++
+ #}}}
+-#Kriging sources {{{
+-if KRIGING
+-kriging_sources = ./classes/kriging/Observations.h\
+- ./classes/kriging/Observations.cpp\
+- ./classes/kriging/Variogram.h \
+- ./classes/kriging/GaussianVariogram.h\
+- ./classes/kriging/GaussianVariogram.cpp\
+- ./classes/kriging/ExponentialVariogram.h\
+- ./classes/kriging/ExponentialVariogram.cpp\
+- ./classes/kriging/SphericalVariogram.h\
+- ./classes/kriging/SphericalVariogram.cpp\
+- ./classes/kriging/PowerVariogram.h\
+- ./classes/kriging/PowerVariogram.cpp\
+- ./classes/kriging/Quadtree.h\
+- ./classes/kriging/Quadtree.cpp\
+- ./classes/kriging/Observation.h\
+- ./classes/kriging/Observation.cpp\
+- ./modules/Krigingx/Krigingx.cpp\
+- ./modules/Krigingx/Krigingx.h\
+- ./modules/Krigingx/pKrigingx.cpp
+-issm_sources +=$(kriging_sources)
+-endif
+-#}}}
+ #Kml sources {{{
+ kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.h\
+ ./modules/Exp2Kmlx/Exp2Kmlx.cpp\
+@@ -844,7 +826,33 @@
+ ./modules/Scotchx/Scotchx.h
+ endif
+ #}}}
++
++#kriging (WRAPPER and executable)
++#Kriging sources {{{
++if KRIGING
++issm_sources +=./classes/kriging/Observations.h\
++ ./classes/kriging/Observations.cpp\
++ ./classes/kriging/Variogram.h \
++ ./classes/kriging/GaussianVariogram.h\
++ ./classes/kriging/GaussianVariogram.cpp\
++ ./classes/kriging/ExponentialVariogram.h\
++ ./classes/kriging/ExponentialVariogram.cpp\
++ ./classes/kriging/SphericalVariogram.h\
++ ./classes/kriging/SphericalVariogram.cpp\
++ ./classes/kriging/PowerVariogram.h\
++ ./classes/kriging/PowerVariogram.cpp\
++ ./classes/kriging/Quadtree.h\
++ ./classes/kriging/Quadtree.cpp\
++ ./classes/kriging/Observation.h\
++ ./classes/kriging/Observation.cpp\
++ ./modules/Krigingx/pKrigingx.cpp
++
++modules_sources +=./modules/Krigingx/Krigingx.cpp\
++ ./modules/Krigingx/Krigingx.h\
++ ./modules/Krigingx/pKrigingx.cpp
++endif
+ #}}}
++#}}}
+ #Library flags and sources {{{
+ ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18318-18319.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18318-18319.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18318-18319.diff (revision 19102)
@@ -0,0 +1,48 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18318)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18319)
+@@ -854,7 +854,7 @@
+ #}}}
+ #}}}
+ #Library flags and sources {{{
+-ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
++ALLCXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS)
+
+ libISSMCore_la_SOURCES = $(issm_sources)
+ libISSMCore_la_CXXFLAGS = $(ALLCXXFLAGS) $(DAKOTAFLAGS)
+Index: ../trunk-jpl/src/wrappers/python/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/wrappers/python/Makefile.am (revision 18318)
++++ ../trunk-jpl/src/wrappers/python/Makefile.am (revision 18319)
+@@ -15,7 +15,7 @@
+ ./io/CheckNumPythonArguments.cpp\
+ ./io/FetchPythonData.cpp
+
+-ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
++ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
+ libISSMPython_la_SOURCES = $(io_sources)
+ libISSMPython_la_CXXFLAGS= $(ALLCXXFLAGS)
+ #}}}
+Index: ../trunk-jpl/src/wrappers/matlab/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 18318)
++++ ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 18319)
+@@ -15,7 +15,7 @@
+ ./io/WriteMatlabData.cpp\
+ ./io/FetchMatlabData.cpp
+
+-ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
++ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
+
+ libISSMMatlab_la_SOURCES = $(io_sources)
+ libISSMMatlab_la_CXXFLAGS= $(ALLCXXFLAGS)
+@@ -89,7 +89,7 @@
+ AM_LDFLAGS += -Wl,-static
+ endif
+
+-AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
++AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -fPIC
+
+ deps += ./libISSMMatlab.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18319-18320.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18319-18320.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18319-18320.diff (revision 19102)
@@ -0,0 +1,17 @@
+Index: ../trunk-jpl/src/m/plot/plot_section.m
+===================================================================
+--- ../trunk-jpl/src/m/plot/plot_section.m (revision 18319)
++++ ../trunk-jpl/src/m/plot/plot_section.m (revision 18320)
+@@ -52,7 +52,11 @@
+ if exist(options,'resolution'),
+ resolution=getfieldvalue(options,'resolution');
+ else %Default resolution
+- resolution=[1000 10*md.mesh.numberoflayers];
++ if is2d,
++ resolution=[1000 1];
++ else
++ resolution=[1000 10*md.mesh.numberoflayers];
++ end
+ disp(['plot_section warning: no resolution specified, use default resolution: [horizontal_resolution vertical_resolution]=[' num2str(resolution) ']']);
+ end
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18320-18321.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18320-18321.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18320-18321.diff (revision 19102)
@@ -0,0 +1,92 @@
+Index: ../trunk-jpl/jenkins/linux64_murdo
+===================================================================
+--- ../trunk-jpl/jenkins/linux64_murdo (revision 18320)
++++ ../trunk-jpl/jenkins/linux64_murdo (revision 18321)
+@@ -8,9 +8,6 @@
+ #Nightly run name
+ NAME="ISSM matlab tests on Linux64 (murdo)"
+
+-#ISSM Architecture
+-ISSM_ARCH="linux-gnu-amd64"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR\
+ --with-matlab-dir=$MATLAB_DIR \
+Index: ../trunk-jpl/jenkins/linux64_murdo_ad
+===================================================================
+--- ../trunk-jpl/jenkins/linux64_murdo_ad (revision 18320)
++++ ../trunk-jpl/jenkins/linux64_murdo_ad (revision 18321)
+@@ -7,9 +7,6 @@
+ #Nightly run name
+ NAME="ISSM tests on Linux64 (murdo). Automatic differentiation validation tests"
+
+-#ISSM Architecture
+-ISSM_ARCH="linux-gnu-amd64"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR\
+ --prefix=$ISSM_DIR \
+Index: ../trunk-jpl/jenkins/linux64_murdo_ampi
+===================================================================
+--- ../trunk-jpl/jenkins/linux64_murdo_ampi (revision 18320)
++++ ../trunk-jpl/jenkins/linux64_murdo_ampi (revision 18321)
+@@ -8,9 +8,6 @@
+ #Nightly run name
+ NAME="ISSM tests on Linux64 (murdo). Automatic differentiation validation tests with ampi"
+
+-#ISSM Architecture
+-ISSM_ARCH="linux-gnu-amd64"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR\
+ --without-kriging \
+Index: ../trunk-jpl/jenkins/imac-012301-gil
+===================================================================
+--- ../trunk-jpl/jenkins/imac-012301-gil (revision 18320)
++++ ../trunk-jpl/jenkins/imac-012301-gil (revision 18321)
+@@ -8,9 +8,6 @@
+ #Nightly run name
+ NAME="ISSM matlab tests on MacOSX"
+
+-#ISSM Architecture
+-ISSM_ARCH="macosx-gnu"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR \
+ --with-matlab-dir=$MATLAB_DIR \
+Index: ../trunk-jpl/jenkins/windows
+===================================================================
+--- ../trunk-jpl/jenkins/windows (revision 18320)
++++ ../trunk-jpl/jenkins/windows (revision 18321)
+@@ -8,9 +8,6 @@
+ #Nightly run name
+ NAME="ISSM matlab tests on Windows"
+
+-#ISSM Architecture
+-ISSM_ARCH="cygwin-intel"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR \
+ --disable-static \
+@@ -20,7 +17,6 @@
+ --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
+ --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \
+ --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
+- --with-petsc-arch=$ISSM_ARCH \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \
+ --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \
+ --with-mpi-libflags="-Wl,libpetsc.lib" \
+Index: ../trunk-jpl/jenkins/linux64_larsen
+===================================================================
+--- ../trunk-jpl/jenkins/linux64_larsen (revision 18320)
++++ ../trunk-jpl/jenkins/linux64_larsen (revision 18321)
+@@ -8,9 +8,6 @@
+ #Nightly run name
+ NAME="ISSM matlab tests on Linux64 (murdo)"
+
+-#ISSM Architecture
+-ISSM_ARCH="linux-gnu-amd64"
+-
+ #ISSM CONFIGURATION
+ ISSM_CONFIG='--prefix=$ISSM_DIR\
+ --with-matlab-dir=$MATLAB_DIR \
Index: /issm/oecreview/Archive/18296-19100/ISSM-18321-18322.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18321-18322.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18321-18322.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/m4/issm_options.m4
+===================================================================
+--- ../trunk-jpl/m4/issm_options.m4 (revision 18321)
++++ ../trunk-jpl/m4/issm_options.m4 (revision 18322)
+@@ -666,7 +666,7 @@
+ if test "x$HAVE_ATLAS" = "xyes" ; then
+ GSLLIB="-dy -L$GSL_ROOT/lib -lgsl -L$ATLAS_ROOT/lib -lcblas -latlas -lm"
+ else
+- GSLLIB="-dy -L$GSL_ROOT/lib -lgsl -lgslcblas -lm"
++ GSLLIB="-L$GSL_ROOT/lib -lgsl -lgslcblas -lm"
+ fi
+ AC_DEFINE([_HAVE_GSL_],[1],[with gsl in ISSM src])
+ AC_SUBST([GSLINCL])
Index: /issm/oecreview/Archive/18296-19100/ISSM-18327-18328.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18327-18328.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18327-18328.diff (revision 19102)
@@ -0,0 +1,22 @@
+Index: ../trunk-jpl/externalpackages/m1qn3/install.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/m1qn3/install.sh (revision 18327)
++++ ../trunk-jpl/externalpackages/m1qn3/install.sh (revision 18328)
+@@ -31,7 +31,7 @@
+ ar -r libm1qn3.\$(LIB_EXT) \$(OBJECTS)
+ ranlib libm1qn3.\$(LIB_EXT)
+ %.o: %.f
+- \$(FC) \$(FFLAGS) -c $< -o \$@
++ \$(FC) \$(FFLAGS) -fPIC -c $< -o \$@
+ clean:
+ rm -rf *.o *.\$(LIB_EXT)
+ EOF
+@@ -51,7 +51,7 @@
+ ar -r libddot.\$(LIB_EXT) \$(OBJECTS)
+ ranlib libddot.\$(LIB_EXT)
+ %.o: %.f
+- \$(FC) \$(FFLAGS) -c $< -o \$@
++ \$(FC) \$(FFLAGS) -fPIC -c $< -o \$@
+ clean:
+ rm -rf *.o *.\$(LIB_EXT)
+ EOF
Index: /issm/oecreview/Archive/18296-19100/ISSM-18328-18329.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18328-18329.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18328-18329.diff (revision 19102)
@@ -0,0 +1,66 @@
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh (revision 0)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh (revision 18329)
+@@ -0,0 +1,54 @@
++#!/bin/bash
++set -eu
++
++#WARNING: make sure you have the right mpi:
++#mpi-selector --query
++#default:openmpi_intel-1.5.4_psm
++
++#Some cleanup
++rm -rf install petsc-3.5.1 src
++mkdir install src
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.5.1.tar.gz' 'petsc-3.5.1.tar.gz'
++
++#Untar and move petsc to install directory
++tar -zxvf petsc-3.5.1.tar.gz
++mv petsc-3.5.1/* src/
++rm -rf petsc-3.5.1
++
++#configure
++cd src
++./config/configure.py \
++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
++ --with-blas-lapack-dir="/opt/intel/mkl/10.2.4.032/" \
++ --with-mpi-dir="/sopt/mpi/openmpi-1.5.4_psm/intel/" \
++ --known-mpi-shared-libraries=1 \
++ --with-debugging=0 \
++ --with-valgrind=0 \
++ --with-batch=1 \
++ --with-shared-libraries=1 \
++ --download-metis=1 \
++ --download-parmetis=1 \
++ --download-scalapack=1 \
++ --download-mumps=1 \
++ --COPTFLAGS="-lmpi -O3" \
++ --FOPTFLAGS="-lmpi -O3" \
++ --CXXOPTFLAGS="-lmpi -O3"
++
++#prepare script to reconfigure petsc
++cat > script.queue << EOF
++#PBS -S /bin/bash
++#PBS -l nodes=1:ppn=1
++#PBS -q c6145
++#PBS -l walltime=10
++
++cd $(echo $ISSM_DIR)/externalpackages/petsc/src/
++mpiexec -np 1 ./conftest-arch-linux2-c-opt
++EOF
++
++#print instructions
++echo "== Now: cd src/ "
++echo "== qsub script.queue "
++echo "== Then run reconfigure script generated by PETSc and follow instructions"
+
+Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18329-18330.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18329-18330.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18329-18330.diff (revision 19102)
@@ -0,0 +1,30 @@
+Index: ../trunk-jpl/etc/environment.csh
+===================================================================
+--- ../trunk-jpl/etc/environment.csh (revision 18329)
++++ ../trunk-jpl/etc/environment.csh (revision 18330)
+@@ -42,10 +42,17 @@
+ #Dakota
+ set DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
+ if (-d $DAKOTA_DIR) then
+- setenv PATH {$PATH}:{$DAKOTA_DIR}/bin
++ setenv PATH {$DAKOTA_DIR}/bin:{$PATH}
+ setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref
+ endif
+
++#Boost
++set BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
++set BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
++if (-d $BOOST_DIR) then
++ setenv PATH {$BOOST_DIR}/bin:{$PATH}
++endif
++
+ #Doxygen
+ set DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
+ if (-d $DOXYGEN_DIR) then
+@@ -99,5 +106,5 @@
+ #SHELL2JUNIT
+ set SHELL2JUNIT_DIR="$ISSM_DIR/externalpackages/shell2junit"
+ if (-d $SHELL2JUNIT_DIR) then
+- setenv PATH {$PATH}:{$SHELL2JUNIT_DIR}/install
++ setenv PATH {$SHELL2JUNIT_DIR}/install:{$PATH}
+ endif
Index: /issm/oecreview/Archive/18296-19100/ISSM-18330-18331.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18330-18331.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18330-18331.diff (revision 19102)
@@ -0,0 +1,63 @@
+Index: ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 0)
++++ ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 18331)
+@@ -0,0 +1,51 @@
++#!/bin/bash
++set -eu
++
++#Some cleanup
++rm -rf Dakota
++rm -rf src
++rm -rf build
++rm -rf install
++mkdir src build install
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz'
++
++#Untar
++tar -zxvf dakota-5.3.1-public-src.tar.gz
++
++#Move Dakota to src directory
++mv dakota-5.3.1.src/* src
++rm -rf dakota-5.3.1.src
++
++#Set up Dakota cmake variables and config
++export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
++export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
++cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
++patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
++patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
++
++#Apply patches
++patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch
++patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch
++patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch
++patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
++patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
++
++#Configure dakota
++cd $DAK_BUILD
++#cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran -D BOOST_ROOT=/opt/local -D Boost_INCLUDE_DIR=/opt/local/include -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran -D LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH -D LDFLAGS="-L/usr/lib -lstdc++" -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++cd ..
++
++#Compile and install dakota
++cd $DAK_BUILD
++if [ $# -eq 0 ];
++then
++ make
++ make install
++else
++ make -j $1
++ make -j $1 install
++fi
++cd ..
+
+Property changes on: ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18331-18332.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18331-18332.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18331-18332.diff (revision 19102)
@@ -0,0 +1,12 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18331)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18332)
+@@ -852,7 +852,6 @@
+ ./modules/Krigingx/pKrigingx.cpp
+ endif
+ #}}}
+-#}}}
+ #Library flags and sources {{{
+ ALLCXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS)
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18332-18333.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18332-18333.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18332-18333.diff (revision 19102)
@@ -0,0 +1,16 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18332)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18333)
+@@ -911,7 +911,10 @@
+ endif
+
+ #Standard libraries
+-LDADD = ./libISSMCore.la ./libISSMOverload.la ./libISSMModules.la $(TRIANGLELIB)
++LDADD = ./libISSMCore.la ./libISSMOverload.la
++if WRAPPERS
++LDADD += ./libISSMModules.la $(TRIANGLELIB)
++endif
+
+ #External packages
+ LDADD += $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
Index: /issm/oecreview/Archive/18296-19100/ISSM-18333-18334.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18333-18334.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18333-18334.diff (revision 19102)
@@ -0,0 +1,25 @@
+Index: ../trunk-jpl/m4/issm_options.m4
+===================================================================
+--- ../trunk-jpl/m4/issm_options.m4 (revision 18333)
++++ ../trunk-jpl/m4/issm_options.m4 (revision 18334)
+@@ -126,6 +126,11 @@
+ export CXX=icpc
+ export CFLAGS=" -D_INTEL_LINUX_"
+ export CXXFLAGS=" -D_INTEL_LINUX_"
++ elif test $VENDOR = intel-gp; then
++ export CC=icc
++ export CXX=icpc
++ export CFLAGS=" -D_INTEL_LINUX_"
++ export CXXFLAGS=" -D_INTEL_LINUX_"
+ elif test $VENDOR = intel-discover; then
+ export CC=icc
+ export CXX=icpc
+@@ -1150,6 +1155,8 @@
+ MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
+ elif test x$VENDOR = xintel-acenet; then
+ MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm"
++ elif test x$VENDOR = xintel-gp; then
++ MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm"
+ else
+ MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64 -lmkl_blacs_sgimpt_ilp64 -lguide -lpthread"
+ fi
Index: /issm/oecreview/Archive/18296-19100/ISSM-18334-18335.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18334-18335.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18334-18335.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/jenkins/linux64_murdo_ampi
+===================================================================
+--- ../trunk-jpl/jenkins/linux64_murdo_ampi (revision 18334)
++++ ../trunk-jpl/jenkins/linux64_murdo_ampi (revision 18335)
+@@ -97,7 +97,7 @@
+
+ #number of cpus used in ISSM installation and compilation (one is usually
+ #safer as some packages are very sensitive to parallel compilation)
+-NUMCPUS_INSTALL=8
++NUMCPUS_INSTALL=1
+
+ #number of cpus used in the nightly runs.
+ NUMCPUS_RUN=8
Index: /issm/oecreview/Archive/18296-19100/ISSM-18335-18336.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18335-18336.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18335-18336.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/m/plot/processdata.m
+===================================================================
+--- ../trunk-jpl/src/m/plot/processdata.m (revision 18335)
++++ ../trunk-jpl/src/m/plot/processdata.m (revision 18336)
+@@ -24,7 +24,7 @@
+ disp([' ' num2str(i) ': ' F{i} ]);
+ end
+ choice=input(['please enter the field number? (between 1 and ' num2str(numel(F)) ') ']);
+- [data datatype]=processdata(md,data.(F{choice}),options);
++ [data datatype]=processdata(md,data(1).(F{choice}),options);
+ end
+
+ %Process NaN if any (do not know before mask is applied)
Index: /issm/oecreview/Archive/18296-19100/ISSM-18336-18337.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18336-18337.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18336-18337.diff (revision 19102)
@@ -0,0 +1,67 @@
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18336)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18337)
+@@ -14,7 +14,6 @@
+ char** requestedoutputs = NULL;
+
+ parameters->AddObject(iomodel->CopyConstantObject(FlowequationIsFSEnum));
+-
+ parameters->AddObject(iomodel->CopyConstantObject(MasstransportIsfreesurfaceEnum));
+ parameters->AddObject(iomodel->CopyConstantObject(MasstransportHydrostaticAdjustmentEnum));
+ parameters->AddObject(iomodel->CopyConstantObject(MasstransportStabilizationEnum));
+@@ -361,27 +360,34 @@
+ Bprime,dim,numnodes,0,
+ &Ke->values[0],1);
+
+- if(stabilization==2){
+- if(dim==1){
+- vel=fabs(vx)+1.e-8;
+- D[0]=h/(2*vel)*vx*vx;
+- }
+- else{
+- /*Streamline upwinding*/
+- vel=sqrt(vx*vx+vy*vy)+1.e-8;
+- D[0*dim+0]=h/(2*vel)*vx*vx;
+- D[1*dim+0]=h/(2*vel)*vy*vx;
+- D[0*dim+1]=h/(2*vel)*vx*vy;
+- D[1*dim+1]=h/(2*vel)*vy*vy;
+- }
++ switch(stabilization){
++ case 0:
++ /*Nothing to be onde*/
++ break;
++ case 1:
++ /*SSA*/
++ vxaverage_input->GetInputAverage(&vx);
++ if(dim==2) vyaverage_input->GetInputAverage(&vy);
++ D[0*dim+0]=h/2.0*fabs(vx);
++ if(dim==2) D[1*dim+1]=h/2.0*fabs(vy);
++ break;
++ case 2:
++ if(dim==1){
++ vel=fabs(vx)+1.e-8;
++ D[0]=h/(2*vel)*vx*vx;
++ }
++ else{
++ /*Streamline upwinding*/
++ vel=sqrt(vx*vx+vy*vy)+1.e-8;
++ D[0*dim+0]=h/(2*vel)*vx*vx;
++ D[1*dim+0]=h/(2*vel)*vy*vx;
++ D[0*dim+1]=h/(2*vel)*vx*vy;
++ D[1*dim+1]=h/(2*vel)*vy*vy;
++ }
++ break;
++ default:
++ _error_("Stabilization "<GetInputAverage(&vx);
+- if(dim==2) vyaverage_input->GetInputAverage(&vy);
+- D[0*dim+0]=h/2.0*fabs(vx);
+- if(dim==2) D[1*dim+1]=h/2.0*fabs(vy);
+- }
+ if(stabilization==1 || stabilization==2){
+ if(dim==1) D[0]=D_scalar*D[0];
+ else{
Index: /issm/oecreview/Archive/18296-19100/ISSM-18339-18340.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18339-18340.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18339-18340.diff (revision 19102)
@@ -0,0 +1,346 @@
+Index: ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 0)
++++ ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 18340)
+@@ -0,0 +1,6 @@
++156c153,155
++< # TODO: Can't this be integrated into the following logic?
++---
++> # TODO: Can't this be integrated into the following logic?
++> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
++> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
+Index: ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 0)
++++ ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 18340)
+@@ -0,0 +1,51 @@
++#!/bin/bash
++set -eu
++
++#Some cleanup
++rm -rf Dakota
++rm -rf src
++rm -rf build
++rm -rf install
++mkdir src build install
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz'
++
++#Untar
++tar -zxvf dakota-5.3.1-public-src.tar.gz
++
++#Move Dakota to src directory
++mv dakota-5.3.1.src/* src
++rm -rf dakota-5.3.1.src
++
++#Set up Dakota cmake variables and config
++export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
++export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
++cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
++patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
++patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
++patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.patch
++
++#Apply patches
++patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch
++patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch
++patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch
++patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
++patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
++
++#Configure dakota
++cd $DAK_BUILD
++cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++cd ..
++
++#Compile and install dakota
++cd $DAK_BUILD
++if [ $# -eq 0 ];
++then
++ make
++ make install
++else
++ make -j $1
++ make -j $1 install
++fi
++cd ..
+
+Property changes on: ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18339)
++++ ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18340)
+@@ -1,61 +0,0 @@
+-#!/bin/bash
+-
+-#Some cleanup
+-rm -rf install petsc-3.4.2 src
+-mkdir install src
+-
+-#Download from ISSM server
+-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
+-
+-#Untar and move petsc to install directory
+-tar -zxvf petsc-3.4.2.tar.gz
+-mv petsc-3.4.2/* src/
+-rm -rf petsc-3.4.2
+-
+-#configure
+-cd src
+-./config/configure.py \
+- --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+- --PETSC_ARCH="$ISSM_ARCH" \
+- --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+- --with-batch=1 \
+- --with-debugging=0 \
+- --with-shared-libraries=1 \
+- --known-mpi-shared-libraries=1 \
+- --with-mpi=1 \
+- --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
+- --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
+- --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
+- --download-scalapack=yes \
+- --download-blacs=yes \
+- --download-mumps=yes \
+- --download-metis=yes \
+- --download-parmetis=yes \
+- --download-trilinos=yes \
+- --download-euclid=yes \
+- --download-hypre=yes \
+- --COPTFLAGS="-lmpi -O3" \
+- --FOPTFLAGS="-lmpi -O3" \
+- --CXXOPTFLAGS="-lmpi -O3"
+-
+-#prepare script to reconfigure petsc
+-cat > script.queue << EOF
+-#PBS -S /bin/bash
+-#PBS -l select=1:ncpus=1:model=wes
+-#PBS -l walltime=200
+-#PBS -W group_list=s1010
+-#PBS -m e
+-
+-. /usr/share/modules/init/bash
+-module load comp-intel/2012.0.032
+-module load mpi-sgi/mpt.2.06rp16
+-
+-export PATH="$PATH:."
+-export MPI_GROUP_MAX=64
+-mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
+-EOF
+-
+-#print instructions
+-echo "== Now: cd src/ "
+-echo "== qsub -q devel script.queue "
+-echo "== Then run reconfigure script generated by PETSc and follow instructions"
+Index: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 0)
++++ ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18340)
+@@ -0,0 +1,61 @@
++#!/bin/bash
++
++#Some cleanup
++rm -rf install petsc-3.4.2 src
++mkdir install src
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
++
++#Untar and move petsc to install directory
++tar -zxvf petsc-3.4.2.tar.gz
++mv petsc-3.4.2/* src/
++rm -rf petsc-3.4.2
++
++#configure
++cd src
++./config/configure.py \
++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
++ --PETSC_ARCH="$ISSM_ARCH" \
++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
++ --with-batch=1 \
++ --with-debugging=0 \
++ --with-shared-libraries=1 \
++ --known-mpi-shared-libraries=1 \
++ --with-mpi=1 \
++ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
++ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
++ --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
++ --download-scalapack=yes \
++ --download-blacs=yes \
++ --download-mumps=yes \
++ --download-metis=yes \
++ --download-parmetis=yes \
++ --download-trilinos=yes \
++ --download-euclid=yes \
++ --download-hypre=yes \
++ --COPTFLAGS="-lmpi -O3" \
++ --FOPTFLAGS="-lmpi -O3" \
++ --CXXOPTFLAGS="-lmpi -O3"
++
++#prepare script to reconfigure petsc
++cat > script.queue << EOF
++#PBS -S /bin/bash
++#PBS -l select=1:ncpus=1:model=wes
++#PBS -l walltime=200
++#PBS -W group_list=s1010
++#PBS -m e
++
++. /usr/share/modules/init/bash
++module load comp-intel/2012.0.032
++module load mpi-sgi/mpt.2.06rp16
++
++export PATH="$PATH:."
++export MPI_GROUP_MAX=64
++mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
++EOF
++
++#print instructions
++echo "== Now: cd src/ "
++echo "== qsub -q devel script.queue "
++echo "== Then run reconfigure script generated by PETSc and follow instructions"
+
+Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 0)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18340)
+@@ -0,0 +1,62 @@
++#!/bin/bash
++set -eu
++
++#Some cleanup
++rm -rf install petsc-3.5.1 src
++mkdir install src
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.5.1.tar.gz' 'petsc-3.5.1.tar.gz'
++
++#Untar and move petsc to install directory
++tar -zxvf petsc-3.5.1.tar.gz
++mv petsc-3.5.1/* src/
++rm -rf petsc-3.5.1
++
++#configure
++cd src
++./config/configure.py \
++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
++ --PETSC_ARCH="$ISSM_ARCH" \
++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
++ --with-batch=1 \
++ --with-debugging=0 \
++ --with-shared-libraries=1 \
++ --known-mpi-shared-libraries=1 \
++ --with-mpi=1 \
++ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
++ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
++ --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
++ --download-scalapack=yes \
++ --download-mumps=yes \
++ --download-metis=yes \
++ --download-parmetis=yes \
++ --download-trilinos=yes \
++ --download-euclid=yes \
++ --download-hypre=yes \
++ --COPTFLAGS="-lmpi -O3" \
++ --FOPTFLAGS="-lmpi -O3" \
++ --CXXOPTFLAGS="-lmpi -O3"
++
++#prepare script to reconfigure petsc
++cat > script.queue << EOF
++#PBS -S /bin/bash
++#PBS -l select=1:ncpus=1:model=wes
++#PBS -l walltime=200
++#PBS -W group_list=s1010
++#PBS -m e
++
++. /usr/share/modules/init/bash
++module load comp-intel/2012.0.032
++module load math/intel_mkl_64_10.0.011
++module load mpi-sgi/mpt.2.06rp16
++
++export PATH="$PATH:."
++export MPI_GROUP_MAX=64
++mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
++EOF
++
++#print instructions
++echo "== Now: cd src/ "
++echo "== qsub -q devel script.queue "
++echo "== Then run reconfigure script generated by PETSc and follow instructions"
+
+Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh (revision 0)
++++ ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh (revision 18340)
+@@ -0,0 +1,47 @@
++#!/bin/bash
++set -eu
++
++#Note of caution: stop after boostrap phase, and run
++#bjam --debug-configuration, to figure out which paths boost is using to include
++#python. make sure everyone of these paths is covered by python. If not, just make
++#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
++#to get the boost library to include python support without doing that.
++
++#Some cleanup
++rm -rf install boost_1_55_0 src
++mkdir install src
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'
++
++#Untar
++tar -zxvf boost_1_55_0.tar.gz
++
++#Move boost into install directory
++mv boost_1_55_0/* src
++rm -rf boost_1_55_0
++
++#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
++#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
++#patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
++#patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
++#patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
++
++#Configure and compile
++cd src
++./bootstrap.sh \
++ --prefix="$ISSM_DIR/externalpackages/boost/install" \
++ --with-python=python2.7 \
++ --with-python-root="$ISSM_DIR/externalpackages/python/install" \
++ --with-toolset=intel-linux
++
++#Compile boost
++# Need gcc with iconv installed in a location that has been added to your path
++./b2 toolset=intel-linux cxxflags=-static-libstdc++ linkflags=-static-libstdc++ threading=multi install
++#./bjam install
++
++#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal
++
++#put bjam into install also:
++mkdir ../install/bin
++cp bjam ../install/bin
+
+Property changes on: ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18340-18341.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18340-18341.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18340-18341.diff (revision 19102)
@@ -0,0 +1,54 @@
+Index: ../trunk-jpl/externalpackages/triangle/install.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/triangle/install.sh (revision 0)
++++ ../trunk-jpl/externalpackages/triangle/install.sh (revision 18341)
+@@ -0,0 +1,27 @@
++#!/bin/bash
++set -eu
++
++#Some cleanup
++rm -rf install src triangle
++mkdir install src
++
++#Download from ISSM server
++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
++
++#Untar
++cd src
++mkdir src
++cp ../triangle.zip ./
++unzip triangle.zip
++
++mv ./*.c ./src
++mv ./*.h ./src
++
++cp ../configs/triangle-libtool.tar.gz ./
++tar -xvf ./triangle-libtool.tar.gz
++
++autoreconf -ivf
++./configure.sh --prefix="${ISSM_DIR}/externalpackages/triangle/install"
++
++make
++make install
+
+Property changes on: ../trunk-jpl/externalpackages/triangle/install.sh
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
+Index: ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
+Index: ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz
+===================================================================
+--- ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz (revision 18340)
++++ ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz (revision 18341)
+
+Property changes on: ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz
+___________________________________________________________________
+Added: svn:mime-type
+## -0,0 +1 ##
++application/octet-stream
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18341-18342.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18341-18342.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18341-18342.diff (revision 19102)
@@ -0,0 +1,30 @@
+Index: ../trunk-jpl/externalpackages/triangle/install.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/triangle/install.sh (revision 18341)
++++ ../trunk-jpl/externalpackages/triangle/install.sh (revision 18342)
+@@ -3,7 +3,7 @@
+
+ #Some cleanup
+ rm -rf install src triangle
+-mkdir install src
++mkdir install src ./src/m4
+
+ #Download from ISSM server
+ $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
+@@ -14,6 +14,7 @@
+ cp ../triangle.zip ./
+ unzip triangle.zip
+
++rm ./makefile
+ mv ./*.c ./src
+ mv ./*.h ./src
+
+@@ -21,7 +22,7 @@
+ tar -xvf ./triangle-libtool.tar.gz
+
+ autoreconf -ivf
+-./configure.sh --prefix="${ISSM_DIR}/externalpackages/triangle/install"
++./configure --prefix="${ISSM_DIR}/externalpackages/triangle/install"
+
+ make
+ make install
Index: /issm/oecreview/Archive/18296-19100/ISSM-18342-18343.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18342-18343.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18342-18343.diff (revision 19102)
@@ -0,0 +1,11 @@
+Index: ../trunk-jpl/externalpackages/triangle/install.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/triangle/install.sh (revision 18342)
++++ ../trunk-jpl/externalpackages/triangle/install.sh (revision 18343)
+@@ -26,3 +26,6 @@
+
+ make
+ make install
++
++#Patch triangle.h
++patch ../install/include/triangle.h ../triangle.h.patch
Index: /issm/oecreview/Archive/18296-19100/ISSM-18343-18344.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18343-18344.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18343-18344.diff (revision 19102)
@@ -0,0 +1,698 @@
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18343)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18344)
+@@ -70,6 +70,9 @@
+ if(stabilization==3){
+ iomodel->FetchDataToInput(elements,MasstransportSpcthicknessEnum); //for DG, we need the spc in the element
+ }
++ if(stabilization==4){
++ iomodel->FetchDataToInput(elements,MasstransportSpcthicknessEnum); //for FCT, we need the spc in the element (penlaties)
++ }
+
+ if(iomodel->domaintype!=Domain2DhorizontalEnum){
+ iomodel->FetchDataToInput(elements,MeshVertexonbaseEnum);
+@@ -147,10 +150,11 @@
+ int stabilization;
+ iomodel->Constant(&stabilization,MasstransportStabilizationEnum);
+
+- /*Do not add constraints in DG, they are weakly imposed*/
++ /*Do not add constraints in DG, they are weakly imposed*/
+ if(stabilization!=3){
+ IoModelToConstraintsx(constraints,iomodel,MasstransportSpcthicknessEnum,MasstransportAnalysisEnum,P1Enum);
+ }
++ /*Do not add constraints in FCT, they are imposed using penalties*/
+ }/*}}}*/
+ void MasstransportAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/
+
+@@ -674,7 +678,7 @@
+
+ }/*}}}*/
+ void MasstransportAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/
+- _error_("not implemented yet");
++ element->GetSolutionFromInputsOneDof(solution,ThicknessEnum);
+ }/*}}}*/
+ void MasstransportAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/
+ _error_("Not implemented yet");
+@@ -772,3 +776,148 @@
+ }
+ return;
+ }/*}}}*/
++
++/*Flux Correction Transport*/
++void MasstransportAnalysis::LumpedMassMatrix(Vector** pMlff,FemModel* femmodel){/*{{{*/
++
++ /*Intermediaries*/
++ int configuration_type;
++
++ /*Initialize Lumped mass matrix (actually we just save its diagonal)*/
++ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
++ int fsize = femmodel->nodes->NumberOfDofs(configuration_type,FsetEnum);
++ int flocalsize = femmodel->nodes->NumberOfDofsLocal(configuration_type,FsetEnum);
++ Vector* Mlff = new Vector(flocalsize,fsize);
++
++ /*Create and assemble matrix*/
++ for(int i=0;ielements->Size();i++){
++ Element* element = dynamic_cast(femmodel->elements->GetObjectByOffset(i));
++ ElementMatrix* MLe = this->CreateMassMatrix(element);
++ if(MLe){
++ MLe->Lump();
++ MLe->AddDiagonalToGlobal(Mlff);
++ }
++ delete MLe;
++ }
++ Mlff->Assemble();
++
++ /*Assign output pointer*/
++ *pMlff=Mlff;
++}/*}}}*/
++ElementMatrix* MasstransportAnalysis::CreateMassMatrix(Element* element){/*{{{*/
++
++ /* Check if ice in element */
++ if(!element->IsIceInElement()) return NULL;
++
++ /*Intermediaries*/
++ IssmDouble D,Jdet;
++ IssmDouble* xyz_list = NULL;
++
++ /*Fetch number of nodes and dof for this finite element*/
++ int numnodes = element->GetNumberOfNodes();
++
++ /*Initialize Element vector and other vectors*/
++ ElementMatrix* Me = element->NewElementMatrix();
++ IssmDouble* basis = xNew(numnodes);
++
++ /*Retrieve all inputs and parameters*/
++ element->GetVerticesCoordinates(&xyz_list);
++
++ /* Start looping on the number of gaussian points: */
++ Gauss* gauss=element->NewGauss(2);
++ for(int ig=gauss->begin();igend();ig++){
++ gauss->GaussPoint(ig);
++
++ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
++ element->NodalFunctions(basis,gauss);
++
++ D=gauss->weight*Jdet;
++ TripleMultiply(basis,1,numnodes,1,
++ &D,1,1,0,
++ basis,1,numnodes,0,
++ &Me->values[0],1);
++ }
++
++ /*Clean up and return*/
++ xDelete(xyz_list);
++ xDelete(basis);
++ delete gauss;
++ return Me;
++}/*}}}*/
++void MasstransportAnalysis::FctKMatrix(Matrix** pKff,Matrix** pKfs,FemModel* femmodel){/*{{{*/
++
++ /*Output*/
++ Matrix* Kff = NULL;
++ Matrix* Kfs = NULL;
++
++ /*Initialize Jacobian Matrix*/
++ AllocateSystemMatricesx(&Kff,&Kfs,NULL,NULL,femmodel);
++
++ /*Create and assemble matrix*/
++ for(int i=0;ielements->Size();i++){
++ Element* element = dynamic_cast(femmodel->elements->GetObjectByOffset(i));
++ ElementMatrix* Ke = this->CreateFctKMatrix(element);
++ if(Ke) Ke->AddToGlobal(Kff,Kfs);
++ delete Ke;
++ }
++ Kff->Assemble();
++ Kfs->Assemble();
++
++ /*Assign output pointer*/
++ *pKff=Kff;
++ *pKfs=Kfs;
++}/*}}}*/
++ElementMatrix* MasstransportAnalysis::CreateFctKMatrix(Element* element){/*{{{*/
++
++ /* Check if ice in element */
++ if(!element->IsIceInElement()) return NULL;
++
++ /*Intermediaries */
++ IssmDouble Jdet;
++ IssmDouble vx,vy;
++ IssmDouble* xyz_list = NULL;
++
++ /*Fetch number of nodes and dof for this finite element*/
++ int numnodes = element->GetNumberOfNodes();
++ int dim = 2;
++
++ /*Initialize Element vector and other vectors*/
++ ElementMatrix* Ke = element->NewElementMatrix();
++ IssmDouble* B = xNew(dim*numnodes);
++ IssmDouble* Bprime = xNew(dim*numnodes);
++ IssmDouble* D = xNewZeroInit(dim*dim);
++
++ /*Retrieve all inputs and parameters*/
++ element->GetVerticesCoordinates(&xyz_list);
++ Input* vxaverage_input=element->GetInput(VxEnum); _assert_(vxaverage_input);
++ Input* vyaverage_input=element->GetInput(VyEnum); _assert_(vyaverage_input);
++
++ /* Start looping on the number of gaussian points: */
++ Gauss* gauss=element->NewGauss(2);
++ for(int ig=gauss->begin();igend();ig++){
++ gauss->GaussPoint(ig);
++
++ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
++ GetB(B,element,dim,xyz_list,gauss);
++ GetBprime(Bprime,element,dim,xyz_list,gauss);
++ vxaverage_input->GetInputValue(&vx,gauss);
++ vyaverage_input->GetInputValue(&vy,gauss);
++
++ D[0*dim+0] = -gauss->weight*vx*Jdet;
++ D[1*dim+1] = -gauss->weight*vy*Jdet;
++
++ TripleMultiply(B,dim,numnodes,1,
++ D,dim,dim,0,
++ Bprime,dim,numnodes,0,
++ &Ke->values[0],1);
++
++ }
++
++ /*Clean up and return*/
++ xDelete(xyz_list);
++ xDelete(B);
++ xDelete(Bprime);
++ xDelete(D);
++ delete gauss;
++ return Ke;
++}/*}}}*/
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h (revision 18343)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h (revision 18344)
+@@ -35,5 +35,11 @@
+ void GradientJ(Vector* gradient,Element* element,int control_type,int control_index);
+ void InputUpdateFromSolution(IssmDouble* solution,Element* element);
+ void UpdateConstraints(FemModel* femmodel);
++
++ /*FCT*/
++ void LumpedMassMatrix(Vector** pMLff,FemModel* femmodel);
++ void FctKMatrix(Matrix** pKff,Matrix** pKfs,FemModel* femmodel);
++ ElementMatrix* CreateMassMatrix(Element* element);
++ ElementMatrix* CreateFctKMatrix(Element* element);
+ };
+ #endif
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 0)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18344)
+@@ -0,0 +1,161 @@
++/*!\file: solutionsequence_linear.cpp
++ * \brief: numerical core of linear solutions
++ */
++
++#include "../toolkits/toolkits.h"
++#include "../classes/classes.h"
++#include "../shared/shared.h"
++#include "../modules/modules.h"
++
++void solutionsequence_fct(FemModel* femmodel){
++
++ /*intermediary: */
++ Vector* Mlf = NULL;
++ Matrix* Kff = NULL;
++ Matrix* Kfs = NULL;
++ Vector* ug = NULL;
++ Vector* uf = NULL;
++ Vector* ys = NULL;
++
++ IssmDouble theta,deltat;
++ int dof,ncols,ncols2,ncols3,rstart,rend;
++ int configuration_type,analysis_type;
++ double d,diagD,mi;
++ double dmax = 0.;
++ int* cols = NULL;
++ int* cols2 = NULL;
++ int* cols3 = NULL;
++ double* vals = NULL;
++ double* vals2 = NULL;
++ double* vals3 = NULL;
++
++ /*Create analysis*/
++ MasstransportAnalysis* analysis = new MasstransportAnalysis();
++
++ /*Recover parameters: */
++ femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
++ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
++ femmodel->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
++ femmodel->UpdateConstraintsx();
++ theta = 0.5;
++
++ /*Create lumped mass matrix*/
++ analysis->LumpedMassMatrix(&Mlf,femmodel);
++ analysis->FctKMatrix(&Kff,&Kfs,femmodel);
++
++ /*Create Dff Matrix*/
++ #ifdef _HAVE_PETSC_
++ Mat Kff_transp = NULL;
++ Mat Dff_petsc = NULL;
++ Mat LHS = NULL;
++ Mat Kff_petsc = Kff->pmatrix->matrix;
++ Vec Mlf_petsc = Mlf->pvector->vector;
++ MatTranspose(Kff_petsc,MAT_INITIAL_MATRIX,&Kff_transp);
++ MatDuplicate(Kff_petsc,MAT_SHARE_NONZERO_PATTERN,&Dff_petsc);
++ MatGetOwnershipRange(Kff_transp,&rstart,&rend);
++ for(int row=rstart; rowdmax) dmax = fabs(d);
++ MatSetValues(LHS,1,&row,1,&cols[j],(const double*)&d,INSERT_VALUES);
++ }
++ MatRestoreRow(Kff_petsc,row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(Dff_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
++ }
++
++ /*Penalize Dirichlet boundary*/
++ dmax = dmax * 1.e+3;
++ for(int i=0;iconstraints->Size();i++){
++ Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
++ if(constraint->InAnalysis(analysis_type)){
++ constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
++ if(dof!=-1){
++ MatSetValues(LHS,1,&dof,1,&dof,(const double*)&dmax,INSERT_VALUES);
++ }
++ }
++ }
++ MatAssemblyBegin(LHS,MAT_FINAL_ASSEMBLY);
++ MatAssemblyEnd( LHS,MAT_FINAL_ASSEMBLY);
++
++ /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
++ GetSolutionFromInputsx(&ug,femmodel);
++ Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
++ delete ug;
++ Vec u = uf->pvector->vector;
++ Vec Ku = NULL;
++ Vec Du = NULL;
++ Vec RHS = NULL;
++ VecDuplicate(u,&Ku);
++ VecDuplicate(u,&Du);
++ VecDuplicate(u,&RHS);
++ MatMult(Kff_petsc,u,Ku);
++ MatMult(Dff_petsc,u,Du);
++ VecPointwiseMult(RHS,Mlf_petsc,u);
++ VecAXPBYPCZ(RHS,(1-theta)*deltat,(1-theta)*deltat,1,Ku,Du);// RHS = M*u + (1-theta)*deltat*K*u + (1-theta)*deltat*D*u
++ VecFree(&Ku);
++ VecFree(&Du);
++ MatFree(&Dff_petsc);
++ delete uf;
++
++ /*Penalize Dirichlet boundary*/
++ for(int i=0;iconstraints->Size();i++){
++ Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
++ if(constraint->InAnalysis(analysis_type)){
++ constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
++ d = d*dmax;
++ if(dof!=-1){
++ VecSetValues(RHS,1,&dof,(const double*)&d,INSERT_VALUES);
++ }
++ }
++ }
++
++ /*Go solve!*/
++ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
++ MatFree(&LHS);
++ VecFree(&RHS);
++ uf =new Vector(u);
++ VecFree(&u);
++
++ Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);delete uf; delete ys;
++ InputUpdateFromSolutionx(femmodel,ug);
++ delete ug;
++
++ #else
++ _error_("PETSc needs to be installed");
++ #endif
++
++ delete Mlf;
++ delete Kff;
++ delete Kfs;
++ delete analysis;
++
++}
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequences.h
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequences.h (revision 18343)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequences.h (revision 18344)
+@@ -15,6 +15,7 @@
+ void solutionsequence_hydro_nonlinear(FemModel* femmodel);
+ void solutionsequence_nonlinear(FemModel* femmodel,bool conserve_loads);
+ void solutionsequence_newton(FemModel* femmodel);
++void solutionsequence_fct(FemModel* femmodel);
+ void solutionsequence_FScoupling_nonlinear(FemModel* femmodel,bool conserve_loads);
+ void solutionsequence_linear(FemModel* femmodel);
+ void solutionsequence_la(FemModel* femmodel);
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18343)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18344)
+@@ -353,6 +353,7 @@
+ ./solutionsequences/solutionsequence_linear.cpp\
+ ./solutionsequences/solutionsequence_nonlinear.cpp\
+ ./solutionsequences/solutionsequence_newton.cpp\
++ ./solutionsequences/solutionsequence_fct.cpp\
+ ./solutionsequences/convergence.cpp\
+ ./classes/Options/Options.h\
+ ./classes/Options/Options.cpp\
+Index: ../trunk-jpl/src/c/cores/masstransport_core.cpp
+===================================================================
+--- ../trunk-jpl/src/c/cores/masstransport_core.cpp (revision 18343)
++++ ../trunk-jpl/src/c/cores/masstransport_core.cpp (revision 18344)
+@@ -15,7 +15,7 @@
+ int numoutputs,domaintype;
+ bool save_results;
+ bool isFS,isfreesurface,dakota_analysis;
+- int solution_type;
++ int solution_type,stabilization;
+ char** requested_outputs = NULL;
+
+ /*activate configuration*/
+@@ -28,6 +28,7 @@
+ femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum);
+ femmodel->parameters->FindParam(&domaintype,DomainTypeEnum);
+ femmodel->parameters->FindParam(&numoutputs,MasstransportNumRequestedOutputsEnum);
++ femmodel->parameters->FindParam(&stabilization,MasstransportStabilizationEnum);
+ if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,MasstransportRequestedOutputsEnum);
+
+ /*Calculate new Surface Mass Balance (SMB)*/
+@@ -48,7 +49,12 @@
+ }
+ else{
+ if(VerboseSolution()) _printf0_(" call computational core\n");
+- solutionsequence_linear(femmodel);
++ if(stabilization==4){
++ solutionsequence_fct(femmodel);
++ }
++ else{
++ solutionsequence_linear(femmodel);
++ }
+ femmodel->parameters->SetParam(ThicknessEnum,InputToExtrudeEnum);
+ extrudefrombase_core(femmodel);
+ femmodel->parameters->SetParam(BaseEnum,InputToExtrudeEnum);
+Index: ../trunk-jpl/src/c/classes/matrix/ElementMatrix.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/matrix/ElementMatrix.cpp (revision 18343)
++++ ../trunk-jpl/src/c/classes/matrix/ElementMatrix.cpp (revision 18344)
+@@ -328,6 +328,39 @@
+
+ }
+ /*}}}*/
++void ElementMatrix::AddDiagonalToGlobal(Vector* pf){/*{{{*/
++
++ IssmDouble* localvalues=NULL;
++
++ /*Check that pf is not NULL*/
++ _assert_(pf);
++
++ /*In debugging mode, check consistency (no NaN, and values not too big)*/
++ this->CheckConsistency();
++
++ if(this->dofsymmetrical){
++ /*only use row dofs to add values into global matrices: */
++
++ if(this->row_fsize){
++ /*first, retrieve values that are in the f-set from the g-set values matrix: */
++ localvalues=xNew(this->row_fsize);
++ for(int i=0;irow_fsize;i++){
++ localvalues[i] = this->values[this->ncols*this->row_flocaldoflist[i]+ this->row_flocaldoflist[i]];
++ }
++
++ /*add local values into global matrix, using the fglobaldoflist: */
++ pf->SetValues(this->row_fsize,this->row_fglobaldoflist,localvalues,ADD_VAL);
++
++ /*Free ressources:*/
++ xDelete(localvalues);
++ }
++ }
++ else{
++ _error_("non dofsymmetrical matrix AddToGlobal routine not support yet!");
++ }
++
++}
++/*}}}*/
+ void ElementMatrix::CheckConsistency(void){/*{{{*/
+ /*Check element matrix values, only in debugging mode*/
+ #ifdef _ISSM_DEBUG_
+Index: ../trunk-jpl/src/c/classes/matrix/ElementMatrix.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/matrix/ElementMatrix.h (revision 18343)
++++ ../trunk-jpl/src/c/classes/matrix/ElementMatrix.h (revision 18344)
+@@ -59,6 +59,7 @@
+ /*ElementMatrix specific routines*/
+ void AddToGlobal(Matrix* Kff, Matrix* Kfs);
+ void AddToGlobal(Matrix* Jff);
++ void AddDiagonalToGlobal(Vector* pf);
+ void Echo(void);
+ void CheckConsistency(void);
+ void StaticCondensation(int numindices,int* indices);
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h (revision 18343)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h (revision 18344)
+@@ -37,6 +37,7 @@
+ /*Constraint virtual functions definitions: {{{*/
+ void ConstrainNode(Nodes* nodes,Parameters* parameters);
+ bool InAnalysis(int analysis_type);
++ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters){_error_("not implemented yet");};
+ /*}}}*/
+ /*SpcDynamic management:{{{ */
+ int GetNodeId();
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h (revision 18343)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h (revision 18344)
+@@ -36,6 +36,7 @@
+ /*Constraint virtual functions definitions: {{{*/
+ void ConstrainNode(Nodes* nodes,Parameters* parameters);
+ bool InAnalysis(int analysis_type);
++ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters){_error_("not implemented yet");};
+ /*}}}*/
+ /*SpcStatic management:{{{ */
+ int GetNodeId();
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h (revision 18343)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h (revision 18344)
+@@ -13,13 +13,14 @@
+ class SpcTransient: public Constraint{
+
+ private:
+- int sid; /*! id, to track it*/
+- int nodeid; /*!node id*/
+- int dof; /*!component*/
+- IssmDouble* values; /*different values in time*/
+- IssmDouble* times; /*different time steps*/
+- int nsteps; /*number of time steps*/
+- int analysis_type;
++ bool penalty; /*Is this a penalty constraint */
++ int sid; /* id, to track it */
++ int nodeid; /*node id */
++ int dof; /*component */
++ IssmDouble *values; /*different values in time */
++ IssmDouble *times; /*different time steps */
++ int nsteps; /*number of time steps */
++ int analysis_type;
+
+ public:
+
+@@ -38,6 +39,7 @@
+ /*Constraint virtual functions definitions: {{{*/
+ void ConstrainNode(Nodes* nodes,Parameters* parameters);
+ bool InAnalysis(int analysis_type);
++ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters);
+ /*}}}*/
+ /*SpcTransient management:{{{ */
+ int GetNodeId();
+Index: ../trunk-jpl/src/c/classes/Constraints/Constraint.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/Constraint.h (revision 18343)
++++ ../trunk-jpl/src/c/classes/Constraints/Constraint.h (revision 18344)
+@@ -20,6 +20,7 @@
+
+ virtual ~Constraint(){};
+ virtual void ConstrainNode(Nodes* nodes,Parameters* parameters)=0;
++ virtual void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters)=0;
+ virtual bool InAnalysis(int analysis_type)=0;
+
+ };
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp (revision 18343)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp (revision 18344)
+@@ -14,25 +14,27 @@
+
+ /*SpcTransient constructors and destructor*/
+ SpcTransient::SpcTransient(){/*{{{*/
+- sid=-1;
+- nodeid=-1;
+- dof=-1;
+- values=NULL;
+- times=NULL;
+- nsteps=-1;
+- analysis_type=-1;
++ penalty = false;
++ sid = -1;
++ nodeid = -1;
++ dof = -1;
++ values = NULL;
++ times = NULL;
++ nsteps = -1;
++ analysis_type = -1;
+ return;
+ }
+ /*}}}*/
+ SpcTransient::SpcTransient(int spc_sid,int spc_nodeid, int spc_dof,int spc_nsteps, IssmDouble* spc_times, IssmDouble* spc_values,int spc_analysis_type){/*{{{*/
+
+- sid=spc_sid;
+- nodeid=spc_nodeid;
+- dof=spc_dof;
+- nsteps=spc_nsteps;
++ penalty= false;
++ sid = spc_sid;
++ nodeid = spc_nodeid;
++ dof = spc_dof;
++ nsteps = spc_nsteps;
+ if(spc_nsteps){
+- values=xNew(spc_nsteps);
+- times=xNew(spc_nsteps);
++ values = xNew(spc_nsteps);
++ times = xNew(spc_nsteps);
+ xMemCpy(values,spc_values,nsteps);
+ xMemCpy(times,spc_times,nsteps);
+ }
+@@ -68,7 +70,9 @@
+ this->Echo();
+ }
+ /*}}}*/
+-int SpcTransient::Id(void){ return sid; }/*{{{*/
++int SpcTransient::Id(void){/*{{{*/
++ return sid;
++}
+ /*}}}*/
+ int SpcTransient::ObjectEnum(void){/*{{{*/
+
+@@ -100,7 +104,7 @@
+ /*Chase through nodes and find the node to which this SpcTransient applys: */
+ node=(Node*)nodes->GetObjectById(NULL,nodeid);
+
+- if(node){ //in case the spc is dealing with a node on another cpu
++ if(!this->penalty && node){ //in case the spc is dealing with a node on another cpu
+
+ /*Retrieve time in parameters: */
+ parameters->FindParam(&time,TimeEnum);
+@@ -136,7 +140,63 @@
+ }
+ }
+ /*}}}*/
++void SpcTransient::PenaltyDofAndValue(int* pdof,IssmDouble* pvalue,Nodes* nodes,Parameters* parameters){/*{{{*/
+
++ if(!this->penalty) _error_("cannot return dof and value for non penalty constraint");
++
++ Node *node = NULL;
++ IssmDouble time = 0.;
++ int i,gdof;
++ IssmDouble alpha = -1.;
++ IssmDouble value;
++ bool found = false;
++
++ /*Chase through nodes and find the node to which this SpcTransient applys: */
++ node=(Node*)nodes->GetObjectById(NULL,nodeid);
++
++ if(node){ //in case the spc is dealing with a node on another cpu
++
++ /*Retrieve time in parameters: */
++ parameters->FindParam(&time,TimeEnum);
++
++ /*Now, go fetch value for this time: */
++ if (time<=times[0]){
++ value=values[0];
++ found=true;
++ }
++ else if (time>=times[nsteps-1]){
++ value=values[nsteps-1];
++ found=true;
++ }
++ else{
++ for(i=0;iGetDof(dof,GsetEnum);
++ if(xIsNan(value)){
++ gdof = -1;
++ }
++ }
++ else{
++ value = NAN;
++ gdof = -1;
++ }
++
++ /*Assign output pointers*/
++ *pdof = gdof;
++ *pvalue = value;
++}
++/*}}}*/
++
+ /*SpcTransient functions*/
+ int SpcTransient::GetDof(){/*{{{*/
+ return dof;
+Index: ../trunk-jpl/src/c
+===================================================================
+--- ../trunk-jpl/src/c (revision 18343)
++++ ../trunk-jpl/src/c (revision 18344)
+
+Property changes on: ../trunk-jpl/src/c
+___________________________________________________________________
+Modified: svn:ignore
+## -4,6 +4,8 ##
+ *.o
+ *.obj
+ *.exe
++issm
++kriging
+ appscan.*
+ ouncemake*
+ list
Index: /issm/oecreview/Archive/18296-19100/ISSM-18344-18345.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18344-18345.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18344-18345.diff (revision 19102)
@@ -0,0 +1,274 @@
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18344)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18345)
+@@ -804,6 +804,26 @@
+ /*Assign output pointer*/
+ *pMlff=Mlff;
+ }/*}}}*/
++void MasstransportAnalysis::MassMatrix(Matrix** pMff,FemModel* femmodel){/*{{{*/
++
++ /*Initialize Mass matrix*/
++ Matrix *Mff = NULL;
++ AllocateSystemMatricesx(&Mff,NULL,NULL,NULL,femmodel);
++
++ /*Create and assemble matrix*/
++ for(int i=0;ielements->Size();i++){
++ Element* element = dynamic_cast(femmodel->elements->GetObjectByOffset(i));
++ ElementMatrix* MLe = this->CreateMassMatrix(element);
++ if(MLe){
++ MLe->AddToGlobal(Mff);
++ }
++ delete MLe;
++ }
++ Mff->Assemble();
++
++ /*Assign output pointer*/
++ *pMff=Mff;
++}/*}}}*/
+ ElementMatrix* MasstransportAnalysis::CreateMassMatrix(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+@@ -865,7 +885,12 @@
+
+ /*Assign output pointer*/
+ *pKff=Kff;
+- *pKfs=Kfs;
++ if(pKfs){
++ *pKfs=Kfs;
++ }
++ else{
++ delete Kfs;
++ }
+ }/*}}}*/
+ ElementMatrix* MasstransportAnalysis::CreateFctKMatrix(Element* element){/*{{{*/
+
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h (revision 18344)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.h (revision 18345)
+@@ -38,6 +38,7 @@
+
+ /*FCT*/
+ void LumpedMassMatrix(Vector** pMLff,FemModel* femmodel);
++ void MassMatrix(Matrix** pMff,FemModel* femmodel);
+ void FctKMatrix(Matrix** pKff,Matrix** pKfs,FemModel* femmodel);
+ ElementMatrix* CreateMassMatrix(Element* element);
+ ElementMatrix* CreateFctKMatrix(Element* element);
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18344)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18345)
+@@ -10,12 +10,12 @@
+ void solutionsequence_fct(FemModel* femmodel){
+
+ /*intermediary: */
+- Vector* Mlf = NULL;
+- Matrix* Kff = NULL;
+- Matrix* Kfs = NULL;
+- Vector* ug = NULL;
+- Vector* uf = NULL;
+- Vector* ys = NULL;
++ Vector* Ml = NULL;
++ Matrix* K = NULL;
++ Matrix* Mc = NULL;
++ Vector* ug = NULL;
++ Vector* uf = NULL;
++ Vector* ys = NULL;
+
+ IssmDouble theta,deltat;
+ int dof,ncols,ncols2,ncols3,rstart,rend;
+@@ -40,56 +40,58 @@
+ theta = 0.5;
+
+ /*Create lumped mass matrix*/
+- analysis->LumpedMassMatrix(&Mlf,femmodel);
+- analysis->FctKMatrix(&Kff,&Kfs,femmodel);
++ analysis->LumpedMassMatrix(&Ml,femmodel);
++ analysis->MassMatrix(&Mc,femmodel);
++ analysis->FctKMatrix(&K,NULL,femmodel);
+
+- /*Create Dff Matrix*/
++ /*Create D Matrix*/
+ #ifdef _HAVE_PETSC_
+- Mat Kff_transp = NULL;
+- Mat Dff_petsc = NULL;
+- Mat LHS = NULL;
+- Mat Kff_petsc = Kff->pmatrix->matrix;
+- Vec Mlf_petsc = Mlf->pvector->vector;
+- MatTranspose(Kff_petsc,MAT_INITIAL_MATRIX,&Kff_transp);
+- MatDuplicate(Kff_petsc,MAT_SHARE_NONZERO_PATTERN,&Dff_petsc);
+- MatGetOwnershipRange(Kff_transp,&rstart,&rend);
++ Mat K_transp = NULL;
++ Mat D_petsc = NULL;
++ Mat LHS = NULL;
++ Mat K_petsc = K->pmatrix->matrix;
++ Vec Ml_petsc = Ml->pvector->vector;
++ Mat Mc_petsc = Mc->pmatrix->matrix;
++ MatTranspose(K_petsc,MAT_INITIAL_MATRIX,&K_transp);
++ MatDuplicate(K_petsc,MAT_SHARE_NONZERO_PATTERN,&D_petsc);
++ MatGetOwnershipRange(K_transp,&rstart,&rend);
+ for(int row=rstart; rowdmax) dmax = fabs(d);
+ MatSetValues(LHS,1,&row,1,&cols[j],(const double*)&d,INSERT_VALUES);
+ }
+- MatRestoreRow(Kff_petsc,row,&ncols, (const int**)&cols, (const double**)&vals);
+- MatRestoreRow(Dff_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
++ MatRestoreRow(K_petsc,row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+ }
+
+ /*Penalize Dirichlet boundary*/
+@@ -117,13 +119,12 @@
+ VecDuplicate(u,&Ku);
+ VecDuplicate(u,&Du);
+ VecDuplicate(u,&RHS);
+- MatMult(Kff_petsc,u,Ku);
+- MatMult(Dff_petsc,u,Du);
+- VecPointwiseMult(RHS,Mlf_petsc,u);
++ MatMult(K_petsc,u,Ku);
++ MatMult(D_petsc,u,Du);
++ VecPointwiseMult(RHS,Ml_petsc,u);
+ VecAXPBYPCZ(RHS,(1-theta)*deltat,(1-theta)*deltat,1,Ku,Du);// RHS = M*u + (1-theta)*deltat*K*u + (1-theta)*deltat*D*u
+ VecFree(&Ku);
+ VecFree(&Du);
+- MatFree(&Dff_petsc);
+ delete uf;
+
+ /*Penalize Dirichlet boundary*/
+@@ -137,11 +138,79 @@
+ }
+ }
+ }
++ VecAssemblyBegin(RHS);
++ VecAssemblyEnd( RHS);
+
+ /*Go solve!*/
+ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
+ MatFree(&LHS);
+ VecFree(&RHS);
++
++ /*Richardson to calculate udot*/
++ Vec udot = NULL;
++ VecDuplicate(u,&udot);
++ VecZeroEntries(udot);
++ Vec temp1 = NULL; VecDuplicate(u,&temp1);
++ Vec temp2 = NULL; VecDuplicate(u,&temp2);
++ for(int i=0;i<5;i++){
++ /*udot_new = udot_old + Ml^-1 (K^(n+1) u -- Mc udot_old)*/
++ MatMult(Mc_petsc,udot,temp1);
++ MatMult(K_petsc, u, temp2);
++ VecAXPBY(temp2,-1.,1.,temp1); // temp2 = (K^(n+1) u -- Mc udot_old)
++ VecPointwiseDivide(temp1,temp2,Ml_petsc); //temp1 = Ml^-1 temp2
++ VecAXPBY(udot,1.,1.,temp1);
++ }
++ VecFree(&temp1);
++ VecFree(&temp2);
++
++ /*Serialize u and udot*/
++ IssmDouble* udot_serial = NULL;
++ IssmDouble* u_serial = NULL;
++ VecToMPISerial(&udot_serial,udot,IssmComm::GetComm());
++ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
++
++
++ /*Anti diffusive fluxes*/
++ Mat F = NULL;
++ Vec Fbar = NULL;
++ VecDuplicate(u,&Fbar);
++ MatDuplicate(D_petsc,MAT_SHARE_NONZERO_PATTERN,&F);
++ for(int row=rstart; row(udot_serial);
++ xDelete(u_serial);
++
++ /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
++ VecDuplicate(u,&temp1);
++ VecPointwiseDivide(temp1,Fbar,Ml_petsc); //temp1 = Ml^-1 temp2
++ VecAXPBY(udot,1.,1.,temp1);
++ VecAXPY(u,deltat,temp1);
++ VecFree(&Fbar);
++ VecFree(&udot);
++ VecFree(&temp1);
++
+ uf =new Vector(u);
+ VecFree(&u);
+
+@@ -153,9 +222,8 @@
+ _error_("PETSc needs to be installed");
+ #endif
+
+- delete Mlf;
+- delete Kff;
+- delete Kfs;
++ delete Ml;
++ delete K;
+ delete analysis;
+
+ }
Index: /issm/oecreview/Archive/18296-19100/ISSM-18345-18346.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18345-18346.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18345-18346.diff (revision 19102)
@@ -0,0 +1,44 @@
+Index: ../trunk-jpl/src/m/classes/masstransport.py
+===================================================================
+--- ../trunk-jpl/src/m/classes/masstransport.py (revision 18345)
++++ ../trunk-jpl/src/m/classes/masstransport.py (revision 18346)
+@@ -34,7 +34,7 @@
+ string="%s\n%s"%(string,fielddisplay(self,'isfreesurface','do we use free surfaces (FS only) are mass conservation'))
+ string="%s\n%s"%(string,fielddisplay(self,'min_thickness','minimum ice thickness allowed [m]'))
+ string="%s\n%s"%(string,fielddisplay(self,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' '))
+- string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin'))
++ string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin, 4: Flux Correction Transport'))
+ string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested'))
+
+ return string
+@@ -73,7 +73,7 @@
+ md = checkfield(md,'fieldname','masstransport.calvingrate','NaN',1,'size',[md.mesh.numberofvertices],'>=',0)
+ md = checkfield(md,'fieldname','masstransport.isfreesurface','values',[0,1])
+ md = checkfield(md,'fieldname','masstransport.hydrostatic_adjustment','values',['Absolute','Incremental'])
+- md = checkfield(md,'fieldname','masstransport.stabilization','values',[0,1,2,3])
++ md = checkfield(md,'fieldname','masstransport.stabilization','values',[0,1,2,3,4])
+ md = checkfield(md,'fieldname','masstransport.min_thickness','>',0)
+ md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1)
+
+Index: ../trunk-jpl/src/m/classes/masstransport.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/masstransport.m (revision 18345)
++++ ../trunk-jpl/src/m/classes/masstransport.m (revision 18346)
+@@ -126,7 +126,7 @@
+
+ md = checkfield(md,'fieldname','masstransport.isfreesurface','values',[0 1]);
+ md = checkfield(md,'fieldname','masstransport.hydrostatic_adjustment','values',{'Absolute' 'Incremental'});
+- md = checkfield(md,'fieldname','masstransport.stabilization','values',[0 1 2 3]);
++ md = checkfield(md,'fieldname','masstransport.stabilization','values',[0 1 2 3 4]);
+ md = checkfield(md,'fieldname','masstransport.min_thickness','>',0);
+ md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1);
+
+@@ -138,7 +138,7 @@
+ fielddisplay(obj,'isfreesurface','do we use free surfaces (FS only) are mass conservation');
+ fielddisplay(obj,'min_thickness','minimum ice thickness allowed [m]');
+ fielddisplay(obj,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ');
+- fielddisplay(obj,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin');
++ fielddisplay(obj,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin, 4: Flux Correction Transport');
+
+ disp(sprintf('\n %s','Penalty options:'));
+ fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset');
Index: /issm/oecreview/Archive/18296-19100/ISSM-18346-18347.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18346-18347.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18346-18347.diff (revision 19102)
@@ -0,0 +1,115 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18346)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18347)
+@@ -166,41 +166,96 @@
+ /*Serialize u and udot*/
+ IssmDouble* udot_serial = NULL;
+ IssmDouble* u_serial = NULL;
+- VecToMPISerial(&udot_serial,udot,IssmComm::GetComm());
+- VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
++ IssmDouble* ml_serial = NULL;
++ VecToMPISerial(&udot_serial,udot ,IssmComm::GetComm());
++ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
++ VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
+
++ /*Anti diffusive fluxes*/
++ Vec Ri_plus = NULL;
++ Vec Ri_minus = NULL;
++ double uiLmax = 3.;
++ double uiLmin = 2.;
++ VecDuplicate(u,&Ri_plus);
++ VecDuplicate(u,&Ri_minus);
++ for(int row=rstart; row0.){
++ Pi_plus += d;
++ }
++ else{
++ Pi_minus += d;
++ }
++ }
++ }
+
+- /*Anti diffusive fluxes*/
+- Mat F = NULL;
++ /*Compute Qis and Ris*/
++ double Qi_plus = ml_serial[row]/deltat*(uiLmax - u_serial[row]);
++ double Qi_minus = ml_serial[row]/deltat*(uiLmin - u_serial[row]);
++ d = 1.;
++ if(Pi_plus!=0.) d = min(1.,Qi_plus/Pi_plus);
++ VecSetValue(Ri_plus,row,(const double)d,INSERT_VALUES);
++ d = 1.;
++ if(Pi_minus!=0.) d = min(1.,Qi_minus/Pi_minus);
++ VecSetValue(Ri_minus,row,(const double)d,INSERT_VALUES);
++
++ MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
++ }
++ VecAssemblyBegin(Ri_plus);
++ VecAssemblyEnd( Ri_plus);
++ VecAssemblyBegin(Ri_minus);
++ VecAssemblyEnd( Ri_minus);
++
++ /*Serialize Ris*/
++ IssmDouble* Ri_plus_serial = NULL;
++ IssmDouble* Ri_minus_serial = NULL;
++ VecToMPISerial(&Ri_plus_serial,Ri_plus,IssmComm::GetComm());
++ VecToMPISerial(&Ri_minus_serial,Ri_minus,IssmComm::GetComm());
++ VecFree(&Ri_plus);
++ VecFree(&Ri_minus);
++
++ /*Build fbar*/
+ Vec Fbar = NULL;
+ VecDuplicate(u,&Fbar);
+- MatDuplicate(D_petsc,MAT_SHARE_NONZERO_PATTERN,&F);
+ for(int row=rstart; row0){
++ d += min(Ri_plus_serial[row],Ri_minus_serial[cols[j]]) * f_ij;
++ }
++ else{
++ d += min(Ri_minus_serial[row],Ri_plus_serial[cols[j]]) * f_ij;
++ }
+ }
+- VecSetValue(Fbar,row,(const double)mi,INSERT_VALUES);
++ VecSetValue(Fbar,row,(const double)d,INSERT_VALUES);
+ MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
+ MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+ }
+- MatAssemblyBegin(F,MAT_FINAL_ASSEMBLY);
+- MatAssemblyEnd( F,MAT_FINAL_ASSEMBLY);
+ VecAssemblyBegin(Fbar);
+ VecAssemblyEnd( Fbar);
+
+ MatFree(&D_petsc);
+- MatFree(&F);
+ delete Mc;
+ xDelete(udot_serial);
+ xDelete(u_serial);
++ xDelete(ml_serial);
++ xDelete(Ri_plus_serial);
++ xDelete(Ri_minus_serial);
+
+ /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
+ VecDuplicate(u,&temp1);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18347-18348.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18347-18348.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18347-18348.diff (revision 19102)
@@ -0,0 +1,270 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18347)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18348)
+@@ -7,6 +7,111 @@
+ #include "../shared/shared.h"
+ #include "../modules/modules.h"
+
++#ifdef _HAVE_PETSC_
++void CreateDMatrix(Mat* pD,Mat K){/*{{{*/
++ /*Create D matrix such that:
++ *
++ * d_ij = max( -k_ij,0,-k_ji) off diagonal
++ *
++ * d_ii = - sum_{i!=j} d_ij for the diagonal
++ *
++ */
++
++ /*Intermediaries*/
++ int ncols,ncols2,rstart,rend;
++ double d,diagD;
++ Mat D = NULL;
++ Mat K_transp = NULL;
++ int* cols = NULL;
++ int* cols2 = NULL;
++ double* vals = NULL;
++ double* vals2 = NULL;
++
++ /*First, we need to transpose K so that we access both k_ij and k_ji*/
++ MatTranspose(K,MAT_INITIAL_MATRIX,&K_transp);
++
++ /*Initialize output (D has the same non zero pattern as K)*/
++ MatDuplicate(K,MAT_SHARE_NONZERO_PATTERN,&D);
++
++ /*Go through the rows of K an K' and build D*/
++ MatGetOwnershipRange(K,&rstart,&rend);
++ for(int row=rstart; rowdmax) dmax = fabs(d);
++ MatSetValue(LHS,row,cols[j],(const double)d,INSERT_VALUES);
++ }
++ MatRestoreRow(K,row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(D,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
++ }
++
++ /*Penalize Dirichlet boundary*/
++ dmax = dmax * 1.e+3;
++ for(int i=0;iconstraints->Size();i++){
++ Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
++ if(constraint->InAnalysis(configuration_type)){
++ constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
++ if(dof!=-1){
++ MatSetValue(LHS,dof,dof,(const double)dmax,INSERT_VALUES);
++ }
++ }
++ }
++ MatAssemblyBegin(LHS,MAT_FINAL_ASSEMBLY);
++ MatAssemblyEnd( LHS,MAT_FINAL_ASSEMBLY);
++
++ /*Clean up and assign output pointer*/
++ *pdmax = dmax;
++ *pLHS = LHS;
++}/*}}}*/
++#endif
+ void solutionsequence_fct(FemModel* femmodel){
+
+ /*intermediary: */
+@@ -17,11 +122,10 @@
+ Vector* uf = NULL;
+ Vector* ys = NULL;
+
+- IssmDouble theta,deltat;
++ IssmDouble theta,deltat,dmax=0.;
+ int dof,ncols,ncols2,ncols3,rstart,rend;
+ int configuration_type,analysis_type;
+- double d,diagD,mi;
+- double dmax = 0.;
++ double d,mi;
+ int* cols = NULL;
+ int* cols2 = NULL;
+ int* cols3 = NULL;
+@@ -44,38 +148,20 @@
+ analysis->MassMatrix(&Mc,femmodel);
+ analysis->FctKMatrix(&K,NULL,femmodel);
+
+- /*Create D Matrix*/
+- #ifdef _HAVE_PETSC_
+- Mat K_transp = NULL;
++ /*Convert matrices to PETSc matrices*/
+ Mat D_petsc = NULL;
+ Mat LHS = NULL;
+ Mat K_petsc = K->pmatrix->matrix;
+ Vec Ml_petsc = Ml->pvector->vector;
+ Mat Mc_petsc = Mc->pmatrix->matrix;
+- MatTranspose(K_petsc,MAT_INITIAL_MATRIX,&K_transp);
+- MatDuplicate(K_petsc,MAT_SHARE_NONZERO_PATTERN,&D_petsc);
+- MatGetOwnershipRange(K_transp,&rstart,&rend);
+- for(int row=rstart; rowparameters->FindParam(&configuration_type,ConfigurationTypeEnum);
++ int numnodes = this->nodes->NumberOfNodes(configuration_type);
++
++ /*Initialize output vectors*/
++ IssmDouble* uLmin_local = xNew(numnodes);
++ IssmDouble* uLmax_local = xNew(numnodes);
++ IssmDouble* uLmin = xNew(numnodes);
++ IssmDouble* uLmax = xNew(numnodes);
++ for(int i=0;ielements->Size();i++){
++ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i));
++ element->GetInputLocalMinMaxOnNodes(uLmin_local,uLmax_local,input_enum);
++ }
++
++ /*Synchronize all CPUs*/
++ ISSM_MPI_Allreduce((void*)uLmin_local,(void*)uLmin,numnodes,ISSM_MPI_DOUBLE,ISSM_MPI_MIN,IssmComm::GetComm());
++ ISSM_MPI_Allreduce((void*)uLmax_local,(void*)uLmax,numnodes,ISSM_MPI_DOUBLE,ISSM_MPI_MAX,IssmComm::GetComm());
++ xDelete(uLmin_local);
++ xDelete(uLmax_local);
++
++ /*Assign output pointers: */
++ *pmin=uLmin;
++ *pmax=uLmax;
++
++}/*}}}*/
+ void FemModel::IceVolumex(IssmDouble* pV){/*{{{*/
+
+ IssmDouble local_ice_volume = 0;
+Index: ../trunk-jpl/src/c/classes/Elements/Element.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18347)
++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18348)
+@@ -84,6 +84,7 @@
+ void GetInputListOnNodesVelocity(IssmDouble* pvalue,int enumtype);
+ void GetInputListOnVertices(IssmDouble* pvalue,int enumtype);
+ void GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue);
++ void GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,int input_enum);
+ void GetInputValue(bool* pvalue,int enum_type);
+ void GetInputValue(int* pvalue,int enum_type);
+ void GetInputValue(IssmDouble* pvalue,int enum_type);
+Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18347)
++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18348)
+@@ -723,6 +723,22 @@
+ delete gauss;
+ }
+ /*}}}*/
++void Element::GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,int input_enum){/*{{{*/
++
++ Input* input = GetInput(input_enum);
++ if(!input){
++ _error_("Input "<GetNumberOfNodes();
++ IssmDouble input_min = input->Min();
++ IssmDouble input_max = input->Max();
++ for(int i=0;iSid()]>input_min) min[nodes[i]->Sid()] = input_min;
++ if(max[nodes[i]->Sid()]Sid()] = input_max;
++ }
++}
++/*}}}*/
+ void Element::GetInputValue(bool* pvalue,int inputenum){/*{{{*/
+
+ Input* input=inputs->GetInput(inputenum);
+Index: ../trunk-jpl/src/c/classes/FemModel.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/FemModel.h (revision 18347)
++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 18348)
+@@ -60,6 +60,7 @@
+ void SetCurrentConfiguration(int configuration_type,int analysis_type);
+
+ /*Modules*/
++ void GetInputLocalMinMaxOnNodesx(IssmDouble** pmin,IssmDouble** pmax,int input_enum);
+ void MassFluxx(IssmDouble* presponse);
+ void MaxAbsVxx(IssmDouble* presponse);
+ void MaxAbsVyx(IssmDouble* presponse);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18348-18349.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18348-18349.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18348-18349.diff (revision 19102)
@@ -0,0 +1,54 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18348)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18349)
+@@ -160,40 +160,8 @@
+ CreateDMatrix(&D_petsc,K_petsc);
+
+ /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
+- MatDuplicate(K_petsc,MAT_SHARE_NONZERO_PATTERN,&LHS);
+- MatGetOwnershipRange(K_petsc,&rstart,&rend);
+- for(int row=rstart; rowdmax) dmax = fabs(d);
+- MatSetValues(LHS,1,&row,1,&cols[j],(const double*)&d,INSERT_VALUES);
+- }
+- MatRestoreRow(K_petsc,row,&ncols, (const int**)&cols, (const double**)&vals);
+- MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+- }
++ CreateLHS(&LHS,&dmax,K_petsc,D_petsc,Ml_petsc,theta,deltat,femmodel,configuration_type);
+
+- /*Penalize Dirichlet boundary*/
+- dmax = dmax * 1.e+3;
+- for(int i=0;iconstraints->Size();i++){
+- Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
+- if(constraint->InAnalysis(analysis_type)){
+- constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
+- if(dof!=-1){
+- MatSetValues(LHS,1,&dof,1,&dof,(const double*)&dmax,INSERT_VALUES);
+- }
+- }
+- }
+- MatAssemblyBegin(LHS,MAT_FINAL_ASSEMBLY);
+- MatAssemblyEnd( LHS,MAT_FINAL_ASSEMBLY);
+-
+ /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
+ GetSolutionFromInputsx(&ug,femmodel);
+ Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
+@@ -264,6 +232,7 @@
+ double uiLmin = 2.;
+ VecDuplicate(u,&Ri_plus);
+ VecDuplicate(u,&Ri_minus);
++ MatGetOwnershipRange(K_petsc,&rstart,&rend);
+ for(int row=rstart; rowconstraints->Size();i++){
++ Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
++ if(constraint->InAnalysis(configuration_type)){
++ constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
++ d = d*dmax;
++ if(dof!=-1){
++ VecSetValues(RHS,1,&dof,(const double*)&d,INSERT_VALUES);
++ }
++ }
++ }
++ VecAssemblyBegin(RHS);
++ VecAssemblyEnd( RHS);
++
++ /*Assign output pointer*/
++ *pRHS = RHS;
++
++}/*}}}*/
+ #endif
+ void solutionsequence_fct(FemModel* femmodel){
+
+@@ -120,18 +167,15 @@
+ Matrix* Mc = NULL;
+ Vector* ug = NULL;
+ Vector* uf = NULL;
+- Vector* ys = NULL;
+
+- IssmDouble theta,deltat,dmax=0.;
+- int dof,ncols,ncols2,ncols3,rstart,rend;
+- int configuration_type,analysis_type;
+- double d,mi;
++ IssmDouble theta,deltat,dmax;
++ int dof,ncols,ncols2,rstart,rend;
++ int configuration_type;
++ double d;
+ int* cols = NULL;
+ int* cols2 = NULL;
+- int* cols3 = NULL;
+ double* vals = NULL;
+ double* vals2 = NULL;
+- double* vals3 = NULL;
+
+ /*Create analysis*/
+ MasstransportAnalysis* analysis = new MasstransportAnalysis();
+@@ -139,7 +183,6 @@
+ /*Recover parameters: */
+ femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
+ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
+- femmodel->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+ femmodel->UpdateConstraintsx();
+ theta = 0.5;
+
+@@ -151,6 +194,8 @@
+ /*Convert matrices to PETSc matrices*/
+ Mat D_petsc = NULL;
+ Mat LHS = NULL;
++ Vec RHS = NULL;
++ Vec u = NULL;
+ Mat K_petsc = K->pmatrix->matrix;
+ Vec Ml_petsc = Ml->pvector->vector;
+ Mat Mc_petsc = Mc->pmatrix->matrix;
+@@ -166,35 +211,9 @@
+ GetSolutionFromInputsx(&ug,femmodel);
+ Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
+ delete ug;
+- Vec u = uf->pvector->vector;
+- Vec Ku = NULL;
+- Vec Du = NULL;
+- Vec RHS = NULL;
+- VecDuplicate(u,&Ku);
+- VecDuplicate(u,&Du);
+- VecDuplicate(u,&RHS);
+- MatMult(K_petsc,u,Ku);
+- MatMult(D_petsc,u,Du);
+- VecPointwiseMult(RHS,Ml_petsc,u);
+- VecAXPBYPCZ(RHS,(1-theta)*deltat,(1-theta)*deltat,1,Ku,Du);// RHS = M*u + (1-theta)*deltat*K*u + (1-theta)*deltat*D*u
+- VecFree(&Ku);
+- VecFree(&Du);
++ CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
+ delete uf;
+
+- /*Penalize Dirichlet boundary*/
+- for(int i=0;iconstraints->Size();i++){
+- Constraint* constraint=(Constraint*)femmodel->constraints->GetObjectByOffset(i);
+- if(constraint->InAnalysis(analysis_type)){
+- constraint->PenaltyDofAndValue(&dof,&d,femmodel->nodes,femmodel->parameters);
+- d = d*dmax;
+- if(dof!=-1){
+- VecSetValues(RHS,1,&dof,(const double*)&d,INSERT_VALUES);
+- }
+- }
+- }
+- VecAssemblyBegin(RHS);
+- VecAssemblyEnd( RHS);
+-
+ /*Go solve!*/
+ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
+ MatFree(&LHS);
+@@ -324,9 +343,8 @@
+ uf =new Vector(u);
+ VecFree(&u);
+
+- Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);delete uf; delete ys;
+- InputUpdateFromSolutionx(femmodel,ug);
+- delete ug;
++ InputUpdateFromSolutionx(femmodel,uf);
++ delete uf;
+
+ #else
+ _error_("PETSc needs to be installed");
Index: /issm/oecreview/Archive/18296-19100/ISSM-18350-18351.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18350-18351.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18350-18351.diff (revision 19102)
@@ -0,0 +1,398 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18350)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18351)
+@@ -158,200 +158,225 @@
+ *pRHS = RHS;
+
+ }/*}}}*/
++void RichardsonUdot(Vec* pudot,Vec u,Vec Ml,Mat K,Mat Mc){/*{{{*/
++ /*Use Richardson's formulato get udot using 5 steps and an initial guess of 0
++ *
++ * udot_new = udot_old + Ml^-1 (K^(n+1) u - Mc udot_old)
++ *
++ * */
++
++ /*Intermediaries*/
++ Vec udot = NULL;
++ Vec temp1 = NULL;
++ Vec temp2 = NULL;
++
++ /*Initialize vectors*/
++ VecDuplicate(u,&udot);
++ VecDuplicate(u,&temp1);
++ VecDuplicate(u,&temp2);
++
++ /*Initial guess*/
++ VecZeroEntries(udot);
++
++ /*Richardson's iterations*/
++ for(int i=0;i<5;i++){
++ MatMult(Mc,udot,temp1);
++ MatMult(K, u, temp2);
++ VecAXPBY(temp2,-1.,1.,temp1); // temp2 = (K^(n+1) u -- Mc udot_old)
++ VecPointwiseDivide(temp1,temp2,Ml); // temp1 = Ml^-1 temp2
++ VecAXPBY(udot,1.,1.,temp1);
++ }
++
++ /*Clean up and assign output pointer*/
++ VecFree(&temp1);
++ VecFree(&temp2);
++ *pudot=udot;
++
++}/*}}}*/
+ #endif
+-void solutionsequence_fct(FemModel* femmodel){
++ void solutionsequence_fct(FemModel* femmodel){
+
+- /*intermediary: */
+- Vector* Ml = NULL;
+- Matrix* K = NULL;
+- Matrix* Mc = NULL;
+- Vector* ug = NULL;
+- Vector* uf = NULL;
++ /*intermediary: */
++ Vector* Ml = NULL;
++ Matrix* K = NULL;
++ Matrix* Mc = NULL;
++ Vector* ug = NULL;
++ Vector* uf = NULL;
+
+- IssmDouble theta,deltat,dmax;
+- int dof,ncols,ncols2,rstart,rend;
+- int configuration_type;
+- double d;
+- int* cols = NULL;
+- int* cols2 = NULL;
+- double* vals = NULL;
+- double* vals2 = NULL;
++ IssmDouble theta,deltat,dmax;
++ int dof,ncols,ncols2,rstart,rend;
++ int configuration_type;
++ double d;
++ int* cols = NULL;
++ int* cols2 = NULL;
++ double* vals = NULL;
++ double* vals2 = NULL;
+
+- /*Create analysis*/
+- MasstransportAnalysis* analysis = new MasstransportAnalysis();
++ /*Create analysis*/
++ MasstransportAnalysis* analysis = new MasstransportAnalysis();
+
+- /*Recover parameters: */
+- femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
+- femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
+- femmodel->UpdateConstraintsx();
+- theta = 0.5;
++ /*Recover parameters: */
++ femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
++ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
++ femmodel->UpdateConstraintsx();
++ theta = 0.5;
+
+- /*Create lumped mass matrix*/
+- analysis->LumpedMassMatrix(&Ml,femmodel);
+- analysis->MassMatrix(&Mc,femmodel);
+- analysis->FctKMatrix(&K,NULL,femmodel);
++ /*Create lumped mass matrix*/
++ analysis->LumpedMassMatrix(&Ml,femmodel);
++ analysis->MassMatrix(&Mc,femmodel);
++ analysis->FctKMatrix(&K,NULL,femmodel);
+
+- /*Convert matrices to PETSc matrices*/
+- Mat D_petsc = NULL;
+- Mat LHS = NULL;
+- Vec RHS = NULL;
+- Vec u = NULL;
+- Mat K_petsc = K->pmatrix->matrix;
+- Vec Ml_petsc = Ml->pvector->vector;
+- Mat Mc_petsc = Mc->pmatrix->matrix;
++ /*Convert matrices to PETSc matrices*/
++ Mat D_petsc = NULL;
++ Mat LHS = NULL;
++ Vec RHS = NULL;
++ Vec u = NULL;
++ Vec udot = NULL;
++ Mat K_petsc = K->pmatrix->matrix;
++ Vec Ml_petsc = Ml->pvector->vector;
++ Mat Mc_petsc = Mc->pmatrix->matrix;
+
+- /*Create D Matrix*/
+- #ifdef _HAVE_PETSC_
+- CreateDMatrix(&D_petsc,K_petsc);
++ /*Create D Matrix*/
++ #ifdef _HAVE_PETSC_
++ CreateDMatrix(&D_petsc,K_petsc);
+
+- /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
+- CreateLHS(&LHS,&dmax,K_petsc,D_petsc,Ml_petsc,theta,deltat,femmodel,configuration_type);
++ /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
++ CreateLHS(&LHS,&dmax,K_petsc,D_petsc,Ml_petsc,theta,deltat,femmodel,configuration_type);
+
+- /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
+- GetSolutionFromInputsx(&ug,femmodel);
+- Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
+- delete ug;
+- CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
+- delete uf;
++ /*Get previous solution u^n*/
++ GetSolutionFromInputsx(&ug,femmodel);
++ Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
++ delete ug;
+
+- /*Go solve!*/
+- SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
+- MatFree(&LHS);
+- VecFree(&RHS);
++ /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
++ CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
++ delete uf;
+
+- /*Richardson to calculate udot*/
+- Vec udot = NULL;
+- VecDuplicate(u,&udot);
+- VecZeroEntries(udot);
+- Vec temp1 = NULL; VecDuplicate(u,&temp1);
+- Vec temp2 = NULL; VecDuplicate(u,&temp2);
+- for(int i=0;i<5;i++){
+- /*udot_new = udot_old + Ml^-1 (K^(n+1) u -- Mc udot_old)*/
+- MatMult(Mc_petsc,udot,temp1);
+- MatMult(K_petsc, u, temp2);
+- VecAXPBY(temp2,-1.,1.,temp1); // temp2 = (K^(n+1) u -- Mc udot_old)
+- VecPointwiseDivide(temp1,temp2,Ml_petsc); //temp1 = Ml^-1 temp2
+- VecAXPBY(udot,1.,1.,temp1);
+- }
+- VecFree(&temp1);
+- VecFree(&temp2);
++ /*Go solve!*/
++ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
++ MatFree(&LHS);
++ VecFree(&RHS);
+
+- /*Serialize u and udot*/
+- IssmDouble* udot_serial = NULL;
+- IssmDouble* u_serial = NULL;
+- IssmDouble* ml_serial = NULL;
+- VecToMPISerial(&udot_serial,udot ,IssmComm::GetComm());
+- VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
+- VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
++ /*Richardson to calculate udot*/
++ RichardsonUdot(&udot,u,Ml_petsc,K_petsc,Mc_petsc);
+
+- /*Anti diffusive fluxes*/
+- Vec Ri_plus = NULL;
+- Vec Ri_minus = NULL;
+- double uiLmax = 3.;
+- double uiLmin = 2.;
+- VecDuplicate(u,&Ri_plus);
+- VecDuplicate(u,&Ri_minus);
+- MatGetOwnershipRange(K_petsc,&rstart,&rend);
+- for(int row=rstart; row0.){
+- Pi_plus += d;
++ /*Serialize u and udot*/
++ IssmDouble* udot_serial = NULL;
++ IssmDouble* u_serial = NULL;
++ IssmDouble* ml_serial = NULL;
++ VecToMPISerial(&udot_serial,udot ,IssmComm::GetComm());
++ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
++ VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
++
++ /*Anti diffusive fluxes*/
++ Vec Ri_plus = NULL;
++ Vec Ri_minus = NULL;
++ double uiLmax = 3.;
++ double uiLmin = 2.;
++ VecDuplicate(u,&Ri_plus);
++ VecDuplicate(u,&Ri_minus);
++ MatGetOwnershipRange(K_petsc,&rstart,&rend);
++ for(int row=rstart; row0.){
++ Pi_plus += d;
++ }
++ else{
++ Pi_minus += d;
++ }
+ }
+- else{
+- Pi_minus += d;
+- }
+ }
+- }
+
+- /*Compute Qis and Ris*/
+- double Qi_plus = ml_serial[row]/deltat*(uiLmax - u_serial[row]);
+- double Qi_minus = ml_serial[row]/deltat*(uiLmin - u_serial[row]);
+- d = 1.;
+- if(Pi_plus!=0.) d = min(1.,Qi_plus/Pi_plus);
+- VecSetValue(Ri_plus,row,(const double)d,INSERT_VALUES);
+- d = 1.;
+- if(Pi_minus!=0.) d = min(1.,Qi_minus/Pi_minus);
+- VecSetValue(Ri_minus,row,(const double)d,INSERT_VALUES);
++ /*Compute Qis and Ris*/
++ double Qi_plus = ml_serial[row]/deltat*(uiLmax - u_serial[row]);
++ double Qi_minus = ml_serial[row]/deltat*(uiLmin - u_serial[row]);
++ d = 1.;
++ if(Pi_plus!=0.) d = min(1.,Qi_plus/Pi_plus);
++ VecSetValue(Ri_plus,row,(const double)d,INSERT_VALUES);
++ d = 1.;
++ if(Pi_minus!=0.) d = min(1.,Qi_minus/Pi_minus);
++ VecSetValue(Ri_minus,row,(const double)d,INSERT_VALUES);
+
+- MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
+- MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+- }
+- VecAssemblyBegin(Ri_plus);
+- VecAssemblyEnd( Ri_plus);
+- VecAssemblyBegin(Ri_minus);
+- VecAssemblyEnd( Ri_minus);
++ MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
++ }
++ VecAssemblyBegin(Ri_plus);
++ VecAssemblyEnd( Ri_plus);
++ VecAssemblyBegin(Ri_minus);
++ VecAssemblyEnd( Ri_minus);
+
+- /*Serialize Ris*/
+- IssmDouble* Ri_plus_serial = NULL;
+- IssmDouble* Ri_minus_serial = NULL;
+- VecToMPISerial(&Ri_plus_serial,Ri_plus,IssmComm::GetComm());
+- VecToMPISerial(&Ri_minus_serial,Ri_minus,IssmComm::GetComm());
+- VecFree(&Ri_plus);
+- VecFree(&Ri_minus);
++ /*Serialize Ris*/
++ IssmDouble* Ri_plus_serial = NULL;
++ IssmDouble* Ri_minus_serial = NULL;
++ VecToMPISerial(&Ri_plus_serial,Ri_plus,IssmComm::GetComm());
++ VecToMPISerial(&Ri_minus_serial,Ri_minus,IssmComm::GetComm());
++ VecFree(&Ri_plus);
++ VecFree(&Ri_minus);
+
+- /*Build fbar*/
+- Vec Fbar = NULL;
+- VecDuplicate(u,&Fbar);
+- for(int row=rstart; row0){
+- d += min(Ri_plus_serial[row],Ri_minus_serial[cols[j]]) * f_ij;
++ /*Build fbar*/
++ Vec Fbar = NULL;
++ VecDuplicate(u,&Fbar);
++ for(int row=rstart; row0){
++ d += min(Ri_plus_serial[row],Ri_minus_serial[cols[j]]) * f_ij;
++ }
++ else{
++ d += min(Ri_minus_serial[row],Ri_plus_serial[cols[j]]) * f_ij;
++ }
+ }
+- else{
+- d += min(Ri_minus_serial[row],Ri_plus_serial[cols[j]]) * f_ij;
+- }
++ VecSetValue(Fbar,row,(const double)d,INSERT_VALUES);
++ MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
++ MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+ }
+- VecSetValue(Fbar,row,(const double)d,INSERT_VALUES);
+- MatRestoreRow(Mc_petsc, row,&ncols, (const int**)&cols, (const double**)&vals);
+- MatRestoreRow(D_petsc,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+- }
+- VecAssemblyBegin(Fbar);
+- VecAssemblyEnd( Fbar);
++ VecAssemblyBegin(Fbar);
++ VecAssemblyEnd( Fbar);
+
+- MatFree(&D_petsc);
+- delete Mc;
+- xDelete(udot_serial);
+- xDelete(u_serial);
+- xDelete(ml_serial);
+- xDelete(Ri_plus_serial);
+- xDelete(Ri_minus_serial);
++ MatFree(&D_petsc);
++ delete Mc;
++ xDelete(udot_serial);
++ xDelete(u_serial);
++ xDelete(ml_serial);
++ xDelete(Ri_plus_serial);
++ xDelete(Ri_minus_serial);
+
+- /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
+- VecDuplicate(u,&temp1);
+- VecPointwiseDivide(temp1,Fbar,Ml_petsc); //temp1 = Ml^-1 temp2
+- VecAXPBY(udot,1.,1.,temp1);
+- VecAXPY(u,deltat,temp1);
+- VecFree(&Fbar);
+- VecFree(&udot);
+- VecFree(&temp1);
++ /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
++ Vec temp1 = NULL; VecDuplicate(u,&temp1);
++ VecDuplicate(u,&temp1);
++ VecPointwiseDivide(temp1,Fbar,Ml_petsc); //temp1 = Ml^-1 temp2
++ VecAXPBY(udot,1.,1.,temp1);
++ VecAXPY(u,deltat,temp1);
++ VecFree(&Fbar);
++ VecFree(&udot);
++ VecFree(&temp1);
+
+- uf =new Vector(u);
+- VecFree(&u);
++ uf =new Vector(u);
++ VecFree(&u);
+
+- InputUpdateFromSolutionx(femmodel,uf);
+- delete uf;
++ InputUpdateFromSolutionx(femmodel,uf);
++ delete uf;
+
+- #else
+- _error_("PETSc needs to be installed");
+- #endif
++ #else
++ _error_("PETSc needs to be installed");
++ #endif
+
+- delete Ml;
+- delete K;
+- delete analysis;
++ delete Ml;
++ delete K;
++ delete analysis;
+
+-}
++ }
Index: /issm/oecreview/Archive/18296-19100/ISSM-18353-18354.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18353-18354.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18353-18354.diff (revision 19102)
@@ -0,0 +1,21 @@
+Index: ../trunk-jpl/externalpackages/triangle/install.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/triangle/install.sh (revision 18353)
++++ ../trunk-jpl/externalpackages/triangle/install.sh (revision 18354)
+@@ -22,10 +22,10 @@
+ tar -xvf ./triangle-libtool.tar.gz
+
+ autoreconf -ivf
+-./configure --prefix="${ISSM_DIR}/externalpackages/triangle/install"
++./configure --prefix="${ISSM_DIR}/externalpackages/triangle/install" --disable-executables
+
+ make
+ make install
+
+ #Patch triangle.h
+-patch ../install/include/triangle.h ../triangle.h.patch
++patch ${ISSM_DIR}/externalpackages/triangle/install/include/triangle.h ${ISSM_DIR}/externalpackages/triangle/triangle.h.patch
+Index: ../trunk-jpl/externalpackages/triangle/configs/triangle-libtool.tar.gz
+===================================================================
+Cannot display: file marked as a binary type.
+svn:mime-type = application/octet-stream
Index: /issm/oecreview/Archive/18296-19100/ISSM-18354-18355.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18354-18355.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18354-18355.diff (revision 19102)
@@ -0,0 +1,253 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18354)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18355)
+@@ -193,13 +193,11 @@
+ *pudot=udot;
+
+ }/*}}}*/
+-void CreateRis(IssmDouble** pRi_plus_serial,IssmDouble** pRi_minus_serial,Mat Mc,Mat D,IssmDouble* ml_serial,Vec uvec,IssmDouble* u,IssmDouble* udot,IssmDouble deltat){/*{{{*/
++void CreateRis(IssmDouble** pRi_plus_serial,IssmDouble** pRi_minus_serial,Mat Mc,Mat D,IssmDouble* ml_serial,Vec uvec,IssmDouble* u,IssmDouble* udot,IssmDouble* ulmin,IssmDouble* ulmax,IssmDouble deltat){/*{{{*/
+
+ /*Intermediaries*/
+ Vec Ri_plus = NULL;
+ Vec Ri_minus = NULL;
+- IssmDouble uiLmax = 3.;
+- IssmDouble uiLmin = 2.;
+ int ncols,ncols2,rstart,rend;
+ double d;
+ int *cols = NULL;
+@@ -233,8 +231,10 @@
+ }
+
+ /*Compute Qis and Ris*/
+- double Qi_plus = ml_serial[row]/deltat*(uiLmax - u[row]);
+- double Qi_minus = ml_serial[row]/deltat*(uiLmin - u[row]);
++ double Qi_plus = ml_serial[row]/deltat*(3. - u[row]);
++ double Qi_minus = ml_serial[row]/deltat*(2. - u[row]);
++ //double Qi_plus = ml_serial[row]/deltat*(ulmax[row] - u[row]);
++ //double Qi_minus = ml_serial[row]/deltat*(ulmin[row] - u[row]);
+ d = 1.;
+ if(Pi_plus!=0.) d = min(1.,Qi_plus/Pi_plus);
+ VecSetValue(Ri_plus,row,(const double)d,INSERT_VALUES);
+@@ -302,119 +302,124 @@
+ /*Assign output pointer*/
+ *pFbar = Fbar;
+ }/*}}}*/
+-#endif
+- void solutionsequence_fct(FemModel* femmodel){
++void UpdateSolution(Vec u,Vec udot,Vec Ml,Vec Fbar,IssmDouble deltat){/*{{{*/
+
+- /*intermediary: */
+- Vector* Ml = NULL;
+- Matrix* K = NULL;
+- Matrix* Mc = NULL;
+- Vector* ug = NULL;
+- Vector* uf = NULL;
++ /*Intermediary*/
++ Vec temp1 = NULL;
+
+- IssmDouble theta,deltat,dmax;
+- int dof,ncols,ncols2,rstart,rend;
+- int configuration_type;
+- double d;
+- int* cols = NULL;
+- int* cols2 = NULL;
+- double* vals = NULL;
+- double* vals2 = NULL;
++ /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
++ VecDuplicate(u,&temp1);
++ VecPointwiseDivide(temp1,Fbar,Ml); //temp1 = Ml^-1 temp2
++ VecAXPBY(udot,1.,1.,temp1);
++ VecAXPY(u,deltat,temp1);
+
+- /*Create analysis*/
+- MasstransportAnalysis* analysis = new MasstransportAnalysis();
++ /*CLean up and return*/
++ VecFree(&temp1);
++}/*}}}*/
++#endif
++void solutionsequence_fct(FemModel* femmodel){
+
+- /*Recover parameters: */
+- femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
+- femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
+- femmodel->UpdateConstraintsx();
+- theta = 0.5;
++ /*intermediary: */
++ IssmDouble theta,deltat,dmax;
++ int configuration_type;
++ Vector* Ml = NULL;
++ Matrix* K = NULL;
++ Matrix* Mc = NULL;
++ Vector* ug = NULL;
++ Vector* uf = NULL;
+
+- /*Create lumped mass matrix*/
+- analysis->LumpedMassMatrix(&Ml,femmodel);
+- analysis->MassMatrix(&Mc,femmodel);
+- analysis->FctKMatrix(&K,NULL,femmodel);
++ /*Create analysis*/
++ MasstransportAnalysis* analysis = new MasstransportAnalysis();
+
+- /*Convert matrices to PETSc matrices*/
+- Mat D_petsc = NULL;
+- Mat LHS = NULL;
+- Vec RHS = NULL;
+- Vec u = NULL;
+- Vec udot = NULL;
+- Mat K_petsc = K->pmatrix->matrix;
+- Vec Ml_petsc = Ml->pvector->vector;
+- Mat Mc_petsc = Mc->pmatrix->matrix;
++ /*Recover parameters: */
++ femmodel->parameters->FindParam(&deltat,TimesteppingTimeStepEnum);
++ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
++ femmodel->UpdateConstraintsx();
++ theta = 0.5;
+
+- /*Create D Matrix*/
+- #ifdef _HAVE_PETSC_
+- CreateDMatrix(&D_petsc,K_petsc);
++ /*Create lumped mass matrix*/
++ analysis->LumpedMassMatrix(&Ml,femmodel);
++ analysis->MassMatrix(&Mc,femmodel);
++ analysis->FctKMatrix(&K,NULL,femmodel);
++ delete analysis;
+
+- /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
+- CreateLHS(&LHS,&dmax,K_petsc,D_petsc,Ml_petsc,theta,deltat,femmodel,configuration_type);
++ /*Convert matrices to PETSc matrices*/
++ Mat D_petsc = NULL;
++ Mat LHS = NULL;
++ Vec RHS = NULL;
++ Vec u = NULL;
++ Vec udot = NULL;
++ Mat K_petsc = K->pmatrix->matrix;
++ Vec Ml_petsc = Ml->pvector->vector;
++ Mat Mc_petsc = Mc->pmatrix->matrix;
+
+- /*Get previous solution u^n*/
+- GetSolutionFromInputsx(&ug,femmodel);
+- Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
+- delete ug;
++ /*Create D Matrix*/
++ #ifdef _HAVE_PETSC_
++ CreateDMatrix(&D_petsc,K_petsc);
+
+- /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
+- CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
+- delete uf;
++ /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
++ CreateLHS(&LHS,&dmax,K_petsc,D_petsc,Ml_petsc,theta,deltat,femmodel,configuration_type);
+
+- /*Go solve lower order solution*/
+- SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
+- MatFree(&LHS);
+- VecFree(&RHS);
++ /*Get previous solution u^n*/
++ GetSolutionFromInputsx(&ug,femmodel);
++ Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters);
++ delete ug;
+
+- /*Richardson to calculate udot*/
+- RichardsonUdot(&udot,u,Ml_petsc,K_petsc,Mc_petsc);
++ /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
++ CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
++ delete uf;
+
+- /*Serialize u and udot*/
+- IssmDouble* udot_serial = NULL;
+- IssmDouble* u_serial = NULL;
+- IssmDouble* ml_serial = NULL;
+- VecToMPISerial(&udot_serial,udot ,IssmComm::GetComm());
+- VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
+- VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
++ /*Go solve lower order solution*/
++ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
++ MatFree(&LHS);
++ VecFree(&RHS);
+
+- /*Anti diffusive fluxes*/
+- Vec Fbar = NULL;
+- IssmDouble* Ri_minus_serial = NULL;
+- IssmDouble* Ri_plus_serial = NULL;
+- CreateRis(&Ri_plus_serial,&Ri_minus_serial,Mc_petsc,D_petsc,ml_serial,u,u_serial,udot_serial,deltat);
+- CreateFbar(&Fbar,Ri_plus_serial,Ri_minus_serial,Mc_petsc,D_petsc,udot_serial,u_serial,u);
++ /*Richardson to calculate udot*/
++ RichardsonUdot(&udot,u,Ml_petsc,K_petsc,Mc_petsc);
++ delete K;
+
+- /*Clean up*/
+- MatFree(&D_petsc);
+- delete Mc;
+- xDelete(udot_serial);
+- xDelete(u_serial);
+- xDelete(ml_serial);
+- xDelete(Ri_plus_serial);
+- xDelete(Ri_minus_serial);
++ /*Serialize u and udot*/
++ IssmDouble* udot_serial = NULL;
++ IssmDouble* u_serial = NULL;
++ IssmDouble* ml_serial = NULL;
++ VecToMPISerial(&udot_serial,udot ,IssmComm::GetComm());
++ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
++ VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
+
+- /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
+- Vec temp1 = NULL;
+- VecDuplicate(u,&temp1);
+- VecPointwiseDivide(temp1,Fbar,Ml_petsc); //temp1 = Ml^-1 temp2
+- VecAXPBY(udot,1.,1.,temp1);
+- VecAXPY(u,deltat,temp1);
+- VecFree(&Fbar);
+- VecFree(&udot);
+- VecFree(&temp1);
++ /*Anti diffusive fluxes*/
++ Vec Fbar = NULL;
++ IssmDouble *Ri_minus_serial = NULL;
++ IssmDouble *Ri_plus_serial = NULL;
++ IssmDouble *ulmin = NULL;
++ IssmDouble *ulmax = NULL;
++ femmodel->GetInputLocalMinMaxOnNodesx(&ulmin,&ulmax,ThicknessEnum);
++ CreateRis(&Ri_plus_serial,&Ri_minus_serial,Mc_petsc,D_petsc,ml_serial,u,u_serial,udot_serial,ulmin,ulmax,deltat);
++ CreateFbar(&Fbar,Ri_plus_serial,Ri_minus_serial,Mc_petsc,D_petsc,udot_serial,u_serial,u);
++ xDelete(Ri_plus_serial);
++ xDelete(Ri_minus_serial);
++ xDelete(ulmin);
++ xDelete(ulmax);
+
+- uf =new Vector(u);
+- VecFree(&u);
++ /*Clean up*/
++ MatFree(&D_petsc);
++ delete Mc;
++ xDelete(udot_serial);
++ xDelete(u_serial);
++ xDelete(ml_serial);
+
+- InputUpdateFromSolutionx(femmodel,uf);
+- delete uf;
++ /*Compute solution u^n+1 = u_L + deltat Ml^-1 fbar*/
++ UpdateSolution(u,udot,Ml_petsc,Fbar,deltat);
++ uf =new Vector(u);
++ VecFree(&u);
++ VecFree(&Fbar);
++ VecFree(&udot);
++ delete Ml;
+
+- #else
+- _error_("PETSc needs to be installed");
+- #endif
++ /*Update Element inputs*/
++ InputUpdateFromSolutionx(femmodel,uf);
++ delete uf;
+
+- delete Ml;
+- delete K;
+- delete analysis;
+-
+- }
++ #else
++ _error_("PETSc needs to be installed");
++ #endif
++}
Index: /issm/oecreview/Archive/18296-19100/ISSM-18357-18358.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18357-18358.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18357-18358.diff (revision 19102)
@@ -0,0 +1,15 @@
+Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18357)
++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18358)
+@@ -734,8 +734,8 @@
+ IssmDouble input_min = input->Min();
+ IssmDouble input_max = input->Max();
+ for(int i=0;iSid()]>input_min) min[nodes[i]->Sid()] = input_min;
+- if(max[nodes[i]->Sid()]Sid()] = input_max;
++ if(min[nodes[i]->GetDof(0,GSetEnum)]>input_min) min[nodes[i]->GetDof(0,GSetEnum)] = input_min;
++ if(max[nodes[i]->GetDof(0,GSetEnum)]GetDof(0,GSetEnum)] = input_max;
+ }
+ }
+ /*}}}*/
Index: /issm/oecreview/Archive/18296-19100/ISSM-18358-18359.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18358-18359.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18358-18359.diff (revision 19102)
@@ -0,0 +1,37 @@
+Index: ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 18358)
++++ ../trunk-jpl/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 18359)
+@@ -22,7 +22,7 @@
+ export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
+ export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
+ cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
+-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
++patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.mac.patch
+ patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
+
+ #Apply patches
+@@ -32,10 +32,21 @@
+ patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
+ patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
+
++export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
++
+ #Configure dakota
++# Set your local gcc compiler here
+ cd $DAK_BUILD
+-#cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran -D BOOST_ROOT=/opt/local -D Boost_INCLUDE_DIR=/opt/local/include -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
+-cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran -D LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH -D LDFLAGS="-L/usr/lib -lstdc++" -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++cmake -DBoost_NO_BOOST_CMAKE=TRUE \
++ -DBoost_NO_SYSTEM_PATHS=TRUE \
++ -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \
++ -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \
++ -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \
++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \
++ -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
++
++#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran
++
+ cd ..
+
+ #Compile and install dakota
Index: /issm/oecreview/Archive/18296-19100/ISSM-18359-18360.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18359-18360.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18359-18360.diff (revision 19102)
@@ -0,0 +1,15 @@
+Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18359)
++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18360)
+@@ -734,8 +734,8 @@
+ IssmDouble input_min = input->Min();
+ IssmDouble input_max = input->Max();
+ for(int i=0;iGetDof(0,GSetEnum)]>input_min) min[nodes[i]->GetDof(0,GSetEnum)] = input_min;
+- if(max[nodes[i]->GetDof(0,GSetEnum)]GetDof(0,GSetEnum)] = input_max;
++ if(min[nodes[i]->GetDof(0,GsetEnum)]>input_min) min[nodes[i]->GetDof(0,GsetEnum)] = input_min;
++ if(max[nodes[i]->GetDof(0,GsetEnum)]GetDof(0,GsetEnum)] = input_max;
+ }
+ }
+ /*}}}*/
Index: /issm/oecreview/Archive/18296-19100/ISSM-18360-18361.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18360-18361.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18360-18361.diff (revision 19102)
@@ -0,0 +1,29 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18360)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18361)
+@@ -231,10 +231,10 @@
+ }
+
+ /*Compute Qis and Ris*/
+- double Qi_plus = ml_serial[row]/deltat*(3. - u[row]);
+- double Qi_minus = ml_serial[row]/deltat*(2. - u[row]);
+- //double Qi_plus = ml_serial[row]/deltat*(ulmax[row] - u[row]);
+- //double Qi_minus = ml_serial[row]/deltat*(ulmin[row] - u[row]);
++ //double Qi_plus = ml_serial[row]/deltat*(3. - u[row]);
++ //double Qi_minus = ml_serial[row]/deltat*(2. - u[row]);
++ double Qi_plus = ml_serial[row]/deltat*(ulmax[row] - u[row]);
++ double Qi_minus = ml_serial[row]/deltat*(ulmin[row] - u[row]);
+ _assert_(Qi_plus >= 0.);
+ _assert_(Qi_minus <= 0.);
+ d = 1.;
+@@ -388,6 +388,9 @@
+ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
+ VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
+
++ /*Push uL to elements*/
++ InputUpdateFromSolutionx(femmodel,u_serial);
++
+ /*Anti diffusive fluxes*/
+ Vec Fbar = NULL;
+ IssmDouble *Ri_minus_serial = NULL;
Index: /issm/oecreview/Archive/18296-19100/ISSM-18361-18362.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18361-18362.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18361-18362.diff (revision 19102)
@@ -0,0 +1,21 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18361)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18362)
+@@ -345,6 +345,8 @@
+ analysis->FctKMatrix(&K,NULL,femmodel);
+ delete analysis;
+
++ #ifdef _HAVE_PETSC_
++
+ /*Convert matrices to PETSc matrices*/
+ Mat D_petsc = NULL;
+ Mat LHS = NULL;
+@@ -356,7 +358,6 @@
+ Mat Mc_petsc = Mc->pmatrix->matrix;
+
+ /*Create D Matrix*/
+- #ifdef _HAVE_PETSC_
+ CreateDMatrix(&D_petsc,K_petsc);
+
+ /*Create LHS: [ML − theta*detlat *(K+D)^n+1]*/
Index: /issm/oecreview/Archive/18296-19100/ISSM-18362-18363.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18362-18363.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18362-18363.diff (revision 19102)
@@ -0,0 +1,109 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18362)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18363)
+@@ -389,16 +389,13 @@
+ VecToMPISerial(&u_serial ,u ,IssmComm::GetComm());
+ VecToMPISerial(&ml_serial ,Ml_petsc,IssmComm::GetComm());
+
+- /*Push uL to elements*/
+- InputUpdateFromSolutionx(femmodel,u_serial);
+-
+ /*Anti diffusive fluxes*/
+ Vec Fbar = NULL;
+ IssmDouble *Ri_minus_serial = NULL;
+ IssmDouble *Ri_plus_serial = NULL;
+ IssmDouble *ulmin = NULL;
+ IssmDouble *ulmax = NULL;
+- femmodel->GetInputLocalMinMaxOnNodesx(&ulmin,&ulmax,ThicknessEnum);
++ femmodel->GetInputLocalMinMaxOnNodesx(&ulmin,&ulmax,u_serial);
+ CreateRis(&Ri_plus_serial,&Ri_minus_serial,Mc_petsc,D_petsc,ml_serial,u,u_serial,udot_serial,ulmin,ulmax,deltat);
+ CreateFbar(&Fbar,Ri_plus_serial,Ri_minus_serial,Mc_petsc,D_petsc,udot_serial,u_serial,u);
+ xDelete(Ri_plus_serial);
+Index: ../trunk-jpl/src/c/classes/FemModel.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18362)
++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18363)
+@@ -1124,7 +1124,7 @@
+ *pdiv=total_divergence;
+
+ }/*}}}*/
+-void FemModel::GetInputLocalMinMaxOnNodesx(IssmDouble** pmin,IssmDouble** pmax,int input_enum){/*{{{*/
++void FemModel::GetInputLocalMinMaxOnNodesx(IssmDouble** pmin,IssmDouble** pmax,IssmDouble* ug){/*{{{*/
+
+ /*Get vector sizes for current configuration*/
+ int configuration_type;
+@@ -1143,7 +1143,7 @@
+
+ for(int i=0;ielements->Size();i++){
+ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i));
+- element->GetInputLocalMinMaxOnNodes(uLmin_local,uLmax_local,input_enum);
++ element->GetInputLocalMinMaxOnNodes(uLmin_local,uLmax_local,ug);
+ }
+
+ /*Synchronize all CPUs*/
+Index: ../trunk-jpl/src/c/classes/Elements/Element.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18362)
++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18363)
+@@ -84,7 +84,7 @@
+ void GetInputListOnNodesVelocity(IssmDouble* pvalue,int enumtype);
+ void GetInputListOnVertices(IssmDouble* pvalue,int enumtype);
+ void GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue);
+- void GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,int input_enum);
++ void GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,IssmDouble* ug);
+ void GetInputValue(bool* pvalue,int enum_type);
+ void GetInputValue(int* pvalue,int enum_type);
+ void GetInputValue(IssmDouble* pvalue,int enum_type);
+Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18362)
++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18363)
+@@ -723,16 +723,27 @@
+ delete gauss;
+ }
+ /*}}}*/
+-void Element::GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,int input_enum){/*{{{*/
++void Element::GetInputLocalMinMaxOnNodes(IssmDouble* min,IssmDouble* max,IssmDouble* ug){/*{{{*/
+
+- Input* input = GetInput(input_enum);
+- if(!input){
+- _error_("Input "<GetNumberOfNodes();
++
++ /*Some checks to avoid segmentation faults*/
++ _assert_(ug);
++ _assert_(numnodes>0);
++ _assert_(nodes);
++
++ /*Get element minimum/maximum*/
++ IssmDouble input_min = ug[nodes[0]->GetDof(0,GsetEnum)];
++ IssmDouble input_max = input_min;
++ for(int i=1;iGetDof(0,GsetEnum)] < input_min) input_min = ug[nodes[i]->GetDof(0,GsetEnum)];
++ if(ug[nodes[i]->GetDof(0,GsetEnum)] > input_max) input_max = ug[nodes[i]->GetDof(0,GsetEnum)];
+ }
+
+- int numnodes = this->GetNumberOfNodes();
+- IssmDouble input_min = input->Min();
+- IssmDouble input_max = input->Max();
++
++ /*Second loop to reassign min and max with local extrema*/
+ for(int i=0;iGetDof(0,GsetEnum)]>input_min) min[nodes[i]->GetDof(0,GsetEnum)] = input_min;
+ if(max[nodes[i]->GetDof(0,GsetEnum)]GetDof(0,GsetEnum)] = input_max;
+Index: ../trunk-jpl/src/c/classes/FemModel.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/FemModel.h (revision 18362)
++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 18363)
+@@ -60,7 +60,7 @@
+ void SetCurrentConfiguration(int configuration_type,int analysis_type);
+
+ /*Modules*/
+- void GetInputLocalMinMaxOnNodesx(IssmDouble** pmin,IssmDouble** pmax,int input_enum);
++ void GetInputLocalMinMaxOnNodesx(IssmDouble** pmin,IssmDouble** pmax,IssmDouble* ug);
+ void MassFluxx(IssmDouble* presponse);
+ void MaxAbsVxx(IssmDouble* presponse);
+ void MaxAbsVyx(IssmDouble* presponse);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18363-18364.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18363-18364.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18363-18364.diff (revision 19102)
@@ -0,0 +1,22 @@
+Index: ../trunk-jpl/test/Exp/SquareOne.exp
+===================================================================
+--- ../trunk-jpl/test/Exp/SquareOne.exp (revision 0)
++++ ../trunk-jpl/test/Exp/SquareOne.exp (revision 18364)
+@@ -0,0 +1,10 @@
++## Name:domainoutline
++## Icon:0
++# Points Count Value
++5 1.
++# X pos Y pos
++0 0
++1 0
++1 1
++0 1
++0 0
+
+Property changes on: ../trunk-jpl/test/Exp/SquareOne.exp
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18364-18365.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18364-18365.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18364-18365.diff (revision 19102)
@@ -0,0 +1,54 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18364)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18365)
+@@ -93,6 +93,12 @@
+ MatRestoreRow(D,row,&ncols2,(const int**)&cols2,(const double**)&vals2);
+ }
+
++ /*Broadcast max(dmax)*/
++ IssmDouble dmax_all;
++ ISSM_MPI_Reduce(&dmax,&dmax_all,1,ISSM_MPI_DOUBLE,ISSM_MPI_MAX,0,IssmComm::GetComm() );
++ ISSM_MPI_Bcast(&dmax_all,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm());
++ dmax = dmax_all;
++
+ /*Penalize Dirichlet boundary*/
+ dmax = dmax * 1.e+3;
+ for(int i=0;iconstraints->Size();i++){
+@@ -209,6 +215,14 @@
+ VecDuplicate(uvec,&Ri_plus);
+ VecDuplicate(uvec,&Ri_minus);
+
++ /*Get global extremas*/
++ IssmDouble uLmin_global = ulmin[0];
++ IssmDouble uLmax_global = ulmax[0];
++ VecGetSize(uvec,&ncols);
++ for(int i=1;iuLmax_global) uLmax_global = ulmax[i];
++ //printf("%g %g\n",uLmin_global,uLmax_global);
++
+ /*Go through D and calculate Ris*/
+ MatGetOwnershipRange(D,&rstart,&rend);
+ for(int row=rstart; row= 0.);
+ _assert_(Qi_minus <= 0.);
+ d = 1.;
+@@ -371,7 +387,7 @@
+ /*Create RHS: [ML + (1 − theta) deltaT L^n] u^n */
+ CreateRHS(&RHS,K_petsc,D_petsc,Ml_petsc,uf->pvector->vector,theta,deltat,dmax,femmodel,configuration_type);
+ delete uf;
+-
++
+ /*Go solve lower order solution*/
+ SolverxPetsc(&u,LHS,RHS,NULL,NULL, femmodel->parameters);
+ MatFree(&LHS);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18365-18366.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18365-18366.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18365-18366.diff (revision 19102)
@@ -0,0 +1,97 @@
+Index: ../trunk-jpl/src/m/classes/clusters/generic_static.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 0)
++++ ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 18366)
+@@ -0,0 +1,85 @@
++%GENERIC cluster class definition
++%
++% Usage:
++% cluster=generic_static.m('name','astrid','np',3);
++
++classdef generic_static.m
++ properties (SetAccess=public)
++ % {{{
++ name='';
++ np=1;
++ codepath=fileparts(which('issm.exe'));
++ shell='/bin/sh';
++ %}}}
++ end
++ methods
++ function cluster=generic_static.m(varargin) % {{{
++
++ %use provided options to change fields
++ options=pairoptions(varargin{:});
++
++ %get name
++ cluster.name=getfieldvalue(options,'name',oshostname());
++
++ %initialize cluster using user settings if provided
++ if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
++
++ %OK get other fields
++ cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
++ end
++ %}}}
++ function disp(cluster) % {{{
++ % display the object
++ disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
++ disp(sprintf(' name: %s',cluster.name));
++ disp(sprintf(' np: %i',cluster.np));
++ disp(sprintf(' codepath: %s',cluster.codepath));
++ disp(sprintf(' shell: %s',cluster.shell));
++ end
++ %}}}
++ function md = checkconsistency(cluster,md,solution,analyses) % {{{
++ if cluster.np<1
++ md = checkmessage(md,['number of processors should be at least 1']);
++ end
++ if isnan(cluster.np),
++ md = checkmessage(md,'number of processors should not be NaN!');
++ end
++ end
++ %}}}
++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
++
++ %write queuing script
++ fid=fopen([modelname '.queue'],'w');
++ fprintf(fid,'#!%s\n',cluster.shell);
++ fprintf(fid,[cluster.codepath '/mpiexec -np %i %s/issm.exe %s %s %s \n'],cluster.np,cluster.codepath,EnumToString(solution),'./',modelname);
++ fclose(fid);
++
++ %in interactive mode, create a run file, and errlog and outlog file
++ fid=fopen([modelname '.errlog'],'w'); fclose(fid);
++ fid=fopen([modelname '.outlog'],'w'); fclose(fid);
++ end
++ %}}}
++ function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
++
++ if ~ispc,
++
++ %figure out what shell extension we will use:
++ if isempty(strfind(cluster.shell,'csh')),
++ shellext='sh';
++ else
++ shellext='csh';
++ end
++
++ disp('launching solution sequence');
++ launchcommand=['source ' modelname '.queue '];
++ issmssh(cluster.name,'',0,launchcommand);
++ else
++ system([modelname '.bat']);
++ end
++ end %}}}
++ function Download(cluster,dirname,filelist)% {{{
++ %do nothing
++ return;
++ end %}}}
++ end
++end
+
+Property changes on: ../trunk-jpl/src/m/classes/clusters/generic_static.m
+___________________________________________________________________
+Added: svn:executable
+## -0,0 +1 ##
++*
+\ No newline at end of property
Index: /issm/oecreview/Archive/18296-19100/ISSM-18366-18367.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18366-18367.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18366-18367.diff (revision 19102)
@@ -0,0 +1,19 @@
+Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp
+===================================================================
+--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18366)
++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_fct.cpp (revision 18367)
+@@ -247,10 +247,10 @@
+ /*Compute Qis and Ris*/
+ //double Qi_plus = ml_serial[row]/deltat*(3. - u[row]);
+ //double Qi_minus = ml_serial[row]/deltat*(2. - u[row]);
+- //double Qi_plus = ml_serial[row]/deltat*(ulmax[row] - u[row]);
+- //double Qi_minus = ml_serial[row]/deltat*(ulmin[row] - u[row]);
+- double Qi_plus = ml_serial[row]/deltat*(uLmax_global - u[row]);
+- double Qi_minus = ml_serial[row]/deltat*(uLmin_global - u[row]);
++ double Qi_plus = ml_serial[row]/deltat*(ulmax[row] - u[row]);
++ double Qi_minus = ml_serial[row]/deltat*(ulmin[row] - u[row]);
++ //double Qi_plus = ml_serial[row]/deltat*(uLmax_global - u[row]);
++ //double Qi_minus = ml_serial[row]/deltat*(uLmin_global - u[row]);
+ _assert_(Qi_plus >= 0.);
+ _assert_(Qi_minus <= 0.);
+ d = 1.;
Index: /issm/oecreview/Archive/18296-19100/ISSM-18367-18368.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18367-18368.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18367-18368.diff (revision 19102)
@@ -0,0 +1,42 @@
+Index: ../trunk-jpl/src/m/solve/waitonlock.m
+===================================================================
+--- ../trunk-jpl/src/m/solve/waitonlock.m (revision 18367)
++++ ../trunk-jpl/src/m/solve/waitonlock.m (revision 18368)
+@@ -26,7 +26,7 @@
+
+
+ %If we are using the generic cluster in interactive mode, job is already complete
+-if isa(cluster,'generic') & cluster.interactive
++if (isa(cluster,'generic') & cluster.interactive) | isa(cluster,'generic_static'),
+ %We are in interactive mode, no need to check for job completion
+ ispresent=1;
+ return;
+Index: ../trunk-jpl/src/m/classes/clusters/generic_static.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 18367)
++++ ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 18368)
+@@ -1,19 +1,21 @@
+ %GENERIC cluster class definition
+ %
+ % Usage:
+-% cluster=generic_static.m('name','astrid','np',3);
++% cluster=generic_static('name','astrid','np',3);
+
+-classdef generic_static.m
++classdef generic_static
+ properties (SetAccess=public)
+ % {{{
+ name='';
+ np=1;
+ codepath=fileparts(which('issm.exe'));
++ executionpath = '.';
++ interactive = 1;
+ shell='/bin/sh';
+ %}}}
+ end
+ methods
+- function cluster=generic_static.m(varargin) % {{{
++ function cluster=generic_static(varargin) % {{{
+
+ %use provided options to change fields
+ options=pairoptions(varargin{:});
Index: /issm/oecreview/Archive/18296-19100/ISSM-18368-18369.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18368-18369.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18368-18369.diff (revision 19102)
@@ -0,0 +1,89 @@
+Index: ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18368)
++++ ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18369)
+@@ -99,16 +99,6 @@
+ vbarobs = sqrt(vbarobs2);
+ hu2 = hobs*hobs*vbarobs2;
+
+- /*H^2 - Hobs^2*/
+- NUMxH2 = 2.*dbasis[0]*dphi[0]*(dphi[0]*dphi[0] + dphi[1]*dphi[1] - hu2);
+- NUMyH2 = 2.*dbasis[1]*dphi[1]*(dphi[0]*dphi[0] + dphi[1]*dphi[1] - hu2);
+- DENH2 = vbarobs2*vbarobs2+1.e-14;
+-
+- /*Ubar-Ubar_obs*/
+- NUMxUbar = (vyobsbar*dphi[0]*dphi[1] - vxobsbar*dphi[1]*dphi[1])*vbarobs*dbasis[0];
+- NUMyUbar = (vyobsbar*dphi[0]*dphi[0] - vxobsbar*dphi[0]*dphi[1])*vbarobs*dbasis[1];
+- DENUbar = pow(dphi[0]*dphi[0] + dphi[1]*dphi[1],3./2.)+1.e-14;
+-
+ /*Loop over all requested responses*/
+ for(int resp=0;respGetInputValue(&weight,gauss,responses[resp]);
+@@ -116,11 +106,26 @@
+ switch(responses[resp]){
+ case Balancethickness2MisfitEnum:
+ /*J = (H^2 - Hobs^2)^2*/
+- //for(i=0;ivalues[i]+=(NUMxH2+NUMyH2)/DENH2 *weight*Jdet*gauss->weight; NOT WORKING
++ for(i=0;ivalues[i]+=(NUMxH2+NUMyH2)/DENH2 *weight*Jdet*gauss->weight;
++ }
+ /*J = phi^2*/
+- //for(i=0;ivalues[i]+= phi*basis[i]*weight*Jdet*gauss->weight; OK
++ //for(i=0;ivalues[i]+= phi*basis[i]*weight*Jdet*gauss->weight; //OK
++ /*J = grad J ^2*/
++ //for(i=0;ivalues[i]+= (dphi[0]*dbasis[0*numnodes+i] + dphi[1]*dbasis[1*numnodes+i])*weight*Jdet*gauss->weight; //OK
+ /*J = (ubar - nux*uobs)^2*/
+- for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
++ //for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
+ break;
+ default:
+ _error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+Index: ../trunk-jpl/src/c/classes/FemModel.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18368)
++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18369)
+@@ -1303,7 +1303,7 @@
+ IssmDouble J=0.;
+ IssmDouble J_sum;
+
+- IssmDouble weight,thicknessobs,thickness,potential;
++ IssmDouble weight,thicknessobs,thickness,potential,dpotential[2];
+ IssmDouble vx,vy,vxbar,vybar,vxobs,vyobs,vxbarobs,vybarobs,nux,nuy;
+ IssmDouble Jdet;
+ IssmDouble* xyz_list = NULL;
+@@ -1342,6 +1342,7 @@
+ thickness_input->GetInputValue(&thickness,gauss);
+ thicknessobs_input->GetInputValue(&thicknessobs,gauss);
+ potential_input->GetInputValue(&potential,gauss);
++ potential_input->GetInputDerivativeValue(&dpotential[0],xyz_list,gauss);
+ vxobs_input->GetInputValue(&vxobs,gauss);
+ vyobs_input->GetInputValue(&vyobs,gauss);
+ vx_input->GetInputValue(&vxbar,gauss);
+@@ -1353,11 +1354,13 @@
+ vybarobs = nuy*vyobs;
+
+ /*J = (H^2 - Hobs^2)^2*/
+- //J +=0.5*(thickness*thickness - thicknessobs*thicknessobs)*(thickness*thickness - thicknessobs*thicknessobs)*weight*Jdet*gauss->weight;
++ J +=0.5*(thickness*thickness - thicknessobs*thicknessobs)*(thickness*thickness - thicknessobs*thicknessobs)*weight*Jdet*gauss->weight;
+ /*J = phi^2*/
+- //J +=.5*potential*potential*weight*Jdet*gauss->weight; OK
++ //J +=.5*potential*potential*weight*Jdet*gauss->weight;// OK
++ /*J = grad phi^2*/
++ //J +=.5*(dpotential[0]*dpotential[0] + dpotential[1]*dpotential[1])*weight*Jdet*gauss->weight;
+ /*J = (ubar - nux*uobs)^2*/
+- J +=0.5*((vxbarobs - vxbar)*(vxbarobs - vxbar) + (vybarobs - vybar)*(vybarobs - vybar))*weight*Jdet*gauss->weight;
++ //J +=0.5*((vxbarobs - vxbar)*(vxbarobs - vxbar) + (vybarobs - vybar)*(vybarobs - vybar))*weight*Jdet*gauss->weight;
+ }
+
+ /*clean up and Return: */
Index: /issm/oecreview/Archive/18296-19100/ISSM-18369-18370.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18369-18370.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18369-18370.diff (revision 19102)
@@ -0,0 +1,37 @@
+Index: ../trunk-jpl/src/c/Makefile.am
+===================================================================
+--- ../trunk-jpl/src/c/Makefile.am (revision 18369)
++++ ../trunk-jpl/src/c/Makefile.am (revision 18370)
+@@ -872,8 +872,12 @@
+ libISSMModules_la_SOURCES += $(kml_sources)
+ endif
+ libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS)
++if STANDALONE_LIBRARIES
++libISSMModules_la_LIBADD = ./libISSMCore.la
++else
+ libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB)
+ endif
++endif
+
+ if VERSION
+ AM_LDFLAGS =
+Index: ../trunk-jpl/configure.ac
+===================================================================
+--- ../trunk-jpl/configure.ac (revision 18369)
++++ ../trunk-jpl/configure.ac (revision 18370)
+@@ -14,7 +14,6 @@
+ AC_PROG_F77([ifort g77 gfortran])
+
+ #Libraries and linking
+-AC_F77_LIBRARY_LDFLAGS
+ AC_PATH_XTRA #figure out X library and include paths
+
+ #AUTOMAKE
+@@ -22,7 +21,6 @@
+ AM_INIT_AUTOMAKE([foreign])
+ AC_CONFIG_HEADERS([./config.h]) #Config file must be config.h
+ AM_SILENT_RULES([yes]) #Do not show compilation command by default
+-AM_PROG_CC_C_O
+ AM_PROG_AR
+
+ #Libtool
Index: /issm/oecreview/Archive/18296-19100/ISSM-18370-18371.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18370-18371.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18370-18371.diff (revision 19102)
@@ -0,0 +1,79 @@
+Index: ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18370)
++++ ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18371)
+@@ -106,26 +106,31 @@
+ switch(responses[resp]){
+ case Balancethickness2MisfitEnum:
+ /*J = (H^2 - Hobs^2)^2*/
+- for(i=0;ivalues[i]+=(NUMxH2+NUMyH2)/DENH2 *weight*Jdet*gauss->weight;
+- }
++ // pe->values[i]+=(NUMxH2+NUMyH2)/DENH2 *weight*Jdet*gauss->weight;
++ //}
+ /*J = phi^2*/
+ //for(i=0;ivalues[i]+= phi*basis[i]*weight*Jdet*gauss->weight; //OK
+ /*J = grad J ^2*/
+ //for(i=0;ivalues[i]+= (dphi[0]*dbasis[0*numnodes+i] + dphi[1]*dbasis[1*numnodes+i])*weight*Jdet*gauss->weight; //OK
+ /*J = (ubar - nux*uobs)^2*/
+- //for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
++ for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
++ }
+ break;
+ default:
+ _error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+Index: ../trunk-jpl/src/c/modules/FloatingiceMeltingRatex
+===================================================================
+--- ../trunk-jpl/src/c/modules/FloatingiceMeltingRatex (revision 18370)
++++ ../trunk-jpl/src/c/modules/FloatingiceMeltingRatex (revision 18371)
+
+Property changes on: ../trunk-jpl/src/c/modules/FloatingiceMeltingRatex
+___________________________________________________________________
+Modified: svn:ignore
+## -1 +1,2 ##
+ .deps
++.dirstamp
+Index: ../trunk-jpl/src/c/classes/FemModel.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18370)
++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 18371)
+@@ -1354,13 +1354,13 @@
+ vybarobs = nuy*vyobs;
+
+ /*J = (H^2 - Hobs^2)^2*/
+- J +=0.5*(thickness*thickness - thicknessobs*thicknessobs)*(thickness*thickness - thicknessobs*thicknessobs)*weight*Jdet*gauss->weight;
++ //J +=0.5*(thickness*thickness - thicknessobs*thicknessobs)*(thickness*thickness - thicknessobs*thicknessobs)*weight*Jdet*gauss->weight;
+ /*J = phi^2*/
+ //J +=.5*potential*potential*weight*Jdet*gauss->weight;// OK
+ /*J = grad phi^2*/
+ //J +=.5*(dpotential[0]*dpotential[0] + dpotential[1]*dpotential[1])*weight*Jdet*gauss->weight;
+ /*J = (ubar - nux*uobs)^2*/
+- //J +=0.5*((vxbarobs - vxbar)*(vxbarobs - vxbar) + (vybarobs - vybar)*(vybarobs - vybar))*weight*Jdet*gauss->weight;
++ J +=0.5*((vxbarobs - vxbar)*(vxbarobs - vxbar) + (vybarobs - vybar)*(vybarobs - vybar))*weight*Jdet*gauss->weight;
+ }
+
+ /*clean up and Return: */
Index: /issm/oecreview/Archive/18296-19100/ISSM-18371-18372.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18371-18372.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18371-18372.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/configure.ac
+===================================================================
+--- ../trunk-jpl/configure.ac (revision 18371)
++++ ../trunk-jpl/configure.ac (revision 18372)
+@@ -13,6 +13,8 @@
+ AC_PROG_CXX([icpc cccl cl icl g++])
+ AC_PROG_F77([ifort g77 gfortran])
+
++AC_F77_LIBRARY_LDFLAGS
++
+ #Libraries and linking
+ AC_PATH_XTRA #figure out X library and include paths
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18372-18373.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18372-18373.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18372-18373.diff (revision 19102)
@@ -0,0 +1,91 @@
+Index: ../trunk-jpl/m4/issm_options.m4
+===================================================================
+--- ../trunk-jpl/m4/issm_options.m4 (revision 18372)
++++ ../trunk-jpl/m4/issm_options.m4 (revision 18373)
+@@ -8,9 +8,10 @@
+
+ dnl ISSM's internal options
+ dnl Build info{{{
++
++ dnl build date
+ AC_PATH_PROGS(DATE, date)
+ AC_MSG_CHECKING(for build date)
+- dnl system checks require uname
+ if test "$DATE" ; then
+ PACKAGE_DATE=`date`
+ else
+@@ -18,6 +19,74 @@
+ fi
+ AC_DEFINE_UNQUOTED(PACKAGE_BUILD_DATE,"$PACKAGE_DATE", Build date)
+ AC_MSG_RESULT($PACKAGE_DATE)
++
++ dnl user name
++ AC_MSG_CHECKING([user name])
++ if test -n "$USER"
++ then
++ user_name="$USER"
++ else
++ if test -n "$LOGNAME"
++ then
++ user_name="$LOGNAME"
++ else
++ user_name=`(whoami) 2>/dev/null` || user_name=unknown
++ fi
++ fi
++ AC_DEFINE_UNQUOTED(USER_NAME, "$user_name", Build user name)
++ AC_MSG_RESULT($user_name)
++
++ AC_MSG_CHECKING([host full OS name and version])
++ dnl normalize some host OS names
++ case ${host_os} in
++ dnl linux is linux is linux, regardless of RMS.
++ linux-gnu* | lignux* ) host_os=linux ;;
++ esac
++ AC_DEFINE_UNQUOTED(HOST_OS, "$host_os", Host full OS name and version)
++ AC_MSG_RESULT($host_os)
++
++ AC_MSG_CHECKING([host cpu])
++ AC_DEFINE_UNQUOTED(HOST_CPU, "$host_cpu",Host cpu)
++ AC_MSG_RESULT($host_cpu)
++
++ AC_MSG_CHECKING([vendor])
++ AC_DEFINE_UNQUOTED(HOST_VENDOR, "$host_vendor",Host vendor)
++ AC_MSG_RESULT($host_vendor)
++
++ AC_MSG_CHECKING([host OS name])
++ host_os_name=`echo $host_os | sed 's/\..*//g'`
++ dnl normalize some OS names
++ case ${host_os_name} in
++ dnl linux is linux is linux, regardless of RMS.
++ linux-gnu* | lignux* ) host_os_name=linux ;;
++ esac
++ AC_DEFINE_UNQUOTED(HOST_OS_NAME, "$host_os_name", Host OS name)
++ AC_MSG_RESULT($host_os_name)
++
++ dnl parse out the OS version of the host
++ AC_MSG_CHECKING([host OS version])
++ host_os_version=`echo $host_os | sed 's/^[[^0-9]]*//g'`
++ if test -z "$host_os_version"
++ then
++ host_os_version=`(uname -r) 2>/dev/null` || host_os_version=unknown
++ fi
++ AC_DEFINE_UNQUOTED(HOST_OS_VERSION, "$host_os_version", Host OS version)
++ AC_MSG_RESULT($host_os_version)
++
++
++ dnl figure out host architecture (different than CPU)
++ AC_MSG_CHECKING([host OS architecture])
++ host_arch=`(uname -m) 2>/dev/null` || host_arch=unknown
++ dnl normalize some names
++ case ${host_arch} in
++ sun4* ) host_arch=sun4 ;;
++ sun3x ) host_arch=sun3 ;;
++ sun ) host_arch=`(arch) 2>/dev/null` || host_arch=unknown ;;
++ i?86 ) host_arch=i386 ;; # all x86 should show up as i386
++ esac
++ AC_DEFINE_UNQUOTED(HOST_ARCH, "$host_arch",Host Archictecture)
++ AC_MSG_RESULT($host_arch)
++
+ dnl }}}
+ dnl Debugging {{{
+ AC_ARG_ENABLE([debugging], dnl feature
Index: /issm/oecreview/Archive/18296-19100/ISSM-18373-18374.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18373-18374.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18373-18374.diff (revision 19102)
@@ -0,0 +1,36 @@
+Index: ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp
+===================================================================
+--- ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp (revision 18373)
++++ ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp (revision 18374)
+@@ -114,6 +114,31 @@
+ svalue =xNew(strlen(PACKAGE_BUILD_DATE)+1);
+ xMemCpy(svalue,PACKAGE_BUILD_DATE,(strlen(PACKAGE_BUILD_DATE)+1));
+ }
++ else if(strcmp(name,"HOST_OS")==0){
++ isstring = true;
++ svalue =xNew(strlen(HOST_OS)+1);
++ xMemCpy(svalue,HOST_OS,(strlen(HOST_OS)+1));
++ }
++ else if(strcmp(name,"USER_NAME")==0){
++ isstring = true;
++ svalue =xNew(strlen(USER_NAME)+1);
++ xMemCpy(svalue,USER_NAME,(strlen(USER_NAME)+1));
++ }
++ else if(strcmp(name,"HOST_VENDOR")==0){
++ isstring = true;
++ svalue =xNew(strlen(HOST_VENDOR)+1);
++ xMemCpy(svalue,HOST_VENDOR,(strlen(HOST_VENDOR)+1));
++ }
++ else if(strcmp(name,"HOST_OS")==0){
++ isstring = true;
++ svalue =xNew(strlen(HOST_OS)+1);
++ xMemCpy(svalue,HOST_OS,(strlen(HOST_OS)+1));
++ }
++ else if(strcmp(name,"HOST_ARCH")==0){
++ isstring = true;
++ svalue =xNew(strlen(HOST_ARCH)+1);
++ xMemCpy(svalue,HOST_ARCH,(strlen(HOST_ARCH)+1));
++ }
+ else{
+ _error_("variable " << name << " not supported yet");
+ }
Index: /issm/oecreview/Archive/18296-19100/ISSM-18374-18375.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18374-18375.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18374-18375.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/m/dev/issmversion.m
+===================================================================
+--- ../trunk-jpl/src/m/dev/issmversion.m (revision 18374)
++++ ../trunk-jpl/src/m/dev/issmversion.m (revision 18375)
+@@ -14,6 +14,8 @@
+ disp(['(website: ' IssmConfig('PACKAGE_URL') ' contact:' IssmConfig('PACKAGE_BUGREPORT') ')']);
+ disp([' ']);
+ disp(['Build date: ' IssmConfig('PACKAGE_BUILD_DATE')]);
++disp(['Compiled on ' IssmConfig('HOST_VENDOR') ' ' IssmConfig('HOST_OS') ' ' IssmConfig('HOST_ARCH') ' by ' IssmConfig('USER_NAME')]);
++disp([' ']);
+ disp(['Copyright (c) 2009-2014 California Institute of Technology']);
+ disp([' ']);
+ disp([' to get started type: issmdoc']);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18375-18376.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18375-18376.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18375-18376.diff (revision 19102)
@@ -0,0 +1,60 @@
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh (revision 18375)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-greenplanet.sh (revision 18376)
+@@ -27,6 +27,7 @@
+ --known-mpi-shared-libraries=1 \
+ --with-debugging=0 \
+ --with-valgrind=0 \
++ --with-x=0 \
+ --with-batch=1 \
+ --with-shared-libraries=1 \
+ --download-metis=1 \
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-macosx64.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-macosx64.sh (revision 18375)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-macosx64.sh (revision 18376)
+@@ -21,6 +21,7 @@
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-debugging=0 \
+ --with-valgrind=0 \
++ --with-x=0 \
+ --with-shared-libraries=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-linux64.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-linux64.sh (revision 18375)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-linux64.sh (revision 18376)
+@@ -21,6 +21,7 @@
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-debugging=0 \
+ --with-valgrind=0 \
++ --with-x=0 \
+ --with-shared-libraries=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades.sh (revision 18375)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades.sh (revision 18376)
+@@ -24,6 +24,7 @@
+ --known-mpi-shared-libraries=1 \
+ --with-debugging=0 \
+ --with-valgrind=0 \
++ --with-x=0 \
+ --with-batch=1 \
+ --with-shared-libraries=1 \
+ --download-metis=1 \
+Index: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
+===================================================================
+--- ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18375)
++++ ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18376)
+@@ -21,6 +21,7 @@
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-batch=1 \
+ --with-debugging=0 \
++ --with-x=0 \
+ --with-shared-libraries=1 \
+ --known-mpi-shared-libraries=1 \
+ --with-mpi=1 \
Index: /issm/oecreview/Archive/18296-19100/ISSM-18376-18377.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18376-18377.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18376-18377.diff (revision 19102)
@@ -0,0 +1,639 @@
+Index: ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim
+===================================================================
+--- ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 18376)
++++ ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 18377)
+@@ -547,6 +547,7 @@
+ syn keyword cType StressbalanceSIAAnalysis
+ syn keyword cType StressbalanceVerticalAnalysis
+ syn keyword cType ThermalAnalysis
++syn keyword cType UzawaPressureAnalysis
+ "ISSM's objects end
+ "ISSM's Enums begin
+ syn keyword cConstant AutodiffIsautodiffEnum
+@@ -707,7 +708,6 @@
+ syn keyword cConstant InversionVyObsEnum
+ syn keyword cConstant InversionVzObsEnum
+ syn keyword cConstant MaskIceLevelsetEnum
+-syn keyword cConstant QmuMaskIceLevelsetEnum
+ syn keyword cConstant MaterialsBetaEnum
+ syn keyword cConstant MaterialsHeatcapacityEnum
+ syn keyword cConstant MaterialsLatentheatEnum
+@@ -720,7 +720,6 @@
+ syn keyword cConstant DamageIsdamageEnum
+ syn keyword cConstant DamageDEnum
+ syn keyword cConstant DamageFEnum
+-syn keyword cConstant QmuDamageDEnum
+ syn keyword cConstant DamageDbarEnum
+ syn keyword cConstant DamageLawEnum
+ syn keyword cConstant DamageC1Enum
+@@ -740,6 +739,7 @@
+ syn keyword cConstant DamageEquivStressEnum
+ syn keyword cConstant DamageEvolutionNumRequestedOutputsEnum
+ syn keyword cConstant DamageEvolutionRequestedOutputsEnum
++syn keyword cConstant NewDamageEnum
+ syn keyword cConstant MaterialsRhoIceEnum
+ syn keyword cConstant MaterialsRhoSeawaterEnum
+ syn keyword cConstant MaterialsRhoFreshwaterEnum
+@@ -793,7 +793,6 @@
+ syn keyword cConstant QmuPartitionEnum
+ syn keyword cConstant QmuResponsedescriptorsEnum
+ syn keyword cConstant QmuVariabledescriptorsEnum
+-syn keyword cConstant QmuMaterialsRheologyBEnum
+ syn keyword cConstant RiftsNumriftsEnum
+ syn keyword cConstant RiftsRiftstructEnum
+ syn keyword cConstant SettingsResultsOnNodesEnum
+@@ -925,6 +924,7 @@
+ syn keyword cConstant ThermalAnalysisEnum
+ syn keyword cConstant ThermalSolutionEnum
+ syn keyword cConstant TransientSolutionEnum
++syn keyword cConstant UzawaPressureAnalysisEnum
+ syn keyword cConstant GiaSolutionEnum
+ syn keyword cConstant GiaAnalysisEnum
+ syn keyword cConstant MeshdeformationSolutionEnum
+@@ -1034,17 +1034,6 @@
+ syn keyword cConstant MisfitEnum
+ syn keyword cConstant PressureEnum
+ syn keyword cConstant PressurePicardEnum
+-syn keyword cConstant QmuPressureEnum
+-syn keyword cConstant QmuVxEnum
+-syn keyword cConstant QmuVyEnum
+-syn keyword cConstant QmuVzEnum
+-syn keyword cConstant QmuThicknessEnum
+-syn keyword cConstant QmuBaseEnum
+-syn keyword cConstant QmuSurfaceEnum
+-syn keyword cConstant QmuMeltingEnum
+-syn keyword cConstant QmuVxMeshEnum
+-syn keyword cConstant QmuVyMeshEnum
+-syn keyword cConstant QmuVzMeshEnum
+ syn keyword cConstant AndroidFrictionCoefficientEnum
+ syn keyword cConstant ResetPenaltiesEnum
+ syn keyword cConstant SegmentOnIceShelfEnum
+@@ -1088,7 +1077,6 @@
+ syn keyword cConstant WatercolumnEnum
+ syn keyword cConstant BasalFrictionEnum
+ syn keyword cConstant ViscousHeatingEnum
+-syn keyword cConstant QmuTemperatureEnum
+ syn keyword cConstant HydrologyWaterVxEnum
+ syn keyword cConstant HydrologyWaterVyEnum
+ syn keyword cConstant SigmaNNEnum
+@@ -1106,6 +1094,13 @@
+ syn keyword cConstant DeviatoricStressyyEnum
+ syn keyword cConstant DeviatoricStressyzEnum
+ syn keyword cConstant DeviatoricStresszzEnum
++syn keyword cConstant StressEnum
++syn keyword cConstant StressxxEnum
++syn keyword cConstant StressxyEnum
++syn keyword cConstant StressxzEnum
++syn keyword cConstant StressyyEnum
++syn keyword cConstant StressyzEnum
++syn keyword cConstant StresszzEnum
+ syn keyword cConstant StrainRateEnum
+ syn keyword cConstant StrainRatexxEnum
+ syn keyword cConstant StrainRatexyEnum
+@@ -1134,6 +1129,7 @@
+ syn keyword cConstant MINIEnum
+ syn keyword cConstant MINIcondensedEnum
+ syn keyword cConstant TaylorHoodEnum
++syn keyword cConstant LATaylorHoodEnum
+ syn keyword cConstant XTaylorHoodEnum
+ syn keyword cConstant OneLayerP4zEnum
+ syn keyword cConstant CrouzeixRaviartEnum
+@@ -1178,6 +1174,9 @@
+ syn keyword cConstant AbsoluteEnum
+ syn keyword cConstant IncrementalEnum
+ syn keyword cConstant AugmentedLagrangianREnum
++syn keyword cConstant AugmentedLagrangianRhopEnum
++syn keyword cConstant AugmentedLagrangianRlambdaEnum
++syn keyword cConstant AugmentedLagrangianRholambdaEnum
+ syn keyword cConstant AugmentedLagrangianThetaEnum
+ syn keyword cConstant NoneEnum
+ syn keyword cConstant AggressiveMigrationEnum
+@@ -1186,7 +1185,6 @@
+ syn keyword cConstant SubelementMigration2Enum
+ syn keyword cConstant ContactEnum
+ syn keyword cConstant MaskGroundediceLevelsetEnum
+-syn keyword cConstant QmuMaskGroundediceLevelsetEnum
+ syn keyword cConstant GaussSegEnum
+ syn keyword cConstant GaussTriaEnum
+ syn keyword cConstant GaussTetraEnum
+Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18376)
++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18377)
+@@ -569,6 +569,13 @@
+ DeviatoricStressyyEnum,
+ DeviatoricStressyzEnum,
+ DeviatoricStresszzEnum,
++ StressEnum,
++ StressxxEnum,
++ StressxyEnum,
++ StressxzEnum,
++ StressyyEnum,
++ StressyzEnum,
++ StresszzEnum,
+ StrainRateEnum,
+ StrainRatexxEnum,
+ StrainRatexyEnum,
+Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18376)
++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18377)
+@@ -560,6 +560,13 @@
+ case DeviatoricStressyyEnum : return "DeviatoricStressyy";
+ case DeviatoricStressyzEnum : return "DeviatoricStressyz";
+ case DeviatoricStresszzEnum : return "DeviatoricStresszz";
++ case StressEnum : return "Stress";
++ case StressxxEnum : return "Stressxx";
++ case StressxyEnum : return "Stressxy";
++ case StressxzEnum : return "Stressxz";
++ case StressyyEnum : return "Stressyy";
++ case StressyzEnum : return "Stressyz";
++ case StresszzEnum : return "Stresszz";
+ case StrainRateEnum : return "StrainRate";
+ case StrainRatexxEnum : return "StrainRatexx";
+ case StrainRatexyEnum : return "StrainRatexy";
+Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18376)
++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18377)
+@@ -572,6 +572,13 @@
+ else if (strcmp(name,"DeviatoricStressyy")==0) return DeviatoricStressyyEnum;
+ else if (strcmp(name,"DeviatoricStressyz")==0) return DeviatoricStressyzEnum;
+ else if (strcmp(name,"DeviatoricStresszz")==0) return DeviatoricStresszzEnum;
++ else if (strcmp(name,"Stress")==0) return StressEnum;
++ else if (strcmp(name,"Stressxx")==0) return StressxxEnum;
++ else if (strcmp(name,"Stressxy")==0) return StressxyEnum;
++ else if (strcmp(name,"Stressxz")==0) return StressxzEnum;
++ else if (strcmp(name,"Stressyy")==0) return StressyyEnum;
++ else if (strcmp(name,"Stressyz")==0) return StressyzEnum;
++ else if (strcmp(name,"Stresszz")==0) return StresszzEnum;
+ else if (strcmp(name,"StrainRate")==0) return StrainRateEnum;
+ else if (strcmp(name,"StrainRatexx")==0) return StrainRatexxEnum;
+ else if (strcmp(name,"StrainRatexy")==0) return StrainRatexyEnum;
+@@ -621,17 +628,17 @@
+ else if (strcmp(name,"MassfluxatgateSegments")==0) return MassfluxatgateSegmentsEnum;
+ else if (strcmp(name,"MisfitName")==0) return MisfitNameEnum;
+ else if (strcmp(name,"MisfitModelEnum")==0) return MisfitModelEnumEnum;
+- else if (strcmp(name,"MisfitObservation")==0) return MisfitObservationEnum;
++ else stage=6;
++ }
++ if(stage==6){
++ if (strcmp(name,"MisfitObservation")==0) return MisfitObservationEnum;
+ else if (strcmp(name,"MisfitObservationEnum")==0) return MisfitObservationEnumEnum;
+ else if (strcmp(name,"MisfitTimeinterpolation")==0) return MisfitTimeinterpolationEnum;
+ else if (strcmp(name,"MisfitWeights")==0) return MisfitWeightsEnum;
+ else if (strcmp(name,"MisfitWeightsEnum")==0) return MisfitWeightsEnumEnum;
+ else if (strcmp(name,"SurfaceObservation")==0) return SurfaceObservationEnum;
+ else if (strcmp(name,"WeightsSurfaceObservation")==0) return WeightsSurfaceObservationEnum;
+- else stage=6;
+- }
+- if(stage==6){
+- if (strcmp(name,"MinVel")==0) return MinVelEnum;
++ else if (strcmp(name,"MinVel")==0) return MinVelEnum;
+ else if (strcmp(name,"MaxVel")==0) return MaxVelEnum;
+ else if (strcmp(name,"MinVx")==0) return MinVxEnum;
+ else if (strcmp(name,"MaxVx")==0) return MaxVxEnum;
+Index: ../trunk-jpl/src/m/enum/QmuVzMeshEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVzMeshEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVzMeshEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVzMeshEnum()
+-%QMUVZMESHENUM - Enum of QmuVzMesh
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVzMeshEnum()
+-
+-macro=StringToEnum('QmuVzMesh');
+Index: ../trunk-jpl/src/m/enum/QmuMeltingEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuMeltingEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuMeltingEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuMeltingEnum()
+-%QMUMELTINGENUM - Enum of QmuMelting
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuMeltingEnum()
+-
+-macro=StringToEnum('QmuMelting');
+Index: ../trunk-jpl/src/m/enum/QmuMaskGroundediceLevelsetEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuMaskGroundediceLevelsetEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuMaskGroundediceLevelsetEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuMaskGroundediceLevelsetEnum()
+-%QMUMASKGROUNDEDICELEVELSETENUM - Enum of QmuMaskGroundediceLevelset
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuMaskGroundediceLevelsetEnum()
+-
+-macro=StringToEnum('QmuMaskGroundediceLevelset');
+Index: ../trunk-jpl/src/m/enum/QmuMaskIceLevelsetEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuMaskIceLevelsetEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuMaskIceLevelsetEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuMaskIceLevelsetEnum()
+-%QMUMASKICELEVELSETENUM - Enum of QmuMaskIceLevelset
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuMaskIceLevelsetEnum()
+-
+-macro=StringToEnum('QmuMaskIceLevelset');
+Index: ../trunk-jpl/src/m/enum/QmuDamageDEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuDamageDEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuDamageDEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuDamageDEnum()
+-%QMUDAMAGEDENUM - Enum of QmuDamageD
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuDamageDEnum()
+-
+-macro=StringToEnum('QmuDamageD');
+Index: ../trunk-jpl/src/m/enum/QmuBaseEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuBaseEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuBaseEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuBaseEnum()
+-%QMUBASEENUM - Enum of QmuBase
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuBaseEnum()
+-
+-macro=StringToEnum('QmuBase');
+Index: ../trunk-jpl/src/m/enum/QmuMaterialsRheologyBEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuMaterialsRheologyBEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuMaterialsRheologyBEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuMaterialsRheologyBEnum()
+-%QMUMATERIALSRHEOLOGYBENUM - Enum of QmuMaterialsRheologyB
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuMaterialsRheologyBEnum()
+-
+-macro=StringToEnum('QmuMaterialsRheologyB');
+Index: ../trunk-jpl/src/m/enum/QmuVxEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVxEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVxEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVxEnum()
+-%QMUVXENUM - Enum of QmuVx
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVxEnum()
+-
+-macro=StringToEnum('QmuVx');
+Index: ../trunk-jpl/src/m/enum/QmuVxMeshEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVxMeshEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVxMeshEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVxMeshEnum()
+-%QMUVXMESHENUM - Enum of QmuVxMesh
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVxMeshEnum()
+-
+-macro=StringToEnum('QmuVxMesh');
+Index: ../trunk-jpl/src/m/enum/QmuVyEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVyEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVyEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVyEnum()
+-%QMUVYENUM - Enum of QmuVy
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVyEnum()
+-
+-macro=StringToEnum('QmuVy');
+Index: ../trunk-jpl/src/m/enum/QmuPressureEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuPressureEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuPressureEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuPressureEnum()
+-%QMUPRESSUREENUM - Enum of QmuPressure
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuPressureEnum()
+-
+-macro=StringToEnum('QmuPressure');
+Index: ../trunk-jpl/src/m/enum/QmuThicknessEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuThicknessEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuThicknessEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuThicknessEnum()
+-%QMUTHICKNESSENUM - Enum of QmuThickness
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuThicknessEnum()
+-
+-macro=StringToEnum('QmuThickness');
+Index: ../trunk-jpl/src/m/enum/QmuVzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVzEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVzEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVzEnum()
+-%QMUVZENUM - Enum of QmuVz
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVzEnum()
+-
+-macro=StringToEnum('QmuVz');
+Index: ../trunk-jpl/src/m/enum/QmuVyMeshEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuVyMeshEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuVyMeshEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuVyMeshEnum()
+-%QMUVYMESHENUM - Enum of QmuVyMesh
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuVyMeshEnum()
+-
+-macro=StringToEnum('QmuVyMesh');
+Index: ../trunk-jpl/src/m/enum/QmuTemperatureEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuTemperatureEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuTemperatureEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuTemperatureEnum()
+-%QMUTEMPERATUREENUM - Enum of QmuTemperature
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuTemperatureEnum()
+-
+-macro=StringToEnum('QmuTemperature');
+Index: ../trunk-jpl/src/m/enum/QmuSurfaceEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/QmuSurfaceEnum.m (revision 18376)
++++ ../trunk-jpl/src/m/enum/QmuSurfaceEnum.m (revision 18377)
+@@ -1,11 +0,0 @@
+-function macro=QmuSurfaceEnum()
+-%QMUSURFACEENUM - Enum of QmuSurface
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=QmuSurfaceEnum()
+-
+-macro=StringToEnum('QmuSurface');
+Index: ../trunk-jpl/src/m/enum/StressxyEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxyEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressxyEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressxyEnum()
++%STRESSXYENUM - Enum of Stressxy
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressxyEnum()
++
++macro=StringToEnum('Stressxy');
+Index: ../trunk-jpl/src/m/enum/StressxzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxzEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressxzEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressxzEnum()
++%STRESSXZENUM - Enum of Stressxz
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressxzEnum()
++
++macro=StringToEnum('Stressxz');
+Index: ../trunk-jpl/src/m/enum/StressyyEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressyyEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressyyEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressyyEnum()
++%STRESSYYENUM - Enum of Stressyy
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressyyEnum()
++
++macro=StringToEnum('Stressyy');
+Index: ../trunk-jpl/src/m/enum/StressyzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressyzEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressyzEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressyzEnum()
++%STRESSYZENUM - Enum of Stressyz
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressyzEnum()
++
++macro=StringToEnum('Stressyz');
+Index: ../trunk-jpl/src/m/enum/StressEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressEnum()
++%STRESSENUM - Enum of Stress
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressEnum()
++
++macro=StringToEnum('Stress');
+Index: ../trunk-jpl/src/m/enum/StresszzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StresszzEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StresszzEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StresszzEnum()
++%STRESSZZENUM - Enum of Stresszz
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StresszzEnum()
++
++macro=StringToEnum('Stresszz');
+Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py
+===================================================================
+--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18376)
++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18377)
+@@ -166,7 +166,6 @@
+ def InversionVyObsEnum(): return StringToEnum("InversionVyObs")[0]
+ def InversionVzObsEnum(): return StringToEnum("InversionVzObs")[0]
+ def MaskIceLevelsetEnum(): return StringToEnum("MaskIceLevelset")[0]
+-def QmuMaskIceLevelsetEnum(): return StringToEnum("QmuMaskIceLevelset")[0]
+ def MaterialsBetaEnum(): return StringToEnum("MaterialsBeta")[0]
+ def MaterialsHeatcapacityEnum(): return StringToEnum("MaterialsHeatcapacity")[0]
+ def MaterialsLatentheatEnum(): return StringToEnum("MaterialsLatentheat")[0]
+@@ -179,7 +178,6 @@
+ def DamageIsdamageEnum(): return StringToEnum("DamageIsdamage")[0]
+ def DamageDEnum(): return StringToEnum("DamageD")[0]
+ def DamageFEnum(): return StringToEnum("DamageF")[0]
+-def QmuDamageDEnum(): return StringToEnum("QmuDamageD")[0]
+ def DamageDbarEnum(): return StringToEnum("DamageDbar")[0]
+ def DamageLawEnum(): return StringToEnum("DamageLaw")[0]
+ def DamageC1Enum(): return StringToEnum("DamageC1")[0]
+@@ -253,7 +251,6 @@
+ def QmuPartitionEnum(): return StringToEnum("QmuPartition")[0]
+ def QmuResponsedescriptorsEnum(): return StringToEnum("QmuResponsedescriptors")[0]
+ def QmuVariabledescriptorsEnum(): return StringToEnum("QmuVariabledescriptors")[0]
+-def QmuMaterialsRheologyBEnum(): return StringToEnum("QmuMaterialsRheologyB")[0]
+ def RiftsNumriftsEnum(): return StringToEnum("RiftsNumrifts")[0]
+ def RiftsRiftstructEnum(): return StringToEnum("RiftsRiftstruct")[0]
+ def SettingsResultsOnNodesEnum(): return StringToEnum("SettingsResultsOnNodes")[0]
+@@ -495,17 +492,6 @@
+ def MisfitEnum(): return StringToEnum("Misfit")[0]
+ def PressureEnum(): return StringToEnum("Pressure")[0]
+ def PressurePicardEnum(): return StringToEnum("PressurePicard")[0]
+-def QmuPressureEnum(): return StringToEnum("QmuPressure")[0]
+-def QmuVxEnum(): return StringToEnum("QmuVx")[0]
+-def QmuVyEnum(): return StringToEnum("QmuVy")[0]
+-def QmuVzEnum(): return StringToEnum("QmuVz")[0]
+-def QmuThicknessEnum(): return StringToEnum("QmuThickness")[0]
+-def QmuBaseEnum(): return StringToEnum("QmuBase")[0]
+-def QmuSurfaceEnum(): return StringToEnum("QmuSurface")[0]
+-def QmuMeltingEnum(): return StringToEnum("QmuMelting")[0]
+-def QmuVxMeshEnum(): return StringToEnum("QmuVxMesh")[0]
+-def QmuVyMeshEnum(): return StringToEnum("QmuVyMesh")[0]
+-def QmuVzMeshEnum(): return StringToEnum("QmuVzMesh")[0]
+ def AndroidFrictionCoefficientEnum(): return StringToEnum("AndroidFrictionCoefficient")[0]
+ def ResetPenaltiesEnum(): return StringToEnum("ResetPenalties")[0]
+ def SegmentOnIceShelfEnum(): return StringToEnum("SegmentOnIceShelf")[0]
+@@ -549,7 +535,6 @@
+ def WatercolumnEnum(): return StringToEnum("Watercolumn")[0]
+ def BasalFrictionEnum(): return StringToEnum("BasalFriction")[0]
+ def ViscousHeatingEnum(): return StringToEnum("ViscousHeating")[0]
+-def QmuTemperatureEnum(): return StringToEnum("QmuTemperature")[0]
+ def HydrologyWaterVxEnum(): return StringToEnum("HydrologyWaterVx")[0]
+ def HydrologyWaterVyEnum(): return StringToEnum("HydrologyWaterVy")[0]
+ def SigmaNNEnum(): return StringToEnum("SigmaNN")[0]
+@@ -567,6 +552,13 @@
+ def DeviatoricStressyyEnum(): return StringToEnum("DeviatoricStressyy")[0]
+ def DeviatoricStressyzEnum(): return StringToEnum("DeviatoricStressyz")[0]
+ def DeviatoricStresszzEnum(): return StringToEnum("DeviatoricStresszz")[0]
++def StressEnum(): return StringToEnum("Stress")[0]
++def StressxxEnum(): return StringToEnum("Stressxx")[0]
++def StressxyEnum(): return StringToEnum("Stressxy")[0]
++def StressxzEnum(): return StringToEnum("Stressxz")[0]
++def StressyyEnum(): return StringToEnum("Stressyy")[0]
++def StressyzEnum(): return StringToEnum("Stressyz")[0]
++def StresszzEnum(): return StringToEnum("Stresszz")[0]
+ def StrainRateEnum(): return StringToEnum("StrainRate")[0]
+ def StrainRatexxEnum(): return StringToEnum("StrainRatexx")[0]
+ def StrainRatexyEnum(): return StringToEnum("StrainRatexy")[0]
+@@ -651,7 +643,6 @@
+ def SubelementMigration2Enum(): return StringToEnum("SubelementMigration2")[0]
+ def ContactEnum(): return StringToEnum("Contact")[0]
+ def MaskGroundediceLevelsetEnum(): return StringToEnum("MaskGroundediceLevelset")[0]
+-def QmuMaskGroundediceLevelsetEnum(): return StringToEnum("QmuMaskGroundediceLevelset")[0]
+ def GaussSegEnum(): return StringToEnum("GaussSeg")[0]
+ def GaussTriaEnum(): return StringToEnum("GaussTria")[0]
+ def GaussTetraEnum(): return StringToEnum("GaussTetra")[0]
+Index: ../trunk-jpl/src/m/enum/StressxxEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxxEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressxxEnum.m (revision 18377)
+@@ -0,0 +1,11 @@
++function macro=StressxxEnum()
++%STRESSXXENUM - Enum of Stressxx
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressxxEnum()
++
++macro=StringToEnum('Stressxx');
Index: /issm/oecreview/Archive/18296-19100/ISSM-18377-18378.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18377-18378.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18377-18378.diff (revision 19102)
@@ -0,0 +1,45 @@
+Index: ../trunk-jpl/src/m/classes/model.m
+===================================================================
+--- ../trunk-jpl/src/m/classes/model.m (revision 18377)
++++ ../trunk-jpl/src/m/classes/model.m (revision 18378)
+@@ -220,8 +220,12 @@
+ end
+
+ %special for thermal modeling:
+- md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
+- md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
++ if ~isnan(md.basalforcings.groundedice_melting_rate),
++ md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
++ end
++ if ~isnan(md.basalforcings.floatingice_melting_rate),
++ md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
++ end
+ md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
+
+ %update of connectivity matrix
+@@ -237,8 +241,12 @@
+ md.geometry.base=project2d(md,md.geometry.base,1);
+ md.geometry.bed=project2d(md,md.geometry.bed,1);
+
+- md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
+- md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
++ if ~isnan(md.mask.groundedice_levelset),
++ md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
++ end
++ if ~isnan(md.mask.ice_levelset),
++ md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
++ end
+
+ %lat long
+ if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
+@@ -824,8 +832,9 @@
+ if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
+ if isfield(structmd,'p'), md.friction.p=structmd.p; end
+ if isfield(structmd,'q'), md.friction.q=structmd.p; end
+- if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
++ if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
+ if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
++ if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
+ if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
+ if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
+ if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
Index: /issm/oecreview/Archive/18296-19100/ISSM-18378-18379.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18378-18379.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18378-18379.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/m/contrib/bamg/gmsh3d.m
+===================================================================
+--- ../trunk-jpl/src/m/contrib/bamg/gmsh3d.m (revision 18378)
++++ ../trunk-jpl/src/m/contrib/bamg/gmsh3d.m (revision 18379)
+@@ -96,7 +96,7 @@
+
+ %call gmsh
+ fprintf('%s\n',' call gmsh...');
+-system([issmdir() '/externalpackages/gmsh/install/gmsh -3 model.geo']);
++system([issmdir() '/externalpackages/gmsh/install/gmsh -3 -v 0 model.geo']);
+
+ %plug new mesh
+ t1=clock; fprintf('\n%s',' reading final mesh files...');
Index: /issm/oecreview/Archive/18296-19100/ISSM-18379-18380.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18379-18380.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18379-18380.diff (revision 19102)
@@ -0,0 +1,12 @@
+Index: ../trunk-jpl/src/m/exp/masktoexp.m
+===================================================================
+--- ../trunk-jpl/src/m/exp/masktoexp.m (revision 18379)
++++ ../trunk-jpl/src/m/exp/masktoexp.m (revision 18380)
+@@ -23,6 +23,7 @@
+
+ %Create exp structure
+ A=struct();
++if(j-1<1), error('no contour found'); end
+ for i=1:j-1,
+ A(i).x=s(i).x;
+ A(i).y=s(i).y;
Index: /issm/oecreview/Archive/18296-19100/ISSM-18380-18381.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18380-18381.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18380-18381.diff (revision 19102)
@@ -0,0 +1,49 @@
+Index: ../trunk-jpl/src/m/miscellaneous/vorticity.m
+===================================================================
+--- ../trunk-jpl/src/m/miscellaneous/vorticity.m (revision 18380)
++++ ../trunk-jpl/src/m/miscellaneous/vorticity.m (revision 18381)
+@@ -28,6 +28,6 @@
+ dvxdy=(vx(index).*beta)*summation;
+ rot=dvxdy - dvydx;
+
+-if strcmpi(meshtype(md.mesh),'3D'),
++if strcmpi(domaintype(md.mesh),'3D'),
+ rot=project3d(md,'vector',rot,'type','element');
+ end
+Index: ../trunk-jpl/src/m/miscellaneous/colinearity.m
+===================================================================
+--- ../trunk-jpl/src/m/miscellaneous/colinearity.m (revision 0)
++++ ../trunk-jpl/src/m/miscellaneous/colinearity.m (revision 18381)
+@@ -0,0 +1,32 @@
++function theta = colinearity(md)
++
++%load some variables (it is much faster if the variab;es are loaded from md once for all)
++if ~strcmpi(meshtype(md.mesh),'3D'),
++ numberofelements=md.mesh.numberofelements;
++ numberofnodes=md.mesh.numberofvertices;
++ index=md.mesh.elements;
++ x=md.mesh.x; y=md.mesh.y;
++else
++ numberofelements=md.mesh.numberofelements2d;
++ numberofnodes=md.mesh.numberofvertices2d;
++ index=md.mesh.elements2d;
++ x=md.mesh.x2d; y=md.mesh.y2d;
++end
++
++%compute nodal functions coefficients N(x,y)=alpha x + beta y + gamma
++[alpha beta]=GetNodalFunctionsCoeff(index,x,y);
++
++s = averaging(md,md.geometry.surface,2);
++
++summation=[1;1;1];
++dsdx=(s(index).*alpha)*summation;
++dsdy=(s(index).*beta)*summation;
++dsdx = -averaging(md,dsdx,0);
++dsdy = -averaging(md,dsdy,0);
++
++vx = md.inversion.vx_obs;
++vy = md.inversion.vy_obs;
++v = md.inversion.vel_obs;
++v2 = sqrt(dsdx.^2 + dsdy.^2);
++
++theta = acos((vx.*dsdx + vy.*dsdy)./(v.*v2+eps));
Index: /issm/oecreview/Archive/18296-19100/ISSM-18381-18382.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18381-18382.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18381-18382.diff (revision 19102)
@@ -0,0 +1,33 @@
+Index: ../trunk-jpl/src/m/contrib/gslib/gslib.m
+===================================================================
+--- ../trunk-jpl/src/m/contrib/gslib/gslib.m (revision 18381)
++++ ../trunk-jpl/src/m/contrib/gslib/gslib.m (revision 18382)
+@@ -1,18 +1,21 @@
+-function [B E] = gslib(x,y,data,xmin,ymin,nx,ny,deltax,deltay)
++function [B E] = gslib(x,y,data,xmin,ymin,nx,ny,deltax,deltay,varargin)
+ %GSLIB - use gslib for Kriging
+ %
+ % Usage:
+ % output = gslib(x,y,data,varargin)
+
++%process options
++options = pairoptions(varargin{:});
++
+ %Variogram
+-nugget=10;
+-sill =164;
+-range =25763;
++nugget= getfieldvalue(options,'nugget',10);
++sill = getfieldvalue(options,'sill',164);
++range = getfieldvalue(options,'range',25763);
+
+ %Kriging options
+-mindata = 1;
+-maxdata = 50;
+-maxsearchradius = 50000;
++mindata = getfieldvalue(options,'mindata',1);
++maxdata = getfieldvalue(options,'maxdata',50);
++maxsearchradius = getfieldvalue(options,'searchrange',50000);
+
+ %Some intermediaries (Convert to gslib's parameters);
+ c = (sill-nugget);
Index: /issm/oecreview/Archive/18296-19100/ISSM-18382-18383.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18382-18383.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18382-18383.diff (revision 19102)
@@ -0,0 +1,207 @@
+Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18382)
++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18383)
+@@ -569,13 +569,6 @@
+ DeviatoricStressyyEnum,
+ DeviatoricStressyzEnum,
+ DeviatoricStresszzEnum,
+- StressEnum,
+- StressxxEnum,
+- StressxyEnum,
+- StressxzEnum,
+- StressyyEnum,
+- StressyzEnum,
+- StresszzEnum,
+ StrainRateEnum,
+ StrainRatexxEnum,
+ StrainRatexyEnum,
+Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18382)
++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18383)
+@@ -560,13 +560,6 @@
+ case DeviatoricStressyyEnum : return "DeviatoricStressyy";
+ case DeviatoricStressyzEnum : return "DeviatoricStressyz";
+ case DeviatoricStresszzEnum : return "DeviatoricStresszz";
+- case StressEnum : return "Stress";
+- case StressxxEnum : return "Stressxx";
+- case StressxyEnum : return "Stressxy";
+- case StressxzEnum : return "Stressxz";
+- case StressyyEnum : return "Stressyy";
+- case StressyzEnum : return "Stressyz";
+- case StresszzEnum : return "Stresszz";
+ case StrainRateEnum : return "StrainRate";
+ case StrainRatexxEnum : return "StrainRatexx";
+ case StrainRatexyEnum : return "StrainRatexy";
+Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18382)
++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18383)
+@@ -572,13 +572,6 @@
+ else if (strcmp(name,"DeviatoricStressyy")==0) return DeviatoricStressyyEnum;
+ else if (strcmp(name,"DeviatoricStressyz")==0) return DeviatoricStressyzEnum;
+ else if (strcmp(name,"DeviatoricStresszz")==0) return DeviatoricStresszzEnum;
+- else if (strcmp(name,"Stress")==0) return StressEnum;
+- else if (strcmp(name,"Stressxx")==0) return StressxxEnum;
+- else if (strcmp(name,"Stressxy")==0) return StressxyEnum;
+- else if (strcmp(name,"Stressxz")==0) return StressxzEnum;
+- else if (strcmp(name,"Stressyy")==0) return StressyyEnum;
+- else if (strcmp(name,"Stressyz")==0) return StressyzEnum;
+- else if (strcmp(name,"Stresszz")==0) return StresszzEnum;
+ else if (strcmp(name,"StrainRate")==0) return StrainRateEnum;
+ else if (strcmp(name,"StrainRatexx")==0) return StrainRatexxEnum;
+ else if (strcmp(name,"StrainRatexy")==0) return StrainRatexyEnum;
+@@ -628,17 +621,17 @@
+ else if (strcmp(name,"MassfluxatgateSegments")==0) return MassfluxatgateSegmentsEnum;
+ else if (strcmp(name,"MisfitName")==0) return MisfitNameEnum;
+ else if (strcmp(name,"MisfitModelEnum")==0) return MisfitModelEnumEnum;
+- else stage=6;
+- }
+- if(stage==6){
+- if (strcmp(name,"MisfitObservation")==0) return MisfitObservationEnum;
++ else if (strcmp(name,"MisfitObservation")==0) return MisfitObservationEnum;
+ else if (strcmp(name,"MisfitObservationEnum")==0) return MisfitObservationEnumEnum;
+ else if (strcmp(name,"MisfitTimeinterpolation")==0) return MisfitTimeinterpolationEnum;
+ else if (strcmp(name,"MisfitWeights")==0) return MisfitWeightsEnum;
+ else if (strcmp(name,"MisfitWeightsEnum")==0) return MisfitWeightsEnumEnum;
+ else if (strcmp(name,"SurfaceObservation")==0) return SurfaceObservationEnum;
+ else if (strcmp(name,"WeightsSurfaceObservation")==0) return WeightsSurfaceObservationEnum;
+- else if (strcmp(name,"MinVel")==0) return MinVelEnum;
++ else stage=6;
++ }
++ if(stage==6){
++ if (strcmp(name,"MinVel")==0) return MinVelEnum;
+ else if (strcmp(name,"MaxVel")==0) return MaxVelEnum;
+ else if (strcmp(name,"MinVx")==0) return MinVxEnum;
+ else if (strcmp(name,"MaxVx")==0) return MaxVxEnum;
+Index: ../trunk-jpl/src/m/enum/StressxyEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxyEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressxyEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressxyEnum()
+-%STRESSXYENUM - Enum of Stressxy
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressxyEnum()
+-
+-macro=StringToEnum('Stressxy');
+Index: ../trunk-jpl/src/m/enum/StressxzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxzEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressxzEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressxzEnum()
+-%STRESSXZENUM - Enum of Stressxz
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressxzEnum()
+-
+-macro=StringToEnum('Stressxz');
+Index: ../trunk-jpl/src/m/enum/StressyyEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressyyEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressyyEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressyyEnum()
+-%STRESSYYENUM - Enum of Stressyy
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressyyEnum()
+-
+-macro=StringToEnum('Stressyy');
+Index: ../trunk-jpl/src/m/enum/StressyzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressyzEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressyzEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressyzEnum()
+-%STRESSYZENUM - Enum of Stressyz
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressyzEnum()
+-
+-macro=StringToEnum('Stressyz');
+Index: ../trunk-jpl/src/m/enum/StressEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressEnum()
+-%STRESSENUM - Enum of Stress
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressEnum()
+-
+-macro=StringToEnum('Stress');
+Index: ../trunk-jpl/src/m/enum/StresszzEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StresszzEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StresszzEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StresszzEnum()
+-%STRESSZZENUM - Enum of Stresszz
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StresszzEnum()
+-
+-macro=StringToEnum('Stresszz');
+Index: ../trunk-jpl/src/m/enum/StressxxEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressxxEnum.m (revision 18382)
++++ ../trunk-jpl/src/m/enum/StressxxEnum.m (revision 18383)
+@@ -1,11 +0,0 @@
+-function macro=StressxxEnum()
+-%STRESSXXENUM - Enum of Stressxx
+-%
+-% WARNING: DO NOT MODIFY THIS FILE
+-% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+-% Please read src/c/shared/Enum/README for more information
+-%
+-% Usage:
+-% macro=StressxxEnum()
+-
+-macro=StringToEnum('Stressxx');
+Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py
+===================================================================
+--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18382)
++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18383)
+@@ -552,13 +552,6 @@
+ def DeviatoricStressyyEnum(): return StringToEnum("DeviatoricStressyy")[0]
+ def DeviatoricStressyzEnum(): return StringToEnum("DeviatoricStressyz")[0]
+ def DeviatoricStresszzEnum(): return StringToEnum("DeviatoricStresszz")[0]
+-def StressEnum(): return StringToEnum("Stress")[0]
+-def StressxxEnum(): return StringToEnum("Stressxx")[0]
+-def StressxyEnum(): return StringToEnum("Stressxy")[0]
+-def StressxzEnum(): return StringToEnum("Stressxz")[0]
+-def StressyyEnum(): return StringToEnum("Stressyy")[0]
+-def StressyzEnum(): return StringToEnum("Stressyz")[0]
+-def StresszzEnum(): return StringToEnum("Stresszz")[0]
+ def StrainRateEnum(): return StringToEnum("StrainRate")[0]
+ def StrainRatexxEnum(): return StringToEnum("StrainRatexx")[0]
+ def StrainRatexyEnum(): return StringToEnum("StrainRatexy")[0]
Index: /issm/oecreview/Archive/18296-19100/ISSM-18383-18384.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18383-18384.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18383-18384.diff (revision 19102)
@@ -0,0 +1,26 @@
+Index: ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim
+===================================================================
+--- ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 18383)
++++ ../trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 18384)
+@@ -1087,6 +1087,7 @@
+ syn keyword cConstant StressTensoryyEnum
+ syn keyword cConstant StressTensoryzEnum
+ syn keyword cConstant StressTensorzzEnum
++syn keyword cConstant StressMaxPrincipalEnum
+ syn keyword cConstant DeviatoricStressEnum
+ syn keyword cConstant DeviatoricStressxxEnum
+ syn keyword cConstant DeviatoricStressxyEnum
+@@ -1094,13 +1095,6 @@
+ syn keyword cConstant DeviatoricStressyyEnum
+ syn keyword cConstant DeviatoricStressyzEnum
+ syn keyword cConstant DeviatoricStresszzEnum
+-syn keyword cConstant StressEnum
+-syn keyword cConstant StressxxEnum
+-syn keyword cConstant StressxyEnum
+-syn keyword cConstant StressxzEnum
+-syn keyword cConstant StressyyEnum
+-syn keyword cConstant StressyzEnum
+-syn keyword cConstant StresszzEnum
+ syn keyword cConstant StrainRateEnum
+ syn keyword cConstant StrainRatexxEnum
+ syn keyword cConstant StrainRatexyEnum
Index: /issm/oecreview/Archive/18296-19100/ISSM-18384-18385.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18384-18385.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18384-18385.diff (revision 19102)
@@ -0,0 +1,227 @@
+Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18384)
++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 18385)
+@@ -562,6 +562,7 @@
+ StressTensoryyEnum,
+ StressTensoryzEnum,
+ StressTensorzzEnum,
++ StressMaxPrincipalEnum,
+ DeviatoricStressEnum,
+ DeviatoricStressxxEnum,
+ DeviatoricStressxyEnum,
+Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18384)
++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 18385)
+@@ -553,6 +553,7 @@
+ case StressTensoryyEnum : return "StressTensoryy";
+ case StressTensoryzEnum : return "StressTensoryz";
+ case StressTensorzzEnum : return "StressTensorzz";
++ case StressMaxPrincipalEnum : return "StressMaxPrincipal";
+ case DeviatoricStressEnum : return "DeviatoricStress";
+ case DeviatoricStressxxEnum : return "DeviatoricStressxx";
+ case DeviatoricStressxyEnum : return "DeviatoricStressxy";
+Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp
+===================================================================
+--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18384)
++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 18385)
+@@ -565,6 +565,7 @@
+ else if (strcmp(name,"StressTensoryy")==0) return StressTensoryyEnum;
+ else if (strcmp(name,"StressTensoryz")==0) return StressTensoryzEnum;
+ else if (strcmp(name,"StressTensorzz")==0) return StressTensorzzEnum;
++ else if (strcmp(name,"StressMaxPrincipal")==0) return StressMaxPrincipalEnum;
+ else if (strcmp(name,"DeviatoricStress")==0) return DeviatoricStressEnum;
+ else if (strcmp(name,"DeviatoricStressxx")==0) return DeviatoricStressxxEnum;
+ else if (strcmp(name,"DeviatoricStressxy")==0) return DeviatoricStressxyEnum;
+@@ -627,11 +628,11 @@
+ else if (strcmp(name,"MisfitWeights")==0) return MisfitWeightsEnum;
+ else if (strcmp(name,"MisfitWeightsEnum")==0) return MisfitWeightsEnumEnum;
+ else if (strcmp(name,"SurfaceObservation")==0) return SurfaceObservationEnum;
+- else if (strcmp(name,"WeightsSurfaceObservation")==0) return WeightsSurfaceObservationEnum;
+ else stage=6;
+ }
+ if(stage==6){
+- if (strcmp(name,"MinVel")==0) return MinVelEnum;
++ if (strcmp(name,"WeightsSurfaceObservation")==0) return WeightsSurfaceObservationEnum;
++ else if (strcmp(name,"MinVel")==0) return MinVelEnum;
+ else if (strcmp(name,"MaxVel")==0) return MaxVelEnum;
+ else if (strcmp(name,"MinVx")==0) return MinVxEnum;
+ else if (strcmp(name,"MaxVx")==0) return MaxVxEnum;
+Index: ../trunk-jpl/src/c/classes/Elements/Element.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18384)
++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 18385)
+@@ -148,6 +148,7 @@
+ void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum);
+ void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array);
+ void ViscousHeatingCreateInput(void);
++ void StressMaxPrincipalCreateInput(void);
+ void ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input);
+ void ViscosityHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input);
+ void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf);
+Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 18384)
++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 18385)
+@@ -244,15 +244,15 @@
+ /*}}}*/
+ void Penta::ComputeStressTensor(){/*{{{*/
+
+- IssmDouble xyz_list[NUMVERTICES][3];
+- IssmDouble pressure,viscosity;
+- IssmDouble epsilon[6]; /* epsilon=[exx,eyy,exy];*/
+- IssmDouble sigma_xx[NUMVERTICES];
+- IssmDouble sigma_yy[NUMVERTICES];
+- IssmDouble sigma_zz[NUMVERTICES];
+- IssmDouble sigma_xy[NUMVERTICES];
+- IssmDouble sigma_xz[NUMVERTICES];
+- IssmDouble sigma_yz[NUMVERTICES];
++ IssmDouble xyz_list[NUMVERTICES][3];
++ IssmDouble pressure,viscosity;
++ IssmDouble epsilon[6]; /* epsilon=[exx,eyy,exy];*/
++ IssmDouble sigma_xx[NUMVERTICES];
++ IssmDouble sigma_yy[NUMVERTICES];
++ IssmDouble sigma_zz[NUMVERTICES];
++ IssmDouble sigma_xy[NUMVERTICES];
++ IssmDouble sigma_xz[NUMVERTICES];
++ IssmDouble sigma_yz[NUMVERTICES];
+ GaussPenta* gauss=NULL;
+
+ /* Get node coordinates and dof list: */
+Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18384)
++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 18385)
+@@ -1157,6 +1157,10 @@
+ this->ViscousHeatingCreateInput();
+ input=this->inputs->GetInput(output_enum);
+ break;
++ case StressMaxPrincipalEnum:
++ this->StressMaxPrincipalCreateInput();
++ input=this->inputs->GetInput(output_enum);
++ break;
+ case StressTensorxxEnum:
+ case StressTensorxyEnum:
+ case StressTensorxzEnum:
+@@ -1337,6 +1341,92 @@
+ _assert_(matpar);
+ return this->matpar->TMeltingPoint(pressure);
+ }/*}}}*/
++void Element::StressMaxPrincipalCreateInput(void){/*{{{*/
++
++ /*Intermediaries*/
++ IssmDouble *xyz_list = NULL;
++ IssmDouble sigma_xx,sigma_yy,sigma_zz,sigma_xy,sigma_xz,sigma_yz;
++ IssmDouble a,b,c,d,x[3],max;
++ int dim,numroots;
++
++ /*First: get stress tensor*/
++ this->ComputeStressTensor();
++
++ /*Get domain dimension*/
++ this->FindParam(&dim,DomainDimensionEnum);
++
++ /*Fetch number vertices and allocate memory*/
++ int numvertices = this->GetNumberOfVertices();
++ IssmDouble* maxprincipal = xNew(numvertices);
++
++ /*Retrieve all inputs and parameters*/
++ this->GetVerticesCoordinatesBase(&xyz_list);
++ Input* sigma_xx_input = this->GetInput(StressTensorxxEnum); _assert_(sigma_xx_input);
++ Input* sigma_yy_input = this->GetInput(StressTensoryyEnum); _assert_(sigma_yy_input);
++ Input* sigma_xy_input = this->GetInput(StressTensorxyEnum); _assert_(sigma_xy_input);
++ Input* sigma_xz_input = NULL;
++ Input* sigma_yz_input = NULL;
++ Input* sigma_zz_input = NULL;
++ if(dim==3){
++ sigma_xz_input = this->GetInput(StressTensorxzEnum); _assert_(sigma_xz_input);
++ sigma_yz_input = this->GetInput(StressTensoryzEnum); _assert_(sigma_yz_input);
++ sigma_zz_input = this->GetInput(StressTensorzzEnum); _assert_(sigma_zz_input);
++ }
++
++ /*loop over vertices: */
++ Gauss* gauss=this->NewGauss();
++ for (int iv=0;ivGaussVertex(iv);
++
++ sigma_xx_input->GetInputValue(&sigma_xx,gauss);
++ sigma_yy_input->GetInputValue(&sigma_yy,gauss);
++ sigma_xy_input->GetInputValue(&sigma_xy,gauss);
++ if(dim==3){
++ sigma_xz_input->GetInputValue(&sigma_xz,gauss);
++ sigma_yz_input->GetInputValue(&sigma_yz,gauss);
++ sigma_zz_input->GetInputValue(&sigma_zz,gauss);
++ }
++
++ if(dim==2){
++ a = 0.;
++ b = 1.;
++ c = -sigma_yy -sigma_xx;
++ d = sigma_xx*sigma_yy - sigma_xy*sigma_xy;
++ }
++ else{
++ a = -1.;
++ b = sigma_xx+sigma_yy+sigma_zz;
++ c = -sigma_xx*sigma_yy -sigma_xx*sigma_zz -sigma_yy*sigma_zz + sigma_xy*sigma_xy +sigma_xz*sigma_xz +sigma_yz*sigma_yz;
++ d = sigma_xx*sigma_yy*sigma_zz - sigma_xx*sigma_yz*sigma_yz -sigma_yy*sigma_xz*sigma_xz - sigma_zz*sigma_xy*sigma_xy + 2.*sigma_xy*sigma_xz*sigma_yz;
++ }
++
++ /*Get roots of polynomials*/
++ cubic(a,b,c,d,x,&numroots);
++
++ /*Initialize maximum eigne value*/
++ if(numroots>0){
++ max = x[0];
++ }
++ else{
++ _error_("No eigen value found");
++ }
++
++ /*Get max*/
++ for(int i=1;imax) max = x[i];
++ }
++
++ maxprincipal[iv]=max;
++ }
++
++ /*Create input*/
++ this->AddInput(StressMaxPrincipalEnum,maxprincipal,P1Enum);
++
++ /*Clean up and return*/
++ xDelete(maxprincipal);
++ delete gauss;
++}
++/*}}}*/
+ void Element::ViscousHeatingCreateInput(void){/*{{{*/
+
+ /*Intermediaries*/
+Index: ../trunk-jpl/src/m/enum/StressMaxPrincipalEnum.m
+===================================================================
+--- ../trunk-jpl/src/m/enum/StressMaxPrincipalEnum.m (revision 0)
++++ ../trunk-jpl/src/m/enum/StressMaxPrincipalEnum.m (revision 18385)
+@@ -0,0 +1,11 @@
++function macro=StressMaxPrincipalEnum()
++%STRESSMAXPRINCIPALENUM - Enum of StressMaxPrincipal
++%
++% WARNING: DO NOT MODIFY THIS FILE
++% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
++% Please read src/c/shared/Enum/README for more information
++%
++% Usage:
++% macro=StressMaxPrincipalEnum()
++
++macro=StringToEnum('StressMaxPrincipal');
+Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py
+===================================================================
+--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18384)
++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 18385)
+@@ -545,6 +545,7 @@
+ def StressTensoryyEnum(): return StringToEnum("StressTensoryy")[0]
+ def StressTensoryzEnum(): return StringToEnum("StressTensoryz")[0]
+ def StressTensorzzEnum(): return StringToEnum("StressTensorzz")[0]
++def StressMaxPrincipalEnum(): return StringToEnum("StressMaxPrincipal")[0]
+ def DeviatoricStressEnum(): return StringToEnum("DeviatoricStress")[0]
+ def DeviatoricStressxxEnum(): return StringToEnum("DeviatoricStressxx")[0]
+ def DeviatoricStressxyEnum(): return StringToEnum("DeviatoricStressxy")[0]
Index: /issm/oecreview/Archive/18296-19100/ISSM-18385-18386.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18385-18386.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18385-18386.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/src/c/shared/Numerics/numerics.h
+===================================================================
+--- ../trunk-jpl/src/c/shared/Numerics/numerics.h (revision 18385)
++++ ../trunk-jpl/src/c/shared/Numerics/numerics.h (revision 18386)
+@@ -32,7 +32,7 @@
+ void BrentSearch(IssmDouble** pJ,OptPars optpars,IssmDouble* X0,IssmDouble (*f)(IssmDouble*,void*),IssmDouble (*g)(IssmDouble**,IssmDouble*,void*),void* usr);
+ void cross(IssmDouble *result,IssmDouble*vector1,IssmDouble*vector2);
+ void XZvectorsToCoordinateSystem(IssmDouble *T,IssmDouble*xzvectors);
+-int cubic(IssmDouble a, IssmDouble b, IssmDouble c, IssmDouble d, double X[3], int *num);
++int cubic(IssmDouble a, IssmDouble b, IssmDouble c, IssmDouble d,IssmDouble X[3], int *num);
+
+ int NewtonSolveDnorm(IssmDouble* pdnorm,IssmDouble c1,IssmDouble c2,IssmDouble c3,IssmDouble n,IssmDouble dnorm);
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18386-18387.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18386-18387.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18386-18387.diff (revision 19102)
@@ -0,0 +1,13 @@
+Index: ../trunk-jpl/jenkins/imac-012301-gil
+===================================================================
+--- ../trunk-jpl/jenkins/imac-012301-gil (revision 18386)
++++ ../trunk-jpl/jenkins/imac-012301-gil (revision 18387)
+@@ -55,7 +55,7 @@
+ matlab install.sh
+ mpich install-3.0-macosx64.sh
+ cmake install.sh
+- petsc install-3.5-macosx64.sh
++ petsc install-3.4-macosx64.sh
+ triangle install-macosx64.sh
+ shell2junit install.sh "
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18387-18388.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18387-18388.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18387-18388.diff (revision 19102)
@@ -0,0 +1,270 @@
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.h (revision 18388)
+@@ -13,38 +13,39 @@
+ class SpcDynamic: public Constraint{
+
+ private:
+- int sid; /*! id, to track it*/
+- int nodeid; /*!node id*/
+- int dof; /*!component*/
+- IssmDouble value; /*value*/
+- bool isset;
+- int analysis_type;
++ int sid; /*! id, to track it */
++ int nodeid; /*!node id */
++ int dof; /*!component */
++ IssmDouble value; /*value */
++ bool isset;
++ int analysis_type;
++ bool penalty; /*Is this a penalty constraint */
+
+ public:
+
+- /*SpcDynamic constructors, destructors:{{{*/
++ /*SpcDynamic constructors, destructors*/
+ SpcDynamic();
+ SpcDynamic(int sid,int nodeid, int dof,int analysis_type);
+ ~SpcDynamic();
+- /*}}}*/
+- /*Object virtual functions definitions:{{{ */
+- void Echo();
+- void DeepEcho();
+- int Id();
+- int ObjectEnum();
+- Object* copy();
+- /*}}}*/
+- /*Constraint virtual functions definitions: {{{*/
+- void ConstrainNode(Nodes* nodes,Parameters* parameters);
+- bool InAnalysis(int analysis_type);
+- void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters){_error_("not implemented yet");};
+- /*}}}*/
+- /*SpcDynamic management:{{{ */
+- int GetNodeId();
+- int GetDof();
++
++ /*Object virtual functions definitions*/
++ void Echo();
++ void DeepEcho();
++ int Id();
++ int ObjectEnum();
++ Object *copy();
++
++ /*Constraint virtual functions definitions*/
++ void ConstrainNode(Nodes* nodes,Parameters* parameters);
++ bool InAnalysis(int analysis_type);
++ void ActivatePenaltyMethod(void);
++ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters){_error_("not implemented yet");};
++
++ /*SpcDynamic management*/
++ int GetNodeId();
++ int GetDof();
+ IssmDouble GetValue();
+- void SetDynamicConstraint(Nodes* nodes,IssmDouble *yg_serial);
+- /*}}}*/
++ void SetDynamicConstraint(Nodes *nodes,IssmDouble *yg_serial);
+
+ };
+
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcStatic.h (revision 18388)
+@@ -13,11 +13,12 @@
+ class SpcStatic: public Constraint{
+
+ private:
+- int sid; /*! id, to track it*/
+- int nodeid; /*!node id*/
+- int dof; /*!component*/
+- IssmDouble value; /*value*/
+- int analysis_type;
++ int sid; /*! id, to track it */
++ int nodeid; /*!node id */
++ int dof; /*!component */
++ IssmDouble value; /*value */
++ int analysis_type;
++ bool penalty; /*Is this a penalty constraint */
+
+ public:
+
+@@ -34,6 +35,7 @@
+ Object* copy();
+ /*}}}*/
+ /*Constraint virtual functions definitions: {{{*/
++ void ActivatePenaltyMethod(void);
+ void ConstrainNode(Nodes* nodes,Parameters* parameters);
+ bool InAnalysis(int analysis_type);
+ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters){_error_("not implemented yet");};
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcTransient.h (revision 18388)
+@@ -13,7 +13,6 @@
+ class SpcTransient: public Constraint{
+
+ private:
+- bool penalty; /*Is this a penalty constraint */
+ int sid; /* id, to track it */
+ int nodeid; /*node id */
+ int dof; /*component */
+@@ -21,6 +20,7 @@
+ IssmDouble *times; /*different time steps */
+ int nsteps; /*number of time steps */
+ int analysis_type;
++ bool penalty; /*Is this a penalty constraint */
+
+ public:
+
+@@ -37,6 +37,7 @@
+ Object* copy();
+ /*}}}*/
+ /*Constraint virtual functions definitions: {{{*/
++ void ActivatePenaltyMethod(void);
+ void ConstrainNode(Nodes* nodes,Parameters* parameters);
+ bool InAnalysis(int analysis_type);
+ void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters);
+Index: ../trunk-jpl/src/c/classes/Constraints/Constraints.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/Constraints.cpp (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/Constraints.cpp (revision 18388)
+@@ -11,6 +11,7 @@
+ #endif
+
+ #include "./Constraints.h"
++#include "./Constraint.h"
+ #include "../../shared/shared.h"
+ #include "../../toolkits/toolkits.h"
+
+@@ -33,3 +34,14 @@
+ return numberofconstraints;
+ }
+ /*}}}*/
++void Constraints::ActivatePenaltyMethod(int in_analysis){/*{{{*/
++
++ for(int i=0;iSize();i++){
++ Constraint* constraint=(Constraint*)this->GetObjectByOffset(i);
++ if(constraint->InAnalysis(in_analysis)){
++ constraint->ActivatePenaltyMethod();
++ }
++ }
++
++}
++/*}}}*/
+Index: ../trunk-jpl/src/c/classes/Constraints/Constraint.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/Constraint.h (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/Constraint.h (revision 18388)
+@@ -22,6 +22,7 @@
+ virtual void ConstrainNode(Nodes* nodes,Parameters* parameters)=0;
+ virtual void PenaltyDofAndValue(int* dof,IssmDouble* value,Nodes* nodes,Parameters* parameters)=0;
+ virtual bool InAnalysis(int analysis_type)=0;
++ virtual void ActivatePenaltyMethod(void)=0;
+
+ };
+ #endif
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.cpp (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcDynamic.cpp (revision 18388)
+@@ -19,12 +19,13 @@
+ /*}}}*/
+ SpcDynamic::SpcDynamic(int spc_sid,int spc_nodeid, int spc_dof,int spc_analysis_type){/*{{{*/
+
+- sid=spc_sid;
+- nodeid=spc_nodeid;
+- dof=spc_dof;
+- value=0;
+- analysis_type=spc_analysis_type;
+- isset=false;
++ sid = spc_sid;
++ nodeid = spc_nodeid;
++ dof = spc_dof;
++ value = 0;
++ analysis_type = spc_analysis_type;
++ isset = false;
++ penalty = false;
+
+ return;
+ }
+@@ -77,6 +78,10 @@
+ /*}}}*/
+
+ /*Constraint virtual functions definitions: */
++void SpcDynamic::ActivatePenaltyMethod(void){/*{{{*/
++ this->penalty = true;
++}
++/*}}}*/
+ bool SpcDynamic::InAnalysis(int in_analysis_type){/*{{{*/
+ if (in_analysis_type==this->analysis_type) return true;
+ else return false;
+Index: ../trunk-jpl/src/c/classes/Constraints/Constraints.h
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/Constraints.h (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/Constraints.h (revision 18388)
+@@ -26,7 +26,8 @@
+ /*}}}*/
+
+ /*numerics*/
+- int NumberOfConstraints(void);
++ int NumberOfConstraints(void);
++ void ActivatePenaltyMethod(int in_analysis);
+
+ };
+
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcStatic.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcStatic.cpp (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcStatic.cpp (revision 18388)
+@@ -24,6 +24,7 @@
+ dof = spc_dof;
+ value = spc_value;
+ analysis_type = spc_analysis_type;
++ penalty = false;
+
+ return;
+ }
+@@ -79,6 +80,10 @@
+ /*}}}*/
+
+ /*Constraint virtual functions definitions: */
++void SpcStatic::ActivatePenaltyMethod(void){/*{{{*/
++ this->penalty = true;
++}
++/*}}}*/
+ bool SpcStatic::InAnalysis(int in_analysis_type){/*{{{*/
+ if (in_analysis_type==this->analysis_type) return true;
+ else return false;
+Index: ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp
+===================================================================
+--- ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp (revision 18387)
++++ ../trunk-jpl/src/c/classes/Constraints/SpcTransient.cpp (revision 18388)
+@@ -27,11 +27,11 @@
+ /*}}}*/
+ SpcTransient::SpcTransient(int spc_sid,int spc_nodeid, int spc_dof,int spc_nsteps, IssmDouble* spc_times, IssmDouble* spc_values,int spc_analysis_type){/*{{{*/
+
+- penalty= false;
+- sid = spc_sid;
+- nodeid = spc_nodeid;
+- dof = spc_dof;
+- nsteps = spc_nsteps;
++ penalty = false;
++ sid = spc_sid;
++ nodeid = spc_nodeid;
++ dof = spc_dof;
++ nsteps = spc_nsteps;
+ if(spc_nsteps){
+ values = xNew(spc_nsteps);
+ times = xNew(spc_nsteps);
+@@ -86,6 +86,10 @@
+ /*}}}*/
+
+ /*Constraint virtual functions definitions:*/
++void SpcTransient::ActivatePenaltyMethod(void){/*{{{*/
++ this->penalty = true;
++}
++/*}}}*/
+ bool SpcTransient::InAnalysis(int in_analysis_type){/*{{{*/
+
+ if (in_analysis_type==this->analysis_type) return true;
Index: /issm/oecreview/Archive/18296-19100/ISSM-18388-18389.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18388-18389.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18388-18389.diff (revision 19102)
@@ -0,0 +1,17 @@
+Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18388)
++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 18389)
+@@ -154,7 +154,11 @@
+ if(stabilization!=3){
+ IoModelToConstraintsx(constraints,iomodel,MasstransportSpcthicknessEnum,MasstransportAnalysisEnum,P1Enum);
+ }
+- /*Do not add constraints in FCT, they are imposed using penalties*/
++
++ /*FCT, constraints are imposed using penalties*/
++ if(stabilization==4){
++ constraints->ActivatePenaltyMethod(MasstransportAnalysisEnum);
++ }
+ }/*}}}*/
+ void MasstransportAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/
+
Index: /issm/oecreview/Archive/18296-19100/ISSM-18389-18390.diff
===================================================================
--- /issm/oecreview/Archive/18296-19100/ISSM-18389-18390.diff (revision 19102)
+++ /issm/oecreview/Archive/18296-19100/ISSM-18389-18390.diff (revision 19102)
@@ -0,0 +1,213 @@
+Index: ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp
+===================================================================
+--- ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18389)
++++ ../trunk-jpl/src/c/analyses/AdjointBalancethickness2Analysis.cpp (revision 18390)
+@@ -107,30 +107,29 @@
+ case Balancethickness2MisfitEnum:
+ /*J = (H^2 - Hobs^2)^2*/
+ //for(i=0;ivalues[i]+=(NUMxH2+NUMyH2)/DENH2 *weight*Jdet*gauss->weight;
+ //}
+ /*J = phi^2*/
+ //for(i=0;ivalues[i]+= phi*basis[i]*weight*Jdet*gauss->weight; //OK
+- /*J = grad J ^2*/
++ /*J = grad phi ^2*/
+ //for(i=0;ivalues[i]+= (dphi[0]*dbasis[0*numnodes+i] + dphi[1]*dbasis[1*numnodes+i])*weight*Jdet*gauss->weight; //OK
+ /*J = (ubar - nux*uobs)^2*/
++ //for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
++ //}
++ /*J = 1/2 (vbar ^ gard(phi))^2*/
+ for(i=0;ivalues[i]+=(NUMxUbar-NUMyUbar)/DENUbar *weight*Jdet*gauss->weight;
++ pe->values[i]+= weight*Jdet*gauss->weight*
++ (nuy*vyobs*dphi[0] - nux*vxobs*dphi[1])*
++ (nuy*vyobs*dbasis[0*numnodes+i] - nux*vxobs*dbasis[1*numnodes+i]);
+ }
++
+ break;
+ default:
+ _error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+@@ -167,11 +166,6 @@
+ element->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+ element->FindParam(&responses,NULL,InversionCostFunctionsEnum);
+
+- /*Check that control_type is supported*/
+- if(control_type!=BalancethicknessApparentMassbalanceEnum){
+- _error_("Control "<(vertexpidlist);
+ delete gauss;
+ }/*}}}*/
++void AdjointBalancethickness2Analysis::GradientJNux(Element* element,Vector* gradient,int control_index){/*{{{*/
++
++ /*Intermediaries*/
++ IssmDouble Jdet,weight;
++ IssmDouble vxobs,vyobs;
++ IssmDouble nux,nuy,dphi[2];
++ IssmDouble *xyz_list= NULL;
++
++ /*Fetch number of vertices for this finite element*/
++ int numvertices = element->GetNumberOfVertices();
++
++ /*Initialize some vectors*/
++ IssmDouble* basis = xNew(numvertices);
++ IssmDouble* ge = xNewZeroInit(numvertices);
++ int* vertexpidlist = xNew(numvertices);
++
++ /*Retrieve all inputs we will be needing: */
++ element->GetVerticesCoordinates(&xyz_list);
++ element->GradientIndexing(&vertexpidlist[0],control_index);
++ Input* weights_input = element->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input);
++ Input* vxobs_input = element->GetInput(BalancethicknessVxObsEnum); _assert_(vxobs_input);
++ Input* vyobs_input = element->GetInput(BalancethicknessVyObsEnum); _assert_(vyobs_input);
++ Input* nux_input = element->GetInput(BalancethicknessNuxEnum); _assert_(nux_input);
++ Input* nuy_input = element->GetInput(BalancethicknessNuyEnum); _assert_(nuy_input);
++ Input* potential_input = element->GetInput(PotentialEnum); _assert_(potential_input);
++
++
++ Gauss* gauss=element->NewGauss(2);
++ for(int ig=gauss->begin();igend();ig++){
++ gauss->GaussPoint(ig);
++
++ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
++ element->NodalFunctionsP1(basis,gauss);
++ weights_input->GetInputValue(&weight,gauss,Balancethickness2MisfitEnum);
++ vxobs_input->GetInputValue(&vxobs,gauss);
++ vyobs_input->GetInputValue(&vyobs,gauss);
++ nux_input->GetInputValue(&nux,gauss);
++ nuy_input->GetInputValue(&nuy,gauss);
++ potential_input->GetInputDerivativeValue(&dphi[0],xyz_list,gauss);
++
++ /*Build gradient vector (actually -dJ/da): */
++ for(int i=0;iweight*(-vxobs)*dphi[1]*(nuy*vyobs*dphi[0] - nux*vxobs*dphi[1])*basis[i];
++ _assert_(!xIsNan(ge[i]));
++ }
++ }
++ gradient->SetValues(numvertices,vertexpidlist,ge,ADD_VAL);
++
++ /*Clean up and return*/
++ xDelete(ge);
++ xDelete(xyz_list);
++ xDelete(basis);
++ xDelete(vertexpidlist);
++ delete gauss;
++}/*}}}*/
++void AdjointBalancethickness2Analysis::GradientJNuy(Element* element,Vector* gradient,int control_index){/*{{{*/
++
++ /*Intermediaries*/
++ IssmDouble Jdet,weight;
++ IssmDouble vxobs,vyobs;
++ IssmDouble nux,nuy,dphi[2];
++ IssmDouble *xyz_list= NULL;
++
++ /*Fetch number of vertices for this finite element*/
++ int numvertices = element->GetNumberOfVertices();
++
++ /*Initialize some vectors*/
++ IssmDouble* basis = xNew(numvertices);
++ IssmDouble* ge = xNewZeroInit(numvertices);
++ int* vertexpidlist = xNew(numvertices);
++
++ /*Retrieve all inputs we will be needing: */
++ element->GetVerticesCoordinates(&xyz_list);
++ element->GradientIndexing(&vertexpidlist[0],control_index);
++ Input* weights_input = element->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input);
++ Input* vxobs_input = element->GetInput(BalancethicknessVxObsEnum); _assert_(vxobs_input);
++ Input* vyobs_input = element->GetInput(BalancethicknessVyObsEnum); _assert_(vyobs_input);
++ Input* nux_input = element->GetInput(BalancethicknessNuxEnum); _assert_(nux_input);
++ Input* nuy_input = element->GetInput(BalancethicknessNuyEnum); _assert_(nuy_input);
++ Input* potential_input = element->GetInput(PotentialEnum); _assert_(potential_input);
++
++
++ Gauss* gauss=element->NewGauss(2);
++ for(int ig=gauss->begin();igend();ig++){
++ gauss->GaussPoint(ig);
++
++ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
++ element->NodalFunctionsP1(basis,gauss);
++ weights_input->GetInputValue(&weight,gauss,Balancethickness2MisfitEnum);
++ vxobs_input->GetInputValue(&vxobs,gauss);
++ vyobs_input->GetInputValue(&vyobs,gauss);
++ nux_input->GetInputValue(&nux,gauss);
++ nuy_input->GetInputValue(&nuy,gauss);
++ potential_input->GetInputDerivativeValue(&dphi[0],xyz_list,gauss);
++
++ /*Build gradient vector (actually -dJ/da): */
++ for(int i=0;iweight*(+vyobs)*dphi[0]*(nuy*vyobs*dphi[0] - nux*vxobs*dphi[1])*basis[i];
++ _assert_(!xIsNan(ge[i]));
++ }
++ }
++ gradient->SetValues(numvertices,vertexpidlist,ge,ADD_VAL);
++
++ /*Clean up and return*/
++ xDelete(ge);
++ xDelete(xyz_list);
++ xDelete(basis);
++ xDelete