Changeset 28012

Timestamp:

11/15/23 12:02:47 (17 months ago)

Author:

Mathieu Morlighem

Message:

merged trunk and trunk-jpl

Location:

issm/trunk-jpl

Files:

• . (modified) (1 prop)
• externalpackages/geocode/geoCode.m (modified) (4 diffs)
• externalpackages/geocode/install.sh (modified) (1 diff)
• externalpackages/hdf5/install-1-parallel-with_tests.sh (modified) (1 diff)
• externalpackages/hdf5/install-1-parallel.sh (modified) (1 diff)
• externalpackages/hdf5/install-1-with_tests.sh (modified) (1 diff)
• externalpackages/hdf5/install-1.sh (modified) (1 diff)
• src (modified) (1 prop)
• src/m/classes/stressbalance.py (modified) (2 diffs)
• src/m/contrib/musselman (copied) (copied from issm/trunk/src/m/contrib/musselman )
• src/m/contrib/musselman/README.txt (modified) (4 diffs)
• src/m/contrib/musselman/read_netCDF_beta.py (added)
• src/m/contrib/musselman/read_netCDF_commit.py (added)
• src/m/contrib/musselman/write_netCDF_beta.py (added)
• src/m/contrib/musselman/write_netCDF_commit.py (added)
• src/m/solve/createMCC.m (copied) (copied from issm/trunk/src/m/solve/createMCC.m )

issm/trunk-jpl/externalpackages/geocode/geoCode.m

@@ -15 +15 @@
 
 % Copyright(c) 2012, Stuart P. Layton <stuart.layton@gmail.com>
-% http://stuartlayton.com
+% https://stuartlayton.com
 %
 % Revision History
@@ -46 +46 @@
 switch lower(service)
     case('google')
-        SERVER_URL = 'http://maps.google.com';
+        SERVER_URL = 'https://maps.google.com';
         queryUrl = sprintf('%s/maps/geo?output=xml&q=%s',SERVER_URL, address);
         parseFcn = @parseGoogleMapsXML;
@@ -52 +52 @@
     case('yahoo')
       
-        SERVER_URL = 'http://where.yahooapis.com/geocode';
+        SERVER_URL = 'https://where.yahooapis.com/geocode';
         queryUrl = sprintf('%s?location=%s',SERVER_URL, address);
        
@@ -67 +67 @@
     case {'osm', 'openstreetmaps', 'open street maps'}
         
-                SERVER_URL = 'https://nominatim.openstreetmap.org/search';
+        SERVER_URL = 'https://nominatim.openstreetmap.org/search';
         queryUrl = sprintf('%s?format=xml&q=%s', SERVER_URL, address);
         parseFcn = @parseOpenStreetMapXML;

issm/trunk-jpl/externalpackages/geocode/install.sh

@@ -1 +1 @@
 #/bin/bash
 unzip geoCode.zip
+sed -i -e 's/http:/https:/g' geoCode.m

issm/trunk-jpl/externalpackages/hdf5/install-1-parallel-with_tests.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="1.10.9"
+VER="1.14.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed

issm/trunk-jpl/externalpackages/hdf5/install-1-parallel.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="1.10.9"
+VER="1.14.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed

issm/trunk-jpl/externalpackages/hdf5/install-1-with_tests.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="1.10.9"
+VER="1.14.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed

issm/trunk-jpl/externalpackages/hdf5/install-1.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="1.10.9"
+VER="1.14.0"
 
 PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed

issm/trunk-jpl/src/m/classes/stressbalance.py

@@ -30 +30 @@
         self.isnewton = 0
         self.FSreconditioning = 0
-        self.icefront = np.nan
+        #self.icefront = np.nan -- no longer in use
         self.maxiter = 0
         self.shelf_dampening = 0
@@ -58 +58 @@
         s += '{}\n'.format(fielddisplay(self, 'spcvy', 'y-axis velocity constraint (NaN means no constraint) [m / yr]'))
         s += '{}\n'.format(fielddisplay(self, 'spcvz', 'z-axis velocity constraint (NaN means no constraint) [m / yr]'))
-        s += '{}\n'.format(fielddisplay(self, 'icefront', 'segments on ice front list (last column 0: Air, 1: Water, 2: Ice'))
+        #s += '{}\n'.format(fielddisplay(self, 'icefront', 'segments on ice front list (last column 0: Air, 1: Water, 2: Ice'))
         s += '      MOLHO boundary conditions:\n'
         s += '{}\n'.format(fielddisplay(self, 'spcvx_base', 'x-axis basal velocity constraint (NaN means no constraint) [m / yr]'))

issm/trunk-jpl/src/m/contrib/musselman/README.txt

@@ -5 +5 @@
 To save a model, call either write_netCDF.py or write_netCDF.m depending on whether your class is in matlab or python. 
 To read a saved model, call either read_netCDF.py or read_netCDF.m depending on what language you prefer to use the model in.
-If you would like to log the names and locations of variables being stored, add the argument verbose = True (verbose = true for matlab).
 
 Usage Instructions:
@@ -15 +14 @@
             md = bamg(model(), foo.csv, .01)
 
-            write_netCDF(md, 'adress_to_save/../filename.nc')            
+            write_netCDF(md, 'md', 'adress_to_save/../filename.nc')
 
         - Reading a model:
@@ -22 +21 @@
             md = read_netCDF('adress_to_file/../filename.nc')
 
-        Verbose examples:
-            write_netCDF(md, adress_to_save/../filename.nc, verbose = True)
-            md = read_netCDF(adress_to_file/../filename.nc, verbose = True)
+    MATLAB:
+        - Saving a model: 
+            import write_netCDF
 
-    MATLAB:
-        - Saving a model:
-
-            write_netCDF(md, adress_to_save/../filename.nc);
+            write_netCDF(md, adress_to_save/../filename.nc)
 
         - Reading a model:
+            import read_netCDF
 
-            md = read_netCDF(adress_to_file/../filename.nc);
+            md = read_netCDF(adress_to_file/../filename.nc)
 
-        Verbose examples:
-            write_netCDF(md, adress_to_save/../filename.nc, verbose = true);
-            
-          or:
 
-            write_netCDF(md, adress_to_save/../filename.nc, verbose);
-            md = read_netCDF(adress_to_file/../filename.nc, verbose = true);
 
 Dependencies:
     Python: 
         - NumPy 
-        - NetCDF4 / NetCDF4.Dataset
+        - NetCDF4.Dataset
         - The model() class
-        - results.solution / results.solutionstep / results.resultsdakota
-        - inversion.inversion / inversion.m1qn3inversion / inversion.taoinversion
 
     MATLAB: 
         - The model() class
-        - inversion.inversion / inversion.m1qn3inversion / inversion.taoinversion
 
 
@@ -59 +47 @@
 
 There are currently datatypes that both write_netCDF and read_netCDF modules may not be able to handle. These datatypes might 
-include lists with multiple datatypes (ie, ['number', 1, 'letter', a, 'color', 'blue']), lists of dicts ect. 
+include dictionaries with multiple value datatypes, lists with multiple datatypes, lists of dicts ect. 
 
 To add functionality for these additional cases, one must simply create a function to handle the case and call it using a 
 conditional case within the create_var() function. To read the data from the NetCDF4 file, add the case to the 
-copy_variable_data_to_new_model() function in read_netCDF so that the data can be added to a new model() instance.
-
-Known issues:
-
-Unlike Python, MATLAB doesn't utilize subclasses in its model class. This leads to a loss of certain subclass instances. 
-For instance, the results.solutionstep() class poses a known issue. In MATLAB, there's no direct equivalent. The fields in 
-'md.results' in MATLAB might correspond to instances of resultsdakota(), solution(), or solutionstep() in Python, but 
-because those classes don't exist in MATLAB, there is no way for python to know which instance it needs. 
-
-The current workaround, while not theoretically sound, involves searching for the class name string in MATLAB's 'results' 
-field names. For instance, 'md.results.TransientSolution' is recorded as a solution() class instance. However, problems arise 
-in cases like 'md.results.StressbalanceSolution', where the code notes a solution() instance, while in Python, it should be a 
-solutionstep() instance.
-
-So far, there have been no recorded problems swapping a solutionstep() instance for a solution() instance.
-
-Potential solutions are:
-
-    - Restructure both Python and MATLAB solve frameworks. In Python, when creating an md.results.<solutionstep()> instance, 
-    embed 'solutionstep' in the class instance name.
-        >> This solution is very involved, and would include the tedious modification of >5 files in total
-    - Create a hash table linking solutions with their corresponding 'md.results.<class>' for reference when saving models to 
-    the netCDF file. 
+copy_variable_data_to_new_model() function so that the data can be added to a new model() instance.