Index: /issm/trunk-jpl/src/m/classes/calvingdev2.m =================================================================== --- /issm/trunk-jpl/src/m/classes/calvingdev2.m (revision 26660) +++ /issm/trunk-jpl/src/m/classes/calvingdev2.m (revision 26661) @@ -42,6 +42,6 @@ if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end - md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'nan',1,'Inf',1); - md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'nan',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'NaN',1,'Inf',1); md = checkfield(md,'fieldname','calving.height_above_floatation','<=',0); end % }}} Index: /issm/trunk-jpl/src/m/classes/calvingvonmises.m =================================================================== --- /issm/trunk-jpl/src/m/classes/calvingvonmises.m (revision 26660) +++ /issm/trunk-jpl/src/m/classes/calvingvonmises.m (revision 26661) @@ -44,6 +44,6 @@ if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end - md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'nan',1,'Inf',1); - md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'nan',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'NaN',1,'Inf',1); md = checkfield(md,'fieldname','calving.min_thickness','>=',0,'NaN',1,'Inf',1,'numel',1); end % }}} Index: /issm/trunk-jpl/src/m/coordsystems/laea.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/laea.py (revision 26660) +++ /issm/trunk-jpl/src/m/coordsystems/laea.py (revision 26661) @@ -1,5 +1,4 @@ def laea(lat, long): #{{{ - ''' - LAEA - Lambert Azimuthal Equal Area projection at lat, long projection + """LAEA - Lambert Azimuthal Equal Area projection at lat, long projection center. @@ -10,5 +9,5 @@ string = laea(45, -90) return string = '+proj=laea +lat_0=45 +lon_0=-90 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs' - ''' + """ return '+proj=laea +lat_0={} +lon_0={} +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs'.format(lat, long) Index: /issm/trunk-jpl/src/m/exp/expwrite.py =================================================================== --- /issm/trunk-jpl/src/m/exp/expwrite.py (revision 26660) +++ /issm/trunk-jpl/src/m/exp/expwrite.py (revision 26661) @@ -3,30 +3,29 @@ def expwrite(contours, filename): - """ - EXPWRITE - write an Argus file from a dictionary given in input + """EXPWRITE - write an Argus file from a dictionary given in input - This routine writes an Argus file from a dict containing the fields: - x and y of the coordinates of the points. - The first argument is the list containing the points coordinates - and the second one the file to be written. + This routine writes an Argus file from a dict containing the fields: + x and y of the coordinates of the points. + The first argument is the list containing the points coordinates and the + second one the file to be written. - Usage: - expwrite(contours, filename) + Usage: + expwrite(contours, filename) - Example: - expwrite(coordstruct, 'domainoutline.exp') + Example: + expwrite(coordstruct, 'domainoutline.exp') - See also EXPDOC, EXPREAD, EXPWRITEASVERTICES + See also EXPDOC, EXPREAD, EXPWRITEASVERTICES """ fid = open(filename, 'w') for x, y in zip(contours['x'], contours['y']): - #if np.size(contour['x']) != np.size(contour['y']): if len(x) != len(y): - raise RuntimeError("contours x and y coordinates must be of identical size") + raise RuntimeError('contours x and y coordinates must be of identical size') + if 'name' in contours: - fid.write("%s%s\n" % (' # Name:', contours['name'])) + fid.write('{}{}\n'.format('# Name:', contours['name'])) else: - fid.write("%s%s\n" % (' # Name:', filename)) + fid.write('{}{}\n'.format('# Name:', filename)) #Add density if it's not there FIXME what is this ever used for? @@ -35,13 +34,17 @@ density = 1 - fid.write("%s\n" % ' # Icon:0') - fid.write("%s\n" % ' # Points Count Value') - #fid.write("%i %f\n" % (np.size(contour['x']), contour['density'])) - fid.write("%i %f\n" % (np.size(x), density)) - fid.write("%s\n" % ' # X pos Y pos') - #for x, y in zip(contour['x'], contour['y']): + fid.write('{}\n'.format('## Icon:0')) + fid.write('{}\n'.format('# Points Count Value') + if 'density' in contours: + if isinstance(contours['density'], int): + fid.write('{} {}\n'.format(np.size(x), density)) + else: + fid.write('{} {}\n'.format(np.size(x), 1.)) + else: + fid.write('{} {}\n'.format(np.size(x), 1.)) + fid.write('{}\n'.format('# X pos Y pos')) for xi, yi in zip(x, y): - fid.write("%10.10f %10.10f\n" % (xi, yi)) - fid.write("\n") + fid.write('%10.10f %10.10f\n' % (xi, yi)) + fid.write('\n') fid.close() Index: /issm/trunk-jpl/src/m/modules/ExpToLevelSet.py =================================================================== --- /issm/trunk-jpl/src/m/modules/ExpToLevelSet.py (revision 26660) +++ /issm/trunk-jpl/src/m/modules/ExpToLevelSet.py (revision 26661) @@ -30,5 +30,5 @@ contourname = shpread(contourname) - # NOTE: This library does not currently exist! See TODO list in function + # NOTE: This module does not currently exist! See TODO list in function # header. distance = ExpToLevelSet_python(x, y, contourname) Index: /issm/trunk-jpl/src/m/shp/shp2exp.m =================================================================== --- /issm/trunk-jpl/src/m/shp/shp2exp.m (revision 26660) +++ /issm/trunk-jpl/src/m/shp/shp2exp.m (revision 26661) @@ -1,4 +1,4 @@ function shp2exp(shpfilename,expfilename) -%SHP2EXP- transform shape file to Argus .exp file +%SHP2EXP - transform shape file to Argus .exp file % % Usage: Index: /issm/trunk-jpl/src/m/shp/shp2exp.py =================================================================== --- /issm/trunk-jpl/src/m/shp/shp2exp.py (revision 26660) +++ /issm/trunk-jpl/src/m/shp/shp2exp.py (revision 26661) @@ -1,12 +1,12 @@ +import os import shapefile -import os from expwrite import expwrite -def shp2exp(shapefilename, * expfilename): - ''' - Convert a shapefile to an .exp file. Optionally, expfilename can be - specified to give a name for the .exp file to be created, otherwise the - .exp file will have the same prefix as the .shp file. +def shp2exp(shapefilename, *expfilename): + """SHP2EXP - Convert a shapefile to an Argus .exp file. Optionally, + expfilename can be specified to give a name for the .exp file to be + created, otherwise the .exp file will have the same prefix as the .shp + file. Usage: @@ -15,10 +15,12 @@ Examples: - shp2exp('Domain.shp') % creates Domain.exp - shp2exp('Domain.shp', 'DomainForISSM.exp') - ''' + shp2exp('Domain.shp') # Creates Domain.exp + shp2exp('Domain.shp', 'Domain.exp') + + See also EXPMASTER, EXPDOC + """ if not os.path.exists(shapefilename): - raise IOError("shp2exp error message: file '%s' not found!" % shapefilename) + raise IOError('shp2exp error message: file {} not found!'.format(shapefilename)) if not len(expfilename): expfile = os.path.splitext(shapefilename)[0] + '.exp' @@ -33,5 +35,5 @@ for i in range(len(shp.shapes())): geom = shp.shapes()[i].shapeType - if geom == 5: # polygon + if geom == 5: # polygon expdict['closed'] = 1 tmpx = [p[0] for p in shp.shapes()[i].points] @@ -39,5 +41,5 @@ x.append(tmpx) y.append(tmpy) - elif geom == 3: # line + elif geom == 3: # line expdict['closed'] = 0 tmpx = [p[0] for p in shp.shapes()[i].points] @@ -45,5 +47,5 @@ x.append(tmpx) y.append(tmpy) - elif geom == 1: # point + elif geom == 1: # point expdict['closed'] = 0 x.append(shp.shapes()[i].points[0][0]) Index: /issm/trunk-jpl/src/m/solve/loadresultsfromcluster.py =================================================================== --- /issm/trunk-jpl/src/m/solve/loadresultsfromcluster.py (revision 26660) +++ /issm/trunk-jpl/src/m/solve/loadresultsfromcluster.py (revision 26661) @@ -22,4 +22,9 @@ md = loadresultsfromcluster(md) md = loadresultsfromcluster(md, 'runtimename', runtimename) + + Options include: 'runtimename', 'nolog' + + Example: + md = loadresultsfromcluster(md, 'runtimename', 'test101-06-15-2021-13-24-18-4883') """ Index: /issm/trunk-jpl/src/m/solvers/asmoptions.m =================================================================== --- /issm/trunk-jpl/src/m/solvers/asmoptions.m (revision 26660) +++ /issm/trunk-jpl/src/m/solvers/asmoptions.m (revision 26661) @@ -1,4 +1,4 @@ function asm=asmoptions(varargin) -%ASMOPTIONS - return Additive Schwartz Method petsc options +%ASMOPTIONS - return Additive Schwartz Method PETSc options % % Usage: Index: /issm/trunk-jpl/src/m/solvers/asmoptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/asmoptions.py (revision 26660) +++ /issm/trunk-jpl/src/m/solvers/asmoptions.py (revision 26661) @@ -3,22 +3,25 @@ def asmoptions(*args): - #ASMOPTIONS - return ASM petsc options - # - # Usage: - # options = asmoptions + """ASMOPTIONS - Return Additive Schwartz Method PETSc options - #retrieve options provided in *args + Usage: + options = asmoptions + """ + + # Retrieve options provided in *args arguments = pairoptions(*args) - options = [['toolkit', 'petsc'], - ['mat_type', 'mpiaij'], - ['ksp_type', 'gmres'], - ['pc_type', 'asm'], - ['sub_pc_type', 'lu'], - ['pc_asm_overlap', 3], - ['ksp_max_it', 100], - ['ksp_rtol', 1e-30]] + options = [ + ['toolkit', 'petsc'], + ['mat_type', 'mpiaij'], + ['ksp_type', 'gmres'], + ['pc_type', 'asm'], + ['sub_pc_type', 'lu'], + ['pc_asm_overlap', 3], + ['ksp_max_it', 100], + ['ksp_rtol', 1e-30] + ] - #now, go through our arguments, and write over default options. + # Now, go through our arguments, and write over default options for i in range(len(arguments.list)): arg1 = arguments.list[i][0] @@ -33,5 +36,5 @@ break if not found: - #this option did not exist, add it: + # This option did not exist; add it options.append([arg1, arg2]) Index: /issm/trunk-jpl/src/m/solvers/asmstokesoptions.m =================================================================== --- /issm/trunk-jpl/src/m/solvers/asmstokesoptions.m (revision 26660) +++ /issm/trunk-jpl/src/m/solvers/asmstokesoptions.m (revision 26661) @@ -1,7 +1,7 @@ -function asm=asmoptions(varargin) -%ASMOPTIONS - return Additive Schwartz Method petsc options +function asm=asmstokesoptions(varargin) +%ASMSTOKESOPTIONS - return Additive Schwartz Method Stokes PETSc options % % Usage: -% options=asmoptions; +% options=asmstokesoptions; %retrieve options provided in varargin Index: /issm/trunk-jpl/src/m/solvers/asmstokesoptions.py =================================================================== --- /issm/trunk-jpl/src/m/solvers/asmstokesoptions.py (revision 26661) +++ /issm/trunk-jpl/src/m/solvers/asmstokesoptions.py (revision 26661) @@ -0,0 +1,46 @@ +from collections import OrderedDict +from pairoptions import pairoptions + +def asmstokesoptions(*args): + """ASMSTOKESOPTIONS - Return Additive Schwartz Method Stokes PETSc options + + Usage: + options = asmstokesoptions + """ + + # Retrieve options provided in *args + arguments = pairoptions(*args) + + options = [ + ['toolkit', 'petsc'], + ['mat_type', 'mpiaij'], + ['ksp_type', 'gmres'], + ['pc_type', 'asm'], + ['sub_pc_type', 'lu'], + ['pc_asm_overlap', 1], # COMSOL's default + ['ksp_max_it', 100], + ['ksp_rtol', 1e-7], # Tuned for best performance and to fit ISMIP-HOM-C 5km with MUMPS + ['ksp_atol', 1e-10] # Tuned for best performance and to fit ISMIP-HOM-C 5km with MUMPS + ] + + # Now, go through our arguments, and write over default options + for i in range(len(arguments.list)): + arg1 = arguments.list[i][0] + arg2 = arguments.list[i][1] + found = 0 + for j in range(len(options)): + joption = options[j][0] + if joption == arg1: + joption[1] = arg2 + options[j] = joption + found = 1 + break + if not found: + # This option did not exist; add it + options.append([arg1, arg2]) + + asmoptions = OrderedDict() + for j in range(len(options)): + asmoptions[options[j][0]]=options[j][1] + + return asmoptions