Index: /issm/trunk-jpl/src/m/mesh/bamg.m =================================================================== --- /issm/trunk-jpl/src/m/mesh/bamg.m (revision 28157) +++ /issm/trunk-jpl/src/m/mesh/bamg.m (revision 28158) @@ -29,5 +29,5 @@ % - NoBoundaryRefinementAllBoundaries: do not refine boundary, only follow contour provided (default 0) % - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) -% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) +% - maxsubdiv : maximum subdivision of existing elements (default is 10) % - metric : matrix (numberofnodes x 3) used as a metric % - Metrictype : 0 -> absolute error c/(err coeff^2) * Abs(H) (default) @@ -58,5 +58,5 @@ options=deleteduplicates(options,1); -%initialize the structures required as input of Bamg +%initialize the structures required as input of BAMG bamg_options=struct(); bamg_geometry=bamggeom(); @@ -65,5 +65,5 @@ subdomain_ref = 1; hole_ref = 1; -% Bamg Geometry parameters {{{ +% BAMG Geometry parameters {{{ if exist(options,'domain'), @@ -453,5 +453,5 @@ end %}}} -% Bamg Mesh parameters {{{ +% BAMG Mesh parameters {{{ if (~exist(options,'domain') & md.mesh.numberofvertices~=0 & strcmp(elementtype(md.mesh),'Tria')), @@ -468,9 +468,9 @@ end %}}} -% Bamg Options {{{ +% BAMG Options {{{ bamg_options.Crack=getfieldvalue(options,'Crack',0); -bamg_options.anisomax=getfieldvalue(options,'anisomax',10.^30); +bamg_options.anisomax=getfieldvalue(options,'anisomax',1e30); bamg_options.coeff=getfieldvalue(options,'coeff',1.); -bamg_options.cutoff=getfieldvalue(options,'cutoff',10.^-5); +bamg_options.cutoff=getfieldvalue(options,'cutoff',1e-5); bamg_options.err=getfieldvalue(options,'err',0.01); bamg_options.errg=getfieldvalue(options,'errg',0.1); @@ -478,11 +478,11 @@ bamg_options.gradation=getfieldvalue(options,'gradation',1.5); bamg_options.Hessiantype=getfieldvalue(options,'Hessiantype',0); -bamg_options.hmin=getfieldvalue(options,'hmin',10.^-100); -bamg_options.hmax=getfieldvalue(options,'hmax',10.^100); +bamg_options.hmin=getfieldvalue(options,'hmin',1e-100); +bamg_options.hmax=getfieldvalue(options,'hmax',1e100); bamg_options.hminVertices=getfieldvalue(options,'hminVertices',[]); bamg_options.hmaxVertices=getfieldvalue(options,'hmaxVertices',[]); bamg_options.hVertices=getfieldvalue(options,'hVertices',[]); bamg_options.KeepVertices=getfieldvalue(options,'KeepVertices',1); -bamg_options.maxnbv=getfieldvalue(options,'maxnbv',10^6); +bamg_options.maxnbv=getfieldvalue(options,'maxnbv',1e6); bamg_options.maxsubdiv=getfieldvalue(options,'maxsubdiv',10.); bamg_options.metric=getfieldvalue(options,'metric',[]); @@ -496,5 +496,5 @@ %}}} -%call Bamg +%call BAMG [bamgmesh_out bamggeom_out]=BamgMesher(bamg_mesh,bamg_geometry,bamg_options); @@ -550,5 +550,5 @@ end -%Bamg private fields +%BAMG private fields md.private.bamg=struct(); md.private.bamg.mesh=bamgmesh(bamgmesh_out); Index: /issm/trunk-jpl/src/m/mesh/bamg.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/bamg.py (revision 28157) +++ /issm/trunk-jpl/src/m/mesh/bamg.py (revision 28158) @@ -19,97 +19,49 @@ def bamg(md, *args): - """BAMG - mesh generation + """bamg - mesh generation Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): - - domain : followed by an ARGUS file that - prescribes the domain outline - - holes : followed by an ARGUS file that - prescribes the holes - - subdomains : followed by an ARGUS file that - prescribes the list of subdomains - (that need to be inside domain) - - - hmin : minimum edge length (default is - 1.0e-100) - - hmax : maximum edge length (default is - 1.0e100) - - hVertices : imposed edge length for each vertex - (geometry or mesh) - - hminVertices : minimum edge length for each vertex - (mesh) - - hmaxVertices : maximum edge length for each vertex - (mesh) - - - anisomax : maximum ratio between the smallest - and largest edges (default is - 1.0e30) - - coeff : coefficient applied to the metric - (2 -> twice as many elements, - default is 1) - - cutoff : scalar used to compute the metric - when metric type 2 or 3 are applied - - err : error used to generate the metric - from a field + - domain : followed by an ARGUS file that prescribes the domain outline + - holes : followed by an ARGUS file that prescribes the holes + - subdomains : followed by an ARGUS file that prescribes the list of subdomains (that need to be inside domain) + + - hmin : minimum edge length (default is 1.0e-100) + - hmax : maximum edge length (default is 1.0e100) + - hVertices : imposed edge length for each vertex (geometry or mesh) + - hminVertices : minimum edge length for each vertex (mesh) + - hmaxVertices : maximum edge length for each vertex (mesh) + + - anisomax : maximum ratio between the smallest and largest edges (default is 1.0e30) + - coeff : coefficient applied to the metric (2 -> twice as many elements, default is 1) + - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied + - err : error used to generate the metric from a field - errg : geometric error (default is 0.1) - - field : field of the model that will be - used to compute the metric to apply - several fields, use one column per - field - - gradation : maximum ratio between two adjacent - edges - - Hessiantype : 0 -> use double P2 projection - (default) + - field : field of the model that will be used to compute the metric to apply several fields, use one column per field + - gradation : maximum ratio between two adjacent edges + - Hessiantype : 0 -> use double P2 projection (default) 1 -> use Green formula - - KeepVertices : try to keep initial vertices when - adaptation is done on an existing - mesh (default 1) - - NoBoundaryRefinement : do not refine boundary, only follow - contour provided (default 0). Allow - subdomain boundary refinement - though - - NoBoundaryRefinementAllBoundaries : do not refine boundary, only follow - contour provided (default 0) - - maxnbv : maximum number of vertices used to - allocate memory (default is 1.0e6) - - maxsubdiv : maximum subdivision of exisiting - elements (default is 10) - - metric : matrix (numberofnodes x 3) used as - a metric - - Metrictype : 1 -> absolute error - c/(err coeff^2) * Abs(H) (default) - 2 -> relative error - c / (err coeff^2) * Abs(H) / - max(s, cutoff * max(s)) - 3 -> rescaled absolute error - c / (err coeff^2) * Abs(H) / - (smax - smin) - - nbjacoby : correction used by Hessiantype = 1 - (default is 1) - - nbsmooth : number of metric smoothing - procedure (default is 3) - - omega : relaxation parameter of the - smoothing procedure (default is - 1.8) - - power : power applied to the metric - (default is 1) - - splitcorners : split triangles which have 3 - vertices on the outline (default is - 1) + - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) + - NoBoundaryRefinement : do not refine boundary, only follow contour provided (default 0). Allow subdomain boundary refinement though + - NoBoundaryRefinementAllBoundaries : do not refine boundary, only follow contour provided (default 0) + - maxnbv : maximum number of vertices used to allocate memory (default is 1.0e6) + - maxsubdiv : maximum subdivision of existing elements (default is 10) + - metric : matrix (numberofnodes x 3) used as a metric + - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) + 2 -> relative error c / (err coeff^2) * Abs(H) / max(s, cutoff * max(s)) + 3 -> rescaled absolute error c / (err coeff^2) * Abs(H) / (smax - smin) + - nbjacoby : correction used by Hessiantype = 1 (default is 1) + - nbsmooth : number of metric smoothing procedure (default is 3) + - omega : relaxation parameter of the smoothing procedure (default is 1.8) + - power : power applied to the metric (default is 1) + - splitcorners : split triangles which have 3 vertices on the outline (default is 1) - verbose : level of verbosity (default is 1) - - rifts : followed by an ARGUS file that - prescribes the rifts - - toltip : tolerance to move tip on an - existing point of the domain - outline - - tracks : followed by an ARGUS file that - prescribes the tracks that the mesh - will stick to - - RequiredVertices : mesh vertices that are required. - [x, y, ref]; ref is optional - - tol : if the distance between 2 points of - the domain outline is less than - tol, they will be merged + - vertical : is this a 2d vertical mesh (flowband, default is 0) + - rifts : followed by an ARGUS file that prescribes the rifts + - toltip : tolerance to move tip on an existing point of the domain outline + - tracks : followed by an ARGUS file that prescribes the tracks that the mesh will stick to + - RequiredVertices : mesh vertices that are required. [x, y, ref]; ref is optional + - tol : if the distance between 2 points of the domain outline is less than tol, they will be merged Examples: @@ -126,5 +78,5 @@ #options = deleteduplicates(options, 1) - # Initialize the structures required as input of Bamg + # Initialize the structures required as input of BAMG bamg_options = OrderedDict() bamg_geometry = bamggeom() @@ -134,5 +86,5 @@ hole_ref = 1 - # Bamg Geometry parameters {{{ + # BAMG Geometry parameters {{{ if options.exist('domain'): #Check that file exists @@ -532,8 +484,8 @@ bamg_geometry = bamggeom(md.private.bamg['geometry'].__dict__) else: - #do nothing... + # Do nothing... pass # }}} - # Bamg mesh parameters {{{ + # BAMG mesh parameters {{{ if not options.exist('domain') and md.mesh.numberofvertices and md.mesh.elementtype() == 'Tria': if isinstance(md.private.bamg, dict) and 'mesh' in md.private.bamg: @@ -548,23 +500,23 @@ if isinstance(md.rifts.riftstruct, dict): - raise TypeError("bamg error message: rifts not supported yet. Do meshprocessrift AFTER bamg") + raise TypeError('bamg error message: rifts not supported yet. Do meshprocessrift AFTER bamg') # }}} - # Bamg options {{{ + # BAMG options {{{ bamg_options['Crack'] = options.getfieldvalue('Crack', 0) - bamg_options['anisomax'] = options.getfieldvalue('anisomax', pow(10.0, 18)) + bamg_options['anisomax'] = options.getfieldvalue('anisomax', 1e30) bamg_options['coeff'] = options.getfieldvalue('coeff', 1.0) - bamg_options['cutoff'] = options.getfieldvalue('cutoff', pow(10.0, -5)) - bamg_options['err'] = options.getfieldvalue('err', np.array([[0.01]])) + bamg_options['cutoff'] = options.getfieldvalue('cutoff', 1e-5) + bamg_options['err'] = options.getfieldvalue('err', 0.01) bamg_options['errg'] = options.getfieldvalue('errg', 0.1) bamg_options['field'] = options.getfieldvalue('field', np.empty((0, 1))) bamg_options['gradation'] = options.getfieldvalue('gradation', 1.5) bamg_options['Hessiantype'] = options.getfieldvalue('Hessiantype', 0) - bamg_options['hmin'] = options.getfieldvalue('hmin', pow(10.0, -100)) - bamg_options['hmax'] = options.getfieldvalue('hmax', pow(10.0, 100)) + bamg_options['hmin'] = options.getfieldvalue('hmin', 1e-100) + bamg_options['hmax'] = options.getfieldvalue('hmax', 1e100) bamg_options['hminVertices'] = options.getfieldvalue('hminVertices', np.empty((0, 1))) bamg_options['hmaxVertices'] = options.getfieldvalue('hmaxVertices', np.empty((0, 1))) bamg_options['hVertices'] = options.getfieldvalue('hVertices', np.empty((0, 1))) bamg_options['KeepVertices'] = options.getfieldvalue('KeepVertices', 1) - bamg_options['maxnbv'] = options.getfieldvalue('maxnbv', pow(10, 6)) + bamg_options['maxnbv'] = options.getfieldvalue('maxnbv', 1e6) bamg_options['maxsubdiv'] = options.getfieldvalue('maxsubdiv', 10.0) bamg_options['metric'] = options.getfieldvalue('metric', np.empty((0, 1))) @@ -578,5 +530,5 @@ # }}} - # Call Bamg + # Call BAMG bamgmesh_out, bamggeom_out = BamgMesher(bamg_mesh.__dict__, bamg_geometry.__dict__, bamg_options) @@ -632,5 +584,5 @@ md.mesh.vertexonboundary[md.mesh.segments[:, 0:2] - 1] = 1 - # Bamg private fields + # BAMG private fields md.private.bamg = OrderedDict() md.private.bamg['mesh'] = bamgmesh(bamgmesh_out) @@ -732,5 +684,5 @@ if num: - print(('WARNING: {} points outside the domain outline have been removed'.format(num))) + print('WARNING: {} points outside the domain outline have been removed'.format(num)) """ Index: /issm/trunk-jpl/src/m/modules/ContourToMesh.py =================================================================== --- /issm/trunk-jpl/src/m/modules/ContourToMesh.py (revision 28157) +++ /issm/trunk-jpl/src/m/modules/ContourToMesh.py (revision 28158) @@ -3,24 +3,20 @@ def ContourToMesh(index, x, y, contourname, interptype, edgevalue): - """ + """ContourToMesh - Flag the elements or nodes inside a contour - CONTOURTOMESH - Flag the elements or nodes inside a contour + Usage: + [in_nod, in_elem] = ContourToMesh(index, x, y, contourname, interptype, edgevalue) - Usage: - [in_nod, in_elem] = ContourToMesh(index, x, y, contourname, interptype, edgevalue) + index, x, y: mesh triangulation. + contourname: name of .exp file containing the contours. + interptype: string defining type of interpolation ('element', or 'node'). + edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons. + in_nod: vector of flags (0 or 1), of size nel if interptype is set to 'node' or 'element and node', or of size 0 otherwise. + in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', or of size 0 otherwise. - index, x, y: mesh triangulation. - contourname: name of .exp file containing the contours. - interptype: string defining type of interpolation ('element', or 'node'). - edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons. - in_nod: vector of flags (0 or 1), of size nel if interptype is set to 'node' or 'element and node', - or of size 0 otherwise. - in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', - or of size 0 otherwise. - - Example: - in_nod = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'node', 1) - in_elements = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'element', 0) - [in_nodes, in_elements] = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'element and node', 0) + Example: + in_nod = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'node', 1) + in_elements = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'element', 0) + [in_nodes, in_elements] = ContourToMesh(md.elements, md.x, md.y, 'Contour.exp', 'element and node', 0) """ #Call mex module Index: /issm/trunk-jpl/src/m/modules/ContourToNodes.py =================================================================== --- /issm/trunk-jpl/src/m/modules/ContourToNodes.py (revision 28157) +++ /issm/trunk-jpl/src/m/modules/ContourToNodes.py (revision 28158) @@ -3,5 +3,5 @@ def ContourToNodes(x, y, contourname, edgevalue): - """CONTOURTONODES - flags vertices inside contour + """ContourToNodes - flags vertices inside contour x, y: list of nodes Index: /issm/trunk-jpl/src/m/solve/WriteData.py =================================================================== --- /issm/trunk-jpl/src/m/solve/WriteData.py (revision 28157) +++ /issm/trunk-jpl/src/m/solve/WriteData.py (revision 28158) @@ -8,5 +8,5 @@ def WriteData(fid, prefix, *args): - """WRITEDATA - write model field in binary file + """WriteData - write model field in binary file Usage: @@ -14,9 +14,9 @@ """ - #process options + # Process options options = pairoptions.pairoptions(*args) - #Get data properties + # Get data properties if options.exist('object'): - #This is an object field, construct enum and data + # This is an object field, construct enum and data obj = options.getfieldvalue('object') fieldname = options.getfieldvalue('fieldname') @@ -27,5 +27,5 @@ data = getattr(obj, fieldname) else: - #No processing required + # No processing required data = options.getfieldvalue('data') name = options.getfieldvalue('name') @@ -35,29 +35,29 @@ timeserieslength = options.getfieldvalue('timeserieslength', -1) - #Process sparse matrices + # Process sparse matrices # if issparse(data), # data = full(data) # end - # Make a copy of the the data so that we do not accidently overwrite any + # Make a copy of the the data so that we do not accidentally overwrite any # model fields. # data = copy(data) - #Scale data if necessary + # Scale data if necessary if datatype == 'MatArray': - #if it is a matrix array we loop over the matrices + # If it is a matrix array we loop over the matrices for i in range(len(data)): if options.exist('scale'): scale = options.getfieldvalue('scale') if np.ndim(data[i]) > 1 and data[i].shape[0] == timeserieslength: - #We scale everything but the last line that holds time + # We scale everything but the last line that holds time data[i][:-1, :] = scale * data[i][:-1, :] else: data[i] = scale * data[i] if np.ndim(data[i]) > 1 and data[i].shape[0] == timeserieslength: - #no scaling given, just get the time right + # No scaling given, just get the time right yts = options.getfieldvalue('yts') - #We scale only the last line that holds time + # We scale only the last line that holds time data[i][-1, :] = yts * data[i][-1, :] else: @@ -65,5 +65,5 @@ scale = options.getfieldvalue('scale') if np.ndim(data) > 1 and data.shape[0] == timeserieslength: - #We scale everything but the last line that holds time + # We scale everything but the last line that holds time data[:-1, :] = scale * data[:-1, :] elif type(data) is list: # Deal with "TypeError: can't multiply sequence by non-int of type 'float'" for type list @@ -72,9 +72,9 @@ scaleddata.append(scale * data[i]) data = scaleddata - else: # + else: data = scale * data if np.ndim(data) > 1 and data.shape[0] == timeserieslength: yts = options.getfieldvalue('yts') - #We scale only the last line that holds time + # We scale only the last line that holds time # scaler = np.ones((np.shape(data))) # scaler[-1, :] = yts @@ -82,16 +82,16 @@ data[-1, :] = yts * data[-1, :] - #Step 1: write the enum to identify this record uniquely + # Step 1: write the enum to identify this record uniquely fid.write(pack('i', len(name))) fid.write(pack('{}s'.format(len(name)), name.encode())) - #Step 2: write the data itself. + # Step 2: write the data itself. if datatype == 'Boolean': # {{{ - #first write length of record + # First write length of record fid.write(pack('q', 4 + 4)) #1 bool (disguised as an int) + code - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - - #now write bool as an integer + # Write data code + fid.write(pack('i', FormatToCode(datatype))) + + # Now write bool as an integer try: fid.write(pack('i', int(data))) #send an int, not easy to send a bool @@ -101,11 +101,11 @@ elif datatype == 'Integer': # {{{ - #first write length of record + # First write length of record fid.write(pack('q', 4 + 4)) #1 integer + code - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - #now write integer - try: - fid.write(pack('i', int(data))) #force an int, + # Write data code: + fid.write(pack('i', FormatToCode(datatype))) + # Now write integer + try: + fid.write(pack('i', int(data))) # force an int except error as Err: raise ValueError('field {} cannot be marshaled, {}'.format(name, Err)) @@ -113,11 +113,11 @@ elif datatype == 'Double': # {{{ - #first write length of record - fid.write(pack('q', 8 + 4)) #1 double + code - - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - - #now write double + # First write length of record + fid.write(pack('q', 8 + 4)) # 1 double + code + + # Write data code + fid.write(pack('i', FormatToCode(datatype))) + + # Now write double try: fid.write(pack('d', data)) @@ -127,9 +127,9 @@ elif datatype == 'String': # {{{ - #first write length of record - fid.write(pack('q', len(data) + 4 + 4)) #string + string size + code - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - #now write string + # First write length of record + fid.write(pack('q', len(data) + 4 + 4)) # string + string size + code + # Write data code + fid.write(pack('i', FormatToCode(datatype))) + # Now write string fid.write(pack('i', len(data))) fid.write(pack('{}s'.format(len(data)), data.encode())) @@ -147,19 +147,19 @@ data = data.reshape(0, 0) - #Get size + # Get size s = data.shape - #if matrix = NaN, then do not write anything + # If matrix = NaN, then do not write anything if np.ndim(data) == 2 and np.product(s) == 1 and np.all(np.isnan(data)): s = (0, 0) - #first write length of record - recordlength = 4 + 4 + 8 * np.product(s) + 4 + 4 #2 integers (32 bits) + the double matrix + code + matrix type + # First write length of record + recordlength = 4 + 4 + 8 * np.product(s) + 4 + 4 # 2 integers (32 bits) + the double matrix + code + matrix type fid.write(pack('q', recordlength)) - #write data code and matrix type: + # Write data code and matrix type fid.write(pack('i', FormatToCode(datatype))) fid.write(pack('i', mattype)) - #now write matrix + # Now write matrix fid.write(pack('i', s[0])) try: @@ -186,12 +186,12 @@ data = data.reshape(0, 0) - #Get size + # Get size s = data.shape - #if matrix = NaN, then do not write anything + # If matrix = NaN, then do not write anything if np.ndim(data) == 1 and np.product(s) == 1 and np.all(np.isnan(data)): s = (0, 0) - #first write length of record - recordlength = 4 + 4 + 8 * np.product(s) + 4 + 4 #2 integers (32 bits) + the double matrix + code + matrix type + # First write length of record + recordlength = 4 + 4 + 8 * np.product(s) + 4 + 4 # 2 integers (32 bits) + the double matrix + code + matrix type try: @@ -200,8 +200,8 @@ raise ValueError('Field {} can not be marshaled, {}, with "number" the length of the record.'.format(name, Err)) - #write data code and matrix type: + # Write data code and matrix type fid.write(pack('i', FormatToCode(datatype))) fid.write(pack('i', mattype)) - #now write matrix + # Now write matrix fid.write(pack('i', s[0])) try: @@ -211,8 +211,8 @@ for i in range(s[0]): if np.ndim(data) == 1: - fid.write(pack('d', float(data[i]))) #get to the "c" convention, hence the transpose + fid.write(pack('d', float(data[i]))) # get to the "c" convention, hence the transpose else: for j in range(s[1]): - fid.write(pack('d', float(data[i][j]))) #get to the "c" convention, hence the transpose + fid.write(pack('d', float(data[i][j]))) # get to the "c" convention, hence the transpose # }}} @@ -228,5 +228,5 @@ data = data.reshape(0, 0) - #Get size + # Get size s = data.shape if np.ndim(data) == 1: @@ -235,11 +235,11 @@ n2 = s[1] - #if matrix = NaN, then do not write anything + # If matrix = NaN, then do not write anything if np.ndim(data) == 1 and np.product(s) == 1 and np.all(np.isnan(data)): s = (0, 0) n2 = 0 - #first write length of record - recordlength = 4 + 4 + 8 + 8 + 1 * (s[0] - 1) * n2 + 8 * n2 + 4 + 4 #2 integers (32 bits) + the matrix + code + matrix type + # First write length of record + recordlength = 4 + 4 + 8 + 8 + 1 * (s[0] - 1) * n2 + 8 * n2 + 4 + 4 # 2 integers (32 bits) + the matrix + code + matrix type try: fid.write(pack('q', recordlength)) @@ -247,9 +247,9 @@ raise ValueError('Field {} can not be marshaled, {}, with "number" the lenght of the record.'.format(name, Err)) - #write data code and matrix type: + # Write data code and matrix type fid.write(pack('i', FormatToCode(datatype))) fid.write(pack('i', mattype)) - #Write offset and range + # Write offset and range A = data[0:s[0] - 1] offsetA = A.min() @@ -261,5 +261,5 @@ A = (A - offsetA) / rangeA * 255. - #now write matrix + # Now write matrix fid.write(pack('i', s[0])) try: @@ -272,10 +272,10 @@ for i in range(s[0] - 1): fid.write(pack('B', int(A[i]))) - fid.write(pack('d', float(data[s[0] - 1]))) #get to the "c" convention, hence the transpose + fid.write(pack('d', float(data[s[0] - 1]))) # get to the "c" convention, hence the transpose elif np.product(s) > 0: for i in range(s[0] - 1): for j in range(s[1]): - fid.write(pack('B', int(A[i][j]))) #get to the "c" convention, hence the transpose + fid.write(pack('B', int(A[i][j]))) # get to the "c" convention, hence the transpose for j in range(s[1]): @@ -285,6 +285,6 @@ elif datatype == 'MatArray': # {{{ - #first get length of record - recordlength = 4 + 4 #number of records + code + # First get length of record + recordlength = 4 + 4 # number of records + code for matrix in data: if isinstance(matrix, (bool, int, float)): @@ -299,13 +299,13 @@ s = matrix.shape - recordlength += 4 * 2 + np.product(s) * 8 #row and col of matrix + matrix of doubles - - #write length of record + recordlength += 4 * 2 + np.product(s) * 8 # row and col of matrix + matrix of doubles + + # Write length of record fid.write(pack('q', recordlength)) - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - - #write data, first number of records + # Write data code + fid.write(pack('i', FormatToCode(datatype))) + + # Write data, first number of records fid.write(pack('i', len(data))) @@ -327,5 +327,5 @@ for i in range(s[0]): if np.ndim(matrix) == 1: - fid.write(pack('d', float(matrix[i]))) #get to the "c" convention, hence the transpose + fid.write(pack('d', float(matrix[i]))) # get to the "c" convention, hence the transpose else: for j in range(s[1]): @@ -334,16 +334,16 @@ elif datatype == 'StringArray': # {{{ - #first get length of record - recordlength = 4 + 4 #for length of array + code + # First get length of record + recordlength = 4 + 4 # for length of array + code for string in data: - recordlength += 4 + len(string) #for each string - - #write length of record + recordlength += 4 + len(string) # for each string + + # Write length of record fid.write(pack('q', recordlength)) - #write data code: - fid.write(pack('i', FormatToCode(datatype))) - #now write length of string array + # Write data code + fid.write(pack('i', FormatToCode(datatype))) + # Now write length of string array fid.write(pack('i', len(data))) - #now write the strings + # Now write the strings for string in data: fid.write(pack('i', len(string))) @@ -357,5 +357,5 @@ def FormatToCode(datatype): # {{{ - """ FORMATTOCODE - This routine takes the datatype string, and hardcodes it + """ FormatToCode - This routine takes the datatype string, and hardcodes it into an integer, which is passed along the record, in order to identify the nature of the dataset being sent. Index: /issm/trunk-jpl/test/NightlyRun/runme.m =================================================================== --- /issm/trunk-jpl/test/NightlyRun/runme.m (revision 28157) +++ /issm/trunk-jpl/test/NightlyRun/runme.m (revision 28158) @@ -12,6 +12,6 @@ % % Available options: -% 'id' followed by the list of ids requested -% 'exclude' ids to be excluded from the test +% 'id' followed by the list of test ID's or names to run +% 'exclude' followed by the list of test ID's or names to exclude % 'benchmark' 'all' : (all of them) % 'nightly' : (nightly run @@ -61,5 +61,5 @@ %Process options -%GET benchmark {{{ +%Get benchmark {{{ benchmark=getfieldvalue(options,'benchmark','nightly'); if ~ismember(benchmark,{'all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc','slc','qmu'}) @@ -68,5 +68,5 @@ end % }}} -%GET procedure {{{ +%Get procedure {{{ procedure=getfieldvalue(options,'procedure','check'); if ~ismember(procedure,{'check','update','valgrind','ncExport'}) @@ -75,5 +75,5 @@ end % }}} -%GET output {{{ +%Get output {{{ output=getfieldvalue(options,'output','none'); if ~ismember(output,{'nightly','none'}) @@ -82,18 +82,18 @@ end % }}} -%GET RANK and NUMPROCS for multithreaded runs {{{ +%Get rank and numprocs for multi-threaded runs {{{ rank=getfieldvalue(options,'rank',1); numprocs=getfieldvalue(options,'numprocs',1); if (numprocs