Index: /issm/trunk-jpl/jenkins/mac-silicon-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/mac-silicon-solid_earth (revision 27844) +++ /issm/trunk-jpl/jenkins/mac-silicon-solid_earth (revision 27845) @@ -100,5 +100,6 @@ # - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") # - Excluding 2091 until it can be debugged (resource starvation) +# - Excluding 2110:2113 until we can compile MEX modules natively for Silicon and then can debug differences in mesh generation between different platforms # MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2051 2052 2053 2085 2424 2425]" -PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2051 2052 2053 2085 2424 2425" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2051 2052 2053 2085 2110:2113 2424 2425" Index: /issm/trunk-jpl/src/c/shared/Exp/exp.h =================================================================== --- /issm/trunk-jpl/src/c/shared/Exp/exp.h (revision 27844) +++ /issm/trunk-jpl/src/c/shared/Exp/exp.h (revision 27845) @@ -115,5 +115,5 @@ closed=xNew(nprof); - /*Reaset file pointer to beginning of file: */ + /*Reset file pointer to beginning of file: */ fseek(fid,0,SEEK_SET); Index: /issm/trunk-jpl/src/m/classes/mesh2d.m =================================================================== --- /issm/trunk-jpl/src/m/classes/mesh2d.m (revision 27844) +++ /issm/trunk-jpl/src/m/classes/mesh2d.m (revision 27845) @@ -76,9 +76,9 @@ function self = setdefaultparameters(self) % {{{ - %the connectivity is the averaged number of nodes linked to a - %given node through an edge. This connectivity is used to initially - %allocate memory to the stiffness matrix. A value of 16 seems to - %give a good memory/time ration. This value can be checked in - %trunk/test/Miscellaneous/runme.m + %The connectivity is the average number of nodes linked to a given + %node through an edge. This connectivity is used to initially allocate + %memory to the stiffness matrix. A value of 16 seems to give a good + %memory/time ratio. This value can be checked in + %test/Miscellaneous/runme.m self.average_vertex_connectivity=25; end % }}} Index: /issm/trunk-jpl/src/m/classes/mesh2d.py =================================================================== --- /issm/trunk-jpl/src/m/classes/mesh2d.py (revision 27844) +++ /issm/trunk-jpl/src/m/classes/mesh2d.py (revision 27845) @@ -1,5 +1,5 @@ import numpy as np +from checkfield import checkfield from fielddisplay import fielddisplay -from checkfield import checkfield import MatlabFuncs as m from WriteData import WriteData @@ -7,36 +7,35 @@ class mesh2d(object): - """ - MESH2D class definition + """mesh2d class definition - Usage: - mesh2d = mesh2d() + Usage: + mesh2d = mesh2d() """ def __init__(self): # {{{ - self.x = float('NaN') - self.y = float('NaN') - self.elements = float('NaN') + self.x = np.nan + self.y = np.nan + self.elements = np.nan self.numberofelements = 0 self.numberofvertices = 0 self.numberofedges = 0 - self.lat = float('NaN') - self.long = float('NaN') + self.lat = np.nan + self.long = np.nan self.epsg = 0 - self.scale_factor = float('NaN') + self.scale_factor = np.nan - self.vertexonboundary = float('NaN') - self.edges = float('NaN') - self.segments = float('NaN') - self.segmentmarkers = float('NaN') - self.vertexconnectivity = float('NaN') - self.elementconnectivity = float('NaN') + self.vertexonboundary = np.nan + self.edges = np.nan + self.segments = np.nan + self.segmentmarkers = np.nan + self.vertexconnectivity = np.nan + self.elementconnectivity = np.nan self.average_vertex_connectivity = 0 - self.extractedvertices = float('NaN') - self.extractedelements = float('NaN') + self.extractedvertices = np.nan + self.extractedelements = np.nan - #set defaults + # Set defaults self.setdefaultparameters() @@ -44,41 +43,42 @@ def __repr__(self): # {{{ - string = " 2D tria Mesh (horizontal):" + s = ' 2D tria Mesh (horizontal):\n' - string = "%s\n%s" % (string, "\n Elements and vertices:") - string = "%s\n%s" % (string, fielddisplay(self, "numberofelements", "number of elements")) - string = "%s\n%s" % (string, fielddisplay(self, "numberofvertices", "number of vertices")) - string = "%s\n%s" % (string, fielddisplay(self, "elements", "vertex indices of the mesh elements")) - string = "%s\n%s" % (string, fielddisplay(self, "x", "vertices x coordinate [m]")) - string = "%s\n%s" % (string, fielddisplay(self, "y", "vertices y coordinate [m]")) - string = "%s\n%s" % (string, fielddisplay(self, "edges", "edges of the 2d mesh (vertex1 vertex2 element1 element2)")) - string = "%s\n%s" % (string, fielddisplay(self, "numberofedges", "number of edges of the 2d mesh")) + s += '{}\n'.format(' Elements and vertices:') + s += '{}\n'.format(fielddisplay(self, 'numberofelements', 'number of elements')) + s += '{}\n'.format(fielddisplay(self, 'numberofvertices', 'number of vertices')) + s += '{}\n'.format(fielddisplay(self, 'elements', 'vertex indices of the mesh elements')) + s += '{}\n'.format(fielddisplay(self, 'x', 'vertices x coordinate [m]')) + s += '{}\n'.format(fielddisplay(self, 'y', 'vertices y coordinate [m]')) + s += '{}\n'.format(fielddisplay(self, 'edges', 'edges of the 2d mesh (vertex1 vertex2 element1 element2)')) + s += '{}\n'.format(fielddisplay(self, 'numberofedges', 'number of edges of the 2d mesh')) + s += '\n' + s += '{}\n'.format(' Properties:') + s += '{}\n'.format(fielddisplay(self, 'vertexonboundary', 'vertices on the boundary of the domain flag list')) + s += '{}\n'.format(fielddisplay(self, 'segments', 'edges on domain boundary (vertex1 vertex2 element)')) + s += '{}\n'.format(fielddisplay(self, 'segmentmarkers', 'number associated to each segment')) + s += '{}\n'.format(fielddisplay(self, 'vertexconnectivity', 'list of elements connected to vertex_i')) + s += '{}\n'.format(fielddisplay(self, 'elementconnectivity', 'list of elements adjacent to element_i')) + s += '{}\n'.format(fielddisplay(self, 'average_vertex_connectivity', 'average number of vertices connected to one vertex')) + s += '\n' + s += '{}\n'.format(' Extracted model:') + s += '{}\n'.format(fielddisplay(self, 'extractedvertices', 'vertices extracted from the model')) + s += '{}\n'.format(fielddisplay(self, 'extractedelements', 'elements extracted from the model')) + s += '\n' + s += '{}\n'.format(' Projection:') + s += '{}\n'.format(fielddisplay(self, 'lat', 'vertices latitude [degrees]')) + s += '{}\n'.format(fielddisplay(self, 'long', 'vertices longitude [degrees]')) + s += '{}\n'.format(fielddisplay(self, 'epsg', 'EPSG code (ex: 3413 for UPS Greenland, 3031 for UPS Antarctica)')) + s += '{}\n'.format(fielddisplay(self, 'scale_factor', 'Projection correction for volume, area, etc. computation')) - string = "%s%s" % (string, "\n\n Properties:") - string = "%s\n%s" % (string, fielddisplay(self, "vertexonboundary", "vertices on the boundary of the domain flag list")) - string = "%s\n%s" % (string, fielddisplay(self, "segments", "edges on domain boundary (vertex1 vertex2 element)")) - string = "%s\n%s" % (string, fielddisplay(self, "segmentmarkers", "number associated to each segment")) - string = "%s\n%s" % (string, fielddisplay(self, "vertexconnectivity", "list of elements connected to vertex_i")) - string = "%s\n%s" % (string, fielddisplay(self, "elementconnectivity", "list of elements adjacent to element_i")) - string = "%s\n%s" % (string, fielddisplay(self, "average_vertex_connectivity", "average number of vertices connected to one vertex")) - - string = "%s%s" % (string, "\n\n Extracted model:") - string = "%s\n%s" % (string, fielddisplay(self, "extractedvertices", "vertices extracted from the model")) - string = "%s\n%s" % (string, fielddisplay(self, "extractedelements", "elements extracted from the model")) - - string = "%s%s" % (string, "\n\n Projection:") - string = "%s\n%s" % (string, fielddisplay(self, "lat", "vertices latitude [degrees]")) - string = "%s\n%s" % (string, fielddisplay(self, "long", "vertices longitude [degrees]")) - string = "%s\n%s" % (string, fielddisplay(self, "epsg", "EPSG code (ex: 3413 for UPS Greenland, 3031 for UPS Antarctica)")) - string = "%s\n%s" % (string, fielddisplay(self, "scale_factor", "Projection correction for volume, area, etc. computation")) - return string + return s # }}} def setdefaultparameters(self): # {{{ - #the connectivity is the averaged number of nodes linked to a - #given node through an edge. This connectivity is used to initially - #allocate memory to the stiffness matrix. A value of 16 seems to - #give a good memory / time ration. This value can be checked in - #trunk / test / Miscellaneous / runme.m + # The connectivity is the average number of nodes linked to a given + # node through an edge. This connectivity is used to initially allocate + # memory to the stiffness matrix. A value of 16 seems to give a good + # memory/time ratio. This value can be checked in + # test/Miscellaneous/runme.m self.average_vertex_connectivity = 25 @@ -95,8 +95,8 @@ md = checkfield(md, 'fieldname', 'mesh.elements', 'size', [md.mesh.numberofelements, 3]) if np.any(np.logical_not(m.ismember(np.arange(1, md.mesh.numberofvertices + 1), md.mesh.elements))): - md.checkmessage("orphan nodes have been found. Check the mesh outline") + md.checkmessage('orphan nodes have been found. Check the mesh outline') md = checkfield(md, 'fieldname', 'mesh.numberofelements', '>', 0) md = checkfield(md, 'fieldname', 'mesh.numberofvertices', '>', 0) - md = checkfield(md, 'fieldname', 'mesh.average_vertex_connectivity', '>=', 9, 'message', "'mesh.average_vertex_connectivity' should be at least 9 in 2d") + md = checkfield(md, 'fieldname', 'mesh.average_vertex_connectivity', '>=', 9, 'message', '\'mesh.average_vertex_connectivity\' should be at least 9 in 2d') md = checkfield(md, 'fieldname', 'mesh.segments', 'NaN', 1, 'Inf', 1, '>', 0, 'size', [np.nan, 3]) if(np.size(self.scale_factor) > 1): @@ -104,5 +104,5 @@ if solution == 'ThermalSolution': - md.checkmessage("thermal not supported for 2d mesh") + md.checkmessage('thermal not supported for 2d mesh') return md @@ -110,5 +110,5 @@ def domaintype(self): # {{{ - return "2Dhorizontal" + return '2Dhorizontal' # }}} @@ -118,9 +118,9 @@ def elementtype(self): # {{{ - return "Tria" + return 'Tria' # }}} def marshall(self, prefix, md, fid): # {{{ - WriteData(fid, prefix, 'name', 'md.mesh.domain_type', 'data', "Domain" + self.domaintype(), 'format', 'String') + WriteData(fid, prefix, 'name', 'md.mesh.domain_type', 'data', 'Domain' + self.domaintype(), 'format', 'String') WriteData(fid, prefix, 'name', 'md.mesh.domain_dimension', 'data', self.dimension(), 'format', 'Integer') WriteData(fid, prefix, 'name', 'md.mesh.elementtype', 'data', self.elementtype(), 'format', 'String') Index: /issm/trunk-jpl/src/m/mesh/roundmesh.m =================================================================== --- /issm/trunk-jpl/src/m/mesh/roundmesh.m (revision 27844) +++ /issm/trunk-jpl/src/m/mesh/roundmesh.m (revision 27845) @@ -2,5 +2,5 @@ %ROUNDMESH - create an unstructured round mesh % -% This script will generate a structured round mesh +% This script will generate an unstructured round mesh % - radius : specifies the radius of the circle in meters % - resolution : specifies the resolution in meters Index: /issm/trunk-jpl/src/m/mesh/roundmesh.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/roundmesh.py (revision 27844) +++ /issm/trunk-jpl/src/m/mesh/roundmesh.py (revision 27845) @@ -10,5 +10,5 @@ """roundmesh - create an unstructured round mesh - This script will generate a structured round mesh + This script will generate an unstructured round mesh - radius : specifies the radius of the circle in meters - resolution : specifies the resolution in meters Index: /issm/trunk-jpl/src/m/mesh/triangle.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/triangle.py (revision 27844) +++ /issm/trunk-jpl/src/m/mesh/triangle.py (revision 27845) @@ -12,8 +12,8 @@ """triangle - create model mesh using the triangle package - This routine creates a model mesh using Triangle and a domain outline, to within a certain resolution - where md is a @model object, domainname is the name of an Argus domain outline file, - and resolution is a characteristic length for the mesh (same unit as the domain outline - unit). Riftname is an optional argument (Argus domain outline) describing rifts. + This routine creates a model mesh using Triangle and a domain outline, to + within a certain resolution where md is a @model object, domainname is the + name of an Argus domain outline file, and resolution is a characteristic + length for the mesh (same unit as the domain outline unit). Riftname is an optional argument (Argus domain outline) describing rifts. Usage: @@ -27,6 +27,6 @@ """ - # Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would - # be made of 1000 * 1000 area squares). + # Figure out a characteristic area. Resolution is a node oriented concept + # (ex a 1000m resolution node would be made of 1000 * 1000 area squares). if len(args) == 1: @@ -37,5 +37,5 @@ resolution = args[1] - # Check that mesh was not already run, and warn user: + # Check that mesh was not already run, and warn user if md.mesh.numberofelements: choice = input('This model already has a mesh. Are you sure you want to go ahead? (y / n)') @@ -49,5 +49,5 @@ area = resolution ** 2 - # Check that file exist (this is a very very common mistake) + # Check that file exists (this is a very common mistake) if not os.path.exists(domainname): raise IOError('file {} not found'.format(domainname)) @@ -86,5 +86,5 @@ md.mesh.segmentmarkers = segmentmarkers.astype(int) - # Fill in rest of fields: + # Fill in rest of fields md.mesh.numberofelements = np.size(md.mesh.elements, axis=0) md.mesh.numberofvertices = np.size(md.mesh.x) @@ -92,5 +92,5 @@ md.mesh.vertexonboundary[md.mesh.segments[:, 0:2] - 1] = 1 - # Now, build the connectivity tables for this mesh. + # Now, build the connectivity tables for this mesh md.mesh.vertexconnectivity = NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) md.mesh.elementconnectivity = ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity)