Changeset 12943

Timestamp:

08/08/12 11:37:55 (13 years ago)

Author:

jschierm

Message:

NEW: Python checkconsistency and marshall methods for mesh sub-class (plus other changes to make them work).

Location:

issm/trunk-jpl/src/m

Files:

• classes/mesh.m (modified) (1 diff)
• classes/mesh.py (modified) (7 diffs)
• classes/private.m (modified) (1 diff)
• classes/private.py (modified) (2 diffs)
• model/WriteData.py (modified) (1 diff)
• model/ismodelselfconsistent.py (modified) (1 diff)
• model/marshall.py (modified) (1 diff)
• utils/consistency/checkfield.py (modified) (6 diffs)

issm/trunk-jpl/src/m/classes/mesh.m

@@ -57 +57 @@
                 function obj = setdefaultparameters(obj) % {{{
 
-                        %the connectivity is the avergaded number of nodes linked to a
+                        %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

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

@@ -1 +1 @@
 #module imports
+import numpy
 from fielddisplay import fielddisplay
+from checkfield import *
+from EnumDefinitions import *
+from MatlabFuncs import *
 
 class mesh:
@@ -65 +69 @@
                 else:
                         string="\n%s"%("      Elements and vertices:")
-
                 string="%s\n%s"%(string,fielddisplay(obj,"numberofelements","number of elements"))
-                
-
-
-
                 string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices","number of vertices"))
                 string="%s\n%s"%(string,fielddisplay(obj,"elements","index into (x,y,z), coordinates of the vertices"))
@@ -80 +79 @@
 
                 string="%s%s"%(string,"\n      Properties:")
-                
                 string="%s\n%s"%(string,fielddisplay(obj,"dimension","mesh dimension (2d or 3d)"))
                 string="%s\n%s"%(string,fielddisplay(obj,"numberoflayers","number of extrusion layers"))
@@ -92 +90 @@
                 string="%s\n%s"%(string,fielddisplay(obj,"lowerelements","lower element list (NaN for element on the lower layer"))
                 string="%s\n%s"%(string,fielddisplay(obj,"vertexonboundary","vertices on the boundary of the domain flag list"))
-                
                 string="%s\n%s"%(string,fielddisplay(obj,"segments","edges on domain boundary (vertex1 vertex2 element)"))
                 string="%s\n%s"%(string,fielddisplay(obj,"segmentmarkers","number associated to each segment"))
@@ -100 +97 @@
 
                 string="%s%s"%(string,"\n      Extracted model:")
-
                 string="%s\n%s"%(string,fielddisplay(obj,"extractedvertices","vertices extracted from the model"))
                 string="%s\n%s"%(string,fielddisplay(obj,"extractedelements","elements extracted from the model"))
@@ -114 +110 @@
                 # {{{setdefaultparameters
                 
-                #the connectivity is the avergaded number of nodes linked to a
+                #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
@@ -124 +120 @@
         #}}}
 
+        def checkconsistency(self,md,solution,analyses):    # {{{
+
+                md = checkfield(md,'mesh.x','NaN',1,'size',[md.mesh.numberofvertices])
+                md = checkfield(md,'mesh.y','NaN',1,'size',[md.mesh.numberofvertices])
+                md = checkfield(md,'mesh.z','NaN',1,'size',[md.mesh.numberofvertices])
+                md = checkfield(md,'mesh.elements','NaN',1,'>',0,'values',range(1,md.mesh.numberofvertices+1))
+                if md.mesh.dimension==2:
+                        md = checkfield(md,'mesh.elements','size',[md.mesh.numberofelements,3])
+                else:
+                        md = checkfield(md,'mesh.elements','size',[md.mesh.numberofelements,6])
+                if any(numpy.logical_not(ismember(range(1,md.mesh.numberofvertices+1),md.mesh.elements))):
+                        md = checkmessage(md,"orphan nodes have been found. Check the mesh outline")
+                md = checkfield(md,'mesh.dimension','values',[2,3])
+                md = checkfield(md,'mesh.numberoflayers','>=',0)
+                md = checkfield(md,'mesh.numberofelements','>',0)
+                md = checkfield(md,'mesh.numberofvertices','>',0)
+                #no checks for numberofedges lat long and hemisphere
+                md = checkfield(md,'mesh.elementonbed','size',[md.mesh.numberofelements],'values',[0,1])
+                md = checkfield(md,'mesh.elementonsurface','size',[md.mesh.numberofelements],'values',[0,1])
+                md = checkfield(md,'mesh.vertexonbed','size',[md.mesh.numberofvertices],'values',[0,1])
+                md = checkfield(md,'mesh.vertexonsurface','size',[md.mesh.numberofvertices],'values',[0,1])
+                if md.mesh.dimension==2:
+                        md = checkfield(md,'mesh.average_vertex_connectivity','>=',9,'message',"'mesh.average_vertex_connectivity' should be at least 9 in 2d")
+                else:
+                        md = checkfield(md,'mesh.average_vertex_connectivity','>=',24,'message',"'mesh.average_vertex_connectivity' should be at least 24 in 3d")
+                md = checkfield(md,'mesh.elementconnectivity','size',[md.mesh.numberofelements,3],'NaN',1)
+
+                #Solution specific checks
+                if   solution==PrognosticSolutionEnum:
+                        if md.prognostic.stabilization==3:
+                                md = checkfield(md,'mesh.dimension','values',2,'message',"Discontinuous Galerkin only supported for 2d meshes")
+                                md = checkfield(md,'mesh.edges','size',[float('NaN'),4])
+                                md = checkfield(md,'mesh.edges[:,1:3]','>',0)
+                elif solution==BalancethicknessSolutionEnum:
+                        if md.balancethickness.stabilization==3:
+                                md = checkfield(md,'mesh.dimension','values',2,'message',"Discontinuous Galerkin only supported for 2d meshes")
+                                md = checkfield(md,'mesh.edges','size',[float('NaN'),4])
+                                md = checkfield(md,'mesh.edges[:,1:3]','>',0)
+                elif solution==TransientSolutionEnum:
+                        if md.transient.isprognostic and md.prognostic.stabilization==3:
+                                md = checkfield(md,'mesh.dimension','values',2,'message',"Discontinuous Galerkin only supported for 2d meshes")
+                                md = checkfield(md,'mesh.edges','size',[float('NaN'),4])
+                                md = checkfield(md,'mesh.edges[:,1:3]','>',0)
+                elif solution==ThermalSolutionEnum:
+                        md = checkfield(md,'mesh.dimension','values',3,'message','thermal solution only supported on 3d meshes')
+
+                return md
+        # }}}
+
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','x','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','y','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','z','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','elements','format','DoubleMat','mattype',2)
+                WriteData(fid,'object',self,'fieldname','dimension','format','Integer')
+                WriteData(fid,'object',self,'fieldname','numberoflayers','format','Integer')
+                WriteData(fid,'object',self,'fieldname','numberofelements','format','Integer')
+                WriteData(fid,'object',self,'fieldname','numberofvertices','format','Integer')
+                WriteData(fid,'object',self,'fieldname','numberofedges','format','Integer')
+                WriteData(fid,'object',self,'fieldname','elementonbed','format','BooleanMat','mattype',2)
+                WriteData(fid,'object',self,'fieldname','elementonsurface','format','BooleanMat','mattype',2)
+                WriteData(fid,'object',self,'fieldname','vertexonbed','format','BooleanMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','vertexonsurface','format','BooleanMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','lowerelements','format','DoubleMat','mattype',2)
+                WriteData(fid,'object',self,'fieldname','upperelements','format','DoubleMat','mattype',2)
+                WriteData(fid,'object',self,'fieldname','edges','format','DoubleMat','mattype',3)
+                WriteData(fid,'object',self,'fieldname','elementconnectivity','format','DoubleMat','mattype',3)
+                WriteData(fid,'object',self,'fieldname','average_vertex_connectivity','format','Integer')
+                WriteData(fid,'object',self,'fieldname','elements2d','format','DoubleMat','mattype',3)
+                WriteData(fid,'object',self,'fieldname','numberofvertices2d','format','Integer')
+                WriteData(fid,'object',self,'fieldname','numberofelements2d','format','Integer')
+        # }}}
+

issm/trunk-jpl/src/m/classes/private.m

@@ -31 +31 @@
                         fielddisplay(obj,'isconsistent','is model self consistent');
                         fielddisplay(obj,'runtimename','name of the run launched');
-                        fielddisplay(obj,'bamg','structure with mesh properties construced if bamg is used to mesh the domain');
+                        fielddisplay(obj,'bamg','structure with mesh properties constructed if bamg is used to mesh the domain');
                         fielddisplay(obj,'solution','type of solution launched');
 

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

@@ -6 +6 @@
         def __init__(self):
                 # {{{ Properties
-                self.runtimename = ''
-                self.bamg        = {}
-                self.solution    = '';
+                self.isconsistent = True;
+                self.runtimename  = ''
+                self.bamg         = {}
+                self.solution     = '';
 
                 #set defaults
@@ -17 +18 @@
                 # {{{ Display
                 string='   private parameters: do not change'
+
+                string="%s\n%s"%(string,fielddisplay(obj,'isconsistent','is model self consistent'))
                 string="%s\n%s"%(string,fielddisplay(obj,'runtimename','name of the run launched'))
-                string="%s\n%s"%(string,fielddisplay(obj,'bamg','structure with mesh properties construced if bamg is used to mesh the domain'))
+                string="%s\n%s"%(string,fielddisplay(obj,'bamg','structure with mesh properties constructed if bamg is used to mesh the domain'))
                 string="%s\n%s"%(string,fielddisplay(obj,'solution','type of solution launched'))
                 return string

issm/trunk-jpl/src/m/model/WriteData.py

@@ -9 +9 @@
  
             Usage:
-               WriteData(fid,*args)
+               WriteData(fid,varargin)
         """
 
         #process options
-        options=pairoptions(args)
+        options=pairoptions(*args)
 
         #Get data properties

issm/trunk-jpl/src/m/model/ismodelselfconsistent.py

@@ -17 +17 @@
 
         #Go through a model fields, check that it is a class, and call checkconsistency
-#       fields=vars('model')
-        fields=dir(md)
-        for field in fields:
+        fields=vars(md)
+        for field in fields.iterkeys():
 
                 #Some properties do not need to be checked

issm/trunk-jpl/src/m/model/marshall.py

@@ -26 +26 @@
         fields=vars(md)
 
-        for field in fields.interkeys():
+        for field in fields.iterkeys():
 
                 #Some properties do not need to be marshalled

issm/trunk-jpl/src/m/utils/consistency/checkfield.py

@@ -8 +8 @@
         CHECKFIELD - check field consistency
 
-            Used to check model consistency.
-            Available options:
-               - NaN: 1 if check that there is no NaN
-               - size: [lines cols], NaN for non checked dimensions
-               - >:  greater than provided value
-               - >=: greater or equal to provided value
-               - <:  smallerthan provided value
-               - <=: smaller or equal to provided value
-               - < vec:  smallerthan provided values on each vertex
-               - forcing: 1 if check forcing consistency (size and time)
-               - values: cell of strings or vector of acceptable values
-               - numel: list of acceptable number of elements
-               - cell: 1 if check that is cell
-               - empty: 1 if check that non empty
-               - message: overloaded error message
+           Used to check model consistency.
+           Available options:
+              - NaN: 1 if check that there is no NaN
+              - size: [lines cols], NaN for non checked dimensions
+              - >:  greater than provided value
+              - >=: greater or equal to provided value
+              - <:  smallerthan provided value
+              - <=: smaller or equal to provided value
+              - < vec:  smallerthan provided values on each vertex
+              - forcing: 1 if check forcing consistency (size and time)
+              - values: cell of strings or vector of acceptable values
+              - numel: list of acceptable number of elements
+              - cell: 1 if check that is cell
+              - empty: 1 if check that non empty
+              - message: overloaded error message
 
-            Usage:
-               md = checkfield(md,fieldname,options);
+           Usage:
+              md = checkfield(md,fieldname,options);
 
-            Example:
-               md = checkfield(md,'mesh.elementonbed','size',[md.mesh.numberofelements 1],'values',[0 1]);
-               md = checkfield(md,'diagnostic.icefront','size',[NaN 4],'NaN',1);
-               md = checkfield(md,'diagnostic.icefront(:,end)','values',[0 1 2]);
+           Example:
+              md = checkfield(md,'mesh.elementonbed','size',[md.mesh.numberofelements 1],'values',[0 1]);
+              md = checkfield(md,'diagnostic.icefront','size',[NaN 4],'NaN',1);
+              md = checkfield(md,'diagnostic.icefront(:,end)','values',[0 1 2]);
         """
 
@@ -37 +37 @@
 
         #get field from model
-        field=getattr(md,fieldname)
+#       field=getattr(md,fieldname)
+        exec("field=md.%s" % fieldname)
 
         #check empty
-        if 'empty' in options:
+        if options.exist('empty'):
                 if not field:
                         md = md.checkmessage(options.getfieldvalue('message',\
@@ -46 +47 @@
 
         #Check size
-        if 'size' in options:
+        if options.exist('size'):
                 fieldsize=options.getfieldvalue('size')
-                if   numpy.isnan(fieldsize[0]):
-                        if not numpy.size(field,1)==fieldsize[1]:
+                if   len(fieldsize) == 1:
+                        if (not numpy.size(field,0)==fieldsize[0]):
                                 md = md.checkmessage(options.getfieldvalue('message',\
-                                        "field '%s' should have %d columns" % (fieldname,fieldsize[1])))
-                elif numpy.isnan(fieldsize[1]):
-                        if not numpy.size(field,0)==fieldsize[0]:
-                                md = md.checkmessage(options.getfieldvalue('message',\
-                                        "field '%s' should have %d lines" % (fieldname,fieldsize[0])))
-                else:
-                        if (not numpy.size(field,0)==fieldsize[0]) or (not numpy.size(field,1)==fieldsize[1]):
-                                md = md.checkmessage(options.getfieldvalue('message',\
-                                        "field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1])))
+                                        "field '%s' size should be %d" % (fieldname,fieldsize[0])))
+                elif len(fieldsize) == 2:
+                        if   numpy.isnan(fieldsize[0]):
+                                if not numpy.size(field,1)==fieldsize[1]:
+                                        md = md.checkmessage(options.getfieldvalue('message',\
+                                                "field '%s' should have %d columns" % (fieldname,fieldsize[1])))
+                        elif numpy.isnan(fieldsize[1]):
+                                if not numpy.size(field,0)==fieldsize[0]:
+                                        md = md.checkmessage(options.getfieldvalue('message',\
+                                                "field '%s' should have %d lines" % (fieldname,fieldsize[0])))
+                        else:
+                                if (not numpy.size(field,0)==fieldsize[0]) or (not numpy.size(field,1)==fieldsize[1]):
+                                        md = md.checkmessage(options.getfieldvalue('message',\
+                                                "field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1])))
         
         #Check numel
-        if 'numel' in options:
+        if options.exist('numel'):
                 fieldnumel=options.getfieldvalue('numel')
                 if not numpy.size(field) in fieldnumel:
@@ -88 +94 @@
 
         #check values
-        if 'values' in options:
+        if options.exist('values'):
                 fieldvalues=options.getfieldvalue('values')
                 if False in ismember(field,fieldvalues):
@@ -102 +108 @@
 
         #check greater
-        if '>=' in options:
+        if options.exist('>='):
                 lowerbound=options.getfieldvalue('>=')
                 if numpy.any(field<lowerbound):
                         md = md.checkmessage(options.getfieldvalue('message',\
                                 "field '%s' should have values above %d" % (fieldname,lowerbound)))
-        if '>' in options:
+        if options.exist('>'):
                 lowerbound=options.getfieldvalue('>')
                 if numpy.any(field<=lowerbound):
@@ -114 +120 @@
 
         #check smaller
-        if '<=' in options:
+        if options.exist('<='):
                 upperbound=options.getfieldvalue('<=')
                 if numpy.any(field>upperbound):
                         md = md.checkmessage(options.getfieldvalue('message',\
                                 "field '%s' should have values below %d" % (fieldname,upperbound)))
-        if '<' in options:
+        if options.exist('<'):
                 upperbound=options.getfieldvalue('<')
                 if numpy.any(field>=upperbound):