Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.m =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.m (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.m (revision 13030) @@ -1,4 +1,4 @@ -%MISCELANEOUS class definition +%MISCELLANEOUS class definition % % Usage: % miscellaneous=miscellaneous(); Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/diagnostic.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/diagnostic.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/diagnostic.py (revision 13030) @@ -138,8 +138,7 @@ md = checkfield(md,'diagnostic.requested_outputs','size',[float('NaN'),1]) #singular solution - #if ~any((~isnan(md.diagnostic.spcvx)+~isnan(md.diagnostic.spcvy))==2), - if not any((numpy.logical_not(numpy.isnan(md.diagnostic.spcvx))+numpy.logical_not(numpy.isnan(md.diagnostic.spcvy)))==2): + if not any(numpy.logical_and(numpy.logical_not(numpy.isnan(md.diagnostic.spcvx)),numpy.logical_not(numpy.isnan(md.diagnostic.spcvy)))): md.checkmessage("model is not well posed (singular). You need at least one node with fixed velocity!") #CHECK THAT EACH LINES CONTAINS ONLY NAN VALUES OR NO NAN VALUES if any(not numpy.sum(numpy.isnan(md.diagnostic.referential),axis=1)==0 and not numpy.sum(numpy.isnan(md.diagnostic.referential),axis=1)==6): Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/radaroverlay.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/radaroverlay.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/radaroverlay.py (revision 13030) @@ -2,6 +2,13 @@ from fielddisplay import fielddisplay class radaroverlay(object): + """ + RADAROVERLAY class definition + + Usage: + radaroverlay=radaroverlay(); + """ + #properties def __init__(self): # {{{ Properties @@ -13,17 +20,17 @@ self.setdefaultparameters() #}}} - def __repr__(obj): + def __repr__(self): # {{{ Display string=' radaroverlay parameters:' - string="%s\n\n%s"%(string,fielddisplay(obj,'pwr','radar power image (matrix)')) - string="%s\n%s"%(string,fielddisplay(obj,'x','corresponding x coordinates')) - string="%s\n%s"%(string,fielddisplay(obj,'y','corresponding y coordinates')) + string="%s\n\n%s"%(string,fielddisplay(self,'pwr','radar power image (matrix)')) + string="%s\n%s"%(string,fielddisplay(self,'x','corresponding x coordinates')) + string="%s\n%s"%(string,fielddisplay(self,'y','corresponding y coordinates')) return string #}}} - def setdefaultparameters(obj): + def setdefaultparameters(self): # {{{setdefaultparameters - return obj + return self #}}} Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.m =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.m (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.m (revision 13030) @@ -46,21 +46,9 @@ if numel(md.qmu.partition)~=md.mesh.numberofvertices, md = checkmessage(md,['user supplied partition for qmu analysis should have size md.mesh.numberofvertices x 1 ']); end - if find(md.qmu.partition)>=md.mesh.numberofvertices, - md = checkmessage(md,['user supplied partition should be indexed from 0 (c-convention)']); - end if min(md.qmu.partition)~=0, md = checkmessage(md,['partition vector not indexed from 0 on']); end - if max(md.qmu.partition)>=md.mesh.numberofvertices, - md = checkmessage(md,['partition vector cannot have maximum index larger than number of nodes']); - end - if ~isempty(find(md.qmu.partition<0)), - md = checkmessage(md,['partition vector cannot have values less than 0']); - end - if ~isempty(find(md.qmu.partition>=md.qmu.numberofpartitions)), - md = checkmessage(md,['partition vector cannot have values more than md.qmu.numberofpartitions-1']); - end if max(md.qmu.partition)>=md.qmu.numberofpartitions, md = checkmessage(md,['for qmu analysis, partitioning vector cannot go over npart, number of partition areas']); end @@ -139,8 +127,8 @@ fnames{j},size(obj.results.(fnames{j})),class(obj.results.(fnames{j})))); end end - fielddisplay(obj,'partition','user provided mesh partitionition, defaults to metis if not specified') - fielddisplay(obj,'numberofpartitions','number of partitions for semi-descrete qmu') + fielddisplay(obj,'partition','user provided mesh partitioning, defaults to metis if not specified') + fielddisplay(obj,'numberofpartitions','number of partitions for semi-discrete qmu') fielddisplay(obj,'variabledescriptors',''); fielddisplay(obj,'responsedescriptors',''); fielddisplay(obj,'method','array of dakota_method class'); Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/model/model.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/model/model.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/model/model.py (revision 13030) @@ -115,7 +115,7 @@ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flaim","[%s,%s]" % ("1x1",obj.flaim.__class__.__name__),"flaim parameters")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties")) - string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) return string Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/qmu.py (revision 13030) @@ -1,7 +1,19 @@ #module imports +import numpy from fielddisplay import fielddisplay +from EnumDefinitions import * +from checkfield import * +from WriteData import * +from MatlabFuncs import * class qmu(object): + """ + QMU class definition + + Usage: + qmu=qmu(); + """ + #properties def __init__(self): # {{{ Properties @@ -26,14 +38,117 @@ self.setdefaultparameters() #}}} - def __repr__(obj): - # {{{ Display - string=" qmu parameters: not implemented yet!" - return string - #}}} - - def setdefaultparameters(obj): + + def setdefaultparameters(self): # {{{setdefaultparameters - return obj + return self #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + + #Early return + if not md.qmu.isdakota: + return + + if not md.qmu.params.evaluation_concurrency==1: + md.checkmessage("concurrency should be set to 1 when running dakota in library mode") + if md.qmu.partition: + if not numpy.size(md.qmu.partition)==md.mesh.numberofvertices: + md.checkmessage("user supplied partition for qmu analysis should have size md.mesh.numberofvertices x 1") + if not min(md.qmu.partition)==0: + md.checkmessage("partition vector not indexed from 0 on") + if max(md.qmu.partition)>=md.qmu.numberofpartitions: + md.checkmessage("for qmu analysis, partitioning vector cannot go over npart, number of partition areas") + + if not strcmpi(md.cluster.name,'none'): + if not md.settings.waitonlock: + md.checkmessage("waitonlock should be activated when running qmu in parallel mode!") + + return md + # }}} + + def __repr__(self): # {{{ + s =' qmu parameters:\n' + + s+="%s\n" % fielddisplay(self,'isdakota','is qmu analysis activated?') + for i,variable in enumerate(self.variables): + s+=" variables%s: (arrays of each variable class)\n" % \ + string_dim(self.variables,i) + fnames=vars(variable) + maxlen=0 + for fname in fnames: + maxlen=max(maxlen,len(fname)) + + for fname in fnames: + s+="' %-*s: [%ix%i] '%s'\n" % \ + (maxlen+1,fname,size(getattr(variable,fname)),type(getattr(variable,fname))) + + for i,response in enumerate(self.responses): + s+=" responses%s: (arrays of each response class)\n" % \ + string_dim(self.responses,i) + fnames=vars(response) + maxlen=0 + for fname in fnames: + maxlen=max(maxlen,len(fname)) + + for fname in fnames: + s+=" %-*s: [%ix%i] '%s'\n" % \ + (maxlen+1,fname,size(getattr(response,fname)),type(getattr(response,fname))) + + s+="%s\n" % fielddisplay(self,'numberofresponses','number of responses') + + for i,method in enumerate(self.method): + if isinstance(method,'dakota_method'): + s+=" method%s : '%s'\n" % \ + (string_dim(method,i),method.method) + + for i,param in enumerate(self.params): + s+=" params%s: (array of method-independent parameters)\n" % \ + string_dim(self.params,i) + fnames=vars(param) + maxlen=0 + for fname in fnames: + maxlen=max(maxlen,len(fname)) + + for fname in fnames: + s+=" %-*s: %s\n" % \ + (maxlen+1,fname,any2str(getattr(param,fname))) + + for i,result in enumerate(self.results): + s+=" results%s: (information from dakota files)\n" % \ + string_dim(self.results,i) + fnames=vars(result) + maxlen=0 + for fname in fnames: + maxlen=max(maxlen,len(fname)) + + for fname in fnames: + s+=" %-*s: [%ix%i] '%s'\n" % \ + (maxlen+1,fname,size(getattr(result,fname)),type(getattr(result,fname))) + + s+="%s\n" % fielddisplay(self,'partition','user provided mesh partitioning, defaults to metis if not specified') + s+="%s\n" % fielddisplay(self,'numberofpartitions','number of partitions for semi-discrete qmu') + s+="%s\n" % fielddisplay(self,'variabledescriptors','') + s+="%s\n" % fielddisplay(self,'responsedescriptors','') + s+="%s\n" % fielddisplay(self,'method','array of dakota_method class') + s+="%s\n" % fielddisplay(self,'mass_flux_profile_directory','directory for mass flux profiles') + s+="%s\n" % fielddisplay(self,'mass_flux_profiles','list of mass_flux profiles') + s+="%s\n" % fielddisplay(self,'mass_flux_segments','') + s+="%s\n" % fielddisplay(self,'adjacency','') + s+="%s\n" % fielddisplay(self,'vertex_weight','weight applied to each mesh vertex') + + return s + # }}} + + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','isdakota','format','Boolean') + if not self.isdakota: + return + WriteData(fid,'object',self,'fieldname','partition','format','DoubleMat','mattype',2) + WriteData(fid,'object',self,'fieldname','numberofpartitions','format','Integer') + WriteData(fid,'object',self,'fieldname','numberofresponses','format','Integer') + WriteData(fid,'object',self,'fieldname','variabledescriptors','format','StringArray') + WriteData(fid,'object',self,'fieldname','responsedescriptors','format','StringArray') + WriteData(fid,'object',self,'fieldname','mass_flux_segments','format','MatArray') + # }}} + Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/miscellaneous.py (revision 13030) @@ -1,7 +1,17 @@ #module imports from fielddisplay import fielddisplay +from EnumDefinitions import * +from checkfield import * +from WriteData import * class miscellaneous(object): + """ + MISCELLANEOUS class definition + + Usage: + miscellaneous=miscellaneous(); + """ + #properties def __init__(self): # {{{ Properties @@ -13,18 +23,27 @@ self.setdefaultparameters() #}}} - def __repr__(obj): + def __repr__(self): # {{{ Display string=' miscellaneous parameters:' - string="%s\n\n%s"%(string,fielddisplay(obj,'notes','notes in a cell of strings')) - string="%s\n%s"%(string,fielddisplay(obj,'name','model name')) - string="%s\n%s"%(string,fielddisplay(obj,'dummy','empty field to store some data')) + string="%s\n\n%s"%(string,fielddisplay(self,'notes','notes in a cell of strings')) + string="%s\n%s"%(string,fielddisplay(self,'name','model name')) + string="%s\n%s"%(string,fielddisplay(self,'dummy','empty field to store some data')) return string #}}} - def setdefaultparameters(obj): + def setdefaultparameters(self): # {{{setdefaultparameters - return obj + return self #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + md = checkfield(md,'miscellaneous.name','empty',1) + return md + # }}} + + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','name','format','String') + # }}} + Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/private.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/private.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/private.py (revision 13030) @@ -1,7 +1,16 @@ #module imports from fielddisplay import fielddisplay +from EnumDefinitions import * +from checkfield import * class private(object): + """ + PRIVATE class definition + + Usage: + private=private(); + """ + #properties def __init__(self): # {{{ Properties @@ -14,19 +23,23 @@ self.setdefaultparameters() #}}} - def __repr__(obj): + def __repr__(self): # {{{ 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 constructed if bamg is used to mesh the domain')) - string="%s\n%s"%(string,fielddisplay(obj,'solution','type of solution launched')) + string="%s\n%s"%(string,fielddisplay(self,'isconsistent','is model self consistent')) + string="%s\n%s"%(string,fielddisplay(self,'runtimename','name of the run launched')) + string="%s\n%s"%(string,fielddisplay(self,'bamg','structure with mesh properties constructed if bamg is used to mesh the domain')) + string="%s\n%s"%(string,fielddisplay(self,'solution','type of solution launched')) return string #}}} - def setdefaultparameters(obj): + def setdefaultparameters(self): # {{{setdefaultparameters - return obj + return self #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + return md + # }}} + Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/inversion.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/inversion.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/inversion.py (revision 13030) @@ -110,6 +110,7 @@ return self #}}} + def checkconsistency(self,md,solution,analyses): # {{{ #Early return @@ -141,6 +142,7 @@ return md # }}} + def marshall(self,fid): # {{{ WriteData(fid,'object',self,'fieldname','iscontrol','format','Boolean') @@ -183,3 +185,4 @@ WriteData(fid,'data',data,'enum',InversionCostFunctionsEnum(),'format','DoubleMat','mattype',3) WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer') # }}} + Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/ismodelselfconsistent.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/ismodelselfconsistent.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/ismodelselfconsistent.py (revision 13030) @@ -1,4 +1,3 @@ -from AnalysisConfiguration import * from EnumDefinitions import * def AnalysisConfiguration(solutiontype): #{{{ Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/checkfield.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/checkfield.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/consistency/checkfield.py (revision 13030) @@ -111,24 +111,24 @@ #check greater if options.exist('>='): lowerbound=options.getfieldvalue('>=') - if numpy.any(field'): lowerbound=options.getfieldvalue('>') - if numpy.any(field<=lowerbound): + if any(field<=lowerbound): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' should have values above %d" % (fieldname,lowerbound))) #check smaller if options.exist('<='): upperbound=options.getfieldvalue('<=') - if numpy.any(field>upperbound): + if any(field>upperbound): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' should have values below %d" % (fieldname,upperbound))) if options.exist('<'): upperbound=options.getfieldvalue('<') - if numpy.any(field>=upperbound): + if any(field>=upperbound): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' should have values below %d" % (fieldname,upperbound))) @@ -144,10 +144,10 @@ md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' should have only one column as there are md.mesh.numberofvertices lines" % fieldname)) elif numpy.size(field,0)==md.mesh.numberofvertices+1: - if not numpy.all(field[-1,:]==numpy.sort(field[-1,:])): + if not all(field[-1,:]==numpy.sort(field[-1,:])): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns should be sorted chronologically" % fieldname)) - if nump.any(field[-1,0:-1]==field[-1,1:]): + if any(field[-1,0:-1]==field[-1,1:]): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns must not contain duplicate timesteps" % fieldname)) else: Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13030) @@ -68,16 +68,16 @@ md.diagnostic.icefront=pressureload #Create zeros basalforcings and surfaceforcings - if numpy.isnan(md.surfaceforcings.precipitation).all(): + if all(numpy.isnan(md.surfaceforcings.precipitation)): md.surfaceforcings.precipitation=numpy.zeros(md.mesh.numberofvertices) print ' no surfaceforcings.precipitation specified: values set as zero' - if numpy.isnan(md.surfaceforcings.mass_balance).all(): + if all(numpy.isnan(md.surfaceforcings.mass_balance)): md.surfaceforcings.mass_balance=numpy.zeros(md.mesh.numberofvertices) print ' no surfaceforcings.mass_balance specified: values set as zero' - if numpy.isnan(md.basalforcings.melting_rate).all(): + if all(numpy.isnan(md.basalforcings.melting_rate)): md.basalforcings.melting_rate=numpy.zeros(md.mesh.numberofvertices) print ' no basalforcings.melting_rate specified: values set as zero' - if numpy.isnan(md.balancethickness.thickening_rate).all(): + if all(numpy.isnan(md.balancethickness.thickening_rate)): md.balancethickness.thickening_rate=numpy.zeros(md.mesh.numberofvertices) print ' no balancethickness.thickening_rate specified: values set as zero' Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/parameterize.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/parameterize.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/parameterize.py (revision 13030) @@ -1,6 +1,5 @@ import os import datetime -from addnote import * def parameterize(md,parametername): """ @@ -28,7 +27,7 @@ if not md.miscellaneous.name: md.miscellaneous.name=os.path.basename(parametername).split('.')[0] - md=addnote(md,"Model created by using parameter file: '%s' on: %s." % (parametername,datetime.datetime.strftime(datetime.datetime.now(),'%c') )) + md.miscellaneous.notes="Model created by using parameter file: '%s' on: %s." % (parametername,datetime.datetime.strftime(datetime.datetime.now(),'%c')) return md Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/setflowequation.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13029) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13030) @@ -62,11 +62,11 @@ pattynflag[numpy.nonzero(numpy.logical_not(numpy.logical_or(hutterflag,numpy.logical_or(macayealflag,stokesflag))))]=1 #check that each element has at least one flag - if not numpy.any(hutterflag+macayealflag+pattynflag+stokesflag): + if not any(hutterflag+macayealflag+pattynflag+stokesflag): raise TypeError("setflowequation error message: elements type not assigned, must be specified") #check that each element has only one flag - if numpy.any(hutterflag+macayealflag+pattynflag+stokesflag>1): + if any(hutterflag+macayealflag+pattynflag+stokesflag>1): print "setflowequation warning message: some elements have several types, higher order type is used for them" hutterflag[numpy.nonzero(numpy.logical_and(hutterflag,macayealflag))]=0 hutterflag[numpy.nonzero(numpy.logical_and(hutterflag,pattynflag))]=0 @@ -74,11 +74,11 @@ #Check that no pattyn or stokes for 2d mesh if md.mesh.dimension==2: - if numpy.any(numpy.logical_or(stokesflag,pattynflag)): + if any(numpy.logical_or(stokesflag,pattynflag)): raise TypeError("setflowequation error message: stokes and pattyn elements not allowed in 2d mesh, extrude it first") #Stokes can only be used alone for now: - if numpy.any(stokesflag) and numpy.any(hutterflag): + if any(stokesflag) and any(hutterflag): raise TypeError("setflowequation error message: stokes cannot be used with any other model for now, put stokes everywhere") #Initialize node fields @@ -129,14 +129,14 @@ bordernodes2d=numpy.nonzero(numpy.logical_and(nodeonpattyn[1:numnodes2d],nodeonmacayeal[1:numnodes2d])) #Nodes connected to two different types of elements #initialize and fill in penalties structure - if numpy.all(numpy.logical_not(numpy.isnan(bordernodes2d))): + if all(numpy.logical_not(numpy.isnan(bordernodes2d))): penalties=numpy.zeros((0,2)) for i in xrange(1,numlayers): penalties=numpy.concatenate((penalties,numpy.concatenate((bordernodes2d,bordernodes2d+md.mesh.numberofvertices2d*(i)),axis=1)),axis=0) md.diagnostic.vertex_pairing=penalties elif strcmpi(coupling_method,'tiling'): - if numpy.any(macayealflag) and numpy.any(pattynflag): #coupling macayeal pattyn + if any(macayealflag) and any(pattynflag): #coupling macayeal pattyn #Find node at the border nodeonmacayealpattyn[numpy.nonzero(numpy.logical_and(nodeonmacayeal,nodeonpattyn))]=1 #Macayeal elements in contact with this layer become MacAyealPattyn elements @@ -151,8 +151,8 @@ #rule out elements that don't touch the 2 boundaries pos=numpy.nonzero(macayealpattynflag) elist=numpy.zeros(len(pos)) - elist = elist + numpy.any(numpy.sum(nodeonmacayeal[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) - elist = elist - numpy.any(numpy.sum(nodeonpattyn[md.mesh.elements[pos,:].astype(int)-1] ,axis=1),axis=1) + elist = elist + any(numpy.sum(nodeonmacayeal[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) + elist = elist - any(numpy.sum(nodeonpattyn[md.mesh.elements[pos,:].astype(int)-1] ,axis=1),axis=1) pos1=[i for i,item in enumerate(elist) if item==1] macayealflag[pos[pos1]]=1 macayealpattynflag[pos[pos1]]=0 @@ -168,7 +168,7 @@ nodeonmacayealpattyn[:]=0 nodeonmacayealpattyn[md.mesh.elements[numpy.nonzero(macayealpattynflag),:].astype(int)-1]=1 - elif numpy.any(pattynflag) and numpy.any(stokesflag): #coupling pattyn stokes + elif any(pattynflag) and any(stokesflag): #coupling pattyn stokes #Find node at the border nodeonpattynstokes[numpy.nonzero(numpy.logical_and(nodeonpattyn,nodeonstokes))]=1 #Stokes elements in contact with this layer become PattynStokes elements @@ -183,8 +183,8 @@ #rule out elements that don't touch the 2 boundaries pos=numpy.nonzero(pattynstokesflag) elist=numpy.zeros(len(pos)) - elist = elist + numpy.any(numpy.sum(nodeonstokes[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) - elist = elist - numpy.any(numpy.sum(nodeonpattyn[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) + elist = elist + any(numpy.sum(nodeonstokes[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) + elist = elist - any(numpy.sum(nodeonpattyn[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) pos1=[i for i,item in enumerate(elist) if item==1] stokesflag[pos[pos1]]=1 pattynstokesflag[pos[pos1]]=0 @@ -200,7 +200,7 @@ nodeonpattynstokes[:]=0 nodeonpattynstokes[md.mesh.elements[numpy.nonzero(pattynstokesflag),:].astype(int)-1]=1 - elif numpy.any(stokesflag) and numpy.any(macayealflag): + elif any(stokesflag) and any(macayealflag): #Find node at the border nodeonmacayealstokes[numpy.nonzero(numpy.logical_and(nodeonmacayeal,nodeonstokes))]=1 #Stokes elements in contact with this layer become MacAyealStokes elements @@ -215,8 +215,8 @@ #rule out elements that don't touch the 2 boundaries pos=numpy.nonzero(macayealstokesflag) elist=numpy.zeros(len(pos)) - elist = elist + numpy.any(numpy.sum(nodeonmacayeal[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) - elist = elist - numpy.any(numpy.sum(nodeonstokes[md.mesh.elements[pos,:].astype(int)-1] ,axis=1),axis=1) + elist = elist + any(numpy.sum(nodeonmacayeal[md.mesh.elements[pos,:].astype(int)-1],axis=1),axis=1) + elist = elist - any(numpy.sum(nodeonstokes[md.mesh.elements[pos,:].astype(int)-1] ,axis=1),axis=1) pos1=[i for i,item in enumerate(elist) if item==1] macayealflag[pos[pos1]]=1 macayealstokesflag[pos[pos1]]=0 @@ -232,7 +232,7 @@ nodeonmacayealstokes[:]=0 nodeonmacayealstokes[md.mesh.elements[numpy.nonzero(macayealstokesflag),:].astype(int)-1]=1 - elif numpy.any(stokesflag) and numpy.any(hutterflag): + elif any(stokesflag) and any(hutterflag): raise TypeError("type of coupling not supported yet") #Create MacaAyealPattynApproximation where needed @@ -265,9 +265,9 @@ md.flowequation.vertex_equation[pos]=5 pos=numpy.nonzero(nodeonstokes) md.flowequation.vertex_equation[pos]=4 - if numpy.any(stokesflag): + if any(stokesflag): pos=numpy.nonzero(numpy.logical_not(nodeonstokes)) - if not (numpy.any(pattynflag) or numpy.any(macayealflag)): + if not (any(pattynflag) or any(macayealflag)): md.flowequation.vertex_equation[pos]=0 pos=numpy.nonzero(nodeonpattynstokes) md.flowequation.vertex_equation[pos]=7 @@ -275,18 +275,18 @@ md.flowequation.vertex_equation[pos]=6 #figure out solution types - md.flowequation.ishutter=float(numpy.any(md.flowequation.element_equation==1)) - md.flowequation.ismacayealpattyn=float(numpy.any(numpy.logical_or(md.flowequation.element_equation==2,md.flowequation.element_equation==3))) - md.flowequation.isstokes=float(numpy.any(md.flowequation.element_equation==4)) + md.flowequation.ishutter=float(any(md.flowequation.element_equation==1)) + md.flowequation.ismacayealpattyn=float(any(numpy.logical_or(md.flowequation.element_equation==2,md.flowequation.element_equation==3))) + md.flowequation.isstokes=float(any(md.flowequation.element_equation==4)) return md #Check that tiling can work: - if numpy.any(md.flowequation.bordermacayeal) and numpy.any(md.flowequation.borderpattyn) and numpy.any(md.flowequation.borderpattyn + md.flowequation.bordermacayeal !=1): + if any(md.flowequation.bordermacayeal) and any(md.flowequation.borderpattyn) and any(md.flowequation.borderpattyn + md.flowequation.bordermacayeal !=1): raise TypeError("error coupling domain too irregular") - if numpy.any(md.flowequation.bordermacayeal) and numpy.any(md.flowequation.borderstokes) and numpy.any(md.flowequation.borderstokes + md.flowequation.bordermacayeal !=1): + if any(md.flowequation.bordermacayeal) and any(md.flowequation.borderstokes) and any(md.flowequation.borderstokes + md.flowequation.bordermacayeal !=1): raise TypeError("error coupling domain too irregular") - if numpy.any(md.flowequation.borderstokes) and numpy.any(md.flowequation.borderpattyn) and numpy.any(md.flowequation.borderpattyn + md.flowequation.borderstokes !=1): + if any(md.flowequation.borderstokes) and any(md.flowequation.borderpattyn) and any(md.flowequation.borderpattyn + md.flowequation.borderstokes !=1): raise TypeError("error coupling domain too irregular") return md