Index: /issm/trunk-jpl/src/py3/boundaryconditions/PattynSMB.py =================================================================== --- /issm/trunk-jpl/src/py3/boundaryconditions/PattynSMB.py (revision 23669) +++ /issm/trunk-jpl/src/py3/boundaryconditions/PattynSMB.py (revision 23670) @@ -1,4 +1,4 @@ import os -import numpy as np +import numpy as np def PattynSMB(md,Tf): """ Index: /issm/trunk-jpl/src/py3/boundaryconditions/SetIceSheetBC.py =================================================================== --- /issm/trunk-jpl/src/py3/boundaryconditions/SetIceSheetBC.py (revision 23669) +++ /issm/trunk-jpl/src/py3/boundaryconditions/SetIceSheetBC.py (revision 23670) @@ -1,4 +1,4 @@ import os -import numpy +import numpy as np from ContourToMesh import ContourToMesh @@ -14,16 +14,16 @@ #node on Dirichlet - pos=numpy.nonzero(md.mesh.vertexonboundary) - md.stressbalance.spcvx=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvy=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvz=float('nan')*numpy.ones(md.mesh.numberofvertices) + pos=np.nonzero(md.mesh.vertexonboundary) + md.stressbalance.spcvx=float('nan')*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=float('nan')*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=float('nan')*np.ones((md.mesh.numberofvertices)) md.stressbalance.spcvx[pos]=0 md.stressbalance.spcvy[pos]=0 md.stressbalance.spcvz[pos]=0 - md.stressbalance.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) - md.stressbalance.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3)) + md.stressbalance.referential=float('nan')*np.ones((md.mesh.numberofvertices,6)) + md.stressbalance.loadingforce=0*np.ones((md.mesh.numberofvertices,3)) #Dirichlet Values - if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: + if isinstance(md.inversion.vx_obs,np.ndarray) and np.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,np.ndarray) and np.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: print(" boundary conditions for stressbalance model: spc set as observed velocities") md.stressbalance.spcvx[pos]=md.inversion.vx_obs[pos] @@ -39,18 +39,18 @@ #Deal with other boundary conditions - if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): - md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(md.balancethickness.thickening_rate)): + md.balancethickness.thickening_rate=np.zeros((md.mesh.numberofvertices)) print(" no balancethickness.thickening_rate specified: values set as zero") - md.masstransport.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.damage.spcdamage=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.masstransport.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.balancethickness.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.damage.spcdamage=float('nan')*np.ones((md.mesh.numberofvertices)) - if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: - md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + if isinstance(md.initialization.temperature,np.ndarray) and np.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: + md.thermal.spctemperature=float('nan')*np.ones((md.mesh.numberofvertices)) if hasattr(md.mesh,'vertexonsurface'): - pos=numpy.nonzero(md.mesh.vertexonsurface)[0] + pos=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface - if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux)==md.mesh.numberofvertices: - md.basalforcings.geothermalflux=50.*10**-3*numpy.ones((md.mesh.numberofvertices,1)) #50 mW/m^2 + if not isinstance(md.basalforcings.geothermalflux,np.ndarray) or not np.size(md.basalforcings.geothermalflux)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=50.*10**-3*np.ones((md.mesh.numberofvertices)) #50 mW/m^2 else: print(" no thermal boundary conditions created: no observed temperature found") Index: /issm/trunk-jpl/src/py3/boundaryconditions/SetIceShelfBC.py =================================================================== --- /issm/trunk-jpl/src/py3/boundaryconditions/SetIceShelfBC.py (revision 23669) +++ /issm/trunk-jpl/src/py3/boundaryconditions/SetIceShelfBC.py (revision 23670) @@ -1,4 +1,4 @@ import os -import numpy +import numpy as np from ContourToMesh import ContourToMesh import MatlabFuncs as m @@ -26,19 +26,19 @@ if not os.path.exists(icefrontfile): raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) - [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) - nodeonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)) + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) + nodeonicefront=np.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)) else: - nodeonicefront=numpy.zeros((md.mesh.numberofvertices),bool) + nodeonicefront=np.zeros((md.mesh.numberofvertices),bool) # pos=find(md.mesh.vertexonboundary & ~nodeonicefront); - pos=numpy.nonzero(numpy.logical_and(md.mesh.vertexonboundary,numpy.logical_not(nodeonicefront)))[0] - md.stressbalance.spcvx=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvy=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvz=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) - md.stressbalance.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3)) + pos=np.nonzero(np.logical_and(md.mesh.vertexonboundary,np.logical_not(nodeonicefront)))[0] + md.stressbalance.spcvx=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.spcvy=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.spcvz=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.referential=float('nan')*np.ones((md.mesh.numberofvertices,6)) + md.stressbalance.loadingforce=0*np.ones((md.mesh.numberofvertices,3)) #Icefront position - pos=numpy.nonzero(nodeonicefront)[0] + pos=np.nonzero(nodeonicefront)[0] md.mask.ice_levelset[pos]=0 @@ -53,10 +53,10 @@ values=md.mask.ice_levelset[md.mesh.segments[:,0:-1]-1] segmentsfront=1-values - numpy.sum(segmentsfront,axis=1)!=numbernodesfront - segments=numpy.nonzero(numpy.sum(segmentsfront,axis=1)!=numbernodesfront)[0] + np.sum(segmentsfront,axis=1)!=numbernodesfront + segments=np.nonzero(np.sum(segmentsfront,axis=1)!=numbernodesfront)[0] #Find all nodes for these segments and spc them pos=md.mesh.segments[segments,0:-1]-1 else: - pos=numpy.nonzero(md.mesh.vertexonboundary)[0] + pos=np.nonzero(md.mesh.vertexonboundary)[0] md.stressbalance.spcvx[pos]=0 md.stressbalance.spcvy[pos]=0 @@ -64,10 +64,10 @@ #Dirichlet Values - if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: + if isinstance(md.inversion.vx_obs,np.ndarray) and np.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,np.ndarray) and np.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: #reshape to rank-2 if necessary to match spc arrays - if numpy.ndim(md.inversion.vx_obs)==1: - md.inversion.vx_obs=md.inversion.vx_obs.reshape(-1,1) - if numpy.ndim(md.inversion.vy_obs)==1: - md.inversion.vy_obs=md.inversion.vy_obs.reshape(-1,1) + if np.ndim(md.inversion.vx_obs)==1: + md.inversion.vx_obs=md.inversion.vx_obs.reshape(-1,) + if np.ndim(md.inversion.vy_obs)==1: + md.inversion.vy_obs=md.inversion.vy_obs.reshape(-1,) print(" boundary conditions for stressbalance model: spc set as observed velocities") md.stressbalance.spcvx[pos]=md.inversion.vx_obs[pos] @@ -81,18 +81,18 @@ #Deal with other boundary conditions - if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): - md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(md.balancethickness.thickening_rate)): + md.balancethickness.thickening_rate=np.zeros((md.mesh.numberofvertices)) print(" no balancethickness.thickening_rate specified: values set as zero") - md.masstransport.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.damage.spcdamage=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.masstransport.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.balancethickness.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.damage.spcdamage=float('nan')*np.ones((md.mesh.numberofvertices)) - if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: - md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + if isinstance(md.initialization.temperature,np.ndarray) and np.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: + md.thermal.spctemperature=float('nan')*np.ones((md.mesh.numberofvertices)) if hasattr(md.mesh,'vertexonsurface'): - pos=numpy.nonzero(md.mesh.vertexonsurface)[0] + pos=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface - if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: - md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) + if not isinstance(md.basalforcings.geothermalflux,np.ndarray) or not np.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=np.zeros((md.mesh.numberofvertices)) else: print(" no thermal boundary conditions created: no observed temperature found") Index: /issm/trunk-jpl/src/py3/boundaryconditions/SetMarineIceSheetBC.py =================================================================== --- /issm/trunk-jpl/src/py3/boundaryconditions/SetMarineIceSheetBC.py (revision 23669) +++ /issm/trunk-jpl/src/py3/boundaryconditions/SetMarineIceSheetBC.py (revision 23670) @@ -1,4 +1,4 @@ import os -import numpy +import numpy as np from ContourToMesh import ContourToMesh import MatlabFuncs as m @@ -28,26 +28,26 @@ if not os.path.exists(icefrontfile): raise IOError("SetMarineIceSheetBC error message: ice front file '%s' not found." % icefrontfile) - [incontour,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) - vertexonicefront=numpy.logical_and(md.mesh.vertexonboundary,incontour.reshape(-1)) + incontour=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) + vertexonicefront=np.logical_and(md.mesh.vertexonboundary,incontour.reshape(-1)) else: #Guess where the ice front is - vertexonfloatingice=numpy.zeros((md.mesh.numberofvertices,1)) - pos=numpy.nonzero(numpy.sum(md.mask.groundedice_levelset[md.mesh.elements-1]<0.,axis=1) >0.)[0] + vertexonfloatingice=np.zeros((md.mesh.numberofvertices)) + pos=np.nonzero(np.sum(md.mask.groundedice_levelset[md.mesh.elements-1]<0.,axis=1) >0.)[0] vertexonfloatingice[md.mesh.elements[pos].astype(int)-1]=1. - vertexonicefront=numpy.logical_and(numpy.reshape(md.mesh.vertexonboundary,(-1,1)),vertexonfloatingice>0.) + vertexonicefront=np.logical_and(np.reshape(md.mesh.vertexonboundary,(-1,)),vertexonfloatingice>0.) # pos=find(md.mesh.vertexonboundary & ~vertexonicefront); - pos=numpy.nonzero(numpy.logical_and(md.mesh.vertexonboundary,numpy.logical_not(vertexonicefront)))[0] - if not numpy.size(pos): + pos=np.nonzero(np.logical_and(md.mesh.vertexonboundary,np.logical_not(vertexonicefront)))[0] + if not np.size(pos): print("SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually.") - md.stressbalance.spcvx=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvy=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.spcvz=float('nan')*numpy.ones(md.mesh.numberofvertices) - md.stressbalance.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) - md.stressbalance.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3)) + md.stressbalance.spcvx=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.spcvy=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.spcvz=float('nan')*np.ones(md.mesh.numberofvertices) + md.stressbalance.referential=float('nan')*np.ones((md.mesh.numberofvertices,6)) + md.stressbalance.loadingforce=0*np.ones((md.mesh.numberofvertices,3)) #Position of ice front - pos=numpy.nonzero(vertexonicefront)[0] + pos=np.nonzero(vertexonicefront)[0] md.mask.ice_levelset[pos]=0 @@ -62,10 +62,10 @@ values=md.mask.ice_levelset[md.mesh.segments[:,0:-1]-1] segmentsfront=1-values - numpy.sum(segmentsfront,axis=1)!=numbernodesfront - segments=numpy.nonzero(numpy.sum(segmentsfront,axis=1)!=numbernodesfront)[0] + np.sum(segmentsfront,axis=1)!=numbernodesfront + segments=np.nonzero(np.sum(segmentsfront,axis=1)!=numbernodesfront)[0] #Find all nodes for these segments and spc them pos=md.mesh.segments[segments,0:-1]-1 else: - pos=numpy.nonzero(md.mesh.vertexonboundary)[0] + pos=np.nonzero(md.mesh.vertexonboundary)[0] md.stressbalance.spcvx[pos]=0 md.stressbalance.spcvy[pos]=0 @@ -73,5 +73,5 @@ #Dirichlet Values - if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: + if isinstance(md.inversion.vx_obs,np.ndarray) and np.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,np.ndarray) and np.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: print(" boundary conditions for stressbalance model: spc set as observed velocities") md.stressbalance.spcvx[pos]=md.inversion.vx_obs[pos] @@ -80,6 +80,6 @@ print(" boundary conditions for stressbalance model: spc set as zero") - md.hydrology.spcwatercolumn=numpy.zeros((md.mesh.numberofvertices,2)) - pos=numpy.nonzero(md.mesh.vertexonboundary)[0] + md.hydrology.spcwatercolumn=np.zeros((md.mesh.numberofvertices,2)) + pos=np.nonzero(md.mesh.vertexonboundary)[0] md.hydrology.spcwatercolumn[pos,0]=1 @@ -89,20 +89,20 @@ #Deal with other boundary conditions - if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): - md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(md.balancethickness.thickening_rate)): + md.balancethickness.thickening_rate=np.zeros((md.mesh.numberofvertices)) print(" no balancethickness.thickening_rate specified: values set as zero") - md.masstransport.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) - md.damage.spcdamage=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.masstransport.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.balancethickness.spcthickness=float('nan')*np.ones((md.mesh.numberofvertices)) + md.damage.spcdamage=float('nan')*np.ones((md.mesh.numberofvertices)) - if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: - md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + if isinstance(md.initialization.temperature,np.ndarray) and np.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: + md.thermal.spctemperature=float('nan')*np.ones((md.mesh.numberofvertices)) if hasattr(md.mesh,'vertexonsurface'): - pos=numpy.nonzero(md.mesh.vertexonsurface)[0] + pos=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface - if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: - md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) - md.basalforcings.geothermalflux[numpy.nonzero(md.mask.groundedice_levelset>0.)]=50.*10.**-3 #50mW/m2 + if not isinstance(md.basalforcings.geothermalflux,np.ndarray) or not np.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=np.zeros((md.mesh.numberofvertices)) + md.basalforcings.geothermalflux[np.nonzero(md.mask.groundedice_levelset>0.)]=50.*10.**-3 #50mW/m2 else: print(" no thermal boundary conditions created: no observed temperature found") Index: /issm/trunk-jpl/src/py3/classes/SMBcomponents.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBcomponents.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBcomponents.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import * from project3d import * @@ -39,14 +38,14 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.accumulation)): - self.accumulation=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.accumulation)): + self.accumulation=np.zeros((md.mesh.numberofvertices)) print(" no SMB.accumulation specified: values set as zero") - if numpy.all(numpy.isnan(self.runoff)): - self.runoff=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.runoff)): + self.runoff=np.zeros((md.mesh.numberofvertices)) print(" no SMB.runoff specified: values set as zero") - if numpy.all(numpy.isnan(self.evaporation)): - self.evaporation=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.evaporation)): + self.evaporation=np.zeros((md.mesh.numberofvertices)) print(" no SMB.evaporation specified: values set as zero") @@ -55,20 +54,20 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.accumulation','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.accumulation','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.runoff','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.runoff','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.evaporation','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.evaporation','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) @@ -77,12 +76,12 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',SmbEnum(),'data',SMBcomponentsEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','smb','fieldname','accumulation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','runoff','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','evaporation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) + WriteData(fid,prefix,'name','md.smb.model','data',2,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accumulation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoff','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','evaporation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) #process requested outputs @@ -92,5 +91,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/SMBd18opdd.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBd18opdd.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBd18opdd.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -21,12 +20,20 @@ self.rlapslgm = 0. self.dpermil = 0. + self.f = 0. self.Tdiff = float('NaN') self.sealev = float('NaN') self.ismungsm = 0 self.isd18opd = 0 + self.issetpddfac = 0 + self.istemperaturescaled = 0 + self.isprecipscaled = 0 self.delta18o = float('NaN') self.delta18o_surface = float('NaN') self.temperatures_presentday = float('NaN') self.precipitations_presentday = float('NaN') + self.temperatures_reconstructed = float('NaN') + self.precipitations_reconstructed = float('NaN') + self.pddfac_snow = float('NaN') + self.pddfac_ice = float('NaN') #set defaults @@ -38,4 +45,5 @@ string="%s\n%s"%(string,fielddisplay(self,'isd18opd','is delta18o parametrisation from present day temperature and precipitation activated (0 or 1, default is 0)')) + string="%s\n%s"%(string,fielddisplay(self,'issetpddfac','is user passing in defined pdd factors at each vertex (0 or 1, default is 0)')) string="%s\n%s"%(string,fielddisplay(self,'desfac','desertification elevation factor (between 0 and 1, default is 0.5) [m]')) string="%s\n%s"%(string,fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]')) @@ -45,6 +53,20 @@ string="%s\n%s"%(string,fielddisplay(self,'temperatures_presentday','monthly present day surface temperatures [K], required if delta18o/mungsm is activated')) string="%s\n%s"%(string,fielddisplay(self,'precipitations_presentday','monthly surface precipitation [m/yr water eq], required if delta18o or mungsm is activated')) + string="%s\n%s"%(string,fielddisplay(self,'istemperaturescaled','if delta18o parametrisation from present day temperature and precipitation is activated, is temperature scaled to delta18o value? (0 or 1, default is 1)')) + string="%s\n%s"%(string,fielddisplay(self,'isprecipscaled','if delta18o parametrisation from present day temperature and precipitation is activated, is precipitation scaled to delta18o value? (0 or 1, default is 1)')) + + if self.istemperaturescaled==0: + string="%s\n%s"%(string,fielddisplay(self,'temperatures_reconstructed','monthly historical surface temperatures [K], required if delta18o/mungsm/d18opd is activated and istemperaturescaled is not activated')) + + if self.isprecipscaled==0: + string="%s\n%s"%(string,fielddisplay(self,'precipitations_reconstructed','monthly historical precipitation [m/yr water eq], required if delta18o/mungsm/d18opd is activated and isprecipscaled is not activated')) + string="%s\n%s"%(string,fielddisplay(self,'delta18o','delta18o [per mil], required if pdd is activated and delta18o activated')) string="%s\n%s"%(string,fielddisplay(self,'dpermil','degree per mil, required if d18opd is activated')) + string="%s\n%s"%(string,fielddisplay(self,'f','precip/temperature scaling factor, required if d18opd is activated')) + + if self.issetpddfac==1: + string="%s\n%s"%(string,fielddisplay(self,'pddfac_snow','Pdd factor for snow, at each vertex [mm ice equiv/day/degree C]')) + string="%s\n%s"%(string,fielddisplay(self,'pddfac_ice','Pdd factor for ice, at each vertex [mm ice equiv/day/degree C]')) string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) @@ -55,4 +77,9 @@ if self.isd18opd: self.temperatures_presentday=project3d(md,'vector',self.temperatures_presentday,'type','node') if self.isd18opd: self.precipitations_presentday=project3d(md,'vector',self.precipitations_presentday,'type','node') + if self.istemperaturescaled==0: self.temperatures_reconstructed=project3d(md,'vector',self.temperatures_reconstructed,'type','node') + if self.isprecipscaled==0: self.temperatures_reconstructed=project3d(md,'vector',self.precipitations_reconstructed,'type','node') + if self.isd18opd: self.precipitations_presentday=project3d(md,'vector',self.precipitations_presentday,'type','node') + if self.issetpddfac: self.pddfac_snow=project3d(md,'vector',self.pddfac_snow,'type','node') + if self.issetpddfac: self.pddfac_ice=project3d(md,'vector',self.pddfac_ice,'type','node') self.s0p=project3d(md,'vector',self.s0p,'type','node') self.s0t=project3d(md,'vector',self.s0t,'type','node') @@ -65,10 +92,10 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.s0p)): - self.s0p=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.s0p)): + self.s0p=np.zeros((md.mesh.numberofvertices)) print(" no SMBd18opdd.s0p specified: values set as zero") - if numpy.all(numpy.isnan(self.s0t)): - self.s0t=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.s0t)): + self.s0t=np.zeros((md.mesh.numberofvertices)) print(" no SMBd18opdd.s0t specified: values set as zero") @@ -80,52 +107,90 @@ self.ismungsm = 0 self.isd18opd = 1 + self.istemperaturescaled = 1 + self.isprecipscaled = 1 self.desfac = 0.5 self.rlaps = 6.5 self.rlapslgm = 6.5 self.dpermil = 2.4 - + self.f = 0.169 + self.issetpddfac = 0 return self #}}} def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',[1]) - md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) - md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',[1]) md = checkfield(md,'fieldname','smb.rlapslgm','>=',0,'numel',[1]) if self.isd18opd: + lent=float(np.size(self.temperatures_presentday,1)) + lenp=float(np.size(self.precipitations_presentday,1)) + multt=np.ceil(lent/12.)*12. + multp=np.ceil(lenp/12.)*12. md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) + + if self.istemperaturescaled==0: + lent=float(np.size(self.temperatures_reconstructed,1)) + multt=np.ceil(lent/12.)*12. + md = checkfield(md,'fieldname','smb.temperatures_reconstructed','size',[md.mesh.numberofvertices+1,multt],'NaN',1,'Inf',1,'timeseries',1) + + if self.isprecipscaled==0: + lenp=float(np.size(self.precipitations_reconstructed,1)) + multp=np.ceil(lent/12.)*12. + md = checkfield(md,'fieldname','smb.precipitations_reconstructed','size',[md.mesh.numberofvertices+1,multt],'NaN',1,'Inf',1,'timeseries',1) + + md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) md = checkfield(md,'fieldname','smb.dpermil','>=',0,'numel',[1]) - + md = checkfield(md,'fieldname','smb.f','>=',0,'numel',[1]) + + if self.issetpddfac: + md = checkfield(md,'fieldname','smb.pddfac_snow','>=',0,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.pddfac_ice','>=',0,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) return md # }}} - def marshall(self,md,fid): # {{{ - - yts=365.0*24.0*3600.0 - - WriteData(fid,'enum',SmbEnum(),'data',SMBd18opddEnum(),'format','Integer') - - WriteData(fid,'object',self,'class','smb','fieldname','ismungsm','format','Boolean') - WriteData(fid,'object',self,'class','smb','fieldname','isd18opd','format','Boolean') - WriteData(fid,'object',self,'class','smb','fieldname','desfac','format','Double') - WriteData(fid,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); - WriteData(fid,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); - WriteData(fid,'object',self,'class','smb','fieldname','rlaps','format','Double') - WriteData(fid,'object',self,'class','smb','fieldname','rlapslgm','format','Double') - WriteData(fid,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2) + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts + + WriteData(fid,prefix,'name','md.smb.model','data',5,'format','Integer') + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','ismungsm','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','isd18opd','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','issetpddfac','format','Boolean'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlapslgm','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) if self.isd18opd: - WriteData(fid,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','dpermil','format','Double') - + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','istemperaturescaled','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','isprecipscaled','format','Boolean') + + if self.istemperaturescaled==0: + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_reconstructed','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + + if self.isprecipscaled==0: + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_reconstructed','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + + WriteData(fid,prefix,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','dpermil','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','f','format','Double') + + if self.issetpddfac: + WriteData(fid,prefix,'object',self,'class','smb','fieldname','pddfac_snow','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','pddfac_ice','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + #process requested outputs outputs = self.requested_outputs @@ -134,5 +199,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/SMBforcing.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBforcing.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBforcing.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -34,6 +33,6 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.mass_balance)): - self.mass_balance=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.mass_balance)): + self.mass_balance=np.zeros((md.mesh.numberofvertices)) print(" no SMBforcing.mass_balance specified: values set as zero") @@ -42,8 +41,8 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.mass_balance','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.mass_balance','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) @@ -51,10 +50,11 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',SmbEnum(),'data',SMBforcingEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) + WriteData(fid,prefix,'name','md.smb.model','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + #WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); #process requested outputs @@ -64,5 +64,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/SMBgradients.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBgradients.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBgradients.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -48,5 +47,5 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.href','timeseries',1,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','smb.smbref','timeseries',1,'NaN',1,'Inf',1) @@ -57,13 +56,13 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',SmbEnum(),'data',SMBgradientsEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','smb','fieldname','href','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','smbref','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) + WriteData(fid,prefix,'name','md.smb.model','data',6,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','href','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','smbref','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) #process requested outputs @@ -73,5 +72,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/SMBmeltcomponents.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBmeltcomponents.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBmeltcomponents.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import * from project3d import * @@ -30,8 +29,8 @@ def extrude(self,md): # {{{ - self.mass_balance=project3d(md,'vector',self.accumulation,'type','node'); - self.mass_balance=project3d(md,'vector',self.evaporation,'type','node'); - self.mass_balance=project3d(md,'vector',self.melt,'type','node'); - self.mass_balance=project3d(md,'vector',self.refreeze,'type','node'); + self.accumulation=project3d(md,'vector',self.accumulation,'type','node'); + self.evaporation=project3d(md,'vector',self.evaporation,'type','node'); + self.melt=project3d(md,'vector',self.melt,'type','node'); + self.refreeze=project3d(md,'vector',self.refreeze,'type','node'); return self #}}} @@ -41,18 +40,18 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.accumulation)): - self.accumulation=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.accumulation)): + self.accumulation=np.zeros((md.mesh.numberofvertices)) print(" no SMB.accumulation specified: values set as zero") - if numpy.all(numpy.isnan(self.evaporation)): - self.evaporation=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.evaporation)): + self.evaporation=np.zeros((md.mesh.numberofvertices)) print(" no SMB.evaporation specified: values set as zero") - if numpy.all(numpy.isnan(self.melt)): - self.melt=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.melt)): + self.melt=np.zeros((md.mesh.numberofvertices)) print(" no SMB.melt specified: values set as zero") - if numpy.all(numpy.isnan(self.refreeze)): - self.refreeze=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.refreeze)): + self.refreeze=np.zeros((md.mesh.numberofvertices)) print(" no SMB.refreeze specified: values set as zero") @@ -61,26 +60,26 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.accumulation','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.accumulation','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.melt','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.melt','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.refreeze','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.refreeze','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.evaporation','timeseries',1,'NaN',1,'Inf',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','smb.evaporation','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) @@ -88,14 +87,14 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',SmbEnum(),'data',SMBmeltcomponentsEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','smb','fieldname','accumulation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','evaporation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','melt','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','refreeze','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - + WriteData(fid,prefix,'name','md.smb.model','data',3,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accumulation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','evaporation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','melt','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','refreeze','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + #process requested outputs outputs = self.requested_outputs @@ -104,5 +103,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/SMBpdd.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/SMBpdd.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/SMBpdd.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -27,4 +26,5 @@ self.isdelta18o = 0 self.ismungsm = 0 + self.issetpddfac = 0 self.delta18o = float('NaN') self.delta18o_surface = float('NaN') @@ -95,10 +95,10 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.s0p)): - self.s0p=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.s0p)): + self.s0p=np.zeros((md.mesh.numberofvertices)) print(" no SMBpdd.s0p specified: values set as zero") - if numpy.all(numpy.isnan(self.s0t)): - self.s0t=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.s0t)): + self.s0t=np.zeros((md.mesh.numberofvertices)) print(" no SMBpdd.s0t specified: values set as zero") @@ -118,8 +118,8 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',[1]) - md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) - md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',[1]) md = checkfield(md,'fieldname','smb.rlapslgm','>=',0,'numel',[1]) @@ -129,12 +129,12 @@ md = checkfield(md,'fieldname','smb.precipitation','NaN',1,'Inf',1,'timeseries',1) elif self.isdelta18o: - md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) - md = checkfield(md,'fieldname','smb.delta18o_surface','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.delta18o_surface','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','smb.temperatures_lgm','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','smb.precipitations_lgm','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','smb.Tdiff','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) - md = checkfield(md,'fieldname','smb.sealev','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.Tdiff','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.sealev','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) elif self.ismungsm: md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) @@ -142,45 +142,46 @@ md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','smb.precipitations_lgm','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','smb.Pfac','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) - md = checkfield(md,'fieldname','smb.Tdiff','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) - md = checkfield(md,'fieldname','smb.sealev','NaN',1,'Inf',1,'size',[2,numpy.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.Pfac','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.Tdiff','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.sealev','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) return md #}}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',SmbEnum(),'data',SMBpddEnum(),'format','Integer') + WriteData(fid,prefix,'name','md.smb.model','data',4,'format','Integer') - WriteData(fid,'object',self,'class','smb','fieldname','isdelta18o','format','Boolean') - WriteData(fid,'object',self,'class','smb','fieldname','ismungsm','format','Boolean') - WriteData(fid,'object',self,'class','smb','fieldname','desfac','format','Double') - WriteData(fid,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); - WriteData(fid,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); - WriteData(fid,'object',self,'class','smb','fieldname','rlaps','format','Double') - WriteData(fid,'object',self,'class','smb','fieldname','rlapslgm','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','isdelta18o','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','ismungsm','format','Boolean') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','issetpddfac','format','Boolean'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlapslgm','format','Double') if (self.isdelta18o==0 and self.ismungsm==0): - WriteData(fid,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) elif self.isdelta18o: - WriteData(fid,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','temperatures_lgm','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitations_lgm','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','delta18o_surface','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_lgm','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_lgm','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','delta18o_surface','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) elif self.ismungsm: - WriteData(fid,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','temperatures_lgm','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','precipitations_lgm','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','smb','fieldname','Pfac','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2) - WriteData(fid,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_presentday','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperatures_lgm','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_presentday','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitations_lgm','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','Pfac','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','Tdiff','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','sealev','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) #process requested outputs @@ -190,5 +191,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SmbRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/autodiff.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/autodiff.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/autodiff.py (revision 23670) @@ -1,7 +1,6 @@ -import numpy +import numpy as np from dependent import dependent from independent import independent from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -15,14 +14,15 @@ """ def __init__(self,*args): # {{{ - self.isautodiff = False - self.dependents = [] - self.independents = [] - self.driver = 'fos_forward' - self.obufsize = float('NaN') - self.lbufsize = float('NaN') - self.cbufsize = float('NaN') - self.tbufsize = float('NaN') - self.gcTriggerMaxSize = float('NaN') - self.gcTriggerRatio = float('NaN') + self.isautodiff = False + self.dependents = [] + self.independents = [] + self.driver = 'fos_forward' + self.obufsize = float('NaN') + self.lbufsize = float('NaN') + self.cbufsize = float('NaN') + self.tbufsize = float('NaN') + self.gcTriggerMaxSize = float('NaN') + self.gcTriggerRatio = float('NaN') + self.tapeAlloc = float('NaN') if not len(args): self.setdefaultparameters() @@ -30,7 +30,7 @@ raise RuntimeError("constructor not supported") # }}} + def __repr__(self): # {{{ s =" automatic differentiation parameters:\n" - s+="%s\n" % fielddisplay(self,'isautodiff',"indicates if the automatic differentiation is activated") s+="%s\n" % fielddisplay(self,'dependents',"list of dependent variables") @@ -43,23 +43,25 @@ s+="%s\n" % fielddisplay(self,'gcTriggerRatio',"free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio") s+="%s\n" % fielddisplay(self,'gcTriggerMaxSize',"free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize)") + s+="%s\n" % fielddisplay(self,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); return s # }}} + def setdefaultparameters(self): # {{{ - - self.obufsize = 524288 - self.lbufsize = 524288 - self.cbufsize = 524288 - self.tbufsize = 524288 - self.gcTriggerRatio=2.0 - self.gcTriggerMaxSize=65536 + self.obufsize = 524288 + self.lbufsize = 524288 + self.cbufsize = 524288 + self.tbufsize = 524288 + self.gcTriggerRatio = 2.0 + self.gcTriggerMaxSize = 65536 + self.tapeAlloc = 15000000; return self # }}} + def checkconsistency(self,md,solution,analyses): # {{{ - - #Early return + #Early return if not self.isautodiff: - return md - + return md + md = checkfield(md,'fieldname','autodiff.obufsize','>=',524288) md = checkfield(md,'fieldname','autodiff.lbufsize','>=',524288) @@ -67,10 +69,11 @@ md = checkfield(md,'fieldname','autodiff.tbufsize','>=',524288) md = checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',2.0) - md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',2000000) + md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536) + md = checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); #Driver value: md = checkfield(md,'fieldname','autodiff.driver','values',['fos_forward','fov_forward','fov_forward_all','fos_reverse','fov_reverse','fov_reverse_all']) - #go through our dependents and independents and check consistency: + #go through our dependents and independents and check consistency: for dep in self.dependents: dep.checkconsistency(md,solution,analyses) @@ -80,54 +83,56 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','isautodiff','format','Boolean') - WriteData(fid,'object',self,'fieldname','driver','format','String') + + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','isautodiff','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','driver','format','String') #early return if not self.isautodiff: - WriteData(fid,'data',False,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean') - WriteData(fid,'data',False,'enum',AutodiffKeepEnum(),'format','Boolean') + WriteData(fid,prefix,'data',False,'name','md.autodiff.mass_flux_segments_present','format','Boolean') + WriteData(fid,prefix,'data',False,'name','md.autodiff.keep','format','Boolean') return - + #buffer sizes {{{ - WriteData(fid,'object',self,'fieldname','obufsize','format','Double'); - WriteData(fid,'object',self,'fieldname','lbufsize','format','Double'); - WriteData(fid,'object',self,'fieldname','cbufsize','format','Double'); - WriteData(fid,'object',self,'fieldname','tbufsize','format','Double'); - WriteData(fid,'object',self,'fieldname','gcTriggerRatio','format','Double'); - WriteData(fid,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','obufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','lbufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','cbufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','tbufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerRatio','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','tapeAlloc','format','Integer'); #}}} #process dependent variables {{{ num_dependent_objects=len(self.dependents) - WriteData(fid,'data',num_dependent_objects,'enum',AutodiffNumDependentObjectsEnum(),'format','Integer') + WriteData(fid,prefix,'data',num_dependent_objects,'name','md.autodiff.num_dependent_objects','format','Integer') if num_dependent_objects: names=[] - types=numpy.zeros(num_dependent_objects) - indices=numpy.zeros(num_dependent_objects) + types=np.zeros(num_dependent_objects) + indices=np.zeros(num_dependent_objects) for i,dep in enumerate(self.dependents): - names[i]=dep.name + names.append(dep.name) types[i]=dep.typetoscalar() indices[i]=dep.index - WriteData(fid,'data',names,'enum',AutodiffDependentObjectNamesEnum(),'format','StringArray') - WriteData(fid,'data',types,'enum',AutodiffDependentObjectTypesEnum(),'format','IntMat','mattype',3) - WriteData(fid,'data',indices,'enum',AutodiffDependentObjectIndicesEnum(),'format','IntMat','mattype',3) + WriteData(fid,prefix,'data',names,'name','md.autodiff.dependent_object_names','format','StringArray') + WriteData(fid,prefix,'data',types,'name','md.autodiff.dependent_object_types','format','IntMat','mattype',3) + WriteData(fid,prefix,'data',indices,'name','md.autodiff.dependent_object_indices','format','IntMat','mattype',3) #}}} #process independent variables {{{ num_independent_objects=len(self.independents) - WriteData(fid,'data',num_independent_objects,'enum',AutodiffNumIndependentObjectsEnum(),'format','Integer') + WriteData(fid,prefix,'data',num_independent_objects,'name','md.autodiff.num_independent_objects','format','Integer') if num_independent_objects: - names=numpy.zeros(num_independent_objects) - types=numpy.zeros(num_independent_objects) + names=[None] * num_independent_objects + types=np.zeros(num_independent_objects) for i,indep in enumerate(self.independents): - names[i]=StringToEnum(indep.name)[0] + names[i]=indep.name types[i]=indep.typetoscalar() - WriteData(fid,'data',names,'enum',AutodiffIndependentObjectNamesEnum(),'format','IntMat','mattype',3) - WriteData(fid,'data',types,'enum',AutodiffIndependentObjectTypesEnum(),'format','IntMat','mattype',3) + WriteData(fid,prefix,'data',names,'name','md.autodiff.independent_object_names','format','StringArray') + WriteData(fid,prefix,'data',types,'name','md.autodiff.independent_object_types','format','IntMat','mattype',3) #}}} #if driver is fos_forward, build index: {{{ @@ -136,5 +141,5 @@ for indep in self.independents: - if not numpy.isnan(indep.fos_forward_index): + if not np.isnan(indep.fos_forward_index): index+=indep.fos_forward_index break @@ -146,5 +151,5 @@ index-=1 #get c-index numbering going - WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer') + WriteData(fid,prefix,'data',index,'name','md.autodiff.fos_forward_index','format','Integer') #}}} #if driver is fos_reverse, build index: {{{ @@ -153,5 +158,5 @@ for dep in self.dependents: - if not numpy.isnan(dep.fos_reverse_index): + if not np.isnan(dep.fos_reverse_index): index+=dep.fos_reverse_index break @@ -163,5 +168,5 @@ index-=1 #get c-index numbering going - WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer') + WriteData(fid,prefix,'data',index,'name','md.autodiff.fos_reverse_index','format','Integer') #}}} #if driver is fov_forward, build indices: {{{ @@ -180,5 +185,5 @@ indices-=1 #get c-indices numbering going - WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum(),'format','IntMat','mattype',3) + WriteData(fid,prefix,'data',indices,'name','md.autodiff.fov_forward_indices','format','IntMat','mattype',3) #}}} #deal with mass fluxes: {{{ @@ -186,22 +191,22 @@ if mass_flux_segments: - WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum(),'format','MatArray') + WriteData(fid,prefix,'data',mass_flux_segments,'name','md.autodiff.mass_flux_segments','format','MatArray') flag=True else: flag=False - WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean') + WriteData(fid,prefix,'data',flag,'name','md.autodiff.mass_flux_segments_present','format','Boolean') #}}} #deal with trace keep on: {{{ keep=False - #From ADOLC userdoc: - # The optional integer argument keep of trace on determines whether the numerical values of all active variables are - # recorded in a buffered temporary array or file called the taylor stack. This option takes effect if keep = 1 and - # prepares the scene for an immediately following gradient evaluation by a call to a routine implementing the reverse - # mode as described in the Section 4 and Section 5. + #From ADOLC userdoc: + # The optional integer argument keep of trace on determines whether the numerical values of all active variables are + # recorded in a buffered temporary array or file called the taylor stack. This option takes effect if keep = 1 and + # prepares the scene for an immediately following gradient evaluation by a call to a routine implementing the reverse + # mode as described in the Section 4 and Section 5. # if len(self.driver)<=3: - keep=False #there is no "_reverse" string within the driver string: + keep=False #there is no "_reverse" string within the driver string: else: if strncmpi(self.driver[3:],'_reverse',8): @@ -209,5 +214,5 @@ else: keep=False - WriteData(fid,'data',keep,'enum',AutodiffKeepEnum(),'format','Boolean') + WriteData(fid,prefix,'data',keep,'name','md.autodiff.keep','format','Boolean') #}}} Index: /issm/trunk-jpl/src/py3/classes/balancethickness.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/balancethickness.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/balancethickness.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -16,4 +15,8 @@ self.thickening_rate = float('NaN') self.stabilization = 0 + + self.omega = float('NaN') + self.slopex = float('NaN') + self.slopey = float('NaN') #set defaults @@ -39,5 +42,5 @@ def checkconsistency(self,md,solution,analyses): # {{{ #Early return - if not solution==BalancethicknessSolutionEnum(): + if not solution=='BalancethicknessSolution': return md @@ -45,13 +48,16 @@ md = checkfield(md,'fieldname','balancethickness.thickening_rate','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) md = checkfield(md,'fieldname','balancethickness.stabilization','size',[1],'values',[0,1,2,3]) - + #md = checkfield(md,'fieldname','balancethickness.omega','size', [md.mesh.numberofvertices],'NaN',1,'Inf',1,'>=',0); return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'object',self,'fieldname','spcthickness','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','thickening_rate','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'fieldname','stabilization','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','spcthickness','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','thickening_rate','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','slopex','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','slopey','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','omega','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk-jpl/src/py3/classes/bamggeom.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/bamggeom.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/bamggeom.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np class bamggeom(object): @@ -10,12 +10,12 @@ def __init__(self,*args): # {{{ - self.Vertices=numpy.empty((0,3)) - self.Edges=numpy.empty((0,3)) - self.TangentAtEdges=numpy.empty((0,4)) - self.Corners=numpy.empty((0,1)) - self.RequiredVertices=numpy.empty((0,1)) - self.RequiredEdges=numpy.empty((0,1)) - self.CrackedEdges=numpy.empty((0,0)) - self.SubDomains=numpy.empty((0,4)) + self.Vertices=np.empty((0,3)) + self.Edges=np.empty((0,3)) + self.TangentAtEdges=np.empty((0,4)) + self.Corners=np.empty((0,1)) + self.RequiredVertices=np.empty((0,1)) + self.RequiredEdges=np.empty((0,1)) + self.CrackedEdges=np.empty((0,0)) + self.SubDomains=np.empty((0,4)) if not len(args): @@ -25,5 +25,5 @@ elif len(args) == 1: object=args[0] - for field in list(object.keys()): + for field in object.keys(): if field in vars(self): setattr(self,field,object[field]) Index: /issm/trunk-jpl/src/py3/classes/bamgmesh.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/bamgmesh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/bamgmesh.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np class bamgmesh(object): @@ -10,20 +10,19 @@ def __init__(self,*args): # {{{ - self.Vertices=numpy.empty((0,3)) - self.Edges=numpy.empty((0,3)) - self.Triangles=numpy.empty((0,0)) - self.Quadrilaterals=numpy.empty((0,0)) - self.IssmEdges=numpy.empty((0,0)) - self.IssmSegments=numpy.empty((0,0)) - self.VerticesOnGeomVertex=numpy.empty((0,0)) - self.VerticesOnGeomEdge=numpy.empty((0,0)) - self.EdgesOnGeomEdge=numpy.empty((0,0)) - self.SubDomains=numpy.empty((0,4)) - self.SubDomainsFromGeom=numpy.empty((0,0)) - self.ElementConnectivity=numpy.empty((0,0)) - self.NodalConnectivity=numpy.empty((0,0)) - self.NodalElementConnectivity=numpy.empty((0,0)) - self.CrackedVertices=numpy.empty((0,0)) - self.CrackedEdges=numpy.empty((0,0)) + self.Vertices=np.empty((0,3)) + self.Edges=np.empty((0,3)) + self.Triangles=np.empty((0,0)) + self.IssmEdges=np.empty((0,0)) + self.IssmSegments=np.empty((0,0)) + self.VerticesOnGeomVertex=np.empty((0,0)) + self.VerticesOnGeomEdge=np.empty((0,0)) + self.EdgesOnGeomEdge=np.empty((0,0)) + self.SubDomains=np.empty((0,4)) + self.SubDomainsFromGeom=np.empty((0,0)) + self.ElementConnectivity=np.empty((0,0)) + self.NodalConnectivity=np.empty((0,0)) + self.NodalElementConnectivity=np.empty((0,0)) + self.CrackedVertices=np.empty((0,0)) + self.CrackedEdges=np.empty((0,0)) if not len(args): @@ -33,5 +32,5 @@ elif len(args) == 1: object=args[0] - for field in list(object.keys()): + for field in object.keys(): if field in vars(self): setattr(self,field,object[field]) @@ -45,5 +44,4 @@ s+=" Edges: %s\n" % str(self.Edges) s+=" Triangles: %s\n" % str(self.Triangles) - s+=" Quadrilaterals: %s\n" % str(self.Quadrilaterals) s+=" IssmEdges: %s\n" % str(self.IssmEdges) s+=" IssmSegments: %s\n" % str(self.IssmSegments) Index: /issm/trunk-jpl/src/py3/classes/basalforcings.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/basalforcings.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/basalforcings.py (revision 23670) @@ -1,8 +1,7 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData -import numpy +import numpy as np class basalforcings(object): @@ -39,11 +38,14 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.groundedice_melting_rate)): - self.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.groundedice_melting_rate)): + self.groundedice_melting_rate=np.zeros((md.mesh.numberofvertices)) print(" no basalforcings.groundedice_melting_rate specified: values set as zero") - if numpy.all(numpy.isnan(self.floatingice_melting_rate)): - self.floatingice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.floatingice_melting_rate)): + self.floatingice_melting_rate=np.zeros((md.mesh.numberofvertices)) print(" no basalforcings.floatingice_melting_rate specified: values set as zero") + #if np.all(np.isnan(self.geothermalflux)): + #self.geothermalflux=np.zeros((md.mesh.numberofvertices)) + #print " no basalforcings.geothermalflux specified: values set as zero" return self @@ -54,13 +56,13 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and not md.transient.ismasstransport): + if 'MasstransportAnalysis' in analyses and not (solution=='TransientSolution' and not md.transient.ismasstransport): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'timeseries',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - if ThermalAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and not md.transient.isthermal): + if 'ThermalAnalysis' in analyses and not (solution=='TransientSolution' and not md.transient.isthermal): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) md = checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'timeseries',1) @@ -69,11 +71,11 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',BasalforcingsEnum(),'data',FloatingMeltRateEnum(),'format','Integer'); - WriteData(fid,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','floatingice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) + WriteData(fid,prefix,'name','md.basalforcings.model','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','floatingice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) # }}} Index: /issm/trunk-jpl/src/py3/classes/calving.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/calving.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/calving.py (revision 23670) @@ -1,6 +1,4 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData @@ -16,6 +14,4 @@ def __init__(self): # {{{ - self.stabilization = 0 - self.spclevelset = float('NaN') self.calvingrate = float('NaN') self.meltingrate = float('NaN') @@ -27,21 +23,13 @@ def __repr__(self): # {{{ string=' Calving parameters:' - string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding')) - string="%s\n%s"%(string,fielddisplay(self,'spclevelset','levelset constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'calvingrate','calving rate at given location [m/a]')) - string="%s\n%s"%(string,fielddisplay(self,'meltingrate','melting rate at given location [m/a]')) return string #}}} def extrude(self,md): # {{{ - self.spclevelset=project3d(md,'vector',self.spclevelset,'type','node') self.calvingrate=project3d(md,'vector',self.calvingrate,'type','node') - self.meltingrate=project3d(md,'vector',self.meltingrate,'type','node') return self #}}} def setdefaultparameters(self): # {{{ - - #stabilization = 2 by default - self.stabilization = 2 return self @@ -50,22 +38,16 @@ #Early return - if (solution!=TransientSolutionEnum()) or (not md.transient.iscalving): + if (solution!='TransientSolution') or (not md.transient.ismovingfront): return md - md = checkfield(md,'fieldname','calving.spclevelset','Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','calving.stabilization','values',[0,1,2]); md = checkfield(md,'fieldname','calving.calvingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1); - md = checkfield(md,'fieldname','calving.meltingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1); return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.*24.*3600. + yts=md.constants.yts - WriteData(fid,'enum',CalvingLawEnum(),'data',DefaultCalvingEnum(),'format','Integer'); - WriteData(fid,'enum',LevelsetStabilizationEnum(),'data',self.stabilization,'format','Integer'); - WriteData(fid,'enum',SpclevelsetEnum(),'data',self.spclevelset,'format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); - WriteData(fid,'object',self,'fieldname','calvingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts) - WriteData(fid,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts) + WriteData(fid,prefix,'name','md.calving.law','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','calvingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts,'scale',1./yts) # }}} Index: /issm/trunk-jpl/src/py3/classes/calvinglevermann.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/calvinglevermann.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/calvinglevermann.py (revision 23670) @@ -1,5 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData @@ -15,6 +13,4 @@ def __init__(self): # {{{ - self.stabilization = 0 - self.spclevelset = float('NaN') self.coeff = float('NaN') self.meltingrate = float('NaN') @@ -26,21 +22,13 @@ def __repr__(self): # {{{ string=' Calving Levermann parameters:' - string="%s\n%s"%(string,fielddisplay(self,'spclevelset','levelset constraints (NaN means no constraint)')) - string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding')) string="%s\n%s"%(string,fielddisplay(self,'coeff','proportionality coefficient in Levermann model')) - string="%s\n%s"%(string,fielddisplay(self,'meltingrate','melting rate at given location [m/a]')) return string #}}} def extrude(self,md): # {{{ - self.spclevelset=project3d(md,'vector',self.spclevelset,'type','node') self.coeff=project3d(md,'vector',self.coeff,'type','node') - self.meltingrate=project3d(md,'vector',self.meltingrate,'type','node') return self #}}} def setdefaultparameters(self): # {{{ - - #stabilization = 2 by default - self.stabilization = 2 #Proportionality coefficient in Levermann model @@ -50,19 +38,13 @@ #Early return - if (solution!=TransientSolutionEnum()) or (not md.transient.iscalving): + if (solution!='TransientSolution') or (not md.transient.ismovingfront): return md - md = checkfield(md,'fieldname','calving.spclevelset','Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','calving.stabilization','values',[0,1,2]); md = checkfield(md,'fieldname','calving.coeff','size',[md.mesh.numberofvertices],'>',0) - md = checkfield(md,'fieldname','calving.meltingrate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>=',0) return md # }}} - def marshall(self,md,fid): # {{{ - yts=365.*24.*3600. - WriteData(fid,'enum',CalvingLawEnum(),'data',CalvingLevermannEnum(),'format','Integer'); - WriteData(fid,'enum',LevelsetStabilizationEnum(),'data',self.stabilization,'format','Integer'); - WriteData(fid,'enum',SpclevelsetEnum(),'data',self.spclevelset,'format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); - WriteData(fid,'enum',CalvinglevermannCoeffEnum(),'data',self.coeff,'format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts) + def marshall(self,prefix,md,fid): # {{{ + yts=md.constants.yts + WriteData(fid,prefix,'name','md.calving.law','data',3,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','coeff','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk-jpl/src/py3/classes/clusters/generic.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/clusters/generic.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/clusters/generic.py (revision 23670) @@ -4,5 +4,4 @@ import subprocess from IssmConfig import IssmConfig -from EnumToString import EnumToString from issmdir import issmdir from pairoptions import pairoptions @@ -18,8 +17,8 @@ Usage: cluster=generic('name','astrid','np',3); - cluster=generic('name',oshostname(),'np',3,'login','username'); + cluster=generic('name',gethostname(),'np',3,'login','username'); """ - def __init__(self,**kwargs): # {{{ + def __init__(self,*args): # {{{ self.name='' @@ -28,5 +27,5 @@ self.port=0 self.interactive=1 - self.codepath=issmdir()+'/bin' + self.codepath=IssmConfig('ISSM_PREFIX')[0]+'/bin' self.executionpath=issmdir()+'/execution' self.valgrind=issmdir()+'/externalpackages/valgrind/install/bin/valgrind' @@ -35,5 +34,5 @@ #use provided options to change fields - options=pairoptions(**kwargs) + options=pairoptions(*args) #get name @@ -69,12 +68,14 @@ return md # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): # {{{ + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ executable='issm.exe'; if isdakota: - version=IssmConfig('_DAKOTA_VERSION_')[0:2] - version=float(version) + version=IssmConfig('_DAKOTA_VERSION_') + version=float(version[0]) if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script @@ -86,12 +87,12 @@ if self.interactive: if IssmConfig('_HAVE_MPI_')[0]: - fid.write('mpiexec -np %i %s/%s %s %s/%s %s ' % (self.np,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname)) + fid.write('mpiexec -np %i %s/%s %s %s/%s %s ' % (self.np,self.codepath,executable,solution,self.executionpath,dirname,modelname)) else: - fid.write('%s/%s %s %s/%s %s ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname)) + fid.write('%s/%s %s %s/%s %s ' % (self.codepath,executable,solution,self.executionpath,dirname,modelname)) else: if IssmConfig('_HAVE_MPI_')[0]: - fid.write('mpiexec -np %i %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.np,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname)) + fid.write('mpiexec -np %i %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.np,self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname)) else: - fid.write('%s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname)) + fid.write('%s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname)) elif isgprof: fid.write('\n gprof %s/%s gmon.out > %s.performance' % (self.codepath,executable,modelname)) @@ -101,8 +102,8 @@ if IssmConfig('_HAVE_MPI_')[0]: fid.write('mpiexec -np %i %s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \ - (self.np,self.valgrind,self.valgrindsup,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname)) + (self.np,self.valgrind,self.valgrindsup,self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname)) else: fid.write('%s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \ - (self.valgrind,self.valgrindsup,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname)) + (self.valgrind,self.valgrindsup,self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname)) if not io_gather: #concatenate the output files: @@ -115,8 +116,8 @@ fid.write('@echo off\n') if self.interactive: - fid.write('"%s/%s" %s "%s/%s" %s ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname)) + fid.write('"%s/%s" %s "%s/%s" %s ' % (self.codepath,executable,solution,self.executionpath,dirname,modelname)) else: fid.write('"%s/%s" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \ - (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname)) + (self.codepath,executable,solution,self.executionpath,dirname,modelname,modelname,modelname)) fid.close() @@ -156,8 +157,8 @@ fid.write('@echo off\n') if self.interactive: - fid.write('"%s/issm.exe" %s "%s/%s" %s ' % (self.codepath,EnumToString(solution)[0],self.executionpath,modelname,modelname)) + fid.write('"%s/issm.exe" %s "%s/%s" %s ' % (self.codepath,solution,self.executionpath,modelname,modelname)) else: fid.write('"%s/issm.exe" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \ - (self.codepath,EnumToString(solution)[0],self.executionpath,modelname,modelname,modelname,modelname)) + (self.codepath,solution,self.executionpath,modelname,modelname,modelname,modelname)) fid.close() @@ -183,5 +184,5 @@ # }}} - def LaunchQueueJob(self,modelname,dirname,filelist,restart): # {{{ + def LaunchQueueJob(self,modelname,dirname,filelist,restart,batch): # {{{ print('launching solution sequence on remote cluster') @@ -189,6 +190,10 @@ launchcommand='cd %s && cd %s chmod 777 %s.queue && ./%s.queue' % (self.executionpath,dirname,modelname,modelname) else: - launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz && chmod 777 %s.queue && ./%s.queue' % \ - (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname,modelname) + if batch: + launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz' % \ + (self.executionpath,dirname,dirname,dirname,dirname,dirname) + else: + launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz && chmod 777 %s.queue && ./%s.queue' % \ + (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname,modelname) issmssh(self.name,self.login,self.port,launchcommand) # }}} Index: /issm/trunk-jpl/src/py3/classes/clusters/pfe.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/clusters/pfe.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/clusters/pfe.py (revision 23670) @@ -4,5 +4,4 @@ import subprocess from fielddisplay import fielddisplay -from EnumToString import EnumToString from pairoptions import pairoptions from issmssh import issmssh @@ -25,5 +24,5 @@ """ - def __init__(self,**kwargs): + def __init__(self,*args): # {{{ @@ -45,5 +44,5 @@ #use provided options to change fields - options=pairoptions(**kwargs) + options=pairoptions(*args) #initialize cluster using user settings if provided @@ -134,5 +133,5 @@ return self # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ @@ -143,4 +142,6 @@ if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script @@ -162,5 +163,5 @@ fid.write('source $ISSM_DIR/etc/environment.sh\n') fid.write('cd %s/%s/\n\n' % (self.executionpath,dirname)) - fid.write('mpiexec -np %i %s/%s %s %s/%s %s\n' % (self.nprocs(),self.codepath,executable,str(EnumToString(solution)[0]),self.executionpath,dirname,modelname)) + fid.write('mpiexec -np %i %s/%s %s %s/%s %s\n' % (self.nprocs(),self.codepath,executable,str(solution),self.executionpath,dirname,modelname)) fid.close() @@ -180,5 +181,5 @@ # }}} - def LaunchQueueJob(self,modelname,dirname,filelist,restart): + def LaunchQueueJob(self,modelname,dirname,filelist,restart,batch): # {{{ Index: /issm/trunk-jpl/src/py3/classes/constants.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/constants.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/constants.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -13,7 +12,8 @@ def __init__(self): # {{{ - self.g = 0 - self.yts = 0 - self.referencetemperature = 0 + self.g = 0. + self.omega = 0. + self.yts = 0. + self.referencetemperature = 0. #set defaults @@ -25,4 +25,5 @@ string="%s\n%s"%(string,fielddisplay(self,"g","gravitational acceleration [m/s^2]")) + string="%s\n%s"%(string,fielddisplay(self,"omega","angular velocity of Earth [rad/s]")) string="%s\n%s"%(string,fielddisplay(self,"yts","number of seconds in a year [s/yr]")) string="%s\n%s"%(string,fielddisplay(self,"referencetemperature","reference temperature used in the enthalpy model [K]")) @@ -35,6 +36,9 @@ self.g=9.81 + #Earth's rotation speed + self.omega = 7.292*1e-5; + #converstion from year to seconds - self.yts=365*24*3600 + self.yts=365.*24.*3600. #the reference temperature for enthalpy model (cf Aschwanden) @@ -45,13 +49,14 @@ def checkconsistency(self,md,solution,analyses): # {{{ - md = checkfield(md,'fieldname','constants.g','>',0,'size',[1]) - md = checkfield(md,'fieldname','constants.yts','>',0,'size',[1]) - md = checkfield(md,'fieldname','constants.referencetemperature','size',[1]) + md = checkfield(md,'fieldname','constants.g','>=',0,'size',[1,1]) + md = checkfield(md,'fieldname','constants.omega','>=',0,'size',[1,1]) + md = checkfield(md,'fieldname','constants.yts','>',0,'size',[1,1]) + md = checkfield(md,'fieldname','constants.referencetemperature','size',[1,1]) return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','g','format','Double') - WriteData(fid,'object',self,'fieldname','yts','format','Double') - WriteData(fid,'object',self,'fieldname','referencetemperature','format','Double') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','g','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','yts','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','referencetemperature','format','Double') # }}} Index: /issm/trunk-jpl/src/py3/classes/damage.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/damage.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/damage.py (revision 23670) @@ -1,9 +1,6 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData -import MatlabFuncs as m class damage(object): @@ -16,27 +13,26 @@ def __init__(self,*args): # {{{ - - #damage: - self.isdamage = 0. - self.D = float('NaN') - self.law = float('NaN') - self.spcdamage = float('NaN') - self.max_damage = float('NaN') - + #damage: + self.isdamage = 0. + self.D = float('NaN') + self.law = float('NaN') + self.spcdamage = float('NaN') + self.max_damage = float('NaN') + #numerical - self.stabilization = float('NaN') - self.maxiter = float('NaN') - self.elementinterp = '' + self.stabilization = float('NaN') + self.maxiter = float('NaN') + self.elementinterp = '' - #general parameters for evolution law: - self.stress_threshold = float('NaN') - self.kappa = float('NaN') - self.c1 = float('NaN') - self.c2 = float('NaN') - self.c3 = float('NaN') - self.c4 = float('NaN') - self.healing = float('NaN') - self.equiv_stress = float('NaN') - self.requested_outputs = [] + #general parameters for evolution law: + self.stress_threshold = float('NaN') + self.kappa = float('NaN') + self.c1 = float('NaN') + self.c2 = float('NaN') + self.c3 = float('NaN') + self.c4 = float('NaN') + self.healing = float('NaN') + self.equiv_stress = float('NaN') + self.requested_outputs = [] if not len(args): @@ -44,9 +40,8 @@ else: raise RuntimeError("constructor not supported") + # }}} - # }}} def __repr__(self): # {{{ s =' Damage:\n' - s+="%s\n" % fielddisplay(self,"isdamage","is damage mechanics being used? [0 (default) or 1]") if self.isdamage: @@ -70,4 +65,5 @@ return s # }}} + def extrude(self,md): # {{{ self.D=project3d(md,'vector',self.D,'type','node') @@ -75,16 +71,15 @@ return self #}}} + def setdefaultparameters(self): # {{{ + #damage parameters: + self.isdamage = 0 + self.D = 0 + self.law = 0 + self.max_damage = 1-1e-5 #if damage reaches 1, solve becomes singular, as viscosity becomes nil - #damage parameters: - self.isdamage=0 - self.D=0 - self.law=0 - - self.max_damage=1-1e-5 #if damage reaches 1, solve becomes singular, as viscosity becomes nil - #Type of stabilization used self.stabilization=4 - + #Maximum number of iterations self.maxiter=100 @@ -93,5 +88,5 @@ self.elementinterp='P1' - #damage evolution parameters + #damage evolution parameters self.stress_threshold=1.3e5 self.kappa=2.8 @@ -108,6 +103,6 @@ return self # }}} + def defaultoutputs(self,md): # {{{ - if md.mesh.domaintype().lower()=='2dhorizontal': list = ['DamageDbar'] @@ -115,8 +110,7 @@ list = ['DamageD'] return list + #}}} - #}}} def checkconsistency(self,md,solution,analyses): # {{{ - md = checkfield(md,'fieldname','damage.isdamage','numel',[1],'values',[0,1]) if self.isdamage: @@ -139,29 +133,29 @@ md = checkfield(md,'fieldname','damage.requested_outputs','stringrow',1) elif self.law != 0: - if (solution==DamageEvolutionSolutionEnum): + if (solution=='DamageEvolutionSolution'): raise RuntimeError('Invalid evolution law (md.damage.law) for a damage solution') return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','isdamage','format','Boolean') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','isdamage','format','Boolean') if self.isdamage: - WriteData(fid,'object',self,'fieldname','D','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','law','format','Integer') - WriteData(fid,'object',self,'fieldname','spcdamage','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','max_damage','format','Double') - WriteData(fid,'object',self,'fieldname','stabilization','format','Integer') - WriteData(fid,'object',self,'fieldname','maxiter','format','Integer') - WriteData(fid,'enum',DamageElementinterpEnum(),'data',StringToEnum(self.elementinterp)[0],'format','Integer') - WriteData(fid,'object',self,'fieldname','stress_threshold','format','Double') - WriteData(fid,'object',self,'fieldname','kappa','format','Double') - WriteData(fid,'object',self,'fieldname','c1','format','Double') - WriteData(fid,'object',self,'fieldname','c2','format','Double') - WriteData(fid,'object',self,'fieldname','c3','format','Double') - WriteData(fid,'object',self,'fieldname','c4','format','Double') - WriteData(fid,'object',self,'fieldname','healing','format','Double') - WriteData(fid,'object',self,'fieldname','equiv_stress','format','Integer') - + WriteData(fid,prefix,'object',self,'fieldname','D','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','law','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','spcdamage','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','max_damage','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','maxiter','format','Integer') + WriteData(fid,prefix,'name','md.damage.elementinterp','data',self.elementinterp,'format','String') + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','kappa','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','c1','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','c2','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','c3','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','c4','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','healing','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','equiv_stress','format','Integer') + #process requested outputs outputs = self.requested_outputs @@ -170,4 +164,5 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',DamageEvolutionRequestedOutputsEnum(),'format','StringArray') + if self.isdamage: + WriteData(fid,prefix,'data',outputs,'name','md.damage.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/debug.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/debug.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/debug.py (revision 23670) @@ -30,5 +30,5 @@ return self #}}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','profiling','format','Boolean') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','profiling','format','Boolean') # }}} Index: /issm/trunk-jpl/src/py3/classes/dependent.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/dependent.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/dependent.py (revision 23670) @@ -1,8 +1,7 @@ import os.path -import numpy +import numpy as np from pairoptions import pairoptions from fielddisplay import fielddisplay -import MatlabFuncs as m -from EnumDefinitions import * +from MatlabFuncs import * from MeshProfileIntersection import MeshProfileIntersection @@ -28,5 +27,5 @@ #use provided options to change fields - options=pairoptions(**kwargs) + options=pairoptions(*args) self.name=options.getfieldvalue('name','') @@ -44,13 +43,13 @@ #process the file and retrieve segments mesh=options.getfieldvalue('mesh') - self.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,self.exp) + self.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,self.exp)[0] # }}} def __repr__(self): # {{{ s =" dependent variable:\n" - s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") + s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding String)") s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") - if not numpy.isnan(self.fos_reverse_index): + if not np.isnan(self.fos_reverse_index): s+="%s\n" % fielddisplay(self,'fos_reverse_index',"index for fos_reverse driver of ADOLC") if self.exp: @@ -71,5 +70,5 @@ raise RuntimeError("dependent checkconsistency error: index for segments should be >=0") - if not numpy.isnan(self.fos_reverse_index): + if not np.isnan(self.fos_reverse_index): if not strcmpi(driver,'fos_reverse'): raise TypeError("cannot declare a dependent with a fos_reverse_index when the driver is not fos_reverse!") Index: /issm/trunk-jpl/src/py3/classes/flowequation.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/flowequation.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/flowequation.py (revision 23670) @@ -1,7 +1,6 @@ -import numpy +import numpy as np import copy from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -17,5 +16,5 @@ def __init__(self): # {{{ - + self.isSIA = 0 self.isSSA = 0 @@ -50,5 +49,5 @@ string="%s\n%s"%(string,fielddisplay(self,'isFS',"are the Full-FS (FS) equations used ?")) string="%s\n%s"%(string,fielddisplay(self,'fe_SSA',"Finite Element for SSA: 'P1', 'P1bubble' 'P1bubblecondensed' 'P2'")) - string="%s\n%s"%(string,fielddisplay(self,'fe_HO' ,"Finite Element for HO: 'P1' 'P1bubble' 'P1bubblecondensed' 'P1xP2' 'P2xP1' 'P2'")) + string="%s\n%s"%(string,fielddisplay(self,'fe_HO' ,"Finite Element for HO: 'P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4'")) string="%s\n%s"%(string,fielddisplay(self,'fe_FS' ,"Finite Element for FS: 'P1P1' (debugging only) 'P1P1GLS' 'MINIcondensed' 'MINI' 'TaylorHood' 'LATaylorHood' 'XTaylorHood'")) string="%s\n%s"%(string,fielddisplay(self,'vertex_equation',"flow equation for each vertex")) @@ -83,5 +82,5 @@ #Early return - if (StressbalanceAnalysisEnum() not in analyses and StressbalanceSIAAnalysisEnum() not in analyses) or (solution==TransientSolutionEnum() and not md.transient.isstressbalance): + if ('StressbalanceAnalysis' not in analyses and 'StressbalanceSIAAnalysis' not in analyses) or (solution=='TransientSolution' and not md.transient.isstressbalance): return md @@ -93,5 +92,5 @@ md = checkfield(md,'fieldname','flowequation.fe_SSA','values',['P1','P1bubble','P1bubblecondensed','P2','P2bubble']) md = checkfield(md,'fieldname','flowequation.fe_HO' ,'values',['P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4']) - md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',['P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart']) + md = checkfield(md,'fieldname','flowequation.fe_FS' ,'values',['P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','LATaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart','LACrouzeixRaviart']) md = checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices],'values',[0,1]) md = checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices],'values',[0,1]) @@ -105,7 +104,10 @@ md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',[1,2]) md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',[1,2]) + elif m.strcmp(md.mesh.domaintype(),'2Dvertical'): + md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',[2,4,5]) + md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',[2,4,5]) elif m.strcmp(md.mesh.domaintype(),'3D'): - md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',numpy.arange(0,8+1)) - md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',numpy.arange(0,8+1)) + md = checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',np.arange(0,8+1)) + md = checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements],'values',np.arange(0,8+1)) else: raise RuntimeError('mesh type not supported yet') @@ -113,50 +115,31 @@ md.checkmessage("no element types set for this model") - if StressbalanceSIAAnalysisEnum() in analyses: + if 'StressbalanceSIAAnalysis' in analyses: if any(self.element_equation==1): - if numpy.any(numpy.logical_and(self.vertex_equation,md.mask.groundedice_levelset)): + if np.any(np.logical_and(self.vertex_equation,md.mask.groundedice_levelset)): print("\n !!! Warning: SIA's model is not consistent on ice shelves !!!\n") return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','isSIA','format','Boolean') - WriteData(fid,'object',self,'fieldname','isSSA','format','Boolean') - WriteData(fid,'object',self,'fieldname','isL1L2','format','Boolean') - WriteData(fid,'object',self,'fieldname','isHO','format','Boolean') - WriteData(fid,'object',self,'fieldname','isFS','format','Boolean') - WriteData(fid,'enum',FlowequationFeSSAEnum(),'data',StringToEnum(self.fe_SSA)[0],'format','Integer') - WriteData(fid,'enum',FlowequationFeHOEnum() ,'data',StringToEnum(self.fe_HO)[0] ,'format','Integer') - WriteData(fid,'enum',FlowequationFeFSEnum() ,'data',StringToEnum(self.fe_FS)[0] ,'format','Integer') - WriteData(fid,'enum',AugmentedLagrangianREnum(),'data',self.augmented_lagrangian_r ,'format','Double') - WriteData(fid,'enum',AugmentedLagrangianRhopEnum(),'data',self.augmented_lagrangian_rhop ,'format','Double') - WriteData(fid,'enum',AugmentedLagrangianRlambdaEnum(),'data',self.augmented_lagrangian_rlambda ,'format','Double') - WriteData(fid,'enum',AugmentedLagrangianRholambdaEnum(),'data',self.augmented_lagrangian_rholambda ,'format','Double') - WriteData(fid,'enum',AugmentedLagrangianThetaEnum() ,'data',self.XTH_theta ,'format','Double') - WriteData(fid,'object',self,'fieldname','borderSSA','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','borderHO','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','borderFS','format','DoubleMat','mattype',1) + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','isSIA','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isSSA','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isL1L2','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isHO','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isFS','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','fe_SSA','data',self.fe_SSA,'format','String') + WriteData(fid,prefix,'object',self,'fieldname','fe_HO','data',self.fe_HO,'format','String') + WriteData(fid,prefix,'object',self,'fieldname','fe_FS','data',self.fe_FS ,'format','String') + WriteData(fid,prefix,'object',self,'fieldname','augmented_lagrangian_r','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','augmented_lagrangian_rhop','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','augmented_lagrangian_rlambda','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','augmented_lagrangian_rholambda','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','XTH_theta','data',self.XTH_theta ,'format','Double') + WriteData(fid,prefix,'object',self,'fieldname','borderSSA','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','borderHO','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','borderFS','format','DoubleMat','mattype',1) #convert approximations to enums - data=copy.deepcopy(self.vertex_equation) - data[numpy.nonzero(data==0)]=NoneApproximationEnum() - data[numpy.nonzero(data==1)]=SIAApproximationEnum() - data[numpy.nonzero(data==2)]=SSAApproximationEnum() - data[numpy.nonzero(data==3)]=L1L2ApproximationEnum() - data[numpy.nonzero(data==4)]=HOApproximationEnum() - data[numpy.nonzero(data==5)]=FSApproximationEnum() - data[numpy.nonzero(data==6)]=SSAHOApproximationEnum() - data[numpy.nonzero(data==7)]=HOFSApproximationEnum() - data[numpy.nonzero(data==8)]=SSAFSApproximationEnum() - WriteData(fid,'data',data,'enum',FlowequationVertexEquationEnum(),'format','DoubleMat','mattype',1) - data=copy.deepcopy(self.element_equation) - data[numpy.nonzero(data==0)]=NoneApproximationEnum() - data[numpy.nonzero(data==1)]=SIAApproximationEnum() - data[numpy.nonzero(data==2)]=SSAApproximationEnum() - data[numpy.nonzero(data==3)]=L1L2ApproximationEnum() - data[numpy.nonzero(data==4)]=HOApproximationEnum() - data[numpy.nonzero(data==5)]=FSApproximationEnum() - data[numpy.nonzero(data==6)]=SSAHOApproximationEnum() - data[numpy.nonzero(data==7)]=SSAFSApproximationEnum() - data[numpy.nonzero(data==8)]=HOFSApproximationEnum() - WriteData(fid,'data',data,'enum',FlowequationElementEquationEnum(),'format','DoubleMat','mattype',2) + WriteData(fid,prefix,'data',self.vertex_equation,'name','md.flowequation.vertex_equation','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'data',self.element_equation,'name','md.flowequation.element_equation','format','DoubleMat','mattype',2) + # }}} Index: /issm/trunk-jpl/src/py3/classes/friction.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/friction.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/friction.py (revision 23670) @@ -1,5 +1,5 @@ +import numpy as np from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -17,5 +17,6 @@ self.p = float('NaN') self.q = float('NaN') - + self.coupling = 0 + self.effective_pressure = float('NaN') #set defaults self.setdefaultparameters() @@ -23,9 +24,11 @@ #}}} def __repr__(self): # {{{ - string="Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b,\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p)" + string="Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b,\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*base, r=q/p and s=1/p)" string="%s\n%s"%(string,fielddisplay(self,"coefficient","friction coefficient [SI]")) string="%s\n%s"%(string,fielddisplay(self,"p","p exponent")) string="%s\n%s"%(string,fielddisplay(self,"q","q exponent")) + string="%s\n%s"%(string,fielddisplay(self,'coupling','Coupling flag 0: uniform sheet (negative pressure ok, default), 1: ice pressure only, 2: water pressure assuming uniform sheet (no negative pressure), 3: use provided effective_pressure, 4: used coupled model (not implemented yet)')) + string="%s\n%s"%(string,fielddisplay(self,'effective_pressure','Effective Pressure for the forcing if not coupled [Pa]')) return string #}}} @@ -34,4 +37,9 @@ self.p=project3d(md,'vector',self.p,'type','element') self.q=project3d(md,'vector',self.q,'type','element') + #if self.coupling==0: #doesnt work with empty loop, so just skip it? + if self.coupling in[3,4]: + self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1) + elif self.coupling > 4: + raise ValueError('md.friction.coupling larger than 4, not supported yet') return self #}}} @@ -42,5 +50,5 @@ #Early return - if StressbalanceAnalysisEnum() not in analyses and ThermalAnalysisEnum() not in analyses: + if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses: return md @@ -48,11 +56,20 @@ md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) md = checkfield(md,'fieldname','friction.p','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) - + md = checkfield(md,'fieldname','friction.coupling','numel',[1],'values',[0,1,2,3,4]) + if self.coupling==3: + md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1) + elif self.coupling > 4: + raise ValueError('md.friction.coupling larger than 4, not supported yet') return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',FrictionLawEnum(),'data',1,'format','Integer') - WriteData(fid,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','p','format','DoubleMat','mattype',2) - WriteData(fid,'object',self,'fieldname','q','format','DoubleMat','mattype',2) + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.friction.law','data',1,'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','p','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'fieldname','q','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer') + if self.coupling in[3,4]: + WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + elif self.coupling > 4: + raise ValueError('md.friction.coupling larger than 4, not supported yet') # }}} Index: /issm/trunk-jpl/src/py3/classes/frictioncoulomb.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/frictioncoulomb.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/frictioncoulomb.py (revision 23670) @@ -1,5 +1,4 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -18,5 +17,6 @@ self.p = float('NaN') self.q = float('NaN') - + self.coupling = 0 + self.effective_pressure = float('NaN') #set defaults self.setdefaultparameters() @@ -30,4 +30,6 @@ string="%s\n%s"%(string,fielddisplay(self,"p","p exponent")) string="%s\n%s"%(string,fielddisplay(self,"q","q exponent")) + string="%s\n%s"%(string,fielddisplay(self,'coupling','Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure) and 2 for coupled(not implemented yet)')) + string="%s\n%s"%(string,fielddisplay(self,'effective_pressure','Effective Pressure for the forcing if not coupled [Pa]')) return string #}}} @@ -37,4 +39,10 @@ self.p=project3d(md,'vector',self.p,'type','element') self.q=project3d(md,'vector',self.q,'type','element') + if self.coupling==1: + self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1) + elif self.coupling==2: + raise ValueError('coupling not supported yet') + elif self.coupling > 2: + raise ValueError('md.friction.coupling larger than 2, not supported yet') return self #}}} @@ -45,5 +53,5 @@ #Early return - if StressbalanceAnalysisEnum() not in analyses and ThermalAnalysisEnum() not in analyses: + if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses: return md @@ -52,12 +60,25 @@ md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) md = checkfield(md,'fieldname','friction.p','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) + if self.coupling==1: + md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1) + elif self.coupling==2: + raise ValueError('coupling not supported yet') + elif self.coupling > 2: + raise ValueError('md.friction.coupling larger than 2, not supported yet') + return md - return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',FrictionLawEnum(),'data',1,'format','Integer') - WriteData(fid,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'enum',FrictionCoefficientEnum()) - WriteData(fid,'object',self,'fieldname','coefficientcoulomb','format','DoubleMat','mattype',1,'enum',FrictionCoefficientcoulombEnum()) - WriteData(fid,'object',self,'fieldname','p','format','DoubleMat','mattype',2,'enum',FrictionPEnum()) - WriteData(fid,'object',self,'fieldname','q','format','DoubleMat','mattype',2,'enum',FrictionQEnum()) + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.friction.law','data',7,'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','coefficientcoulomb','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','p','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'fieldname','q','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer') + if self.coupling==1: + WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + elif self.coupling==2: + raise ValueError('coupling not supported yet') + elif self.coupling > 2: + raise ValueError('md.friction.coupling larger than 2, not supported yet') # }}} Index: /issm/trunk-jpl/src/py3/classes/frictionweertman.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/frictionweertman.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/frictionweertman.py (revision 23670) @@ -1,5 +1,4 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -34,5 +33,5 @@ #Early return - if StressbalanceAnalysisEnum() not in analyses and ThermalAnalysisEnum() not in analyses: + if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses: return md @@ -42,7 +41,7 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',FrictionLawEnum(),'data',2,'format','Integer') - WriteData(fid,'class','friction','object',self,'fieldname','C','format','DoubleMat','mattype',1) - WriteData(fid,'class','friction','object',self,'fieldname','m','format','DoubleMat','mattype',2) + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.friction.law','data',2,'format','Integer') + WriteData(fid,prefix,'class','friction','object',self,'fieldname','C','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'class','friction','object',self,'fieldname','m','format','DoubleMat','mattype',2) # }}} Index: /issm/trunk-jpl/src/py3/classes/geometry.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/geometry.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/geometry.py (revision 23670) @@ -1,5 +1,4 @@ from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -14,9 +13,9 @@ def __init__(self): # {{{ - self.surface = float('NaN') - self.thickness = float('NaN') + self.surface = float('NaN') + self.thickness = float('NaN') self.base = float('NaN') - self.bed = float('NaN') - self.hydrostatic_ratio = float('NaN') + self.bed = float('NaN') + self.hydrostatic_ratio = float('NaN') #set defaults @@ -46,19 +45,24 @@ def checkconsistency(self,md,solution,analyses): # {{{ - md = checkfield(md,'fieldname','geometry.surface' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','geometry.base' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','geometry.thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0,'timeseries',1) - if any(abs(self.thickness-self.surface+self.base)>10**-9): - md.checkmessage("equality thickness=surface-base violated") - if solution==TransientSolutionEnum() and md.transient.isgroundingline: - md = checkfield(md,'fieldname','geometry.bed','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + if (solution=='TransientSolution' and md.transient.isgia) or (solution=='GiaSolution'): + md = checkfield(md,'fieldname','geometry.thickness','NaN',1,'Inf',1,'>=',0,'timeseries',1) + elif solution=='LoveSolution': + return + else: + md = checkfield(md,'fieldname','geometry.surface' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','geometry.base' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','geometry.thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0,'timeseries',1) + if any(abs(self.thickness-self.surface+self.base)>10**-9): + md.checkmessage("equality thickness=surface-base violated") + if solution=='TransientSolution' and md.transient.isgroundingline: + md = checkfield(md,'fieldname','geometry.bed','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'data',self.surface,'format','DoubleMat','mattype',1,'enum',SurfaceEnum()) - WriteData(fid,'data',self.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum(),'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'data',self.base,'format','DoubleMat','mattype',1,'enum',BaseEnum()) - WriteData(fid,'data',self.bed,'format','DoubleMat','mattype',1,'enum',BedEnum()) - WriteData(fid,'object',self,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1) + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','surface','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','thickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','base','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','bed','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk-jpl/src/py3/classes/groundingline.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/groundingline.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/groundingline.py (revision 23670) @@ -1,6 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData @@ -17,4 +15,6 @@ def __init__(self): # {{{ self.migration='' + self.friction_interpolation='' + self.melt_interpolation='' #set defaults @@ -25,5 +25,7 @@ string=' grounding line migration parameters:' - string="%s\n%s"%(string,fielddisplay(self,'migration','type of grounding line migration: ''SoftMigration'',''AggressiveMigration'',''SubelementMigration'',''SubelementMigration2'',''Contact'',''None''')) + string="%s\n%s"%(string,fielddisplay(self,'migration','type of grounding line migration: ''SoftMigration'',''SubelementMigration'',''AggressiveMigration'',''Contact'',''None''')) + string="%s\n%s"%(string,fielddisplay(self,'migration','type of friction interpolation on partially floating elements: ''SubelementFriction1'',''SubelementFriction2'',''NoFrictionOnPartiallyFloating''')) + string="%s\n%s"%(string,fielddisplay(self,'migration','type of melt interpolation on partially floating elements: ''SubelementMelt1'',''SubelementMelt2'',''NoMeltOnPartiallyFloating'',''FullMeltOnPartiallyFloating''')) return string #}}} @@ -31,5 +33,7 @@ #Type of migration - self.migration='None' + self.migration='SubelementMigration' + self.friction_interpolation='SubelementFriction1' + self.melt_interpolation='NoMeltOnPartiallyFloating' return self @@ -37,11 +41,13 @@ def checkconsistency(self,md,solution,analyses): # {{{ - md = checkfield(md,fieldname='groundingline.migration',values=['None','AggressiveMigration','SoftMigration','SubelementMigration','SubelementMigration2','Contact','GroundingOnly']) + md = checkfield(md,'fieldname','groundingline.migration','values',['None','SubelementMigration','AggressiveMigration','SoftMigration','Contact','GroundingOnly']) + md = checkfield(md,'fieldname','groundingline.friction_interpolation','values',['SubelementFriction1','SubelementFriction2','NoFrictionOnPartiallyFloating']) + md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',['SubelementMelt1','SubelementMelt2','NoMeltOnPartiallyFloating','FullMeltOnPartiallyFloating']) - if not m.strcmp(self.migration,'None'): - if numpy.any(numpy.isnan(md.geometry.bed)): + if(not m.strcmp(self.migration,'None') and md.transient.isgroundingline and solution=='TransientSolution'): + if np.any(np.isnan(md.geometry.bed)): md.checkmessage("requesting grounding line migration, but bathymetry is absent!") - pos=numpy.nonzero(md.mask.groundedice_levelset>0.)[0] - if any(numpy.abs(md.geometry.base[pos]-md.geometry.bed[pos])>10**-10): + pos=np.nonzero(md.mask.groundedice_levelset>0.)[0] + if any(np.abs(md.geometry.base[pos]-md.geometry.bed[pos])>10**-10): md.checkmessage("base not equal to bed on grounded ice!") if any(md.geometry.bed - md.geometry.base > 10**-9): @@ -50,5 +56,7 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'data',StringToEnum(self.migration)[0],'enum',GroundinglineMigrationEnum(),'format','Integer') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'data',self.migration,'name','md.groundingline.migration','format','String') + WriteData(fid,prefix,'data',self.friction_interpolation,'name','md.groundingline.friction_interpolation','format','String') + WriteData(fid,prefix,'data',self.melt_interpolation,'name','md.groundingline.melt_interpolation','format','String') # }}} Index: /issm/trunk-jpl/src/py3/classes/hydrologydc.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/hydrologydc.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/hydrologydc.py (revision 23670) @@ -1,6 +1,5 @@ -import numpy +import numpy as np from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -21,19 +20,22 @@ self.rel_tol = 0 self.max_iter = 0 + self.steps_per_step = 0 self.sedimentlimit_flag = 0 self.sedimentlimit = 0 self.transfer_flag = 0 + self.unconfined_flag = 0 self.leakage_factor = 0 - self.basal_moulin_input = float('NaN') - - self.spcsediment_head = float('NaN') - self.sediment_transmitivity = float('NaN') + self.basal_moulin_input = np.nan + self.requested_outputs = [] + + self.spcsediment_head = np.nan + self.mask_thawed_node = np.nan + self.sediment_transmitivity = np.nan self.sediment_compressibility = 0 self.sediment_porosity = 0 self.sediment_thickness = 0 - - self.spcepl_head = float('NaN') - self.mask_eplactive_node = float('NaN') + self.spcepl_head = np.nan + self.mask_eplactive_node = np.nan self.epl_compressibility = 0 self.epl_porosity = 0 @@ -44,5 +46,5 @@ self.epl_conductivity = 0 self.eplflip_lock = 0 - + #set defaults self.setdefaultparameters() @@ -57,5 +59,7 @@ string="%s\n%s"%(string,fielddisplay(self,'rel_tol','tolerance of the nonlinear iteration for the transfer between layers [dimensionless]')) string="%s\n%s"%(string,fielddisplay(self,'max_iter','maximum number of nonlinear iteration')) + string="%s\n%s"%(string,fielddisplay(self,'steps_per_step','number of hydrology steps per time step')) string="%s\n%s"%(string,fielddisplay(self,'basal_moulin_input','water flux at a given point [m3 s-1]')) + string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) string="%s\n%s"%(string,fielddisplay(self,'sedimentlimit_flag','what kind of upper limit is applied for the inefficient layer')) string="%s\n\t\t%s"%(string,'0: no limit') @@ -63,5 +67,5 @@ string="%s\n\t\t%s"%(string,'2: hydrostatic pressure') string="%s\n\t\t%s"%(string,'3: normal stress') - + if self.sedimentlimit_flag==1: string="%s\n%s"%(string,fielddisplay(self,'sedimentlimit','user defined upper limit for the inefficient layer [m]')) @@ -70,7 +74,11 @@ string="%s\n\t\t%s"%(string,'0: no transfer') string="%s\n\t\t%s"%(string,'1: constant leakage factor: leakage_factor') - + if self.transfer_flag is 1: string="%s\n%s"%(string,fielddisplay(self,'leakage_factor','user defined leakage factor [m]')) + + string="%s\n%s"%(string,fielddisplay(self,'unconfined_flag','using an unconfined scheme or not (transitory)')) + string="%s\n\t\t%s"%(string,'0: Confined only') + string="%s\n\t\t%s"%(string,'1: Confined-Unconfined') string="%s\n%s"%(string,' - for the sediment layer') @@ -80,4 +88,5 @@ string="%s\n%s"%(string,fielddisplay(self,'sediment_thickness','sediment thickness [m]')) string="%s\n%s"%(string,fielddisplay(self,'sediment_transmitivity','sediment transmitivity [m^2/s]')) + string="%s\n%s"%(string,fielddisplay(self,'mask_thawed_node','IDS is deactivaed (0) on frozen nodes')) if self.isefficientlayer==1: @@ -87,6 +96,6 @@ string="%s\n%s"%(string,fielddisplay(self,'epl_compressibility','epl compressibility [Pa^-1]')) string="%s\n%s"%(string,fielddisplay(self,'epl_porosity','epl [dimensionless]')) - string="%s\n%s"%(string,fielddisplay(self,'epl_max_thickness','epl initial thickness [m]')) - string="%s\n%s"%(string,fielddisplay(self,'epl_initial_thickness','epl initial thickness [m]')) + string="%s\n%s"%(string,fielddisplay(self,'epl_max_thickness','epl maximal thickness [m]')) + string="%s\n%s"%(string,fielddisplay(self,'epl_initial_thickness','epl initial thickness [m]')) string="%s\n%s"%(string,fielddisplay(self,'epl_colapse_thickness','epl colapsing thickness [m]')) string="%s\n%s"%(string,fielddisplay(self,'epl_thick_comp','epl thickness computation flag')) @@ -97,14 +106,13 @@ def extrude(self,md): # {{{ self.spcsediment_head=project3d(md,'vector',self.spcsediment_head,'type','node','layer',1) - self.spcepl_head=project3d(md,'vector',self.spcepl_head,'type','node','layer',1) - self.mask_eplactive_node=project3d(md,'vector',self.mask_eplactive_node,'type','node','layer',1) self.sediment_transmitivity=project3d(md,'vector',self.sediment_transmitivity,'type','node','layer',1) self.basal_moulin_input=project3d(md,'vector',self.basal_moulin_input,'type','node','layer',1) + self.mask_thawed_node=project3d(md,'vector',self.mask_thawed_node,'type','node','layer',1) if self.isefficientlayer==1 : self.spcepl_head=project3d(md,'vector',self.spcepl_head,'type','node','layer',1) + self.mask_eplactive_node=project3d(md,'vector',self.mask_eplactive_node,'type','node','layer',1) return self #}}} - def setdefaultparameters(self): #{{{ - + def setdefaultparameters(self): #{{{ #Parameters from de Fleurian 2014 self.water_compressibility = 5.04e-10 @@ -114,8 +122,11 @@ self.rel_tol = 1.0e-06 self.max_iter = 100 + self.steps_per_step = 1 self.sedimentlimit_flag = 0 self.sedimentlimit = 0 self.transfer_flag = 0 + self.unconfined_flag = 0 self.leakage_factor = 10.0 + self.requested_outputs = ['default'] self.sediment_compressibility = 1.0e-08 @@ -125,25 +136,38 @@ self.epl_compressibility = 1.0e-08 + self.epl_conductivity = 8.0e-02 self.epl_porosity = 0.4 self.epl_initial_thickness = 1.0 - self.epl_colapse_thickness = 1.0e-3 + self.epl_colapse_thickness = self.sediment_transmitivity/self.epl_conductivity self.epl_thick_comp = 1 self.epl_max_thickness = 5.0 - self.epl_conductivity = 8.0e-02 self.eplflip_lock = 0 - + return self # }}} + + def defaultoutputs(self,md): # {{{ + list = ['SedimentHeadHydrostep','SedimentHeadResidual','EffectivePressureHydrostep'] + if self.isefficientlayer==1: + list.extend(['EplHeadHydrostep','HydrologydcMaskEplactiveNode','HydrologydcMaskEplactiveElt','EplHeadSlopeX','EplHeadSlopeY','HydrologydcEplThicknessHydrostep']) + if self.steps_per_step>1: + list.extend(['EffectivePressure','SedimentHead']) + if self.isefficientlayer==1: + list.extend(['EplHead','HydrologydcEplThickness']) + return list + #}}} + def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.basal_moulin_input)): - self.basal_moulin_input=numpy.zeros((md.mesh.numberofvertices,1)) + self.epl_colapse_thickness = self.sediment_transmitivity/self.epl_conductivity + if np.all(np.isnan(self.basal_moulin_input)): + self.basal_moulin_input=np.zeros((md.mesh.numberofvertices)) print(" no hydrology.basal_moulin_input specified: values set as zero") return self # }}} - def checkconsistency(self,md,solution,analyses): #{{{ + def checkconsistency(self,md,solution,analyses): #{{{ #Early return - if HydrologyDCInefficientAnalysisEnum() not in analyses and HydrologyDCEfficientAnalysisEnum() not in analyses: + if 'HydrologyDCInefficientAnalysis' not in analyses and 'HydrologyDCEfficientAnalysis' not in analyses: return md @@ -154,6 +178,9 @@ md = checkfield(md,'fieldname','hydrology.rel_tol','>',0.,'numel',[1]) md = checkfield(md,'fieldname','hydrology.max_iter','>',0.,'numel',[1]) + md = checkfield(md,'fieldname','hydrology.steps_per_step','>',0.,'numel',[1]) md = checkfield(md,'fieldname','hydrology.sedimentlimit_flag','numel',[1],'values',[0,1,2,3]) md = checkfield(md,'fieldname','hydrology.transfer_flag','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','hydrology.unconfined_flag','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','hydrology.requested_outputs','stringrow',1) if self.sedimentlimit_flag==1: @@ -168,8 +195,9 @@ md = checkfield(md,'fieldname','hydrology.sediment_porosity','>',0.,'numel',[1]) md = checkfield(md,'fieldname','hydrology.sediment_thickness','>',0.,'numel',[1]) - md = checkfield(md,'fieldname','hydrology.sediment_transmitivity','>=',0,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','hydrology.sediment_transmitivity','>=',0,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','hydrology.mask_thawed_node','size',[md.mesh.numberofvertices],'values',[0,1]) if self.isefficientlayer==1: md = checkfield(md,'fieldname','hydrology.spcepl_head','Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','hydrology.mask_eplactive_node','size',[md.mesh.numberofvertices,1],'values',[0,1]) + md = checkfield(md,'fieldname','hydrology.mask_eplactive_node','size',[md.mesh.numberofvertices],'values',[0,1]) md = checkfield(md,'fieldname','hydrology.epl_compressibility','>',0.,'numel',[1]) md = checkfield(md,'fieldname','hydrology.epl_porosity','>',0.,'numel',[1]) @@ -183,37 +211,48 @@ md = checkfield(md,'fieldname','hydrology.epl_conductivity','numel',[1],'>',0.) # }}} - def marshall(self,md,fid): #{{{ - WriteData(fid,'enum',HydrologyModelEnum(),'data',HydrologydcEnum(),'format','Integer') - WriteData(fid,'object',self,'fieldname','water_compressibility','format','Double') - WriteData(fid,'object',self,'fieldname','isefficientlayer','format','Boolean') - WriteData(fid,'object',self,'fieldname','penalty_factor','format','Double') - WriteData(fid,'object',self,'fieldname','penalty_lock','format','Integer') - WriteData(fid,'object',self,'fieldname','rel_tol','format','Double') - WriteData(fid,'object',self,'fieldname','max_iter','format','Integer') - WriteData(fid,'object',self,'fieldname','sedimentlimit_flag','format','Integer') - WriteData(fid,'object',self,'fieldname','transfer_flag','format','Integer') + def marshall(self,prefix,md,fid): #{{{ + WriteData(fid,prefix,'name','md.hydrology.model','data',1,'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','water_compressibility','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','isefficientlayer','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','penalty_factor','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','penalty_lock','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','rel_tol','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','max_iter','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','steps_per_step','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','sedimentlimit_flag','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','transfer_flag','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','unconfined_flag','format','Integer') if self.sedimentlimit_flag==1: - WriteData(fid,'object',self,'fieldname','sedimentlimit','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','sedimentlimit','format','Double') if self.transfer_flag==1: - WriteData(fid,'object',self,'fieldname','leakage_factor','format','Double') - - WriteData(fid,'object',self,'fieldname','basal_moulin_input','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','spcsediment_head','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','sediment_compressibility','format','Double') - WriteData(fid,'object',self,'fieldname','sediment_porosity','format','Double') - WriteData(fid,'object',self,'fieldname','sediment_thickness','format','Double') - WriteData(fid,'object',self,'fieldname','sediment_transmitivity','format','DoubleMat','mattype',1) - - if self.isefficientlayer==1: - WriteData(fid,'object',self,'fieldname','spcepl_head','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','mask_eplactive_node','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','epl_compressibility','format','Double') - WriteData(fid,'object',self,'fieldname','epl_porosity','format','Double') - WriteData(fid,'object',self,'fieldname','epl_max_thickness','format','Double') - WriteData(fid,'object',self,'fieldname','epl_initial_thickness','format','Double') - WriteData(fid,'object',self,'fieldname','epl_colapse_thickness','format','Double') - WriteData(fid,'object',self,'fieldname','epl_thick_comp','format','Integer') - WriteData(fid,'object',self,'fieldname','epl_conductivity','format','Double') - WriteData(fid,'object',self,'fieldname','eplflip_lock','format','Integer') - # }}} + WriteData(fid,prefix,'object',self,'fieldname','leakage_factor','format','Double') + + WriteData(fid,prefix,'object',self,'fieldname','basal_moulin_input','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','spcsediment_head','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','sediment_compressibility','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','sediment_porosity','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','sediment_thickness','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','sediment_transmitivity','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','mask_thawed_node','format','DoubleMat','mattype',1) + + if self.isefficientlayer==1: + WriteData(fid,prefix,'object',self,'fieldname','spcepl_head','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','mask_eplactive_node','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','epl_compressibility','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','epl_porosity','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','epl_max_thickness','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','epl_initial_thickness','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','epl_colapse_thickness','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','epl_thick_comp','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','epl_conductivity','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','eplflip_lock','format','Integer') + + #process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] + outputs =outputscopy + WriteData(fid,prefix,'data',outputs,'name','md.hydrology.requested_outputs','format','StringArray') + # }}} Index: /issm/trunk-jpl/src/py3/classes/hydrologyshreve.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/hydrologyshreve.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/hydrologyshreve.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -15,5 +14,5 @@ self.spcwatercolumn = float('NaN') self.stabilization = 0 - + self.requested_outputs = [] #set defaults self.setdefaultparameters() @@ -25,4 +24,5 @@ string="%s\n%s"%(string,fielddisplay(self,'spcwatercolumn','water thickness constraints (NaN means no constraint) [m]')) string="%s\n%s"%(string,fielddisplay(self,'stabilization','artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.')) + string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) return string #}}} @@ -34,21 +34,34 @@ #Type of stabilization to use 0:nothing 1:artificial_diffusivity self.stabilization=1 - + self.requested_outputs= ['default'] return self #}}} + def defaultoutputs(self,md): # {{{ + list = ['Watercolumn','HydrologyWaterVx','HydrologyWaterVy'] + return list + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ #Early return - if HydrologyShreveAnalysisEnum() not in analyses: + if 'HydrologyShreveAnalysis' not in analyses: return md md = checkfield(md,'fieldname','hydrology.spcwatercolumn','Inf',1,'timeseries',1) md = checkfield(md,'fieldname','hydrology.stabilization','>=',0) - + md = checkfield(md,'fieldname','hydrology.requested_outputs','stringrow',1) return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',HydrologyModelEnum(),'data',HydrologyshreveEnum(),'format','Integer'); - WriteData(fid,'object',self,'fieldname','spcwatercolumn','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','stabilization','format','Double') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.hydrology.model','data',2,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','spcwatercolumn','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Double') + #process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] + outputs =outputscopy + WriteData(fid,prefix,'data',outputs,'name','md.hydrology.requested_outputs','format','StringArray') + # }}} Index: /issm/trunk-jpl/src/py3/classes/independent.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/independent.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/independent.py (revision 23670) @@ -1,7 +1,7 @@ -import numpy +import numpy as np from pairoptions import pairoptions from fielddisplay import fielddisplay -import MatlabFuncs as m -from EnumDefinitions import * +from checkfield import checkfield +from MatlabFuncs import * class independent(object): @@ -13,9 +13,9 @@ """ - def __init__(self,**kwargs): # {{{ + def __init__(self,*args): # {{{ self.name = '' self.type = '' self.fos_forward_index = float('NaN') - self.fov_forward_indices = numpy.array([]) + self.fov_forward_indices = np.array([]) self.nods = 0 @@ -24,5 +24,5 @@ #use provided options to change fields - options=pairoptions(**kwargs) + options=pairoptions(*args) #OK get other fields @@ -32,9 +32,9 @@ s =" independent variable:\n" - s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") + s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding String)") s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") - if not numpy.isnan(self.fos_forward_index): + if not np.isnan(self.fos_forward_index): s+="%s\n" % fielddisplay(self,'fos_forward_index',"index for fos_foward driver of ADOLC") - if numpy.any(numpy.logical_not(numpy.isnan(self.fov_forward_indices))): + if np.any(np.logical_not(np.isnan(self.fov_forward_indices))): s+="%s\n" % fielddisplay(self,'fov_forward_indices',"indices for fov_foward driver of ADOLC") @@ -46,5 +46,5 @@ # }}} def checkconsistency(self,md,i,solution,analyses,driver): # {{{ - if not numpy.isnan(self.fos_forward_index): + if not np.isnan(self.fos_forward_index): if not strcmpi(driver,'fos_forward'): raise TypeError("cannot declare an independent with a fos_forward_index when the driver is not fos_forward!") @@ -52,10 +52,10 @@ raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") - if self.fov_forward_indices: + if len(self.fov_forward_indices) > 0: if not strcmpi(driver,'fov_forward'): raise TypeError("cannot declare an independent with fov_forward_indices when the driver is not fov_forward!") if self.nods==0: raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") - md = checkfield(md,'fieldname',"autodiff.independents[%d].fov_forward_indices" % i,'>=',1,'<=',self.nods,'size',[float('NaN'),1]) + md = checkfield(md,'fieldname',"autodiff.independents[%d].fov_forward_indices" % i,'>=',1,'<=',self.nods) return md Index: /issm/trunk-jpl/src/py3/classes/initialization.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/initialization.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/initialization.py (revision 23670) @@ -1,6 +1,5 @@ -import numpy +import numpy as np from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -62,5 +61,13 @@ #Lithostatic pressure by default - self.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z.reshape(-1,1)) + # self.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface[:,0]-md.mesh.z) + #self.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z.reshape(-1,)) + + if np.ndim(md.geometry.surface)==2: + print('Reshaping md.geometry.surface for you convenience but you should fix it in you files') + self.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface.reshape(-1,)-md.mesh.z) + else: + self.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z) + return self #}}} @@ -69,19 +76,19 @@ #}}} def checkconsistency(self,md,solution,analyses): # {{{ - if StressbalanceAnalysisEnum() in analyses: - if not numpy.any(numpy.logical_or(numpy.isnan(md.initialization.vx),numpy.isnan(md.initialization.vy))): + if 'StressbalanceAnalysis' in analyses: + if not np.any(np.logical_or(np.isnan(md.initialization.vx),np.isnan(md.initialization.vy))): md = checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - if MasstransportAnalysisEnum() in analyses: + if 'MasstransportAnalysis' in analyses: md = checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) #Triangle with zero velocity - if numpy.any(numpy.logical_and(numpy.sum(numpy.abs(md.initialization.vx[md.mesh.elements-1]),axis=1)==0,\ - numpy.sum(numpy.abs(md.initialization.vy[md.mesh.elements-1]),axis=1)==0)): + if np.any(np.logical_and(np.sum(np.abs(md.initialization.vx[md.mesh.elements-1]),axis=1)==0,\ + np.sum(np.abs(md.initialization.vy[md.mesh.elements-1]),axis=1)==0)): md.checkmessage("at least one triangle has all its vertices with a zero velocity") - if ThermalAnalysisEnum() in analyses: + if 'ThermalAnalysis' in analyses: md = checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) @@ -90,43 +97,45 @@ md = checkfield(md,'fieldname','initialization.vz','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.pressure','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - if (EnthalpyAnalysisEnum() in analyses and md.thermal.isenthalpy): + if ('EnthalpyAnalysis' in analyses and md.thermal.isenthalpy): md = checkfield(md,'fieldname','initialization.waterfraction','>=',0,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.watercolumn' ,'>=',0,'size',[md.mesh.numberofvertices]) - if HydrologyShreveAnalysisEnum() in analyses: + pos = np.nonzero(md.initialization.waterfraction > 0.)[0] + if(pos.size): + md = checkfield(md,'fieldname', 'delta Tpmp', 'field', np.absolute(md.initialization.temperature[pos]-(md.materials.meltingpoint-md.materials.beta*md.initialization.pressure[pos])),'<',1e-11, 'message','set temperature to pressure melting point at locations with waterfraction>0'); + if 'HydrologyShreveAnalysis' in analyses: if hasattr(md.hydrology,'hydrologyshreve'): md = checkfield(md,'fieldname','initialization.watercolumn','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - if HydrologyDCInefficientAnalysisEnum() in analyses: + if 'HydrologyDCInefficientAnalysis' in analyses: if hasattr(md.hydrology,'hydrologydc'): - md = checkfield(md,'fieldname','initialization.sediment_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) - if HydrologyDCEfficientAnalysisEnum() in analyses: + md = checkfield(md,'fieldname','initialization.sediment_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + if 'HydrologyDCEfficientAnalysis' in analyses: if hasattr(md.hydrology,'hydrologydc'): if md.hydrology.isefficientlayer==1: - md = checkfield(md,'fieldname','initialization.epl_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) - md = checkfield(md,'fieldname','initialization.epl_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) + md = checkfield(md,'fieldname','initialization.epl_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'fieldname','initialization.epl_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'data',self.vx,'format','DoubleMat','mattype',1,'enum',VxEnum(),'scale',1./yts) - WriteData(fid,'data',self.vy,'format','DoubleMat','mattype',1,'enum',VyEnum(),'scale',1./yts) - WriteData(fid,'data',self.vz,'format','DoubleMat','mattype',1,'enum',VzEnum(),'scale',1./yts) - WriteData(fid,'data',self.pressure,'format','DoubleMat','mattype',1,'enum',PressureEnum()) - WriteData(fid,'data',self.temperature,'format','DoubleMat','mattype',1,'enum',TemperatureEnum()) - WriteData(fid,'data',self.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum()) - WriteData(fid,'data',self.watercolumn,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum()) - WriteData(fid,'data',self.sediment_head,'format','DoubleMat','mattype',1,'enum',SedimentHeadEnum()) - WriteData(fid,'data',self.epl_head,'format','DoubleMat','mattype',1,'enum',EplHeadEnum()) - WriteData(fid,'data',self.epl_thickness,'format','DoubleMat','mattype',1,'enum',HydrologydcEplThicknessEnum()) - + WriteData(fid,prefix,'object',self,'fieldname','vx','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','vy','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','vz','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','pressure','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','temperature','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','waterfraction','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','sediment_head','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','epl_head','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','epl_thickness','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','watercolumn','format','DoubleMat','mattype',1) if md.thermal.isenthalpy: tpmp = md.materials.meltingpoint - md.materials.beta*md.initialization.pressure; - pos = numpy.nonzero(md.initialization.temperature > tpmp)[0] + pos = np.nonzero(md.initialization.waterfraction > 0.)[0] enthalpy = md.materials.heatcapacity*(md.initialization.temperature-md.constants.referencetemperature); - enthalpy[pos] = md.materials.heatcapacity*tpmp[pos].reshape(-1,1) - md.constants.referencetemperature + md.materials.latentheat*md.initialization.waterfraction[pos].reshape(-1,1) - WriteData(fid,'data',enthalpy,'format','DoubleMat','mattype',1,'enum',EnthalpyEnum()); + enthalpy[pos] = md.materials.heatcapacity*(tpmp[pos].reshape(-1,) - md.constants.referencetemperature) + md.materials.latentheat*md.initialization.waterfraction[pos].reshape(-1,) + WriteData(fid,prefix,'data',enthalpy,'format','DoubleMat','mattype',1,'name','md.initialization.enthalpy'); # }}} Index: /issm/trunk-jpl/src/py3/classes/inversion.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/inversion.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/inversion.py (revision 23670) @@ -1,7 +1,5 @@ -import numpy +import numpy as np from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData @@ -24,5 +22,5 @@ self.nsteps = 0 self.maxiter_per_step = float('NaN') - self.cost_functions = float('NaN') + self.cost_functions = '' self.cost_functions_coefficients = float('NaN') self.gradient_scaling = float('NaN') @@ -78,9 +76,9 @@ self.vel_obs=project3d(md,'vector',self.vel_obs,'type','node') self.thickness_obs=project3d(md,'vector',self.thickness_obs,'type','node') - if not numpy.any(numpy.isnan(self.cost_functions_coefficients)): + if not np.any(np.isnan(self.cost_functions_coefficients)): self.cost_functions_coefficients=project3d(md,'vector',self.cost_functions_coefficients,'type','node') - if not numpy.any(numpy.isnan(self.min_parameters)): + if not np.any(np.isnan(self.min_parameters)): self.min_parameters=project3d(md,'vector',self.min_parameters,'type','node') - if not numpy.any(numpy.isnan(self.max_parameters)): + if not np.any(np.isnan(self.max_parameters)): self.max_parameters=project3d(md,'vector',self.max_parameters,'type','node') return self @@ -100,5 +98,5 @@ #maximum number of iteration in the optimization algorithm for #each step - self.maxiter_per_step=20*numpy.ones(self.nsteps) + self.maxiter_per_step=20*np.ones(self.nsteps) #the inversed parameter is updated as follows: @@ -107,13 +105,13 @@ #inversed parameter (10^8 for B, 50 for drag) and can be decreased #after the first iterations - self.gradient_scaling=50*numpy.ones((self.nsteps,1)) + self.gradient_scaling=50*np.ones((self.nsteps,1)) #several responses can be used: - self.cost_functions=101 + self.cost_functions=[101,] #step_threshold is used to speed up control method. When #misfit(1)/misfit(0) < self.step_threshold, we go directly to #the next step - self.step_threshold=.7*numpy.ones(self.nsteps) #30 per cent decrement + self.step_threshold=.7*np.ones(self.nsteps) #30 per cent decrement #cost_function_threshold is a criteria to stop the control methods. @@ -130,6 +128,6 @@ return md - num_controls=numpy.size(md.inversion.control_parameters) - num_costfunc=numpy.size(md.inversion.cost_functions) + num_controls=np.size(md.inversion.control_parameters) + num_costfunc=np.size(md.inversion.cost_functions) md = checkfield(md,'fieldname','inversion.iscontrol','values',[0,1]) @@ -146,9 +144,9 @@ #Only SSA, HO and FS are supported right now - if solution==StressbalanceSolutionEnum(): + if solution=='StressbalanceSolution': if not (md.flowequation.isSSA or md.flowequation.isHO or md.flowequation.isFS or md.flowequation.isL1L2): md.checkmessage("'inversion can only be performed for SSA, HO or FS ice flow models"); - if solution==BalancethicknessSolutionEnum(): + if solution=='BalancethicknessSolution': md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) else: @@ -158,37 +156,37 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - WriteData(fid,'enum',InversionTypeEnum(),'data',0,'format','Integer') - WriteData(fid,'object',self,'fieldname','iscontrol','format','Boolean') - WriteData(fid,'object',self,'fieldname','incomplete_adjoint','format','Boolean') + WriteData(fid,prefix,'name','md.inversion.type','data',0,'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','iscontrol','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','incomplete_adjoint','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','vel_obs','format','DoubleMat','mattype',1,'scale',1./yts) if not self.iscontrol: return - WriteData(fid,'object',self,'fieldname','nsteps','format','Integer') - WriteData(fid,'object',self,'fieldname','maxiter_per_step','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','gradient_scaling','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'fieldname','cost_function_threshold','format','Double') - WriteData(fid,'object',self,'fieldname','min_parameters','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'fieldname','max_parameters','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'fieldname','step_threshold','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'fieldname','thickness_obs','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'fieldname','surface_obs','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','nsteps','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','maxiter_per_step','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','gradient_scaling','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'fieldname','cost_function_threshold','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','min_parameters','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'fieldname','max_parameters','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'fieldname','step_threshold','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','thickness_obs','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','surface_obs','format','DoubleMat','mattype',1) #process control parameters num_control_parameters=len(self.control_parameters) - data=numpy.array([StringToEnum(control_parameter)[0] for control_parameter in self.control_parameters]).reshape(1,-1) - WriteData(fid,'data',data,'enum',InversionControlParametersEnum(),'format','DoubleMat','mattype',3) - WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum(),'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','control_parameters','format','StringArray') + WriteData(fid,prefix,'data',num_control_parameters,'name','md.inversion.num_control_parameters','format','Integer') #process cost functions - num_cost_functions=numpy.size(self.cost_functions) + num_cost_functions=np.size(self.cost_functions) data=marshallcostfunctions(self.cost_functions) - WriteData(fid,'data',numpy.array(data).reshape(1,-1),'enum',InversionCostFunctionsEnum(),'format','DoubleMat','mattype',3) - WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer') + WriteData(fid,prefix,'data',data,'name','md.inversion.cost_functions','format','StringArray') + WriteData(fid,prefix,'data',num_cost_functions,'name','md.inversion.num_cost_functions','format','Integer') # }}} Index: /issm/trunk-jpl/src/py3/classes/linearbasalforcings.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/linearbasalforcings.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/linearbasalforcings.py (revision 23670) @@ -1,7 +1,6 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData -import numpy +import numpy as np class linearbasalforcings(object): @@ -52,6 +51,6 @@ def initialize(self,md): # {{{ - if numpy.all(numpy.isnan(self.groundedice_melting_rate)): - self.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) + if np.all(np.isnan(self.groundedice_melting_rate)): + self.groundedice_melting_rate=np.zeros((md.mesh.numberofvertices)) print(" no basalforcings.groundedice_melting_rate specified: values set as zero") @@ -68,41 +67,34 @@ def checkconsistency(self,md,solution,analyses): # {{{ - if MasstransportAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and not md.transient.ismasstransport): + if 'MasstransportAnalysis' in analyses and not (solution=='TransientSolution' and not md.transient.ismasstransport): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0); - md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<',md.basalforcings.upperwater_elevation); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0); + md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'singletimeseries',1) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0); - md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<',md.basalforcings.upperwater_elevation); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0); + md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'singletimeseries',1) - if ThermalAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and not md.transient.isthermal): + if 'ThermalAnalysis' in analyses and not (solution=='TransientSolution' and not md.transient.isthermal): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) - md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0); - md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<',md.basalforcings.upperwater_elevation); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0); + md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','singletimeseries',1) + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'singletimeseries',1) md = checkfield(md,'fieldname','basalforcings.geothermalflux','NaN',1,'Inf',1,'timeseries',1,'>=',0) return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ - yts=365.0*24.0*3600.0 + yts=md.constants.yts - floatingice_melting_rate = numpy.zeros((md.mesh.numberofvertices,1)) - pos=numpy.nonzero(md.geometry.base<=md.basalforcings.deepwater_elevation) - floatingice_melting_rate[pos]=md.basalforcings.deepwater_melting_rate - pos=numpy.nonzero(numpy.logical_and(md.geometry.base>md.basalforcings.deepwater_elevation,md.geometry.base',0,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements]) - md = checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey','Paterson','Arrhenius','LliboutryDuval']) + md = checkfield(md,'fieldname','materials.rheology_law','values',['None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson','Arrhenius','LliboutryDuval']) md = checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.mantle_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.mantle_density','>',0,'numel',[1]); + md = checkfield(md,'fieldname','materials.earth_density','>',0,'numel',[1]); + return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',MaterialsEnum(),'data',MatdamageiceEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','materials','fieldname','rho_ice','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rho_water','enum',MaterialsRhoSeawaterEnum(),'format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rho_freshwater','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','mu_water','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','heatcapacity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','latentheat','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','thermalconductivity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','meltingpoint','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','beta','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2) - WriteData(fid,'data',StringToEnum(self.rheology_law)[0],'enum',MaterialsRheologyLawEnum(),'format','Integer') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.materials.type','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_ice','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_water','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_freshwater','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mu_water','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','heatcapacity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','latentheat','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermalconductivity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','meltingpoint','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','beta','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'data',self.rheology_law,'name','md.materials.rheology_law','format','String') - WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); - WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.); - WriteData(fid,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double'); - WriteData(fid,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','earth_density','format','Double'); + # }}} Index: /issm/trunk-jpl/src/py3/classes/matice.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/matice.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/matice.py (revision 23670) @@ -1,6 +1,4 @@ from fielddisplay import fielddisplay from project3d import project3d -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData @@ -31,9 +29,14 @@ self.rheology_law = '' - #gia: + #giaivins: self.lithosphere_shear_modulus = 0. self.lithosphere_density = 0. self.mantle_shear_modulus = 0. - self.mantle_density = 0. + self.mantle_density = 0. + + #SLR + self.earth_density= 5512; + + self.setdefaultparameters() @@ -54,11 +57,13 @@ string="%s\n%s"%(string,fielddisplay(self,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")) string="%s\n%s"%(string,fielddisplay(self,"thermal_exchange_velocity","thermal exchange velocity [m/s]")) - string="%s\n%s"%(string,fielddisplay(self,"rheology_B","flow law parameter [Pa/s^(1/n)]")) + string="%s\n%s"%(string,fielddisplay(self,"rheology_B","flow law parameter [Pa s^(1/n)]")) string="%s\n%s"%(string,fielddisplay(self,"rheology_n","Glen's flow law exponent")) - string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Cuffey', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) + string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_shear_modulus","Lithosphere shear modulus [Pa]")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_density","Lithosphere density [g/cm^-3]")) string="%s\n%s"%(string,fielddisplay(self,"mantle_shear_modulus","Mantle shear modulus [Pa]")) string="%s\n%s"%(string,fielddisplay(self,"mantle_density","Mantle density [g/cm^-3]")) + string="%s\n%s"%(string,fielddisplay(self,"earth_density","Mantle density [kg/m^-3]")) + return string @@ -115,4 +120,8 @@ self.mantle_shear_modulus = 1.45*10**11 # (Pa) self.mantle_density = 3.34 # (g/cm^-3) + + #SLR + self.earth_density= 5512; # average density of the Earth, (kg/m^3) + return self @@ -125,33 +134,36 @@ md = checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements]) - md = checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey','Paterson','Arrhenius','LliboutryDuval']) + md = checkfield(md,'fieldname','materials.rheology_law','values',['None','BuddJacka','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']) md = checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.mantle_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.mantle_density','>',0,'numel',[1]); + md = checkfield(md,'fieldname','materials.earth_density','>',0,'numel',[1]); + return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',MaterialsEnum(),'data',MaticeEnum(),'format','Integer'); - WriteData(fid,'object',self,'class','materials','fieldname','rho_ice','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rho_water','enum',MaterialsRhoSeawaterEnum(),'format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rho_freshwater','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','mu_water','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','heatcapacity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','latentheat','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','thermalconductivity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','meltingpoint','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','beta','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double') - WriteData(fid,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2) - WriteData(fid,'data',StringToEnum(self.rheology_law)[0],'enum',MaterialsRheologyLawEnum(),'format','Integer') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'name','md.materials.type','data',3,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_ice','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_water','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_freshwater','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mu_water','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','heatcapacity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','latentheat','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermalconductivity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','meltingpoint','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','beta','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double') + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'data',self.rheology_law,'name','md.materials.rheology_law','format','String') - WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); - WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.); - WriteData(fid,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double'); - WriteData(fid,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','earth_density','format','Double'); + # }}} Index: /issm/trunk-jpl/src/py3/classes/mesh2d.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/mesh2d.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/mesh2d.py (revision 23670) @@ -1,8 +1,7 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay from checkfield import checkfield +import MatlabFuncs as m from WriteData import WriteData -from EnumDefinitions import * -import MatlabFuncs as m class mesh2d(object): @@ -25,4 +24,5 @@ self.long = float('NaN'); self.epsg = 0; + self.scale_factor = float('NaN'); self.vertexonboundary = float('NaN'); @@ -57,6 +57,6 @@ 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 vertices connected to vertex_i")) - string="%s\n%s"%(string,fielddisplay(self,"elementconnectivity","list of vertices connected to element_i")) + 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")) @@ -69,4 +69,5 @@ 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 #}}} @@ -83,17 +84,21 @@ #}}} def checkconsistency(self,md,solution,analyses): # {{{ + if(solution=='LoveSolution'): + return md = checkfield(md,'fieldname','mesh.x','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','mesh.y','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',numpy.arange(1,md.mesh.numberofvertices+1)) + md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',np.arange(1,md.mesh.numberofvertices+1)) md = checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements,3]) -# if numpy.any(numpy.logical_not(m.ismember(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements))): - if any(numpy.logical_not(m.ismember(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements))): - [x for x in A if not x in B] + 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 = 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") - if solution==ThermalSolutionEnum(): + md = checkfield(md,'fieldname','mesh.segments','NaN',1,'Inf',1,'>',0,'size',[np.nan,3]); + if(np.size(self.scale_factor)>1): + md = checkfield(md,'fieldname','mesh.scale_factor','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) + + if solution=='ThermalSolution': md.checkmessage("thermal not supported for 2d mesh") @@ -109,14 +114,20 @@ return "Tria" #}}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',DomainTypeEnum(),'data',StringToEnum("Domain"+self.domaintype())[0],'format','Integer'); - WriteData(fid,'enum',DomainDimensionEnum(),'data',self.dimension(),'format','Integer'); - WriteData(fid,'enum',MeshElementtypeEnum(),'data',StringToEnum(self.elementtype())[0],'format','Integer'); - WriteData(fid,'object',self,'class','mesh','fieldname','x','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','y','format','DoubleMat','mattype',1) - WriteData(fid,'enum',MeshZEnum(),'data',numpy.zeros(self.numberofvertices),'format','DoubleMat','mattype',1); - WriteData(fid,'object',self,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2) - WriteData(fid,'object',self,'class','mesh','fieldname','numberofelements','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','numberofvertices','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','average_vertex_connectivity','format','Integer') + 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_dimension','data',self.dimension(),'format','Integer'); + WriteData(fid,prefix,'name','md.mesh.elementtype','data',self.elementtype(),'format','String'); + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','x','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','y','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'name','md.mesh.z','data',np.zeros(self.numberofvertices),'format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofelements','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofvertices','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','average_vertex_connectivity','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','vertexonboundary','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','segments','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','scale_factor','format','DoubleMat','mattype',1) + if md.transient.isoceancoupling: + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','lat','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','long','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk-jpl/src/py3/classes/mesh3dprisms.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/mesh3dprisms.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/mesh3dprisms.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import * import MatlabFuncs as m @@ -26,4 +25,5 @@ self.long = float('NaN'); self.epsg = 0; + self.scale_factor = float('NaN'); self.vertexonbase = float('NaN'); @@ -74,11 +74,11 @@ string="%s\n%s"%(string,fielddisplay(self,"vertexonbase","lower vertices flags list")) string="%s\n%s"%(string,fielddisplay(self,"vertexonsurface","upper vertices flags list")) - string="%s\n%s"%(string,fielddisplay(self,"uppervertex","upper vertex list (-1 for vertex on the upper surface)")) - string="%s\n%s"%(string,fielddisplay(self,"upperelements","upper element list (-1 for element on the upper layer)")) - string="%s\n%s"%(string,fielddisplay(self,"lowervertex","lower vertex list (-1 for vertex on the lower surface)")) - string="%s\n%s"%(string,fielddisplay(self,"lowerelements","lower element list (-1 for element on the lower layer)")) + string="%s\n%s"%(string,fielddisplay(self,"uppervertex","upper vertex list (NaN for vertex on the upper surface)")) + string="%s\n%s"%(string,fielddisplay(self,"upperelements","upper element list (NaN for element on the upper layer)")) + string="%s\n%s"%(string,fielddisplay(self,"lowervertex","lower vertex list (NaN for vertex on the lower surface)")) + string="%s\n%s"%(string,fielddisplay(self,"lowerelements","lower element list (NaN for element on the lower layer)")) string="%s\n%s"%(string,fielddisplay(self,"vertexonboundary","vertices on the boundary of the domain flag list")) - string="%s\n%s"%(string,fielddisplay(self,"vertexconnectivity","list of vertices connected to vertex_i")) - string="%s\n%s"%(string,fielddisplay(self,"elementconnectivity","list of vertices connected to element_i")) + 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")) @@ -91,4 +91,5 @@ 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 #}}} @@ -109,7 +110,7 @@ md = checkfield(md,'fieldname','mesh.y','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','mesh.z','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',numpy.arange(1,md.mesh.numberofvertices+1)) + md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',np.arange(1,md.mesh.numberofvertices+1)) md = checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements,6]) - if numpy.any(numpy.logical_not(m.ismember(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements))): + 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 mesh3dprisms outline") md = checkfield(md,'fieldname','mesh.numberoflayers','>=',0) @@ -119,4 +120,6 @@ md = checkfield(md,'fieldname','mesh.vertexonsurface','size',[md.mesh.numberofvertices],'values',[0,1]) md = checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',24,'message',"'mesh.average_vertex_connectivity' should be at least 24 in 3d") + if(np.size(self.scale_factor)>1): + md = checkfield(md,'fieldname','mesh.scale_factor','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) return md @@ -131,22 +134,26 @@ return "Penta" #}}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'enum',DomainTypeEnum(),'data',StringToEnum("Domain"+self.domaintype())[0],'format','Integer'); - WriteData(fid,'enum',DomainDimensionEnum(),'data',self.dimension(),'format','Integer'); - WriteData(fid,'enum',MeshElementtypeEnum(),'data',StringToEnum(self.elementtype())[0],'format','Integer'); - WriteData(fid,'object',self,'class','mesh','fieldname','x','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','y','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','z','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2) - WriteData(fid,'object',self,'class','mesh','fieldname','numberoflayers','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','numberofelements','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','numberofvertices','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','vertexonbase','format','BooleanMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','vertexonsurface','format','BooleanMat','mattype',1) - WriteData(fid,'object',self,'class','mesh','fieldname','lowerelements','format','DoubleMat','mattype',2) - WriteData(fid,'object',self,'class','mesh','fieldname','upperelements','format','DoubleMat','mattype',2) - WriteData(fid,'object',self,'class','mesh','fieldname','average_vertex_connectivity','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','elements2d','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'class','mesh','fieldname','numberofvertices2d','format','Integer') - WriteData(fid,'object',self,'class','mesh','fieldname','numberofelements2d','format','Integer') + 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_dimension','data',self.dimension(),'format','Integer'); + WriteData(fid,prefix,'name','md.mesh.elementtype','data',self.elementtype(),'format','String'); + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','x','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','y','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','z','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberoflayers','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofelements','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofvertices','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','vertexonbase','format','BooleanMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','vertexonsurface','format','BooleanMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','lowerelements','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','upperelements','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','average_vertex_connectivity','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','elements2d','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofvertices2d','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofelements2d','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','scale_factor','format','DoubleMat','mattype',1) + if md.transient.isoceancoupling: + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','lat','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','long','format','DoubleMat','mattype',1) # }}} Index: /issm/trunk-jpl/src/py3/classes/miscellaneous.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/miscellaneous.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/miscellaneous.py (revision 23670) @@ -1,5 +1,4 @@ from collections import OrderedDict from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -37,5 +36,5 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','name','format','String') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','name','format','String'); # }}} Index: /issm/trunk-jpl/src/py3/classes/mismipbasalforcings.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/mismipbasalforcings.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/mismipbasalforcings.py (revision 23670) @@ -1,10 +1,10 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * +from project3d import project3d from checkfield import checkfield from WriteData import WriteData -import numpy +import numpy as np class mismipbasalforcings(object): - """ + """ MISMIP Basal Forcings class definition @@ -13,5 +13,5 @@ """ - def __init__(self,md): # {{{ + def __init__(self): # {{{ self.groundedice_melting_rate = float('NaN') @@ -20,8 +20,4 @@ self.upperdepth_melt = float('NaN') self.geothermalflux = float('NaN') - - if numpy.all(numpy.isnan(self.groundedice_melting_rate)): - self.groundedice_melting_rate=numpy.zeros(md.mesh.numberofvertices) - print(' no basalforcings.groundedice_melting_rate specified: values set as zero') self.setdefaultparameters() @@ -35,20 +31,25 @@ string="%s\n%s"%(string,fielddisplay(self,"upperdepth_melt","Depth above which melt rate is zero [m]")) string="%s\n%s"%(string,fielddisplay(self,"geothermalflux","Geothermal heat flux [W/m^2]")) - return string #}}} def extrude(self,md): # {{{ - self.coefficient=project3d(md,'vector',self.coefficient,'type','node','layer',1) - self.p=project3d(md,'vector',self.p,'type','element') - self.q=project3d(md,'vector',self.q,'type','element') + self.groundedice_melting_rate=project3d(md,'vector',self.groundedice_melting_rate,'type','node','layer',1) + self.geothermalflux=project3d(md,'vector',self.geothermalflux,'type','node','layer',1) #bedrock only gets geothermal flux return self #}}} + def initialize(self,md): # {{{ + if np.all(np.isnan(self.groundedice_melting_rate)): + self.groundedice_melting_rate=np.zeros((md.mesh.numberofvertices)) + print(' no basalforcings.groundedice_melting_rate specified: values set as zero') + if np.all(np.isnan(self.geothermalflux)): + self.geothermalflux=np.zeros((md.mesh.numberofvertices)) + print(" no basalforcings.geothermalflux specified: values set as zero") + return self + #}}} def setdefaultparameters(self): # {{{ - # default values for melting parameterization self.meltrate_factor = 0.2 self.threshold_thickness = 75. self.upperdepth_melt = -100. - return self #}}} @@ -56,5 +57,5 @@ #Early return - if MasstransportAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and md.transient.ismasstransport==0): + if 'MasstransportAnalysis' in analyses and not (solution=='TransientSolution' and md.transient.ismasstransport==0): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) @@ -63,5 +64,5 @@ md = checkfield(md,'fieldname','basalforcings.upperdepth_melt','<=',0,'numel',[1]) - if BalancethicknessAnalysisEnum() in analyses: + if 'BalancethicknessAnalysis' in analyses: md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) @@ -70,5 +71,5 @@ md = checkfield(md,'fieldname','basalforcings.upperdepth_melt','<=',0,'numel',[1]) - if ThermalAnalysisEnum() in analyses and not (solution==TransientSolutionEnum() and md.transient.isthermal==0): + if 'ThermalAnalysis' in analyses and not (solution=='TransientSolution' and md.transient.isthermal==0): md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1) @@ -79,5 +80,5 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ yts=md.constants.yts @@ -85,14 +86,10 @@ print('WARNING: value of yts for MISMIP+ runs different from ISSM default!') - floatingice_melting_rate = numpy.zeros((md.mesh.numberofvertices,1)) - floatingice_melting_rate = md.basalforcings.meltrate_factor*numpy.tanh((md.geometry.base-md.geometry.bed)/md.basalforcings.threshold_thickness)*numpy.amax(md.basalforcings.upperdepth_melt-md.geometry.base,0) - - WriteData(fid,'enum',BasalforcingsEnum(),'data',MismipFloatingMeltRateEnum(),'format','Integer') - WriteData(fid,'data',floatingice_melting_rate,'format','DoubleMat','enum',BasalforcingsFloatingiceMeltingRateEnum(),'mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','enum',BasalforcingsGroundediceMeltingRateEnum(),'mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','geothermalflux','enum',BasalforcingsGeothermalfluxEnum(),'format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','meltrate_factor','format','Double','enum',BasalforcingsMeltrateFactorEnum(),'scale',1./yts) - WriteData(fid,'object',self,'fieldname','threshold_thickness','format','Double','enum',BasalforcingsThresholdThicknessEnum()) - WriteData(fid,'object',self,'fieldname','upperdepth_melt','format','Double','enum',BasalforcingsUpperdepthMeltEnum()) + WriteData(fid,prefix,'name','md.basalforcings.model','data',3,'format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','name','md.basalforcings.groundedice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','geothermalflux','name','md.basalforcings.geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','meltrate_factor','format','Double','scale',1./yts) + WriteData(fid,prefix,'object',self,'fieldname','threshold_thickness','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','upperdepth_melt','format','Double') # }}} Index: /issm/trunk-jpl/src/py3/classes/model.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/model.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/model.py (revision 23670) @@ -1,156 +1,281 @@ #module imports {{{ -import numpy +import numpy as np import copy import sys -import MatlabFuncs as m +from mesh2d import mesh2d +from mesh3dprisms import mesh3dprisms +from mask import mask +from geometry import geometry +from constants import constants +from SMBforcing import SMBforcing +from SMBpdd import SMBpdd +from SMBd18opdd import SMBd18opdd +from SMBgradients import SMBgradients +from SMBcomponents import SMBcomponents +from SMBmeltcomponents import SMBmeltcomponents +from basalforcings import basalforcings +from matice import matice +from levelset import levelset +from calving import calving +from fourierlove import fourierlove +from calvinglevermann import calvinglevermann +#from calvingpi import calvingpi +from frontalforcings import frontalforcings +from damage import damage +from friction import friction +from flowequation import flowequation +from timestepping import timestepping +from timesteppingadaptive import timesteppingadaptive +from initialization import initialization +from rifts import rifts +from slr import slr +from debug import debug +from verbose import verbose +from issmsettings import issmsettings +from toolkits import toolkits +from generic import generic +from pfe import pfe +from vilje import vilje +from hexagon import hexagon +from cyclone import cyclone +from stallo import stallo +from balancethickness import balancethickness +from stressbalance import stressbalance +from groundingline import groundingline +from hydrologyshreve import hydrologyshreve +from hydrologydc import hydrologydc +from masstransport import masstransport +from thermal import thermal +from steadystate import steadystate +from transient import transient +from giaivins import giaivins +from esa import esa +from autodiff import autodiff +from inversion import inversion +from outputdefinition import outputdefinition +from qmu import qmu +from amr import amr +from results import results +from radaroverlay import radaroverlay +from miscellaneous import miscellaneous +from private import private +from mumpsoptions import mumpsoptions +from iluasmoptions import iluasmoptions +from project3d import project3d +from project2d import project2d +from FlagElements import FlagElements +from NodeConnectivity import NodeConnectivity +from ElementConnectivity import ElementConnectivity +from contourenvelope import contourenvelope +from DepthAverage import DepthAverage #}}} class model(object): #properties - def __init__(self,*filename):#{{{ - - def netCDFread(filename): - def walktree(data): - keys = data.groups.keys() - yield keys - for key in keys: - for children in walktree(data.groups[str(key)]): - yield children - - if path.exists(filename): - print ('Opening {} for reading '.format(filename)) - NCData=Dataset(filename, 'r') - class_dict={} - - for children in walktree(NCData): - for child in children: - class_dict[str(child)]=str(getattr(NCData.groups[str(child)],'classtype')) - - return class_dict - - if filename: - classtype=netCDFread(filename[0]) - else: - classtype=self.properties() - - VT=[v[0] for v in dict.values(classtype)] - classnames=[classname for classname in dict.keys(classtype)] - module=map(__import__,VT) - - for i,mod in enumerate(module): - self.__dict__[classnames[i]] = getattr(mod,str(classtype[str(classnames[i])][0]))() - - #}}} - + def __init__(self):#{{{ + + # classtype=model.properties + + # for classe in dict.keys(classtype): + # print classe + # self.__dict__[classe] = classtype[str(classe)] + + self.mesh = mesh2d() + self.mask = mask() + self.geometry = geometry() + self.constants = constants() + self.smb = SMBforcing() + self.basalforcings = basalforcings() + self.materials = matice() + self.damage = damage() + self.friction = friction() + self.flowequation = flowequation() + self.timestepping = timestepping() + self.initialization = initialization() + self.rifts = rifts() + self.slr = slr() + + self.debug = debug() + self.verbose = verbose() + self.settings = issmsettings() + self.toolkits = toolkits() + self.cluster = generic() + + self.balancethickness = balancethickness() + self.stressbalance = stressbalance() + self.groundingline = groundingline() + self.hydrology = hydrologyshreve() + self.masstransport = masstransport() + self.thermal = thermal() + self.steadystate = steadystate() + self.transient = transient() + self.levelset = levelset() + self.calving = calving() + self.frontalforcings = frontalforcings() + self.gia = giaivins() + self.love = fourierlove() + self.esa = esa() + self.autodiff = autodiff() + self.inversion = inversion() + self.qmu = qmu() + self.amr = amr() + + self.results = results() + self.outputdefinition = outputdefinition() + self.radaroverlay = radaroverlay() + self.miscellaneous = miscellaneous() + self.private = private() + #}}} def properties(self): # {{{ # ordered list of properties since vars(self) is random - return {'mesh':['mesh2d','mesh properties'],\ - 'mask':['mask','defines grounded and floating elements'],\ - 'geometry':['geometry','surface elevation, bedrock topography, ice thickness,...'],\ - 'constants':['constants','physical constants'],\ - 'smb':['SMBpdd','surface forcings'],\ - 'basalforcings':['basalforcings','bed forcings'],\ - 'materials':['matice','material properties'],\ - 'damage':['damage','damage propagation laws'],\ - 'friction':['friction','basal friction/drag properties'],\ - 'flowequation':['flowequation','flow equations'],\ - 'timestepping':['timestepping','time stepping for transient models'],\ - 'initialization':['initialization','initial guess/state'],\ - 'rifts':['rifts','rifts properties'],\ - 'debug':['debug','debugging tools (valgrind, gprof)'],\ - 'verbose':['verbose','verbosity level in solve'],\ - 'settings':['settings','settings properties'],\ - 'toolkits':['toolkits','PETSc options for each solution'],\ - 'cluster':['generic','cluster parameters (number of cpus...)'],\ - 'balancethickness':['balancethickness','parameters for balancethickness solution'],\ - 'stressbalance':['stressbalance','parameters for stressbalance solution'],\ - 'groundingline':['groundingline','parameters for groundingline solution'],\ - 'hydrology':['hydrologyshreve','parameters for hydrology solution'],\ - 'masstransport':['masstransport','parameters for masstransport solution'],\ - 'thermal':['thermal','parameters for thermal solution'],\ - 'steadystate':['steadystate','parameters for steadystate solution'],\ - 'transient':['transient','parameters for transient solution'],\ - 'calving':['calving','parameters for calving'],\ - 'gia':['gia','Parameters for gia model'],\ - 'autodiff':['autodiff','automatic differentiation parameters'],\ - 'flaim':['flaim','flaim parameters'],\ - 'inversion':['inversion','parameters for inverse methods'],\ - 'qmu':['qmu','dakota properties'],\ - 'outputdefinition':['outputdefinition','output definition'],\ - 'results':['results','model results'],\ - 'radaroverlay':['radaroverlay','radar image for plot overlay'],\ - 'miscellaneous':['miscellaneous','miscellaneous fields'],\ - 'private':['private','...']} + return ['mesh', + 'mask', + 'geometry', + 'constants', + 'smb', + 'basalforcings', + 'materials', + 'damage', + 'friction', + 'flowequation', + 'timestepping', + 'initialization', + 'rifts', + 'slr', + 'debug', + 'verbose', + 'settings', + 'toolkits', + 'cluster', + 'balancethickness', + 'stressbalance', + 'groundingline', + 'hydrology', + 'masstransport', + 'thermal', + 'steadystate', + 'transient', + 'levelset', + 'calving', + 'frontalforcings', + 'love', + 'gia', + 'esa', + 'autodiff', + 'inversion', + 'qmu', + 'amr', + 'outputdefinition', + 'results', + 'radaroverlay', + 'miscellaneous', + 'private'] # }}} - def __repr__(obj): #{{{ - string = "Model Description" - for i,mod in enumerate(dict.keys(obj.properties())): - tmp="%19s: %-22s -- %s" % (mod,"[%s,%s]" % ("1x1",obj.__dict__[mod].__class__.__name__),obj.properties()[mod][1]) - string="\n".join([string, tmp]) + #print "Here %s the number: %d" % ("is", 37) + string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties") + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("mask","[%s,%s]" % ("1x1",obj.mask.__class__.__name__),"defines grounded and floating elements")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("geometry","[%s,%s]" % ("1x1",obj.geometry.__class__.__name__),"surface elevation, bedrock topography, ice thickness,...")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("constants","[%s,%s]" % ("1x1",obj.constants.__class__.__name__),"physical constants")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("smb","[%s,%s]" % ("1x1",obj.smb.__class__.__name__),"surface mass balance")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("basalforcings","[%s,%s]" % ("1x1",obj.basalforcings.__class__.__name__),"bed forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("materials","[%s,%s]" % ("1x1",obj.materials.__class__.__name__),"material properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("damage","[%s,%s]" % ("1x1",obj.damage.__class__.__name__),"damage propagation laws")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("friction","[%s,%s]" % ("1x1",obj.friction.__class__.__name__),"basal friction/drag properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flowequation","[%s,%s]" % ("1x1",obj.flowequation.__class__.__name__),"flow equations")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("timestepping","[%s,%s]" % ("1x1",obj.timestepping.__class__.__name__),"time stepping for transient models")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("initialization","[%s,%s]" % ("1x1",obj.initialization.__class__.__name__),"initial guess/state")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("rifts","[%s,%s]" % ("1x1",obj.rifts.__class__.__name__),"rifts properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("slr","[%s,%s]" % ("1x1",obj.slr.__class__.__name__),"slr forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("debug","[%s,%s]" % ("1x1",obj.debug.__class__.__name__),"debugging tools (valgrind, gprof)")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("toolkits","[%s,%s]" % ("1x1",obj.toolkits.__class__.__name__),"PETSc options for each solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("stressbalance","[%s,%s]" % ("1x1",obj.stressbalance.__class__.__name__),"parameters for stressbalance solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("groundingline","[%s,%s]" % ("1x1",obj.groundingline.__class__.__name__),"parameters for groundingline solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("hydrology","[%s,%s]" % ("1x1",obj.hydrology.__class__.__name__),"parameters for hydrology solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("masstransport","[%s,%s]" % ("1x1",obj.masstransport.__class__.__name__),"parameters for masstransport solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("thermal","[%s,%s]" % ("1x1",obj.thermal.__class__.__name__),"parameters for thermal solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("steadystate","[%s,%s]" % ("1x1",obj.steadystate.__class__.__name__),"parameters for steadystate solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("transient","[%s,%s]" % ("1x1",obj.transient.__class__.__name__),"parameters for transient solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("levelset","[%s,%s]" % ("1x1",obj.levelset.__class__.__name__),"parameters for moving boundaries (level-set method)")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("calving","[%s,%s]" % ("1x1",obj.calving.__class__.__name__),"parameters for calving")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("frontalforcings","[%s,%s]" % ("1x1",obj.frontalforcings.__class__.__name__),"parameters for frontalforcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("gia","[%s,%s]" % ("1x1",obj.gia.__class__.__name__),"parameters for gia solution")) + string="%s\n%s" % (string,'%19s: %-22s -- %s' % ("love","[%s,%s]" % ("1x1",obj.love.__class__.__name__),"parameters for love solution")) + string="%s\n%s" % (string,'%19s: %-22s -- %s' % ("esa","[%s,%s]" % ("1x1",obj.esa.__class__.__name__),"parameters for elastic adjustment solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("autodiff","[%s,%s]" % ("1x1",obj.autodiff.__class__.__name__),"automatic differentiation 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" % ("amr","[%s,%s]" % ("1x1",obj.amr.__class__.__name__),"adaptive mesh refinement properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("outputdefinition","[%s,%s]" % ("1x1",obj.outputdefinition.__class__.__name__),"output definition")) + 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 # }}} - def checkmessage(self,string): # {{{ - print(("model not consistent: ", string)) + print("model not consistent: ", string) self.private.isconsistent=False return self # }}} - - def extract(md,area): # {{{ + #@staticmethod + def extract(self,area): # {{{ """ extract - extract a model according to an Argus contour or flag list - This routine extracts a submodel from a bigger model with respect to a given contour - md must be followed by the corresponding exp file or flags list - It can either be a domain file (argus type, .exp extension), or an array of element flags. - If user wants every element outside the domain to be - extract2d, add '~' to the name of the domain file (ex: '~HO.exp') - an empty string '' will be considered as an empty domain - a string 'all' will be considered as the entire domain - - Usage: - md2=extract(md,area) - - Examples: - md2=extract(md,'Domain.exp') - - See also: EXTRUDE, COLLAPSE + This routine extracts a submodel from a bigger model with respect to a given contour + md must be followed by the corresponding exp file or flags list + It can either be a domain file (argus type, .exp extension), or an array of element flags. + If user wants every element outside the domain to be + extract2d, add '~' to the name of the domain file (ex: '~HO.exp') + an empty string '' will be considered as an empty domain + a string 'all' will be considered as the entire domain + + Usage: + md2=extract(md,area) + + Examples: + md2=extract(md,'Domain.exp') + + See also: EXTRUDE, COLLAPSE """ #copy model - md1=copy.deepcopy(md) + md1=copy.deepcopy(self) #get elements that are inside area flag_elem=FlagElements(md1,area) - if not numpy.any(flag_elem): + if not np.any(flag_elem): raise RuntimeError("extracted model is empty") #kick out all elements with 3 dirichlets - spc_elem=numpy.nonzero(numpy.logical_not(flag_elem))[0] - spc_node=numpy.unique(md1.mesh.elements[spc_elem,:])-1 - flag=numpy.ones(md1.mesh.numberofvertices) + spc_elem=np.nonzero(np.logical_not(flag_elem))[0] + spc_node=np.unique(md1.mesh.elements[spc_elem,:])-1 + flag=np.ones(md1.mesh.numberofvertices) flag[spc_node]=0 - pos=numpy.nonzero(numpy.logical_not(numpy.sum(flag[md1.mesh.elements-1],axis=1)))[0] + pos=np.nonzero(np.logical_not(np.sum(flag[md1.mesh.elements-1],axis=1)))[0] flag_elem[pos]=0 - + #extracted elements and nodes lists - pos_elem=numpy.nonzero(flag_elem)[0] - pos_node=numpy.unique(md1.mesh.elements[pos_elem,:])-1 - + pos_elem=np.nonzero(flag_elem)[0] + pos_node=np.unique(md1.mesh.elements[pos_elem,:])-1 + #keep track of some fields numberofvertices1=md1.mesh.numberofvertices numberofelements1=md1.mesh.numberofelements - numberofvertices2=numpy.size(pos_node) - numberofelements2=numpy.size(pos_elem) - flag_node=numpy.zeros(numberofvertices1) + numberofvertices2=np.size(pos_node) + numberofelements2=np.size(pos_elem) + flag_node=np.zeros(numberofvertices1) flag_node[pos_node]=1 - + #Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements) - Pelem=numpy.zeros(numberofelements1,int) - Pelem[pos_elem]=numpy.arange(1,numberofelements2+1) - Pnode=numpy.zeros(numberofvertices1,int) - Pnode[pos_node]=numpy.arange(1,numberofvertices2+1) - + Pelem=np.zeros(numberofelements1,int) + Pelem[pos_elem]=np.arange(1,numberofelements2+1) + Pnode=np.zeros(numberofvertices1,int) + Pnode[pos_node]=np.arange(1,numberofvertices2+1) + #renumber the elements (some node won't exist anymore) elements_1=copy.deepcopy(md1.mesh.elements) @@ -165,8 +290,10 @@ #OK, now create the new model! + #take every field from model md2=copy.deepcopy(md1) #automatically modify fields + #loop over model fields model_fields=vars(md1) @@ -174,18 +301,18 @@ #get field field=getattr(md1,fieldi) - fieldsize=numpy.shape(field) - if hasattr(field,'__dict__') and not m.ismember(fieldi,['results'])[0]: #recursive call + fieldsize=np.shape(field) + if hasattr(field,'__dict__') and not fieldi in ['results']: #recursive call object_fields=vars(field) for fieldj in object_fields: #get field field=getattr(getattr(md1,fieldi),fieldj) - fieldsize=numpy.shape(field) + fieldsize=np.shape(field) if len(fieldsize): #size = number of nodes * n - if fieldsize[0]==numberofvertices1: + if fieldsize[0]==numberofvertices1: setattr(getattr(md2,fieldi),fieldj,field[pos_node]) elif fieldsize[0]==numberofvertices1+1: - setattr(getattr(md2,fieldi),fieldj,numpy.vstack((field[pos_node],field[-1,:]))) - #size = number of elements * n + setattr(getattr(md2,fieldi),fieldj,np.vstack((field[pos_node],field[-1,:]))) + #size = number of elements * n elif fieldsize[0]==numberofelements1: setattr(getattr(md2,fieldi),fieldj,field[pos_elem]) @@ -196,6 +323,6 @@ setattr(md2,fieldi,field[pos_node]) elif fieldsize[0]==numberofvertices1+1: - setattr(md2,fieldi,numpy.hstack((field[pos_node],field[-1,:]))) - #size = number of elements * n + setattr(md2,fieldi,np.hstack((field[pos_node],field[-1,:]))) + #size = number of elements * n elif fieldsize[0]==numberofelements1: setattr(md2,fieldi,field[pos_elem]) @@ -207,59 +334,58 @@ md2.mesh.numberofvertices=numberofvertices2 md2.mesh.elements=elements_2 - + #mesh.uppervertex mesh.lowervertex if md1.mesh.__class__.__name__=='mesh3dprisms': md2.mesh.uppervertex=md1.mesh.uppervertex[pos_node] - pos=numpy.nonzero(numpy.logical_not(md2.mesh.uppervertex==-1))[0] - md2.mesh.uppervertex[pos]=Pnode[md2.mesh.uppervertex[pos]-1] - + pos=np.where(~np.isnan(md2.mesh.uppervertex))[0] + md2.mesh.uppervertex[pos]=Pnode[md2.mesh.uppervertex[pos].astype(int)-1] + md2.mesh.lowervertex=md1.mesh.lowervertex[pos_node] - pos=numpy.nonzero(numpy.logical_not(md2.mesh.lowervertex==-1))[0] - md2.mesh.lowervertex[pos]=Pnode[md2.mesh.lowervertex[pos]-1] - + pos=np.where(~np.isnan(md2.mesh.lowervertex))[0] + md2.mesh.lowervertex[pos]=Pnode[md2.mesh.lowervertex[pos].astype(int)-1] + md2.mesh.upperelements=md1.mesh.upperelements[pos_elem] - pos=numpy.nonzero(numpy.logical_not(md2.mesh.upperelements==-1))[0] - md2.mesh.upperelements[pos]=Pelem[md2.mesh.upperelements[pos]-1] - + pos=np.where(~np.isnan(md2.mesh.upperelements))[0] + md2.mesh.upperelements[pos]=Pelem[md2.mesh.upperelements[pos].astype(int)-1] + md2.mesh.lowerelements=md1.mesh.lowerelements[pos_elem] - pos=numpy.nonzero(numpy.logical_not(md2.mesh.lowerelements==-1))[0] - md2.mesh.lowerelements[pos]=Pelem[md2.mesh.lowerelements[pos]-1] - - #Initial 2d mesh + pos=np.where(~np.isnan(md2.mesh.lowerelements))[0] + md2.mesh.lowerelements[pos]=Pelem[md2.mesh.lowerelements[pos].astype(int)-1] + + #Initial 2d mesh if md1.mesh.__class__.__name__=='mesh3dprisms': - flag_elem_2d=flag_elem[numpy.arange(0,md1.mesh.numberofelements2d)] - pos_elem_2d=numpy.nonzero(flag_elem_2d)[0] - flag_node_2d=flag_node[numpy.arange(0,md1.mesh.numberofvertices2d)] - pos_node_2d=numpy.nonzero(flag_node_2d)[0] - - md2.mesh.numberofelements2d=numpy.size(pos_elem_2d) - md2.mesh.numberofvertices2d=numpy.size(pos_node_2d) + flag_elem_2d=flag_elem[np.arange(0,md1.mesh.numberofelements2d)] + pos_elem_2d=np.nonzero(flag_elem_2d)[0] + flag_node_2d=flag_node[np.arange(0,md1.mesh.numberofvertices2d)] + pos_node_2d=np.nonzero(flag_node_2d)[0] + + md2.mesh.numberofelements2d=np.size(pos_elem_2d) + md2.mesh.numberofvertices2d=np.size(pos_node_2d) md2.mesh.elements2d=md1.mesh.elements2d[pos_elem_2d,:] md2.mesh.elements2d[:,0]=Pnode[md2.mesh.elements2d[:,0]-1] md2.mesh.elements2d[:,1]=Pnode[md2.mesh.elements2d[:,1]-1] md2.mesh.elements2d[:,2]=Pnode[md2.mesh.elements2d[:,2]-1] - + md2.mesh.x2d=md1.mesh.x[pos_node_2d] md2.mesh.y2d=md1.mesh.y[pos_node_2d] - + #Edges - if m.strcmp(md.mesh.domaintype(),'2Dhorizontal'): - if numpy.ndim(md2.mesh.edges)>1 and numpy.size(md2.mesh.edges,axis=1)>1: - #do not use ~isnan because there are some numpy.nans... + if md1.mesh.domaintype()=='2Dhorizontal': + if np.ndim(md2.mesh.edges)>1 and np.size(md2.mesh.edges,axis=1)>1: #do not use ~isnan because there are some np.nans... #renumber first two columns - pos=numpy.nonzero(md2.mesh.edges[:,3]!=-1)[0] - md2.mesh.edges[: ,0]=Pnode[md2.mesh.edges[:,0]-1] - md2.mesh.edges[: ,1]=Pnode[md2.mesh.edges[:,1]-1] - md2.mesh.edges[: ,2]=Pelem[md2.mesh.edges[:,2]-1] + pos=np.nonzero(md2.mesh.edges[:,3]!=-1)[0] + md2.mesh.edges[:,0]=Pnode[md2.mesh.edges[:,0]-1] + md2.mesh.edges[:,1]=Pnode[md2.mesh.edges[:,1]-1] + md2.mesh.edges[:,2]=Pelem[md2.mesh.edges[:,2]-1] md2.mesh.edges[pos,3]=Pelem[md2.mesh.edges[pos,3]-1] #remove edges when the 2 vertices are not in the domain. - md2.mesh.edges=md2.mesh.edges[numpy.nonzero(numpy.logical_and(md2.mesh.edges[:,0],md2.mesh.edges[:,1]))[0],:] + md2.mesh.edges=md2.mesh.edges[np.nonzero(np.logical_and(md2.mesh.edges[:,0],md2.mesh.edges[:,1]))[0],:] #Replace all zeros by -1 in the last two columns - pos=numpy.nonzero(md2.mesh.edges[:,2]==0)[0] + pos=np.nonzero(md2.mesh.edges[:,2]==0)[0] md2.mesh.edges[pos,2]=-1 - pos=numpy.nonzero(md2.mesh.edges[:,3]==0)[0] + pos=np.nonzero(md2.mesh.edges[:,3]==0)[0] md2.mesh.edges[pos,3]=-1 #Invert -1 on the third column with last column (Also invert first two columns!!) - pos=numpy.nonzero(md2.mesh.edges[:,2]==-1)[0] + pos=np.nonzero(md2.mesh.edges[:,2]==-1)[0] md2.mesh.edges[pos,2]=md2.mesh.edges[pos,3] md2.mesh.edges[pos,3]=-1 @@ -268,60 +394,60 @@ md2.mesh.edges[pos,0]=values #Finally remove edges that do not belong to any element - pos=numpy.nonzero(numpy.logical_and(md2.mesh.edges[:,1]==-1,md2.mesh.edges[:,2]==-1))[0] - md2.mesh.edges=numpy.delete(md2.mesh.edges,pos,axis=0) + pos=np.nonzero(np.logical_and(md2.mesh.edges[:,1]==-1,md2.mesh.edges[:,2]==-1))[0] + md2.mesh.edges=np.delete(md2.mesh.edges,pos,axis=0) #Penalties - if numpy.any(numpy.logical_not(numpy.isnan(md2.stressbalance.vertex_pairing))): - for i in range(numpy.size(md1.stressbalance.vertex_pairing,axis=0)): + if np.any(np.logical_not(np.isnan(md2.stressbalance.vertex_pairing))): + for i in range(np.size(md1.stressbalance.vertex_pairing,axis=0)): md2.stressbalance.vertex_pairing[i,:]=Pnode[md1.stressbalance.vertex_pairing[i,:]] - md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing[numpy.nonzero(md2.stressbalance.vertex_pairing[:,0])[0],:] - if numpy.any(numpy.logical_not(numpy.isnan(md2.masstransport.vertex_pairing))): - for i in range(numpy.size(md1.masstransport.vertex_pairing,axis=0)): + md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing[np.nonzero(md2.stressbalance.vertex_pairing[:,0])[0],:] + if np.any(np.logical_not(np.isnan(md2.masstransport.vertex_pairing))): + for i in range(np.size(md1.masstransport.vertex_pairing,axis=0)): md2.masstransport.vertex_pairing[i,:]=Pnode[md1.masstransport.vertex_pairing[i,:]] - md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing[numpy.nonzero(md2.masstransport.vertex_pairing[:,0])[0],:] + md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing[np.nonzero(md2.masstransport.vertex_pairing[:,0])[0],:] #recreate segments if md1.mesh.__class__.__name__=='mesh2d': - [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices) - [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity) + md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices)[0] + md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity)[0] md2.mesh.segments=contourenvelope(md2) - md2.mesh.vertexonboundary=numpy.zeros(numberofvertices2,bool) + md2.mesh.vertexonboundary=np.zeros(numberofvertices2,bool) md2.mesh.vertexonboundary[md2.mesh.segments[:,0:2]-1]=True else: #First do the connectivity for the contourenvelope in 2d - [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d) - [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity) + md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d)[0] + md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity)[0] segments=contourenvelope(md2) - md2.mesh.vertexonboundary=numpy.zeros(numberofvertices2/md2.mesh.numberoflayers,bool) + md2.mesh.vertexonboundary=np.zeros(numberofvertices2/md2.mesh.numberoflayers,bool) md2.mesh.vertexonboundary[segments[:,0:2]-1]=True - md2.mesh.vertexonboundary=numpy.tile(md2.mesh.vertexonboundary,md2.mesh.numberoflayers) + md2.mesh.vertexonboundary=np.tile(md2.mesh.vertexonboundary,md2.mesh.numberoflayers) #Then do it for 3d as usual - [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices) - [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity) + md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices)[0] + md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity)[0] #Boundary conditions: Dirichlets on new boundary #Catch the elements that have not been extracted - orphans_elem=numpy.nonzero(numpy.logical_not(flag_elem))[0] - orphans_node=numpy.unique(md1.mesh.elements[orphans_elem,:])-1 + orphans_elem=np.nonzero(np.logical_not(flag_elem))[0] + orphans_node=np.unique(md1.mesh.elements[orphans_elem,:])-1 #Figure out which node are on the boundary between md2 and md1 - nodestoflag1=numpy.intersect1d(orphans_node,pos_node) + nodestoflag1=np.intersect1d(orphans_node,pos_node) nodestoflag2=Pnode[nodestoflag1].astype(int)-1 - if numpy.size(md1.stressbalance.spcvx)>1 and numpy.size(md1.stressbalance.spcvy)>2 and numpy.size(md1.stressbalance.spcvz)>2: - if numpy.size(md1.inversion.vx_obs)>1 and numpy.size(md1.inversion.vy_obs)>1: - md2.stressbalance.spcvx[nodestoflag2]=md2.inversion.vx_obs[nodestoflag2] + if np.size(md1.stressbalance.spcvx)>1 and np.size(md1.stressbalance.spcvy)>2 and np.size(md1.stressbalance.spcvz)>2: + if np.size(md1.inversion.vx_obs)>1 and np.size(md1.inversion.vy_obs)>1: + md2.stressbalance.spcvx[nodestoflag2]=md2.inversion.vx_obs[nodestoflag2] md2.stressbalance.spcvy[nodestoflag2]=md2.inversion.vy_obs[nodestoflag2] else: - md2.stressbalance.spcvx[nodestoflag2]=numpy.nan - md2.stressbalance.spcvy[nodestoflag2]=numpy.nan + md2.stressbalance.spcvx[nodestoflag2]=np.nan + md2.stressbalance.spcvy[nodestoflag2]=np.nan print("\n!! extract warning: spc values should be checked !!\n\n") #put 0 for vz md2.stressbalance.spcvz[nodestoflag2]=0 - if numpy.any(numpy.logical_not(numpy.isnan(md1.thermal.spctemperature))): - md2.thermal.spctemperature[nodestoflag2,0]=1 + if np.any(np.logical_not(np.isnan(md1.thermal.spctemperature))): + md2.thermal.spctemperature[nodestoflag2]=1 #Results fields if md1.results: md2.results=results() - for solutionfield,field in list(md1.results.__dict__.items()): + for solutionfield,field in md1.results.__dict__.items(): if isinstance(field,list): setattr(md2.results,solutionfield,[]) @@ -332,8 +458,8 @@ fieldr=getattr(md2.results,solutionfield)[i] #get subfields - for solutionsubfield,subfield in list(fieldi.__dict__.items()): - if numpy.size(subfield)==numberofvertices1: + for solutionsubfield,subfield in fieldi.__dict__.items(): + if np.size(subfield)==numberofvertices1: setattr(fieldr,solutionsubfield,subfield[pos_node]) - elif numpy.size(subfield)==numberofelements1: + elif np.size(subfield)==numberofelements1: setattr(fieldr,solutionsubfield,subfield[pos_elem]) else: @@ -346,18 +472,35 @@ fieldr=getattr(md2.results,solutionfield) #get subfields - for solutionsubfield,subfield in list(field.__dict__.items()): - if numpy.size(subfield)==numberofvertices1: + for solutionsubfield,subfield in field.__dict__.items(): + if np.size(subfield)==numberofvertices1: setattr(fieldr,solutionsubfield,subfield[pos_node]) - elif numpy.size(subfield)==numberofelements1: + elif np.size(subfield)==numberofelements1: setattr(fieldr,solutionsubfield,subfield[pos_elem]) else: setattr(fieldr,solutionsubfield,subfield) + #OutputDefinitions fields + if md1.outputdefinition.definitions: + for solutionfield,field in md1.outputdefinition.__dict__.items(): + if isinstance(field,list): + #get each definition + for i,fieldi in enumerate(field): + if fieldi: + fieldr=getattr(md2.outputdefinition,solutionfield)[i] + #get subfields + for solutionsubfield,subfield in fieldi.__dict__.items(): + if np.size(subfield)==numberofvertices1: + setattr(fieldr,solutionsubfield,subfield[pos_node]) + elif np.size(subfield)==numberofelements1: + setattr(fieldr,solutionsubfield,subfield[pos_elem]) + else: + setattr(fieldr,solutionsubfield,subfield) + #Keep track of pos_node and pos_elem md2.mesh.extractedvertices=pos_node+1 md2.mesh.extractedelements=pos_elem+1 + return md2 # }}} - def extrude(md,*args): # {{{ """ @@ -369,5 +512,5 @@ - follow two polynomial laws, one for the lower part and one for the upper part of the mesh - be discribed by a list of coefficients (between 0 and 1) - + Usage: @@ -402,5 +545,5 @@ raise TypeError("extrusionexponent must be >=0") numlayers=args[0] - extrusionlist=(numpy.arange(0.,float(numlayers-1)+1.,1.)/float(numlayers-1))**args[1] + extrusionlist=(np.arange(0.,float(numlayers-1)+1.,1.)/float(numlayers-1))**args[1] elif len(args)==3: #two polynomial laws @@ -412,7 +555,7 @@ raise TypeError("lower and upper extrusionexponents must be >=0") - lowerextrusionlist=(numpy.arange(0.,1.+2./float(numlayers-1),2./float(numlayers-1)))**lowerexp/2. - upperextrusionlist=(numpy.arange(0.,1.+2./float(numlayers-1),2./float(numlayers-1)))**upperexp/2. - extrusionlist=numpy.unique(numpy.concatenate((lowerextrusionlist,1.-upperextrusionlist))) + lowerextrusionlist=(np.arange(0.,1.+2./float(numlayers-1),2./float(numlayers-1)))**lowerexp/2. + upperextrusionlist=(np.arange(0.,1.+2./float(numlayers-1),2./float(numlayers-1)))**upperexp/2. + extrusionlist=np.unique(np.concatenate((lowerextrusionlist,1.-upperextrusionlist))) if numlayers<2: @@ -429,20 +572,21 @@ md.mesh.numberofelements = mesh2d.numberofelements md.mesh.numberofvertices = mesh2d.numberofvertices - + md.mesh.lat = mesh2d.lat md.mesh.long = mesh2d.long md.mesh.epsg = mesh2d.epsg - + md.mesh.scale_factor = mesh2d.scale_factor + md.mesh.vertexonboundary = mesh2d.vertexonboundary md.mesh.vertexconnectivity = mesh2d.vertexconnectivity md.mesh.elementconnectivity = mesh2d.elementconnectivity md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity - + md.mesh.extractedvertices = mesh2d.extractedvertices md.mesh.extractedelements = mesh2d.extractedelements - - x3d=numpy.empty((0)) - y3d=numpy.empty((0)) - z3d=numpy.empty((0)) #the lower node is on the bed + + x3d=np.empty((0)) + y3d=np.empty((0)) + z3d=np.empty((0)) #the lower node is on the bed thickness3d=md.geometry.thickness #thickness and bed for these nodes bed3d=md.geometry.base @@ -450,33 +594,33 @@ #Create the new layers for i in range(numlayers): - x3d=numpy.concatenate((x3d,md.mesh.x)) - y3d=numpy.concatenate((y3d,md.mesh.y)) + x3d=np.concatenate((x3d,md.mesh.x)) + y3d=np.concatenate((y3d,md.mesh.y)) #nodes are distributed between bed and surface accordingly to the given exponent - z3d=numpy.concatenate((z3d,(bed3d+thickness3d*extrusionlist[i]).reshape(-1))) - number_nodes3d=numpy.size(x3d) #number of 3d nodes for the non extruded part of the mesh - - #Extrude elements - elements3d=numpy.empty((0,6),int) + z3d=np.concatenate((z3d,(bed3d+thickness3d*extrusionlist[i]).reshape(-1))) + number_nodes3d=np.size(x3d) #number of 3d nodes for the non extruded part of the mesh + + #Extrude elements + elements3d=np.empty((0,6),int) for i in range(numlayers-1): - elements3d=numpy.vstack((elements3d,numpy.hstack((md.mesh.elements+i*md.mesh.numberofvertices,md.mesh.elements+(i+1)*md.mesh.numberofvertices)))) #Create the elements of the 3d mesh for the non extruded part - number_el3d=numpy.size(elements3d,axis=0) #number of 3d nodes for the non extruded part of the mesh + elements3d=np.vstack((elements3d,np.hstack((md.mesh.elements+i*md.mesh.numberofvertices,md.mesh.elements+(i+1)*md.mesh.numberofvertices)))) #Create the elements of the 3d mesh for the non extruded part + number_el3d=np.size(elements3d,axis=0) #number of 3d nodes for the non extruded part of the mesh #Keep a trace of lower and upper nodes - lowervertex=-1*numpy.ones(number_nodes3d,int) - uppervertex=-1*numpy.ones(number_nodes3d,int) - lowervertex[md.mesh.numberofvertices:]=numpy.arange(1,(numlayers-1)*md.mesh.numberofvertices+1) - uppervertex[:(numlayers-1)*md.mesh.numberofvertices]=numpy.arange(md.mesh.numberofvertices+1,number_nodes3d+1) + lowervertex=np.nan*np.ones(number_nodes3d,int) + uppervertex=np.nan*np.ones(number_nodes3d,int) + lowervertex[md.mesh.numberofvertices:]=np.arange(1,(numlayers-1)*md.mesh.numberofvertices+1) + uppervertex[:(numlayers-1)*md.mesh.numberofvertices]=np.arange(md.mesh.numberofvertices+1,number_nodes3d+1) md.mesh.lowervertex=lowervertex md.mesh.uppervertex=uppervertex #same for lower and upper elements - lowerelements=-1*numpy.ones(number_el3d,int) - upperelements=-1*numpy.ones(number_el3d,int) - lowerelements[md.mesh.numberofelements:]=numpy.arange(1,(numlayers-2)*md.mesh.numberofelements+1) - upperelements[:(numlayers-2)*md.mesh.numberofelements]=numpy.arange(md.mesh.numberofelements+1,(numlayers-1)*md.mesh.numberofelements+1) + lowerelements=np.nan*np.ones(number_el3d,int) + upperelements=np.nan*np.ones(number_el3d,int) + lowerelements[md.mesh.numberofelements:]=np.arange(1,(numlayers-2)*md.mesh.numberofelements+1) + upperelements[:(numlayers-2)*md.mesh.numberofelements]=np.arange(md.mesh.numberofelements+1,(numlayers-1)*md.mesh.numberofelements+1) md.mesh.lowerelements=lowerelements md.mesh.upperelements=upperelements - #Save old mesh + #Save old mesh md.mesh.x2d=md.mesh.x md.mesh.y2d=md.mesh.y @@ -485,5 +629,5 @@ md.mesh.numberofvertices2d=md.mesh.numberofvertices - #Build global 3d mesh + #Build global 3d mesh md.mesh.elements=elements3d md.mesh.x=x3d @@ -497,6 +641,6 @@ #bedinfo and surface info - md.mesh.vertexonbase=project3d(md,'vector',numpy.ones(md.mesh.numberofvertices2d,bool),'type','node','layer',1) - md.mesh.vertexonsurface=project3d(md,'vector',numpy.ones(md.mesh.numberofvertices2d,bool),'type','node','layer',md.mesh.numberoflayers) + md.mesh.vertexonbase=project3d(md,'vector',np.ones(md.mesh.numberofvertices2d,bool),'type','node','layer',1) + md.mesh.vertexonsurface=project3d(md,'vector',np.ones(md.mesh.numberofvertices2d,bool),'type','node','layer',md.mesh.numberoflayers) md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node') @@ -504,4 +648,5 @@ md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node') md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node') + md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node') md.geometry.extrude(md) @@ -518,21 +663,25 @@ # Calving variables md.hydrology.extrude(md) + md.levelset.extrude(md) md.calving.extrude(md) + md.frontalforcings.extrude(md) #connectivity - md.mesh.elementconnectivity=numpy.tile(md.mesh.elementconnectivity,(numlayers-1,1)) - md.mesh.elementconnectivity[numpy.nonzero(md.mesh.elementconnectivity==0)]=-sys.maxsize-1 - if not numpy.isnan(md.mesh.elementconnectivity).all(): + md.mesh.elementconnectivity=np.tile(md.mesh.elementconnectivity,(numlayers-1,1)) + md.mesh.elementconnectivity[np.nonzero(md.mesh.elementconnectivity==0)]=-sys.maxsize-1 + if not np.isnan(md.mesh.elementconnectivity).all(): for i in range(1,numlayers-1): md.mesh.elementconnectivity[i*md.mesh.numberofelements2d:(i+1)*md.mesh.numberofelements2d,:] \ - =md.mesh.elementconnectivity[i*md.mesh.numberofelements2d:(i+1)*md.mesh.numberofelements2d,:]+md.mesh.numberofelements2d - md.mesh.elementconnectivity[numpy.nonzero(md.mesh.elementconnectivity<0)]=0 + =md.mesh.elementconnectivity[i*md.mesh.numberofelements2d:(i+1)*md.mesh.numberofelements2d,:]+md.mesh.numberofelements2d + md.mesh.elementconnectivity[np.nonzero(md.mesh.elementconnectivity<0)]=0 md.materials.extrude(md) - md.damage.extrude(md) + if md.damage.isdamage==1: + md.damage.extrude(md) md.gia.extrude(md) md.mask.extrude(md) md.qmu.extrude(md) md.basalforcings.extrude(md) + md.outputdefinition.extrude(md) #increase connectivity if less than 25: @@ -541,58 +690,90 @@ return md - # }}} + # }}} def collapse(md): #{{{ ''' collapses a 3d mesh into a 2d mesh - + This routine collapses a 3d model into a 2d model and collapses all the fileds of the 3d model by taking their depth-averaged values - + Usage: md=collapse(md) - ''' + ''' #Check that the model is really a 3d model if md.mesh.domaintype().lower() != '3d': raise Exception("only a 3D model can be collapsed") - + + #dealing with the friction law #drag is limited to nodes that are on the bedrock. - md.friction.coefficient=project2d(md,md.friction.coefficient,1) + if hasattr(md.friction,'coefficient'): + md.friction.coefficient=project2d(md,md.friction.coefficient,1) #p and q (same deal, except for element that are on the bedrock: ) - md.friction.p=project2d(md,md.friction.p,1) - md.friction.q=project2d(md,md.friction.q,1) + if hasattr(md.friction,'p'): + md.friction.p=project2d(md,md.friction.p,1) + if hasattr(md.friction,'q'): + md.friction.q=project2d(md,md.friction.q,1) + + if hasattr(md.friction,'coefficientcoulomb'): + md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1) + if hasattr(md.friction,'C'): + md.friction.C=project2d(md,md.friction.C,1) + if hasattr(md.friction,'As'): + md.friction.As=project2d(md,md.friction.As,1) + if hasattr(md.friction,'effective_pressure') and not np.isnan(md.friction.effective_pressure).all(): + md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1) + if hasattr(md.friction,'water_layer'): + md.friction.water_layer=project2d(md,md.friction.water_layer,1) + if hasattr(md.friction,'m'): + md.friction.m=project2d(md,md.friction.m,1) #observations - if not numpy.isnan(md.inversion.vx_obs).all(): md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers) - if not numpy.isnan(md.inversion.vy_obs).all(): md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers) - if not numpy.isnan(md.inversion.vel_obs).all(): md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers) - if not numpy.isnan(md.inversion.cost_functions_coefficients).all(): md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers) - if isinstance(md.inversion.min_parameters,numpy.ndarray): - if md.inversion.min_parameters.size>1: md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers) - if isinstance(md.inversion.max_parameters,numpy.ndarray): - if md.inversion.max_parameters.size>1: md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers) - if not numpy.isnan(md.smb.mass_balance).all(): - md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers) - - if not numpy.isnan(md.balancethickness.thickening_rate).all(): md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers) + if not np.isnan(md.inversion.vx_obs).all(): + md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers) + if not np.isnan(md.inversion.vy_obs).all(): + md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers) + if not np.isnan(md.inversion.vel_obs).all(): + md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers) + if not np.isnan(md.inversion.cost_functions_coefficients).all(): + md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers) + if isinstance(md.inversion.min_parameters,np.ndarray): + if md.inversion.min_parameters.size>1: + md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers) + if isinstance(md.inversion.max_parameters,np.ndarray): + if md.inversion.max_parameters.size>1: + md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers) + if not np.isnan(md.smb.mass_balance).all(): + md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers) #results - if not numpy.isnan(md.initialization.vx).all(): md.initialization.vx=DepthAverage(md,md.initialization.vx) - if not numpy.isnan(md.initialization.vy).all(): md.initialization.vy=DepthAverage(md,md.initialization.vy) - if not numpy.isnan(md.initialization.vz).all(): md.initialization.vz=DepthAverage(md,md.initialization.vz) - if not numpy.isnan(md.initialization.vel).all(): md.initialization.vel=DepthAverage(md,md.initialization.vel) - if not numpy.isnan(md.initialization.temperature).all(): md.initialization.temperature=DepthAverage(md,md.initialization.temperature) - if not numpy.isnan(md.initialization.pressure).all(): md.initialization.pressure=project2d(md,md.initialization.pressure,1) - if not numpy.isnan(md.initialization.sediment_head).all(): md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1) - if not numpy.isnan(md.initialization.epl_head).all(): md.initialization.epl_head=project2d(md,md.initialization.epl_head,1) - if not numpy.isnan(md.initialization.epl_thickness).all(): md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1) - - #gia - if not numpy.isnan(md.gia.mantle_viscosity).all(): md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1) - if not numpy.isnan(md.gia.lithosphere_thickness).all(): md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1) + if not np.isnan(md.initialization.vx).all(): + md.initialization.vx=DepthAverage(md,md.initialization.vx) + if not np.isnan(md.initialization.vy).all(): + md.initialization.vy=DepthAverage(md,md.initialization.vy) + if not np.isnan(md.initialization.vz).all(): + md.initialization.vz=DepthAverage(md,md.initialization.vz) + if not np.isnan(md.initialization.vel).all(): + md.initialization.vel=DepthAverage(md,md.initialization.vel) + if not np.isnan(md.initialization.temperature).all(): + md.initialization.temperature=DepthAverage(md,md.initialization.temperature) + if not np.isnan(md.initialization.pressure).all(): + md.initialization.pressure=project2d(md,md.initialization.pressure,1) + if not np.isnan(md.initialization.sediment_head).all(): + md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1) + if not np.isnan(md.initialization.epl_head).all(): + md.initialization.epl_head=project2d(md,md.initialization.epl_head,1) + if not np.isnan(md.initialization.epl_thickness).all(): + md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1) + + #giaivins + if not np.isnan(md.gia.mantle_viscosity).all(): + md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1) + if not np.isnan(md.gia.lithosphere_thickness).all(): + md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1) #elementstype - if not numpy.isnan(md.flowequation.element_equation).all(): + if not np.isnan(md.flowequation.element_equation).all(): md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1) md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1) @@ -602,10 +783,11 @@ # Hydrologydc variables - if hasattr(md.hydrology,'hydrologydc'): + if type(md.hydrology) is 'hydrologydc': md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1) - md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1) md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1) md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1) + md.hydrology.mask_thawed_node=project2d(md,md.hydrology.mask_thawed_node,1) if md.hydrology.isefficientlayer == 1: + md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1) md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1) @@ -617,18 +799,19 @@ md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers) md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers) - if not numpy.isnan(md.damage.spcdamage).all(): md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers-1) md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers-1) + if not np.isnan(md.damage.spcdamage).all(): + md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers-1) #materials md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B) md.materials.rheology_n=project2d(md,md.materials.rheology_n,1) - - #damage: + + #damage: if md.damage.isdamage: md.damage.D=DepthAverage(md,md.damage.D) #special for thermal modeling: - md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1) - md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1) + md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1) + md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1) md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1) #bedrock only gets geothermal flux @@ -644,14 +827,24 @@ md.geometry.thickness=project2d(md,md.geometry.thickness,1) md.geometry.base=project2d(md,md.geometry.base,1) - if isinstance(md.geometry.bed,numpy.ndarray): + if isinstance(md.geometry.bed,np.ndarray): md.geometry.bed=project2d(md,md.geometry.bed,1) - md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1) - md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1) - - #lat long - if isinstance(md.mesh.lat,numpy.ndarray): - if md.mesh.lat.size==md.mesh.numberofvertices: md.mesh.lat=project2d(md,md.mesh.lat,1) - if isinstance(md.mesh.long,numpy.ndarray): - if md.mesh.long.size==md.mesh.numberofvertices: md.mesh.long=project2d(md,md.mesh.long,1) + md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1) + md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1) + + #OutputDefinitions + if md.outputdefinition.definitions: + for solutionfield,field in md.outputdefinition.__dict__.items(): + if isinstance(field,list): + #get each definition + for i,fieldi in enumerate(field): + if fieldi: + fieldr=getattr(md.outputdefinition,solutionfield)[i] + #get subfields + for solutionsubfield,subfield in fieldi.__dict__.items(): + if np.size(subfield)==md.mesh.numberofvertices: + setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) + elif np.size(subfield)==md.mesh.numberofelements: + setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) + #Initialize with the 2d mesh @@ -662,7 +855,22 @@ mesh.numberofelements=md.mesh.numberofelements2d mesh.elements=md.mesh.elements2d - if not numpy.isnan(md.mesh.vertexonboundary).all(): mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1) - if not numpy.isnan(md.mesh.elementconnectivity).all(): mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1) + if not np.isnan(md.mesh.vertexonboundary).all(): + mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1) + if not np.isnan(md.mesh.elementconnectivity).all(): + mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1) + if isinstance(md.mesh.lat,np.ndarray): + if md.mesh.lat.size==md.mesh.numberofvertices: + mesh.lat=project2d(md,md.mesh.lat,1) + if isinstance(md.mesh.long,np.ndarray): + if md.mesh.long.size==md.mesh.numberofvertices: + md.mesh.long=project2d(md,md.mesh.long,1) + mesh.epsg=md.mesh.epsg + if isinstance(md.mesh.scale_factor,np.ndarray): + if md.mesh.scale_factor.size==md.mesh.numberofvertices: + md.mesh.scale_factor=project2d(md,md.mesh.scale_factor,1) md.mesh=mesh + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices)[0] + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity)[0] + md.mesh.segments=contourenvelope(md) return md Index: /issm/trunk-jpl/src/py3/classes/organizer.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/organizer.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/organizer.py (revision 23670) @@ -6,5 +6,5 @@ from savevars import savevars from model import model -from dbm.ndbm import whichdb +from dbm import whichdb import MatlabFuncs as m @@ -26,5 +26,5 @@ """ - def __init__(self,**kwargs): # {{{ + def __init__(self,*args): # {{{ self._currentstep =0 self.repository ='./' @@ -35,5 +35,5 @@ #process options - options=pairoptions.pairoptions(**kwargs) + options=pairoptions.pairoptions(*args) #Get prefix @@ -86,5 +86,5 @@ if os.path.exists(path): struc=loadvars(path) - name=name=[key for key in list(struc.keys())] + name=name=[key for key in struc.keys()] md=struc.name[0] else: @@ -98,5 +98,5 @@ if not isinstance(string,str): raise TypeError("argument provided is not a string") - path1=os.path.join(self.repository,self.prefix+'.step#'+string+'.python') + path1=os.path.join(self.repository,self.prefix+string+'.python') path2=os.path.join(self.repository,string) @@ -115,5 +115,5 @@ raise IOError("Could find neither '%s' nor '%s'" % (path,path2)) else: - print(("--> Branching '%s' from trunk '%s'" % (self.prefix,self.trunkprefix))) + print("--> Branching '%s' from trunk '%s'" % (self.prefix,self.trunkprefix)) md=loadmodel(path2) return md @@ -142,10 +142,10 @@ if 0 in self.requestedsteps: if self._currentstep==1: - print((" prefix: %s" % self.prefix)) - print((" step #%i : %s" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string']))) + print(" prefix: %s" % self.prefix) + print(" step #%i : %s" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string'])) #Ok, now if _currentstep is a member of steps, return true if self._currentstep in self.requestedsteps: - print(("\n step #%i : %s\n" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string']))) + print("\n step #%i : %s\n" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string'])) bool=True @@ -164,8 +164,8 @@ if (name=='default'): - name=os.path.join(self.repository,self.prefix+'step#'+self.steps[self._currentstep-1]['string']+'.python') - else: - name=os.path.join(self.repository,name) - print(("saving model as: '%s'" % name)) + name=os.path.join(self.repository,self.prefix+self.steps[self._currentstep-1]['string']+'.python') + else: + name=os.path.join(self.repository,name) + print("saving model as: '%s'" % name) #check that md is a model Index: /issm/trunk-jpl/src/py3/classes/outputdefinition.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/outputdefinition.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/outputdefinition.py (revision 23670) @@ -1,8 +1,6 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * -from StringToEnum import StringToEnum from checkfield import checkfield from WriteData import WriteData -import numpy as np +import numpy as np class outputdefinition(object): @@ -24,4 +22,10 @@ return string #}}} + def extrude(self,md): # {{{ + for definition in self.definitions: + definition.extrude(md); + + return self + #}}} def setdefaultparameters(self): # {{{ return self @@ -34,16 +38,13 @@ # }}} - def marshall(self,md,fid): # {{{ - - enums=np.zeros(len(self.definitions),) - + def marshall(self,prefix,md,fid): # {{{ + data=[]; for i in range(len(self.definitions)): - self.definitions[i].marshall(md,fid); - classdefinition=self.definitions[i].__class__.__name__ + self.definitions[i].marshall(prefix,md,fid); + classdefinition=self.definitions[i].__class__.__name__; classdefinition=classdefinition[0].upper()+classdefinition[1:] - enums[i]=StringToEnum(classdefinition)[0] - - enums=np.unique(enums); - - WriteData(fid,'data',enums,'enum',OutputdefinitionListEnum(),'format','DoubleMat','mattype',1); + data.append(classdefinition) + + data=np.unique(data); + WriteData(fid,prefix,'data',data,'name','md.outputdefinition.list','format','StringArray'); # }}} Index: /issm/trunk-jpl/src/py3/classes/pairoptions.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/pairoptions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/pairoptions.py (revision 23670) @@ -11,5 +11,5 @@ """ - def __init__(self,**kwargs): # {{{ + def __init__(self,*arg): # {{{ self.functionname = '' self.list = OrderedDict() @@ -21,8 +21,8 @@ #initialize list - if not len(kwargs): + if not len(arg): pass #Do nothing, else: - self.buildlist(**kwargs) + self.buildlist(*arg) # }}} def __repr__(self): # {{{ @@ -30,5 +30,5 @@ if self.list: s+=" list: (%ix%i)\n\n" % (len(self.list),2) - for item in list(self.list.items()): + for item in self.list.items(): if isinstance(item[1],str): s+=" field: %-10s value: '%s'\n" % (item[0],item[1]) @@ -41,29 +41,25 @@ return s # }}} - def buildlist(self,**kwargs): # {{{ + def buildlist(self,*arg): # {{{ """BUILDLIST - build list of objects from input""" - # #check length of input - # if len(arg) % 2: - # raise TypeError('Invalid parameter/value pair arguments') - # numoptions = len(arg)/2 - # #go through arg and build list of objects - # for i in xrange(numoptions): - # if isinstance(arg[2*i],(str,unicode)): - # self.list[arg[2*i]] = arg[2*i+1]; - # else: - # #option is not a string, ignore it - # print "WARNING: option number %d is not a string and will be ignored." % (i+1) + #check length of input + if len(arg) % 2: + raise TypeError('Invalid parameter/value pair arguments') + numoptions = len(arg)/2 #go through arg and build list of objects - print(kwargs) - for name,value in kwargs.items(): - self.list[name] = value - # }}} + for i in range(numoptions): + if isinstance(arg[2*i],str): + self.list[arg[2*i]] = arg[2*i+1]; + else: + #option is not a string, ignore it + print("WARNING: option number %d is not a string and will be ignored." % (i+1)) + # }}} def addfield(self,field,value): # {{{ """ADDFIELD - add a field to an options list""" if isinstance(field,str): if field in self.list: - print(("WARNING: field '%s' with value=%s exists and will be overwritten with value=%s." % (field,str(self.list[field]),str(value)))) + print("WARNING: field '%s' with value=%s exists and will be overwritten with value=%s." % (field,str(self.list[field]),str(value))) self.list[field] = value # }}} @@ -76,9 +72,9 @@ def AssignObjectFields(self,obj2): # {{{ """ASSIGNOBJECTFIELDS - assign object fields from options""" - for item in list(self.list.items()): + for item in self.list.items(): if item[0] in dir(obj2): setattr(obj2,item[0],item[1]) else: - print(("WARNING: field '%s' is not a property of '%s'." % (item[0],type(obj2)))) + print("WARNING: field '%s' is not a property of '%s'." % (item[0],type(obj2))) return obj2 # }}} @@ -154,5 +150,5 @@ #warn user if requested if warn: - print(("removefield info: option '%s' has been removed from the list of options." % field)) + print("removefield info: option '%s' has been removed from the list of options." % field) # }}} def marshall(self,md,fid,firstindex): # {{{ @@ -162,13 +158,15 @@ value = item[1] - #Write option name - WriteData(fid,'enum',(firstindex-1)+2*i+1,'data',name,'format','String') + raise NameError('need to sync with MATLAB') - #Write option value - if isinstance(value,str): - WriteData(fid,'enum',(firstindex-1)+2*i+2,'data',value,'format','String') - elif isinstance(value,(bool,int,float)): - WriteData(fid,'enum',(firstindex-1)+2*i+2,'data',value,'format','Double') - else: - raise TypeError("Cannot marshall option '%s': format not supported yet." % name) + ##Write option name + #WriteData(fid,prefix,'enum',(firstindex-1)+2*i+1,'data',name,'format','String') + + ##Write option value + #if isinstance(value,(str,unicode)): + # WriteData(fid,prefix,'enum',(firstindex-1)+2*i+2,'data',value,'format','String') + #elif isinstance(value,(bool,int,long,float)): + # WriteData(fid,prefix,'enum',(firstindex-1)+2*i+2,'data',value,'format','Double') + #else: + #raise TypeError("Cannot marshall option '%s': format not supported yet." % name) # }}} Index: /issm/trunk-jpl/src/py3/classes/plotoptions.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/plotoptions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/plotoptions.py (revision 23670) @@ -7,13 +7,13 @@ Usage: - plotoptions=plotoptions(**kwargs) + plotoptions=plotoptions(*arg) ''' - def __init__(self,**kwargs):# {{{ + def __init__(self,*arg):# {{{ self.numberofplots = 0 self.figurenumber = 1 self.list = OrderedDict() - self.buildlist(**kwargs) + self.buildlist(*arg) #}}} def __repr__(self): #{{{ @@ -23,5 +23,5 @@ if self.list: s+=" list: (%ix%i)\n" % (len(self.list),2) - for item in list(self.list.items()): + for item in self.list.items(): #s+=" options of plot number %i\n" % item if isinstance(item[1],str): @@ -35,15 +35,27 @@ return s #}}} - def buildlist(self,**kwargs): #{{{ + def buildlist(self,*arg): #{{{ + #check length of input + if len(arg) % 2: + raise TypeError('Invalid parameter/value pair arguments') - for name,value in kwargs.items(): - self.rawlist[name] = value + #go through args and build list (like pairoptions) + rawoptions=pairoptions.pairoptions(*arg) + numoptions=len(arg)/2 + rawlist=[] # cannot be a dict since they do not support duplicate keys - #get figure number + for i in range(numoptions): + if isinstance(arg[2*i],str): + rawlist.append([arg[2*i],arg[2*i+1]]) + else: + #option is not a string, ignore it + print("WARNING: option number %d is not a string and will be ignored." % (i+1)) + + #get figure number self.figurenumber=rawoptions.getfieldvalue('figure',1) rawoptions.removefield('figure',0) - #get number of subplots - numberofplots=Counter(x for sublist in rawlist for x in sublist if isinstance(x,str))['data'] + #get number of subplots + numberofplots=len([1 for sublist in rawlist for x in sublist if str(x)=='data']) self.numberofplots=numberofplots @@ -64,5 +76,5 @@ #if alloptions flag is on, apply to all plots if (allflag and 'data' not in rawlist[i][0] and '#' not in rawlist[i][0]): - + for j in range(numberofplots): self.list[j].addfield(rawlist[i][0],rawlist[i][1]) @@ -94,5 +106,5 @@ raise ValueError('error: in option i-j both i and j must be integers') for j in range(int(nums[0])-1,int(nums[1])): - self.list[j].addfield(field,rawlist[i][1]) + self.list[j].addfield(field,rawlist[i][1]) # Deal with #i @@ -103,5 +115,5 @@ self.list[int(plotnum)-1].addfield(field,rawlist[i][1]) else: - + #go through all subplots and assign key-value pairs j=0 @@ -113,4 +125,4 @@ j=j+1 if j+1>numberofplots: - print(("WARNING: too many instances of '%s' in options" % rawlist[i][0])) + print("WARNING: too many instances of '%s' in options" % rawlist[i][0]) #}}} Index: /issm/trunk-jpl/src/py3/classes/private.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/private.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/private.py (revision 23670) @@ -1,5 +1,4 @@ from collections import OrderedDict from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield @@ -20,4 +19,5 @@ #set defaults self.setdefaultparameters() + #}}} def __repr__(self): # {{{ Index: /issm/trunk-jpl/src/py3/classes/qmu.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/qmu.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/qmu.py (revision 23670) @@ -1,10 +1,12 @@ -import numpy +import numpy as np +from MatlabFuncs import * +from IssmConfig import * from project3d import project3d from collections import OrderedDict from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData -import MatlabFuncs as m +from helpers import * +from dakota_method import * class qmu(object): @@ -18,8 +20,8 @@ def __init__(self): # {{{ self.isdakota = 0 - self.variables = OrderedDict() - self.responses = OrderedDict() + self.variables = OrderedStruct() + self.responses = OrderedStruct() self.method = OrderedDict() - self.params = OrderedDict() + self.params = OrderedStruct() self.results = OrderedDict() self.partition = float('NaN') @@ -42,38 +44,43 @@ s+="%s\n" % fielddisplay(self,'isdakota','is qmu analysis activated?') - for i,variable in enumerate(self.variables.items()): - 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)) + maxlen = 0 + s+=" variables: (arrays of each variable class)\n" - for fname in fnames: - s+="' %-*s: [%ix%i] '%s'\n" % \ - (maxlen+1,fname,size(getattr(variable,fname)),type(getattr(variable,fname))) + # OrderedStruct's iterator returns individual name/array-of-functions pairs + for variable in self.variables: + fname=variable[0] + maxlen=max(maxlen,len(fname)) + size = np.shape(variable[1]) + a = size[0] + b = 1 if len(size) < 2 else size[1] + s+=" %-*s: [%ix%i] '%s'\n" % (maxlen+1,fname,a,b,type(variable[1][0])) - for i,response in enumerate(self.responses.items()): - 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)) + s+=" responses: (arrays of each response class)\n" + for response in self.responses: + fname=response[0] + maxlen=max(maxlen,len(fname)) + size = np.shape(response[1]) + a = size[0] + b = 1 if len(size) < 2 else size[1] + s+=" %-*s: [%ix%i] '%s'\n" % (maxlen+1,fname,a,b,type(response[1][0])) - 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') - s+="%s\n" % fielddisplay(self,'numberofresponses','number of responses') + if type(self.method) != OrderedDict: + self.method = [self.method] + # self.method must be iterable + for method in self.method: + if isinstance(method,dakota_method): + s+=" method : '%s'\n" % (method.method) - for i,method in enumerate(self.method.items()): - if isinstance(method,'dakota_method'): - s+=" method%s : '%s'\n" % \ - (string_dim(method,i),method.method) - - for i,param in enumerate(self.params.items()): - s+=" params%s: (array of method-independent parameters)\n" % \ - string_dim(self.params,i) + # params could be have a number of forms (mainly 1 struct or many) + if type(self.params) == OrderedStruct: + params = [self.params] + else: + params = np.hstack(np.atleast_1d(np.array(self.params))) + for param in params: + print(type(param)) + print(param) + s+=" params: (array of method-independent parameters)\n" fnames=vars(param) maxlen=0 @@ -82,10 +89,10 @@ for fname in fnames: - s+=" %-*s: %s\n" % \ - (maxlen+1,fname,any2str(getattr(param,fname))) + s+=" %-*s: %s\n" % (maxlen+1,fname,str(getattr(param,fname))) - for i,result in enumerate(self.results.items()): - s+=" results%s: (information from dakota files)\n" % \ - string_dim(self.results,i) + # results could be have a number of forms (mainly 1 struct or many) + results = np.hstack(np.atleast_1d(np.array(self.results))) + for result in results: + s+=" results: (information from dakota files)\n" fnames=vars(result) maxlen=0 @@ -94,6 +101,9 @@ for fname in fnames: - s+=" %-*s: [%ix%i] '%s'\n" % \ - (maxlen+1,fname,size(getattr(result,fname)),type(getattr(result,fname))) + size = np.shape(response[1]) + a = size[0] + b = 0 if len(size) < 2 else size[1] + size = np.shape(getattr(result,fname)) + s+=" %-*s: [%ix%i] '%s'\n" % (maxlen+1,fname,a,b,type(getattr(result,fname))) s+="%s\n" % fielddisplay(self,'partition','user provided mesh partitioning, defaults to metis if not specified') @@ -111,5 +121,5 @@ # }}} def extrude(self,md): # {{{ - self.partition=project3d(md,'vector',numpy.transpose(self.partition),'type','node') + self.partition=project3d(md,'vector',np.transpose(self.partition),'type','node') return self #}}} @@ -123,35 +133,48 @@ 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: + version=IssmConfig('_DAKOTA_VERSION_') + version=float(version[0]) + + if version < 6: + if not md.qmu.params.evaluation_concurrency==1: + md.checkmessage("concurrency should be set to 1 when running dakota in library mode") + else: + if not strcmpi(self.params.evaluation_scheduling,'master'): + md.checkmessage('evaluation_scheduling in qmu.params should be set to "master"') + + if md.cluster.np <= 1: + md.checkmessage('in parallel library mode, Dakota needs to run on at least 2 cpus, 1 cpu for the master, 1 cpu for the slave. Modify md.cluser.np accordingly.') + + if self.params.processors_per_evaluation < 1: + md.checkmessage('in parallel library mode, Dakota needs to run at least one slave on one cpu (md.qmu.params.processors_per_evaluation >=1)!') + + if np.mod(md.cluster.np-1,self.params.processors_per_evaluation): + md.checkmessage('in parallel library mode, the requirement is for md.cluster.np = md.qmu.params.processors_per_evaluation * number_of_slaves, where number_of_slaves will automatically be determined by Dakota. Modify md.cluster.np accordingly') + + if np.size(md.qmu.partition) > 0: + if np.size(md.qmu.partition)!=md.mesh.numberofvertices and np.size(md.qmu.partition) != md.mesh.numberofelements: + md.checkmessage("user supplied partition for qmu analysis should have size (md.mesh.numberofvertices x 1) or (md.mesh.numberofelements x 1)") + if not min(md.qmu.partition.flatten())==0: md.checkmessage("partition vector not indexed from 0 on") - if max(md.qmu.partition)>=md.qmu.numberofpartitions: + if max(md.qmu.partition.flatten())>=md.qmu.numberofpartitions: md.checkmessage("for qmu analysis, partitioning vector cannot go over npart, number of partition areas") - - if not m.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 marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','isdakota','format','Boolean') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','isdakota','format','Boolean') if not self.isdakota: - WriteData(fid,'data',False,'enum',QmuMassFluxSegmentsPresentEnum(),'format','Boolean'); + WriteData(fid,prefix,'data',False,'name','md.qmu.mass_flux_segments_present','format','Boolean'); 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') - if not self.mass_flux_segments: - WriteData(fid,'data',self.mass_flux_segments,'enum',MassFluxSegmentsEnum(),'format','MatArray'); + WriteData(fid,prefix,'object',self,'fieldname','partition','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'fieldname','numberofpartitions','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','numberofresponses','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','variabledescriptors','format','StringArray') + WriteData(fid,prefix,'object',self,'fieldname','responsedescriptors','format','StringArray') + if not isempty(self.mass_flux_segments): + WriteData(fid,prefix,'data',self.mass_flux_segments,'name','md.qmu.mass_flux_segments','format','MatArray'); flag=True; else: flag=False; - WriteData(fid,'data',flag,'enum',QmuMassFluxSegmentsPresentEnum(),'format','Boolean'); + WriteData(fid,prefix,'data',flag,'name','md.qmu.mass_flux_segments_present','format','Boolean'); # }}} Index: /issm/trunk-jpl/src/py3/classes/results.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/results.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/results.py (revision 23670) @@ -1,6 +1,6 @@ -import numpy +import numpy as np +from pairoptions import pairoptions from fielddisplay import fielddisplay import MatlabFuncs as m -from EnumDefinitions import * class results(object): @@ -12,5 +12,5 @@ """ - def __init__(self): # {{{ + def __init__(self,*args): # {{{ pass # }}} @@ -25,5 +25,5 @@ s+="%s\n" % fielddisplay(self,'SolutionType',"solution type") - for name in list(self.__dict__.keys()): + for name in self.__dict__.keys(): if name not in ['step','time','SolutionType','errlog','outlog']: if isinstance(getattr(self,name),list): @@ -48,5 +48,5 @@ return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ pass # }}} Index: /issm/trunk-jpl/src/py3/classes/rifts.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/rifts.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/rifts.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -34,5 +33,5 @@ #}}} def checkconsistency(self,md,solution,analyses): # {{{ - if (not self.riftstruct) or numpy.any(isnans(self.riftstruct)): + if (not self.riftstruct) or np.any(isnans(self.riftstruct)): numrifts=0 else: @@ -44,19 +43,19 @@ if not isinstance(self.riftstruct,list): md.checkmessage("rifts.riftstruct should be a structure!") - if numpy.any(md.mesh.segmentmarkers>=2): + if np.any(md.mesh.segmentmarkers>=2): #We have segments with rift markers, but no rift structure! md.checkmessage("model should be processed for rifts (run meshprocessrifts)!") for i,rift in enumerate(self.riftstruct): - md = checkfield(md,'fieldname',"rifts.riftstruct[%d]['fill']" % i,'values',[WaterEnum(),AirEnum(),IceEnum(),MelangeEnum()]) + md = checkfield(md,'fieldname',"rifts.riftstruct[%d]['fill']" % i,'values',['Water','Air','Ice','Melange',0,1,2,3]) else: - if self.riftstruct and numpy.any(numpy.logical_not(isnans(self.riftstruct))): + if self.riftstruct and np.any(np.logical_not(isnans(self.riftstruct))): md.checkmessage("riftstruct should be NaN since numrifts is 0!") return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ #Process rift info - if (not self.riftstruct) or numpy.any(isnans(self.riftstruct)): + if (not self.riftstruct) or np.any(isnans(self.riftstruct)): numrifts=0 else: @@ -65,11 +64,20 @@ numpairs=0 for rift in self.riftstruct: - numpairs+=numpy.size(rift['penaltypairs'],axis=0) + numpairs+=np.size(rift['penaltypairs'],axis=0) + + # Convert strings in riftstruct to hard coded numbers + FillDict={'Air':0, + 'Ice':1, + 'Melange':2, + 'Water':3} + for rift in self.riftstruct: + if rift['fill'] in ['Air','Ice','Melange','Water']: + rift['fill'] = FillDict[rift['fill']] # 2 for nodes + 2 for elements+ 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. - data=numpy.zeros((numpairs,12)) + data=np.zeros((numpairs,12)) count=0 for rift in self.riftstruct: - numpairsforthisrift=numpy.size(rift['penaltypairs'],0) + numpairsforthisrift=np.size(rift['penaltypairs'],0) data[count:count+numpairsforthisrift,0:7]=rift['penaltypairs'] data[count:count+numpairsforthisrift,7]=rift['fill'] @@ -80,5 +88,5 @@ count+=numpairsforthisrift - WriteData(fid,'data',numrifts,'enum',RiftsNumriftsEnum(),'format','Integer') - WriteData(fid,'data',data,'enum',RiftsRiftstructEnum(),'format','DoubleMat','mattype',3) + WriteData(fid,prefix,'data',numrifts,'name','md.rifts.numrifts','format','Integer') + WriteData(fid,prefix,'data',data,'name','md.rifts.riftstruct','format','DoubleMat','mattype',3) # }}} Index: /issm/trunk-jpl/src/py3/classes/steadystate.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/steadystate.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/steadystate.py (revision 23670) @@ -1,5 +1,4 @@ -import numpy +import numpy as np from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -49,5 +48,5 @@ #Early return - if not solution==SteadystateSolutionEnum(): + if not solution=='SteadystateSolution': return md @@ -55,5 +54,5 @@ md.checkmessage("for a steadystate computation, timestepping.time_step must be zero.") - if numpy.isnan(md.stressbalance.reltol): + if np.isnan(md.stressbalance.reltol): md.checkmessage("for a steadystate computation, stressbalance.reltol (relative convergence criterion) must be defined!") @@ -62,7 +61,7 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','reltol','format','Double') - WriteData(fid,'object',self,'fieldname','maxiter','format','Integer') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','reltol','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','maxiter','format','Integer') #process requested outputs @@ -72,4 +71,4 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',SteadystateRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.steadystate.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/stressbalance.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/stressbalance.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/stressbalance.py (revision 23670) @@ -1,8 +1,7 @@ -import numpy +import numpy as np import sys import copy from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -123,5 +122,5 @@ #Early return - if StressbalanceAnalysisEnum() not in analyses: + if 'StressbalanceAnalysis' not in analyses: return md @@ -142,51 +141,53 @@ #singular solution # if ~any((~isnan(md.stressbalance.spcvx)+~isnan(md.stressbalance.spcvy))==2), - if not numpy.any(numpy.logical_and(numpy.logical_not(numpy.isnan(md.stressbalance.spcvx)),numpy.logical_not(numpy.isnan(md.stressbalance.spcvy)))): + if not np.any(np.logical_and(np.logical_not(np.isnan(md.stressbalance.spcvx)),np.logical_not(np.isnan(md.stressbalance.spcvy)))): print("\n !!! Warning: no spc applied, model might not be well posed if no basal friction is applied, check for solution crash\n") #CHECK THAT EACH LINES CONTAINS ONLY NAN VALUES OR NO NAN VALUES # if any(sum(isnan(md.stressbalance.referential),2)~=0 & sum(isnan(md.stressbalance.referential),2)~=6), - if numpy.any(numpy.logical_and(numpy.sum(numpy.isnan(md.stressbalance.referential),axis=1)!=0,numpy.sum(numpy.isnan(md.stressbalance.referential),axis=1)!=6)): + if np.any(np.logical_and(np.sum(np.isnan(md.stressbalance.referential),axis=1)!=0,np.sum(np.isnan(md.stressbalance.referential),axis=1)!=6)): md.checkmessage("Each line of stressbalance.referential should contain either only NaN values or no NaN values") #CHECK THAT THE TWO VECTORS PROVIDED ARE ORTHOGONAL # if any(sum(isnan(md.stressbalance.referential),2)==0), - if numpy.any(numpy.sum(numpy.isnan(md.stressbalance.referential),axis=1)==0): - pos=[i for i,item in enumerate(numpy.sum(numpy.isnan(md.stressbalance.referential),axis=1)) if item==0] -# numpy.inner (and numpy.dot) calculate all the dot product permutations, resulting in a full matrix multiply -# if numpy.any(numpy.abs(numpy.inner(md.stressbalance.referential[pos,0:2],md.stressbalance.referential[pos,3:5]).diagonal())>sys.float_info.epsilon): + if np.any(np.sum(np.isnan(md.stressbalance.referential),axis=1)==0): + pos=[i for i,item in enumerate(np.sum(np.isnan(md.stressbalance.referential),axis=1)) if item==0] +# np.inner (and np.dot) calculate all the dot product permutations, resulting in a full matrix multiply +# if np.any(np.abs(np.inner(md.stressbalance.referential[pos,0:2],md.stressbalance.referential[pos,3:5]).diagonal())>sys.float_info.epsilon): # md.checkmessage("Vectors in stressbalance.referential (columns 1 to 3 and 4 to 6) must be orthogonal") for item in md.stressbalance.referential[pos,:]: - if numpy.abs(numpy.inner(item[0:2],item[3:5]))>sys.float_info.epsilon: + if np.abs(np.inner(item[0:2],item[3:5]))>sys.float_info.epsilon: md.checkmessage("Vectors in stressbalance.referential (columns 1 to 3 and 4 to 6) must be orthogonal") #CHECK THAT NO rotation specified for FS Grounded ice at base if m.strcmp(md.mesh.domaintype(),'3D') and md.flowequation.isFS: - pos=numpy.nonzero(numpy.logical_and(md.mask.groundedice_levelset,md.mesh.vertexonbase)) - if numpy.any(numpy.logical_not(numpy.isnan(md.stressbalance.referential[pos,:]))): + pos=np.nonzero(np.logical_and(md.mask.groundedice_levelset,md.mesh.vertexonbase)) + if np.any(np.logical_not(np.isnan(md.stressbalance.referential[pos,:]))): md.checkmessage("no referential should be specified for basal vertices of grounded ice") return md # }}} - def marshall(self,md,fid): # {{{ - - yts=365.0*24.0*3600.0 - - WriteData(fid,'object',self,'class','stressbalance','fieldname','spcvx','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','stressbalance','fieldname','spcvy','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','stressbalance','fieldname','spcvz','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'class','stressbalance','fieldname','restol','format','Double') - WriteData(fid,'object',self,'class','stressbalance','fieldname','reltol','format','Double') - WriteData(fid,'object',self,'class','stressbalance','fieldname','abstol','format','Double','scale',1./yts) - WriteData(fid,'object',self,'class','stressbalance','fieldname','isnewton','format','Integer') - WriteData(fid,'object',self,'class','stressbalance','fieldname','FSreconditioning','format','Double') - WriteData(fid,'object',self,'class','stressbalance','fieldname','maxiter','format','Integer') - WriteData(fid,'object',self,'class','stressbalance','fieldname','shelf_dampening','format','Integer') - WriteData(fid,'object',self,'class','stressbalance','fieldname','vertex_pairing','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'class','stressbalance','fieldname','penalty_factor','format','Double') - WriteData(fid,'object',self,'class','stressbalance','fieldname','rift_penalty_lock','format','Integer') - WriteData(fid,'object',self,'class','stressbalance','fieldname','rift_penalty_threshold','format','Integer') - WriteData(fid,'object',self,'class','stressbalance','fieldname','referential','format','DoubleMat','mattype',1) - - WriteData(fid,'data',self.loadingforce[:,0],'format','DoubleMat','mattype',1,'enum',LoadingforceXEnum()) - WriteData(fid,'data',self.loadingforce[:,1],'format','DoubleMat','mattype',1,'enum',LoadingforceYEnum()) - WriteData(fid,'data',self.loadingforce[:,2],'format','DoubleMat','mattype',1,'enum',LoadingforceZEnum()) + def marshall(self,prefix,md,fid): # {{{ + + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','vertex_pairing','format','DoubleMat','mattype',3) + + yts=md.constants.yts + + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','spcvx','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','spcvy','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','spcvz','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','restol','format','Double') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','reltol','format','Double') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','abstol','format','Double','scale',1./yts) + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','isnewton','format','Integer') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','FSreconditioning','format','Double') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','maxiter','format','Integer') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','shelf_dampening','format','Integer') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','penalty_factor','format','Double') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','rift_penalty_lock','format','Integer') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','rift_penalty_threshold','format','Integer') + WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','referential','format','DoubleMat','mattype',1) + + if isinstance(self.loadingforce, (list, tuple, np.ndarray)) and np.size(self.loadingforce,1) == 3: + WriteData(fid,prefix,'data',self.loadingforce[:,0],'format','DoubleMat','mattype',1,'name','md.stressbalance.loadingforcex') + WriteData(fid,prefix,'data',self.loadingforce[:,1],'format','DoubleMat','mattype',1,'name','md.stressbalance.loadingforcey') + WriteData(fid,prefix,'data',self.loadingforce[:,2],'format','DoubleMat','mattype',1,'name','md.stressbalance.loadingforcez') #process requested outputs @@ -196,4 +197,4 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',StressbalanceRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.stressbalance.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/taoinversion.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/taoinversion.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/taoinversion.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from project3d import project3d from WriteData import WriteData @@ -5,31 +5,32 @@ from fielddisplay import fielddisplay from IssmConfig import IssmConfig -from EnumDefinitions import * from marshallcostfunctions import marshallcostfunctions +from supportedcontrols import * +from supportedcostfunctions import * - -class taoinversion: +class taoinversion(object): def __init__(self): - iscontrol = 0 - incomplete_adjoint = 0 - control_parameters = float('NaN') - maxsteps = 0 - maxiter = 0 - fatol = 0 - frtol = 0 - gatol = 0 - grtol = 0 - gttol = 0 - algorithm = '' - cost_functions = float('NaN') - cost_functions_coefficients = float('NaN') - min_parameters = float('NaN') - max_parameters = float('NaN') - vx_obs = float('NaN') - vy_obs = float('NaN') - vz_obs = float('NaN') - vel_obs = float('NaN') - thickness_obs = float('NaN') - surface_obs = float('NaN') + self.iscontrol = 0 + self.incomplete_adjoint = 0 + self.control_parameters = float('NaN') + self.maxsteps = 0 + self.maxiter = 0 + self.fatol = 0 + self.frtol = 0 + self.gatol = 0 + self.grtol = 0 + self.gttol = 0 + self.algorithm = '' + self.cost_functions = float('NaN') + self.cost_functions_coefficients = float('NaN') + self.min_parameters = float('NaN') + self.max_parameters = float('NaN') + self.vx_obs = float('NaN') + self.vy_obs = float('NaN') + self.vz_obs = float('NaN') + self.vel_obs = float('NaN') + self.thickness_obs = float('NaN') + self.surface_obs = float('NaN') + self.setdefaultparameters() def __repr__(self): @@ -90,14 +91,13 @@ #minimization algorithm - PETSCMAJOR = IssmConfig('_PETSC_MAJOR_') - PETSCMINOR = IssmConfig('_PETSC_MINOR_') + PETSCMAJOR = IssmConfig('_PETSC_MAJOR_')[0] + PETSCMINOR = IssmConfig('_PETSC_MINOR_')[0] if(PETSCMAJOR>3 or (PETSCMAJOR==3 and PETSCMINOR>=5)): self.algorithm = 'blmvm'; else: self.algorithm = 'tao_blmvm'; - + #several responses can be used: self.cost_functions=101; - return self @@ -110,8 +110,8 @@ if numel(self.cost_functions_coefficients) > 1: self.cost_functions_coefficients=project3d(md,'vector',self.cost_functions_coefficients,'type','node') - + if numel(self.min_parameters) > 1: self.min_parameters=project3d(md,'vector',self.min_parameters,'type','node') - + if numel(self.max_parameters)>1: self.max_parameters=project3d(md,'vector',self.max_parameters,'type','node') @@ -120,15 +120,15 @@ def checkconsistency(self,md,solution,analyses): - if not self.control: + if not self.iscontrol: return md - if not IssmConfig('_HAVE_TAO_'): - md = checkmessage(md,['TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO']) + if not IssmConfig('_HAVE_TAO_')[0]: + md = md.checkmessage('TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO') - num_controls= numpy.numel(md.inversion.control_parameters) - num_costfunc= numpy.size(md.inversion.cost_functions,2) + num_controls= np.size(md.inversion.control_parameters) + num_costfunc= np.size(md.inversion.cost_functions) md = checkfield(md,'fieldname','inversion.iscontrol','values',[0, 1]) - md = checkfield(md,'fieldname','inversion.incomplete_adjoint','values',[0, 1]) + md = checkfield(md,'fieldname','inversion.incomplete_adjoint','values',[0,1]) md = checkfield(md,'fieldname','inversion.control_parameters','cell',1,'values',supportedcontrols()) md = checkfield(md,'fieldname','inversion.maxsteps','numel',1,'>=',0) @@ -141,13 +141,13 @@ - PETSCMAJOR = IssmConfig('_PETSC_MAJOR_') - PETSCMINOR = IssmConfig('_PETSC_MINOR_') + PETSCMAJOR = IssmConfig('_PETSC_MAJOR_')[0] + PETSCMINOR = IssmConfig('_PETSC_MINOR_')[0] if(PETSCMAJOR>3 or (PETSCMAJOR==3 and PETSCMINOR>=5)): - md = checkfield(md,'fieldname','inversion.algorithm','values',{'blmvm','cg','lmvm'}) + md = checkfield(md,'fieldname','inversion.algorithm','values',['blmvm','cg','lmvm']) else: - md = checkfield(md,'fieldname','inversion.algorithm','values',{'tao_blmvm','tao_cg','tao_lmvm'}) + md = checkfield(md,'fieldname','inversion.algorithm','values',['tao_blmvm','tao_cg','tao_lmvm']) - md = checkfield(md,'fieldname','inversion.cost_functions','size',[1, num_costfunc],'values',supportedcostfunctions()) + md = checkfield(md,'fieldname','inversion.cost_functions','size', [num_costfunc],'values',supportedcostfunctions()) md = checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices, num_costfunc],'>=',0) md = checkfield(md,'fieldname','inversion.min_parameters','size',[md.mesh.numberofvertices, num_controls]) @@ -155,46 +155,45 @@ - if solution==BalancethicknessSolutionEnum(): - md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices, 1],'NaN',1,'Inf',1) - elif solution==BalancethicknessSoftSolutionEnum(): - md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices, 1],'NaN',1,'Inf',1) + if solution=='BalancethicknessSolution': + md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) + elif solution=='BalancethicknessSoftSolution': + md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) else: - md = checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices, 1],'NaN',1,'Inf',1) - md = checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices, 1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) - def marshall(self, md, fid): + def marshall(self,prefix,md,fid): - yts=365.0*24.0*3600.0; - WriteData(fid,'object',self,'class','inversion','fieldname','iscontrol','format','Boolean') - WriteData(fid,'enum',InversionTypeEnum(),'data',1,'format','Integer') - if not self.iscontrol: - return - WriteData(fid,'object',self,'class','inversion','fieldname','incomplete_adjoint','format','Boolean') - WriteData(fid,'object',self,'class','inversion','fieldname','maxsteps','format','Integer') - WriteData(fid,'object',self,'class','inversion','fieldname','maxiter','format','Integer') - WriteData(fid,'object',self,'class','inversion','fieldname','fatol','format','Double') - WriteData(fid,'object',self,'class','inversion','fieldname','frtol','format','Double') - WriteData(fid,'object',self,'class','inversion','fieldname','gatol','format','Double') - WriteData(fid,'object',self,'class','inversion','fieldname','grtol','format','Double') - WriteData(fid,'object',self,'class','inversion','fieldname','gttol','format','Double') - WriteData(fid,'object',self,'class','inversion','fieldname','algorithm','format','String') - WriteData(fid,'object',self,'class','inversion','fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','inversion','fieldname','min_parameters','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'class','inversion','fieldname','max_parameters','format','DoubleMat','mattype',3) - WriteData(fid,'object',self,'class','inversion','fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'class','inversion','fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'class','inversion','fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts) - WriteData(fid,'object',self,'class','inversion','fieldname','thickness_obs','format','DoubleMat','mattype',1) - WriteData(fid,'object',self,'class','inversion','fieldname','surface_obs','format','DoubleMat','mattype',1) + yts=md.constants.yts; + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','iscontrol','format','Boolean') + WriteData(fid,prefix,'name','md.inversion.type','data',1,'format','Integer') + if not self.iscontrol: + return + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','incomplete_adjoint','format','Boolean') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','maxsteps','format','Integer') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','maxiter','format','Integer') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','fatol','format','Double') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','frtol','format','Double') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','gatol','format','Double') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','grtol','format','Double') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','gttol','format','Double') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','algorithm','format','String') + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','min_parameters','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','max_parameters','format','DoubleMat','mattype',3) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','thickness_obs','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'class','inversion','fieldname','surface_obs','format','DoubleMat','mattype',1) - #process control parameters - num_control_parameters = numpy.numel(self.control_parameters) - data = numpy.array([StringToEnum(self.control_parameter[0]) for control_parameter in self.control_parameters]).reshape(1,-1) - WriteData(fid,'data',data,'enum',InversionControlParametersEnum(),'format','DoubleMat','mattype',3) - WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum(),'format','Integer') + #process control parameters + num_control_parameters = np.size(self.control_parameters) + WriteData(fid,prefix,'object',self,'fieldname','control_parameters','format','StringArray') + WriteData(fid,prefix,'data',num_control_parameters,'name','md.inversion.num_control_parameters','format','Integer') - #process cost functions - num_cost_functions = numpy.size(self.cost_functions,2) - data= marshallcostfunctions(self.cost_functions) - WriteData(fid,'data',data,'enum',InversionCostFunctionsEnum(),'format','DoubleMat','mattype',3) - WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer') + #process cost functions + num_cost_functions = np.size(self.cost_functions) + data= marshallcostfunctions(self.cost_functions) + WriteData(fid,prefix,'data',data,'name','md.inversion.cost_functions','format','StringArray') + WriteData(fid,prefix,'data',num_cost_functions,'name','md.inversion.num_cost_functions','format','Integer') Index: /issm/trunk-jpl/src/py3/classes/thermal.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/thermal.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/thermal.py (revision 23670) @@ -1,9 +1,7 @@ -import numpy +import numpy as np from project3d import project3d from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData -import MatlabFuncs as m class thermal(object): @@ -24,5 +22,6 @@ self.penalty_factor = 0 self.isenthalpy = 0 - self.isdynamicbasalspc = 0; + self.isdynamicbasalspc = 0 + self.fe = 'P1' self.requested_outputs = [] @@ -45,8 +44,8 @@ #}}} def extrude(self,md): # {{{ - self.spctemperature=project3d(md,'vector',self.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',numpy.nan) - if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: - self.spctemperature=numpy.nan*numpy.ones((md.mesh.numberofvertices,1)) - pos=numpy.nonzero(md.mesh.vertexonsurface)[0] + self.spctemperature=project3d(md,'vector',self.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',np.nan) + if isinstance(md.initialization.temperature,np.ndarray) and np.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: + self.spctemperature=float('NaN')*np.ones((md.mesh.numberofvertices)) + pos=np.where(md.mesh.vertexonsurface)[0] self.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface return self @@ -81,5 +80,8 @@ #will basal boundary conditions be set dynamically - self.isdynamicbasalspc=0; + self.isdynamicbasalspc=0 + + #Finite element interpolation + self.fe='P1' #default output @@ -91,33 +93,45 @@ #Early return - if (ThermalAnalysisEnum() not in analyses and EnthalpyAnalysisEnum() not in analyses) or (solution==TransientSolutionEnum() and not md.transient.isthermal): + if ('ThermalAnalysis' not in analyses and 'EnthalpyAnalysis' not in analyses) or (solution=='TransientSolution' and not md.transient.isthermal): return md md = checkfield(md,'fieldname','thermal.stabilization','numel',[1],'values',[0,1,2]) md = checkfield(md,'fieldname','thermal.spctemperature','Inf',1,'timeseries',1) - if EnthalpyAnalysisEnum() in analyses and md.thermal.isenthalpy and md.mesh.dimension()==3: - pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices]))) - replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) - md = checkfield(md,'fieldname','thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'fieldname','thermal.requested_outputs','stringrow',1) + + if 'EnthalpyAnalysis' in analyses and md.thermal.isenthalpy and md.mesh.dimension()==3: + TEMP = md.thermal.spctemperature[:-1].flatten(-1) + pos=np.where(~np.isnan(TEMP)) + try: + spccol=np.size(md.thermal.spctemperature,1) + except IndexError: + spccol=1 + + replicate=np.tile(md.geometry.surface-md.mesh.z,(spccol)).flatten(-1) + + control=md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate+10**-5 + + md = checkfield(md,'fieldname','thermal.spctemperature','field',md.thermal.spctemperature.flatten(-1)[pos],'<=',control[pos],'message',"spctemperature should be below the adjusted melting point") md = checkfield(md,'fieldname','thermal.isenthalpy','numel',[1],'values',[0,1]) md = checkfield(md,'fieldname','thermal.isdynamicbasalspc','numel',[1],'values',[0,1]); if(md.thermal.isenthalpy): - if numpy.isnan(md.stressbalance.reltol): + if np.isnan(md.stressbalance.reltol): md.checkmessage("for a steadystate computation, thermal.reltol (relative convergence criterion) must be defined!") md = checkfield(md,'fieldname','thermal.reltol','>',0.,'message',"reltol must be larger than zero"); - md = checkfield(md,'fieldname','thermal.requested_outputs','stringrow',1) + return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','spctemperature','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1) - WriteData(fid,'object',self,'fieldname','penalty_threshold','format','Integer') - WriteData(fid,'object',self,'fieldname','stabilization','format','Integer') - WriteData(fid,'object',self,'fieldname','reltol','format','Double'); - WriteData(fid,'object',self,'fieldname','maxiter','format','Integer') - WriteData(fid,'object',self,'fieldname','penalty_lock','format','Integer') - WriteData(fid,'object',self,'fieldname','penalty_factor','format','Double') - WriteData(fid,'object',self,'fieldname','isenthalpy','format','Boolean') - WriteData(fid,'object',self,'fieldname','isdynamicbasalspc','format','Boolean'); + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','spctemperature','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'fieldname','penalty_threshold','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','reltol','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','maxiter','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','penalty_lock','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','penalty_factor','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','isenthalpy','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','fe','format','String'); + WriteData(fid,prefix,'object',self,'fieldname','isdynamicbasalspc','format','Boolean'); #process requested outputs @@ -127,4 +141,4 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',ThermalRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.thermal.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/timestepping.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/timestepping.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/timestepping.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -16,7 +15,6 @@ self.final_time = 0. self.time_step = 0. - self.time_adapt = 0 - self.cfl_coefficient = 0. self.interp_forcings = 1 + self.coupling_time = 0. #set defaults @@ -29,7 +27,6 @@ string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yr]")) string="%s\n%s"%(string,fielddisplay(self,"time_step","length of time steps [yr]")) - string="%s\n%s"%(string,fielddisplay(self,"time_adapt","use cfl condition to define time step ? (0 or 1) ")) - string="%s\n%s"%(string,fielddisplay(self,"cfl_coefficient","coefficient applied to cfl condition")) string="%s\n%s"%(string,fielddisplay(self,"interp_forcings","interpolate in time between requested forcing values ? (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(self,"coupling_time","length of coupling time steps with ocean model [yr]")) return string #}}} @@ -42,8 +39,4 @@ self.final_time=10.*self.time_step - #time adaptation? - self.time_adapt=0 - self.cfl_coefficient=0.5 - #should we interpolate forcings between timesteps? self.interp_forcings=1 @@ -56,21 +49,19 @@ md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1) md = checkfield(md,'fieldname','timestepping.time_step','numel',[1],'>=',0,'NaN',1,'Inf',1) - md = checkfield(md,'fieldname','timestepping.time_adapt','numel',[1],'values',[0,1]) - md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1) if self.final_time-self.start_time<0: md.checkmessage("timestepping.final_time should be larger than timestepping.start_time") + md = checkfield(md,'fieldname','timestepping.coupling_time','numel',[1],'>=',0,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]) return md # }}} - def marshall(self,md,fid): # {{{ + def marshall(self,prefix,md,fid): # {{{ yts=md.constants.yts - - WriteData(fid,'object',self,'fieldname','start_time','format','Double','scale',yts) - WriteData(fid,'object',self,'fieldname','final_time','format','Double','scale',yts) - WriteData(fid,'object',self,'fieldname','time_step','format','Double','scale',yts) - WriteData(fid,'object',self,'fieldname','time_adapt','format','Boolean') - WriteData(fid,'object',self,'fieldname','cfl_coefficient','format','Double') - WriteData(fid,'object',self,'fieldname','interp_forcings','format','Boolean') + WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','start_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','final_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','time_step','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','interp_forcings','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','coupling_time','format','Double','scale',yts) # }}} Index: /issm/trunk-jpl/src/py3/classes/toolkits.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/toolkits.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/toolkits.py (revision 23670) @@ -2,8 +2,8 @@ from mumpsoptions import mumpsoptions from iluasmoptions import iluasmoptions -from EnumToString import EnumToString from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield +from issmgslsolver import issmgslsolver +from issmmumpssolver import issmmumpssolver class toolkits(object): @@ -30,10 +30,10 @@ else: raise IOError("ToolkitsFile error: need at least Mumps or Gsl to define issm solver type") + #The other properties are dynamic # }}} def __repr__(self): # {{{ - print('enter repr') s ="List of toolkits options per analysis:\n\n" - for analysis in list(vars(self).keys()): + for analysis in vars(self).keys(): s+="%s\n" % fielddisplay(self,analysis,'') @@ -41,15 +41,10 @@ # }}} def addoptions(self,analysis,*args): # {{{ - print('enter addoption') # Usage example: - # md.toolkits=addoptions(md.toolkits,StressbalanceAnalysisEnum(),FSoptions()); - # md.toolkits=addoptions(md.toolkits,StressbalanceAnalysisEnum()); - - #Convert analysis from enum to string - [analysis]=EnumToString(analysis) + # md.toolkits=addoptions(md.toolkits,'StressbalanceAnalysis',FSoptions()); + # md.toolkits=addoptions(md.toolkits,'StressbalanceAnalysis'); #Create dynamic property if property does not exist yet if not hasattr(self,analysis): -# exec("self.%s = None" % analysis) setattr(self,analysis,None) @@ -61,6 +56,5 @@ # }}} def checkconsistency(self,md,solution,analyses): # {{{ - print('enter check') - for analysis in list(vars(self).keys()): + for analysis in vars(self).keys(): if not getattr(self,analysis): md.checkmessage("md.toolkits.%s is empty" % analysis) @@ -86,15 +80,14 @@ #write header - fid.write("%s%s%s\n" % ('%Petsc options file: ',filename,' written from Matlab toolkits array')) + fid.write("%s%s%s\n" % ('%Toolkits options file: ',filename,' written from Python toolkits array')) #start writing options - for analysis in list(vars(self).keys()): + for analysis in vars(self).keys(): options=getattr(self,analysis) #first write analysis: fid.write("\n+%s\n" % analysis) #append a + to recognize it's an analysis enum - #now, write options - for optionname,optionvalue in list(options.items()): + for optionname,optionvalue in options.items(): if not optionvalue: Index: /issm/trunk-jpl/src/py3/classes/transient.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/transient.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/transient.py (revision 23670) @@ -1,4 +1,3 @@ from fielddisplay import fielddisplay -from EnumDefinitions import * from checkfield import checkfield from WriteData import WriteData @@ -13,5 +12,5 @@ def __init__(self): # {{{ - self.issmb = False + self.issmb = False self.ismasstransport = False self.isstressbalance = False @@ -19,8 +18,12 @@ self.isgroundingline = False self.isgia = False + self.isesa = False self.isdamageevolution = False - self.islevelset = False - self.iscalving = False + self.ismovingfront = False self.ishydrology = False + self.isslr = False + self.iscoupler = False + self.amr_frequency = 0 + self.isoceancoupling = False self.requested_outputs = [] @@ -37,8 +40,12 @@ string="%s\n%s"%(string,fielddisplay(self,'isgroundingline','indicates if a groundingline migration is used in the transient')) string="%s\n%s"%(string,fielddisplay(self,'isgia','indicates if a postglacial rebound is used in the transient')) + string="%s\n%s"%(string,fielddisplay(self,'isesa','indicates whether an elastic adjustment model is used in the transient')) string="%s\n%s"%(string,fielddisplay(self,'isdamageevolution','indicates whether damage evolution is used in the transient')) - string="%s\n%s"%(string,fielddisplay(self,'islevelset','LEVELSET METHOD DESCRIPTION')) - string="%s\n%s"%(string,fielddisplay(self,'iscalving','indicates whether calving is used in the transient')) + string="%s\n%s"%(string,fielddisplay(self,'ismovingfront','indicates whether a moving front capability is used in the transient')) string="%s\n%s"%(string,fielddisplay(self,'ishydrology','indicates whether an hydrology model is used')) + string="%s\n%s"%(string,fielddisplay(self,'isslr','indicates if a sea level rise solution is used in the transient')) + string="%s\n%s"%(string,fielddisplay(self,'isoceancoupling','indicates whether coupling with an ocean model is used in the transient')) + string="%s\n%s"%(string,fielddisplay(self,'iscoupler','indicates whether different models are being run with need for coupling')) + string="%s\n%s"%(string,fielddisplay(self,'amr_frequency','frequency at which mesh is refined in simulations with multiple time_steps')) string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','list of additional outputs requested')) return string @@ -61,8 +68,32 @@ self.isgroundingline = False self.isgia = False + self.isesa = False self.isdamageevolution = False - self.islevelset = False - self.iscalving = False + self.ismovingfront = False self.ishydrology = False + self.isoceancoupling = False + self.isslr = False + self.iscoupler = False + self.amr_frequency = 0 + + #default output + self.requested_outputs=[] + return self + #}}} + def deactivateall(self):#{{{ + self.issmb = False + self.ismasstransport = False + self.isstressbalance = False + self.isthermal = False + self.isgroundingline = False + self.isgia = False + self.isesa = False + self.isdamageevolution = False + self.ismovingfront = False + self.ishydrology = False + self.isslr = False + self.isoceancoupling = False + self.iscoupler = False + self.amr_frequency = 0 #default output @@ -73,14 +104,18 @@ #full analysis: Stressbalance, Masstransport and Thermal but no groundingline migration for now - self.issmb = True - self.ismasstransport = True - self.isstressbalance = True - self.isthermal = True - self.isgroundingline = False - self.isgia = False + self.issmb = True + self.ismasstransport = True + self.isstressbalance = True + self.isthermal = True + self.isgroundingline = False + self.isgia = False + self.isesa = False self.isdamageevolution = False - self.islevelset = False - self.iscalving = False - self.ishydrology = False + self.ismovingfront = False + self.ishydrology = False + self.isslr = False + self.isoceancoupling = False + self.iscoupler = False + self.amr_frequency = 0 #default output @@ -91,5 +126,5 @@ #Early return - if not solution==TransientSolutionEnum(): + if not solution=='TransientSolution': return md @@ -100,23 +135,34 @@ md = checkfield(md,'fieldname','transient.isgroundingline','numel',[1],'values',[0,1]) md = checkfield(md,'fieldname','transient.isgia','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.isesa','numel',[1],'values',[0,1]) md = checkfield(md,'fieldname','transient.isdamageevolution','numel',[1],'values',[0,1]) - md = checkfield(md,'fieldname','transient.islevelset','numel',[1],'values',[0,1]) md = checkfield(md,'fieldname','transient.ishydrology','numel',[1],'values',[0,1]) - md = checkfield(md,'fieldname','transient.iscalving','numel',[1],'values',[0,1]); + md = checkfield(md,'fieldname','transient.ismovingfront','numel',[1],'values',[0,1]); + md = checkfield(md,'fieldname','transient.isslr','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.isoceancoupling','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.iscoupler','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.amr_frequency','numel',[1],'>=',0,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','transient.requested_outputs','stringrow',1) + + if (solution!='TransientSolution') and (md.transient.iscoupling): + md.checkmessage("Coupling with ocean can only be done in transient simulations!") return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'object',self,'fieldname','issmb','format','Boolean') - WriteData(fid,'object',self,'fieldname','ismasstransport','format','Boolean') - WriteData(fid,'object',self,'fieldname','isstressbalance','format','Boolean') - WriteData(fid,'object',self,'fieldname','isthermal','format','Boolean') - WriteData(fid,'object',self,'fieldname','isgroundingline','format','Boolean') - WriteData(fid,'object',self,'fieldname','isgia','format','Boolean') - WriteData(fid,'object',self,'fieldname','isdamageevolution','format','Boolean') - WriteData(fid,'object',self,'fieldname','islevelset','format','Boolean') - WriteData(fid,'object',self,'fieldname','ishydrology','format','Boolean') - WriteData(fid,'object',self,'fieldname','iscalving','format','Boolean') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','issmb','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','ismasstransport','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isstressbalance','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isthermal','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isgroundingline','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isgia','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isesa','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isdamageevolution','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','ishydrology','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','ismovingfront','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isslr','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isoceancoupling','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','iscoupler','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','amr_frequency','format','Integer') #process requested outputs @@ -126,4 +172,4 @@ outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] outputs =outputscopy - WriteData(fid,'data',outputs,'enum',TransientRequestedOutputsEnum(),'format','StringArray') + WriteData(fid,prefix,'data',outputs,'name','md.transient.requested_outputs','format','StringArray') # }}} Index: /issm/trunk-jpl/src/py3/classes/verbose.py =================================================================== --- /issm/trunk-jpl/src/py3/classes/verbose.py (revision 23669) +++ /issm/trunk-jpl/src/py3/classes/verbose.py (revision 23670) @@ -1,5 +1,4 @@ from pairoptions import pairoptions import MatlabFuncs as m -from EnumDefinitions import * from WriteData import WriteData @@ -29,5 +28,5 @@ """ - def __init__(self,*args,**kwargs): # {{{ + def __init__(self,*args): # {{{ #BEGINFIELDS self.mprocessor = False @@ -42,5 +41,5 @@ #ENDFIELDS - if not kwargs and not args: + if not len(args): #Don't do anything self.solution=True; @@ -64,9 +63,9 @@ else: #Use options to initialize object - self=pairoptions(**kwargs).AssignObjectFields(self) + self=pairoptions(*args).AssignObjectFields(self) #Cast to logicals listproperties=vars(self) - for fieldname,fieldvalue in list(listproperties.items()): + for fieldname,fieldvalue in listproperties.items(): if isinstance(fieldvalue,bool) or isinstance(fieldvalue,(int,float)): setattr(self,fieldname,bool(fieldvalue)) @@ -134,5 +133,5 @@ return md # }}} - def marshall(self,md,fid): # {{{ - WriteData(fid,'data',self.VerboseToBinary(),'enum',VerboseEnum(),'format','Integer') + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'data',self.VerboseToBinary(),'name','md.verbose','format','Integer') # }}} Index: /issm/trunk-jpl/src/py3/consistency/checkfield.py =================================================================== --- /issm/trunk-jpl/src/py3/consistency/checkfield.py (revision 23669) +++ /issm/trunk-jpl/src/py3/consistency/checkfield.py (revision 23670) @@ -1,14 +1,14 @@ -import numpy +import numpy as np import os from pairoptions import pairoptions import MatlabFuncs as m -def checkfield(md,**kwargs): +def checkfield(md,*args): """ CHECKFIELD - check field consistency Used to check model consistency., - Requires: - 'field' or 'fieldname' option. If 'fieldname' is provided, it will retrieve it from the model md. (md.(fieldname)) + Requires: + 'field' or 'fieldname' option. If 'fieldname' is provided, it will retrieve it from the model md. (md.(fieldname)) If 'field' is provided, it will assume the argument following 'field' is a numeric array. @@ -33,5 +33,5 @@ #get options - options=pairoptions(**kwargs) + options=pairoptions(*args) #get field from model @@ -40,9 +40,9 @@ fieldname=options.getfieldvalue('fieldname','no fieldname') else: - fieldname=options.getfieldvalue('fieldname') - exec("field=md.%s" % fieldname) + fieldname=options.getfieldvalue('fieldname') + exec("field=md.{}".format(fieldname)) if isinstance(field,(bool,int,float)): - field=numpy.array([field]) + field=np.array([field]) #check empty @@ -55,28 +55,34 @@ if options.exist('size'): fieldsize=options.getfieldvalue('size') - if len(fieldsize) == 1: - if numpy.isnan(fieldsize[0]): + if len(fieldsize) == 1: + if np.isnan(fieldsize[0]): pass - elif not numpy.size(field,0)==fieldsize[0]: - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' size should be %d" % (fieldname,fieldsize[0]))) + elif np.ndim(field)==1: + if not np.size(field)==fieldsize[0]: + md = md.checkmessage(options.getfieldvalue('message',"field {} size should be {}".format(fieldname,fieldsize[0]))) + else: + try: + exec("md.{}=np.squeeze(field)".format(fieldname)) + print(('{} had been squeezed if it was a matrix with only one column'.format(fieldname))) + except IndexError: + md = md.checkmessage(options.getfieldvalue('message',"field {} should have {} dimension".format(fieldname,len(fieldsize)))) 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]))) - + if np.isnan(fieldsize[0]): + if not np.size(field,1)==fieldsize[1]: + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have %d columns" % (fieldname,fieldsize[1]))) + elif np.isnan(fieldsize[1]): + if not np.size(field,0)==fieldsize[0]: + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have %d lines" % (fieldname,fieldsize[0]))) + elif fieldsize[1]==1: + if (not np.size(field,0)==fieldsize[0]): + md = md.checkmessage(options.getfieldvalue('message',"field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1]))) + else: + if (not np.size(field,0)==fieldsize[0]) or (not np.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 options.exist('numel'): fieldnumel=options.getfieldvalue('numel') - if numpy.size(field) not in fieldnumel: + if (type(fieldnumel) == int and np.size(field) != fieldnumel) or (type(fieldnumel) == list and np.size(field) not in fieldnumel): if len(fieldnumel)==1: md = md.checkmessage(options.getfieldvalue('message',\ @@ -91,13 +97,15 @@ #check NaN if options.getfieldvalue('NaN',0): - if numpy.any(numpy.isnan(field)): + if np.any(np.isnan(field)): md = md.checkmessage(options.getfieldvalue('message',\ "NaN values found in field '%s'" % fieldname)) + #check Inf if options.getfieldvalue('Inf',0): - if numpy.any(numpy.isinf(field)): + if np.any(np.isinf(field)): md = md.checkmessage(options.getfieldvalue('message',\ "Inf values found in field '%s'" % fieldname)) + #check cell @@ -123,25 +131,75 @@ #check greater if options.exist('>='): - lowerbound=options.getfieldvalue('>=') - if numpy.any(field=') + if np.size(lowerbound)>1: #checking elementwise + if any(field'): lowerbound=options.getfieldvalue('>') - if numpy.any(field<=lowerbound): - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have values above %d" % (fieldname,lowerbound))) + if np.size(lowerbound)>1: #checking elementwise + if any(field<=upperbound): + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have values below %d" % (fieldname,upperbound))) + else: + minval=np.nanmin(field) + if options.getfieldvalue('timeseries',0) : + minval=np.nanmin(field[:-1]) + elif options.getfieldvalue('singletimeseries',0): + if np.size(field)==1: #some singletimeseries are just one value + minval=field + else: + minval=np.nanmin(field[0]) + + if minval<=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): - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have values below %d" % (fieldname,upperbound))) + if np.size(upperbound)>1: #checking elementwise + if any(field>upperbound): + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have values below %d" % (fieldname,upperbound))) + else: + maxval=np.nanmax(field) + if options.getfieldvalue('timeseries',0): + maxval=np.nanmax(field[:-1]) + elif options.getfieldvalue('singletimeseries',0): + if np.size(field)==1: #some singletimeseries are just one value + maxval=field + else: + maxval=np.nanmax(field[0]) + if maxval>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): - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have values below %d" % (fieldname,upperbound))) + if np.size(upperbound)>1: #checking elementwise + if any(field>=upperbound): + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have values below %d" % (fieldname,upperbound))) + + else: + maxval=np.nanmax(field) + if options.getfieldvalue('timeseries',0): + maxval=np.nanmax(field[:-1]) + elif options.getfieldvalue('singletimeseries',0): + if np.size(field)==1: #some singletimeseries are just one value + maxval=field.copy() + else: + maxval=np.nanmax(field[0]) + + if maxval>=upperbound: + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have values below %d" % (fieldname,upperbound))) #check file @@ -158,13 +216,13 @@ #Check forcings (size and times) if options.getfieldvalue('timeseries',0): - if numpy.size(field,0)==md.mesh.numberofvertices: - if numpy.ndim(field)>1 and not numpy.size(field,1)==1: + if np.size(field,0)==md.mesh.numberofvertices or np.size(field,0)==md.mesh.numberofelements: + if np.ndim(field)>1 and not np.size(field,1)==1: 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 or numpy.size(field,0)==2: - if not all(field[-1,:]==numpy.sort(field[-1,:])): + elif np.size(field,0)==md.mesh.numberofvertices+1 or np.size(field,0)==md.mesh.numberofelements+1: + if np.ndim(field) > 1 and not all(field[-1,:]==np.sort(field[-1,:])): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns should be sorted chronologically" % fieldname)) - if any(field[-1,0:-1]==field[-1,1:]): + if np.ndim(field) > 1 and any(field[-1,0:-1]==field[-1,1:]): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns must not contain duplicate timesteps" % fieldname)) @@ -175,6 +233,6 @@ #Check single value forcings (size and times) if options.getfieldvalue('singletimeseries',0): - if numpy.size(field,0)==2: - if not all(field[-1,:]==numpy.sort(field[-1,:])): + if np.size(field,0)==2: + if not all(field[-1,:]==np.sort(field[-1,:])): md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns should be sorted chronologically" % fieldname)) @@ -182,8 +240,11 @@ md = md.checkmessage(options.getfieldvalue('message',\ "field '%s' columns must not contain duplicate timesteps" % fieldname)) - else: - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have 2 lines" % fieldname)) + elif np.size(field,0) == 1: + if np.ndim(field) > 1 and not np.size(field,1) == 1: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should be either a scalar or have 2 lines" % fieldname)) + else: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have 2 lines or be a scalar" % fieldname)) return md - Index: /issm/trunk-jpl/src/py3/consistency/ismodelselfconsistent.py =================================================================== --- /issm/trunk-jpl/src/py3/consistency/ismodelselfconsistent.py (revision 23669) +++ /issm/trunk-jpl/src/py3/consistency/ismodelselfconsistent.py (revision 23670) @@ -1,5 +1,2 @@ -from EnumDefinitions import * -from EnumToString import EnumToString - def AnalysisConfiguration(solutiontype): #{{{ """ @@ -10,45 +7,45 @@ """ - if solutiontype == StressbalanceSolutionEnum(): - analyses=[StressbalanceAnalysisEnum(),StressbalanceVerticalAnalysisEnum(),StressbalanceSIAAnalysisEnum(),L2ProjectionBaseAnalysisEnum()] + if solutiontype == 'StressbalanceSolution': + analyses=['StressbalanceAnalysis','StressbalanceVerticalAnalysis','StressbalanceSIAAnalysis','L2ProjectionBaseAnalysis'] - elif solutiontype == SteadystateSolutionEnum(): - analyses=[StressbalanceAnalysisEnum(),StressbalanceVerticalAnalysisEnum(),StressbalanceSIAAnalysisEnum(),L2ProjectionBaseAnalysisEnum(),ThermalAnalysisEnum(),MeltingAnalysisEnum()] + elif solutiontype == 'SteadystateSolution': + analyses=['StressbalanceAnalysis','StressbalanceVerticalAnalysis','StressbalanceSIAAnalysis','L2ProjectionBaseAnalysis','ThermalAnalysis','MeltingAnalysis','EnthalpyAnalysis'] - elif solutiontype == ThermalSolutionEnum(): - analyses=[EnthalpyAnalysisEnum(),ThermalAnalysisEnum(),MeltingAnalysisEnum()] + elif solutiontype == 'ThermalSolution': + analyses=['EnthalpyAnalysis','ThermalAnalysis','MeltingAnalysis'] - elif solutiontype == MasstransportSolutionEnum(): - analyses=[MasstransportAnalysisEnum()] + elif solutiontype == 'MasstransportSolution': + analyses=['MasstransportAnalysis'] - elif solutiontype == BalancethicknessSolutionEnum(): - analyses=[BalancethicknessAnalysisEnum()] + elif solutiontype == 'BalancethicknessSolution': + analyses=['BalancethicknessAnalysis'] - elif solutiontype == SurfaceSlopeSolutionEnum(): - analyses=[L2ProjectionBaseAnalysisEnum()] + elif solutiontype == 'SurfaceSlopeSolution': + analyses=['L2ProjectionBaseAnalysis'] - elif solutiontype == BalancevelocitySolutionEnum(): - analyses=[BalancevelocityAnalysisEnum()] + elif solutiontype == 'BalancevelocitySolution': + analyses=['BalancevelocityAnalysis'] - elif solutiontype == BedSlopeSolutionEnum(): - analyses=[L2ProjectionBaseAnalysisEnum()] + elif solutiontype == 'BedSlopeSolution': + analyses=['L2ProjectionBaseAnalysis'] - elif solutiontype == GiaSolutionEnum(): - analyses=[GiaAnalysisEnum()] + elif solutiontype == 'GiaSolution': + analyses=['GiaIvinsAnalysis'] - elif solutiontype == TransientSolutionEnum(): - analyses=[StressbalanceAnalysisEnum(),StressbalanceVerticalAnalysisEnum(),StressbalanceSIAAnalysisEnum(),L2ProjectionBaseAnalysisEnum(),ThermalAnalysisEnum(),MeltingAnalysisEnum(),EnthalpyAnalysisEnum(),MasstransportAnalysisEnum()] + elif solutiontype == 'LoveSolution': + analyses=['LoveAnalysis'] - elif solutiontype == FlaimSolutionEnum(): - analyses=[FlaimAnalysisEnum()] + elif solutiontype == 'TransientSolution': + analyses=['StressbalanceAnalysis','StressbalanceVerticalAnalysis','StressbalanceSIAAnalysis','L2ProjectionBaseAnalysis','ThermalAnalysis','MeltingAnalysis','EnthalpyAnalysis','MasstransportAnalysis'] - elif solutiontype == HydrologySolutionEnum(): - analyses=[L2ProjectionBaseAnalysisEnum(),HydrologyShreveAnalysisEnum(),HydrologyDCInefficientAnalysisEnum(),HydrologyDCEfficientAnalysisEnum()] + elif solutiontype == 'HydrologySolution': + analyses=['L2ProjectionBaseAnalysis','HydrologyShreveAnalysis','HydrologyDCInefficientAnalysis','HydrologyDCEfficientAnalysis'] - elif DamageEvolutionSolutionEnum(): - analyses=[DamageEvolutionAnalysisEnum()] + elif 'DamageEvolutionSolution': + analyses=['DamageEvolutionAnalysis'] else: - raise TypeError("solution type: '%s' not supported yet!" % EnumToString(solutiontype)[0]) + raise TypeError("solution type: '%s' not supported yet!" % solutiontype) return analyses @@ -84,5 +81,5 @@ #Check consistency of the object - exec("md.%s.checkconsistency(md,solution,analyses)" % field) + exec("md.{}.checkconsistency(md,solution,analyses)".format(field)) #error message if mode is not consistent Index: /issm/trunk-jpl/src/py3/contrib/bamg/YamsCall.py =================================================================== --- /issm/trunk-jpl/src/py3/contrib/bamg/YamsCall.py (revision 23669) +++ /issm/trunk-jpl/src/py3/contrib/bamg/YamsCall.py (revision 23670) @@ -29,19 +29,19 @@ #Compute Hessian t1=time.time() - print("%s" % ' computing Hessian...') + print(("%s" % ' computing Hessian...')) hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node') t2=time.time() - print("%s%d%s\n" % (' done (',t2-t1,' seconds)')) + print(("%s%d%s\n" % (' done (',t2-t1,' seconds)'))) #Compute metric t1=time.time() - print("%s" % ' computing metric...') + print(("%s" % ' computing metric...')) metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,numpy.empty(0,int)) t2=time.time() - print("%s%d%s\n" % (' done (',t2-t1,' seconds)')) + print(("%s%d%s\n" % (' done (',t2-t1,' seconds)'))) #write files t1=time.time() - print("%s" % ' writing initial mesh files...') + print(("%s" % ' writing initial mesh files...')) numpy.savetxt('carre0.met',metric) @@ -80,8 +80,8 @@ f.close() t2=time.time() - print("%s%d%s\n" % (' done (',t2-t1,' seconds)')) + print(("%s%d%s\n" % (' done (',t2-t1,' seconds)'))) #call yams - print("%s\n" % ' call Yams...') + print(("%s\n" % ' call Yams...')) if m.ispc(): #windows @@ -96,5 +96,5 @@ #plug new mesh t1=time.time() - print("\n%s" % ' reading final mesh files...') + print(("\n%s" % ' reading final mesh files...')) Tria=numpy.loadtxt('carre1.tria',int) Coor=numpy.loadtxt('carre1.coor',float) @@ -107,9 +107,9 @@ numberofelements2=md.mesh.numberofelements t2=time.time() - print("%s%d%s\n\n" % (' done (',t2-t1,' seconds)')) + print(("%s%d%s\n\n" % (' done (',t2-t1,' seconds)'))) #display number of elements - print("\n%s %i" % (' inital number of elements:',numberofelements1)) - print("\n%s %i\n\n" % (' new number of elements:',numberofelements2)) + print(("\n%s %i" % (' inital number of elements:',numberofelements1))) + print(("\n%s %i\n\n" % (' new number of elements:',numberofelements2))) #clean up: Index: /issm/trunk-jpl/src/py3/contrib/netCDF/export_netCDF.py =================================================================== --- /issm/trunk-jpl/src/py3/contrib/netCDF/export_netCDF.py (revision 23669) +++ /issm/trunk-jpl/src/py3/contrib/netCDF/export_netCDF.py (revision 23670) @@ -12,5 +12,5 @@ if path.exists(filename): print(('File {} allready exist'.format(filename))) - newname=input('Give a new name or "delete" to replace: ') + newname=eval(input('Give a new name or "delete" to replace: ')) if newname=='delete': remove(filename) @@ -72,5 +72,5 @@ for field in subfields: if str(field)!='errlog' and str(field)!='outlog' and str(field)!='SolutionType': - print('Treating '+str(group)+'.'+str(supfield)+'.'+str(field)) + print(('Treating '+str(group)+'.'+str(supfield)+'.'+str(field))) Var=md.results.__dict__[supfield].__dict__[field] DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict,False) @@ -80,5 +80,5 @@ for field in fields: - print('Treating ' +str(group)+'.'+str(field)) + print(('Treating ' +str(group)+'.'+str(field))) NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__) Var=md.__dict__[group].__dict__[field] @@ -119,5 +119,5 @@ charvar=stringtochar(numpy.array(var)) print(charvar) - print(charvar.shape) + print((charvar.shape)) for elt in range(0,val_dim): try: @@ -152,7 +152,7 @@ if time!=0: timevar=md.results.__dict__[supfield].__getitem__(time).__dict__[field] - print('Treating results.'+str(supfield)+'.'+str(field)+' for time '+str(time)) + print(('Treating results.'+str(supfield)+'.'+str(field)+' for time '+str(time))) vartab=numpy.column_stack((vartab,timevar)) - print(numpy.shape(vartab)) + print((numpy.shape(vartab))) try: ncvar[:,:]=vartab[:,:] @@ -190,5 +190,5 @@ DimDict[len(NewDim)]='Dimension'+str(index) output=output+[str(DimDict[shape[dim]])] - print('Defining dimension ' +'Dimension'+str(index)) + print(('Defining dimension ' +'Dimension'+str(index))) elif type(shape[0])==str:#dealling with a dictionnary try: @@ -199,5 +199,5 @@ DimDict[len(NewDim)]='Dimension'+str(index) output=[str(DimDict[numpy.shape(dict.keys(var))[0]])]+['Dimension6'] - print('Defining dimension ' +'Dimension'+str(index)) + print(('Defining dimension ' +'Dimension'+str(index))) break if istime: @@ -215,4 +215,4 @@ DimDict[len(NewDim)]='Dimension'+str(index) output=output+[str(DimDict[stringlength])] - print('Defining dimension ' +'Dimension'+str(index)) + print(('Defining dimension ' +'Dimension'+str(index))) return tuple(output), DimDict Index: /issm/trunk-jpl/src/py3/contrib/paraview/exportVTK.py =================================================================== --- /issm/trunk-jpl/src/py3/contrib/paraview/exportVTK.py (revision 23669) +++ /issm/trunk-jpl/src/py3/contrib/paraview/exportVTK.py (revision 23670) @@ -28,5 +28,5 @@ if os.path.exists(filename): print(('File {} allready exist'.format(filename))) - newname=input('Give a new name or "delete" to replace: ') + newname=eval(input('Give a new name or "delete" to replace: ')) if newname=='delete': filelist = glob.glob(filename+'/*') Index: /issm/trunk-jpl/src/py3/coordsystems/ll2xy.py =================================================================== --- /issm/trunk-jpl/src/py3/coordsystems/ll2xy.py (revision 23669) +++ /issm/trunk-jpl/src/py3/coordsystems/ll2xy.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def ll2xy(lat,lon,sgn=-1,central_meridian=0,standard_parallel=71): Index: /issm/trunk-jpl/src/py3/coordsystems/xy2ll.py =================================================================== --- /issm/trunk-jpl/src/py3/coordsystems/xy2ll.py (revision 23669) +++ /issm/trunk-jpl/src/py3/coordsystems/xy2ll.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from math import pi @@ -37,8 +37,8 @@ raise Exception('bad usage: type "help(xy2ll)" for details') - # if x,y passed as lists, convert to numpy arrays - if type(x) != "numpy.ndarray": + # if x,y passed as lists, convert to np.arrays + if type(x) != "np.ndarray": x=np.array(x) - if type(y) != "numpy.ndarray": + if type(y) != "np.ndarray": y=np.array(y) @@ -73,5 +73,5 @@ res1 = np.nonzero(rho <= 0.1)[0] if len(res1) > 0: - lat[res1] = 90. * sgn + lat[res1] = pi/2. * sgn lon[res1] = 0.0 Index: /issm/trunk-jpl/src/py3/dev/devpath.py =================================================================== --- /issm/trunk-jpl/src/py3/dev/devpath.py (revision 23669) +++ /issm/trunk-jpl/src/py3/dev/devpath.py (revision 23670) @@ -4,13 +4,11 @@ #Recover ISSM_DIR and USERNAME -ISSM_DIR = os.getenv('ISSM_DIRPY3') +ISSM_DIR = os.getenv('ISSM_DEV_DIR') USERNAME = os.getenv('USER') JPL_SVN = os.getenv('JPL_SVN') if(ISSM_DIR==None): raise NameError('"ISSM_DIR" environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!') -if(JPL_SVN==None): - warnings.warn('"JPL_SVN" environment variable is empty! add it to your .cshrc or .bashrc if you want to do distant computing') -#Go through src/m and append any directory that contains a *.py file to PATH +#Go through src/m and append any directory that contains a *.py file to PATH for root,dirs,files in os.walk(ISSM_DIR+ '/src/py3'): if '.svn' in dirs: @@ -21,5 +19,8 @@ if root not in sys.path: sys.path.append(root) - + +#Also add the Nightly run directory +sys.path.append(ISSM_DIR + '/test/NightlyRun') + sys.path.append(ISSM_DIR + '/lib') sys.path.append(ISSM_DIR + '/src/wrappers/python/.libs') @@ -29,8 +30,9 @@ sys.path.append(JPL_SVN + '/usr/' + USERNAME) else: - raise NameError ('cluster settings should be in, '+ JPL_SVN +'/usr/' + USERNAME) + warnings.warn('cluster settings should be in, '+ JPL_SVN +'/usr/' + USERNAME) #Manual imports for commonly used functions -#from plotmodel import plotmodel +from runme import runme #first because plotmodel may fail +from plotmodel import plotmodel #c = get_ipython().config @@ -40,3 +42,4 @@ #c.InteractiveShellApp.exec_lines.append('print "Warning: disable autoreload in startup.py to improve performance." ') -print("\n ISSM development path correctly loaded\n\n") +print("\n ISSM development path correctly loaded") +print(("Current path is {}\n\n".format(ISSM_DIR))) Index: /issm/trunk-jpl/src/py3/dev/issmversion.py =================================================================== --- /issm/trunk-jpl/src/py3/dev/issmversion.py (revision 23669) +++ /issm/trunk-jpl/src/py3/dev/issmversion.py (revision 23670) @@ -15,5 +15,5 @@ print(' ') print('Build date: '+IssmConfig('PACKAGE_BUILD_DATE')[0]) -print('Copyright (c) 2009-2015 California Institute of Technology') +print('Copyright (c) 2009-2018 California Institute of Technology') print(' ') print(' to get started type: issmdoc') Index: /issm/trunk-jpl/src/py3/exp/expcoarsen.py =================================================================== --- /issm/trunk-jpl/src/py3/exp/expcoarsen.py (revision 23669) +++ /issm/trunk-jpl/src/py3/exp/expcoarsen.py (revision 23670) @@ -1,4 +1,4 @@ import os.path -import numpy as np +import numpy as np from collections import OrderedDict from expread import expread Index: /issm/trunk-jpl/src/py3/exp/expdisp.py =================================================================== --- /issm/trunk-jpl/src/py3/exp/expdisp.py (revision 23669) +++ /issm/trunk-jpl/src/py3/exp/expdisp.py (revision 23670) @@ -1,27 +1,59 @@ from expread import expread -import numpy as np +import numpy as np +from matplotlib.path import Path +import matplotlib.patches as patches -def expdisp(domainoutline,ax,linestyle='--k',linewidth=1,unitmultiplier=1.): +def expdisp(ax,options): ''' plot the contents of a domain outline file - This routine reads in a domain outline file and plots all of the x,y contours + This routine reads in an exp file and plots all of the x,y points/lines/patches - 'ax' is a handle to the current plot axes, onto which the contours are to be drawn + 'ax' is a handle to the current plot axes, onto which we want to plot Usage: - expdisp(domainoutline,ax) + expdisp(ax,options) - Example: - expdisp('domain.exp',plt.gca(),linestyle='--k',linewidth=2,unitmultiplier=1.e3) + List of options passable to plotmodel: + 'expdisp' : path (or list of paths) to the exp file to be plotted + 'explinewidth' : linewidth + 'explinestyle' : matplotlib linestyle string + 'explinecolor' : matplotlib color string + 'expfill' : (True/False) fill a closed contour + 'expfillcolor' : Color for a filled contour, only used if expfill is True + 'expfillalpha' : alpha transparency for filled contour + + All options should be passed as lists of length len(number of exp files passed) ''' - domain=expread(domainoutline) - - for i in range(len(domain)): - if domain[i]['nods']==1: - ax.plot(domain[i]['x']*unitmultiplier,domain[i]['y']*unitmultiplier,'o',mec='k',mfc='r',ms=10) - else: - x=domain[i]['x'].tolist() # since expread returns a string representation of the arrays - y=domain[i]['y'].tolist() - ax.plot(x*unitmultiplier,y*unitmultiplier,linestyle,linewidth=linewidth) + filenames=options.getfieldvalue('expdisp') + linewidth=options.getfieldvalue('explinewidth',[1]*len(filenames)) + linestyle=options.getfieldvalue('explinestyle',['-']*len(filenames)) + linecolor=options.getfieldvalue('explinecolor',['k']*len(filenames)) + fill=options.getfieldvalue('expfill',[0]*len(filenames)) + alpha=options.getfieldvalue('expfillalpha',[1]*len(filenames)) + facecolor=options.getfieldvalue('expfillcolor',['r']*len(filenames)) + unitmultiplier=options.getfieldvalue('unit',1) + for i in range(len(filenames)): + linestylei=linestyle[i] + linecolori=linecolor[i] + linewidthi=linewidth[i] + alphai=alpha[i] + facecolori=facecolor[i] + filenamei=filenames[i] + filli=fill[i] + domain=expread(filenamei) + for j in range(len(domain)): + if domain[j]['nods']==1: + ax.plot(domain[j]['x']*unitmultiplier,domain[j]['y']*unitmultiplier,'o',mec='k',mfc='r',ms=10) + elif filli: + verts=np.column_stack((domain[j]['x'],domain[j]['y'])) + codes=[Path.MOVETO] + [Path.LINETO]*(len(domain[j]['x'])-2) + [Path.CLOSEPOLY] + path=Path(verts, codes) + patch=patches.PathPatch(path,facecolor=facecolori,edgecolor=linecolori,alpha=alphai, + lw=linewidthi) + ax.add_patch(patch) + else: + x=domain[j]['x'].tolist() # since expread returns a string representation of the arrays + y=domain[j]['y'].tolist() + ax.plot(x*unitmultiplier,y*unitmultiplier,ls=linestylei,lw=linewidthi,c=linecolori) Index: /issm/trunk-jpl/src/py3/exp/expread.py =================================================================== --- /issm/trunk-jpl/src/py3/exp/expread.py (revision 23669) +++ /issm/trunk-jpl/src/py3/exp/expread.py (revision 23670) @@ -1,9 +1,11 @@ import os.path -import numpy +import numpy as np from collections import OrderedDict import MatlabFuncs as m def expread(filename): + """ + EXPREAD - read a file exp and build a Structure @@ -23,6 +25,6 @@ See also EXPDOC, EXPWRITEASVERTICES + """ - #some checks if not os.path.exists(filename): @@ -31,14 +33,10 @@ #initialize number of profile contours=[] - #open file fid=open(filename,'r') - #loop over the number of profiles while True: - #update number of profiles contour=OrderedDict() - #Get file name A=fid.readline() @@ -50,4 +48,5 @@ if not (len(A) == 2 and m.strcmp(A[0],'##') and m.strncmp(A[1],'Name:',5)): break + if len(A[1])>5: contour['name']=A[1][5:-1] @@ -59,5 +58,4 @@ if not (len(A) == 2 and m.strcmp(A[0],'##') and m.strncmp(A[1],'Icon:',5)): break - #Get Info A=fid.readline().split() @@ -72,11 +70,10 @@ #Get Info A=fid.readline().split() - if not (len(A) == 5 and m.strcmp(A[0],'#') and m.strcmp(A[1],'X') and m.strcmp(A[2],'pos') \ - and m.strcmp(A[3],'Y') and m.strcmp(A[4],'pos')): + if not (len(A) == 5 and m.strcmp(A[0],'#') and m.strcmp(A[1],'X') and m.strcmp(A[2],'pos') + and m.strcmp(A[3],'Y') and m.strcmp(A[4],'pos')): break - #Get Coordinates - contour['x']=numpy.empty(contour['nods']) - contour['y']=numpy.empty(contour['nods']) + contour['x']=np.empty(contour['nods']) + contour['y']=np.empty(contour['nods']) for i in range(int(contour['nods'])): A=fid.readline().split() @@ -93,8 +90,5 @@ contours.append(contour) - #close file fid.close() - return contours - Index: /issm/trunk-jpl/src/py3/exp/expwrite.py =================================================================== --- /issm/trunk-jpl/src/py3/exp/expwrite.py (revision 23669) +++ /issm/trunk-jpl/src/py3/exp/expwrite.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def expwrite(contours,filename): @@ -21,5 +21,5 @@ fid=open(filename,'w') for x,y in zip(contours['x'],contours['y']): - #if numpy.size(contour['x'])!=numpy.size(contour['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") @@ -36,6 +36,6 @@ fid.write("%s\n" % '## Icon:0') fid.write("%s\n" % '# Points Count Value') - #fid.write("%i %f\n" % (numpy.size(contour['x']),contour['density'])) - fid.write("%i %f\n" % (numpy.size(x),density)) + #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']): Index: /issm/trunk-jpl/src/py3/extrusion/DepthAverage.py =================================================================== --- /issm/trunk-jpl/src/py3/extrusion/DepthAverage.py (revision 23669) +++ /issm/trunk-jpl/src/py3/extrusion/DepthAverage.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from project2d import project2d @@ -46,5 +46,5 @@ if vec2d: - vector_average=vector_average.reshape(-1,1) + vector_average=vector_average.reshape(-1,) return vector_average Index: /issm/trunk-jpl/src/py3/extrusion/project2d.py =================================================================== --- /issm/trunk-jpl/src/py3/extrusion/project2d.py (revision 23669) +++ /issm/trunk-jpl/src/py3/extrusion/project2d.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def project2d(md3d,value,layer): @@ -45,5 +45,5 @@ if vec2d: - projection_value=projection_value.reshape(-1,1) + projection_value=projection_value.reshape(-1,) return projection_value Index: /issm/trunk-jpl/src/py3/extrusion/project3d.py =================================================================== --- /issm/trunk-jpl/src/py3/extrusion/project3d.py (revision 23669) +++ /issm/trunk-jpl/src/py3/extrusion/project3d.py (revision 23670) @@ -1,6 +1,6 @@ -import numpy +import numpy as np from pairoptions import pairoptions -def project3d(md,**kwargs): +def project3d(md,*args): """ PROJECT3D - vertically project a vector from 2d mesh @@ -30,5 +30,5 @@ #retrieve parameters from options. - options = pairoptions(**kwargs) + options = pairoptions(*args) vector2d = options.getfieldvalue('vector') #mandatory vectype = options.getfieldvalue('type') #mandatory @@ -37,9 +37,9 @@ vector1d=False - if isinstance(vector2d,numpy.ndarray) and numpy.ndim(vector2d)==1: + if isinstance(vector2d,np.ndarray) and np.ndim(vector2d)==1: vector1d=True - vector2d=vector2d.reshape(-1,1) + vector2d=vector2d.reshape(-1,) - if isinstance(vector2d,(bool,int,float)) or numpy.size(vector2d)==1: + if isinstance(vector2d,(bool,int,float)) or np.size(vector2d)==1: projected_vector=vector2d @@ -47,38 +47,69 @@ #Initialize 3d vector - if vector2d.shape[0]==md.mesh.numberofvertices2d: - projected_vector=(paddingvalue*numpy.ones((md.mesh.numberofvertices, numpy.size(vector2d,axis=1)))).astype(vector2d.dtype) - elif vector2d.shape[0]==md.mesh.numberofvertices2d+1: - projected_vector=(paddingvalue*numpy.ones((md.mesh.numberofvertices+1,numpy.size(vector2d,axis=1)))).astype(vector2d.dtype) - projected_vector[-1,:]=vector2d[-1,:] - vector2d=vector2d[:-1,:] + if np.ndim(vector2d)==1: + if vector2d.shape[0]==md.mesh.numberofvertices2d: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofvertices))).astype(vector2d.dtype) + elif vector2d.shape[0]==md.mesh.numberofvertices2d+1: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofvertices+1))).astype(vector2d.dtype) + projected_vector[-1]=vector2d[-1] + vector2d=vector2d[:-1] + else: + raise TypeError("vector length not supported") + #Fill in + if layer==0: + for i in range(md.mesh.numberoflayers): + projected_vector[(i*md.mesh.numberofvertices2d):((i+1)*md.mesh.numberofvertices2d)]=vector2d + else: + projected_vector[((layer-1)*md.mesh.numberofvertices2d):(layer*md.mesh.numberofvertices2d)]=vector2d else: - raise TypeError("vector length not supported") + if vector2d.shape[0]==md.mesh.numberofvertices2d: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofvertices,np.size(vector2d,axis=1)))).astype(vector2d.dtype) + elif vector2d.shape[0]==md.mesh.numberofvertices2d+1: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofvertices+1,np.size(vector2d,axis=1)))).astype(vector2d.dtype) + projected_vector[-1,:]=vector2d[-1,:] + vector2d=vector2d[:-1,:] + else: + raise TypeError("vector length not supported") + #Fill in + if layer==0: + for i in range(md.mesh.numberoflayers): + projected_vector[(i*md.mesh.numberofvertices2d):((i+1)*md.mesh.numberofvertices2d),:]=vector2d + else: + projected_vector[((layer-1)*md.mesh.numberofvertices2d):(layer*md.mesh.numberofvertices2d),:]=vector2d - #Fill in - if layer==0: - for i in range(md.mesh.numberoflayers): - projected_vector[(i*md.mesh.numberofvertices2d):((i+1)*md.mesh.numberofvertices2d),:]=vector2d - else: - projected_vector[((layer-1)*md.mesh.numberofvertices2d):(layer*md.mesh.numberofvertices2d),:]=vector2d elif vectype.lower()=='element': #Initialize 3d vector - if vector2d.shape[0]==md.mesh.numberofelements2d: - projected_vector=(paddingvalue*numpy.ones((md.mesh.numberofelements, numpy.size(vector2d,axis=1)))).astype(vector2d.dtype) - elif vector2d.shape[0]==md.mesh.numberofelements2d+1: - projected_vector=(paddingvalue*numpy.ones((md.mesh.numberofelements+1,numpy.size(vector2d,axis=1)))).astype(vector2d.dtype) - projected_vector[-1,:]=vector2d[-1,:] - vector2d=vector2d[:-1,:] + if np.ndim(vector2d)==1: + if vector2d.shape[0]==md.mesh.numberofelements2d: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofelements))).astype(vector2d.dtype) + elif vector2d.shape[0]==md.mesh.numberofelements2d+1: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofelements+1))).astype(vector2d.dtype) + projected_vector[-1]=vector2d[-1] + vector2d=vector2d[:-1] + else: + raise TypeError("vector length not supported") + #Fill in + if layer==0: + for i in range(md.mesh.numberoflayers-1): + projected_vector[(i*md.mesh.numberofelements2d):((i+1)*md.mesh.numberofelements2d)]=vector2d + else: + projected_vector[((layer-1)*md.mesh.numberofelements2d):(layer*md.mesh.numberofelements2d)]=vector2d else: - raise TypeError("vector length not supported") - - #Fill in - if layer==0: - for i in range(md.mesh.numberoflayers-1): - projected_vector[(i*md.mesh.numberofelements2d):((i+1)*md.mesh.numberofelements2d),:]=vector2d - else: - projected_vector[((layer-1)*md.mesh.numberofelements2d):(layer*md.mesh.numberofelements2d),:]=vector2d + if vector2d.shape[0]==md.mesh.numberofelements2d: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofelements, np.size(vector2d,axis=1)))).astype(vector2d.dtype) + elif vector2d.shape[0]==md.mesh.numberofelements2d+1: + projected_vector=(paddingvalue*np.ones((md.mesh.numberofelements+1,np.size(vector2d,axis=1)))).astype(vector2d.dtype) + projected_vector[-1,:]=vector2d[-1,:] + vector2d=vector2d[:-1,:] + else: + raise TypeError("vector length not supported") + #Fill in + if layer==0: + for i in range(md.mesh.numberoflayers-1): + projected_vector[(i*md.mesh.numberofelements2d):((i+1)*md.mesh.numberofelements2d),:]=vector2d + else: + projected_vector[((layer-1)*md.mesh.numberofelements2d):(layer*md.mesh.numberofelements2d),:]=vector2d else: Index: /issm/trunk-jpl/src/py3/geometry/FlagElements.py =================================================================== --- /issm/trunk-jpl/src/py3/geometry/FlagElements.py (revision 23669) +++ /issm/trunk-jpl/src/py3/geometry/FlagElements.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np import os #from basinzoom import basinzoon @@ -24,8 +24,8 @@ if isinstance(region,str): if not region: - flag=numpy.zeros(md.mesh.numberofelements,bool) + flag=np.zeros(md.mesh.numberofelements,bool) invert=0 elif m.strcmpi(region,'all'): - flag=numpy.ones(md.mesh.numberofelements,bool) + flag=np.ones(md.mesh.numberofelements,bool) invert=0 else: @@ -44,18 +44,18 @@ xlim,ylim=basinzoom('basin',region) flag_nodes=p.logical_and_n(md.mesh.xxlim[0],md.mesh.yylim[0]) - flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1).astype(bool) + flag=np.prod(flag_nodes[md.mesh.elements],axis=1).astype(bool) else: #ok, flag elements - [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3].copy(),md.mesh.x,md.mesh.y,region,'element',1) + flag=ContourToMesh(md.mesh.elements[:,0:3].copy(),md.mesh.x,md.mesh.y,region,'element',1) flag=flag.astype(bool) if invert: - flag=numpy.logical_not(flag) + flag=np.logical_not(flag) - elif isinstance(region,numpy.ndarray) or isinstance(region,bool): - if numpy.size(region,0)==md.mesh.numberofelements: + elif isinstance(region,np.ndarray) or isinstance(region,bool): + if np.size(region,0)==md.mesh.numberofelements: flag=region - elif numpy.size(region,0)==md.mesh.numberofvertices: - flag=(numpy.sum(region[md.mesh.elements-1]>0,axis=1)==numpy.size(md.mesh.elements,1)) + elif np.size(region,0)==md.mesh.numberofvertices: + flag=(np.sum(region[md.mesh.elements-1]>0,axis=1)==np.size(md.mesh.elements,1)) else: raise TypeError("Flaglist for region must be of same size as number of elements in model.") Index: /issm/trunk-jpl/src/py3/geometry/GetAreas.py =================================================================== --- /issm/trunk-jpl/src/py3/geometry/GetAreas.py (revision 23669) +++ /issm/trunk-jpl/src/py3/geometry/GetAreas.py (revision 23670) @@ -1,5 +1,5 @@ -import numpy +import numpy as np -def GetAreas(index,x,y,z=numpy.array([])): +def GetAreas(index,x,y,z=np.array([])): """ GETAREAS - compute areas or volumes of elements @@ -18,19 +18,19 @@ #get number of elements and number of nodes - nels=numpy.size(index,axis=0) - nods=numpy.size(x) + nels=np.size(index,axis=0) + nods=np.size(x) #some checks - if numpy.size(y)!=nods or (z and numpy.size(z)!=nods): + if np.size(y)!=nods or (z and np.size(z)!=nods): raise TypeError("GetAreas error message: x,y and z do not have the same length.") - if numpy.max(index)>nods: + if np.max(index)>nods: raise TypeError("GetAreas error message: index should not have values above %d." % nods) - if (not z and numpy.size(index,axis=1)!=3): + if (not z and np.size(index,axis=1)!=3): raise TypeError("GetAreas error message: index should have 3 columns for 2d meshes.") - if (z and numpy.size(index,axis=1)!=6): + if (z and np.size(index,axis=1)!=6): raise TypeError("GetAreas error message: index should have 6 columns for 3d meshes.") #initialization - areas=numpy.zeros(nels) + areas=np.zeros(nels) x1=x[index[:,0]-1] x2=x[index[:,1]-1] @@ -46,5 +46,5 @@ else: #V=area(triangle)*1/3(z1+z2+z3) - thickness=numpy.mean(z[index[:,3:6]-1])-numpy.mean(z[index[:,0:3]-1]) + thickness=np.mean(z[index[:,3:6]-1])-np.mean(z[index[:,0:3]-1]) areas=(0.5*((x2-x1)*(y3-y1)-(y2-y1)*(x3-x1)))*thickness Index: /issm/trunk-jpl/src/py3/geometry/SegIntersect.py =================================================================== --- /issm/trunk-jpl/src/py3/geometry/SegIntersect.py (revision 23669) +++ /issm/trunk-jpl/src/py3/geometry/SegIntersect.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def SegIntersect(seg1,seg2): @@ -24,14 +24,14 @@ yD=seg2[1,1] - O2A=numpy.array([xA,yA])-numpy.array([xD/2.+xC/2.,yD/2.+yC/2.]) - O2B=numpy.array([xB,yB])-numpy.array([xD/2.+xC/2.,yD/2.+yC/2.]) - O1C=numpy.array([xC,yC])-numpy.array([xA/2.+xB/2.,yB/2.+yA/2.]) - O1D=numpy.array([xD,yD])-numpy.array([xA/2.+xB/2.,yB/2.+yA/2.]) + O2A=np.array([xA,yA])-np.array([xD/2.+xC/2.,yD/2.+yC/2.]) + O2B=np.array([xB,yB])-np.array([xD/2.+xC/2.,yD/2.+yC/2.]) + O1C=np.array([xC,yC])-np.array([xA/2.+xB/2.,yB/2.+yA/2.]) + O1D=np.array([xD,yD])-np.array([xA/2.+xB/2.,yB/2.+yA/2.]) - n1=numpy.array([yA-yB,xB-xA]) #normal vector to segA - n2=numpy.array([yC-yD,xD-xC]) #normal vector to segB + n1=np.array([yA-yB,xB-xA]) #normal vector to segA + n2=np.array([yC-yD,xD-xC]) #normal vector to segB - test1=numpy.dot(n2,O2A) - test2=numpy.dot(n2,O2B) + test1=np.dot(n2,O2A) + test2=np.dot(n2,O2B) if test1*test2>0: @@ -39,6 +39,6 @@ return bval - test3=numpy.dot(n1,O1C) - test4=numpy.dot(n1,O1D) + test3=np.dot(n1,O1C) + test4=np.dot(n1,O1D) if test3*test4>0: @@ -47,12 +47,12 @@ #if colinear - if test1*test2==0 and test3*test4==0 and numpy.linalg.det(numpy.hstack((n1.reshape((-1,1)),n2.reshape(-1,1))))==0: + if test1*test2==0 and test3*test4==0 and np.linalg.det(np.hstack((n1.reshape((-1,)),n2.reshape(-1,))))==0: #projection on the axis O1O2 - O2O1=numpy.array([xA/2.+xB/2.,yB/2.+yA/2.])-numpy.array([xD/2.+xC/2.,yD/2.+yC/2.]) - O1A=numpy.dot(O2O1,(O2A-O2O1)) - O1B=numpy.dot(O2O1,(O2B-O2O1)) - O1C=numpy.dot(O2O1,O1C) - O1D=numpy.dot(O2O1,O1D) + O2O1=np.array([xA/2.+xB/2.,yB/2.+yA/2.])-np.array([xD/2.+xC/2.,yD/2.+yC/2.]) + O1A=np.dot(O2O1,(O2A-O2O1)) + O1B=np.dot(O2O1,(O2B-O2O1)) + O1C=np.dot(O2O1,O1C) + O1D=np.dot(O2O1,O1D) #test if one point is included in the other segment (->bval=1) Index: /issm/trunk-jpl/src/py3/geometry/slope.py =================================================================== --- /issm/trunk-jpl/src/py3/geometry/slope.py (revision 23669) +++ /issm/trunk-jpl/src/py3/geometry/slope.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from GetNodalFunctionsCoeff import GetNodalFunctionsCoeff @@ -34,6 +34,6 @@ summation=np.array([[1],[1],[1]]) - sx=np.dot(surf[index-1]*alpha,summation).reshape(-1,) - sy=np.dot(surf[index-1]*beta,summation).reshape(-1,) + sx=np.dot(surf[index-1,0]*alpha,summation).reshape(-1,) + sy=np.dot(surf[index-1,0]*beta,summation).reshape(-1,) s=np.sqrt(sx**2+sy**2) Index: /issm/trunk-jpl/src/py3/interp/SectionValues.py =================================================================== --- /issm/trunk-jpl/src/py3/interp/SectionValues.py (revision 23669) +++ /issm/trunk-jpl/src/py3/interp/SectionValues.py (revision 23670) @@ -1,5 +1,5 @@ import os from expread import expread -import numpy as np +import numpy as np from project2d import project2d #from InterpFromMesh2d import InterpFromMesh2d @@ -127,5 +127,5 @@ #Interpolation of data on specified points - data_interp=InterpFromMeshToMesh3d(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z,data,X3,Y3,Z3,np.nan) + data_interp=InterpFromMeshToMesh3d(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z,data,X3,Y3,Z3,np.nan)[0] #build outputs Index: /issm/trunk-jpl/src/py3/interp/averaging.py =================================================================== --- /issm/trunk-jpl/src/py3/interp/averaging.py (revision 23669) +++ /issm/trunk-jpl/src/py3/interp/averaging.py (revision 23670) @@ -1,6 +1,9 @@ -import numpy as np +import numpy as np from GetAreas import GetAreas -from scipy.sparse import csc_matrix import MatlabFuncs as m +try: + from scipy.sparse import csc_matrix +except ImportError: + print("could not import scipy, no averaging capabilities enabled") def averaging(md,data,iterations,layer=0): Index: /issm/trunk-jpl/src/py3/interp/holefiller.py =================================================================== --- /issm/trunk-jpl/src/py3/interp/holefiller.py (revision 23669) +++ /issm/trunk-jpl/src/py3/interp/holefiller.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from scipy.spatial import cKDTree Index: /issm/trunk-jpl/src/py3/interp/interp.py =================================================================== --- /issm/trunk-jpl/src/py3/interp/interp.py (revision 23669) +++ /issm/trunk-jpl/src/py3/interp/interp.py (revision 23670) @@ -1,4 +1,4 @@ # module for inperpolating/smoothing data -import numpy as np +import numpy as np from scipy.interpolate import CloughTocher2DInterpolator, Rbf from scipy.spatial import cKDTree Index: /issm/trunk-jpl/src/py3/inversions/marshallcostfunctions.py =================================================================== --- /issm/trunk-jpl/src/py3/inversions/marshallcostfunctions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/inversions/marshallcostfunctions.py (revision 23670) @@ -1,33 +1,45 @@ import copy -from EnumDefinitions import * def marshallcostfunctions(cost_functions): - #copy list first - data=copy.deepcopy(cost_functions) + cfDict={101:'SurfaceAbsVelMisfit', + 102:'SurfaceRelVelMisfit', + 103:'SurfaceLogVelMisfit', + 104:'SurfaceLogVxVyMisfit', + 105:'SurfaceAverageVelMisfit', + 201:'ThicknessAbsMisfit', + 501:'DragCoefficientAbsGradient', + 502:'RheologyBbarAbsGradient', + 503:'ThicknessAbsGradient', + 504:'ThicknessAlongGradient', + 505:'ThicknessAcrossGradient',} - #convert to Enums - pos=[i for i,x in enumerate(cost_functions) if x==101]; - for i in pos: data[i]=SurfaceAbsVelMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==102]; - for i in pos: data[i]=SurfaceRelVelMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==103]; - for i in pos: data[i]=SurfaceLogVelMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==104]; - for i in pos: data[i]=SurfaceLogVxVyMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==105]; - for i in pos: data[i]=SurfaceAverageVelMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==201]; - for i in pos: data[i]=ThicknessAbsMisfitEnum() - pos=[i for i,x in enumerate(cost_functions) if x==501]; - for i in pos: data[i]=DragCoefficientAbsGradientEnum() - pos=[i for i,x in enumerate(cost_functions) if x==502]; - for i in pos: data[i]=RheologyBbarAbsGradientEnum() - pos=[i for i,x in enumerate(cost_functions) if x==503]; - for i in pos: data[i]=ThicknessAbsGradientEnum() - pos=[i for i,x in enumerate(cost_functions) if x==504]; - for i in pos: data[i]=ThicknessAlongGradientEnum() - pos=[i for i,x in enumerate(cost_functions) if x==505]; - for i in pos: data[i]=ThicknessAcrossGradientEnum() + data=[cfDict[cf] for cf in cost_functions] + # #copy list first + # data=copy.deepcopy(cost_functions) + + # #convert to strings + # pos=[i for i,x in enumerate(cost_functions) if x==101]; + # for i in pos: data[i]='SurfaceAbsVelMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==102]; + # for i in pos: data[i]='SurfaceRelVelMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==103]; + # for i in pos: data[i]='SurfaceLogVelMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==104]; + # for i in pos: data[i]='SurfaceLogVxVyMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==105]; + # for i in pos: data[i]='SurfaceAverageVelMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==201]; + # for i in pos: data[i]='ThicknessAbsMisfit' + # pos=[i for i,x in enumerate(cost_functions) if x==501]; + # for i in pos: data[i]='DragCoefficientAbsGradient' + # pos=[i for i,x in enumerate(cost_functions) if x==502]; + # for i in pos: data[i]='RheologyBbarAbsGradient' + # pos=[i for i,x in enumerate(cost_functions) if x==503]; + # for i in pos: data[i]='ThicknessAbsGradient' + # pos=[i for i,x in enumerate(cost_functions) if x==504]; + # for i in pos: data[i]='ThicknessAlongGradient' + # pos=[i for i,x in enumerate(cost_functions) if x==505]; + # for i in pos: data[i]='ThicknessAcrossGradient' return data Index: /issm/trunk-jpl/src/py3/inversions/parametercontroldrag.py =================================================================== --- /issm/trunk-jpl/src/py3/inversions/parametercontroldrag.py (revision 23669) +++ /issm/trunk-jpl/src/py3/inversions/parametercontroldrag.py (revision 23670) @@ -20,5 +20,5 @@ #process options - options=pairoptions(**kwargs) + options=pairoptions(*args) #control type Index: /issm/trunk-jpl/src/py3/io/loadmodel.py =================================================================== --- /issm/trunk-jpl/src/py3/io/loadmodel.py (revision 23669) +++ /issm/trunk-jpl/src/py3/io/loadmodel.py (revision 23670) @@ -1,4 +1,5 @@ from loadvars import loadvars from dbm import whichdb +from netCDF4 import Dataset def loadmodel(path): @@ -17,19 +18,17 @@ pass else: - raise IOError("loadmodel error message: file '%s' does not exist" % path) + try: + NCFile=Dataset(path,mode='r') + NCFile.close() + pass + except RuntimeError: + raise IOError("loadmodel error message: file '%s' does not exist" % path) + # try: + #recover model on file and name it md + struc=loadvars(path) + name=[key for key in struc.keys()] + if len(name)>1: + raise IOError("loadmodel error message: file '%s' contains several variables. Only one model should be present." % path) - try: - #recover model on file and name it md - struc=loadvars(path) - - name=[key for key in struc.keys()] - if len(name)>1: - raise IOError("loadmodel error message: file '%s' contains several variables. Only one model should be present." % path) - - md=struc[name[0]] - return md - - except Exception as me: - print(me) - raise IOError("could not load model '%s'" % path) - + md=struc[name[0]] + return md Index: /issm/trunk-jpl/src/py3/io/loadvars.py =================================================================== --- /issm/trunk-jpl/src/py3/io/loadvars.py (revision 23669) +++ /issm/trunk-jpl/src/py3/io/loadvars.py (revision 23670) @@ -1,5 +1,12 @@ import shelve import os.path +import numpy as np +from netCDF4 import Dataset +from netCDF4 import chartostring +from re import findall +from os import path +from collections import OrderedDict from dbm import whichdb +from model import * def loadvars(*args): @@ -51,25 +58,156 @@ if whichdb(filename): print("Loading variables from file '%s'." % filename) - else: - raise IOError("File '%s' not found." % filename) - - my_shelf = shelve.open(filename,'r') # 'r' for read-only - - if nvdict: - for name in nvdict.keys(): - try: + + my_shelf = shelve.open(filename,'r') # 'r' for read-only + if nvdict: + for name in nvdict.keys(): + try: + nvdict[name] = my_shelf[name] + print("Variable '%s' loaded." % name) + except KeyError: + value = None + print("Variable '%s' not found." % name) + + else: + for name in my_shelf.keys(): nvdict[name] = my_shelf[name] print("Variable '%s' loaded." % name) - except KeyError: - value = None - print("Variable '%s' not found." % name) + + my_shelf.close() else: - for name in my_shelf.keys(): - nvdict[name] = my_shelf[name] - print("Variable '%s' loaded." % name) - - my_shelf.close() - + try: + NCFile=Dataset(filename,mode='r') + NCFile.close() + except RuntimeError: + raise IOError("File '%s' not found." % filename) + + classtype,classtree=netCDFread(filename) + nvdict['md']=model() + NCFile=Dataset(filename,mode='r') + for mod in dict.keys(classtype): + if np.size(classtree[mod])>1: + curclass=NCFile.groups[classtree[mod][0]].groups[classtree[mod][1]] + if classtype[mod][0]=='list': + keylist=[key for key in curclass.groups] + try: + steplist=[int(key) for key in curclass.groups] + except ValueError: + steplist=[int(findall(r'\d+',key)[0]) for key in keylist] + indexlist=[index*(len(curclass.groups)-1)/max(1,max(steplist)) for index in steplist] + listtype=curclass.groups[keylist[0]].classtype + if listtype=='dict': + nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [OrderedDict() for i in range(max(1,len(curclass.groups)))] + else: + nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [getattr(__import__(listtype),listtype)() for i in range(max(1,len(curclass.groups)))] + Tree=nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]][:] + else: + nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = getattr(classtype[mod][1],classtype[mod][0])() + Tree=nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] + else: + curclass=NCFile.groups[classtree[mod][0]] + nvdict['md'].__dict__[mod] = getattr(classtype[mod][1],classtype[mod][0])() + Tree=nvdict['md'].__dict__[classtree[mod][0]] + #treating groups that are lists + for i in range(0,max(1,len(curclass.groups))): + if len(curclass.groups)>0: + listclass=curclass.groups[keylist[i]] + else: + listclass=curclass + for var in listclass.variables: + if var not in ['errlog','outlog']: + varval=listclass.variables[str(var)] + vardim=varval.ndim + try: + val_type=str(varval.dtype) + except AttributeError: + val_type=type(varval) + if vardim==0: + if type(Tree)==list: + t=indexlist[i] + if listtype=='dict': + Tree[t][str(var)]=varval[0] + else: + Tree[t].__dict__[str(var)]=varval[0] + else: + if str(varval[0])=='': + Tree.__dict__[str(var)]=[] + elif varval[0]=='True': + Tree.__dict__[str(var)]=True + elif varval[0]=='False': + Tree.__dict__[str(var)]=False + else: + Tree.__dict__[str(var)]=varval[0] + + elif vardim==1: + if varval.dtype==str: + if varval.shape[0]==1: + Tree.__dict__[str(var)]=[str(varval[0]),] + elif 'True' in varval[:] or 'False' in varval[:]: + Tree.__dict__[str(var)]=np.asarray([V=='True' for V in varval[:]],dtype=bool) + else: + Tree.__dict__[str(var)]=[str(vallue) for vallue in varval[:]] + else: + if type(Tree)==list: + t=indexlist[i] + if listtype=='dict': + Tree[t][str(var)]=varval[:] + else: + Tree[t].__dict__[str(var)]=varval[:] + else: + try: + #some thing specifically require a list + mdtype=type(Tree.__dict__[str(var)]) + except KeyError: + mdtype=float + if mdtype==list: + Tree.__dict__[str(var)]=[mdval for mdval in varval[:]] + else: + Tree.__dict__[str(var)]=varval[:] + elif vardim==2: + #dealling with dict + if varval.dtype==str: #that is for toolkits wich needs to be ordered + if any(varval[:,0]=='toolkit'): #toolkit definition have to be first + Tree.__dict__[str(var)]=OrderedDict([('toolkit', str(varval[np.where(varval[:,0]=='toolkit')[0][0],1]))]) + + strings1=[str(arg[0]) for arg in varval if arg[0]!='toolkits'] + strings2=[str(arg[1]) for arg in varval if arg[0]!='toolkits'] + Tree.__dict__[str(var)].update(list(zip(strings1, strings2))) + else: + if type(Tree)==list: + #t=int(keylist[i][-1])-1 + t=indexlist[i] + if listtype=='dict': + Tree[t][str(var)]=varval[:,:] + else: + Tree[t].__dict__[str(var)]=varval[:,:] + else: + Tree.__dict__[str(var)]=varval[:,:] + elif vardim==3: + if type(Tree)==list: + t=indexlist[i] + if listtype=='dict': + Tree[t][str(var)]=varval[:,:,:] + else: + Tree[t].__dict__[str(var)]=varval[:,:,:] + else: + Tree.__dict__[str(var)]=varval[:,:,:] + else: + print('table dimension greater than 3 not implemented yet') + for attr in listclass.ncattrs(): + if attr!='classtype': #classtype is for treatment, don't get it back + if type(Tree)==list: + t=indexlist[i] + if listtype=='dict': + Tree[t][str(attr).swapcase()]=str(listclass.getncattr(attr)) + else: + Tree[t].__dict__[str(attr).swapcase()]=str(listclass.getncattr(attr)) + else: + Tree.__dict__[str(attr).swapcase()]=str(listclass.getncattr(attr)) + if listclass.getncattr(attr)=='True': + Tree.__dict__[str(attr).swapcase()]=True + elif listclass.getncattr(attr)=='False': + Tree.__dict__[str(attr).swapcase()]=False + NCFile.close() if len(args) >= 2 and isinstance(args[1],str): # (value) value=[nvdict[name] for name in args[1:]] @@ -83,2 +221,28 @@ return nvdict + +def netCDFread(filename): + print(('Opening {} for reading '.format(filename))) + NCData=Dataset(filename, 'r') + class_dict={} + class_tree={} + + for group in NCData.groups: + if len(NCData.groups[group].groups)>0: + for subgroup in NCData.groups[group].groups: + classe=str(group)+'.'+str(subgroup) + class_dict[classe]=[str(getattr(NCData.groups[group].groups[subgroup],'classtype')),] + if class_dict[classe][0] not in ['dict','list','cell']: + class_dict[classe].append(__import__(class_dict[classe][0])) + class_tree[classe]=[group,subgroup] + else: + classe=str(group) + try: + class_dict[classe]=[str(getattr(NCData.groups[group],'classtype')),] + if class_dict[classe][0] not in ['dict','list','cell']: + class_dict[classe].append(__import__(class_dict[classe][0])) + class_tree[classe]=[group,] + except AttributeError: + print(('group {} is empty'.format(group))) + NCData.close() + return class_dict,class_tree Index: /issm/trunk-jpl/src/py3/materials/TMeltingPoint.py =================================================================== --- /issm/trunk-jpl/src/py3/materials/TMeltingPoint.py (revision 23669) +++ /issm/trunk-jpl/src/py3/materials/TMeltingPoint.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def TMeltingPoint(reftemp,pressure): Index: /issm/trunk-jpl/src/py3/materials/cuffey.py =================================================================== --- /issm/trunk-jpl/src/py3/materials/cuffey.py (revision 23669) +++ /issm/trunk-jpl/src/py3/materials/cuffey.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def cuffey(temperature): @@ -6,5 +6,5 @@ rigidity (in s^(1/3)Pa) is the flow law parameter in the flow law sigma=B*e(1/3) - (Cuffey and Paterson, p75). + (Cuffey and Paterson, p75). temperature is in Kelvin degrees @@ -12,38 +12,55 @@ rigidity=cuffey(temperature) """ - - if numpy.any(temperature<0.): + + if np.any(temperature<0.): raise RuntimeError("input temperature should be in Kelvin (positive)") - - T = temperature.reshape(-1,)-273.15 - rigidity=numpy.zeros_like(T) - pos=numpy.nonzero(T<=-45) - rigidity[pos]=10**8*(-0.000396645116301*(T[pos]+50)**3+ 0.013345579471334*(T[pos]+50)**2 -0.356868703259105*(T[pos]+50)+7.272363035371383) - pos=numpy.nonzero(numpy.logical_and(-45<=T,T<-40)) - rigidity[pos]=10**8*(-0.000396645116301*(T[pos]+45)**3+ 0.007395902726819*(T[pos]+45)**2 -0.253161292268336*(T[pos]+45)+5.772078366321591) - pos=numpy.nonzero(numpy.logical_and(-40<=T,T<-35)) - rigidity[pos]=10**8*(0.000408322072669*(T[pos]+40)**3+ 0.001446225982305*(T[pos]+40)**2 -0.208950648722716*(T[pos]+40)+4.641588833612773) - pos=numpy.nonzero(numpy.logical_and(-35<=T,T<-30)) - rigidity[pos]=10**8*(-0.000423888728124*(T[pos]+35)**3+ 0.007571057072334*(T[pos]+35)**2 -0.163864233449525*(T[pos]+35)+3.684031498640382) - pos=numpy.nonzero(numpy.logical_and(-30<=T,T<-25)) - rigidity[pos]=10**8*(0.000147154327025*(T[pos]+30)**3+ 0.001212726150476*(T[pos]+30)**2 -0.119945317335478*(T[pos]+30)+3.001000667185614) - pos=numpy.nonzero(numpy.logical_and(-25<=T,T<-20)) - rigidity[pos]=10**8*(-0.000193435838672*(T[pos]+25)**3+ 0.003420041055847*(T[pos]+25)**2 -0.096781481303861*(T[pos]+25)+2.449986525148220) - pos=numpy.nonzero(numpy.logical_and(-20<=T,T<-15)) - rigidity[pos]=10**8*(0.000219771255067*(T[pos]+20)**3+ 0.000518503475772*(T[pos]+20)**2 -0.077088758645767*(T[pos]+20)+2.027400665191131) - pos=numpy.nonzero(numpy.logical_and(-15<=T,T<-10)) - rigidity[pos]=10**8*(-0.000653438900191*(T[pos]+15)**3+ 0.003815072301777*(T[pos]+15)**2 -0.055420879758021*(T[pos]+15)+1.682390865739973) - pos=numpy.nonzero(numpy.logical_and(-10<=T,T<-5)) - rigidity[pos]=10**8*(0.000692439419762*(T[pos]+10)**3 -0.005986511201093 *(T[pos]+10)**2 -0.066278074254598*(T[pos]+10)+1.418983411970382) - pos=numpy.nonzero(numpy.logical_and(-5<=T,T<-2)) - rigidity[pos]=10**8*(-0.000132282004110*(T[pos]+5)**3 +0.004400080095332*(T[pos]+5)**2 -0.074210229783403*(T[pos]+5)+ 1.024485188140279) - pos=numpy.nonzero(-2<=T) - rigidity[pos]=10**8*(-0.000132282004110*(T[pos]+2)**3 +0.003209542058346*(T[pos]+2)**2 -0.051381363322371*(T[pos]+2)+ 0.837883605537096) + if np.ndim(temperature)==2: + #T = temperature.reshape(-1,)-273.15 + T = temperature.flatten()-273.15 + elif isinstance(temperature,float) or isinstance(temperature,int): + T = np.array([temperature])-273.15 + else: + T = temperature-273.15 + + + rigidity=np.zeros_like(T) + pos=np.nonzero(T<=-45) + if len(pos): + rigidity[pos]=10**8*(-0.000396645116301*(T[pos]+50)**3+ 0.013345579471334*(T[pos]+50)**2 -0.356868703259105*(T[pos]+50)+7.272363035371383) + pos=np.nonzero(np.logical_and(-45<=T,T<-40)) + if len(pos): + rigidity[pos]=10**8*(-0.000396645116301*(T[pos]+45)**3+ 0.007395902726819*(T[pos]+45)**2 -0.253161292268336*(T[pos]+45)+5.772078366321591) + pos=np.nonzero(np.logical_and(-40<=T,T<-35)) + if len(pos): + rigidity[pos]=10**8*(0.000408322072669*(T[pos]+40)**3+ 0.001446225982305*(T[pos]+40)**2 -0.208950648722716*(T[pos]+40)+4.641588833612773) + pos=np.nonzero(np.logical_and(-35<=T,T<-30)) + if len(pos): + rigidity[pos]=10**8*(-0.000423888728124*(T[pos]+35)**3+ 0.007571057072334*(T[pos]+35)**2 -0.163864233449525*(T[pos]+35)+3.684031498640382) + pos=np.nonzero(np.logical_and(-30<=T,T<-25)) + if len(pos): + rigidity[pos]=10**8*(0.000147154327025*(T[pos]+30)**3+ 0.001212726150476*(T[pos]+30)**2 -0.119945317335478*(T[pos]+30)+3.001000667185614) + pos=np.nonzero(np.logical_and(-25<=T,T<-20)) + if len(pos): + rigidity[pos]=10**8*(-0.000193435838672*(T[pos]+25)**3+ 0.003420041055847*(T[pos]+25)**2 -0.096781481303861*(T[pos]+25)+2.449986525148220) + pos=np.nonzero(np.logical_and(-20<=T,T<-15)) + if len(pos): + rigidity[pos]=10**8*(0.000219771255067*(T[pos]+20)**3+ 0.000518503475772*(T[pos]+20)**2 -0.077088758645767*(T[pos]+20)+2.027400665191131) + pos=np.nonzero(np.logical_and(-15<=T,T<-10)) + if len(pos): + rigidity[pos]=10**8*(-0.000653438900191*(T[pos]+15)**3+ 0.003815072301777*(T[pos]+15)**2 -0.055420879758021*(T[pos]+15)+1.682390865739973) + pos=np.nonzero(np.logical_and(-10<=T,T<-5)) + if len(pos): + rigidity[pos]=10**8*(0.000692439419762*(T[pos]+10)**3 -0.005986511201093 *(T[pos]+10)**2 -0.066278074254598*(T[pos]+10)+1.418983411970382) + pos=np.nonzero(np.logical_and(-5<=T,T<-2)) + if len(pos): + rigidity[pos]=10**8*(-0.000132282004110*(T[pos]+5)**3 +0.004400080095332*(T[pos]+5)**2 -0.074210229783403*(T[pos]+5)+ 1.024485188140279) + pos=np.nonzero(-2<=T) + if len(pos): + rigidity[pos]=10**8*(-0.000132282004110*(T[pos]+2)**3 +0.003209542058346*(T[pos]+2)**2 -0.051381363322371*(T[pos]+2)+ 0.837883605537096) #Now make sure that rigidity is positive - pos=numpy.nonzero(rigidity<0) - rigidity[pos]=1**6 + pos=np.nonzero(rigidity<0) + rigidity[pos]=1**6 return rigidity - Index: /issm/trunk-jpl/src/py3/materials/paterson.py =================================================================== --- /issm/trunk-jpl/src/py3/materials/paterson.py (revision 23669) +++ /issm/trunk-jpl/src/py3/materials/paterson.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def paterson(temperature): @@ -12,12 +12,12 @@ """ - if numpy.any(temperature<0.): + if np.any(temperature<0.): raise RuntimeError("input temperature should be in Kelvin (positive)") - if numpy.ndim(temperature)==2: + if np.ndim(temperature)==2: #T = temperature.reshape(-1,)-273.15 T = temperature.flatten()-273.15 elif isinstance(temperature,float) or isinstance(temperature,int): - T = numpy.array([temperature])-273.15 + T = np.array([temperature])-273.15 else: T = temperature-273.15 @@ -36,41 +36,41 @@ # rigidity=fittedmodel(temperature); - rigidity=numpy.zeros_like(T) - pos1=numpy.nonzero(T<=-45)[0] + rigidity=np.zeros_like(T) + pos1=np.nonzero(T<=-45)[0] if len(pos1): rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) - pos2=numpy.nonzero(numpy.logical_and(-45<=T,T<-40))[0] + pos2=np.nonzero(np.logical_and(-45<=T,T<-40))[0] if len(pos2): rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) - pos3=numpy.nonzero(numpy.logical_and(-40<=T,T<-35))[0] + pos3=np.nonzero(np.logical_and(-40<=T,T<-35))[0] if len(pos3): rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) - pos4=numpy.nonzero(numpy.logical_and(-35<=T,T<-30))[0] + pos4=np.nonzero(np.logical_and(-35<=T,T<-30))[0] if len(pos4): rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) - pos5=numpy.nonzero(numpy.logical_and(-30<=T,T<-25))[0] + pos5=np.nonzero(np.logical_and(-30<=T,T<-25))[0] if len(pos5): rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) - pos6=numpy.nonzero(numpy.logical_and(-25<=T,T<-20))[0] + pos6=np.nonzero(np.logical_and(-25<=T,T<-20))[0] if len(pos6): rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) - pos7=numpy.nonzero(numpy.logical_and(-20<=T,T<-15))[0] + pos7=np.nonzero(np.logical_and(-20<=T,T<-15))[0] if len(pos7): rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) - pos8=numpy.nonzero(numpy.logical_and(-15<=T,T<-10))[0] + pos8=np.nonzero(np.logical_and(-15<=T,T<-10))[0] if len(pos8): rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) - pos9=numpy.nonzero(numpy.logical_and(-10<=T,T<-5))[0] + pos9=np.nonzero(np.logical_and(-10<=T,T<-5))[0] if len(pos9): rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) - pos10=numpy.nonzero(numpy.logical_and(-5<=T,T<-2))[0] + pos10=np.nonzero(np.logical_and(-5<=T,T<-2))[0] if len(pos10): rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) - pos11=numpy.nonzero(-2<=T)[0] + pos11=np.nonzero(-2<=T)[0] if len(pos11): rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) #Now make sure that rigidity is positive - pos=numpy.nonzero(rigidity<0)[0] + pos=np.nonzero(rigidity<0)[0] if len(pos): rigidity[pos]=1.e6 Index: /issm/trunk-jpl/src/py3/mech/analyticaldamage.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/analyticaldamage.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/analyticaldamage.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from averaging import averaging #from plotmodel import plotmodel Index: /issm/trunk-jpl/src/py3/mech/backstressfrominversion.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/backstressfrominversion.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/backstressfrominversion.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from averaging import averaging from thomasparams import thomasparams Index: /issm/trunk-jpl/src/py3/mech/calcbackstress.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/calcbackstress.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/calcbackstress.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from averaging import averaging from thomasparams import thomasparams Index: /issm/trunk-jpl/src/py3/mech/damagefrominversion.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/damagefrominversion.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/damagefrominversion.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def damagefrominversion(md): Index: /issm/trunk-jpl/src/py3/mech/mechanicalproperties.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/mechanicalproperties.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/mechanicalproperties.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from GetNodalFunctionsCoeff import GetNodalFunctionsCoeff from results import results @@ -109,5 +109,5 @@ #eigenvalues and vectors for stress value,directions=np.linalg.eig(stress); - idx=abs(value).argsort()[::-1] # sort in descending order + idx=value.argsort()[::-1] # sort in descending algebraic (not absolute) order value=value[idx] directions=directions[:,idx] @@ -117,5 +117,5 @@ #eigenvalues and vectors for strain value,directions=np.linalg.eig(strain); - idx=abs(value).argsort()[::-1] # sort in descending order + idx=value.argsort()[::-1] # sort in descending order value=value[idx] directions=directions[:,idx] @@ -125,14 +125,4 @@ ##plug onto the model ##NB: Matlab sorts the eigen value in increasing order, we want the reverse - stress=results() - stress.xx=tau_xx - stress.yy=tau_yy - stress.xy=tau_xy - stress.principalvalue1=valuesstress[:,0] - stress.principalaxis1=directionsstress[:,0:2] - stress.principalvalue2=valuesstress[:,1] - stress.principalaxis2=directionsstress[:,2:4] - stress.effectivevalue=1./np.sqrt(2.)*np.sqrt(stress.xx**2+stress.yy**2+2.*stress.xy**2) - md.results.stress=stress strainrate=results() Index: /issm/trunk-jpl/src/py3/mech/robintemperature.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/robintemperature.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/robintemperature.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from scipy.special import erf Index: /issm/trunk-jpl/src/py3/mech/steadystateiceshelftemp.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/steadystateiceshelftemp.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/steadystateiceshelftemp.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def steadystateiceshelftemp(md,surfacetemp,basaltemp): @@ -18,5 +18,4 @@ temperature=steadystateiceshelftemp(md,surfacetemp,basaltemp) """ - if len(md.geometry.thickness)!=md.mesh.numberofvertices: raise ValueError('steadystateiceshelftemp error message: thickness should have a length of ' + md.mesh.numberofvertices) Index: /issm/trunk-jpl/src/py3/mech/thomasparams.py =================================================================== --- /issm/trunk-jpl/src/py3/mech/thomasparams.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mech/thomasparams.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from averaging import averaging Index: /issm/trunk-jpl/src/py3/mesh/ComputeHessian.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/ComputeHessian.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/ComputeHessian.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from GetNodalFunctionsCoeff import GetNodalFunctionsCoeff from GetAreas import GetAreas @@ -20,9 +20,9 @@ #some variables - numberofnodes=numpy.size(x) - numberofelements=numpy.size(index,axis=0) + numberofnodes=np.size(x) + numberofelements=np.size(index,axis=0) #some checks - if numpy.size(field)!=numberofnodes and numpy.size(field)!=numberofelements: + if np.size(field)!=numberofnodes and np.size(field)!=numberofelements: raise TypeError("ComputeHessian error message: the given field size not supported yet") if not m.strcmpi(type,'node') and not m.strcmpi(type,'element'): @@ -33,34 +33,33 @@ linesize=3*numberofelements - #get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma + #get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma [alpha,beta,dum]=GetNodalFunctionsCoeff(index,x,y) areas=GetAreas(index,x,y) #compute weights that hold the volume of all the element holding the node i - weights=m.sparse(line,numpy.ones((linesize,1)),numpy.tile(areas.reshape(-1,1),(3,1)),numberofnodes,1) + weights=m.sparse(line,np.ones((linesize,1),dtype=int),np.tile(areas,(3,1)),numberofnodes,1) #compute field on nodes if on elements - if numpy.size(field,axis=0)==numberofelements: - field=m.sparse(line,numpy.ones((linesize,1)),numpy.tile(areas*field,(3,1)),numberofnodes,1)/weights + if np.size(field,axis=0)==numberofelements: + field=m.sparse(line,np.ones((linesize,1),dtype=int),np.tile(areas*field,(3,1)),numberofnodes,1)/weights #Compute gradient for each element - grad_elx=numpy.sum(field[index-1,0]*alpha,axis=1) - grad_ely=numpy.sum(field[index-1,0]*beta,axis=1) + grad_elx=np.sum(field[index-1]*alpha,axis=1) + grad_ely=np.sum(field[index-1]*beta,axis=1) #Compute gradient for each node (average of the elements around) - gradx=m.sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*grad_elx).reshape(-1,1),(3,1)),numberofnodes,1) - grady=m.sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*grad_ely).reshape(-1,1),(3,1)),numberofnodes,1) + gradx=m.sparse(line,np.ones((linesize,1),dtype=int),np.tile((areas*grad_elx),(3,1)),numberofnodes,1) + grady=m.sparse(line,np.ones((linesize,1),dtype=int),np.tile((areas*grad_ely),(3,1)),numberofnodes,1) gradx=gradx/weights grady=grady/weights #Compute hessian for each element - hessian=numpy.hstack((numpy.sum(gradx[index-1,0]*alpha,axis=1).reshape(-1,1),numpy.sum(grady[index-1,0]*alpha,axis=1).reshape(-1,1),numpy.sum(grady[index-1,0]*beta,axis=1).reshape(-1,1))) + hessian=np.vstack((np.sum(gradx[index-1,0]*alpha,axis=1),np.sum(grady[index-1,0]*alpha,axis=1),np.sum(grady[index-1,0]*beta,axis=1))).T if m.strcmpi(type,'node'): #Compute Hessian on the nodes (average of the elements around) - hessian=numpy.hstack((m.sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,0]).reshape(-1,1),(3,1)),numberofnodes,1)/weights, \ - m.sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,1]).reshape(-1,1),(3,1)),numberofnodes,1)/weights, \ - m.sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,2]).reshape(-1,1),(3,1)),numberofnodes,1)/weights )) + hessian=np.hstack((m.sparse(line,np.ones((linesize,1),dtype=int),np.tile((areas*hessian[:,0]),(3,1)),numberofnodes,1)/weights, + m.sparse(line,np.ones((linesize,1),dtype=int),np.tile((areas*hessian[:,1]),(3,1)),numberofnodes,1)/weights, + m.sparse(line,np.ones((linesize,1),dtype=int),np.tile((areas*hessian[:,2]),(3,1)),numberofnodes,1)/weights )) return hessian - Index: /issm/trunk-jpl/src/py3/mesh/ComputeMetric.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/ComputeMetric.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/ComputeMetric.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos): @@ -17,21 +17,21 @@ b=hessian[:,1] d=hessian[:,2] - lambda1=0.5*((a+d)+numpy.sqrt(4.*b**2+(a-d)**2)) - lambda2=0.5*((a+d)-numpy.sqrt(4.*b**2+(a-d)**2)) - pos1=numpy.nonzero(lambda1==0.)[0] - pos2=numpy.nonzero(lambda2==0.)[0] - pos3=numpy.nonzero(numpy.logical_and(b==0.,lambda1==lambda2))[0] + lambda1=0.5*((a+d)+np.sqrt(4.*b**2+(a-d)**2)) + lambda2=0.5*((a+d)-np.sqrt(4.*b**2+(a-d)**2)) + pos1=np.nonzero(lambda1==0.)[0] + pos2=np.nonzero(lambda2==0.)[0] + pos3=np.nonzero(np.logical_and(b==0.,lambda1==lambda2))[0] #Modify the eigen values to control the shape of the elements - lambda1=numpy.minimum(numpy.maximum(numpy.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) - lambda2=numpy.minimum(numpy.maximum(numpy.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) + lambda1=np.minimum(np.maximum(np.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) + lambda2=np.minimum(np.maximum(np.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) #compute eigen vectors - norm1=numpy.sqrt(8.*b**2+2.*(d-a)**2+2.*(d-a)*numpy.sqrt((a-d)**2+4.*b**2)) + norm1=np.sqrt(8.*b**2+2.*(d-a)**2+2.*(d-a)*np.sqrt((a-d)**2+4.*b**2)) v1x=2.*b/norm1 - v1y=((d-a)+numpy.sqrt((a-d)**2+4.*b**2))/norm1 - norm2=numpy.sqrt(8.*b**2+2.*(d-a)**2-2.*(d-a)*numpy.sqrt((a-d)**2+4.*b**2)) + v1y=((d-a)+np.sqrt((a-d)**2+4.*b**2))/norm1 + norm2=np.sqrt(8.*b**2+2.*(d-a)**2-2.*(d-a)*np.sqrt((a-d)**2+4.*b**2)) v2x=2.*b/norm2 - v2y=((d-a)-numpy.sqrt((a-d)**2+4.*b**2))/norm2 + v2y=((d-a)-np.sqrt((a-d)**2+4.*b**2))/norm2 v1x[pos3]=1. @@ -41,32 +41,32 @@ #Compute new metric (for each node M=V*Lambda*V^-1) - metric=numpy.hstack((((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v2y*v1x-lambda2*v1y*v2x)).reshape(-1,1), \ - ((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v1y*v2y-lambda2*v1y*v2y)).reshape(-1,1), \ - ((v1x*v2y-v1y*v2x)**(-1)*(-lambda1*v2x*v1y+lambda2*v1x*v2y)).reshape(-1,1))) + metric=np.vstack((((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v2y*v1x-lambda2*v1y*v2x)).reshape(-1,), + ((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v1y*v2y-lambda2*v1y*v2y)).reshape(-1,), + ((v1x*v2y-v1y*v2x)**(-1)*(-lambda1*v2x*v1y+lambda2*v1x*v2y)).reshape(-1,))).T #some corrections for 0 eigen values - metric[pos1,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos1),1)) - metric[pos2,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos2),1)) + metric[pos1,:]=np.tile(np.array([[1./hmax**2,0.,1./hmax**2]]),(np.size(pos1),1)) + metric[pos2,:]=np.tile(np.array([[1./hmax**2,0.,1./hmax**2]]),(np.size(pos2),1)) #take care of water elements - metric[pos ,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos ),1)) + metric[pos ,:]=np.tile(np.array([[1./hmax**2,0.,1./hmax**2]]),(np.size(pos ),1)) #take care of NaNs if any (use Numpy eig in a loop) - pos=numpy.nonzero(numpy.isnan(metric))[0] - if numpy.size(pos): - print((" %i NaN found in the metric. Use Numpy routine..." % numpy.size(pos))) + pos=np.nonzero(np.isnan(metric))[0] + if np.size(pos): + print((" %i NaN found in the metric. Use Numpy routine..." % np.size(pos))) for posi in pos: - H=numpy.array([[hessian[posi,0],hessian[posi,1]],[hessian[posi,1],hessian[posi,2]]]) - [v,u]=numpy.linalg.eig(H) - v=numpy.diag(v) + H=np.array([[hessian[posi,0],hessian[posi,1]],[hessian[posi,1],hessian[posi,2]]]) + [v,u]=np.linalg.eig(H) + v=np.diag(v) lambda1=v[0,0] lambda2=v[1,1] - v[0,0]=numpy.minimum(numpy.maximum(numpy.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) - v[1,1]=numpy.minimum(numpy.maximum(numpy.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) + v[0,0]=np.minimum(np.maximum(np.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) + v[1,1]=np.minimum(np.maximum(np.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) - metricTria=numpy.dot(numpy.dot(u,v),numpy.linalg.inv(u)) - metric[posi,:]=numpy.array([metricTria[0,0],metricTria[0,1],metricTria[1,1]]) + metricTria=np.dot(np.dot(u,v),np.linalg.inv(u)) + metric[posi,:]=np.array([metricTria[0,0],metricTria[0,1],metricTria[1,1]]) - if numpy.any(numpy.isnan(metric)): + if np.any(np.isnan(metric)): raise RunTimeError("ComputeMetric error message: NaN in the metric despite our efforts...") Index: /issm/trunk-jpl/src/py3/mesh/ElementsFromEdge.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/ElementsFromEdge.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/ElementsFromEdge.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np import PythonFuncs as p @@ -12,11 +12,11 @@ """ - edgeelements=numpy.nonzero(\ - p.logical_or_n(numpy.logical_and(elements[:,0]==A,elements[:,1]==B), \ - numpy.logical_and(elements[:,0]==A,elements[:,2]==B), \ - numpy.logical_and(elements[:,1]==A,elements[:,2]==B), \ - numpy.logical_and(elements[:,1]==A,elements[:,0]==B), \ - numpy.logical_and(elements[:,2]==A,elements[:,0]==B), \ - numpy.logical_and(elements[:,2]==A,elements[:,1]==B), \ + edgeelements=np.nonzero(\ + p.logical_or_n(np.logical_and(elements[:,0]==A,elements[:,1]==B), \ + np.logical_and(elements[:,0]==A,elements[:,2]==B), \ + np.logical_and(elements[:,1]==A,elements[:,2]==B), \ + np.logical_and(elements[:,1]==A,elements[:,0]==B), \ + np.logical_and(elements[:,2]==A,elements[:,0]==B), \ + np.logical_and(elements[:,2]==A,elements[:,1]==B), \ ))[0]+1 Index: /issm/trunk-jpl/src/py3/mesh/GetNodalFunctionsCoeff.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/GetNodalFunctionsCoeff.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/GetNodalFunctionsCoeff.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def GetNodalFunctionsCoeff(index,x,y): @@ -23,18 +23,18 @@ #get nels and nods - nels=numpy.size(index,axis=0) - nods=numpy.size(x) + nels=np.size(index,axis=0) + nods=np.size(x) #some checks - if numpy.size(y)!=nods: + if np.size(y)!=nods: raise TypeError("GetNodalFunctionsCoeff error message: x and y do not have the same length.") - if numpy.max(index)>nods: + if np.max(index)>nods: raise TypeError("GetNodalFunctionsCoeff error message: index should not have values above %d." % nods) - if numpy.size(index,axis=1)!=3: + if np.size(index,axis=1)!=3: raise TypeError("GetNodalFunctionsCoeff error message: only 2d meshes supported. index should have 3 columns.") #initialize output - alpha=numpy.zeros((nels,3)) - beta=numpy.zeros((nels,3)) + alpha=np.zeros((nels,3)) + beta=np.zeros((nels,3)) #compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma @@ -48,10 +48,10 @@ #get alpha and beta - alpha=numpy.hstack(((invdet*(y2-y3)).reshape(-1,1),(invdet*(y3-y1)).reshape(-1,1),(invdet*(y1-y2)).reshape(-1,1))) - beta =numpy.hstack(((invdet*(x3-x2)).reshape(-1,1),(invdet*(x1-x3)).reshape(-1,1),(invdet*(x2-x1)).reshape(-1,1))) + alpha=np.vstack(((invdet*(y2-y3)).reshape(-1,),(invdet*(y3-y1)).reshape(-1,),(invdet*(y1-y2)).reshape(-1,))).T + beta =np.vstack(((invdet*(x3-x2)).reshape(-1,),(invdet*(x1-x3)).reshape(-1,),(invdet*(x2-x1)).reshape(-1,))).T #get gamma if requested - gamma=numpy.zeros((nels,3)) - gamma=numpy.hstack(((invdet*(x2*y3-x3*y2)).reshape(-1,1),(invdet*(y1*x3-y3*x1)).reshape(-1,1),(invdet*(x1*y2-x2*y1)).reshape(-1,1))) + gamma=np.zeros((nels,3)) + gamma=np.vstack(((invdet*(x2*y3-x3*y2)).reshape(-1,),(invdet*(y1*x3-y3*x1)).reshape(-1,),(invdet*(x1*y2-x2*y1)).reshape(-1,))).T return alpha,beta,gamma Index: /issm/trunk-jpl/src/py3/mesh/bamg.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/bamg.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/bamg.py (revision 23670) @@ -1,5 +1,7 @@ import os.path -import numpy -from mesh2d import mesh2d +import numpy as np +from mesh2d import * +from mesh2dvertical import * +from mesh3dsurface import * from collections import OrderedDict from pairoptions import pairoptions @@ -13,5 +15,5 @@ from ContourToNodes import ContourToNodes -def bamg(md,*kwargs): +def bamg(md,*args): """ BAMG - mesh generation @@ -20,4 +22,8 @@ - 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 10^-100) - hmax : maximum edge length (default is 10^100) @@ -37,5 +43,4 @@ 1 -> use Green formula - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) - - MaxCornerAngle : maximum angle of corners in degree (default is 10) - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) - maxsubdiv : maximum subdivision of exisiting elements (default is 10) @@ -49,5 +54,4 @@ - power : power applied to the metric (default is 1) - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) - - geometricalmetric : take the geometry into account to generate the metric (default is 0) - verbose : level of verbosity (default is 1) @@ -66,5 +70,5 @@ #process options - options=pairoptions(**kwargs) + options=pairoptions(*args) # options=deleteduplicates(options,1); @@ -74,36 +78,133 @@ bamg_mesh=bamgmesh() + subdomain_ref = 1 + hole_ref = 1 + # Bamg Geometry parameters {{{ if options.exist('domain'): - #Check that file exists domainfile=options.getfieldvalue('domain') - if not os.path.exists(domainfile): - raise IOError("bamg error message: file '%s' not found" % domainfile) - domain=expread(domainfile) + if type(domainfile) == str: + if not os.path.exists(domainfile): + raise IOError("bamg error message: file '%s' not found" % domainfile) + domain=expread(domainfile) + else: + domain=domainfile #Build geometry count=0 for i,domaini in enumerate(domain): - #Check that the domain is closed if (domaini['x'][0]!=domaini['x'][-1] or domaini['y'][0]!=domaini['y'][-1]): raise RuntimeError("bamg error message: all contours provided in ''domain'' should be closed") - #Checks that all holes are INSIDE the principle domain outline + #Checks that all holes are INSIDE the principle domain outline princial domain should be index 0 if i: - flags=ContourToNodes(domaini['x'],domaini['y'],domainfile,0) - if numpy.any(numpy.logical_not(flags)): + flags=ContourToNodes(domaini['x'],domaini['y'],domainfile,0)[0] + if np.any(np.logical_not(flags)): raise RuntimeError("bamg error message: All holes should be strictly inside the principal domain") + + #Check orientation + nods=domaini['nods']-1#the domain are closed 1=end; + + test = np.sum((domaini['x'][1:nods+1] - domaini['x'][0:nods])*(domaini['y'][1:nods+1] + domaini['y'][0:nods])) + if (i==0 and test>0) or (i>0 and test<0): + print('At least one contour was not correctly oriented and has been re-oriented') + domaini['x'] = np.flipud(domaini['x']) + domaini['y'] = np.flipud(domaini['y']) + #Add all points to bamg_geometry nods=domaini['nods']-1 #the domain are closed 0=end - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((domaini['x'][0:nods].reshape(-1,1),domaini['y'][0:nods].reshape(-1,1),numpy.ones((nods,1)))))) - bamg_geometry.Edges =numpy.vstack((bamg_geometry.Edges, numpy.hstack((numpy.arange(count+1,count+nods+1).reshape(-1,1),numpy.hstack((numpy.arange(count+2,count+nods+1),count+1)).reshape(-1,1),1.*numpy.ones((nods,1)))))) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.vstack((domaini['x'][0:nods],domaini['y'][0:nods],np.ones((nods)))).T)) + bamg_geometry.Edges =np.vstack((bamg_geometry.Edges,np.vstack((np.arange(count+1,count+nods+1),np.hstack((np.arange(count+2,count+nods+1),count+1)),1.*np.ones((nods)))).T)) if i: - bamg_geometry.SubDomains=numpy.vstack((bamg_geometry.SubDomains,[2,count+1,1,1])) - + bamg_geometry.SubDomains=np.vstack((bamg_geometry.SubDomains,[2,count+1,1,-subdomain_ref])) + subdomain_ref = subdomain_ref+1; + else: + bamg_geometry.SubDomains=np.vstack((bamg_geometry.SubDomains,[2,count+1,1,0])) + #update counter count+=nods + + #Deal with domain holes + if options.exist('holes'): + holesfile=options.getfieldvalue('holes') + if type(holesfile) == str: + if not os.path.exists(holesfile): + raise IOError("bamg error message: file '%s' not found" % holesfile) + holes=expread(holesfile) + else: + holes=holesfile + + #Build geometry + for i,holei in enumerate(holes): + #Check that the hole is closed + if (holei['x'][0]!=holei['x'][-1] or holei['y'][0]!=holei['y'][-1]): + raise RuntimeError("bamg error message: all contours provided in ''hole'' should be closed") + + #Checks that all holes are INSIDE the principle domain outline princial domain should be index 0 + flags=ContourToNodes(holei['x'],holei['y'],domainfile,0)[0] + if np.any(np.logical_not(flags)): + raise RuntimeError("bamg error message: All holes should be strictly inside the principal domain") + + #Check orientation + nods=holei['nods']-1#the hole are closed 1=end; + test = np.sum((holei['x'][1:nods+1] - holei['x'][0:nods])*(holei['y'][1:nods+1] + holei['y'][0:nods])) + if test<0: + print('At least one hole was not correctly oriented and has been re-oriented') + holei['x'] = np.flipud(holei['x']) + holei['y'] = np.flipud(holei['y']) + + #Add all points to bamg_geometry + nods=holei['nods']-1 #the hole are closed 0=end + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.vstack((holei['x'][0:nods],holei['y'][0:nods],np.ones((nods)))).T)) + bamg_geometry.Edges =np.vstack((bamg_geometry.Edges,np.vstack((np.arange(count+1,count+nods+1),np.hstack((np.arange(count+2,count+nods+1),count+1)),1.*np.ones((nods)))).T)) + #update counter + count+=nods + + #And subdomains + if options.exist('subdomains'): + subdomainfile=options.getfieldvalue('subdomains') + if type(subdomainfile) == str: + if not os.path.exists(subdomainfile): + raise IOError("bamg error message: file '%s' not found" % subdomainfile) + subdomains=expread(subdomainfile) + else: + subdomains=subdomainfile + + #Build geometry + for i,subdomaini in enumerate(subdomains): + #Check that the subdomain is closed + if (subdomaini['x'][0]!=subdomaini['x'][-1] or subdomaini['y'][0]!=subdomaini['y'][-1]): + raise RuntimeError("bamg error message: all contours provided in ''subdomain'' should be closed") + + #Checks that all subdomains are INSIDE the principle subdomain outline princial domain should be index 0 + if i: + flags=ContourToNodes(subdomaini['x'],subdomaini['y'],domainfile,0)[0] + if np.any(np.logical_not(flags)): + raise RuntimeError("bamg error message: All subdomains should be strictly inside the principal subdomain") + + #Check orientation + nods=subdomaini['nods']-1#the subdomain are closed 1=end; + + test = np.sum((subdomaini['x'][1:nods+1] - subdomaini['x'][0:nods])*(subdomaini['y'][1:nods+1] + subdomaini['y'][0:nods])) + if test>0: + print('At least one subcontour was not correctly oriented and has been re-oriented') + subdomaini['x'] = np.flipud(subdomaini['x']) + subdomaini['y'] = np.flipud(subdomaini['y']) + + #Add all points to bamg_geometry + nods=subdomaini['nods']-1 #the subdomain are closed 0=end + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.vstack((subdomaini['x'][0:nods],subdomaini['y'][0:nods],np.ones((nods)))).T)) + bamg_geometry.Edges =np.vstack((bamg_geometry.Edges,np.vstack((np.arange(count+1,count+nods+1),np.hstack((np.arange(count+2,count+nods+1),count+1)),1.*np.ones((nods)))).T)) + #update counter + count+=nods + + if options.getfieldvalue('vertical',0): + if np.size(options.getfieldvalue('Markers',[]))!=np.size(bamg_geometry.Edges,0): + raise RuntimeError('for 2d vertical mesh, ''Markers'' option is required, and should be of size ' + str(np.size(bamg_geometry.Edges,0))) + if np.size(options.getfieldvalue('Markers',[]))==np.size(bamg_geometry.Edges,0): + bamg_geometry.Edges[:,2]=options.getfieldvalue('Markers') #take care of rifts @@ -119,14 +220,14 @@ #detect whether all points of the rift are inside the domain - flags=ContourToNodes(rifti['x'],rifti['y'],domain[0],0) - if numpy.all(numpy.logical_not(flags)): + flags=ContourToNodes(rifti['x'],rifti['y'],domain[0],0)[0] + if np.all(np.logical_not(flags)): raise RuntimeError("one rift has all its points outside of the domain outline") - elif numpy.any(numpy.logical_not(flags)): + elif np.any(np.logical_not(flags)): #We LOTS of work to do print("Rift tip outside of or on the domain has been detected and is being processed...") #check that only one point is outside (for now) - if numpy.sum(numpy.logical_not(flags).astype(int))!=1: + if np.sum(np.logical_not(flags).astype(int))!=1: raise RuntimeError("bamg error message: only one point outside of the domain is supported yet") @@ -136,6 +237,6 @@ pass elif not flags[-1]: - rifti['x']=numpy.flipud(rifti['x']) - rifti['y']=numpy.flipud(rifti['y']) + rifti['x']=np.flipud(rifti['x']) + rifti['y']=np.flipud(rifti['y']) else: raise RuntimeError("bamg error message: only a rift tip can be outside of the domain") @@ -146,6 +247,6 @@ x2=rifti['x'][1] y2=rifti['y'][1] - for j in range(0,numpy.size(domain[0]['x'])-1): - if SegIntersect(numpy.array([[x1,y1],[x2,y2]]),numpy.array([[domain[0]['x'][j],domain[0]['y'][j]],[domain[0]['x'][j+1],domain[0]['y'][j+1]]])): + for j in range(0,np.size(domain[0]['x'])-1): + if SegIntersect(np.array([[x1,y1],[x2,y2]]),np.array([[domain[0]['x'][j],domain[0]['y'][j]],[domain[0]['x'][j+1],domain[0]['y'][j+1]]])): #Get position of the two nodes of the edge in domain @@ -161,11 +262,11 @@ # x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); # y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); - x=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),x3-x4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) - y=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),y3-y4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) + x=np.linalg.det(np.array([[np.linalg.det(np.array([[x1,y1],[x2,y2]])),x1-x2],[np.linalg.det(np.array([[x3,y3],[x4,y4]])),x3-x4]]))/np.linalg.det(np.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) + y=np.linalg.det(np.array([[np.linalg.det(np.array([[x1,y1],[x2,y2]])),y1-y2],[np.linalg.det(np.array([[x3,y3],[x4,y4]])),y3-y4]]))/np.linalg.det(np.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) segdis= sqrt((x4-x3)**2+(y4-y3)**2) - tipdis=numpy.array([sqrt((x-x3)**2+(y-y3)**2),sqrt((x-x4)**2+(y-y4)**2)]) - - if numpy.min(tipdis)/segdis < options.getfieldvalue('toltip',0): + tipdis=np.array([sqrt((x-x3)**2+(y-y3)**2),sqrt((x-x4)**2+(y-y4)**2)]) + + if np.min(tipdis)/segdis < options.getfieldvalue('toltip',0): print("moving tip-domain intersection point") @@ -179,8 +280,8 @@ #OK, now we can add our own rift nods=rifti['nods']-1 - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((rifti['x'][1:].reshape(-1,1),rifti['y'][1:].reshape(-1,1),numpy.ones((nods,1)))))) - bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges,\ - numpy.array([[pos,count+1,(1+i)]]),\ - numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),(1+i)*numpy.ones((nods-1,1)))))) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.hstack((rifti['x'][1:].reshape(-1,),rifti['y'][1:].reshape(-1,),np.ones((nods,1)))))) + bamg_geometry.Edges=np.vstack((bamg_geometry.Edges,\ + np.array([[pos,count+1,(1+i)]]),\ + np.hstack((np.arange(count+1,count+nods).reshape(-1,),np.arange(count+2,count+nods+1).reshape(-1,),(1+i)*np.ones((nods-1,1)))))) count+=nods @@ -189,22 +290,22 @@ else: #Add intersection point to Vertices - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.array([[x,y,1]]))) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.array([[x,y,1]]))) count+=1 #Decompose the crossing edge into 2 subedges - pos=numpy.nonzero(numpy.logical_and(bamg_geometry.Edges[:,0]==i1,bamg_geometry.Edges[:,1]==i2))[0] + pos=np.nonzero(np.logical_and(bamg_geometry.Edges[:,0]==i1,bamg_geometry.Edges[:,1]==i2))[0] if not pos: raise RuntimeError("bamg error message: a problem occurred...") - bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges[0:pos-1,:],\ - numpy.array([[bamg_geometry.Edges[pos,0],count ,bamg_geometry.Edges[pos,2]]]),\ - numpy.array([[count ,bamg_geometry.Edges[pos,1],bamg_geometry.Edges[pos,2]]]),\ + bamg_geometry.Edges=np.vstack((bamg_geometry.Edges[0:pos-1,:],\ + np.array([[bamg_geometry.Edges[pos,0],count ,bamg_geometry.Edges[pos,2]]]),\ + np.array([[count ,bamg_geometry.Edges[pos,1],bamg_geometry.Edges[pos,2]]]),\ bamg_geometry.Edges[pos+1:,:])) #OK, now we can add our own rift nods=rifti['nods']-1 - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((rifti['x'][1:].reshape(-1,1),rifti['y'][1:].reshape(-1,1),numpy.ones((nods,1)))))) - bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges,\ - numpy.array([[count,count+1,2]]),\ - numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),(1+i)*numpy.ones((nods-1,1)))))) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,np.hstack((rifti['x'][1:].reshape(-1,),rifti['y'][1:].reshape(-1,),np.ones((nods,1)))))) + bamg_geometry.Edges=np.vstack((bamg_geometry.Edges,\ + np.array([[count,count+1,2]]),\ + np.hstack((np.arange(count+1,count+nods).reshape(-1,),np.arange(count+2,count+nods+1).reshape(-1,),(1+i)*np.ones((nods-1,1)))))) count+=nods @@ -213,6 +314,6 @@ else: nods=rifti['nods']-1 - bamg_geometry.Vertices=numpy.vstack(bamg_geometry.Vertices, numpy.hstack(rifti['x'][:],rifti['y'][:],numpy.ones((nods+1,1)))) - bamg_geometry.Edges =numpy.vstack(bamg_geometry.Edges, numpy.hstack(numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),i*numpy.ones((nods,1)))) + bamg_geometry.Vertices=np.vstack(bamg_geometry.Vertices, np.hstack(rifti['x'][:],rifti['y'][:],np.ones((nods+1,1)))) + bamg_geometry.Edges =np.vstack(bamg_geometry.Edges, np.hstack(np.arange(count+1,count+nods).reshape(-1,),np.arange(count+2,count+nods+1).reshape(-1,),i*np.ones((nods,1)))) count=+nods+1 @@ -224,18 +325,18 @@ if all(isinstance(track,str)): A=expread(track) - track=numpy.hstack((A.x.reshape(-1,1),A.y.reshape(-1,1))) + track=np.hstack((A.x.reshape(-1,),A.y.reshape(-1,))) else: track=float(track) #for some reason, it is of class "single" - if numpy.size(track,axis=1)==2: - track=numpy.hstack((track,3.*numpy.ones((size(track,axis=0),1)))) + if np.size(track,axis=1)==2: + track=np.hstack((track,3.*np.ones((size(track,axis=0),1)))) #only keep those inside - flags=ContourToNodes(track[:,0],track[:,1],domainfile,0) - track=track[numpy.nonzero(flags),:] + flags=ContourToNodes(track[:,0],track[:,1],domainfile,0)[0] + track=track[np.nonzero(flags),:] #Add all points to bamg_geometry - nods=numpy.size(track,axis=0) - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,track)) - bamg_geometry.Edges =numpy.vstack((bamg_geometry.Edges,numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),3.*numpy.ones((nods-1,1)))))) + nods=np.size(track,axis=0) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,track)) + bamg_geometry.Edges =np.vstack((bamg_geometry.Edges,np.hstack((np.arange(count+1,count+nods).reshape(-1,),np.arange(count+2,count+nods+1).reshape(-1,),3.*np.ones((nods-1,1)))))) #update counter @@ -247,15 +348,13 @@ #recover RequiredVertices requiredvertices=options.getfieldvalue('RequiredVertices') #for some reason, it is of class "single" - if numpy.size(requiredvertices,axis=1)==2: - requiredvertices=numpy.hstack((requiredvertices,4.*numpy.ones((numpy.size(requiredvertices,axis=0),1)))) - + if np.size(requiredvertices,axis=1)==2: + requiredvertices=np.hstack((requiredvertices,4.*np.ones((np.size(requiredvertices,axis=0),1)))) #only keep those inside flags=ContourToNodes(requiredvertices[:,0],requiredvertices[:,1],domainfile,0)[0] - requiredvertices=requiredvertices[numpy.nonzero(flags)[0],:] - + requiredvertices=requiredvertices[np.nonzero(flags)[0],:] #Add all points to bamg_geometry - nods=numpy.size(requiredvertices,axis=0) - bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,requiredvertices)) + nods=np.size(requiredvertices,axis=0) + bamg_geometry.Vertices=np.vstack((bamg_geometry.Vertices,requiredvertices)) #update counter @@ -277,6 +376,7 @@ bamg_mesh=bamgmesh(md.private.bamg['mesh'].__dict__) else: - bamg_mesh.Vertices=numpy.hstack((md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),numpy.ones((md.mesh.numberofvertices,1)))) - bamg_mesh.Triangles=numpy.hstack((md.mesh.elements,numpy.ones((md.mesh.numberofelements,1)))) + bamg_mesh.Vertices=np.vstack((md.mesh.x,md.mesh.y,np.ones((md.mesh.numberofvertices)))).T + #bamg_mesh.Vertices=np.hstack((md.mesh.x.reshape(-1,),md.mesh.y.reshape(-1,),np.ones((md.mesh.numberofvertices,1)))) + bamg_mesh.Triangles=np.hstack((md.mesh.elements,np.ones((md.mesh.numberofelements,1)))) if isinstance(md.rifts.riftstruct,dict): @@ -288,19 +388,18 @@ bamg_options['coeff']=options.getfieldvalue('coeff',1.) bamg_options['cutoff']=options.getfieldvalue('cutoff',10.**-5) - bamg_options['err']=options.getfieldvalue('err',numpy.array([[0.01]])) + bamg_options['err']=options.getfieldvalue('err',np.array([[0.01]])) bamg_options['errg']=options.getfieldvalue('errg',0.1) - bamg_options['field']=options.getfieldvalue('field',numpy.empty((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',10.**-100) bamg_options['hmax']=options.getfieldvalue('hmax',10.**100) - bamg_options['hminVertices']=options.getfieldvalue('hminVertices',numpy.empty((0,1))) - bamg_options['hmaxVertices']=options.getfieldvalue('hmaxVertices',numpy.empty((0,1))) - bamg_options['hVertices']=options.getfieldvalue('hVertices',numpy.empty((0,1))) + 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['MaxCornerAngle']=options.getfieldvalue('MaxCornerAngle',10.) bamg_options['maxnbv']=options.getfieldvalue('maxnbv',10**6) bamg_options['maxsubdiv']=options.getfieldvalue('maxsubdiv',10.) - bamg_options['metric']=options.getfieldvalue('metric',numpy.empty((0,1))) + bamg_options['metric']=options.getfieldvalue('metric',np.empty((0,1))) bamg_options['Metrictype']=options.getfieldvalue('Metrictype',0) bamg_options['nbjacobi']=options.getfieldvalue('nbjacobi',1) @@ -309,37 +408,76 @@ bamg_options['power']=options.getfieldvalue('power',1.) bamg_options['splitcorners']=options.getfieldvalue('splitcorners',1) - bamg_options['geometricalmetric']=options.getfieldvalue('geometricalmetric',0) - bamg_options['random']=options.getfieldvalue('rand',True) bamg_options['verbose']=options.getfieldvalue('verbose',1) #}}} #call Bamg - [bamgmesh_out,bamggeom_out]=BamgMesher(bamg_mesh.__dict__,bamg_geometry.__dict__,bamg_options) + bamgmesh_out,bamggeom_out=BamgMesher(bamg_mesh.__dict__,bamg_geometry.__dict__,bamg_options) # plug results onto model + if options.getfieldvalue('vertical',0): + md.mesh=mesh2dvertical() + md.mesh.x=bamgmesh_out['Vertices'][:,0].copy() + md.mesh.y=bamgmesh_out['Vertices'][:,1].copy() + md.mesh.elements=bamgmesh_out['Triangles'][:,0:3].astype(int) + md.mesh.edges=bamgmesh_out['IssmEdges'].astype(int) + md.mesh.segments=bamgmesh_out['IssmSegments'][:,0:3].astype(int) + md.mesh.segmentmarkers=bamgmesh_out['IssmSegments'][:,3].astype(int) + + #Fill in rest of fields: + md.mesh.numberofelements=np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices=np.size(md.mesh.x) + md.mesh.numberofedges=np.size(md.mesh.edges,axis=0) + md.mesh.vertexonboundary=np.zeros(md.mesh.numberofvertices,bool) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True + + #Now, build the connectivity tables for this mesh. Doubled in matlab for some reason + md.mesh.vertexonboundary=np.zeros(md.mesh.numberofvertices,) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=1 + + elif options.getfieldvalue('3dsurface',0): + md.mesh=mesh3dsurface() + md.mesh.x=bamgmesh_out['Vertices'][:,0].copy() + md.mesh.y=bamgmesh_out['Vertices'][:,1].copy() + md.mesh.z=md.mesh.x + md.mesh.z[:]=0 + md.mesh.elements=bamgmesh_out['Triangles'][:,0:3].astype(int) + md.mesh.edges=bamgmesh_out['IssmEdges'].astype(int) + md.mesh.segments=bamgmesh_out['IssmSegments'][:,0:3].astype(int) + md.mesh.segmentmarkers=bamgmesh_out['IssmSegments'][:,3].astype(int) + + #Fill in rest of fields: + md.mesh.numberofelements=np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices=np.size(md.mesh.x) + md.mesh.numberofedges=np.size(md.mesh.edges,axis=0) + md.mesh.vertexonboundary=np.zeros(md.mesh.numberofvertices,bool) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True + + else: + md.mesh=mesh2d() + md.mesh.x=bamgmesh_out['Vertices'][:,0].copy() + md.mesh.y=bamgmesh_out['Vertices'][:,1].copy() + md.mesh.elements=bamgmesh_out['Triangles'][:,0:3].astype(int) + md.mesh.edges=bamgmesh_out['IssmEdges'].astype(int) + md.mesh.segments=bamgmesh_out['IssmSegments'][:,0:3].astype(int) + md.mesh.segmentmarkers=bamgmesh_out['IssmSegments'][:,3].astype(int) + + #Fill in rest of fields: + md.mesh.numberofelements=np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices=np.size(md.mesh.x) + md.mesh.numberofedges=np.size(md.mesh.edges,axis=0) + md.mesh.vertexonboundary=np.zeros(md.mesh.numberofvertices,bool) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True + + #Bamg private fields md.private.bamg=OrderedDict() md.private.bamg['mesh']=bamgmesh(bamgmesh_out) md.private.bamg['geometry']=bamggeom(bamggeom_out) - md.mesh = mesh2d() - md.mesh.x=bamgmesh_out['Vertices'][:,0].copy() - md.mesh.y=bamgmesh_out['Vertices'][:,1].copy() - md.mesh.elements=bamgmesh_out['Triangles'][:,0:3].astype(int) - md.mesh.edges=bamgmesh_out['IssmEdges'].astype(int) - md.mesh.segments=bamgmesh_out['IssmSegments'][:,0:3].astype(int) - md.mesh.segmentmarkers=bamgmesh_out['IssmSegments'][:,3].astype(int) - - #Fill in rest of fields: - md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) - md.mesh.numberofvertices=numpy.size(md.mesh.x) - md.mesh.numberofedges=numpy.size(md.mesh.edges,axis=0) - md.mesh.vertexonboundary=numpy.zeros(md.mesh.numberofvertices,bool) - md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True md.mesh.elementconnectivity=md.private.bamg['mesh'].ElementConnectivity - md.mesh.elementconnectivity[numpy.nonzero(numpy.isnan(md.mesh.elementconnectivity))]=0 + md.mesh.elementconnectivity[np.nonzero(np.isnan(md.mesh.elementconnectivity))]=0 md.mesh.elementconnectivity=md.mesh.elementconnectivity.astype(int) #Check for orphan - if numpy.any(numpy.logical_not(numpy.in1d(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements.flat))): - raise RuntimeError("Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)") + if np.any(np.logical_not(np.in1d(np.arange(1,md.mesh.numberofvertices+1),md.mesh.elements.flat))): + raise RuntimeError("Output mesh has orphans. Check your Domain and/or RequiredVertices") return md @@ -351,5 +489,5 @@ print("Checking Edge crossing...") i=0 - while (ii) + posedges=np.nonzero(geom.Edges>i) geom.Edges[posedges]=geom.Edges[posedges]-1 Index: /issm/trunk-jpl/src/py3/mesh/meshconvert.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/meshconvert.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/meshconvert.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from collections import OrderedDict from BamgConvertMesh import BamgConvertMesh @@ -43,8 +43,8 @@ #Fill in rest of fields: - md.mesh.numberofelements = numpy.size(md.mesh.elements,axis=0) - md.mesh.numberofvertices = numpy.size(md.mesh.x) - md.mesh.numberofedges = numpy.size(md.mesh.edges,axis=0) - md.mesh.vertexonboundary = numpy.zeros(md.mesh.numberofvertices,bool) + md.mesh.numberofelements = np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices = np.size(md.mesh.x) + md.mesh.numberofedges = np.size(md.mesh.edges,axis=0) + md.mesh.vertexonboundary = np.zeros(md.mesh.numberofvertices,bool) md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1] = True Index: /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessoutsiderifts.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessoutsiderifts.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessoutsiderifts.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from ElementsFromEdge import ElementsFromEdge import MatlabFuncs as m @@ -19,5 +19,5 @@ tips=rift.tips - outsidetips=tips[numpy.nonzero(flags[rift.tips-1])[0]] + outsidetips=tips[np.nonzero(flags[rift.tips-1])[0]] #we have found outsidetips, tips that touch the domain outline. go through them @@ -26,10 +26,10 @@ #find tip in the segments, take first segment (there should be 2) that holds tip, #and node_connected_to_tip is the other node on this segment: - tipindex=numpy.nonzero(rift.segments[:,0]==tip)[0] + tipindex=np.nonzero(rift.segments[:,0]==tip)[0] if tipindex: tipindex=tipindex[0] node_connected_to_tip=rift.segments[tipindex,1] else: - tipindex=numpy.nonzero(rift.segments[:,1]==tip)[0] + tipindex=np.nonzero(rift.segments[:,1]==tip)[0] tipindex=tipindex[0] node_connected_to_tip=rift.segments[tipindex,1] @@ -41,5 +41,5 @@ B=node_connected_to_tip - elements=numpy.empty(0,int) + elements=np.empty(0,int) while flags(B): #as long as B does not belong to the domain outline, keep looking. @@ -48,37 +48,37 @@ #rule out those we already detected already_detected=m.ismember(edgeelements,elements) - nextelement=edgeelements(numpy.nonzero(numpy.logical_not(already_detected))[0]) + nextelement=edgeelements(np.nonzero(np.logical_not(already_detected))[0]) #add new detected element to the list of elements we are looking for. - elements=numpy.concatenate((elements,nextelement)) + elements=np.concatenate((elements,nextelement)) #new B: - B=md.mesh.elements[nextelement-1,numpy.nonzero(numpy.logical_not(m.ismember(md.mesh.elements[nextelement-1,:],numpy.array([A,B]))))] + B=md.mesh.elements[nextelement-1,np.nonzero(np.logical_not(m.ismember(md.mesh.elements[nextelement-1,:],np.array([A,B]))))] #take the list of elements on one side of the rift that connect to the tip, #and duplicate the tip on them, so as to open the rift to the outside. - num=numpy.size(md.mesh.x)+1 - md.mesh.x=numpy.concatenate((md.mesh.x,md.mesh.x[tip])) - md.mesh.y=numpy.concatenate((md.mesh.y,md.mesh.y[tip])) + num=np.size(md.mesh.x)+1 + md.mesh.x=np.concatenate((md.mesh.x,md.mesh.x[tip])) + md.mesh.y=np.concatenate((md.mesh.y,md.mesh.y[tip])) md.mesh.numberofvertices=num #replace tip in elements newelements=md.mesh.elements[elements-1,:] - pos=numpy.nonzero(newelements==tip) + pos=np.nonzero(newelements==tip) newelements[pos]=num md.mesh.elements[elements-1,:]=newelements - rift.tips=numpy.concatenate((rift.tips,num)) + rift.tips=np.concatenate((rift.tips,num)) #deal with segments - tipsegments=numpy.nonzero(numpy.logical_or(md.mesh.segments[:,0]==tip,md.mesh.segments[:,1]==tip))[0] + tipsegments=np.nonzero(np.logical_or(md.mesh.segments[:,0]==tip,md.mesh.segments[:,1]==tip))[0] for segment_index in tipsegments: - pos=numpy.nonzero(md.mesh.segments[segment_index,0:2]!=tip)[0] + pos=np.nonzero(md.mesh.segments[segment_index,0:2]!=tip)[0] other_node=md.mesh.segments[segment_index,pos] if not isconnected(md.mesh.elements,other_node,tip): - pos=numpy.nonzero(md.mesh.segments[segment_index,0:2]==tip)[0] + pos=np.nonzero(md.mesh.segments[segment_index,0:2]==tip)[0] md.mesh.segments[segment_index,pos]=num #Fill in rest of fields: - md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) - md.mesh.numberofvertices=numpy.size(md.mesh.x) - md.mesh.vertexonboundary=numpy.zeros(numpy.size(md.mesh.x),bool) + md.mesh.numberofelements=np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices=np.size(md.mesh.x) + md.mesh.vertexonboundary=np.zeros(np.size(md.mesh.x),bool) md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True md.rifts.numrifts=length(md.rifts.riftstruct) Index: /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessrifts.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessrifts.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/rifts/meshprocessrifts.py (revision 23670) @@ -1,4 +1,4 @@ -import numpy -from TriMeshProcessRifts import TriMeshProcessRifts +import numpy as np +from ProcessRifts import ProcessRifts from ContourToMesh import ContourToMesh from meshprocessoutsiderifts import meshprocessoutsiderifts @@ -22,5 +22,5 @@ #Call MEX file - [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers) + md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct=ProcessRifts(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers) md.mesh.elements=md.mesh.elements.astype(int) md.mesh.x=md.mesh.x.reshape(-1) @@ -29,20 +29,20 @@ md.mesh.segmentmarkers=md.mesh.segmentmarkers.astype(int) if not isinstance(md.rifts.riftstruct,list) or not md.rifts.riftstruct: - raise RuntimeError("TriMeshProcessRifts did not find any rift") + raise RuntimeError("ProcessRifts did not find any rift") #Fill in rest of fields: numrifts=len(md.rifts.riftstruct) - md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) - md.mesh.numberofvertices=numpy.size(md.mesh.x) - md.mesh.vertexonboundary=numpy.zeros(numpy.size(md.mesh.x),bool) + md.mesh.numberofelements=np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices=np.size(md.mesh.x) + md.mesh.vertexonboundary=np.zeros(np.size(md.mesh.x),bool) md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1]=True #get coordinates of rift tips for rift in md.rifts.riftstruct: - rift['tip1coordinates']=numpy.hstack((md.mesh.x[rift['tips'][0,0].astype(int)-1].reshape(-1,1),md.mesh.y[rift['tips'][0,0].astype(int)-1].reshape(-1,1))) - rift['tip2coordinates']=numpy.hstack((md.mesh.x[rift['tips'][0,1].astype(int)-1].reshape(-1,1),md.mesh.y[rift['tips'][0,1].astype(int)-1].reshape(-1,1))) + rift['tip1coordinates']=np.hstack((md.mesh.x[rift['tips'][0,0].astype(int)-1].reshape(-1,),md.mesh.y[rift['tips'][0,0].astype(int)-1].reshape(-1,))) + rift['tip2coordinates']=np.hstack((md.mesh.x[rift['tips'][0,1].astype(int)-1].reshape(-1,),md.mesh.y[rift['tips'][0,1].astype(int)-1].reshape(-1,))) #In case we have rifts that open up the domain outline, we need to open them: - [flags,dum]=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainoutline,'node',0) + flags=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainoutline,'node',0) found=0 for rift in md.rifts.riftstruct: @@ -58,6 +58,6 @@ #get elements that are not correctly oriented in the correct direction: aires=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y) - pos=numpy.nonzero(aires<0)[0] - md.mesh.elements[pos,:]=numpy.hstack((md.mesh.elements[pos,1].reshape(-1,1),md.mesh.elements[pos,0].reshape(-1,1),md.mesh.elements[pos,2].reshape(-1,1))) + pos=np.nonzero(aires<0)[0] + md.mesh.elements[pos,:]=np.vstack((md.mesh.elements[pos,1],md.mesh.elements[pos,0],md.mesh.elements[pos,2])).T return md Index: /issm/trunk-jpl/src/py3/mesh/roundmesh.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/roundmesh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/roundmesh.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np import os from collections import OrderedDict @@ -20,12 +20,10 @@ #Get number of points on the circle - pointsonedge=numpy.floor((2.*numpy.pi*radius) / resolution) + pointsonedge=np.floor((2.*np.pi*radius) / resolution)+1 #+1 to close the outline #Calculate the cartesians coordinates of the points - x_list=numpy.ones(pointsonedge) - y_list=numpy.ones(pointsonedge) - theta=numpy.linspace(0.,2.*numpy.pi,num=pointsonedge,endpoint=False) - x_list=roundsigfig(radius*x_list*numpy.cos(theta),12) - y_list=roundsigfig(radius*y_list*numpy.sin(theta),12) + theta=np.linspace(0.,2.*np.pi,pointsonedge) + x_list=roundsigfig(radius*np.cos(theta),12) + y_list=roundsigfig(radius*np.sin(theta),12) A=OrderedDict() A['x']=[x_list] @@ -39,5 +37,5 @@ #move the closest node to the center - pos=numpy.argmin(md.mesh.x**2+md.mesh.y**2) + pos=np.argmin(md.mesh.x**2+md.mesh.y**2) md.mesh.x[pos]=0. md.mesh.y[pos]=0. @@ -50,10 +48,10 @@ def roundsigfig(x,n): - digits=numpy.ceil(numpy.log10(numpy.abs(x))) + digits=np.ceil(np.log10(np.abs(x))) x=x/10.**digits - x=numpy.round(x,decimals=n) + x=np.round(x,decimals=n) x=x*10.**digits - pos=numpy.nonzero(numpy.isnan(x)) + pos=np.nonzero(np.isnan(x)) x[pos]=0. Index: /issm/trunk-jpl/src/py3/mesh/squaremesh.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/squaremesh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/squaremesh.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from NodeConnectivity import NodeConnectivity from ElementConnectivity import ElementConnectivity @@ -22,7 +22,7 @@ #initialization - index=numpy.zeros((nel,3),int) - x=numpy.zeros((nx*ny)) - y=numpy.zeros((nx*ny)) + index=np.zeros((nel,3),int) + x=np.zeros((nx*ny)) + y=np.zeros((nx*ny)) #create coordinates @@ -43,17 +43,17 @@ #Scale x and y - x=x/numpy.max(x)*Lx - y=y/numpy.max(y)*Ly + x=x/np.max(x)*Lx + y=y/np.max(y)*Ly #create segments - segments=numpy.zeros((2*(nx-1)+2*(ny-1),3),int) + segments=np.zeros((2*(nx-1)+2*(ny-1),3),int) #left edge: - segments[0:ny-1,:]=numpy.hstack((numpy.arange(2,ny+1).reshape(-1,1),numpy.arange(1,ny).reshape(-1,1),(2*numpy.arange(1,ny)-1).reshape(-1,1))) + segments[0:ny-1,:]=np.vstack((np.arange(2,ny+1),np.arange(1,ny),(2*np.arange(1,ny)-1))).T #right edge: - segments[ny-1:2*(ny-1),:]=numpy.hstack((numpy.arange(ny*(nx-1)+1,nx*ny).reshape(-1,1),numpy.arange(ny*(nx-1)+2,nx*ny+1).reshape(-1,1),2*numpy.arange((ny-1)*(nx-2)+1,(nx-1)*(ny-1)+1).reshape(-1,1))) + segments[ny-1:2*(ny-1),:]=np.vstack((np.arange(ny*(nx-1)+1,nx*ny),np.arange(ny*(nx-1)+2,nx*ny+1),2*np.arange((ny-1)*(nx-2)+1,(nx-1)*(ny-1)+1))).T #front edge: - segments[2*(ny-1):2*(ny-1)+(nx-1),:]=numpy.hstack((numpy.arange(2*ny,ny*nx+1,ny).reshape(-1,1),numpy.arange(ny,ny*(nx-1)+1,ny).reshape(-1,1),numpy.arange(2*(ny-1),2*(nx-1)*(ny-1)+1,2*(ny-1)).reshape(-1,1))) + segments[2*(ny-1):2*(ny-1)+(nx-1),:]=np.vstack((np.arange(2*ny,ny*nx+1,ny),np.arange(ny,ny*(nx-1)+1,ny),np.arange(2*(ny-1),2*(nx-1)*(ny-1)+1,2*(ny-1)))).T #back edge - segments[2*(ny-1)+(nx-1):2*(nx-1)+2*(ny-1),:]=numpy.hstack((numpy.arange(1,(nx-2)*ny+2,ny).reshape(-1,1),numpy.arange(ny+1,ny*(nx-1)+2,ny).reshape(-1,1),numpy.arange(1,2*(nx-2)*(ny-1)+2,2*(ny-1)).reshape(-1,1))) + segments[2*(ny-1)+(nx-1):2*(nx-1)+2*(ny-1),:]=np.vstack((np.arange(1,(nx-2)*ny+2,ny),np.arange(ny+1,ny*(nx-1)+2,ny),np.arange(1,2*(nx-2)*(ny-1)+2,2*(ny-1)))).T #plug coordinates and nodes @@ -62,5 +62,5 @@ md.mesh.y=y md.mesh.numberofvertices=nods - md.mesh.vertexonboundary=numpy.zeros((nods),bool) + md.mesh.vertexonboundary=np.zeros((nods),bool) md.mesh.vertexonboundary[segments[:,0:2]-1]=True @@ -71,6 +71,6 @@ #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) + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices)[0] + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity)[0] return md Index: /issm/trunk-jpl/src/py3/mesh/triangle.py =================================================================== --- /issm/trunk-jpl/src/py3/mesh/triangle.py (revision 23669) +++ /issm/trunk-jpl/src/py3/mesh/triangle.py (revision 23670) @@ -1,7 +1,8 @@ -import numpy +import os.path +import numpy as np from mesh2d import mesh2d -from TriMesh import TriMesh from NodeConnectivity import NodeConnectivity from ElementConnectivity import ElementConnectivity +from Triangle_python import Triangle_python import MatlabFuncs as m @@ -10,5 +11,5 @@ TRIANGLE - create model mesh using the triangle package - This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution + 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 @@ -43,7 +44,11 @@ area = resolution**2 - #Mesh using TriMesh + #Check that file exist (this is a very very common mistake) + if not os.path.exists(domainname): + raise IOError("file '%s' not found" % domainname) + + #Mesh using Triangle md.mesh=mesh2d() - [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area) + md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers=Triangle_python(domainname,riftname,area) md.mesh.elements=md.mesh.elements.astype(int) md.mesh.segments=md.mesh.segments.astype(int) @@ -51,12 +56,12 @@ #Fill in rest of fields: - md.mesh.numberofelements = numpy.size(md.mesh.elements,axis=0) - md.mesh.numberofvertices = numpy.size(md.mesh.x) - md.mesh.vertexonboundary = numpy.zeros(md.mesh.numberofvertices,bool) + md.mesh.numberofelements = np.size(md.mesh.elements,axis=0) + md.mesh.numberofvertices = np.size(md.mesh.x) + md.mesh.vertexonboundary = np.zeros(md.mesh.numberofvertices,bool) md.mesh.vertexonboundary[md.mesh.segments[:,0:2]-1] = True #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) + md.mesh.vertexconnectivity = NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices)[0] + md.mesh.elementconnectivity = ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity)[0] return md Index: /issm/trunk-jpl/src/py3/miscellaneous/MatlabFuncs.py =================================================================== --- /issm/trunk-jpl/src/py3/miscellaneous/MatlabFuncs.py (revision 23669) +++ /issm/trunk-jpl/src/py3/miscellaneous/MatlabFuncs.py (revision 23670) @@ -49,27 +49,27 @@ def ismember(a,s): - import numpy + import numpy as np - if not isinstance(s,(tuple,list,dict,numpy.ndarray)): + if not isinstance(s,(tuple,list,dict,np.ndarray)): s=[s] - if not isinstance(a,(tuple,list,dict,numpy.ndarray)): + if not isinstance(a,(tuple,list,dict,np.ndarray)): a=[a] - if not isinstance(a,numpy.ndarray): + if not isinstance(a,np.ndarray): b=[item in s for item in a] else: - if not isinstance(s,numpy.ndarray): - b=numpy.empty_like(a) + if not isinstance(s,np.ndarray): + b=np.empty_like(a) for i,item in enumerate(a.flat): b.flat[i]=item in s else: - b=numpy.in1d(a.flat,s.flat).reshape(a.shape) + b=np.in1d(a.flat,s.flat).reshape(a.shape) return b def det(a): - import numpy + import numpy as np if a.shape==(1,): @@ -83,12 +83,12 @@ def sparse(ivec,jvec,svec,m=0,n=0,nzmax=0): - import numpy + import numpy as np if not m: - m=numpy.max(ivec) + m=np.max(ivec) if not n: - n=numpy.max(jvec) + n=np.max(jvec) - a=numpy.zeros((m,n)) + a=np.zeros((m,n)) for i,j,s in zip(ivec.reshape(-1,order='F'),jvec.reshape(-1,order='F'),svec.reshape(-1,order='F')): @@ -98,10 +98,9 @@ def heaviside(x): - import numpy + import numpy as np - y=numpy.zeros_like(x) - y[numpy.nonzero(x> 0.)]=1. - y[numpy.nonzero(x==0.)]=0.5 + y=np.zeros_like(x) + y[np.nonzero(x> 0.)]=1. + y[np.nonzero(x==0.)]=0.5 return y - Index: /issm/trunk-jpl/src/py3/miscellaneous/PythonFuncs.py =================================================================== --- /issm/trunk-jpl/src/py3/miscellaneous/PythonFuncs.py (revision 23669) +++ /issm/trunk-jpl/src/py3/miscellaneous/PythonFuncs.py (revision 23670) @@ -1,5 +1,6 @@ +import numpy as np + def logical_and_n(*arg): - from numpy import logical_and - + if len(arg): result=arg[0] @@ -12,6 +13,5 @@ def logical_or_n(*arg): - from numpy import logical_or - + if len(arg): result=arg[0] Index: /issm/trunk-jpl/src/py3/miscellaneous/fielddisplay.py =================================================================== --- /issm/trunk-jpl/src/py3/miscellaneous/fielddisplay.py (revision 23669) +++ /issm/trunk-jpl/src/py3/miscellaneous/fielddisplay.py (revision 23670) @@ -1,4 +1,4 @@ #Module import -import numpy +import numpy as np from math import isnan import MatlabFuncs as m @@ -33,5 +33,5 @@ #matrix - elif isinstance(field,numpy.ndarray): + elif isinstance(field,np.ndarray): string=displayunit(offset,name,str(field.shape),comment) Index: /issm/trunk-jpl/src/py3/miscellaneous/isnans.py =================================================================== --- /issm/trunk-jpl/src/py3/miscellaneous/isnans.py (revision 23669) +++ /issm/trunk-jpl/src/py3/miscellaneous/isnans.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def isnans(array): @@ -13,5 +13,5 @@ returnvalue=0 else: - returnvalue=numpy.isnan(array) + returnvalue=np.isnan(array) return returnvalue Index: /issm/trunk-jpl/src/py3/os/issmssh.py =================================================================== --- /issm/trunk-jpl/src/py3/os/issmssh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/os/issmssh.py (revision 23670) @@ -1,3 +1,4 @@ from socket import gethostname +from sys import platform as _platform import subprocess import os @@ -45,15 +46,16 @@ # (from http://code.google.com/p/robotframework/issues/detail?id=995) - # Make FreeBSD use blocking I/O like other platforms - import sys - import fcntl - from os import O_NONBLOCK + if _platform == "darwin": + # Make FreeBSD use blocking I/O like other platforms + import sys + import fcntl + from os import O_NONBLOCK + + fd = sys.stdin.fileno() + flags = fcntl.fcntl(fd, fcntl.F_GETFL) + fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK) + + fd = sys.stdout.fileno() + flags = fcntl.fcntl(fd, fcntl.F_GETFL) + fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK) - fd = sys.stdin.fileno() - flags = fcntl.fcntl(fd, fcntl.F_GETFL) - fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK) - - fd = sys.stdout.fileno() - flags = fcntl.fcntl(fd, fcntl.F_GETFL) - fcntl.fcntl(fd, fcntl.F_SETFL, flags & ~O_NONBLOCK) - Index: /issm/trunk-jpl/src/py3/parameterization/contourenvelope.py =================================================================== --- /issm/trunk-jpl/src/py3/parameterization/contourenvelope.py (revision 23669) +++ /issm/trunk-jpl/src/py3/parameterization/contourenvelope.py (revision 23670) @@ -1,4 +1,4 @@ import os.path -import numpy +import numpy as np import copy from NodeConnectivity import NodeConnectivity @@ -40,8 +40,8 @@ #Now, build the connectivity tables for this mesh. #Computing connectivity - if numpy.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices and numpy.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices2d: - [md.mesh.vertexconnectivity]=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices) - if numpy.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements and numpy.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements2d: - [md.mesh.elementconnectivity]=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity) + if np.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices and np.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices2d: + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices)[0] + if np.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements and np.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements2d: + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity)[0] #get nodes inside profile @@ -65,22 +65,22 @@ #get flag list of elements and nodes inside the contour nodein=ContourToMesh(elements,x,y,file,'node',1) - elemin=(numpy.sum(nodein(elements),axis=1)==numpy.size(elements,axis=1)) + elemin=(np.sum(nodein(elements),axis=1)==np.size(elements,axis=1)) #modify element connectivity - elemout=numpy.nonzero(numpy.logical_not(elemin))[0] + elemout=np.nonzero(np.logical_not(elemin))[0] elementconnectivity[elemout,:]=0 - elementconnectivity[numpy.nonzero(m.ismember(elementconnectivity,elemout+1))]=0 + elementconnectivity[np.nonzero(m.ismember(elementconnectivity,elemout+1))]=0 else: #get flag list of elements and nodes inside the contour - nodein=numpy.zeros(numberofvertices) - elemin=numpy.zeros(numberofelements) + nodein=np.zeros(numberofvertices) + elemin=np.zeros(numberofelements) - pos=numpy.nonzero(flags) + pos=np.nonzero(flags) elemin[pos]=1 nodein[elements[pos,:]-1]=1 #modify element connectivity - elemout=numpy.nonzero(numpy.logical_not(elemin))[0] + elemout=np.nonzero(np.logical_not(elemin))[0] elementconnectivity[elemout,:]=0 - elementconnectivity[numpy.nonzero(m.ismember(elementconnectivity,elemout+1))]=0 + elementconnectivity[np.nonzero(m.ismember(elementconnectivity,elemout+1))]=0 #Find element on boundary @@ -88,23 +88,23 @@ flag=copy.deepcopy(elementconnectivity) if len(args)==1: - flag[numpy.nonzero(flag)]=elemin[flag[numpy.nonzero(flag)]] - elementonboundary=numpy.logical_and(numpy.prod(flag,axis=1)==0,numpy.sum(flag,axis=1)>0) + flag[np.nonzero(flag)]=elemin[flag[np.nonzero(flag)]] + elementonboundary=np.logical_and(np.prod(flag,axis=1)==0,np.sum(flag,axis=1)>0) #Find segments on boundary - pos=numpy.nonzero(elementonboundary)[0] - num_segments=numpy.size(pos) - segments=numpy.zeros((num_segments*3,3),int) + pos=np.nonzero(elementonboundary)[0] + num_segments=np.size(pos) + segments=np.zeros((num_segments*3,3),int) count=0 for el1 in pos: - els2=elementconnectivity[el1,numpy.nonzero(elementconnectivity[el1,:])[0]]-1 - if numpy.size(els2)>1: - flag=numpy.intersect1d(numpy.intersect1d(elements[els2[0],:],elements[els2[1],:]),elements[el1,:]) + els2=elementconnectivity[el1,np.nonzero(elementconnectivity[el1,:])[0]]-1 + if np.size(els2)>1: + flag=np.intersect1d(np.intersect1d(elements[els2[0],:],elements[els2[1],:]),elements[el1,:]) nods1=elements[el1,:] - nods1=numpy.delete(nods1,numpy.nonzero(nods1==flag)) + nods1=np.delete(nods1,np.nonzero(nods1==flag)) segments[count,:]=[nods1[0],nods1[1],el1+1] - ord1=numpy.nonzero(nods1[0]==elements[el1,:])[0][0] - ord2=numpy.nonzero(nods1[1]==elements[el1,:])[0][0] + ord1=np.nonzero(nods1[0]==elements[el1,:])[0][0] + ord2=np.nonzero(nods1[1]==elements[el1,:])[0][0] #swap segment nodes if necessary @@ -113,20 +113,20 @@ segments[count,0]=segments[count,1] segments[count,1]=temp - segments[count,0:2]=numpy.flipud(segments[count,0:2]) + segments[count,0:2]=np.flipud(segments[count,0:2]) count+=1 else: nods1=elements[el1,:] - flag=numpy.setdiff1d(nods1,elements[els2,:]) + flag=np.setdiff1d(nods1,elements[els2,:]) for j in range(0,3): - nods=numpy.delete(nods1,j) - if numpy.any(m.ismember(flag,nods)): + nods=np.delete(nods1,j) + if np.any(m.ismember(flag,nods)): segments[count,:]=[nods[0],nods[1],el1+1] - ord1=numpy.nonzero(nods[0]==elements[el1,:])[0][0] - ord2=numpy.nonzero(nods[1]==elements[el1,:])[0][0] + ord1=np.nonzero(nods[0]==elements[el1,:])[0][0] + ord2=np.nonzero(nods[1]==elements[el1,:])[0][0] if ( (ord1==0 and ord2==1) or (ord1==1 and ord2==2) or (ord1==2 and ord2==0) ): temp=segments[count,0] segments[count,0]=segments[count,1] segments[count,1]=temp - segments[count,0:2]=numpy.flipud(segments[count,0:2]) + segments[count,0:2]=np.flipud(segments[count,0:2]) count+=1 segments=segments[0:count,:] Index: /issm/trunk-jpl/src/py3/parameterization/setflowequation.py =================================================================== --- /issm/trunk-jpl/src/py3/parameterization/setflowequation.py (revision 23669) +++ /issm/trunk-jpl/src/py3/parameterization/setflowequation.py (revision 23670) @@ -1,10 +1,8 @@ -import numpy +import numpy as np from model import model from pairoptions import pairoptions -import MatlabFuncs as m -import PythonFuncs as p from FlagElements import FlagElements -def setflowequation(md,**kwargs): +def setflowequation(md,*args): """ SETFLOWEQUATION - associate a solution type to each element @@ -28,15 +26,14 @@ #some checks on list of arguments - if not isinstance(md,model) or not len(kwargs): + if not isinstance(md,model) or not len(args): raise TypeError("setflowequation error message") #process options - options=pairoptions(**kwargs) - print(options) -# options=deleteduplicates(options,1); + options=pairoptions(*args) + # options=deleteduplicates(options,1); #Find_out what kind of coupling to use coupling_method=options.getfieldvalue('coupling','tiling') - if coupling_method is not 'tiling' or not 'penalties': + if not coupling_method in ['tiling','penalties']: raise TypeError("coupling type can only be: tiling or penalties") @@ -48,13 +45,11 @@ FSflag = FlagElements(md,options.getfieldvalue('FS','')) filltype = options.getfieldvalue('fill','none') - #Flag the elements that have not been flagged as filltype - if filltype is 'SIA': - SIAflag[numpy.nonzero(numpy.logical_not(p.logical_or_n(SSAflag,HOflag)))]=True - elif filltype is 'SSA': - SSAflag[numpy.nonzero(numpy.logical_not(p.logical_or_n(SIAflag,HOflag,FSflag)))]=True - elif filltype is 'HO': - HOflag[numpy.nonzero(numpy.logical_not(p.logical_or_n(SIAflag,SSAflag,FSflag)))]=True - + if 'SIA' in filltype: + SIAflag= ~SSAflag & ~HOflag + elif 'SSA' in filltype: + SSAflag=~SIAflag & ~HOflag & ~FSflag + elif 'HO' in filltype: + HOflag=~SIAflag & ~SSAflag & ~FSflag #check that each element has at least one flag if not any(SIAflag+SSAflag+L1L2flag+HOflag+FSflag): @@ -64,7 +59,16 @@ if any(SIAflag+SSAflag+L1L2flag+HOflag+FSflag>1): print("setflowequation warning message: some elements have several types, higher order type is used for them") - SIAflag[numpy.nonzero(numpy.logical_and(SIAflag,SSAflag))]=False - SIAflag[numpy.nonzero(numpy.logical_and(SIAflag,HOflag))]=False - SSAflag[numpy.nonzero(numpy.logical_and(SSAflag,HOflag))]=False + SIAflag[np.where(np.logical_and(SIAflag,SSAflag))]=False + SIAflag[np.where(np.logical_and(SIAflag,HOflag))]=False + SSAflag[np.where(np.logical_and(SSAflag,HOflag))]=False + + #check that L1L2 is not coupled to any other model for now + if any(L1L2flag) and any(SIAflag+SSAflag+HOflag+FSflag): + raise TypeError('L1L2 cannot be coupled to any other model') + + #Check that no HO or FS for 2d mesh + if domaintype(md.mesh)=='2Dhorizontal': + if any(FSflag+HOflag): + raise TypeError('FS and HO elements not allowed in 2d mesh, extrude it first') #FS can only be used alone for now: @@ -73,81 +77,76 @@ #Initialize node fields - nodeonSIA=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonSIA[md.mesh.elements[numpy.nonzero(SIAflag),:]-1]=True - nodeonSSA=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonSSA[md.mesh.elements[numpy.nonzero(SSAflag),:]-1]=True - nodeonL1L2=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonL1L2[md.mesh.elements[numpy.nonzero(L1L2flag),:]-1]=True - nodeonHO=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonHO[md.mesh.elements[numpy.nonzero(HOflag),:]-1]=True - nodeonFS=numpy.zeros(md.mesh.numberofvertices,bool) - noneflag=numpy.zeros(md.mesh.numberofelements,bool) + nodeonSIA=np.zeros(md.mesh.numberofvertices,bool) + nodeonSIA[md.mesh.elements[np.where(SIAflag),:]-1]=True + nodeonSSA=np.zeros(md.mesh.numberofvertices,bool) + nodeonSSA[md.mesh.elements[np.where(SSAflag),:]-1]=True + nodeonL1L2=np.zeros(md.mesh.numberofvertices,bool) + nodeonL1L2[md.mesh.elements[np.where(L1L2flag),:]-1]=True + nodeonHO=np.zeros(md.mesh.numberofvertices,bool) + nodeonHO[md.mesh.elements[np.where(HOflag),:]-1]=True + nodeonFS=np.zeros(md.mesh.numberofvertices,bool) + noneflag=np.zeros(md.mesh.numberofelements,bool) #First modify FSflag to get rid of elements contrained everywhere (spc + border with HO or SSA) if any(FSflag): -# fullspcnodes=double((~isnan(md.stressbalance.spcvx)+~isnan(md.stressbalance.spcvy)+~isnan(md.stressbalance.spcvz))==3 | (nodeonHO & nodeonFS)); %find all the nodes on the boundary of the domain without icefront - fullspcnodes=numpy.logical_or(numpy.logical_not(numpy.isnan(md.stressbalance.spcvx)).astype(int)+ \ - numpy.logical_not(numpy.isnan(md.stressbalance.spcvy)).astype(int)+ \ - numpy.logical_not(numpy.isnan(md.stressbalance.spcvz)).astype(int)==3, \ - numpy.logical_and(nodeonHO,nodeonFS)).astype(int) #find all the nodes on the boundary of the domain without icefront -# fullspcelems=double(sum(fullspcnodes(md.mesh.elements),2)==6); %find all the nodes on the boundary of the domain without icefront - fullspcelems=(numpy.sum(fullspcnodes[md.mesh.elements-1],axis=1)==6).astype(int) #find all the nodes on the boundary of the domain without icefront - FSflag[numpy.nonzero(fullspcelems.reshape(-1))]=False - nodeonFS[md.mesh.elements[numpy.nonzero(FSflag),:]-1]=True + fullspcnodes=np.logical_or(~np.isnan(md.stressbalance.spcvx)+~np.isnan(md.stressbalance.spcvy)+~np.isnan(md.stressbalance.spcvz),np.logical_and(nodeonHO,nodeonFS)) #find all the nodes on the boundary of the domain without icefront + fullspcelems=np.sum(fullspcnodes[md.mesh.elements-1],axis=1)==6 #find all the nodes on the boundary of the domain without icefront + FSflag[np.where(fullspcelems.reshape(-1))]=False + nodeonFS[md.mesh.elements[np.where(FSflag),:]-1]=True #Then complete with NoneApproximation or the other model used if there is no FS if any(FSflag): if any(HOflag): #fill with HO - HOflag[numpy.logical_not(FSflag)]=True - nodeonHO[md.mesh.elements[numpy.nonzero(HOflag),:]-1]=True + HOflag[~FSflag]=True + nodeonHO[md.mesh.elements[np.where(HOflag),:]-1]=True elif any(SSAflag): #fill with SSA - SSAflag[numpy.logical_not(FSflag)]=True - nodeonSSA[md.mesh.elements[numpy.nonzero(SSAflag),:]-1]=True + SSAflag[~FSflag]=True + nodeonSSA[md.mesh.elements[np.where(SSAflag),:]-1]=True else: #fill with none - noneflag[numpy.nonzero(numpy.logical_not(FSflag))]=True + noneflag[np.where(~FSflag)]=True #Now take care of the coupling between SSA and HO - md.stressbalance.vertex_pairing=numpy.array([]) - nodeonSSAHO=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonHOFS=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonSSAFS=numpy.zeros(md.mesh.numberofvertices,bool) - SSAHOflag=numpy.zeros(md.mesh.numberofelements,bool) - SSAFSflag=numpy.zeros(md.mesh.numberofelements,bool) - HOFSflag=numpy.zeros(md.mesh.numberofelements,bool) - if coupling_method is 'penalties': + md.stressbalance.vertex_pairing=np.array([]) + nodeonSSAHO=np.zeros(md.mesh.numberofvertices,bool) + nodeonHOFS=np.zeros(md.mesh.numberofvertices,bool) + nodeonSSAFS=np.zeros(md.mesh.numberofvertices,bool) + SSAHOflag=np.zeros(md.mesh.numberofelements,bool) + SSAFSflag=np.zeros(md.mesh.numberofelements,bool) + HOFSflag=np.zeros(md.mesh.numberofelements,bool) + if coupling_method=='penalties': #Create the border nodes between HO and SSA and extrude them numnodes2d=md.mesh.numberofvertices2d numlayers=md.mesh.numberoflayers - bordernodes2d=numpy.nonzero(numpy.logical_and(nodeonHO[0:numnodes2d],nodeonSSA[0:numnodes2d]))[0]+1 #Nodes connected to two different types of elements + bordernodes2d=np.where(np.logical_and(nodeonHO[0:numnodes2d],nodeonSSA[0:numnodes2d]))[0]+1 #Nodes connected to two different types of elements #initialize and fill in penalties structure - if numpy.all(numpy.logical_not(numpy.isnan(bordernodes2d))): - penalties=numpy.zeros((0,2)) + if np.all(np.logical_not(np.isnan(bordernodes2d))): + penalties=np.zeros((0,2)) for i in range(1,numlayers): - penalties=numpy.vstack((penalties,numpy.hstack((bordernodes2d.reshape(-1,1),bordernodes2d.reshape(-1,1)+md.mesh.numberofvertices2d*(i))))) + penalties=np.vstack((penalties,np.vstack((bordernodes2d,bordernodes2d+md.mesh.numberofvertices2d*(i))).T)) md.stressbalance.vertex_pairing=penalties - elif coupling_method is 'tiling': - if any(SSAflag) and any(HOflag): #coupling SSA HO + elif coupling_method=='tiling': + if any(SSAflag) and any(HOflag): #coupling SSA HO #Find node at the border - nodeonSSAHO[numpy.nonzero(numpy.logical_and(nodeonSSA,nodeonHO))]=True + nodeonSSAHO[np.where(np.logical_and(nodeonSSA,nodeonHO))]=True #SSA elements in contact with this layer become SSAHO elements - matrixelements=m.ismember(md.mesh.elements-1,numpy.nonzero(nodeonSSAHO)[0]) - commonelements=numpy.sum(matrixelements,axis=1)!=0 - commonelements[numpy.nonzero(HOflag)]=False #only one layer: the elements previously in SSA - SSAflag[numpy.nonzero(commonelements)]=False #these elements are now SSAHOelements - SSAHOflag[numpy.nonzero(commonelements)]=True + matrixelements=nodeonSSAHO[md.mesh.elements-1] + commonelements=np.sum(matrixelements,axis=1)!=0 + commonelements[np.where(HOflag)]=False #only one layer: the elements previously in SSA + SSAflag[np.where(commonelements)]=False #these elements are now SSAHOelements + SSAHOflag[np.where(commonelements)]=True nodeonSSA[:]=False - nodeonSSA[md.mesh.elements[numpy.nonzero(SSAflag),:]-1]=True + nodeonSSA[md.mesh.elements[np.where(SSAflag),:]-1]=True #rule out elements that don't touch the 2 boundaries - pos=numpy.nonzero(SSAHOflag)[0] - elist=numpy.zeros(numpy.size(pos),dtype=int) - elist = elist + numpy.sum(nodeonSSA[md.mesh.elements[pos,:]-1],axis=1).astype(bool) - elist = elist - numpy.sum(nodeonHO[md.mesh.elements[pos,:]-1] ,axis=1).astype(bool) - pos1=numpy.nonzero(elist==1)[0] + pos=np.where(SSAHOflag)[0] + elist=np.zeros(np.size(pos),dtype=int) + elist = elist + np.sum(nodeonSSA[md.mesh.elements[pos,:]-1],axis=1).astype(bool) + elist = elist - np.sum(nodeonHO[md.mesh.elements[pos,:]-1] ,axis=1).astype(bool) + pos1=np.where(elist==1)[0] SSAflag[pos[pos1]]=True SSAHOflag[pos[pos1]]=False - pos2=numpy.nonzero(elist==-1)[0] + pos2=np.where(elist==-1)[0] HOflag[pos[pos2]]=True SSAHOflag[pos[pos2]]=False @@ -155,31 +154,31 @@ #Recompute nodes associated to these elements nodeonSSA[:]=False - nodeonSSA[md.mesh.elements[numpy.nonzero(SSAflag),:]-1]=True + nodeonSSA[md.mesh.elements[np.where(SSAflag),:]-1]=True nodeonHO[:]=False - nodeonHO[md.mesh.elements[numpy.nonzero(HOflag),:]-1]=True + nodeonHO[md.mesh.elements[np.where(HOflag),:]-1]=True nodeonSSAHO[:]=False - nodeonSSAHO[md.mesh.elements[numpy.nonzero(SSAHOflag),:]-1]=True + nodeonSSAHO[md.mesh.elements[np.where(SSAHOflag),:]-1]=True elif any(HOflag) and any(FSflag): #coupling HO FS #Find node at the border - nodeonHOFS[numpy.nonzero(numpy.logical_and(nodeonHO,nodeonFS))]=True + nodeonHOFS[np.where(np.logical_and(nodeonHO,nodeonFS))]=True #FS elements in contact with this layer become HOFS elements - matrixelements=m.ismember(md.mesh.elements-1,numpy.nonzero(nodeonHOFS)[0]) - commonelements=numpy.sum(matrixelements,axis=1)!=0 - commonelements[numpy.nonzero(HOflag)]=False #only one layer: the elements previously in SSA - FSflag[numpy.nonzero(commonelements)]=False #these elements are now SSAHOelements - HOFSflag[numpy.nonzero(commonelements)]=True - nodeonFS=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonFS[md.mesh.elements[numpy.nonzero(FSflag),:]-1]=True + matrixelements=nodeonHOFS[md.mesh.elements-1] + commonelements=np.sum(matrixelements,axis=1)!=0 + commonelements[np.where(HOflag)]=False #only one layer: the elements previously in SSA + FSflag[np.where(commonelements)]=False #these elements are now SSAHOelements + HOFSflag[np.where(commonelements)]=True + nodeonFS=np.zeros(md.mesh.numberofvertices,bool) + nodeonFS[md.mesh.elements[np.where(FSflag),:]-1]=True #rule out elements that don't touch the 2 boundaries - pos=numpy.nonzero(HOFSflag)[0] - elist=numpy.zeros(numpy.size(pos),dtype=int) - elist = elist + numpy.sum(nodeonFS[md.mesh.elements[pos,:]-1],axis=1).astype(bool) - elist = elist - numpy.sum(nodeonHO[md.mesh.elements[pos,:]-1],axis=1).astype(bool) - pos1=numpy.nonzero(elist==1)[0] + pos=np.where(HOFSflag)[0] + elist=np.zeros(np.size(pos),dtype=int) + elist = elist + np.sum(nodeonFS[md.mesh.elements[pos,:]-1],axis=1).astype(bool) + elist = elist - np.sum(nodeonHO[md.mesh.elements[pos,:]-1],axis=1).astype(bool) + pos1=np.where(elist==1)[0] FSflag[pos[pos1]]=True HOFSflag[pos[pos1]]=False - pos2=numpy.nonzero(elist==-1)[0] + pos2=np.where(elist==-1)[0] HOflag[pos[pos2]]=True HOFSflag[pos[pos2]]=False @@ -187,31 +186,30 @@ #Recompute nodes associated to these elements nodeonFS[:]=False - nodeonFS[md.mesh.elements[numpy.nonzero(FSflag),:]-1]=True + nodeonFS[md.mesh.elements[np.where(FSflag),:]-1]=True nodeonHO[:]=False - nodeonHO[md.mesh.elements[numpy.nonzero(HOflag),:]-1]=True + nodeonHO[md.mesh.elements[np.where(HOflag),:]-1]=True nodeonHOFS[:]=False - nodeonHOFS[md.mesh.elements[numpy.nonzero(HOFSflag),:]-1]=True - + nodeonHOFS[md.mesh.elements[np.where(HOFSflag),:]-1]=True elif any(FSflag) and any(SSAflag): #Find node at the border - nodeonSSAFS[numpy.nonzero(numpy.logical_and(nodeonSSA,nodeonFS))]=True + nodeonSSAFS[np.where(np.logical_and(nodeonSSA,nodeonFS))]=True #FS elements in contact with this layer become SSAFS elements - matrixelements=m.ismember(md.mesh.elements-1,numpy.nonzero(nodeonSSAFS)[0]) - commonelements=numpy.sum(matrixelements,axis=1)!=0 - commonelements[numpy.nonzero(SSAflag)]=False #only one layer: the elements previously in SSA - FSflag[numpy.nonzero(commonelements)]=False #these elements are now SSASSAelements - SSAFSflag[numpy.nonzero(commonelements)]=True - nodeonFS=numpy.zeros(md.mesh.numberofvertices,bool) - nodeonFS[md.mesh.elements[numpy.nonzero(FSflag),:]-1]=True + matrixelements=nodeonSSAFS[md.mesh.elements-1] + commonelements=np.sum(matrixelements,axis=1)!=0 + commonelements[np.where(SSAflag)]=False #only one layer: the elements previously in SSA + FSflag[np.where(commonelements)]=False #these elements are now SSASSAelements + SSAFSflag[np.where(commonelements)]=True + nodeonFS=np.zeros(md.mesh.numberofvertices,bool) + nodeonFS[md.mesh.elements[np.where(FSflag),:]-1]=True #rule out elements that don't touch the 2 boundaries - pos=numpy.nonzero(SSAFSflag)[0] - elist=numpy.zeros(numpy.size(pos),dtype=int) - elist = elist + numpy.sum(nodeonSSA[md.mesh.elements[pos,:]-1],axis=1).astype(bool) - elist = elist - numpy.sum(nodeonFS[md.mesh.elements[pos,:]-1] ,axis=1).astype(bool) - pos1=numpy.nonzero(elist==1)[0] + pos=np.where(SSAFSflag)[0] + elist=np.zeros(np.size(pos),dtype=int) + elist = elist + np.sum(nodeonSSA[md.mesh.elements[pos,:]-1],axis=1).astype(bool) + elist = elist - np.sum(nodeonFS[md.mesh.elements[pos,:]-1],axis=1).astype(bool) + pos1=np.where(elist==1)[0] SSAflag[pos[pos1]]=True SSAFSflag[pos[pos1]]=False - pos2=numpy.nonzero(elist==-1)[0] + pos2=np.where(elist==-1)[0] FSflag[pos[pos2]]=True SSAFSflag[pos[pos2]]=False @@ -219,9 +217,9 @@ #Recompute nodes associated to these elements nodeonSSA[:]=False - nodeonSSA[md.mesh.elements[numpy.nonzero(SSAflag),:]-1]=True + nodeonSSA[md.mesh.elements[np.where(SSAflag),:]-1]=True nodeonFS[:]=False - nodeonFS[md.mesh.elements[numpy.nonzero(FSflag),:]-1]=True + nodeonFS[md.mesh.elements[np.where(FSflag),:]-1]=True nodeonSSAFS[:]=False - nodeonSSAFS[md.mesh.elements[numpy.nonzero(SSAFSflag),:]-1]=True + nodeonSSAFS[md.mesh.elements[np.where(SSAFSflag),:]-1]=True elif any(FSflag) and any(SIAflag): @@ -229,14 +227,14 @@ #Create SSAHOApproximation where needed - md.flowequation.element_equation=numpy.zeros(md.mesh.numberofelements,int) - md.flowequation.element_equation[numpy.nonzero(noneflag)]=0 - md.flowequation.element_equation[numpy.nonzero(SIAflag)]=1 - md.flowequation.element_equation[numpy.nonzero(SSAflag)]=2 - md.flowequation.element_equation[numpy.nonzero(L1L2flag)]=3 - md.flowequation.element_equation[numpy.nonzero(HOflag)]=4 - md.flowequation.element_equation[numpy.nonzero(FSflag)]=5 - md.flowequation.element_equation[numpy.nonzero(SSAHOflag)]=6 - md.flowequation.element_equation[numpy.nonzero(SSAFSflag)]=7 - md.flowequation.element_equation[numpy.nonzero(HOFSflag)]=8 + md.flowequation.element_equation=np.zeros(md.mesh.numberofelements,int) + md.flowequation.element_equation[np.where(noneflag)]=0 + md.flowequation.element_equation[np.where(SIAflag)]=1 + md.flowequation.element_equation[np.where(SSAflag)]=2 + md.flowequation.element_equation[np.where(L1L2flag)]=3 + md.flowequation.element_equation[np.where(HOflag)]=4 + md.flowequation.element_equation[np.where(FSflag)]=5 + md.flowequation.element_equation[np.where(SSAHOflag)]=6 + md.flowequation.element_equation[np.where(SSAFSflag)]=7 + md.flowequation.element_equation[np.where(HOFSflag)]=8 #border @@ -246,25 +244,25 @@ #Create vertices_type - md.flowequation.vertex_equation=numpy.zeros(md.mesh.numberofvertices,int) - pos=numpy.nonzero(nodeonSSA) + md.flowequation.vertex_equation=np.zeros(md.mesh.numberofvertices,int) + pos=np.where(nodeonSSA) md.flowequation.vertex_equation[pos]=2 - pos=numpy.nonzero(nodeonL1L2) + pos=np.where(nodeonL1L2) md.flowequation.vertex_equation[pos]=3 - pos=numpy.nonzero(nodeonHO) + pos=np.where(nodeonHO) md.flowequation.vertex_equation[pos]=4 - pos=numpy.nonzero(nodeonFS) + pos=np.where(nodeonFS) md.flowequation.vertex_equation[pos]=5 #DO SIA LAST! Otherwise spcs might not be set up correctly (SIA should have priority) - pos=numpy.nonzero(nodeonSIA) + pos=np.where(nodeonSIA) md.flowequation.vertex_equation[pos]=1 if any(FSflag): - pos=numpy.nonzero(numpy.logical_not(nodeonFS)) + pos=np.where(np.logical_not(nodeonFS)) if not (any(HOflag) or any(SSAflag)): md.flowequation.vertex_equation[pos]=0 - pos=numpy.nonzero(nodeonSSAHO) + pos=np.where(nodeonSSAHO) md.flowequation.vertex_equation[pos]=6 - pos=numpy.nonzero(nodeonHOFS) + pos=np.where(nodeonHOFS) md.flowequation.vertex_equation[pos]=7 - pos=numpy.nonzero(nodeonSSAFS) + pos=np.where(nodeonSSAFS) md.flowequation.vertex_equation[pos]=8 Index: /issm/trunk-jpl/src/py3/parameterization/sethydrostaticmask.py =================================================================== --- /issm/trunk-jpl/src/py3/parameterization/sethydrostaticmask.py (revision 23669) +++ /issm/trunk-jpl/src/py3/parameterization/sethydrostaticmask.py (revision 23670) @@ -1,6 +1,7 @@ -import numpy +import numpy as np import os from model import model from FlagElements import FlagElements +import pairoptions from ContourToMesh import ContourToMesh @@ -19,5 +20,5 @@ """ - if numpy.size(md.geometry.bed,axis=0)!=md.mesh.numberofvertices or numpy.size(md.geometry.base,axis=0)!=md.mesh.numberofvertices or numpy.size(md.geometry.thickness,axis=0)!=md.mesh.numberofvertices: + if np.size(md.geometry.bed,axis=0)!=md.mesh.numberofvertices or np.size(md.geometry.base,axis=0)!=md.mesh.numberofvertices or np.size(md.geometry.thickness,axis=0)!=md.mesh.numberofvertices: raise IOError("hydrostaticmask error message: fields in md.geometry do not have the right size.") @@ -26,8 +27,8 @@ #Check consistency of geometry - if any(md.geometry.base[numpy.nonzero(md.mask.groundedice_levelset>0.)]!=md.geometry.bed[numpy.nonzero(md.mask.groundedice_levelset>0.)]): + if any(md.geometry.base[np.nonzero(md.mask.groundedice_levelset>0.)]!=md.geometry.bed[np.nonzero(md.mask.groundedice_levelset>0.)]): print "WARNING: md.geometry.bed and md.geometry.base not equal on grounded ice" - if any(md.geometry.base[numpy.nonzero(md.mask.groundedice_levelset<=0.)]0: lims=[data.min(),data.max()] -else: lims=[0,1] -#}}} - - #shading + elif options.exist('caxis'): + lims=options.getfieldvalue('caxis') + assert len(lims)==2, 'error, caxis should be passed as a list of length 2' + options.addfielddefault('clim',lims) + else: + if len(data)>0: + lims=[data.min(),data.max()] + else: + lims=[0,1] + # }}} + # {{{ shading TODO #if options.exist('shading'): - - #grid {{{ + # }}} + # {{{ grid if options.exist('grid'): if 'on' in options.getfieldvalue('grid','on'): ax.grid() - #}}} - - #colormap {{{ - # default sequential colormap - defaultmap=truncate_colormap(mpl.cm.gnuplot2,0.1,0.9,128) - cmap=options.getfieldvalue('colormap',defaultmap) - norm = mpl.colors.Normalize(vmin=lims[0], vmax=lims[1]) - options.addfield('colornorm',norm) + # }}} + # {{{ colormap + if options.exist('colornorm'): + norm=options.getfieldvalue('colornorm') + if options.exist('colormap'): + cmap=options.getfieldvalue('colormap') cbar_extend=0 if options.exist('cmap_set_over'): - over=options.getfieldvalue('cmap_set_over','0.5') - cmap.set_over(over) cbar_extend+=1 - if options.exist('cmap_set_under'): - under=options.getfieldvalue('cmap_set_under','0.5') - cmap.set_under(under) - cbar_extend+=2 - options.addfield('colormap',cmap) - #}}} - - #contours {{{ + if options.exist('cmap_set_under'): + cbar_extend+=2 + # }}} + # {{{ contours if options.exist('contourlevels'): plot_contour(md,data,options,ax) - #}}} - - #wrapping - - #colorbar {{{ + # }}} + # {{{ wrapping TODO + # }}} + # {{{ colorbar if options.getfieldvalue('colorbar',1)==1: if cbar_extend==0: extend='neither' -elif cbar_extend==1: - extend='max' -elif cbar_extend==2: - extend='min' -elif cbar_extend==3: - extend='both' - cb = mpl.colorbar.ColorbarBase(ax.cax, cmap=cmap, norm=norm, extend=extend) - if options.exist('alpha'): - cb.set_alpha(options.getfieldvalue('alpha')) + elif cbar_extend==1: + extend='max' + elif cbar_extend==2: + extend='min' + elif cbar_extend==3: + extend='both' + cb = mpl.colorbar.ColorbarBase(ax.cax,cmap=cmap, norm=norm, extend=extend) + if options.exist('alpha'): + cb.set_alpha(options.getfieldvalue('alpha')) if options.exist('colorbarnumticks'): cb.locator=MaxNLocator(nbins=options.getfieldvalue('colorbarnumticks',5)) -else: - cb.locator=MaxNLocator(nbins=5) # default 5 ticks - if options.exist('colorbartickspacing'): - locs=np.arange(lims[0],lims[1]+1,options.getfieldvalue('colorbartickspacing')) - cb.set_ticks(locs) + else: + cb.locator=MaxNLocator(nbins=5) # default 5 ticks + if options.exist('colorbartickspacing'): + locs=np.arange(lims[0],lims[1]+1,options.getfieldvalue('colorbartickspacing')) + cb.set_ticks(locs) if options.exist('colorbarlines'): locs=np.arange(lims[0],lims[1]+1,options.getfieldvalue('colorbarlines')) cb.add_lines(locs,['k' for i in range(len(locs))],np.ones_like(locs)) - if options.exist('colorbarlineatvalue'): - locs=options.getfieldvalue('colorbarlineatvalue') - colors=options.getfieldvalue('colorbarlineatvaluecolor',['k' for i in range (len(locs))]) - widths=options.getfieldvalue('colorbarlineatvaluewidth',np.ones_like(locs)) - cb.add_lines(locs,colors,widths) - if options.exist('colorbartitle'): - if options.exist('colorbartitlepad'): - cb.set_label(options.getfieldvalue('colorbartitle'),labelpad=options.getfieldvalue('colorbartitlepad'),fontsize=fontsize) -else: - cb.set_label(options.getfieldvalue('colorbartitle'),fontsize=fontsize) - cb.ax.tick_params(labelsize=fontsize) - cb.solids.set_rasterized(True) - cb.update_ticks() - cb.set_alpha(1) - cb.draw_all() - plt.sca(ax) # return to original axes control - #}}} - - #expdisp {{{ - if options.exist('expdisp'): - filename=options.getfieldvalue('expdisp') - style=options.getfieldvalue('expstyle','k') - linewidth=options.getfieldvalue('explinewidth',1) - for i in range(len(filename)): - filenamei=filename[i] - stylei=style[i] - if type(linewidth)==list: - linewidthi=linewidth[i] -else: - linewidthi=linewidth - expdisp(filenamei,ax,linestyle=stylei,linewidth=linewidthi,unitmultiplier=options.getfieldvalue('unit',1)) - #}}} - - #area - - #text {{{ + if options.exist('colorbarlineatvalue'): + locs=options.getfieldvalue('colorbarlineatvalue') + colors=options.getfieldvalue('colorbarlineatvaluecolor',['k' for i in range (len(locs))]) + widths=options.getfieldvalue('colorbarlineatvaluewidth',np.ones_like(locs)) + cb.add_lines(locs,colors,widths) + if options.exist('colorbartitle'): + if options.exist('colorbartitlepad'): + cb.set_label(options.getfieldvalue('colorbartitle'), + labelpad=options.getfieldvalue('colorbartitlepad'),fontsize=fontsize) + else: + cb.set_label(options.getfieldvalue('colorbartitle'),fontsize=fontsize) + cb.ax.tick_params(labelsize=fontsize) + cb.solids.set_rasterized(True) + cb.update_ticks() + cb.draw_all() + if options.exist('colorbarfontsize'): + colorbarfontsize=options.getfieldvalue('colorbarfontsize') + cb.ax.tick_params(labelsize=colorbarfontsize) + # cb.set_ticks([0,-10]) + # cb.set_ticklabels([-10,0,10]) + if options.exist('colorbarticks'): + colorbarticks=options.getfieldvalue('colorbarticks') + cb.set_ticks(colorbarticks) + plt.sca(ax) # return to original axes control + # }}} + # {{{ expdisp + if options.exist('expdisp'): + expdisp(ax,options) + # }}} + # {{{ area TODO + # }}} + # {{{ text if options.exist('text'): text=options.getfieldvalue('text') @@ -281,35 +259,33 @@ for label,x,y,size,color,weight,rotation in zip(text,textx,texty,textfontsize,textcolor,textweight,textrotation): ax.text(x,y,label,transform=ax.transAxes,fontsize=size,color=color,weight=weight,rotation=rotation) - #}}} - - #north arrow - - #scale ruler - - #streamlines + # }}} + # {{{ north arrow TODO + # }}} + # {{{ scale ruler TODO + # }}} + # {{{ streamlines TOFIX if options.exist('streamlines'): plot_streamlines(md,options,ax) - - - #axis positions - - #figure position - - #axes position - - #showregion - - #flat edges of a partition - - #scatter - - #backgroundcolor - - #figurebackgroundcolor - - #lighting - - #point cloud - - #inset - + # }}} + # {{{ axis positions TODO + # }}} + # {{{ figure position TODO + # }}} + # {{{ axes position TODO + # }}} + # {{{ showregion TODO + # }}} + # {{{ flat edges of a partition TODO + # }}} + # {{{ scatter TODO + # }}} + # {{{ backgroundcolor TODO + # }}} + # {{{ figurebackgroundcolor TODO + # }}} + # {{{ lighting TODO + # }}} + # {{{ point cloud TODO + # }}} + # {{{ inset TODO + # }}} Index: /issm/trunk-jpl/src/py3/plot/checkplotoptions.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/checkplotoptions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/checkplotoptions.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np def checkplotoptions(md,options): @@ -13,6 +13,5 @@ ''' - - #units + # {{{ units if options.exist('unit'): if 'km' in options.getfieldvalue('unit','km'): @@ -20,26 +19,26 @@ elif '100km' in options.getfieldvalue('unit','100km'): options.changefieldvalue('unit',10**-5) - - #density + # }}} + # {{{ density if options.exist('density'): density=options.getfieldvalue('density') options.changefieldvalue('density',abs(ceil(density))) - - #show section + # }}} + # {{{ show section if options.exist('showsection'): if 'on' in options.getfieldvalue('showsection','on'): options.changefieldvalue('showsection',4) - - #smooth values + # }}} + # {{{ smooth values if options.exist('smooth'): if 'on' in options.getfieldvalue('smooth','on'): options.changefieldvalue('smooth',0) - - #contouronly values + # }}} + # {{{ contouronly values if options.exist('contouronly'): if 'on' in options.getfieldvalue('contouronly','on'): options.changefieldvalue('contouronly',1) - - #colorbar + # }}} + # {{{ colorbar if options.exist('colorbar'): if 'on' in options.getfieldvalue('colorbar','on'): @@ -47,8 +46,7 @@ elif 'off' in options.getfieldvalue('colorbar','off'): options.changefieldvalue('colorbar',0) - - #text + # }}} + # {{{ text if options.exist('text'): - # text values (coerce to list for consistent functionality) textlist=[] @@ -56,27 +54,26 @@ textlist.extend([text] if isinstance(text,str) else text) numtext=len(textlist) - # text position textpos=options.getfieldvalue('textposition',[0.5,0.5]) if not isinstance(textpos,list): raise Exception('textposition should be passed as a list') - if any(isinstance(i,list) for i in textpos): - textx=[item[0] for item in textpos] - texty=[item[1] for item in textpos] - else: - textx=[textpos[0]] - texty=[textpos[1]] + if any(isinstance(i,list) for i in textpos): + textx=[item[0] for item in textpos] + texty=[item[1] for item in textpos] + else: + textx=[textpos[0]] + texty=[textpos[1]] if len(textx)!=numtext or len(texty)!=numtext: raise Exception('textposition should contain one list of x,y vertices for every text instance') # font size - if options.exist('textfontsize'): - textfontsize=options.getfieldvalue('textfontsize',12) - sizelist=[] - sizelist.extend(textsize if isinstance(textfontsize,list) else [textfontsize]) - else: - sizelist=[12] - if len(sizelist)==1: - sizelist=np.tile(sizelist,numtext) + if options.exist('textfontsize'): + textfontsize=options.getfieldvalue('textfontsize',12) + sizelist=[] + sizelist.extend(textsize if isinstance(textfontsize,list) else [textfontsize]) + else: + sizelist=[12] + if len(sizelist)==1: + sizelist=np.tile(sizelist,numtext) # font color @@ -108,5 +105,5 @@ rotationlist=[0] if len(rotationlist)==1: - rotationlist=np.tile(rotationlist,numtext) + rotationlist=np.tile(rotationlist,numtext) options.changefieldvalue('text',textlist) @@ -117,6 +114,6 @@ options.changefieldvalue('textweight',weightlist) options.changefieldvalue('textrotation',rotationlist) - - #expdisp + # }}} + # {{{ expdisp expdispvaluesarray=[] expstylevaluesarray=[] @@ -136,14 +133,13 @@ else: expstylevaluesarray.append('-k') - options.changefieldvalue('expstyle',expstylevaluesarray) options.changefieldvalue('expdisp',expdispvaluesarray) - - #latlonnumbering + # }}} + # {{{ latlonnumbering if options.exist('latlonclick'): if 'on' in options.getfieldvalue('latlonclick','on'): options.changefieldvalue('latlonclick',1) - - #northarrow + # }}} + # {{{ northarrow if options.exist('northarrow'): if 'on' in options.getfieldvalue('northarrow','on'): @@ -152,17 +148,15 @@ Ly=max(md.mesh.y)-min(md.mesh.y) options.changefieldvalue('northarrow',[min(md.mesh.x)+1./6.*Lx, min(md.mesh.y)+5./6.*Ly, 1./15.*Ly, 0.25, 1./250.*Ly]) - - #scale ruler + # }}} + # {{{ scale ruler if options.exist('scaleruler'): - if 'on' in options.exist('scaleruler','on'): + if 'on' in options.getfieldvalue('scaleruler','off'): Lx=max(md.mesh.x)-min(md.mesh.x) Ly=max(md.mesh.y)-min(md.mesh.y) - options.changefieldvalue('scaleruler',[min(md.mesh.x)+6./8.*Lx, min(md.mesh.y)+1./10.*Ly, 10**(ceil(log10(Lx)))/5, floor(Lx/100), 5]) - - #log scale + options.changefieldvalue('scaleruler',[min(md.mesh.x)+6./8.*Lx, min(md.mesh.y)+1./10.*Ly, 10**(np.ceil(np.log10(Lx)))/5, np.floor(Lx/100), 5]) + # }}} + # {{{ log scale if options.exist('log'): - if options.exist('clim'): - options.changefieldvalue('clim',log(options.getfieldvalue('clim'))/log(options.getfieldvalue('log'))) - options.changefieldvalue('cutoff',log(options.getfieldvalue('cutoff',1.5))/log(options.getfieldvalue('log'))) - + options.changefieldvalue('cutoff',np.log10(options.getfieldvalue('cutoff',1.5))/np.log10(options.getfieldvalue('log'))) + # }}} return options Index: /issm/trunk-jpl/src/py3/plot/colormaps/cmaptools.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/colormaps/cmaptools.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/colormaps/cmaptools.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np try: Index: /issm/trunk-jpl/src/py3/plot/export_gl.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/export_gl.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/export_gl.py (revision 23670) @@ -2,5 +2,5 @@ from checkplotoptions import checkplotoptions from model import model -import numpy as np +import numpy as np import math from writejsfile import writejsfile Index: /issm/trunk-jpl/src/py3/plot/plot_contour.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_contour.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_contour.py (revision 23670) @@ -1,6 +1,9 @@ from averaging import averaging -import matplotlib.pyplot as plt from processmesh import processmesh from processdata import processdata +try: + import matplotlib.pyplot as plt +except ImportError: + print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") def plot_contour(md,datain,options,ax): @@ -31,8 +34,8 @@ # retrieve necessary options levels=options.getfieldvalue('contourlevels') - colors=options.getfieldvalue('contourcolors') norm=options.getfieldvalue('colornorm') - linestyles=options.getfieldvalue('contourlinestyles') - linewidths=options.getfieldvalue('contourlinewidths') + colors=options.getfieldvalue('contourcolors','y') + linestyles=options.getfieldvalue('contourlinestyles','-') + linewidths=options.getfieldvalue('contourlinewidths',1) ax.tricontour(x,y,elements,data,levels,colors=colors,norm=norm,linestyles=linestyles,linewidths=linewidths) Index: /issm/trunk-jpl/src/py3/plot/plot_manager.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_manager.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_manager.py (revision 23670) @@ -7,4 +7,7 @@ from checkplotoptions import checkplotoptions from plot_mesh import plot_mesh +from plot_BC import plot_BC +from plot_elementnumbering import plot_elementnumbering +from plot_vertexnumbering import plot_vertexnumbering from processmesh import processmesh from processdata import processdata @@ -22,5 +25,5 @@ from plot_overlay import plot_overlay -def plot_manager(md,options,fig,ax): +def plot_manager(md,options,fig,axgrid,gridindex): ''' PLOT_MANAGER - distribute the plots called by plotmodel @@ -39,8 +42,62 @@ #parse options and get a structure of options options=checkplotoptions(md,options) + #get data to be plotted + data=options.getfieldvalue('data') + #add ticklabel has a default option + options.addfielddefault('ticklabels','on') - #get data to be plotted - data=options.getfieldvalue('data'); + ax=axgrid[gridindex] + # {{{ basemap plot TOFIX + #if options.exist('basemap'): + # plot_basemap(md,data,options,nrows,ncols,i) + # }}} + # {{{ overlay plot + if options.exist('overlay') and overlaysupport: + plot_overlay(md,data,options,ax) + options.addfielddefault('alpha',0.5) + options.addfielddefault('xlim',[min(md.mesh.x),max(md.mesh.x)]) + options.addfielddefault('ylim',[min(md.mesh.y),max(md.mesh.y)]) + # }}} + # {{{ dealing with special plot + if isinstance(data,str): + if data=='mesh': + plot_mesh(md,options,fig,axgrid,gridindex) + #fig.delaxes(fig.axes[1]) # hack to remove colorbar after the fact + return + elif data=='BC': + plot_BC(md,options,fig,axgrid,gridindex) + return + elif data=='elementnumbering': + plot_elementnumbering(md,options,fig,axgrid,gridindex) + return + elif data=='vertexnumbering': + plot_vertexnumbering(md,options,fig,axgrid,gridindex) + return + elif data=='none': + print('no data provided to plot (TODO: write plot_none.py)') + applyoptions(md,[],options,fig,axgrid,gridindex) + return + else: + print("WARNING: '%s' is not implemented or is not a valid string for option 'data'" % data) + # }}} + # {{{ Gridded plot TODO + # }}} + # {{{ Section plot TODO + # }}} + # {{{ Profile plot TODO + # }}} + + #process data and model + x,y,z,elements,is2d,isplanet=processmesh(md,data,options) + data2,datatype=processdata(md,data,options) + #plot unit + plot_unit(x,y,z,elements,data2,is2d,isplanet,datatype,options,fig,axgrid,gridindex) + #apply all options + applyoptions(md,data2,options,fig,axgrid,gridindex) + + #ground overlay on kml plot_unit + + # Bits and pieces #initialize plot handle variable #handle=None @@ -49,54 +106,9 @@ #p.subplot(nrows,ncols,i,aspect='equal') - ##basemap plot - #if options.exist('basemap'): - # plot_basemap(md,data,options,nrows,ncols,i) - - #overlay plot - if options.exist('overlay') and overlaysupport: - plot_overlay(md,data,options,ax) - options.addfielddefault('alpha',0.5) - options.addfielddefault('xlim',[min(md.mesh.x),max(md.mesh.x)]) - options.addfielddefault('ylim',[min(md.mesh.y),max(md.mesh.y)]) - - #figure out if this is a special plot - if isinstance(data,str): - - # convert string to lower case for a case-insensitive comparison - if data.lower()=='mesh': - plot_mesh(md,options,ax) - applyoptions(md,[],options,fig,ax) - fig.delaxes(fig.axes[1]) # hack to remove colorbar after the fact - return - elif data.lower()=='none': - print('no data provided to plot (TODO: write plot_none.py)') - applyoptions(md,[],options,fig,ax) - return - else: - print(("WARNING: '%s' is not implemented or is not a valid string for option 'data'" % data)) + #standard plot + #if not handle: + # p.subplot(nrows,ncols,i,aspect='equal') #elif data in vars(md): #else: #print "'data' not a string, plotting model properties yet to be implemented..." - - #Gridded plot - - #Section plot - - #Profile plot - - #process data and model - x,y,z,elements,is2d,isplanet=processmesh(md,data,options) - data2,datatype=processdata(md,data,options) - - #standard plot - #if not handle: - # p.subplot(nrows,ncols,i,aspect='equal') - - #plot unit - plot_unit(x,y,z,elements,data2,is2d,isplanet,datatype,options,ax) - - #apply all options - applyoptions(md,data2,options,fig,ax) - - #ground overlay on kml plot_unit Index: /issm/trunk-jpl/src/py3/plot/plot_mesh.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_mesh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_mesh.py (revision 23670) @@ -4,8 +4,11 @@ print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") +import numpy as np from processmesh import processmesh from applyoptions import applyoptions - -def plot_mesh(md,options,ax): +from mpl_toolkits.mplot3d.art3d import Line3DCollection +from mpl_toolkits.axes_grid1 import inset_locator +from mpl_toolkits.mplot3d import Axes3D +def plot_mesh(md,options,fig,axgrid,gridindex): ''' PLOT_MESH - plot model mesh @@ -16,14 +19,41 @@ See also: PLOTMODEL ''' + x,y,z,elements,is2d,isplanet=processmesh(md,'mesh',options) - x,y,z,elements,is2d,isplanet=processmesh(md,[],options) - + ax=axgrid[gridindex] + fig.delaxes(axgrid.cbar_axes[gridindex]) + if is2d: ax.triplot(x,y,elements) else: - print('WARNING: only 2D mesh plot is currently implemented') - + ax=inset_locator.inset_axes(axgrid[gridindex],width='100%',height='100%',loc=3,borderpad=0,axes_class=Axes3D) + + AB=elements[:,0:2] + BC=elements[:,1:3] + CA=np.vstack((elements[:,2],elements[:,0])).T + DE=elements[:,3:5] + EF=elements[:,4:] + FD=np.vstack((elements[:,5],elements[:,3])).T + AD=np.vstack((elements[:,0],elements[:,3])).T + BE=np.vstack((elements[:,1],elements[:,4])).T + CF=np.vstack((elements[:,2],elements[:,5])).T + + tmpa=np.vstack((AB,BC,CA,DE,EF,FD,AD,BE,CF)) + #deleting segments that appear multiple times + tmpb = np.ascontiguousarray(tmpa).view(np.dtype((np.void, tmpa.dtype.itemsize * tmpa.shape[1]))) + _, idx = np.unique(tmpb, return_index=True) + triel= tmpa[idx] + + for triangle in triel: + tri=list(zip(x[triangle],y[triangle],z[triangle])) + pl3=Line3DCollection([tri],edgecolor='r') + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) #apply options options.addfielddefault('title','Mesh') options.addfielddefault('colorbar','off') options.addfielddefault('ticklabels','on') + applyoptions(md,[],options,fig,axgrid,gridindex) Index: /issm/trunk-jpl/src/py3/plot/plot_overlay.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_overlay.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_overlay.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy as np +import numpy as np from processmesh import processmesh from processdata import processdata @@ -5,13 +5,11 @@ import matplotlib.pyplot as plt import matplotlib as mpl +import os try: - from mpl_toolkits.basemap import Basemap + from mpl_toolkits.basemap import Basemap except ImportError: - print('Basemap toolkit not installed') - -import os - + print('Basemap toolkit not installed') try: - from osgeo import gdal + from osgeo import gdal except ImportError: print('osgeo/gdal for python not installed, plot_overlay is disabled') @@ -25,24 +23,23 @@ x,y,z,elements,is2d,isplanet=processmesh(md,[],options) - - if data=='none' or data==None: + try: + data,datatype=processdata(md,data,options) + imageonly=0 + except (TypeError,ValueError):#that should catch None and 'none' but may also catch unwanted errors imageonly=1 data=np.float('nan')*np.ones((md.mesh.numberofvertices,)) datatype=1 - else: - imageonly=0 - data,datatype=processdata(md,data,options) if not is2d: raise Exception('overlay plot not supported for 3D meshes, project on a 2D layer first') - if not options.exist('geotiff_name'): - raise Exception('overlay error: provide geotiff_name with path to geotiff file') - geotiff=options.getfieldvalue('geotiff_name') + if not options.exist('overlay_image'): + raise Exception('overlay error: provide overlay_image with path to geotiff file') + image=options.getfieldvalue('overlay_image') xlim=options.getfieldvalue('xlim',[min(md.mesh.x),max(md.mesh.x)]) ylim=options.getfieldvalue('ylim',[min(md.mesh.y),max(md.mesh.y)]) - gtif=gdal.Open(geotiff) + gtif=gdal.Open(image) trans=gtif.GetGeoTransform() xmin=trans[0] @@ -50,6 +47,5 @@ ymin=trans[3]+gtif.RasterYSize*trans[5] ymax=trans[3] - - # allow supplied geotiff to have limits smaller than basemap or model limits + # allow supplied image to have limits smaller than basemap or model limits x0=max(min(xlim),xmin) x1=min(max(xlim),xmax) @@ -57,10 +53,10 @@ y1=min(max(ylim),ymax) inputname='temp.tif' - os.system('gdal_translate -quiet -projwin ' + str(x0) + ' ' + str(y1) + ' ' + str(x1) + ' ' + str(y0) + ' ' + geotiff + ' ' + inputname) - + os.system('gdal_translate -quiet -projwin ' + str(x0) + ' ' + str(y1) + ' ' + str(x1) + ' ' + str(y0) + ' ' + image+ ' ' + inputname) + gtif=gdal.Open(inputname) arr=gtif.ReadAsArray() #os.system('rm -rf ./temp.tif') - + if gtif.RasterCount>=3: # RGB array r=gtif.GetRasterBand(1).ReadAsArray() @@ -84,7 +80,7 @@ plt.hist(arr.flatten(),bins=256,range=(0.,1.)) plt.title('histogram of overlay image, use for setting overlaylims') - plt.show() + plt.show() plt.sca(ax) # return to original axes/figure - + # get parameters from cropped geotiff trans=gtif.GetGeoTransform() @@ -94,6 +90,6 @@ ymax=trans[3] dx=trans[1] - dy=trans[5] - + dy=trans[5] + xarr=np.arange(xmin,xmax,dx) yarr=np.arange(ymin,ymax,-dy) # -dy since origin='upper' (not sure how robust this is) @@ -102,31 +98,35 @@ norm=mpl.colors.Normalize(vmin=overlaylims[0],vmax=overlaylims[1]) + pc=ax.pcolormesh(xg, yg, np.flipud(arr), cmap=mpl.cm.Greys, norm=norm) + if options.exist('basemap'): # create coordinate grid in map projection units (for plotting) - lat,lon=xy2ll(xlim,ylim,-1,0,71) - #plt.sca(ax) - width=xmax-xmin - height=ymax-ymin - lat_0,lon_0=xy2ll(xmin+width/2.,ymin+height/2.,-1,0,71) - m=Basemap(projection='spstere', - llcrnrlon=lon[0],llcrnrlat=lat[0],urcrnrlon=lon[1],urcrnrlat=lat[1], - epsg=3031, - resolution='c') - #width=width,height=height,lon_0=lon_0,lat_0=lat_0, - #lat_0=-90,lon_0=0,lat_ts=-71, - #llcrnrx=x0,llcrnry=y0,urcrnrx=x1,urcrnry=y1) - #test - #m.ax=ax - meridians=np.arange(-180.,181.,1.) - parallels=np.arange(-80.,80.,1.) - m.drawparallels(parallels,labels=[0,0,1,1]) # labels=[left,right,top,bottom] - m.drawmeridians(meridians,labels=[1,1,0,0]) - m.drawcoastlines() - pc=m.pcolormesh(xg, yg, np.flipud(arr), cmap=mpl.cm.Greys, norm=norm, ax=ax) + if md.mesh.epsg==3413: + hemisphere=1 + st_lat=70 + lon_0=45 + elif md.mesh.epsg==3031: + hemisphere=-1 + st_lat=71 + lon_0=0 + else: + hemisphere=input('epsg code {} is not supported chose your hemisphere (1 for North, -1 for south)'.format(mesh.epsg)) - else: - pc=ax.pcolormesh(xg, yg, np.flipud(arr), cmap=mpl.cm.Greys, norm=norm) - - #rasterization? + lat,lon=xy2ll(xlim,ylim,hemisphere,lon_0,st_lat) + extent=[np.diff(xlim)[0],np.diff(ylim)[0]] + center=[lon[0]+np.diff(lon)[0]*0.5,lat[0]+np.diff(lat)[0]*0.5] + m=Basemap(llcrnrlon=lon[0],llcrnrlat=lat[0],urcrnrlon=lon[1],urcrnrlat=lat[1], + lon_0=center[0],lat_0=center[1],#width=extent[0],height=extent[1],# + epsg=md.mesh.epsg,anchor='NW', + resolution='i',ax=ax) + + meridians=np.arange(np.floor(lon[0]),np.ceil(lon[1]),1.) + parallels=np.arange(np.floor(lat[0]),np.ceil(lat[1]),1.) + m.drawparallels(parallels,labels=[1,0,0,0],ax=ax) # labels=[left,right,top,bottom] + m.drawmeridians(meridians,labels=[0,0,1,0],ax=ax) + m.drawcoastlines(ax=ax) + m.drawmapboundary(ax=ax) + + #rasterization? if options.getfieldvalue('rasterized',0): pc.set_rasterized(True) Index: /issm/trunk-jpl/src/py3/plot/plot_streamlines.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_streamlines.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_streamlines.py (revision 23670) @@ -1,13 +1,16 @@ -import numpy as np -import matplotlib.pyplot as plt -import matplotlib.tri as tri +import numpy as np from processmesh import processmesh from processdata import processdata -from scipy.interpolate import griddata from ContourToMesh import ContourToMesh +try: + import matplotlib.pyplot as plt + import matplotlib.tri as tri + from scipy.interpolate import griddata +except ImportError: + print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") def plot_streamlines(md,options,ax): ''' - plot streamlines on a figure, using by default vx and vy components in md.initialization. + plot streamlines on a figure, using by default vx and vy components in md.initialization. Usage: @@ -22,5 +25,5 @@ streamlineswidthscale: scaling multiplier for linewidth scaled by velocity streamlinesarrowsize: size of arrows on lines (default 1) - + ''' @@ -33,5 +36,5 @@ arrowsize=options.getfieldvalue('streamlinesarrowsize',1) - #process mesh and data + #process mesh and data x,y,z,elements,is2d,isplanet=processmesh(md,vx,options) u,datatype=processdata(md,vx,options) Index: /issm/trunk-jpl/src/py3/plot/plot_unit.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plot_unit.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plot_unit.py (revision 23670) @@ -1,92 +1,236 @@ from cmaptools import truncate_colormap +from plot_quiver import plot_quiver +from scipy.interpolate import griddata +import numpy as np try: - import pylab as p - import matplotlib as mpl - import matplotlib.pyplot as plt - import numpy as np + import matplotlib as mpl + import matplotlib.pyplot as plt + from mpl_toolkits.axes_grid1 import inset_locator + from mpl_toolkits.mplot3d import Axes3D + from mpl_toolkits.mplot3d.art3d import Poly3DCollection except ImportError: - print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") - -def plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options,ax): - """ - PLOT_UNIT - unit plot, display data - - Usage: - plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - - See also: PLOTMODEL, PLOT_MANAGER - """ - - #edgecolor - edgecolor=options.getfieldvalue('edgecolor','None') - - #number of colorlevels for plots - colorlevels=options.getfieldvalue('colorlevels',128) - - alpha=options.getfieldvalue('alpha',1) - - #colormap - # default sequential colormap - defaultmap=truncate_colormap(mpl.cm.gnuplot2,0.1,0.9,128) - cmap=options.getfieldvalue('colormap',defaultmap) - if options.exist('cmap_set_over'): - over=options.getfieldvalue('cmap_set_over','0.5') - cmap.set_over(over) - if options.exist('cmap_set_under'): - under=options.getfieldvalue('cmap_set_under','0.5') - cmap.set_under(under) - - #normalize colormap if clim/caxis specified - if options.exist('clim'): - lims=options.getfieldvalue('clim',[np.amin(data),np.amax(data)]) - elif options.exist('caxis'): - lims=options.getfieldvalue('caxis',[np.amin(data),np.amax(data)]) - else: - if np.amin(data)==np.amax(data): - lims=[np.amin(data)-0.5,np.amax(data)+0.5] - else: - lims=[np.amin(data),np.amax(data)] - norm = mpl.colors.Normalize(vmin=lims[0], vmax=lims[1]) - if datatype==1: - #element plot - if is2d: - tri=ax.tripcolor(x,y,elements,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,edgecolors=edgecolor) - else: - raise ValueError('plot_unit error: 3D element plot not supported yet') - return - - elif datatype==2: - #node plot - if is2d: - tri=ax.tricontourf(x,y,elements,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,extend='both') - if edgecolor != 'None': - ax.triplot(x,y,elements,color=edgecolor) - else: - raise ValueError('plot_unit error: 3D node plot not supported yet') - return - - elif datatype==3: - vx=data[:,0] - vy=data[:,1] - #TODO write plot_quiver.py to handle this here - color=np.sqrt(vx**2+vy**2) - scale=options.getfieldvalue('scale',1000) - width=options.getfieldvalue('width',0.005*(np.amax(x)-np.amin(y))) - headwidth=options.getfieldvalue('headwidth',3) - headlength=options.getfieldvalue('headlength',5) - Q=ax.quiver(x,y,vx,vy,color,cmap=cmap,norm=norm,scale=scale, - width=width,headwidth=headwidth,headlength=headlength) - return - - elif datatype==4: - #P1 patch plot - print('plot_unit message: P1 patch plot not implemented yet') - return - - elif datatype==5: - print('plot_unit message: P0 patch plot not implemented yet') - return - - else: - raise ValueError('datatype=%d not supported' % datatype) - + print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") + +def plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options,fig,axgrid,gridindex): + """ + PLOT_UNIT - unit plot, display data + + Usage: + plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) + + See also: PLOTMODEL, PLOT_MANAGER + """ + #if we are plotting 3d replace the current axis + if not is2d: + axgrid[gridindex].axis('off') + ax=inset_locator.inset_axes(axgrid[gridindex],width='100%',height='100%',loc=3,borderpad=0,axes_class=Axes3D) + ax.set_axis_bgcolor((0.7,0.7,0.7)) + else: + ax=axgrid[gridindex] + + #edgecolor + edgecolor=options.getfieldvalue('edgecolor','None') + + # colormap + # {{{ give number of colorlevels and transparency + colorlevels=options.getfieldvalue('colorlevels',128) + alpha=options.getfieldvalue('alpha',1) + if alpha<1: + antialiased=True + else: + antialiased=False + # }}} + # {{{ define wich colormap to use + try: + defaultmap=plt.cm.get_cmap('viridis',colorlevels) + except AttributeError: + print("Viridis can't be found (probably too old Matplotlib) reverting to gnuplot colormap") + defaultmap=truncate_colormap('gnuplot2',0.1,0.9,colorlevels) + cmap=options.getfieldvalue('colormap',defaultmap) + if options.exist('cmap_set_over'): + over=options.getfieldvalue('cmap_set_over','0.5') + cmap.set_over(over) + if options.exist('cmap_set_under'): + under=options.getfieldvalue('cmap_set_under','0.5') + cmap.set_under(under) + options.addfield('colormap',cmap) + # }}} + # {{{ if plotting only one of several layers reduce dataset, same for surface + if options.getfieldvalue('layer',0)>=1: + plotlayer=options.getfieldvalue('layer',0) + if datatype==1: + slicesize=np.shape(elements)[0] + elif datatype in [2,3]: + slicesize=len(x) + data=data[(plotlayer-1)*slicesize:plotlayer*slicesize] + # }}} + # {{{ Get the colormap limits + if options.exist('clim'): + lims=options.getfieldvalue('clim',[np.amin(data),np.amax(data)]) + elif options.exist('caxis'): + lims=options.getfieldvalue('caxis',[np.amin(data),np.amax(data)]) + else: + if np.amin(data)==np.amax(data): + lims=[np.amin(data)-0.5,np.amax(data)+0.5] + else: + lims=[np.amin(data),np.amax(data)] + # }}} + # {{{ Set the spread of the colormap (default is normal + if options.exist('log'): + norm = mpl.colors.LogNorm(vmin=lims[0], vmax=lims[1]) + else: + norm = mpl.colors.Normalize(vmin=lims[0], vmax=lims[1]) + if options.exist('log'): + norm = mpl.colors.LogNorm(vmin=lims[0], vmax=lims[1]) + else: + norm = mpl.colors.Normalize(vmin=lims[0], vmax=lims[1]) + options.addfield('colornorm',norm) + # }}} + + # Plot depending on the datatype + # {{{ data are on elements + + if datatype==1: + if is2d: + if options.exist('mask'): + triangles=mpl.tri.Triangulation(x,y,elements,data.mask) + else: + triangles=mpl.tri.Triangulation(x,y,elements) + tri=ax.tripcolor(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,edgecolors=edgecolor) + else: + #first deal with colormap + loccmap = plt.cm.ScalarMappable(cmap=cmap) + loccmap.set_array([min(data),max(data)]) + loccmap.set_clim(vmin=min(data),vmax=max(data)) + + #dealing with prism sides + recface=np.vstack((elements[:,0],elements[:,1],elements[:,4],elements[:,3])).T + eltind=np.arange(0,np.shape(elements)[0]) + recface=np.vstack((recface,np.vstack((elements[:,1],elements[:,2],elements[:,5],elements[:,4])).T)) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + recface=np.vstack((recface,np.vstack((elements[:,2],elements[:,0],elements[:,3],elements[:,5])).T)) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + tmp = np.ascontiguousarray(np.sort(recface)).view(np.dtype((np.void, recface.dtype.itemsize * recface.shape[1]))) + _, idx, recur = np.unique(tmp, return_index=True, return_counts=True) + recel= recface[idx[np.where(recur==1)]] + recindex=eltind[idx[np.where(recur==1)]] + for i,rectangle in enumerate(recel): + rec=list(zip(x[rectangle],y[rectangle],z[rectangle])) + pl3=Poly3DCollection([rec]) + color=loccmap.to_rgba(data[recindex[i]]) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + #dealing with prism bases + triface=np.vstack((elements[:,0:3],elements[:,3:6])) + eltind=np.arange(0,np.shape(elements)[0]) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + tmp = np.ascontiguousarray(triface).view(np.dtype((np.void, triface.dtype.itemsize * triface.shape[1]))) + _, idx,recur = np.unique(tmp, return_index=True,return_counts=True) + #we keep only top and bottom elements + triel= triface[idx[np.where(recur==1)]] + triindex=eltind[idx[np.where(recur==1)]] + for i,triangle in enumerate(triel): + tri=list(zip(x[triangle],y[triangle],z[triangle])) + pl3=Poly3DCollection([tri]) + color=loccmap.to_rgba(data[triindex[i]]) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) + + #raise ValueError('plot_unit error: 3D element plot not supported yet') + return + + # }}} + # {{{ data are on nodes + + elif datatype==2: + if is2d: + if np.ma.is_masked(data): + EltMask=np.asarray([np.any(np.in1d(index,np.where(data.mask))) for index in elements]) + triangles=mpl.tri.Triangulation(x,y,elements,EltMask) + else: + triangles=mpl.tri.Triangulation(x,y,elements) + #tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) + if options.exist('log'): + if alpha<1:#help with antialiasing + tri=ax.tricontour(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=0.1,antialiased=antialiased) + tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,antialiased=antialiased) + else: + if alpha<1:#help with antialiasing + tri=ax.tricontour(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=0.1,antialiased=antialiased) + tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,extend='both',antialiased=antialiased) + if edgecolor != 'None': + ax.triplot(x,y,elements,color=edgecolor) + else: + #first deal with the colormap + loccmap = plt.cm.ScalarMappable(cmap=cmap) + loccmap.set_array([min(data),max(data)]) + loccmap.set_clim(vmin=min(data),vmax=max(data)) + + #deal with prism sides + recface=np.vstack((elements[:,0],elements[:,1],elements[:,4],elements[:,3])).T + recface=np.vstack((recface,np.vstack((elements[:,1],elements[:,2],elements[:,5],elements[:,4])).T)) + recface=np.vstack((recface,np.vstack((elements[:,2],elements[:,0],elements[:,3],elements[:,5])).T)) + tmp = np.ascontiguousarray(np.sort(recface)).view(np.dtype((np.void, recface.dtype.itemsize * recface.shape[1]))) + _, idx, recur = np.unique(tmp, return_index=True, return_counts=True) + recel= recface[idx[np.where(recur==1)]] + for rectangle in recel: + rec=list(zip(x[rectangle],y[rectangle],z[rectangle])) + pl3=Poly3DCollection([rec]) + color=loccmap.to_rgba(np.mean(data[rectangle])) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + #deal with prism faces + triface=np.vstack((elements[:,0:3],elements[:,3:6])) + tmp = np.ascontiguousarray(triface).view(np.dtype((np.void, triface.dtype.itemsize * triface.shape[1]))) + _, idx,recur = np.unique(tmp, return_index=True,return_counts=True) + #we keep only top and bottom elements + triel= triface[idx[np.where(recur==1)]] + for triangle in triel: + tri=list(zip(x[triangle],y[triangle],z[triangle])) + pl3=Poly3DCollection([tri]) + color=loccmap.to_rgba(np.mean(data[triangle])) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) + #raise ValueError('plot_unit error: 3D element plot not supported yet') + return + + # }}} + # {{{ plotting quiver + elif datatype==3: + if is2d: + Q=plot_quiver(x,y,data,options,ax) + else: + raise ValueError('plot_unit error: 3D node plot not supported yet') + return + + # }}} + # {{{ plotting P1 Patch (TODO) + + elif datatype==4: + print('plot_unit message: P1 patch plot not implemented yet') + return + + # }}} + # {{{ plotting P0 Patch (TODO) + + elif datatype==5: + print('plot_unit message: P0 patch plot not implemented yet') + return + + # }}} + else: + raise ValueError('datatype=%d not supported' % datatype) Index: /issm/trunk-jpl/src/py3/plot/plotmodel.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/plotmodel.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/plotmodel.py (revision 23670) @@ -1,4 +1,7 @@ -import numpy as np +import numpy as np from plotoptions import plotoptions +from plotdoc import plotdoc +from plot_manager import plot_manager +from math import ceil, sqrt try: @@ -6,21 +9,17 @@ import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import ImageGrid, AxesGrid + from mpl_toolkits.mplot3d import Axes3D except ImportError: print("could not import pylab, matplotlib has not been installed, no plotting capabilities enabled") -from plot_manager import plot_manager -from math import ceil, sqrt - def plotmodel(md,*args): - ''' - at command prompt, type 'plotdoc' for additional documentation + ''' at command prompt, type 'plotdoc()' for additional documentation ''' - #First process options + #First process options options=plotoptions(*args) #get number of subplots subplotwidth=ceil(sqrt(options.numberofplots)) - #Get figure number and number of plots figurenumber=options.figurenumber @@ -37,5 +36,5 @@ nrows=np.ceil(numberofplots/subplotwidth) nr=False - + if options.list[0].exist('ncols'): ncols=options.list[0].getfieldvalue('ncols') @@ -46,12 +45,11 @@ ncols=int(ncols) nrows=int(nrows) - + #check that nrows and ncols were given at the same time! if not nr==nc: raise Exception('error: nrows and ncols need to be specified together, or not at all') - + #Go through plots if numberofplots: - #if plt.fignum_exists(figurenumber): # plt.cla() @@ -60,22 +58,32 @@ if options.list[0].exist('figsize'): figsize=options.list[0].getfieldvalue('figsize') - fig=plt.figure(figurenumber,figsize=(figsize[0],figsize[1]),tight_layout=True) + fig=plt.figure(figurenumber,figsize=(figsize[0],figsize[1]))#,tight_layout=True) else: - fig=plt.figure(figurenumber,tight_layout=True) + fig=plt.figure(figurenumber)#,tight_layout=True) fig.clf() + backgroundcolor=options.list[0].getfieldvalue('backgroundcolor',(0.7,0.7,0.7)) + fig.set_facecolor(backgroundcolor) + + + translator={'on':'each', + 'off':'None', + 'one':'single'} # options needed to define plot grid + plotnum=options.numberofplots direction=options.list[0].getfieldvalue('direction','row') # row,column axes_pad=options.list[0].getfieldvalue('axes_pad',0.25) add_all=options.list[0].getfieldvalue('add_all',True) # True,False share_all=options.list[0].getfieldvalue('share_all',True) # True,False - label_mode=options.list[0].getfieldvalue('label_mode','1') # 1,L,all - cbar_mode=options.list[0].getfieldvalue('cbar_mode','each') # none,single,each - cbar_location=options.list[0].getfieldvalue('cbar_location','right') # right,top - cbar_size=options.list[0].getfieldvalue('cbar_size','5%') - cbar_pad=options.list[0].getfieldvalue('cbar_pad','2.5%') # None or % - - axgrid=ImageGrid(fig, 111, + label_mode=options.list[0].getfieldvalue('label_mode','L') # 1,L,all + colorbar=options.list[0].getfieldvalue('colorbar','on') # on, off (single) + cbar_mode=translator[colorbar] + cbar_location=options.list[0].getfieldvalue('colorbarpos','right') # right,top + cbar_size=options.list[0].getfieldvalue('colorbarsize','5%') + cbar_pad=options.list[0].getfieldvalue('colorbarpad','2.5%') # None or % + + axgrid=ImageGrid(fig,111, nrows_ncols=(nrows,ncols), + ngrids=plotnum, direction=direction, axes_pad=axes_pad, @@ -86,13 +94,12 @@ cbar_location=cbar_location, cbar_size=cbar_size, - cbar_pad=cbar_pad - ) + cbar_pad=cbar_pad) - if cbar_mode=='none': - for ax in axgrid.cbar_axes: fig._axstack.remove(ax) + if cbar_mode=='None': + for ax in axgrid.cbar_axes: + fig._axstack.remove(ax) - for i in range(numberofplots): - plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],fig,axgrid[i]) - + for i,ax in enumerate(axgrid.axes_all): + plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],fig,axgrid,i) fig.show() else: Index: /issm/trunk-jpl/src/py3/plot/processdata.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/processdata.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/processdata.py (revision 23670) @@ -1,108 +1,138 @@ -from math import isnan -import numpy as np +import numpy as np def processdata(md,data,options): - """ - PROCESSDATA - process data to be plotted + """ + PROCESSDATA - process data to be plotted + + datatype = 1 -> elements + datatype = 2 -> nodes + datatype = 3 -> node quivers + datatype = 4 -> patch + + Usage: + data,datatype=processdata(md,data,options); + + See also: PLOTMODEL, PROCESSMESH + """ + # {{{ Initialisation and grabbing auxiliaries + # check format + if (len(data)==0 or (len(data)==1 and not isinstance(data,dict) and np.isnan(data).all())): + raise ValueError("processdata error message: 'data' provided is empty") + # get the shape + if 'numberofvertices2d' in dir(md.mesh): + numberofvertices2d=md.mesh.numberofvertices2d + numberofelements2d=md.mesh.numberofelements2d + else: + numberofvertices2d=np.nan + numberofelements2d=np.nan + procdata=np.copy(data) + #initialize datatype + datatype=0 + # get datasize + if np.ndim(procdata)==1: + datasize=(np.shape(procdata)[0],1) + elif np.ndim(procdata)==2: + datasize=np.shape(procdata) + elif np.ndim(procdata)==3: + if np.shape(procdata)[0]==2: + #treating a dim two list that needs to be stacked + procdata=np.hstack((procdata[0,:,:],procdata[1,:,:])) + datasize=np.shape(procdata) + else: + raise ValueError('data list contains more than two vectore, we can not cope with that') + else: + raise ValueError('data passed to plotmodel has bad dimensions; check that column vectors are rank-1') + # }}} + # {{{ process NaN's if any + nanfill=options.getfieldvalue('nan',-9999) + if np.any(np.isnan(procdata)): + lb=np.nanmin(procdata) + ub=np.nanmax(procdata) + if lb==ub: + lb=lb-0.5 + ub=ub+0.5 + nanfill=lb-1 + #procdata[np.isnan(procdata)]=nanfill + procdata=np.ma.array(procdata,mask=np.isnan(procdata)) + options.addfielddefault('clim',[lb,ub]) + options.addfielddefault('cmap_set_under','1') + print("WARNING: nan's treated as", nanfill, "by default. Change using pairoption 'nan',nan_fill_value in plotmodel call") + # }}} + # {{{ log + if options.exist('log'): + cutoff=options.getfieldvalue('log',1) + procdata[np.where(procdata1 and datasize[0]!= md.mesh.numberofvertices+1: + if datasize[0]==md.mesh.numberofvertices and datasize[1]==2: + datatype=3 + else: + raise ValueError('plotmodel error message: data should have two columns of length md.mesh.numberofvertices for a quiver plot') + # }}} + # {{{ element data + + if datasize[0]==md.mesh.numberofelements and datasize[1]==1: + #initialize datatype if non patch + if datatype!=4 and datatype!=5: + datatype=1 + # {{{mask + if options.exist('mask'): + flags=options.getfieldvalue('mask') + hide=np.invert(flags) + if np.size(flags)==md.mesh.numberofvertices: + EltMask=np.asarray([np.any(np.in1d(index,np.where(hide))) for index in md.mesh.elements-1]) + procdata=np.ma.array(procdata,mask=EltMask) + options.addfielddefault('cmap_set_bad','w') + elif np.size(flags)==md.mesh.numberofelements: + procdata=np.ma.array(procdata,mask=hide) + options.addfielddefault('cmap_set_bad','w') + else: + print('plotmodel warning: mask length not supported yet (supported length are md.mesh.numberofvertices and md.mesh.numberofelements') + # }}} + + # }}} + # {{{ node data + if datasize[0]==md.mesh.numberofvertices and datasize[1]==1: + datatype=2 + # {{{ Mask + if options.exist('mask'): + flags=options.getfieldvalue('mask') + hide=np.invert(flags) + if np.size(flags)==md.mesh.numberofvertices: + procdata=np.ma.array(procdata,mask=hide) + options.addfielddefault('cmap_set_bad','w') + elif np.size(flags)==md.mesh.numberofelements: + NodeMask=np.zeros(np.shape(md.mesh.x),dtype=bool) + HideElt=md.mesh.elements[np.where(hide)[0]]-1 + NodeMask[HideElt]=True + procdata=np.ma.array(procdata,mask=NodeMask) + options.addfielddefault('cmap_set_bad','w') + else: + print('plotmodel warning: mask length not supported yet (supported length are md.mesh.numberofvertices and md.mesh.numberofelements') + # }}} + # }}} + # {{{ spc time series + if datasize[0]==md.mesh.numberofvertices+1: + datatype=2 + spccol=options.getfieldvalue('spccol',0) + print('multiple-column spc field; specify column to plot using option "spccol"') + print('column ', spccol, ' plotted for time: ', procdata[-1,spccol]) + procdata=procdata[0:-1,spccol] - datatype = 1 -> elements - datatype = 2 -> nodes - datatype = 3 -> node quivers - datatype = 4 -> patch - - Usage: - data,datatype=processdata(md,data,options); - - See also: PLOTMODEL, PROCESSMESH - """ - - #check format - if (len(data)==0 or (len(data)==1 and not isinstance(data,dict) and isnan(data).all())): - raise ValueError("processdata error message: 'data' provided is empty") - - #needed later on - if 'numberofvertices2d' in dir(md.mesh): - numberofvertices2d=md.mesh.numberofvertices2d - numberofelements2d=md.mesh.numberofelements2d - else: - numberofvertices2d=np.nan - numberofelements2d=np.nan - - procdata=np.copy(data) - - #process patch - - #initialize datatype - datatype=0 - - #get datasize - if np.ndim(procdata)==1: - datasize=np.array([len(procdata),1]) - else: - datasize=np.shape(procdata) - if len(datasize)>2: - raise ValueError('data passed to plotmodel has more than 2 dimensions; check that column vectors are rank-1') - - #process NaN's if any - nanfill=options.getfieldvalue('nan',-9999) - if np.any(np.isnan(procdata)): - lb=np.min(data[~np.isnan(data)]) - ub=np.max(data[~np.isnan(data)]) - if lb==ub: - lb=lb-0.5 - ub=ub+0.5 - nanfill=lb-1 - procdata[np.isnan(procdata)]=nanfill - options.addfielddefault('clim',[lb,ub]) - options.addfielddefault('cmap_set_under','1') - print(("WARNING: nan's treated as", nanfill, "by default. Change using pairoption 'nan',nan_fill_value in plotmodel call")) - - #quiver plot - if datasize[1]>1 and datasize[0]!= md.mesh.numberofvertices+1: - if datasize[0]==md.mesh.numberofvertices and datasize[1]==2: - datatype=3 - else: - raise ValueError('plotmodel error message: data should have two columns of length md.mesh.numberofvertices for a quiver plot') - - #non-patch processing - - #element data - if datasize[0]==md.mesh.numberofelements and datasize[1]==1: - - #initialize datatype if non patch - if datatype!=4 and datatype!=5: - datatype=1 - - #mask? - - #log? - - #node data - if datasize[0]==md.mesh.numberofvertices and datasize[1]==1: - datatype=2 - - #spc time series? - if datasize[0]==md.mesh.numberofvertices+1: - datatype=2 - spccol=options.getfieldvalue('spccol',0) - print('multiple-column spc field; specify column to plot using option "spccol"') - print(('column ', spccol, ' plotted for time: ', procdata[-1,spccol])) - procdata=procdata[0:-1,spccol] - - #mask? - - #log? + #mask? #layer projection? #control arrow density if quiver plot - - #convert rank-2 array to rank-1 - if np.ndim(procdata)==2 and np.shape(procdata)[1]==1: - procdata=procdata.reshape(-1,) - - #if datatype is still zero, error out - if datatype==0: - raise ValueError("processdata error: data provided not recognized or not supported") - else: - return procdata, datatype + # }}} + # {{{ convert rank-2 array to rank-1 + if np.ndim(procdata)==2 and np.shape(procdata)[1]==1: + procdata=procdata.reshape(-1,) + # }}} + # {{{ if datatype is still zero, error out + if datatype==0: + raise ValueError("processdata error: data provided not recognized or not supported") + else: + return procdata, datatype + # }}} Index: /issm/trunk-jpl/src/py3/plot/processmesh.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/processmesh.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/processmesh.py (revision 23670) @@ -1,71 +1,47 @@ from math import isnan -import MatlabFuncs as m -import numpy as np +import numpy as np def processmesh(md,data,options): """ PROCESSMESH - process the mesh for plotting - + Usage: - x,y,z,elements,is2d=processmech(md,data,options) - + x,y,z,elements,is2d=processmech(md,data,options) + See also: PLOTMODEL, PROCESSDATA """ - - #some checks + + # {{{ check mesh size parameters if md.mesh.numberofvertices==0: raise ValueError('processmesh error: mesh is empty') if md.mesh.numberofvertices==md.mesh.numberofelements: raise ValueError('processmesh error: the number of elements is the same as the number of nodes') + # }}} + # {{{ treating coordinates - if len(data)==0 or not isinstance(data,dict): + try: + z=md.mesh.z + except AttributeError: + z=np.zeros(np.shape(md.mesh.x)) + elements=md.mesh.elements-1 + + if options.getfieldvalue('layer',0)>=1: + x=md.mesh.x2d + y=md.mesh.y2d + z=np.zeros(np.shape(x)) + elements=md.mesh.elements2d-1 + elif 'latlon' in options.getfieldvalue('coord','xy'): + x=md.mesh.long + y=md.mesh.lat + else: + x=md.mesh.x + y=md.mesh.y + + #is it a 2D plot? + if md.mesh.dimension()==2 or options.getfieldvalue('layer',0)>=1: + is2d=1 + else: + is2d=0 - if 'latlon' not in options.getfieldvalue('coord','xy').lower(): #convert to lower case for comparison - x=md.mesh.x - if 'x2d' in dir(md.mesh): x2d=md.mesh.x2d - y=md.mesh.y - if 'y2d' in dir(md.mesh): y2d=md.mesh.x2d - else: - x=md.mesh.long - y=md.mesh.lat - - if 'z' in dir(md.mesh): - z=md.mesh.z - else: - z=np.zeros_like(md.mesh.x) - - if 'elements2d' in dir(md.mesh): - elements2d=md.mesh.elements2d - elements2d=elements2d-1 # subtract one since python indexes from zero - elements=md.mesh.elements - elements=elements-1 - - #is it a 2D plot? - if md.mesh.dimension()==2: - is2d=1 - else: - if options.getfieldvalue('layer',0)>=1: - is2d=1 - else: - is2d=0 - - #layer projection? - if options.getfieldvalue('layer',0)>=1: - if 'latlon' in options.getfieldvalue('coord','xy').lower(): - raise ValueError('processmesh error: cannot work with 3D mesh in lat-lon coords') - #we modify the mesh temporarily to a 2D mesh from which the 3D mesh was extruded - x=x2d - y=y2d - z=zeros(size(x2d)) - elements=elements2d - - else: - #Process mesh for plotting - if md.mesh.dimension()==2: - is2d=1 - else: - # process polycollection here for 3D plot - is2d=0 - #units if options.exist('unit'): Index: /issm/trunk-jpl/src/py3/plot/writejsfield.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/writejsfield.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/writejsfield.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np def writejsfield(fid,name,variable,nods): #WRITEJSFIELD - write variable to javascript file @@ -8,5 +8,5 @@ #write array: #if not isinstance(variable, list): - if type(variable[0])==numpy.float64: + if type(variable[0])==np.float64: fid.write('\n'.format(name)) fid.write('{0}=['.format(name)) Index: /issm/trunk-jpl/src/py3/plot/writejsfile.py =================================================================== --- /issm/trunk-jpl/src/py3/plot/writejsfile.py (revision 23669) +++ /issm/trunk-jpl/src/py3/plot/writejsfile.py (revision 23670) @@ -1,3 +1,3 @@ -import numpy +import numpy as np from writejsfield import writejsfield def writejsfile(filename,model,keyname): @@ -48,5 +48,5 @@ fid.write('result["shortlabel"]="{0}";\n'.format(results[i].shortlabel)) fid.write('result["unit"]="{0}";\n'.format(results[i].unit)) - if type(results[i].data)==numpy.float64: + if type(results[i].data)==np.float64: fid.write('result["time_range"]=[{0},{1}];\n'.format(results[i].time_range[0],results[i].time_range[1])) fid.write('results["{0}"]=result;\n'.format(i)) Index: /issm/trunk-jpl/src/py3/shp/shp2exp.py =================================================================== --- /issm/trunk-jpl/src/py3/shp/shp2exp.py (revision 23669) +++ /issm/trunk-jpl/src/py3/shp/shp2exp.py (revision 23670) @@ -33,5 +33,5 @@ geom=shp.shapes()[i].shapeType if geom==5: # polygon - expdict['closed']=1 + expdict['closed']=1 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -39,5 +39,5 @@ y.append(tmpy) elif geom==3: # line - expdict['closed']=0 + expdict['closed']=0 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -45,5 +45,5 @@ y.append(tmpy) elif geom==1: # point - expdict['closed']=0 + expdict['closed']=0 x.append(shp.shapes()[i].points[0][0]) y.append(shp.shapes()[i].points[0][1]) Index: /issm/trunk-jpl/src/py3/solve/WriteData.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/WriteData.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/WriteData.py (revision 23670) @@ -1,14 +1,11 @@ -import numpy -import math +import numpy as np import struct import pairoptions import MatlabFuncs as m -from EnumDefinitions import * -from EnumToString import EnumToString - -def WriteData(fid,**kwargs): + +def WriteData(fid,prefix,*args): """ WRITEDATA - write model field in binary file - + Usage: WriteData(fid,varargin) @@ -16,5 +13,5 @@ #process options - options=pairoptions.pairoptions(**kwargs) + options=pairoptions.pairoptions(*args) #Get data properties @@ -24,13 +21,14 @@ fieldname = options.getfieldvalue('fieldname') classname = options.getfieldvalue('class',str(type(obj)).rsplit('.')[-1].split("'")[0]) - if options.exist('enum'): - enum = options.getfieldvalue('enum') - else: - enum = BuildEnum(classname+'_'+fieldname) - data = getattr(obj,fieldname) + name = options.getfieldvalue('name',prefix+'.'+fieldname); + if options.exist('data'): + data = options.getfieldvalue('data') + else: + data = getattr(obj,fieldname) else: #No processing required data = options.getfieldvalue('data') - enum = options.getfieldvalue('enum') + name = options.getfieldvalue('name') + format = options.getfieldvalue('format') mattype = options.getfieldvalue('mattype',0) #only required for matrices @@ -44,31 +42,31 @@ #Scale data if necesarry if options.exist('scale'): + data=np.array(data) scale = options.getfieldvalue('scale') - if numpy.size(data) > 1 : - if numpy.size(data,0)==timeserieslength: - data=numpy.array(data) - data[0:-1,:] = scale*data[0:-1,:] - else: - data = scale*data + if np.size(data) > 1 and np.ndim(data) > 1 and np.size(data,0)==timeserieslength: + data[0:-1,:] = scale*data[0:-1,:] else: data = scale*data - if numpy.size(data) > 1 : - if numpy.size(data,0)==timeserieslength: - yts=365.0*24.0*3600.0 + if np.size(data) > 1 and np.size(data,0)==timeserieslength: + yts = options.getfieldvalue('yts') + if np.ndim(data) > 1: data[-1,:] = yts*data[-1,:] + else: + data[-1] = yts*data[-1] #Step 1: write the enum to identify this record uniquely - fid.write(struct.pack('i',enum)) + fid.write(struct.pack('i',len(name))) + fid.write(struct.pack('%ds' % len(name),name)) #Step 2: write the data itself. if m.strcmpi(format,'Boolean'): # {{{ # if len(data) !=1: -# raise ValueError('field %s cannot be marshalled as it has more than one element!' % EnumToString(enum)[0]) +# raise ValueError('field %s cannot be marshalled as it has more than one element!' % name[0]) #first write length of record fid.write(struct.pack('i',4+4)) #1 bool (disguised as an int)+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer @@ -78,28 +76,28 @@ elif m.strcmpi(format,'Integer'): # {{{ # if len(data) !=1: -# raise ValueError('field %s cannot be marshalled as it has more than one element!' % EnumToString(enum)[0]) +# raise ValueError('field %s cannot be marshalled as it has more than one element!' % name[0]) #first write length of record fid.write(struct.pack('i',4+4)) #1 integer + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer - fid.write(struct.pack('i',data)) + fid.write(struct.pack('i',data)) # }}} elif m.strcmpi(format,'Double'): # {{{ # if len(data) !=1: -# raise ValueError('field %s cannot be marshalled as it has more than one element!' % EnumToString(enum)[0]) +# raise ValueError('field %s cannot be marshalled as it has more than one element!' % name[0]) #first write length of record fid.write(struct.pack('i',8+4)) #1 double+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write double - fid.write(struct.pack('d',data)) + fid.write(struct.pack('d',data)) # }}} @@ -108,10 +106,10 @@ fid.write(struct.pack('i',len(data)+4+4)) #string + string size + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write string - fid.write(struct.pack('i',len(data))) - fid.write(struct.pack('%ds' % len(data),data)) + fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('%ds' % len(data),data)) # }}} @@ -119,10 +117,10 @@ if isinstance(data,bool): - data=numpy.array([data]) + data=np.array([data]) elif isinstance(data,(list,tuple)): - data=numpy.array(data).reshape(-1,1) - if numpy.ndim(data) == 1: - if numpy.size(data): - data=data.reshape(numpy.size(data),1) + data=np.array(data).reshape(-1,) + if np.ndim(data) == 1: + if np.size(data): + data=data.reshape(np.size(data),) else: data=data.reshape(0,0) @@ -131,20 +129,26 @@ s=data.shape #if matrix = NaN, then do not write anything - if s[0]==1 and s[1]==1 and math.isnan(data[0][0]): + if np.ndim(data)==2 and np.product(s)==1 and np.all(np.isnan(data)): s=(0,0) #first write length of record - fid.write(struct.pack('i',4+4+8*s[0]*s[1]+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type + + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) - for i in range(s[0]): - for j in range(s[1]): - fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose + if np.ndim(data)==1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + for i in range(s[0]): + fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose + else: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + for i in range(s[0]): + for j in range(s[1]): + fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose # }}} @@ -152,10 +156,10 @@ if isinstance(data,int): - data=numpy.array([data]) + data=np.array([data]) elif isinstance(data,(list,tuple)): - data=numpy.array(data).reshape(-1,1) - if numpy.ndim(data) == 1: - if numpy.size(data): - data=data.reshape(numpy.size(data),1) + data=np.array(data).reshape(-1,) + if np.ndim(data) == 1: + if np.size(data): + data=data.reshape(np.size(data),) else: data=data.reshape(0,0) @@ -164,20 +168,26 @@ s=data.shape #if matrix = NaN, then do not write anything - if s[0]==1 and s[1]==1 and math.isnan(data[0][0]): + if np.ndim(data)==2 and np.product(s)==1 and np.all(np.isnan(data)): s=(0,0) #first write length of record - fid.write(struct.pack('i',4+4+8*s[0]*s[1]+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type + + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) - for i in range(s[0]): - for j in range(s[1]): - fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose + if np.ndim(data) == 1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + for i in range(s[0]): + fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose + else: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + for i in range(s[0]): + for j in range(s[1]): + fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose # }}} @@ -185,10 +195,10 @@ if isinstance(data,(bool,int,float)): - data=numpy.array([data]) + data=np.array([data]) elif isinstance(data,(list,tuple)): - data=numpy.array(data).reshape(-1,1) - if numpy.ndim(data) == 1: - if numpy.size(data): - data=data.reshape(numpy.size(data),1) + data=np.array(data).reshape(-1,) + if np.ndim(data) == 1: + if np.size(data): + data=data.reshape(np.size(data),) else: data=data.reshape(0,0) @@ -197,24 +207,100 @@ s=data.shape #if matrix = NaN, then do not write anything - if s[0]==1 and s[1]==1 and math.isnan(data[0][0]): + 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*s[0]*s[1]+4+4; #2 integers (32 bits) + the double matrix + code + matrix type - if recordlength > 2**31 : - raise ValueError('field %s cannot be marshalled because it is larger than 4^31 bytes!' % EnumToString(enum)[0]) + recordlength=4+4+8*np.product(s)+4+4; #2 integers (32 bits) + the double matrix + code + matrix type + if recordlength > 4**31 : + raise ValueError('field %s cannot be marshalled because it is larger than 4^31 bytes!' % enum) fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) - for i in range(s[0]): + if np.ndim(data) == 1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + for i in range(s[0]): + fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose + else: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + for i in range(s[0]): + for j in range(s[1]): + fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose + # }}} + + elif m.strcmpi(format,'CompressedMat'): # {{{ + + if isinstance(data,(bool,int,float)): + data=np.array([data]) + elif isinstance(data,(list,tuple)): + data=np.array(data).reshape(-1,) + if np.ndim(data) == 1: + if np.size(data): + data=data.reshape(np.size(data),) + else: + data=data.reshape(0,0) + + #Get size + s=data.shape + if np.ndim(data) == 1: + n2=1 + else: + n2=s[1] + + #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 + if recordlength > 4**31 : + raise ValueError('field %s cannot be marshalled because it is larger than 4^31 bytes!' % enum) + + fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the matrix + code + matrix type + + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',mattype)) + + #Write offset and range + A = data[0:s[0]-1] + offsetA = A.min() + rangeA = A.max() - offsetA + + if rangeA == 0: + A = A*0 + else: + A = (A-offsetA)/rangeA*255. + + #now write matrix + if np.ndim(data) == 1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + fid.write(struct.pack('d',float(offsetA))) + fid.write(struct.pack('d',float(rangeA))) + for i in range(s[0]-1): + fid.write(struct.pack('B',int(A[i]))) + + fid.write(struct.pack('d',float(data[s[0]-1]))) #get to the "c" convention, hence the transpose + + elif np.product(s) > 0: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('d',float(offsetA))) + fid.write(struct.pack('d',float(rangeA))) + for i in range(s[0]-1): + for j in range(s[1]): + fid.write(struct.pack('B',int(A[i][j]))) #get to the "c" convention, hence the transpose + for j in range(s[1]): - fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose + fid.write(struct.pack('d',float(data[s[0]-1][j]))) + # }}} @@ -225,40 +311,46 @@ for matrix in data: if isinstance(matrix,(bool,int,float)): - matrix=numpy.array([matrix]) + matrix=np.array([matrix]) elif isinstance(matrix,(list,tuple)): - matrix=numpy.array(matrix).reshape(-1,1) - if numpy.ndim(matrix) == 1: - if numpy.size(matrix): - matrix=matrix.reshape(numpy.size(matrix),1) + matrix=np.array(matrix).reshape(-1,) + if np.ndim(matrix) == 1: + if np.size(matrix): + matrix=matrix.reshape(np.size(matrix),) else: matrix=matrix.reshape(0,0) s=matrix.shape - recordlength+=4*2+s[0]*s[1]*8 #row and col of matrix + matrix of doubles + recordlength+=4*2+np.product(s)*8 #row and col of matrix + matrix of doubles #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #write data, first number of records - fid.write(struct.pack('i',len(data))) - - #write each matrix: + fid.write(struct.pack('i',len(data))) + for matrix in data: if isinstance(matrix,(bool,int,float)): - matrix=numpy.array([matrix]) + matrix=np.array([matrix]) elif isinstance(matrix,(list,tuple)): - matrix=numpy.array(matrix).reshape(-1,1) - if numpy.ndim(matrix) == 1: - matrix=matrix.reshape(numpy.size(matrix),1) + matrix=np.array(matrix).reshape(-1,) + if np.ndim(matrix) == 1: + matrix=matrix.reshape(np.size(matrix),) s=matrix.shape - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) - for i in range(s[0]): - for j in range(s[1]): - fid.write(struct.pack('d',float(matrix[i][j]))) + + if np.ndim(matrix) == 1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + for i in range(s[0]): + fid.write(struct.pack('d',float(matrix[i]))) #get to the "c" convention, hence the transpose + else: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + for i in range(s[0]): + for j in range(s[1]): + fid.write(struct.pack('d',float(matrix[i][j]))) # }}} @@ -271,49 +363,26 @@ #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write length of string array - fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('i',len(data))) #now write the strings for string in data: - fid.write(struct.pack('i',len(string))) - fid.write(struct.pack('%ds' % len(string),string)) + fid.write(struct.pack('i',len(string))) + fid.write(struct.pack('%ds' % len(string),string)) # }}} else: # {{{ - raise TypeError('WriteData error message: data type: %d not supported yet! (%s)' % (format,EnumToString(enum)[0])) + raise TypeError('WriteData error message: data type: %d not supported yet! (%s)' % (format,enum)) # }}} - -def BuildEnum(string): # {{{ - """ - BUILDENUM - build enum out of string - - Usage: - enum=BuildEnum(string) - """ - - if '_' in string: - substrs=string.split('_') - string='' - for substr in substrs: - string+=substr[0].upper()+substr[1:] - else: - #take first letter of string and make it uppercase: - string=string[0].upper()+string[1:] - - #Get Enum - enum=StringToEnum(string)[0] - - return enum -# }}} def FormatToCode(format): # {{{ """ - This routine takes the format string, and hardcodes it into an integer, which - is passed along the record, in order to identify the nature of the dataset being + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being sent. """ @@ -337,4 +406,6 @@ elif m.strcmpi(format,'StringArray'): code=9 + elif m.strcmpi(format,'CompressedMat'): + code=10 else: raise InputError('FormatToCode error message: data type not supported yet!') @@ -342,3 +413,2 @@ return code # }}} - Index: /issm/trunk-jpl/src/py3/solve/loadresultsfromcluster.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/loadresultsfromcluster.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/loadresultsfromcluster.py (revision 23670) @@ -3,4 +3,6 @@ import platform from loadresultsfromdisk import loadresultsfromdisk + +from helpers import * def loadresultsfromcluster(md,runtimename=False): @@ -23,6 +25,6 @@ filelist.append(md.miscellaneous.name+'.qmu.err') filelist.append(md.miscellaneous.name+'.qmu.out') - if 'tabular_graphics_data' in md.qmu.params: - if md.qmu.params['tabular_graphics_data']: + if 'tabular_graphics_data' in fieldnames(md.qmu.params): + if md.qmu.params.tabular_graphics_data: filelist.append('dakota_tabular.dat') else: @@ -31,9 +33,21 @@ #If we are here, no errors in the solution sequence, call loadresultsfromdisk. - md=loadresultsfromdisk(md,md.miscellaneous.name+'.outbin') - + if os.path.exists(md.miscellaneous.name+'.outbin'): + if os.path.getsize(md.miscellaneous.name+'.outbin')>0: + md=loadresultsfromdisk(md,md.miscellaneous.name+'.outbin') + else: + print('WARNING, outbin file is empty for run '+md.miscellaneous.name) + elif not md.qmu.isdakota: + print('WARNING, outbin file does not exist '+md.miscellaneous.name) + #erase the log and output files if md.qmu.isdakota: - filename=os.path.join('qmu'+str(os.getpid()),md.miscellaneous.name) + #filename=os.path.join('qmu'+str(os.getpid()),md.miscellaneous.name) + filename = md.miscellaneous.name + + # this will not work like normal as dakota doesn't generate outbin files, + # instead calls postqmu to store results directly in the model + # at md.results.dakota via dakota_out_parse + md=loadresultsfromdisk(md,md.miscellaneous.name+'.outbin') else: filename=md.miscellaneous.name @@ -49,5 +63,6 @@ if hostname==cluster.name: if md.qmu.isdakota: - filename=os.path.join('qmu'+str(os.getpid()),md.miscellaneous.name) + #filename=os.path.join('qmu'+str(os.getpid()),md.miscellaneous.name) + filename = md.miscellaneous.name TryRem('.queue',filename) else: @@ -59,10 +74,16 @@ TryRem('.bat',filename) + # remove this for bin file debugging TryRem('.bin',filename) + + #cwd = os.getcwd().split('/')[-1] + if md.qmu.isdakota: + os.chdir('..') + #TryRem('',cwd) return md def TryRem(extension,filename): - try: + try: os.remove(filename+extension) except OSError: Index: /issm/trunk-jpl/src/py3/solve/loadresultsfromdisk.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/loadresultsfromdisk.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/loadresultsfromdisk.py (revision 23670) @@ -2,6 +2,6 @@ from results import results from parseresultsfromdisk import parseresultsfromdisk -from EnumToString import EnumToString import MatlabFuncs as m +from postqmu import postqmu def loadresultsfromdisk(md,filename): @@ -28,5 +28,5 @@ #load results onto model - structure=parseresultsfromdisk(filename,not md.settings.io_gather) + structure=parseresultsfromdisk(md,filename,not md.settings.io_gather) if not len(structure): raise RuntimeError("No result found in binary file '%s'. Check for solution crash." % filename) @@ -58,10 +58,5 @@ #post processes qmu results if necessary else: - - if not isinstance(md.private.solution,str): - [md.private.solution]=EnumToString(md.private.solution) - md=postqmu(md) - os.chdir('..') + md=postqmu(md,filename) return md - Index: /issm/trunk-jpl/src/py3/solve/marshall.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/marshall.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/marshall.py (revision 23670) @@ -1,4 +1,3 @@ from WriteData import WriteData -from EnumDefinitions import * def marshall(md): @@ -12,6 +11,6 @@ marshall(md) """ - - print("marshalling file '%s.bin'." % md.miscellaneous.name) + if md.verbose.solution: + print("marshalling file '%s.bin'." % md.miscellaneous.name) #open file for binary writing @@ -21,15 +20,8 @@ raise IOError("marshall error message: could not open '%s.bin' file for binary writing." % md.miscellaneous.name) - #First, write MaximumNumberOfEnum to make sure that the Enums are synchronized - WriteData(fid,'enum',MaximumNumberOfDefinitionsEnum(),'data',True,'format','Boolean') - - #Go through all model fields: check that it is a class and call checkconsistency - fields=vars(md) - -# for field in fields.iterkeys(): for field in md.properties(): #Some properties do not need to be marshalled - if field in ['results','radaroverlay','toolkits','cluster','flaim','private']: + if field in ['results','radaroverlay','toolkits','cluster','private']: continue @@ -40,8 +32,8 @@ #Marshall current object #print "marshalling %s ..." % field - exec("md.%s.marshall(md,fid)" % field) + exec("md.{}.marshall('md.{}',md,fid)".format(field,field)) - #Last, write MaximumNumberOfEnum+1 to make sure that the binary file is not corrupt - WriteData(fid,'enum',MaximumNumberOfDefinitionsEnum()+1,'data',True,'format','Boolean'); + #Last, write "md.EOF" to make sure that the binary file is not corrupt + WriteData(fid,'XXX','name','md.EOF','data',True,'format','Boolean'); #close file Index: /issm/trunk-jpl/src/py3/solve/parseresultsfromdisk.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/parseresultsfromdisk.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/parseresultsfromdisk.py (revision 23670) @@ -1,31 +1,16 @@ import struct -import numpy +import numpy as np from collections import OrderedDict import results as resultsclass -import MatlabFuncs as m - -def parseresultsfromdisk(filename,iosplit): - """ - PARSERESULTSFROMDISK - ... - - Usage: - results=parseresultsfromdisk(filename,iosplit) - """ - + +def parseresultsfromdisk(md,filename,iosplit): if iosplit: - results=parseresultsfromdiskiosplit(filename) + saveres=parseresultsfromdiskiosplit(md,filename) else: - results=parseresultsfromdiskioserial(filename) - - return results - -def parseresultsfromdiskioserial(filename): # {{{ - """ - PARSERESULTSFROMDISK - ... - - Usage: - results=parseresultsfromdiskioserial(filename) - """ - + saveres=parseresultsfromdiskioserial(md,filename) + + return saveres + +def parseresultsfromdiskioserial(md,filename): # {{{ #Open file try: @@ -35,72 +20,58 @@ #initialize results: - results=[] - results.append(None) + saveres=[] #Read fields until the end of the file. - result=ReadData(fid) + loadres=ReadData(fid,md) counter=0 check_nomoresteps=0 - step=result['step'] - - while result: - + step=loadres['step'] + + while loadres: + #check that the new result does not add a step, which would be an error: if check_nomoresteps: - #check that the new result does not add a step, which would be an error: - if result['step']>=1: + if loadres['step']>=1: raise TypeError("parsing results for a steady-state core, which incorporates transient results!") #Check step, increase counter if this is a new step - if(step!=result['step'] and result['step']>1): + if(step!=loadres['step'] and loadres['step']>1): counter = counter + 1 - step = result['step'] - - #Add result - if result['step']==0: + step = loadres['step'] + + #Add result + if loadres['step']==0: #if we have a step = 0, this is a steady state solution, don't expect more steps. index = 0; check_nomoresteps=1 - - elif result['step']==1: + elif loadres['step']==1: index = 0 else: index = counter; - - if index > len(results)-1: - for i in range(len(results)-1,index-1): - results.append(None) - results.append(resultsclass.results()) - elif results[index] is None: - results[index]=resultsclass.results() - + if index > len(saveres)-1: + for i in range(len(saveres)-1,index-1): + saveres.append(None) + saveres.append(resultsclass.results()) + elif saveres[index] is None: + saveres[index]=resultsclass.results() #Get time and step - if result['step'] != -9999.: - setattr(results[index],'step',result['step']) - if result['time'] != -9999.: - setattr(results[index],'time',result['time']) - - #Add result - if hasattr(results[index],result['fieldname']) and not m.strcmp(result['fieldname'],'SolutionType'): - setattr(results[index],result['fieldname'],numpy.vstack((getattr(results[index],result['fieldname']),result['field']))) - else: - setattr(results[index],result['fieldname'],result['field']) - - #read next result - result=ReadData(fid) + if loadres['step'] != -9999.: + saveres[index].__dict__['step']=loadres['step'] + if loadres['time'] != -9999.: + saveres[index].__dict__['time']=loadres['time'] + + #Add result + saveres[index].__dict__[loadres['fieldname']]=loadres['field'] + + #read next result + loadres=ReadData(fid,md) fid.close() - return results - # }}} -def parseresultsfromdiskiosplit(filename): # {{{ - """ - PARSERESULTSFROMDISKIOSPLIT - ... - - Usage: - results=parseresultsfromdiskiosplit(filename) - """ + return saveres + # }}} +def parseresultsfromdiskiosplit(md,filename): # {{{ #Open file @@ -110,63 +81,63 @@ raise IOError("loadresultsfromdisk error message: could not open '%s' for binary reading." % filename) - results=[] + saveres=[] #if we have done split I/O, ie, we have results that are fragmented across patches, #do a first pass, and figure out the structure of results - result=ReadDataDimensions(fid) - while result: + loadres=ReadDataDimensions(fid) + while loadres: #Get time and step - if result['step'] > len(results): - for i in range(len(results),result['step']-1): - results.append(None) - results.append(resultsclass.results()) - setattr(results[result['step']-1],'step',result['step']) - setattr(results[result['step']-1],'time',result['time']) - - #Add result - setattr(results[result['step']-1],result['fieldname'],float('NaN')) - - #read next result - result=ReadDataDimensions(fid) + if loadres['step'] > len(saveres): + for i in range(len(saveres),loadres['step']-1): + saveres.append(None) + saveres.append(resultsclass.results()) + setattr(saveres[loadres['step']-1],'step',loadres['step']) + setattr(saveres[loadres['step']-1],'time',loadres['time']) + + #Add result + setattr(saveres[loadres['step']-1],loadres['fieldname'],float('NaN')) + + #read next result + loadres=ReadDataDimensions(fid) #do a second pass, and figure out the size of the patches fid.seek(0) #rewind - result=ReadDataDimensions(fid) - while result: - - #read next result - result=ReadDataDimensions(fid) + loadres=ReadDataDimensions(fid) + while loadres: + + #read next result + loadres=ReadDataDimensions(fid) #third pass, this time to read the real information fid.seek(0) #rewind - result=ReadData(fid) - while result: + loadres=ReadData(fid,md) + while loadres: #Get time and step - if result['step']> len(results): - for i in range(len(results),result['step']-1): - results.append(None) - results.append(resultsclass.results()) - setattr(results[result['step']-1],'step',result['step']) - setattr(results[result['step']-1],'time',result['time']) - - #Add result - setattr(results[result['step']-1],result['fieldname'],result['field']) - - #read next result - result=ReadData(fid) + if loadres['step']> len(saveres): + for i in range(len(saveres),loadres['step']-1): + saveres.append(None) + saveres.append(saveresclass.saveres()) + setattr(saveres[loadres['step']-1],'step',loadres['step']) + setattr(saveres[loadres['step']-1],'time',loadres['time']) + + #Add result + setattr(saveres[loadres['step']-1],loadres['fieldname'],loadres['field']) + + #read next result + loadres=ReadData(fid,md) #close file fid.close() - return results - # }}} -def ReadData(fid): # {{{ + return saveres + # }}} +def ReadData(fid,md): # {{{ """ READDATA - ... Usage: - field=ReadData(fid) + field=ReadData(fid,md) """ @@ -182,5 +153,5 @@ M=struct.unpack('i',fid.read(struct.calcsize('i')))[0] if type==1: - field=numpy.array(struct.unpack('%dd' % M,fid.read(M*struct.calcsize('d'))),dtype=float) + field=np.array(struct.unpack('%dd' % M,fid.read(M*struct.calcsize('d'))),dtype=float) elif type==2: field=struct.unpack('%ds' % M,fid.read(M))[0][:-1] @@ -188,48 +159,97 @@ N=struct.unpack('i',fid.read(struct.calcsize('i')))[0] # field=transpose(fread(fid,[N M],'double')); - field=numpy.zeros(shape=(M,N),dtype=float) + field=np.zeros(shape=(M,N),dtype=float) for i in range(M): field[i,:]=struct.unpack('%dd' % N,fid.read(N*struct.calcsize('d'))) + elif type==4: + N=struct.unpack('i',fid.read(struct.calcsize('i')))[0] +# field=transpose(fread(fid,[N M],'int')); + field=np.zeros(shape=(M,N),dtype=int) + for i in range(M): + field[i,:]=struct.unpack('%ii' % N,fid.read(N*struct.calcsize('i'))) else: raise TypeError("cannot read data of type %d" % type) #Process units here FIXME: this should not be done here! - yts=365.0*24.0*3600.0 - if m.strcmp(fieldname,'BalancethicknessThickeningRate'): - field = field*yts - elif m.strcmp(fieldname,'Time'): - field = field/yts - elif m.strcmp(fieldname,'HydrologyWaterVx'): - field = field*yts - elif m.strcmp(fieldname,'HydrologyWaterVy'): - field = field*yts - elif m.strcmp(fieldname,'Vx'): - field = field*yts - elif m.strcmp(fieldname,'Vy'): - field = field*yts - elif m.strcmp(fieldname,'Vz'): - field = field*yts - elif m.strcmp(fieldname,'Vel'): - field = field*yts - elif m.strcmp(fieldname,'BasalforcingsGroundediceMeltingRate'): - field = field*yts - elif m.strcmp(fieldname,'TotalSmb'): - field = field/10.**12.*yts #(GigaTon/year) - elif m.strcmp(fieldname,'SmbMassBalance'): - field = field*yts - elif m.strcmp(fieldname,'CalvingCalvingrate'): - field = field*yts - - - result=OrderedDict() - result['fieldname']=fieldname - result['time']=time - result['step']=step - result['field']=field + yts=md.constants.yts + if fieldname=='BalancethicknessThickeningRate': + field = field*yts + elif fieldname=='HydrologyWaterVx': + field = field*yts + elif fieldname=='HydrologyWaterVy': + field = field*yts + elif fieldname=='Vx': + field = field*yts + elif fieldname=='Vy': + field = field*yts + elif fieldname=='Vz': + field = field*yts + elif fieldname=='Vel': + field = field*yts + elif fieldname=='BasalforcingsGroundediceMeltingRate': + field = field*yts + elif fieldname=='BasalforcingsFloatingiceMeltingRate': + field = field*yts + elif fieldname=='TotalFloatingBmb': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='TotalFloatingBmbScaled': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='TotalGroundedBmb': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='TotalGroundedBmbScaled': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='TotalSmb': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='TotalSmbScaled': + field = field/10.**12*yts #(GigaTon/year) + elif fieldname=='SmbMassBalance': + field = field*yts + elif fieldname=='SmbPrecipitation': + field = field*yts + elif fieldname=='SmbRunoff': + field = field*yts + elif fieldname=='SmbEvaporation': + field = field*yts; + elif fieldname=='SmbRefreeze': + field = field*yts; + elif fieldname=='SmbEC': + field = field*yts + elif fieldname=='SmbAccumulation': + field = field*yts + elif fieldname=='SmbMelt': + field = field*yts + elif fieldname=='SmbMAdd': + field = field*yts + elif fieldname=='CalvingCalvingrate': + field = field*yts + elif fieldname=='LoveKernelsReal' or fieldname=='LoveKernelsImag': + nlayer = md.materials.numlayers + degmax = md.love.sh_nmax + nfreq = md.love.nfreq + #for numpy 1.8+ only + #temp_field = np.full((degmax+1,nfreq,nlayer+1,6),0.0) + temp_field = np.empty((degmax+1,nfreq,nlayer+1,6)) + temp_field.fill(0.0) + for ii in range(degmax+1): + for jj in range(nfreq): + for kk in range(nlayer+1): + ll = ii*(nlayer+1)*6 + (kk*6+1) + for mm in range(6): + temp_field[ii,jj,kk,mm] = field[ll+mm-1,jj] + field=temp_field + + if time !=-9999: + time = time/yts + + saveres=OrderedDict() + saveres['fieldname']=fieldname + saveres['time']=time + saveres['step']=step + saveres['field']=field except struct.error as e: - result=None - - return result + saveres=None + + return saveres # }}} def ReadDataDimensions(fid): # {{{ @@ -262,14 +282,14 @@ raise TypeError("cannot read data of type %d" % type) - result=OrderedDict() - result['fieldname']=fieldname - result['time']=time - result['step']=step - result['M']=M - result['N']=N + saveres=OrderedDict() + saveres['fieldname']=fieldname + saveres['time']=time + saveres['step']=step + saveres['M']=M + saveres['N']=N except struct.error as e: - result=None - - return result - # }}} + saveres=None + + return saveres + # }}} Index: /issm/trunk-jpl/src/py3/solve/solve.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/solve.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/solve.py (revision 23670) @@ -3,61 +3,94 @@ import shutil from pairoptions import pairoptions -from EnumDefinitions import * -from EnumToString import EnumToString from ismodelselfconsistent import ismodelselfconsistent from marshall import marshall from waitonlock import waitonlock from loadresultsfromcluster import loadresultsfromcluster -import MatlabFuncs as m +from preqmu import * +#from MatlabFuncs import * -def solve(md,solutionenum,**kwargs): +def solve(md,solutionstring,*args): """ SOLVE - apply solution sequence for this model Usage: - md=solve(md,solutionenum,varargin) + md=solve(md,solutionstring,varargin) where varargin is a list of paired arguments of string OR enums - solution types available comprise: - - StressbalanceSolutionEnum - - MasstransportSolutionEnum - - ThermalSolutionEnum - - SteadystateSolutionEnum - - TransientSolutionEnum - - BalancethicknessSolutionEnum - - BedSlopeSolutionEnum - - SurfaceSlopeSolutionEnum - - HydrologySolutionEnum - - FlaimSolutionEnum - + solution types available comprise: + - 'Stressbalance' or 'sb' + - 'Masstransport' or 'mt' + - 'Thermal' or 'th' + - 'Steadystate' or 'ss' + - 'Transient' or 'tr' + - 'Balancethickness' or 'mc' + - 'Balancevelocity' or 'bv' + - 'BedSlope' or 'bsl' + - 'SurfaceSlope' or 'ssl' + - 'Hydrology' or 'hy' + - 'DamageEvolution' or 'da' + - 'Gia' or 'gia' + - 'Esa' or 'esa' + - 'Sealevelrise' or 'slr' + - 'Love' or 'lv' + extra options: - - loadonly : does not solve. only load results + - loadonly : does not solve. only load results - checkconsistency : 'yes' or 'no' (default is 'yes'), ensures checks on consistency of model - restart: 'directory name (relative to the execution directory) where the restart file is located. Examples: - md=solve(md,StressbalanceSolutionEnum); + md=solve(md,'Stressbalance'); + md=solve(md,'sb'); """ #recover and process solve options - if EnumToString(solutionenum)[0][-8:] != 'Solution': - raise ValueError("solutionenum '%s' not supported!" % EnumToString(solutionenum)[0]) - options=pairoptions(solutionenum=solutionenum,**kwargs) + if solutionstring.lower() == 'sb' or solutionstring.lower() == 'stressbalance': + solutionstring = 'StressbalanceSolution'; + elif solutionstring.lower() == 'mt' or solutionstring.lower() == 'masstransport': + solutionstring = 'MasstransportSolution'; + elif solutionstring.lower() == 'th' or solutionstring.lower() == 'thermal': + solutionstring = 'ThermalSolution'; + elif solutionstring.lower() == 'st' or solutionstring.lower() == 'steadystate': + solutionstring = 'SteadystateSolution'; + elif solutionstring.lower() == 'tr' or solutionstring.lower() == 'transient': + solutionstring = 'TransientSolution'; + elif solutionstring.lower() == 'mc' or solutionstring.lower() == 'balancethickness': + solutionstring = 'BalancethicknessSolution'; + elif solutionstring.lower() == 'bv' or solutionstring.lower() == 'balancevelocity': + solutionstring = 'BalancevelocitySolution'; + elif solutionstring.lower() == 'bsl' or solutionstring.lower() == 'bedslope': + solutionstring = 'BedSlopeSolution'; + elif solutionstring.lower() == 'ssl' or solutionstring.lower() == 'surfaceslope': + solutionstring = 'SurfaceSlopeSolution'; + elif solutionstring.lower() == 'hy' or solutionstring.lower() == 'hydrology': + solutionstring = 'HydrologySolution'; + elif solutionstring.lower() == 'da' or solutionstring.lower() == 'damageevolution': + solutionstring = 'DamageEvolutionSolution'; + elif solutionstring.lower() == 'gia' or solutionstring.lower() == 'gia': + solutionstring = 'GiaSolution'; + elif solutionstring.lower() == 'lv' or solutionstring.lower() == 'love': + solutionstring = 'LoveSolution'; + elif solutionstring.lower() == 'esa': + solutionstring = 'EsaSolution'; + elif solutionstring.lower() == 'slr' or solutionstring.lower() == 'sealevelrise': + solutionstring = 'SealevelriseSolution'; + else: + raise ValueError("solutionstring '%s' not supported!" % solutionstring) + options=pairoptions('solutionstring',solutionstring,*args) #recover some fields - md.private.solution=solutionenum - cluster=md.cluster + md.private.solution=solutionstring + cluster=md.cluster + if options.getfieldvalue('batch','no')=='yes': + batch=1 + else: + batch=0; #check model consistency - if m.strcmpi(options.getfieldvalue('checkconsistency','yes'),'yes'): - print("checking model consistency") - if solutionenum == FlaimSolutionEnum(): - md.private.isconsistent=True - md.mesh.checkconsistency(md,solutionenum) - md.flaim.checkconsistency(md,solutionenum) - if not md.private.isconsistent: - raise RuntimeError("Model not consistent, see messages above.") - else: - ismodelselfconsistent(md) + if options.getfieldvalue('checkconsistency','yes')=='yes': + if md.verbose.solution: + print("checking model consistency") + ismodelselfconsistent(md) #First, build a runtime name that is unique @@ -80,10 +113,4 @@ md=preqmu(md,options) - #flaim analysis - if solutionenum == FlaimSolutionEnum(): - md=flaim_sol(md,options) - [md.private.solution]=EnumToString(solutionenum) - return md - #Do we load results only? if options.getfieldvalue('loadonly',False): @@ -95,8 +122,8 @@ marshall(md) # bin file md.toolkits.ToolkitsFile(md.miscellaneous.name+'.toolkits') # toolkits file - cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota) # queue file + cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota,md.transient.isoceancoupling) # queue file #Stop here if batch mode - if m.strcmpi(options.getfieldvalue('batch','no'),'yes'): + if options.getfieldvalue('batch','no')=='yes': print('batch mode requested: not launching job interactively') print('launch solution sequence on remote cluster by hand') @@ -113,5 +140,5 @@ #Launch job - cluster.LaunchQueueJob(md.miscellaneous.name,md.private.runtimename,filelist,restart) + cluster.LaunchQueueJob(md.miscellaneous.name,md.private.runtimename,filelist,restart,batch) #wait on lock @@ -122,10 +149,11 @@ print('The results must be loaded manually with md=loadresultsfromcluster(md).') else: #load results - print('loading results from cluster') + if md.verbose.solution: + print('loading results from cluster') md=loadresultsfromcluster(md) #post processes qmu results if necessary if md.qmu.isdakota: - if not strncmpi(options['keep'],'y',1): + if not strncmpi(options.getfieldvalue('keep','y'),'y',1): shutil.rmtree('qmu'+str(os.getpid())) Index: /issm/trunk-jpl/src/py3/solve/waitonlock.py =================================================================== --- /issm/trunk-jpl/src/py3/solve/waitonlock.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solve/waitonlock.py (revision 23670) @@ -48,5 +48,5 @@ #loop till file .lock exist or time is up while ispresent==0 and etime8.: + mumps['pc_factor_mat_solver_type']=options.getfieldvalue('pc_factor_mat_solver_type','mumps') + else: + mumps['pc_factor_mat_solver_package']=options.getfieldvalue('pc_factor_mat_solver_package','mumps') mumps['mat_mumps_icntl_14']=options.getfieldvalue('mat_mumps_icntl_14',120) - mumps['pc_factor_shift_positive_definite']=options.getfieldvalue('pc_factor_shift_positive_definite','true') return mumps - Index: /issm/trunk-jpl/src/py3/solvers/soroptions.py =================================================================== --- /issm/trunk-jpl/src/py3/solvers/soroptions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solvers/soroptions.py (revision 23670) @@ -1,5 +1,5 @@ import pairoptions -def soroptions(**kwargs): +def soroptions(*args): #SOROPTIONS - return Relaxation Solver petsc options # @@ -8,7 +8,7 @@ #retrieve options provided in varargin - arguments=pairoptions.pairoptions(**kwargs) + arguments=pairoptions.pairoptions(*args) - options=[['toolkit','petsc'],['mat_type','aij'],['ksp_type','cg'],['pc_type','sor'],['pc_sor_omega',1.1],['pc_sor_its',2]]; + options=[['toolkit','petsc'],['mat_type','mpiaij'],['ksp_type','cg'],['pc_type','sor'],['pc_sor_omega',1.1],['pc_sor_its',2]]; #now, go through our arguments, and write over default options. Index: /issm/trunk-jpl/src/py3/solvers/stokesoptions.py =================================================================== --- /issm/trunk-jpl/src/py3/solvers/stokesoptions.py (revision 23669) +++ /issm/trunk-jpl/src/py3/solvers/stokesoptions.py (revision 23670) @@ -2,5 +2,5 @@ from IssmConfig import IssmConfig -def stokesoptions(**kwargs): +def stokesoptions(*args): #STOKESOPTIONS - return STOKES multi-physics solver petsc options # @@ -9,5 +9,5 @@ #retrieve options provided in varargin - arguments=pairoptions.pairoptions(**kwargs) + arguments=pairoptions.pairoptions(*args)