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MCorr.py
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MCorr.py
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import proteus
from proteus.mprans.cMCorr import *
class Coefficients(proteus.TransportCoefficients.TC_base):
from proteus.ctransportCoefficients import levelSetConservationCoefficientsEvaluate
from proteus.ctransportCoefficients import levelSetConservationCoefficientsEvaluate_sd
def __init__(self,applyCorrection=True,epsFactHeaviside=0.0,epsFactDirac=1.0,epsFactDiffusion=2.0,LSModel_index=3,V_model=2,me_model=5,VOFModel_index=4,checkMass=True,sd=True,nd=None,applyCorrectionToDOF=True,useMetrics=0.0,useConstantH=False):
self.useConstantH=useConstantH
self.useMetrics=useMetrics
self.sd=sd
self.checkMass=checkMass
self.variableNames=['phiCorr']
nc=1
mass={}
advection={}
hamiltonian={}
diffusion={0:{0:{0:'constant'}}}
potential={0:{0:'u'}}
reaction={0:{0:'nonlinear'}}
#reaction={}
if self.sd:
assert nd!=None,"You must set the number of dimensions to use sparse diffusion in LevelSetConservationCoefficients"
sdInfo = {(0,0):(numpy.arange(start=0,stop=nd+1,step=1,dtype='i'),
numpy.arange(start=0,stop=nd,step=1,dtype='i'))}
else:
sdInfo={}
TC_base.__init__(self,
nc,
mass,
advection,
diffusion,
potential,
reaction,
hamiltonian,
self.variableNames,
sparseDiffusionTensors=sdInfo,
useSparseDiffusion = sd)
self.levelSetModelIndex=LSModel_index
self.flowModelIndex=V_model
self.epsFactHeaviside=epsFactHeaviside
self.epsFactDirac=epsFactDirac
self.epsFactDiffusion=epsFactDiffusion
self.me_model=me_model
self.VOFModelIndex=VOFModel_index
self.useC = True
self.applyCorrection=applyCorrection
if self.applyCorrection:
self.applyCorrectionToDOF = applyCorrectionToDOF
else:
self.applyCorrectionToDOF = False
self.massConservationError=0.0
def initializeMesh(self,mesh):
self.h=mesh.h
self.epsHeaviside = self.epsFactHeaviside*mesh.h
self.epsDirac = self.epsFactDirac*mesh.h
self.epsDiffusion = self.epsFactDiffusion*mesh.h
def attachModels(self,modelList):
import copy
logEvent("Attaching models in LevelSetConservation")
#level set
self.lsModel = modelList[self.levelSetModelIndex]
self.q_u_ls = modelList[self.levelSetModelIndex].q[('u',0)]
self.q_n_ls = modelList[self.levelSetModelIndex].q[('grad(u)',0)]
self.ebqe_u_ls = modelList[self.levelSetModelIndex].ebqe[('u',0)]
self.ebqe_n_ls = modelList[self.levelSetModelIndex].ebqe[('grad(u)',0)]
if modelList[self.levelSetModelIndex].ebq.has_key(('u',0)):
self.ebq_u_ls = modelList[self.levelSetModelIndex].ebq[('u',0)]
else:
self.ebq_u_ls = None
#volume of fluid
self.vofModel = modelList[self.VOFModelIndex]
self.q_H_vof = modelList[self.VOFModelIndex].q[('u',0)]
self.q_porosity = modelList[self.VOFModelIndex].coefficients.q_porosity
self.ebqe_H_vof = modelList[self.VOFModelIndex].ebqe[('u',0)]
if modelList[self.VOFModelIndex].ebq.has_key(('u',0)):
self.ebq_H_vof = modelList[self.VOFModelIndex].ebq[('u',0)]
else:
self.ebq_H_vof = None
#correction
self.massCorrModel = modelList[self.me_model]
self.vofModel.q[('m_last',0)][:] = self.vofModel.q[('m',0)]
if self.checkMass:
self.m_tmp = copy.deepcopy(self.massCorrModel.q[('r',0)])
if self.checkMass:
# self.vofGlobalMass = Norms.scalarDomainIntegral(self.vofModel.q['dV'],
# self.vofModel.q[('u',0)],
# self.massCorrModel.mesh.nElements_owned)
# self.lsGlobalMass = Norms.scalarHeavisideDomainIntegral(self.vofModel.q['dV'],
# self.lsModel.q[('u',0)],
# self.massCorrModel.mesh.nElements_owned)
#self.vofGlobalMass = 0.0
#self.lsGlobalMass = self.massCorrModel.calculateMass(self.lsModel.q[('u',0)])
#logEvent("Attach Models MCorr: mass correction %12.5e" % (Norms.scalarDomainIntegral(self.vofModel.q['dV'],
# self.massCorrModel.q[('r',0)],
# self.massCorrModel.mesh.nElements_owned),),level=2)
self.fluxGlobal = 0.0
self.totalFluxGlobal = 0.0
self.vofGlobalMassArray = []#self.vofGlobalMass]
self.lsGlobalMassArray = []#self.lsGlobalMass]
self.vofGlobalMassErrorArray = []#self.vofGlobalMass - self.vofGlobalMassArray[0]]# + self.vofModel.timeIntegration.dt*self.vofModel.coefficients.fluxIntegral]
self.lsGlobalMassErrorArray = []#self.lsGlobalMass - self.lsGlobalMassArray[0]]# + self.vofModel.timeIntegration.dt*self.vofModel.coefficients.fluxIntegral]
self.fluxArray = []#0.0]#self.vofModel.coefficients.fluxIntegral]
self.timeArray = []#self.vofModel.timeIntegration.t]
#logEvent("Attach Models MCorr: Phase 0 mass after mass correction (VOF) %12.5e" % (self.vofGlobalMass,),level=2)
#logEvent("Attach Models MCorr: Phase 0 mass after mass correction (LS) %12.5e" % (self.lsGlobalMass,),level=2)
#logEvent("Attach Models MCorr: Phase 0 mass conservation (VOF) after step = %12.5e" % (self.vofGlobalMass - self.vofModel.coefficients.m_pre + self.vofModel.timeIntegration.dt*self.vofModel.coefficients.fluxIntegral,),level=2)
#logEvent("Attach Models MCorr: Phase 0 mass conservation (LS) after step = %12.5e" % (self.lsGlobalMass - self.lsModel.coefficients.m_pre + self.vofModel.timeIntegration.dt*self.vofModel.coefficients.fluxIntegral,),level=2)
def initializeElementQuadrature(self,t,cq):
if self.sd and cq.has_key(('a',0,0)):
cq[('a',0,0)].fill(self.epsDiffusion)
def initializeElementBoundaryQuadrature(self,t,cebq,cebq_global):
if self.sd and cebq.has_key(('a',0,0)):
cebq[('a',0,0)].fill(self.epsDiffusion)
def initializeGlobalExteriorElementBoundaryQuadrature(self,t,cebqe):
if self.sd and cebqe.has_key(('a',0,0)):
cebqe[('a',0,0)].fill(self.epsDiffusion)
def preStep(self,t,firstStep=False):
if self.checkMass:
logEvent("Phase 0 mass before mass correction (VOF) %12.5e" % (Norms.scalarDomainIntegral(self.vofModel.q['dV'],
self.vofModel.q[('m',0)],
self.massCorrModel.mesh.nElements_owned),),level=2)
logEvent("Phase 0 mass (primitive) before mass correction (LS) %12.5e" % (Norms.scalarSmoothedHeavisideDomainIntegral(self.epsFactHeaviside,
self.massCorrModel.elementDiameter,
self.vofModel.q['dV'],
self.lsModel.q[('m',0)],
self.massCorrModel.mesh.nElements_owned),),level=2)
logEvent("Phase 0 mass (consistent) before mass correction (LS) %12.5e" % (self.massCorrModel.calculateMass(self.lsModel.q[('m',0)]),),level=2)
copyInstructions = {'clear_uList':True}
return copyInstructions
def postStep(self,t,firstStep=False):
if self.applyCorrection:
#ls
self.lsModel.u[0].dof += self.massCorrModel.u[0].dof
self.lsModel.q[('u',0)] += self.massCorrModel.q[('u',0)]
self.lsModel.ebqe[('u',0)] += self.massCorrModel.ebqe[('u',0)]
self.lsModel.q[('grad(u)',0)] += self.massCorrModel.q[('grad(u)',0)]
self.lsModel.ebqe[('grad(u)',0)] += self.massCorrModel.ebqe[('grad(u)',0)]
#vof
self.massCorrModel.setMassQuadrature()
#self.vofModel.q[('u',0)] += self.massCorrModel.q[('r',0)]
#####print "********************max VOF************************",max(self.vofModel.q[('u',0)].flat[:])
if self.checkMass:
logEvent("Phase 0 mass after mass correction (VOF) %12.5e" % (Norms.scalarDomainIntegral(self.vofModel.q['dV'],
self.vofModel.q[('m',0)],
self.massCorrModel.mesh.nElements_owned),),level=2)
logEvent("Phase 0 mass (primitive) after mass correction (LS) %12.5e" % (Norms.scalarSmoothedHeavisideDomainIntegral(self.epsFactHeaviside,
self.massCorrModel.elementDiameter,
self.vofModel.q['dV'],
self.lsModel.q[('m',0)],
self.massCorrModel.mesh.nElements_owned),),level=2)
logEvent("Phase 0 mass (consistent) after mass correction (LS) %12.5e" % (self.massCorrModel.calculateMass(self.lsModel.q[('m',0)]),),level=2)
copyInstructions = {}
#get the waterline on the obstacle if option set in NCLS (boundary==7)
self.lsModel.computeWaterline(t)
return copyInstructions
def evaluate(self,t,c):
import math
if c[('u',0)].shape == self.q_u_ls.shape:
u_ls = self.q_u_ls
H_vof = self.q_H_vof
elif c[('u',0)].shape == self.ebqe_u_ls.shape:
u_ls = self.ebqe_u_ls
H_vof = self.ebqe_H_vof
elif self.ebq_u_ls != None and c[('u',0)].shape == self.ebq_u_ls.shape:
u_ls = self.ebq_u_ls
H_vof = self.ebq_H_vof
else:
#\todo trap errors in TransportCoefficients.py
u_ls = None
H_vof = None
if u_ls != None and H_vof != None:
if self.useC:
if self.sd:
self.levelSetConservationCoefficientsEvaluate_sd(self.epsHeaviside,
self.epsDirac,
u_ls,
H_vof,
c[('u',0)],
c[('r',0)],
c[('dr',0,0)])
else:
self.levelSetConservationCoefficientsEvaluate(self.epsHeaviside,
self.epsDirac,
self.epsDiffusion,
u_ls,
H_vof,
c[('u',0)],
c[('r',0)],
c[('dr',0,0)],
c[('a',0,0)])
if (self.checkMass and c[('u',0)].shape == self.q_u_ls.shape):
self.m_tmp[:] = H_vof
self.m_tmp += self.massCorrModel.q[('r',0)]
logEvent("mass correction during Newton %12.5e" % (Norms.scalarDomainIntegral(self.vofModel.q['dV'],
self.massCorrModel.q[('r',0)],
self.massCorrModel.mesh.nElements_owned),),level=2)
logEvent("Phase 0 mass during Newton %12.5e" % (Norms.scalarDomainIntegral(self.vofModel.q['dV'],
self.m_tmp,
self.massCorrModel.mesh.nElements_owned),),level=2)
class LevelModel(proteus.Transport.OneLevelTransport):
nCalls=0
def __init__(self,
uDict,
phiDict,
testSpaceDict,
matType,
dofBoundaryConditionsDict,
dofBoundaryConditionsSetterDict,
coefficients,
elementQuadrature,
elementBoundaryQuadrature,
fluxBoundaryConditionsDict=None,
advectiveFluxBoundaryConditionsSetterDict=None,
diffusiveFluxBoundaryConditionsSetterDictDict=None,
stressTraceBoundaryConditionsSetterDict=None,
stabilization=None,
shockCapturing=None,
conservativeFluxDict=None,
numericalFluxType=None,
TimeIntegrationClass=None,
massLumping=False,
reactionLumping=False,
options=None,
name='defaultName',
reuse_trial_and_test_quadrature=True,
sd = True,
movingDomain=False):#,
self.useConstantH=coefficients.useConstantH
from proteus import Comm
#
#set the objects describing the method and boundary conditions
#
self.movingDomain=movingDomain
self.tLast_mesh=None
#
self.name=name
self.sd=sd
self.Hess=False
self.lowmem=True
self.timeTerm=True#allow turning off the time derivative
#self.lowmem=False
self.testIsTrial=True
self.phiTrialIsTrial=True
self.u = uDict
self.ua = {}#analytical solutions
self.phi = phiDict
self.dphi={}
self.matType = matType
#mwf try to reuse test and trial information across components if spaces are the same
self.reuse_test_trial_quadrature = reuse_trial_and_test_quadrature#True#False
if self.reuse_test_trial_quadrature:
for ci in range(1,coefficients.nc):
assert self.u[ci].femSpace.__class__.__name__ == self.u[0].femSpace.__class__.__name__, "to reuse_test_trial_quad all femSpaces must be the same!"
## Simplicial Mesh
self.mesh = self.u[0].femSpace.mesh #assume the same mesh for all components for now
self.testSpace = testSpaceDict
self.dirichletConditions = dofBoundaryConditionsDict
self.dirichletNodeSetList=None #explicit Dirichlet conditions for now, no Dirichlet BC constraints
self.coefficients = coefficients
self.coefficients.initializeMesh(self.mesh)
self.nc = self.coefficients.nc
self.stabilization = stabilization
self.shockCapturing = shockCapturing
self.conservativeFlux = conservativeFluxDict #no velocity post-processing for now
self.fluxBoundaryConditions=fluxBoundaryConditionsDict
self.advectiveFluxBoundaryConditionsSetterDict=advectiveFluxBoundaryConditionsSetterDict
self.diffusiveFluxBoundaryConditionsSetterDictDict = diffusiveFluxBoundaryConditionsSetterDictDict
#determine whether the stabilization term is nonlinear
self.stabilizationIsNonlinear = False
#cek come back
if self.stabilization != None:
for ci in range(self.nc):
if coefficients.mass.has_key(ci):
for flag in coefficients.mass[ci].values():
if flag == 'nonlinear':
self.stabilizationIsNonlinear=True
if coefficients.advection.has_key(ci):
for flag in coefficients.advection[ci].values():
if flag == 'nonlinear':
self.stabilizationIsNonlinear=True
if coefficients.diffusion.has_key(ci):
for diffusionDict in coefficients.diffusion[ci].values():
for flag in diffusionDict.values():
if flag != 'constant':
self.stabilizationIsNonlinear=True
if coefficients.potential.has_key(ci):
for flag in coefficients.potential[ci].values():
if flag == 'nonlinear':
self.stabilizationIsNonlinear=True
if coefficients.reaction.has_key(ci):
for flag in coefficients.reaction[ci].values():
if flag == 'nonlinear':
self.stabilizationIsNonlinear=True
if coefficients.hamiltonian.has_key(ci):
for flag in coefficients.hamiltonian[ci].values():
if flag == 'nonlinear':
self.stabilizationIsNonlinear=True
#determine if we need element boundary storage
self.elementBoundaryIntegrals = {}
for ci in range(self.nc):
self.elementBoundaryIntegrals[ci] = ((self.conservativeFlux != None) or
(numericalFluxType != None) or
(self.fluxBoundaryConditions[ci] == 'outFlow') or
(self.fluxBoundaryConditions[ci] == 'mixedFlow') or
(self.fluxBoundaryConditions[ci] == 'setFlow'))
#
#calculate some dimensions
#
self.nSpace_global = self.u[0].femSpace.nSpace_global #assume same space dim for all variables
self.nDOF_trial_element = [u_j.femSpace.max_nDOF_element for u_j in self.u.values()]
self.nDOF_phi_trial_element = [phi_k.femSpace.max_nDOF_element for phi_k in self.phi.values()]
self.n_phi_ip_element = [phi_k.femSpace.referenceFiniteElement.interpolationConditions.nQuadraturePoints for phi_k in self.phi.values()]
self.nDOF_test_element = [femSpace.max_nDOF_element for femSpace in self.testSpace.values()]
self.nFreeDOF_global = [dc.nFreeDOF_global for dc in self.dirichletConditions.values()]
self.nVDOF_element = sum(self.nDOF_trial_element)
self.nFreeVDOF_global = sum(self.nFreeDOF_global)
#
NonlinearEquation.__init__(self,self.nFreeVDOF_global)
#
#build the quadrature point dictionaries from the input (this
#is just for convenience so that the input doesn't have to be
#complete)
#
elementQuadratureDict={}
elemQuadIsDict = isinstance(elementQuadrature,dict)
if elemQuadIsDict: #set terms manually
for I in self.coefficients.elementIntegralKeys:
if elementQuadrature.has_key(I):
elementQuadratureDict[I] = elementQuadrature[I]
else:
elementQuadratureDict[I] = elementQuadrature['default']
else:
for I in self.coefficients.elementIntegralKeys:
elementQuadratureDict[I] = elementQuadrature
if self.stabilization != None:
for I in self.coefficients.elementIntegralKeys:
if elemQuadIsDict:
if elementQuadrature.has_key(I):
elementQuadratureDict[('stab',)+I[1:]] = elementQuadrature[I]
else:
elementQuadratureDict[('stab',)+I[1:]] = elementQuadrature['default']
else:
elementQuadratureDict[('stab',)+I[1:]] = elementQuadrature
if self.shockCapturing != None:
for ci in self.shockCapturing.components:
if elemQuadIsDict:
if elementQuadrature.has_key(('numDiff',ci,ci)):
elementQuadratureDict[('numDiff',ci,ci)] = elementQuadrature[('numDiff',ci,ci)]
else:
elementQuadratureDict[('numDiff',ci,ci)] = elementQuadrature['default']
else:
elementQuadratureDict[('numDiff',ci,ci)] = elementQuadrature
if massLumping:
for ci in self.coefficients.mass.keys():
elementQuadratureDict[('m',ci)] = Quadrature.SimplexLobattoQuadrature(self.nSpace_global,1)
for I in self.coefficients.elementIntegralKeys:
elementQuadratureDict[('stab',)+I[1:]] = Quadrature.SimplexLobattoQuadrature(self.nSpace_global,1)
if reactionLumping:
for ci in self.coefficients.mass.keys():
elementQuadratureDict[('r',ci)] = Quadrature.SimplexLobattoQuadrature(self.nSpace_global,1)
for I in self.coefficients.elementIntegralKeys:
elementQuadratureDict[('stab',)+I[1:]] = Quadrature.SimplexLobattoQuadrature(self.nSpace_global,1)
elementBoundaryQuadratureDict={}
if isinstance(elementBoundaryQuadrature,dict): #set terms manually
for I in self.coefficients.elementBoundaryIntegralKeys:
if elementBoundaryQuadrature.has_key(I):
elementBoundaryQuadratureDict[I] = elementBoundaryQuadrature[I]
else:
elementBoundaryQuadratureDict[I] = elementBoundaryQuadrature['default']
else:
for I in self.coefficients.elementBoundaryIntegralKeys:
elementBoundaryQuadratureDict[I] = elementBoundaryQuadrature
#
# find the union of all element quadrature points and
# build a quadrature rule for each integral that has a
# weight at each point in the union
#mwf include tag telling me which indices are which quadrature rule?
(self.elementQuadraturePoints,self.elementQuadratureWeights,
self.elementQuadratureRuleIndeces) = Quadrature.buildUnion(elementQuadratureDict)
self.nQuadraturePoints_element = self.elementQuadraturePoints.shape[0]
self.nQuadraturePoints_global = self.nQuadraturePoints_element*self.mesh.nElements_global
#
#Repeat the same thing for the element boundary quadrature
#
(self.elementBoundaryQuadraturePoints,
self.elementBoundaryQuadratureWeights,
self.elementBoundaryQuadratureRuleIndeces) = Quadrature.buildUnion(elementBoundaryQuadratureDict)
self.nElementBoundaryQuadraturePoints_elementBoundary = self.elementBoundaryQuadraturePoints.shape[0]
self.nElementBoundaryQuadraturePoints_global = (self.mesh.nElements_global*
self.mesh.nElementBoundaries_element*
self.nElementBoundaryQuadraturePoints_elementBoundary)
if type(self.u[0].femSpace) == C0_AffineLinearOnSimplexWithNodalBasis:
#print self.nQuadraturePoints_element
if self.nSpace_global == 3:
assert(self.nQuadraturePoints_element == 5)
elif self.nSpace_global == 2:
assert(self.nQuadraturePoints_element == 6)
elif self.nSpace_global == 1:
assert(self.nQuadraturePoints_element == 3)
#print self.nElementBoundaryQuadraturePoints_elementBoundary
if self.nSpace_global == 3:
assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 4)
elif self.nSpace_global == 2:
assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 4)
elif self.nSpace_global == 1:
assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 1)
#pdb.set_trace()
#
#simplified allocations for test==trial and also check if space is mixed or not
#
self.q={}
self.ebq={}
self.ebq_global={}
self.ebqe={}
self.phi_ip={}
#mesh
#self.q['x'] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element,3),'d')
self.q[('u',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('grad(u)',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element,self.nSpace_global),'d')
self.q[('r',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.ebqe[('u',0)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('grad(u)',0)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,self.nSpace_global),'d')
self.points_elementBoundaryQuadrature= set()
self.scalars_elementBoundaryQuadrature= set([('u',ci) for ci in range(self.nc)])
self.vectors_elementBoundaryQuadrature= set()
self.tensors_elementBoundaryQuadrature= set()
logEvent(memory("element and element boundary Jacobians","OneLevelTransport"),level=4)
self.inflowBoundaryBC = {}
self.inflowBoundaryBC_values = {}
self.inflowFlux = {}
for cj in range(self.nc):
self.inflowBoundaryBC[cj] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,),'i')
self.inflowBoundaryBC_values[cj] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nDOF_trial_element[cj]),'d')
self.inflowFlux[cj] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.internalNodes = set(range(self.mesh.nNodes_global))
#identify the internal nodes this is ought to be in mesh
##\todo move this to mesh
for ebNE in range(self.mesh.nExteriorElementBoundaries_global):
ebN = self.mesh.exteriorElementBoundariesArray[ebNE]
eN_global = self.mesh.elementBoundaryElementsArray[ebN,0]
ebN_element = self.mesh.elementBoundaryLocalElementBoundariesArray[ebN,0]
for i in range(self.mesh.nNodes_element):
if i != ebN_element:
I = self.mesh.elementNodesArray[eN_global,i]
self.internalNodes -= set([I])
self.nNodes_internal = len(self.internalNodes)
self.internalNodesArray=numpy.zeros((self.nNodes_internal,),'i')
for nI,n in enumerate(self.internalNodes):
self.internalNodesArray[nI]=n
#
del self.internalNodes
self.internalNodes = None
logEvent("Updating local to global mappings",2)
self.updateLocal2Global()
logEvent("Building time integration object",2)
logEvent(memory("inflowBC, internalNodes,updateLocal2Global","OneLevelTransport"),level=4)
#mwf for interpolating subgrid error for gradients etc
if self.stabilization and self.stabilization.usesGradientStabilization:
self.timeIntegration = TimeIntegrationClass(self,integrateInterpolationPoints=True)
else:
self.timeIntegration = TimeIntegrationClass(self)
if options != None:
self.timeIntegration.setFromOptions(options)
logEvent(memory("TimeIntegration","OneLevelTransport"),level=4)
logEvent("Calculating numerical quadrature formulas",2)
self.calculateQuadrature()
self.setupFieldStrides()
comm = Comm.get()
self.comm=comm
if comm.size() > 1:
assert numericalFluxType != None and numericalFluxType.useWeakDirichletConditions,"You must use a numerical flux to apply weak boundary conditions for parallel runs"
logEvent(memory("stride+offset","OneLevelTransport"),level=4)
if numericalFluxType != None:
if options == None or options.periodicDirichletConditions == None:
self.numericalFlux = numericalFluxType(self,
dofBoundaryConditionsSetterDict,
advectiveFluxBoundaryConditionsSetterDict,
diffusiveFluxBoundaryConditionsSetterDictDict)
else:
self.numericalFlux = numericalFluxType(self,
dofBoundaryConditionsSetterDict,
advectiveFluxBoundaryConditionsSetterDict,
diffusiveFluxBoundaryConditionsSetterDictDict,
options.periodicDirichletConditions)
else:
self.numericalFlux = None
#set penalty terms
#cek todo move into numerical flux initialization
if self.ebq_global.has_key('penalty'):
for ebN in range(self.mesh.nElementBoundaries_global):
for k in range(self.nElementBoundaryQuadraturePoints_elementBoundary):
self.ebq_global['penalty'][ebN,k] = self.numericalFlux.penalty_constant/(self.mesh.elementBoundaryDiametersArray[ebN]**self.numericalFlux.penalty_power)
#penalty term
#cek move to Numerical flux initialization
if self.ebqe.has_key('penalty'):
for ebNE in range(self.mesh.nExteriorElementBoundaries_global):
ebN = self.mesh.exteriorElementBoundariesArray[ebNE]
for k in range(self.nElementBoundaryQuadraturePoints_elementBoundary):
self.ebqe['penalty'][ebNE,k] = self.numericalFlux.penalty_constant/self.mesh.elementBoundaryDiametersArray[ebN]**self.numericalFlux.penalty_power
logEvent(memory("numericalFlux","OneLevelTransport"),level=4)
self.elementEffectiveDiametersArray = self.mesh.elementInnerDiametersArray
#use post processing tools to get conservative fluxes, None by default
from proteus import PostProcessingTools
self.velocityPostProcessor = PostProcessingTools.VelocityPostProcessingChooser(self)
logEvent(memory("velocity postprocessor","OneLevelTransport"),level=4)
#helper for writing out data storage
from proteus import Archiver
self.elementQuadratureDictionaryWriter = Archiver.XdmfWriter()
self.elementBoundaryQuadratureDictionaryWriter = Archiver.XdmfWriter()
self.exteriorElementBoundaryQuadratureDictionaryWriter = Archiver.XdmfWriter()
self.globalResidualDummy = None
compKernelFlag = 0
if self.coefficients.useConstantH:
self.elementDiameter = self.mesh.elementDiametersArray.copy()
self.elementDiameter[:] = max(self.mesh.elementDiametersArray)
else:
self.elementDiameter = self.mesh.elementDiametersArray
self.mcorr = cMCorr_base(self.nSpace_global,
self.nQuadraturePoints_element,
self.u[0].femSpace.elementMaps.localFunctionSpace.dim,
self.u[0].femSpace.referenceFiniteElement.localFunctionSpace.dim,
self.testSpace[0].referenceFiniteElement.localFunctionSpace.dim,
self.nElementBoundaryQuadraturePoints_elementBoundary,
compKernelFlag)
#mwf these are getting called by redistancing classes,
def calculateCoefficients(self):
pass
def calculateElementResidual(self):
if self.globalResidualDummy != None:
self.getResidual(self.u[0].dof,self.globalResidualDummy)
def getResidual(self,u,r):
import pdb
import copy
from proteus.flcbdfWrappers import globalSum
"""
Calculate the element residuals and add in to the global residual
"""
r.fill(0.0)
#Load the unknowns into the finite element dof
self.setUnknowns(u)
#no flux boundary conditions
self.mcorr.calculateResidual(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_global,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.coefficients.q_porosity,
self.offset[0],self.stride[0],
r,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray)
logEvent("Global residual",level=9,data=r)
self.coefficients.massConservationError = fabs(globalSum(sum(r.flat[:self.mesh.nNodes_owned])))
assert self.coefficients.massConservationError == fabs(globalSum(r[:self.mesh.nNodes_owned].sum()))
logEvent(" Mass Conservation Error",level=3,data=self.coefficients.massConservationError)
self.nonlinear_function_evaluations += 1
if self.globalResidualDummy == None:
self.globalResidualDummy = numpy.zeros(r.shape,'d')
def getJacobian(self,jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian,jacobian)
self.mcorr.calculateJacobian(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
self.mesh.nElements_global,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.q_H_vof,
self.coefficients.q_porosity,
self.csrRowIndeces[(0,0)],self.csrColumnOffsets[(0,0)],
jacobian)
logEvent("Jacobian ",level=10,data=jacobian)
#mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def elementSolve(self,u,r):
import pdb
import copy
"""
Calculate the element residuals and add in to the global residual
"""
r.fill(0.0)
#Load the unknowns into the finite element dof
self.setUnknowns(u)
#no flux boundary conditions
self.mcorr.elementSolve(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_global,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.coefficients.q_porosity,
self.offset[0],self.stride[0],
r,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.maxIts,
self.atol)
def elementConstantSolve(self,u,r):
import pdb
import copy
"""
Calculate the element residuals and add in to the global residual
"""
r.fill(0.0)
#Load the unknowns into the finite element dof
self.setUnknowns(u)
#no flux boundary conditions
self.mcorr.elementConstantSolve(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_global,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.coefficients.q_porosity,
self.offset[0],self.stride[0],
r,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.maxIts,
self.atol)
def globalConstantRJ(self,u,r,U):
from proteus.flcbdfWrappers import globalSum
import pdb
import copy
"""
Calculate the element residuals and add in to the global residual
"""
r.fill(0.0)
#Load the unknowns into the finite element dof
self.setUnknowns(u)
#no flux boundary conditions
(R,J) = self.mcorr.globalConstantRJ(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_owned,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,
self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.offset[0],self.stride[0],
r,
self.coefficients.q_porosity,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.maxIts,
self.atol,
U)
R = globalSum(R)
J = globalSum(J)
self.coefficients.massConservationError = fabs(R)
return (R,J)
def globalConstantSolve(self,u,r):
U=0.0
R=0.0
J=0.0
(R,J) = self.globalConstantRJ(u,r,U)
its=0
logEvent(" Mass Conservation Residual 0 ",level=3,data=R)
RNORM_OLD=fabs(R)
while ((fabs(R) > self.atol and its < self.maxIts) or its<1):
U -= R/(J+1.0e-8)
(R,J) = self.globalConstantRJ(u,r,U)
lsits=0
while(fabs(R) > 0.99*RNORM_OLD and lsits < self.maxLSits):
lsits +=1
U += (0.5)**lsits * (R/(J+1.0e-8))
(R,J) = self.globalConstantRJ(u,r,U)
its+=1
logEvent(" Mass Conservation Residual "+`its`+" ",level=3,data=R)
self.u[0].dof.flat[:] = U
def calculateElementQuadrature(self):
"""
Calculate the physical location and weights of the quadrature rules
and the shape information at the quadrature points.
This function should be called only when the mesh changes.
"""
#self.u[0].femSpace.elementMaps.getValues(self.elementQuadraturePoints,
# self.q['x'])
self.u[0].femSpace.elementMaps.getBasisValuesRef(self.elementQuadraturePoints)
self.u[0].femSpace.elementMaps.getBasisGradientValuesRef(self.elementQuadraturePoints)
self.u[0].femSpace.getBasisValuesRef(self.elementQuadraturePoints)
self.u[0].femSpace.getBasisGradientValuesRef(self.elementQuadraturePoints)
self.coefficients.initializeElementQuadrature(self.timeIntegration.t,self.q)
if self.stabilization != None:
self.stabilization.initializeElementQuadrature(self.mesh,self.timeIntegration.t,self.q)
self.stabilization.initializeTimeIntegration(self.timeIntegration)
if self.shockCapturing != None:
self.shockCapturing.initializeElementQuadrature(self.mesh,self.timeIntegration.t,self.q)
def calculateElementBoundaryQuadrature(self):
pass
def calculateExteriorElementBoundaryQuadrature(self):
self.u[0].femSpace.elementMaps.getBasisValuesTraceRef(self.elementBoundaryQuadraturePoints)
self.u[0].femSpace.elementMaps.getBasisGradientValuesTraceRef(self.elementBoundaryQuadraturePoints)
self.u[0].femSpace.getBasisValuesTraceRef(self.elementBoundaryQuadraturePoints)
self.u[0].femSpace.getBasisGradientValuesTraceRef(self.elementBoundaryQuadraturePoints)
def estimate_mt(self):
pass
def calculateAuxiliaryQuantitiesAfterStep(self):
pass
def calculateMass(self,q_phi):
from proteus.flcbdfWrappers import globalSum
return globalSum(self.mcorr.calculateMass(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_owned,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.u[0].dof,
q_phi,#self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.coefficients.q_porosity,
self.offset[0],self.stride[0],
self.u[0].dof,#dummy r,not used
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray))
def setMassQuadrature(self):
self.mcorr.setMassQuadrature(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.elementNodesArray,
self.elementQuadratureWeights[('u',0)],
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
self.u[0].femSpace.psi,
self.u[0].femSpace.grad_psi,
#element boundary
self.u[0].femSpace.elementMaps.psi_trace,
self.u[0].femSpace.elementMaps.grad_psi_trace,
self.elementBoundaryQuadratureWeights[('u',0)],
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.psi_trace,
self.u[0].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.mesh.nElements_global,
self.coefficients.useMetrics,
self.coefficients.epsFactHeaviside,
self.coefficients.epsFactDirac,
self.coefficients.epsFactDiffusion,
self.coefficients.lsModel.u[0].femSpace.dofMap.l2g,
self.elementDiameter,#self.mesh.elementDiametersArray,
self.mesh.nodeDiametersArray,
self.coefficients.lsModel.u[0].dof,
self.coefficients.q_u_ls,
self.coefficients.q_n_ls,
self.coefficients.ebqe_u_ls,
self.coefficients.ebqe_n_ls,
self.coefficients.q_H_vof,
self.q[('u',0)],
self.q[('grad(u)',0)],
self.ebqe[('u',0)],
self.ebqe[('grad(u)',0)],
self.q[('r',0)],
self.coefficients.q_porosity,
self.offset[0],self.stride[0],
self.u[0].dof,#dummy r,not used
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.coefficients.vofModel.u[0].dof)
#self.coefficients.q_H_vof.flat[:]=777.0
def calculateSolutionAtQuadrature(self):
pass
def updateAfterMeshMotion(self):
pass
class DummyNewton(proteus.NonlinearSolvers.NonlinearSolver):
def __init__(self,
linearSolver,
F,J=None,du=None,par_du=None,
rtol_r = 1.0e-4,
atol_r = 1.0e-16,