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RDLS.py
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RDLS.py
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from __future__ import division
from builtins import range
from past.utils import old_div
import proteus
from proteus import TimeIntegration
from proteus.mprans.cRDLS import *
from proteus.Comm import globalMax
import numpy as np
from proteus.Transport import OneLevelTransport, memory
from proteus.Transport import TC_base, NonlinearEquation, Quadrature, logEvent
from proteus.Transport import cfemIntegrals
from . import cArgumentsDict
class SubgridError(proteus.SubgridError.SGE_base):
def __init__(self, coefficients, nd):
proteus.SubgridError.SGE_base.__init__(self, coefficients, nd, False)
def initializeElementQuadrature(self, mesh, t, cq):
for ci in range(self.nc):
cq[('dH_sge', ci, ci)] = cq[('dH', ci, ci)]
def calculateSubgridError(self, q):
pass
def updateSubgridErrorHistory(self, initializationPhase=False):
pass
class ShockCapturing(proteus.ShockCapturing.ShockCapturing_base):
def __init__(self, coefficients, nd, shockCapturingFactor=0.25, lag=True, nStepsToDelay=None):
proteus.ShockCapturing.ShockCapturing_base.__init__(self, coefficients, nd, shockCapturingFactor, lag)
self.nStepsToDelay = nStepsToDelay
self.nSteps = 0
def initializeElementQuadrature(self, mesh, t, cq):
self.mesh = mesh
self.numDiff = []
self.numDiff_last = []
for ci in range(self.nc):
self.numDiff.append(cq[('numDiff', ci, ci)])
self.numDiff_last.append(cq[('numDiff', ci, ci)])
def updateShockCapturingHistory(self):
self.nSteps += 1
if self.lag:
for ci in range(self.nc):
self.numDiff_last[ci][:] = self.numDiff[ci]
if self.lag == False and self.nStepsToDelay is not None and self.nSteps > self.nStepsToDelay:
self.lag = True
self.numDiff_last = []
for ci in range(self.nc):
self.numDiff_last.append(self.numDiff[ci].copy())
logEvent("RDLS: max numDiff %e" % (globalMax(self.numDiff_last[0].max()),))
class PsiTC(proteus.StepControl.SC_base):
def __init__(self, model, nOptions):
proteus.StepControl.SC_base.__init__(self, model, nOptions)
for ci in list(nOptions.atol_res.keys()):
self.atol = nOptions.atol_res[ci]
self.rtol = nOptions.rtol_res[ci]
self.stepExact = True
for m in model.levelModelList:
m.timeIntegration.isAdaptive = False
self.nSteps = 0
self.nStepsOsher = nOptions.psitc['nStepsForce']
self.red_ratio = nOptions.psitc['reduceRatio']
self.start_ratio = nOptions.psitc['startRatio']
self.nStepsMax = nOptions.psitc['nStepsMax']
def stepExact_model(self, tOut):
# pseudo time step
for m in self.model.levelModelList:
m.timeIntegration.choose_dt()
self.dt_model = self.start_ratio * m.timeIntegration.dt
self.set_dt_allLevels()
# physical time step
self.t_model = tOut
self.setSubsteps([tOut])
def initialize_dt_model(self, t0, tOut):
self.saveSolution()
self.t_model_last = t0
self.t_model = tOut
# pseudo time step
for m in self.model.levelModelList:
m.timeIntegration.initialize_dt(t0, tOut, m.q)
# set the starting time steps
self.dt_model = self.start_ratio * m.timeIntegration.dt
self.set_dt_allLevels()
# physical time step
self.t = tOut
self.setSubsteps([tOut])
self.nSteps = 0
logEvent("Initializing time step on model %s to dt = %12.5e" % (self.model.name,
self.dt_model),
level=1)
def updateSubstep(self):
# choose a new dt and add a substep without increasing t
# if the steady state has been reached then append the new t to the substeps
self.solverFailures = 0
self.errorFailures = 0
self.saveSolution()
# here we just need to test the error and set to tOut if steady state
if self.nSteps == 0:
self.res0 = self.model.solver.solverList[-1].norm_r0
for m in self.model.levelModelList:
m.timeIntegration.choose_dt()
self.dt_model = self.start_ratio * self.model.levelModelList[0].timeIntegration.dt
res = self.model.solver.solverList[-1].norm_r0
ssError = old_div(res, (self.res0 * self.rtol + self.atol))
for m in self.model.levelModelList:
m.updateTimeHistory(self.t_model)
m.timeIntegration.updateTimeHistory()
if ((self.nSteps < self.nStepsOsher or
ssError >= 1.0) and
self.nSteps < self.nStepsMax):
self.nSteps += 1
self.dt_model = m.timeIntegration.dt
if self.nSteps >= self.nStepsOsher: # start ramping up the time step
self.dt_model = self.dt_model * self.red_ratio
#logEvent("Osher-PsiTC dt %12.5e" %(self.dt_model),level=1)
self.set_dt_allLevels()
# physical time step
self.t_model = self.substeps[0]
self.substeps.append(self.substeps[0])
logEvent("Osher-PsiTC iteration %d dt = %12.5e |res| = %12.5e %g " % (self.nSteps, self.dt_model, res, (old_div(res, self.res0)) * 100.0), level=1)
elif self.nSteps >= self.nStepsMax:
logEvent("Osher-PsiTC DID NOT Converge |res| = %12.5e but quitting anyway" % (res,))
logEvent("Osher-PsiTC tolerance %12.5e " % (self.res0 * self.rtol + self.atol,))
self.nSteps = 0
else:
logEvent("Osher-PsiTC converged |res| = %12.5e %12.5e" % (res, ssError * 100.0))
logEvent("Osher-PsiTC tolerance %12.5e " % (self.res0 * self.rtol + self.atol,))
self.nSteps = 0
def choose_dt_model(self):
# don't modify dt_model
self.solverFailures = 0
self.errorFailures = 0
self.saveSolution()
# pseudo time step
for m in self.model.levelModelList:
m.timeIntegration.choose_dt()
self.dt_model = self.start_ratio * m.timeIntegration.dt
self.set_dt_allLevels()
# physical time step
self.t_model = self.substeps[0]
self.setSubsteps([self.substeps[0]])
logEvent("Osher-PsiTC choosing dt = %12.5e " % (self.dt_model,))
class Coefficients(proteus.TransportCoefficients.TC_base):
from proteus.ctransportCoefficients import redistanceLevelSetCoefficientsEvaluate
def __init__(self,
applyRedistancing=True,
epsFact=2.0,
nModelId=None,
u0=None,
rdModelId=0,
penaltyParameter=0.0,
useMetrics=0.0,
useConstantH=False,
weakDirichletFactor=10.0,
backgroundDiffusionFactor=0.01,
# Parameters for elliptic re-distancing
computeMetrics = False,
ELLIPTIC_REDISTANCING=0, #Linear elliptic re-distancing by default
alpha=1.0E9,
backgroundDissipationEllipticRedist=1.0,
# OUTPUT quantDOFs
outputQuantDOFs=False,
# NULLSpace info
nullSpace='NoNullSpace', #penalization param for elliptic re-distancing
useExact=False,
copyList=True,
initialize=True):
self.copyList=copyList
self.useExact=useExact
self.useConstantH = useConstantH
self.useMetrics = useMetrics
variableNames = ['phid']
nc = 1
mass = {0: {0: 'linear'}}
hamiltonian = {0: {0: 'nonlinear'}}
advection = {}
diffusion = {}
potential = {}
reaction = {0: {0: 'constant'}}
TC_base.__init__(self,
nc,
mass,
advection,
diffusion,
potential,
reaction,
hamiltonian,
variableNames)
self.nModelId = nModelId
self.rdModelId = rdModelId
self.epsFact = epsFact
self.q_u0 = None
self.ebq_u0 = None
self.ebqe_u0 = None
self.dof_u0 = None
self.u0 = u0
self.applyRedistancing = applyRedistancing
self.weakBC_on = True # False
self.penaltyParameter = penaltyParameter
self.backgroundDiffusionFactor = backgroundDiffusionFactor
self.weakDirichletFactor = weakDirichletFactor
self.outputQuantDOFs=outputQuantDOFs
self.computeMetrics=computeMetrics
self.ELLIPTIC_REDISTANCING=ELLIPTIC_REDISTANCING
assert (ELLIPTIC_REDISTANCING >= 0 and ELLIPTIC_REDISTANCING <= 3), "ELLIPTIC_REDISTANCING=0,1,2 or 3."
#ELLIPTIC_REDISTANCING:
#0: Use default re-distancing in Proteus
#1: Non-linear elliptic re-distancing via single or doble pot.
# Uses single/double pot. with(out) |grad(u)| reconstructed. See c++ code
#2: Linear elliptic re-distancing via C0 normal reconstruction and single pot.
#3: Non-linear elliptic re-distancing via C0 normal reconstruction and single pot.
self.alpha=alpha
self.backgroundDissipationEllipticRedist=backgroundDissipationEllipticRedist
self.freeze_interface_within_elliptic_redist = False
if alpha=='inf':
self.alpha = 0
self.freeze_interface_within_elliptic_redist = True
self.nullSpace = nullSpace
if initialize:
self.initialize()
def initialize(self):
pass
def attachModels(self, modelList):
if self.nModelId is not None:
self.nModel = modelList[self.nModelId]
self.q_u0 = self.nModel.q[('u', 0)]
if ('u', 0) in self.nModel.ebq:
self.ebq_u0 = self.nModel.ebq[('u', 0)]
self.ebqe_u0 = self.nModel.ebqe[('u', 0)]
self.dof_u0 = self.nModel.u[0].dof
else:
self.nModel = None
self.rdModel = modelList[self.rdModelId]
def initializeMesh(self, mesh):
self.h = mesh.h
self.eps = self.epsFact * mesh.h
def initializeElementQuadrature(self, t, cq):
if self.nModelId is None:
if self.q_u0 is None:
self.q_u0 = np.zeros(cq[('u', 0)].shape, 'd')
if self.u0 is not None:
for i in range(len(cq[('u', 0)].flat)):
self.q_u0.flat[i] = self.u0.uOfXT(cq['x'].flat[3 * i:3 * (i + 1)], 0.)
def initializeElementBoundaryQuadrature(self, t, cebq, cebq_global):
if self.nModelId is None:
if self.ebq_u0 is None:
self.ebq_u0 = np.zeros(cebq[('u', 0)].shape, 'd')
if self.u0 is not None:
for i in range(len(cebq[('u', 0)].flat)):
self.ebq_u0.flat[i] = self.u0.uOfXT(cebq['x'].flat[3 * i:3 * (i + 1)], 0.)
def initializeGlobalExteriorElementBoundaryQuadrature(self, t, cebqe):
if self.nModelId is None:
if self.ebqe_u0 is None:
self.ebqe_u0 = np.zeros(cebqe[('u', 0)].shape, 'd')
if self.u0 is not None:
for i in range(len(cebqe[('u', 0)].flat)):
self.ebqe_u0.flat[i] = self.u0.uOfXT(cebqe['x'].flat[3 * i:3 * (i + 1)], 0.)
def preStep(self, t, firstStep=False):
# reset ellipticStage flag
self.rdModel.stage = 1
self.rdModel.auxEllipticFlag = 1
# COMPUTE NORMAL RECONSTRUCTION
if self.ELLIPTIC_REDISTANCING == 2: # linear via C0 normal reconstruction
self.rdModel.getNormalReconstruction()
# END OF NORMAL RECONSTRUCTION #
if self.nModel is not None:
logEvent("resetting signed distance level set to current level set", level=2)
self.rdModel.u[0].dof[:] = self.nModel.u[0].dof[:]
self.rdModel.calculateCoefficients()
self.rdModel.calculateElementResidual()
self.rdModel.timeIntegration.updateTimeHistory(resetFromDOF=True)
self.rdModel.timeIntegration.resetTimeHistory(resetFromDOF=True)
self.rdModel.updateTimeHistory(t, resetFromDOF=True)
# now do again because of subgrid error lagging
#\todo modify subgrid error lagging so this won't be necessary
self.rdModel.calculateCoefficients()
self.rdModel.calculateElementResidual()
self.rdModel.timeIntegration.updateTimeHistory(resetFromDOF=True)
self.rdModel.timeIntegration.resetTimeHistory(resetFromDOF=True)
self.rdModel.updateTimeHistory(t, resetFromDOF=True)
#copyInstructions = {'copy_uList': False,
# 'uList_model': self.nModelId}
#copyInstructions = {'reset_uList': False}
copyInstructions = {'copy_uList': self.copyList,
'uList_model': self.nModelId}
copyInstructions = {'reset_uList': self.copyList}
return copyInstructions
else:
return {}
def postStep(self, t, firstStep=False):
self.rdModel.quantDOFs[:] = self.rdModel.interface_locator
if self.nModel is not None:
if self.applyRedistancing == True:
logEvent("resetting level set to signed distance")
self.nModel.u[0].dof.flat[:] = self.rdModel.u[0].dof.flat[:]
self.nModel.calculateCoefficients()
self.nModel.calculateElementResidual()
# save the boundary level set in the numerical flux to use for
self.nModel.numericalFlux.ebqe[('u', 0)][:] = self.rdModel.ebqe[('u', 0)]
copyInstructions = {}
return copyInstructions
else:
return {}
def getICDofs(self, cj):
return self.dof_u0
def updateToMovingDomain(self, t, c):
# the redistancing equations is not physical so it just needs the updated mesh
pass
def evaluate(self, t, c):
if c[('H', 0)].shape == self.q_u0.shape:
u0 = self.q_u0
# print "numdiff",c[('numDiff',0,0)].min(),c[('numDiff',0,0)].max()
# print "tau",self.rdModel.stabilization.tau[0].min(),self.rdModel.stabilization.tau[0].max(),
elif c[('H', 0)].shape == self.ebqe_u0.shape:
u0 = self.ebqe_u0
else:
u0 = self.ebq_u0
assert u0 is not None
# \todo make redistancing epsilon depend on local element diamater instead of global max
self.redistanceLevelSetCoefficientsEvaluate(self.eps,
u0,
c[('u', 0)],
c[('grad(u)', 0)],
c[('m', 0)],
c[('dm', 0, 0)],
c[('H', 0)],
c[('dH', 0, 0)],
c[('r', 0)])
# weak Dirichlet conditions on level set (boundary conditions of Eikonal equation)
# \todo clean up weak Dirichlet conditions for Eikonal equation in transport coefficents
def setZeroLSweakDirichletBCs(vt):
if vt.coefficients.weakBC_on:
# print "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=========================Setting new weak BC's=======================!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
vt.dirichletNodeSetList[0] = []
vt.dirichletGlobalNodeSet[0] = set()
vt.dirichletValues[0] = {}
for eN in range(vt.mesh.nElements_global):
vt.dirichletNodeSetList[0].append(set())
signU = 0
j0 = 0
eps = vt.u[0].femSpace.mesh.elementDiametersArray[eN]
# loop over nodes looking for a node not within eps of zero
while ((signU == 0) and
(j0 < vt.nDOF_trial_element[0])):
J0 = vt.u[0].femSpace.dofMap.l2g[eN, j0]
if vt.u[0].dof[J0] < -eps:
signU = -1
elif vt.u[0].dof[J0] > eps:
signU = 1
else: # freeze this node within eps of zero
vt.dirichletNodeSetList[0][eN].add(j0)
vt.dirichletValues[0][(eN, j0)] = vt.u[0].dof[J0]
vt.dirichletGlobalNodeSet[0].add(J0)
j0 += 1
# loop over remaining nodes to see if the zero level set cuts element
for j in range(j0, vt.nDOF_trial_element[0]):
J = vt.u[0].femSpace.dofMap.l2g[eN, j]
if (((vt.u[0].dof[J] < -eps) and
(signU == 1)) or
((vt.u[0].dof[J] > eps) and
(signU == -1))): # level set cuts element, freeze whole element
for jj in range(vt.nDOF_trial_element[0]):
JJ = vt.u[0].femSpace.dofMap.l2g[eN, jj]
vt.dirichletNodeSetList[0][eN].add(jj)
vt.dirichletValues[0][(eN, jj)] = float(vt.u[0].dof[JJ])
vt.dirichletGlobalNodeSet[0].add(JJ)
break
elif (fabs(vt.u[0].dof[J]) < eps): # freeze this node within eps of zero
vt.dirichletNodeSetList[0][eN].add(j)
vt.dirichletValues[0][(eN, j)] = float(vt.u[0].dof[J])
vt.dirichletGlobalNodeSet[0].add(J)
# get all frozen dof and make sure they're frozen on each element
for eN in range(vt.mesh.nElements_global):
for j in range(vt.nDOF_trial_element[0]):
J = vt.u[0].femSpace.dofMap.l2g[eN, j]
if J in vt.dirichletGlobalNodeSet[0]:
vt.dirichletNodeSetList[0][eN].add(j)
vt.dirichletValues[0][(eN, j)] = float(vt.u[0].dof[J])
else:
# print "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=========================Unsetting weak BC's=======================!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
vt.dirichletNodeSetList[0] = []
vt.dirichletGlobalNodeSet[0] = set()
vt.dirichletValues[0] = {}
for eN in range(vt.mesh.nElements_global):
vt.dirichletNodeSetList[0].append(set())
def setZeroLSweakDirichletBCs2(vt):
# just look for cut edges and nodes
vt.dirichletNodeSetList[0] = []
vt.dirichletGlobalNodeSet[0] = set()
vt.dirichletValues[0] = {}
for eN in range(vt.mesh.nElements_global):
vt.dirichletNodeSetList[0].append(set())
signU = 0
j0 = 0
eps = .1 * vt.u[0].femSpace.mesh.elementDiametersArray[eN]
eps = 0.0
for j0 in range(vt.nDOF_trial_element[0]):
J0 = vt.u[0].femSpace.dofMap.l2g[eN, j0]
if vt.u[0].dof[J0] < -eps:
signU = -1
elif vt.u[0].dof[J0] > eps:
signU = 1
else:
vt.dirichletNodeSetList[0][eN].add(j0)
vt.dirichletValues[0][(eN, j0)] = float(vt.u[0].dof[J0])
vt.dirichletGlobalNodeSet[0].add(J0)
if signU != 0:
for j in (list(range(0, j0)) + list(range(j0 + 1, vt.nDOF_trial_element[0]))):
J = vt.u[0].femSpace.dofMap.l2g[eN, j]
if (((vt.u[0].dof[J] < -eps) and
(signU == 1)) or
((vt.u[0].dof[J] > eps) and
(signU == -1))):
vt.dirichletNodeSetList[0][eN].add(j)
vt.dirichletValues[0][(eN, j)] = float(vt.u[0].dof[J])
vt.dirichletGlobalNodeSet[0].add(J)
vt.dirichletNodeSetList[0][eN].add(j0)
vt.dirichletValues[0][(eN, j0)] = float(vt.u[0].dof[j0])
vt.dirichletGlobalNodeSet[0].add(j0)
for eN in range(vt.mesh.nElements_global):
for j in range(vt.nDOF_trial_element[0]):
J = vt.u[0].femSpace.dofMap.l2g[eN, j]
if J in vt.dirichletGlobalNodeSet[0]:
vt.dirichletNodeSetList[0][eN].add(j)
vt.dirichletValues[0][(eN, j)] = float(vt.u[0].dof[J])
def setZeroLSweakDirichletBCs3(vt):
if vt.coefficients.weakBC_on:
# print "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=========================Setting new weak BC's=======================!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
vt.dirichletNodeSetList[0] = []
vt.dirichletGlobalNodeSet[0] = set()
vt.dirichletValues[0] = {}
for eN in range(vt.mesh.nElements_global):
vt.dirichletNodeSetList[0].append(set())
eps = vt.coefficients.epsFact * vt.u[0].femSpace.mesh.elementDiametersArray[eN]
#eps = 1.5*vt.u[0].femSpace.mesh.elementDiametersArray[eN]
# loop over nodes looking for a node not within eps of zero
for j in range(vt.nDOF_trial_element[0]):
J = vt.u[0].femSpace.dofMap.l2g[eN, j]
if (fabs(vt.u[0].dof[J]) < eps): # freeze this node within eps of zero
vt.dirichletNodeSetList[0][eN].add(j)
vt.dirichletValues[0][(eN, j)] = float(vt.u[0].dof[J])
vt.dirichletGlobalNodeSet[0].add(J)
else:
# print "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=========================Unsetting weak BC's=======================!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
vt.dirichletNodeSetList[0] = []
vt.dirichletGlobalNodeSet[0] = set()
vt.dirichletValues[0] = {}
for eN in range(vt.mesh.nElements_global):
vt.dirichletNodeSetList[0].append(set())
# def
setZeroLSweakDirichletBCs = staticmethod(setZeroLSweakDirichletBCs)
setZeroLSweakDirichletBCs2 = staticmethod(setZeroLSweakDirichletBCs2)
setZeroLSweakDirichletBCs3 = staticmethod(setZeroLSweakDirichletBCs3)
debugRDLS = False # True
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,
bdyNullSpace=False):
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.bdyNullSpace = bdyNullSpace
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 is not None:
for ci in range(self.nc):
if ci in coefficients.mass:
for flag in list(coefficients.mass[ci].values()):
if flag == 'nonlinear':
self.stabilizationIsNonlinear = True
if ci in coefficients.advection:
for flag in list(coefficients.advection[ci].values()):
if flag == 'nonlinear':
self.stabilizationIsNonlinear = True
if ci in coefficients.diffusion:
for diffusionDict in list(coefficients.diffusion[ci].values()):
for flag in list(diffusionDict.values()):
if flag != 'constant':
self.stabilizationIsNonlinear = True
if ci in coefficients.potential:
for flag in list(coefficients.potential[ci].values()):
if flag == 'nonlinear':
self.stabilizationIsNonlinear = True
if ci in coefficients.reaction:
for flag in list(coefficients.reaction[ci].values()):
if flag == 'nonlinear':
self.stabilizationIsNonlinear = True
if ci in coefficients.hamiltonian:
for flag in list(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 is not None) or
(numericalFluxType is not 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 list(self.u.values())]
self.nDOF_phi_trial_element = [phi_k.femSpace.max_nDOF_element for phi_k in list(self.phi.values())]
self.n_phi_ip_element = [phi_k.femSpace.referenceFiniteElement.interpolationConditions.nQuadraturePoints for phi_k in list(self.phi.values())]
self.nDOF_test_element = [femSpace.max_nDOF_element for femSpace in list(self.testSpace.values())]
self.nFreeDOF_global = [dc.nFreeDOF_global for dc in list(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 I in elementQuadrature:
elementQuadratureDict[I] = elementQuadrature[I]
else:
elementQuadratureDict[I] = elementQuadrature['default']
else:
for I in self.coefficients.elementIntegralKeys:
elementQuadratureDict[I] = elementQuadrature
if self.stabilization is not None:
for I in self.coefficients.elementIntegralKeys:
if elemQuadIsDict:
if I in elementQuadrature:
elementQuadratureDict[('stab',) + I[1:]] = elementQuadrature[I]
else:
elementQuadratureDict[('stab',) + I[1:]] = elementQuadrature['default']
else:
elementQuadratureDict[('stab',) + I[1:]] = elementQuadrature
if self.shockCapturing is not None:
for ci in self.shockCapturing.components:
if elemQuadIsDict:
if ('numDiff', ci, ci) in elementQuadrature:
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 list(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 list(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 I in elementBoundaryQuadrature:
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 isinstance(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)
#
# 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'] = np.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element,3),'d')
self.ebqe['x'] = np.zeros((self.mesh.nExteriorElementBoundaries_global, self.nElementBoundaryQuadraturePoints_elementBoundary, 3), 'd')
self.q[('u', 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element), 'd')
self.q[('grad(u)', 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element, self.nSpace_global), 'd')
self.q[('m_last', 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element), 'd')
self.q[('m_tmp', 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element), 'd')
self.q[('m', 0)] = self.q[('u', 0)] # for time integration by VBDF and probably FLCBDF
# needed by PsiTCtte
self.q[('mt', 0)] = np.zeros(self.q[('u', 0)].shape, 'd')
self.q[('dH', 0, 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element, self.nSpace_global), 'd')
self.q[('dH_sge', 0, 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element, self.nSpace_global), 'd')
self.q[('cfl', 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element), 'd')
self.q[('numDiff', 0, 0)] = np.zeros((self.mesh.nElements_global, self.nQuadraturePoints_element), 'd')
self.ebqe[('u', 0)] = np.zeros((self.mesh.nExteriorElementBoundaries_global, self.nElementBoundaryQuadraturePoints_elementBoundary), 'd')
self.ebqe[('grad(u)', 0)] = np.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()
self.inflowBoundaryBC = {}
self.inflowBoundaryBC_values = {}
self.inflowFlux = {}
for cj in range(self.nc):
self.inflowBoundaryBC[cj] = np.zeros((self.mesh.nExteriorElementBoundaries_global,), 'i')
self.inflowBoundaryBC_values[cj] = np.zeros((self.mesh.nExteriorElementBoundaries_global, self.nDOF_trial_element[cj]), 'd')
self.inflowFlux[cj] = np.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 = np.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 is not 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 is not None and numericalFluxType.useWeakDirichletConditions, "You must use a numerical flux to apply weak boundary conditions for parallel runs"
# add some structures for elliptic re-distancing
self.quantDOFs = np.zeros(self.u[0].dof.shape, 'd')
self.interface_locator = None
self.lumped_qx = np.zeros(self.u[0].dof.shape,'d')
self.lumped_qy = np.zeros(self.u[0].dof.shape,'d')
self.lumped_qz = np.zeros(self.u[0].dof.shape,'d')
self.stage = 1
self.auxEllipticFlag = 1
if self.coefficients.ELLIPTIC_REDISTANCING==2:
self.useTwoStageNewton = True
# ASSERT: If ELLIPTIC_REDISTANCING>0 make sure that a two stage newton solver is used
if self.coefficients.ELLIPTIC_REDISTANCING>0:
assert options.levelNonlinearSolver == proteus.NonlinearSolvers.TwoStageNewton, "If ELLIPTIC REDISTANCING>0, use levelNonlinearSolver=TwoStageNewton"
# ASSERT: if order>1 and ELLIPTIC_REDISTANCING>0 then use bernstein polynomials
if self.coefficients.ELLIPTIC_REDISTANCING>0 and self.u[0].femSpace.order>1:
isBernsteinOnCube = isinstance(self.u[0].femSpace,
proteus.FemTools.C0_AffineBernsteinOnCube)
isBernsteinOnSimplex = isinstance(self.u[0].femSpace,
proteus.FemTools.C0_AffineBernsteinOnSimplex)
isBernstein = isBernsteinOnCube or isBernsteinOnSimplex
assert isBernstein==True, "If order>1 and ELLIPTIC_REDISTANCING=True, use Bernstein polynomials"
logEvent(memory("stride+offset", "OneLevelTransport"), level=4)
if numericalFluxType is not None:
if options is None or options.periodicDirichletConditions is 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 'penalty' in self.ebq_global:
for ebN in range(self.mesh.nElementBoundaries_global):
for k in range(self.nElementBoundaryQuadraturePoints_elementBoundary):
self.ebq_global['penalty'][ebN, k] = old_div(self.numericalFlux.penalty_constant, \
(self.mesh.elementBoundaryDiametersArray[ebN]**self.numericalFlux.penalty_power))
# penalty term
# cek move to Numerical flux initialization
if 'penalty' in self.ebqe:
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] = old_div(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()
# TODO get rid of this
for ci, fbcObject in list(self.fluxBoundaryConditionsObjectsDict.items()):
self.ebqe[('advectiveFlux_bc_flag', ci)] = np.zeros(self.ebqe[('advectiveFlux_bc', ci)].shape, 'i')
for t, g in list(fbcObject.advectiveFluxBoundaryConditionsDict.items()):
if ci in self.coefficients.advection:
self.ebqe[('advectiveFlux_bc', ci)][t[0], t[1]] = g(self.ebqe[('x')][t[0], t[1]], self.timeIntegration.t)
self.ebqe[('advectiveFlux_bc_flag', ci)][t[0], t[1]] = 1
# reduced quad
if hasattr(self.numericalFlux, 'setDirichletValues'):
self.numericalFlux.setDirichletValues(self.ebqe)
if not hasattr(self.numericalFlux, 'isDOFBoundary'):
self.numericalFlux.isDOFBoundary = {0: np.zeros(self.ebqe[('u', 0)].shape, 'i')}
if not hasattr(self.numericalFlux, 'ebqe'):
self.numericalFlux.ebqe = {('u', 0): np.zeros(self.ebqe[('u', 0)].shape, 'd')}
# TODO how to handle redistancing calls for calculateCoefficients,calculateElementResidual etc
self.globalResidualDummy = None
# create storage for enforcing weak dirichlet boundary conditions around zero level set contour
self.freezeLevelSet = 1 # True
self.u_dof_last = np.zeros(self.u[0].dof.shape, 'd')
self.weakDirichletConditionFlags = np.zeros(self.u[0].dof.shape, 'i')
self.dofFlag_element = np.zeros((self.nDOF_trial_element[0],), 'i')
# allow Newton solves for redistancing
if self.timeIntegration.__class__ == TimeIntegration.NoIntegration:
self.timeIntegration.m_tmp = {0: np.zeros(self.q[('m_tmp', 0)].shape, 'd')}
self.timeIntegration.m_last = {0: np.zeros(self.q[('m_tmp', 0)].shape, 'd')}
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.rdls = cRDLS_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)
###########
# METRICS #
###########
self.hasExactSolution = False
if ('exactSolution') in dir (options):
self.hasExactSolution = True
self.exactSolution = options.exactSolution
# metrics
self.global_I_err = 0.0
self.global_V_err = 0.0
self.global_D_err = 0.0
if self.coefficients.computeMetrics:
self.metricsAtEOS = open(self.name+"_metricsAtEOS.csv","w")
self.metricsAtEOS.write('global_I_err'+","+
'global_V_err'+","+
'global_D_err'+"\n")
####################################3
def runAtEOS(self):
if self.coefficients.computeMetrics==True and self.hasExactSolution==True:
# Get exact solution at quad points
u_exact = np.zeros(self.q[('u',0)].shape,'d')
X = {0:self.q[('x')][:,:,0],
1:self.q[('x')][:,:,1],
2:self.q[('x')][:,:,2]}
t = self.timeIntegration.t
u_exact[:] = self.exactSolution[0](X,t)
self.getMetricsAtEOS(u_exact)
self.metricsAtEOS.write(repr(self.global_I_err)+","+
repr(self.global_V_err)+","+
repr(self.global_D_err)+"\n")
self.metricsAtEOS.flush()
def getMetricsAtEOS(self,u_exact):
import copy
"""
Calculate the element residuals and add in to the global residual
"""
degree_polynomial = 1
try:
degree_polynomial = self.u[0].femSpace.order
except:
pass
argsDict = cArgumentsDict.ArgumentsDict()
argsDict["mesh_trial_ref"] = self.u[0].femSpace.elementMaps.psi
argsDict["mesh_grad_trial_ref"] = self.u[0].femSpace.elementMaps.grad_psi
argsDict["mesh_dof"] = self.mesh.nodeArray
argsDict["mesh_l2g"] = self.mesh.elementNodesArray
argsDict["dV_ref"] = self.elementQuadratureWeights[('u',0)]
argsDict["u_trial_ref"] = self.u[0].femSpace.psi
argsDict["u_grad_trial_ref"] = self.u[0].femSpace.grad_psi
argsDict["u_test_ref"] = self.u[0].femSpace.psi
argsDict["nElements_global"] = self.mesh.nElements_global
argsDict["u_l2g"] = self.u[0].femSpace.dofMap.l2g
argsDict["elementDiameter"] = self.mesh.elementDiametersArray
argsDict["degree_polynomial"] = degree_polynomial
argsDict["epsFact_redist"] = self.coefficients.epsFact
argsDict["u_dof"] = self.u[0].dof
argsDict["u_exact"] = u_exact
argsDict["offset_u"] = self.offset[0]
argsDict["stride_u)"] = self.stride[0]
(self.global_I_err,
self.global_V_err,
self.global_D_err) = self.rdls.calculateMetricsAtEOS(argsDict)
###############################################
def calculateCoefficients(self):
pass
def calculateElementResidual(self):
pass
def getNormalReconstruction(self):
argsDict = cArgumentsDict.ArgumentsDict()
argsDict["mesh_trial_ref"] = self.u[0].femSpace.elementMaps.psi
argsDict["mesh_grad_trial_ref"] = self.u[0].femSpace.elementMaps.grad_psi
argsDict["mesh_dof"] = self.mesh.nodeArray
argsDict["mesh_l2g"] = self.mesh.elementNodesArray
argsDict["dV_ref"] = self.elementQuadratureWeights[('u',0)]
argsDict["u_trial_ref"] = self.u[0].femSpace.psi
argsDict["u_grad_trial_ref"] = self.u[0].femSpace.grad_psi
argsDict["u_test_ref"] = self.u[0].femSpace.psi
argsDict["nElements_global"] = self.mesh.nElements_global
argsDict["u_l2g"] = self.u[0].femSpace.dofMap.l2g
argsDict["elementDiameter"] = self.mesh.elementDiametersArray
argsDict["u_dof"] = self.u[0].dof
argsDict["offset_u"] = self.offset[0]
argsDict["stride_u"] = self.stride[0]
argsDict["numDOFs"] = self.nFreeDOF_global[0]
argsDict["lumped_qx"] = self.lumped_qx
argsDict["lumped_qy"] = self.lumped_qy
argsDict["lumped_qz"] = self.lumped_qz
self.rdls.normalReconstruction(argsDict)
def getResidual(self, u, r):
import pdb
import copy
if self.interface_locator is None:
if self.coefficients.nModel is not None:
self.interface_locator = self.coefficients.nModel.interface_locator
else:
self.interface_locator = np.zeros(self.u[0].dof.shape,'d')
# try to use 1d,2d,3d specific modules
r.fill(0.0)
# Load the unknowns into the finite element dof
self.timeIntegration.calculateCoefs()
self.timeIntegration.calculateU(u)
self.setUnknowns(self.timeIntegration.u)
# cek can put in logic to skip of BC's don't depend on t or u
# Dirichlet boundary conditions
if hasattr(self.numericalFlux, 'setDirichletValues'):
self.numericalFlux.setDirichletValues(self.ebqe)
# flux boundary conditions, SHOULDN'T HAVE
# for now force time integration
useTimeIntegration = 1
#assert self.timeIntegration.__class__ != TimeIntegration.NoIntegration
if self.timeIntegration.__class__ == TimeIntegration.NoIntegration or not self.timeTerm:
useTimeIntegration = 0