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RANS3P.py
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RANS3P.py
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import proteus
from proteus.mprans.cRANS3P import *
class Coefficients(proteus.TransportCoefficients.TC_base):
"""
The coefficients for two incompresslble fluids governed by the Navier-Stokes equations and separated by a sharp interface represented by a level set function
"""
from proteus.ctransportCoefficients import TwophaseNavierStokes_ST_LS_SO_2D_Evaluate
from proteus.ctransportCoefficients import TwophaseNavierStokes_ST_LS_SO_3D_Evaluate
from proteus.ctransportCoefficients import TwophaseNavierStokes_ST_LS_SO_2D_Evaluate_sd
from proteus.ctransportCoefficients import TwophaseNavierStokes_ST_LS_SO_3D_Evaluate_sd
def __init__(self,
epsFact=1.5,
sigma=72.8,
rho_0=998.2,nu_0=1.004e-6,
rho_1=1.205,nu_1=1.500e-5,
g=[0.0,-9.8],
nd=2,
SED_model_ID=None,
LS_model=None,
KN_model=None,
epsFact_density=None,
stokes=False,
sd=True,
movingDomain=False,
useRBLES=0.0,
useMetrics=0.0,useConstantH=False):
self.useConstantH = useConstantH
self.useRBLES=useRBLES
self.useMetrics=useMetrics
self.sd=sd
if epsFact_density != None:
self.epsFact_density = epsFact_density
else:
self.epsFact_density = epsFact
self.stokes=stokes
self.SED_model_ID=SED_model_ID
self.LS_model=LS_model
self.KN_model=KN_model
self.epsFact=epsFact
self.eps=None
self.sigma=sigma
self.rho_0 = rho_0
self.nu_0 = nu_0
#cek for debugging using single phase test problems
self.rho=rho_0
self.nu=nu_0
self.rho_1 = rho_1
self.nu_1 = nu_1
self.g = numpy.array(g)
self.nd=nd
mass={}
advection={}
diffusion={}
potential={}
reaction={}
hamiltonian={}
if nd==2:
variableNames=['p','u','v']
mass= {0:{0:'linear'},#really constant
1:{1:'linear'},
2:{2:'linear'}}
advection = {0:{0:'linear',
1:'linear',
2:'linear'},
1:{0:'nonlinear',
1:'nonlinear',
2:'nonlinear'},
2:{0:'nonlinear',
1:'nonlinear',
2:'nonlinear'}}
diffusion = {1:{1:{1:'constant'},2:{2:'constant'}},
2:{2:{2:'constant'},1:{1:'constant'}}}
sdInfo = {(1,1):(numpy.array([0,1,2],dtype='i'),
numpy.array([0,1],dtype='i')),
(1,2):(numpy.array([0,0,1],dtype='i'),
numpy.array([0],dtype='i')),
(2,2):(numpy.array([0,1,2],dtype='i'),
numpy.array([0,1],dtype='i')),
(2,1):(numpy.array([0,1,1],dtype='i'),
numpy.array([1],dtype='i'))}
potential= {1:{1:'u'},
2:{2:'u'}}
reaction = {0:{0:'constant'},#added for Lin, Liu wave forcing
1:{1:'constant'},
2:{2:'constant'}}
hamiltonian = {1:{0:'linear'},
2:{0:'linear'}}
TC_base.__init__(self,
3,
mass,
advection,
diffusion,
potential,
reaction,
hamiltonian,
variableNames,
sparseDiffusionTensors=sdInfo,
useSparseDiffusion = sd,
movingDomain=movingDomain)
self.vectorComponents=[1,2]
elif nd==3:
variableNames=['p','u','v','w']
mass = {0:{0:'linear'},#really constant
1:{1:'linear'},
2:{2:'linear'},
3:{3:'linear'}}
advection = {0:{1:'linear',
2:'linear',
3:'linear'},
1:{0:'nonlinear',
1:'nonlinear',
2:'nonlinear',
3:'nonlinear'},
2:{0:'nonlinear',
1:'nonlinear',
2:'nonlinear',
3:'nonlinear'},
3:{0:'nonlinear',
1:'nonlinear',
2:'nonlinear',
3:'nonlinear'}}
diffusion = {1:{1:{1:'constant'},2:{2:'constant'},3:{3:'constant'}},
2:{1:{1:'constant'},2:{2:'constant'},3:{3:'constant'}},
3:{1:{1:'constant'},2:{2:'constant'},3:{3:'constant'}}}
sdInfo={}
sdInfo = {(1,1):(numpy.array([0,1,2,3],dtype='i'),numpy.array([0,1,2],dtype='i')),
(1,2):(numpy.array([0,0,1,1],dtype='i'),numpy.array([0],dtype='i')),
(1,3):(numpy.array([0,0,0,1],dtype='i'),numpy.array([0],dtype='i')),
(2,1):(numpy.array([0,1,1,1],dtype='i'),numpy.array([1],dtype='i')),
(2,2):(numpy.array([0,1,2,3],dtype='i'),numpy.array([0,1,2],dtype='i')),
(2,3):(numpy.array([0,0,0,1],dtype='i'),numpy.array([1],dtype='i')),
(3,1):(numpy.array([0,1,1,1],dtype='i'),numpy.array([2],dtype='i')),
(3,2):(numpy.array([0,0,1,1],dtype='i'),numpy.array([2],dtype='i')),
(3,3):(numpy.array([0,1,2,3],dtype='i'),numpy.array([0,1,2],dtype='i'))}
potential= {1:{1:'u'},
2:{2:'u'},
3:{3:'u'}}
reaction = {0:{0:'constant'},#added for Lin, Liu wave forcing,
1:{1:'constant'},
2:{2:'constant'},
3:{3:'constant'}}
hamiltonian = {1:{0:'linear'},
2:{0:'linear'},
3:{0:'linear'}}
TC_base.__init__(self,
4,
mass,
advection,
diffusion,
potential,
reaction,
hamiltonian,
variableNames,
sparseDiffusionTensors=sdInfo,
useSparseDiffusion = sd,
movingDomain=movingDomain)
self.vectorComponents=[1,2,3]
def attachModels(self,modelList):
#level set
self.model = modelList[0]
if self.SED_model_ID != None:
self.SED_model = modelList[self.SED_model_ID]
self.C_dof = self.SED_model.u[0].dof
self.q_sedimentForce = self.SED_model.q['sedimentForce']
else:
self.SED_model = None
self.C_dof = self.model.u[0].dof.copy()
self.C_dof[:]=0.5
self.q_sedimentForce = self.model.q[('velocity',0)].copy()
self.q_sedimentForce[:]=0.0
if self.LS_model != None:
self.q_phi = modelList[self.LS_model].q[('u',0)]
if modelList[self.LS_model].ebq.has_key(('u',0)):
self.ebq_phi = modelList[self.LS_model].ebq[('u',0)]
else:
self.ebq_phi = None
self.ebqe_phi = modelList[self.LS_model].ebqe[('u',0)]
#normal
self.q_n = modelList[self.LS_model].q[('grad(u)',0)]
if modelList[self.LS_model].ebq.has_key(('grad(u)',0)):
self.ebq_n = modelList[self.LS_model].ebq[('grad(u)',0)]
else:
self.ebq_n = None
self.ebqe_n = modelList[self.LS_model].ebqe[('grad(u)',0)]
#curvature
if self.KN_model != None:
self.q_kappa = modelList[self.KN_model].q[('u',0)]
self.ebqe_kappa = modelList[self.KN_model].ebqe[('u',0)]
if modelList[self.KN_model].ebq.has_key(('u',0)):
self.ebq_kappa = modelList[self.KN_model].ebq[('u',0)]
else:
self.ebq_kappa = None
def initializeMesh(self,mesh):
#cek we eventually need to use the local element diameter
self.eps_density = self.epsFact_density*mesh.h
self.eps_viscosity = self.epsFact*mesh.h
#initialize so it can run as single phase
def initializeElementQuadrature(self,t,cq):
if self.LS_model == None:
self.q_phi = -numpy.ones(cq[('u',1)].shape,'d')
self.q_n = -numpy.ones(cq[('velocity',0)].shape,'d')
if self.KN_model == None:
self.q_kappa = -numpy.zeros(cq[('u',1)].shape,'d')
def initializeElementBoundaryQuadrature(self,t,cebq,cebq_global):
if self.LS_model == None:
self.ebq_phi = -numpy.ones(cebq[('u',1)].shape,'d')
self.ebq_n = -numpy.ones(cebq[('velocity',0)].shape,'d')
if self.KN_model == None:
self.ebq_kappa = -numpy.zeros(cebq[('u',1)].shape,'d')
def initializeGlobalExteriorElementBoundaryQuadrature(self,t,cebqe):
if self.LS_model == None:
self.ebqe_phi = -numpy.ones(cebqe[('u',1)].shape,'d')
self.ebqe_n = -numpy.ones(cebqe[('velocity',0)].shape,'d')
if self.KN_model == None:
self.ebqe_kappa = -numpy.zeros(cebqe[('u',1)].shape,'d')
def updateToMovingDomain(self,t,c):
pass
def evaluate(self,t,c):
import math
#self.rho_0 = 1000.0*self.rho_1
#self.nu_0 = 0.1*self.nu_1
if c[('u',0)].shape == self.q_phi.shape:
phi = self.q_phi
n = self.q_n
kappa = self.q_kappa
#slopeAngle=0.1*math.pi/2.0#math.pi/4.0
#surfaceNormal = [-sin(slopeAngle),cos(slopeAngle)]
#waterLevel=0.5
#for eN in range(phi.shape[0]):
# for k in range(phi.shape[1]):
# phi[eN,k] = (c['x'][eN,k,0] - 0.5)*surfaceNormal[0]+(c['x'][eN,k,1] - waterLevel)*surfaceNormal[1]
elif c[('u',0)].shape == self.ebqe_phi.shape:
phi = self.ebqe_phi
n = self.ebqe_n
kappa = self.ebqe_kappa
else:
phi = self.ebq_phi
n = self.ebq_n
kappa = self.ebq_kappa
#mwf debug
#waterLevelBase = 0.529
#for i in range(len(phi.flat)):
#if abs(phi.flat[i]) > 0.0:
# assert abs(phi.flat[i] - (c['x'].flat[3*i+1] - waterLevelBase)) <= 1.0e-5, "Problem with phi t=%s phi.shape=%s i=%s phi=%s y=%s wl=%s " % (t,phi.shape,i,phi.flat[i],c['x'].flat[3*i+1],waterLevelBase)
#phi.flat[i] = c['x'].flat[3*i+1] - waterLevelBase#self.waterLevel
#self.sd=False
if self.nd==2:
if self.sd:
self.TwophaseNavierStokes_ST_LS_SO_2D_Evaluate_sd(self.eps_density,
self.eps_viscosity,
self.sigma,
self.rho_0,
self.nu_0,
self.rho_1,
self.nu_1,
self.g,
phi,
n,
kappa,
c[('u',0)],
c[('grad(u)',0)],
c[('u',1)],
c[('u',2)],
c[('m',1)],
c[('dm',1,1)],
c[('m',2)],
c[('dm',2,2)],
c[('f',0)],
c[('df',0,1)],
c[('df',0,2)],
c[('f',1)],
c[('df',1,1)],
c[('df',1,2)],
c[('f',2)],
c[('df',2,1)],
c[('df',2,2)],
c[('a',1,1)],
c[('a',2,2)],
c[('a',1,2)],
c[('a',2,1)],
c[('r',1)],
c[('r',2)],
c[('H',1)],
c[('dH',1,0)],
c[('H',2)],
c[('dH',2,0)])
else:
self.TwophaseNavierStokes_ST_LS_SO_2D_Evaluate(self.eps_density,
self.eps_viscosity,
self.sigma,
self.rho_0,
self.nu_0,
self.rho_1,
self.nu_1,
self.g,
phi,
n,
kappa,
c[('u',0)],
c[('grad(u)',0)],
c[('u',1)],
c[('u',2)],
c[('m',1)],
c[('dm',1,1)],
c[('m',2)],
c[('dm',2,2)],
c[('f',0)],
c[('df',0,1)],
c[('df',0,2)],
c[('f',1)],
c[('df',1,1)],
c[('df',1,2)],
c[('f',2)],
c[('df',2,1)],
c[('df',2,2)],
c[('a',1,1)],
c[('a',2,2)],
c[('a',1,2)],
c[('a',2,1)],
c[('r',1)],
c[('r',2)],
c[('H',1)],
c[('dH',1,0)],
c[('H',2)],
c[('dH',2,0)])
if self.stokes:
c[('f',1)].flat[:] = 0.0
c[('df',1,1)].flat[:] = 0.0
c[('df',1,2)].flat[:] = 0.0
c[('f',2)].flat[:] = 0.0
c[('df',2,1)].flat[:] = 0.0
c[('df',2,2)].flat[:] = 0.0
elif self.nd==3:
if self.sd:
self.TwophaseNavierStokes_ST_LS_SO_3D_Evaluate_sd(self.eps_density,
self.eps_viscosity,
self.sigma,
self.rho_0,
self.nu_0,
self.rho_1,
self.nu_1,
self.g,
phi,
n,
kappa,
c[('u',0)],
c[('grad(u)',0)],
c[('u',1)],
c[('u',2)],
c[('u',3)],
c[('m',1)],
c[('dm',1,1)],
c[('m',2)],
c[('dm',2,2)],
c[('m',3)],
c[('dm',3,3)],
c[('f',0)],
c[('df',0,1)],
c[('df',0,2)],
c[('df',0,3)],
c[('f',1)],
c[('df',1,1)],
c[('df',1,2)],
c[('df',1,3)],
c[('f',2)],
c[('df',2,1)],
c[('df',2,2)],
c[('df',2,3)],
c[('f',3)],
c[('df',3,1)],
c[('df',3,2)],
c[('df',3,3)],
c[('a',1,1)],
c[('a',2,2)],
c[('a',3,3)],
c[('a',1,2)],
c[('a',1,3)],
c[('a',2,1)],
c[('a',2,3)],
c[('a',3,1)],
c[('a',3,2)],
c[('r',1)],
c[('r',2)],
c[('r',3)],
c[('H',1)],
c[('dH',1,0)],
c[('H',2)],
c[('dH',2,0)],
c[('H',3)],
c[('dH',3,0)])
else:
self.TwophaseNavierStokes_ST_LS_SO_3D_Evaluate(self.eps_density,
self.eps_viscosity,
self.sigma,
self.rho_0,
self.nu_0,
self.rho_1,
self.nu_1,
self.g,
phi,
n,
kappa,
c[('u',0)],
c[('grad(u)',0)],
c[('u',1)],
c[('u',2)],
c[('u',3)],
c[('m',1)],
c[('dm',1,1)],
c[('m',2)],
c[('dm',2,2)],
c[('m',3)],
c[('dm',3,3)],
c[('f',0)],
c[('df',0,1)],
c[('df',0,2)],
c[('df',0,3)],
c[('f',1)],
c[('df',1,1)],
c[('df',1,2)],
c[('df',1,3)],
c[('f',2)],
c[('df',2,1)],
c[('df',2,2)],
c[('df',2,3)],
c[('f',3)],
c[('df',3,1)],
c[('df',3,2)],
c[('df',3,3)],
c[('a',1,1)],
c[('a',2,2)],
c[('a',3,3)],
c[('a',1,2)],
c[('a',1,3)],
c[('a',2,1)],
c[('a',2,3)],
c[('a',3,1)],
c[('a',3,2)],
c[('r',1)],
c[('r',2)],
c[('r',3)],
c[('H',1)],
c[('dH',1,0)],
c[('H',2)],
c[('dH',2,0)],
c[('H',3)],
c[('dH',3,0)])
if self.stokes:
c[('f',1)].flat[:] = 0.0
c[('df',1,1)].flat[:] = 0.0
c[('df',1,2)].flat[:] = 0.0
c[('df',1,3)].flat[:] = 0.0
c[('f',2)].flat[:] = 0.0
c[('df',2,1)].flat[:] = 0.0
c[('df',2,2)].flat[:] = 0.0
c[('df',2,3)].flat[:] = 0.0
c[('f',3)].flat[:] = 0.0
c[('df',3,1)].flat[:] = 0.0
c[('df',3,2)].flat[:] = 0.0
c[('df',3,3)].flat[:] = 0.0
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,
stressTraceBoundaryConditionsSetterDictDict=None,
stabilization=None,
shockCapturing=None,
conservativeFluxDict=None,
numericalFluxType=None,
TimeIntegrationClass=None,
massLumping=False,
reactionLumping=False,
options=None,
name='RANS3P',
reuse_trial_and_test_quadrature=True,
sd = True,
movingDomain=False):
useConstantH=coefficients.useConstantH#this is a hack to test the effect of using a constant smoothing width
self.postProcessing = False#this is a hack to test the effect of post-processing
if self.postProcessing:
from proteus import RANS3P as oldRANS3P
self.tmpvt = oldRANS3P.OneLevelRANS3P(uDict,
phiDict,
testSpaceDict,
matType,
dofBoundaryConditionsDict,
dofBoundaryConditionsSetterDict,
coefficients,
elementQuadrature,
elementBoundaryQuadrature,
fluxBoundaryConditionsDict,
advectiveFluxBoundaryConditionsSetterDict,
diffusiveFluxBoundaryConditionsSetterDictDict,
stressTraceBoundaryConditionsSetterDictDict,
stabilization,
shockCapturing,
conservativeFluxDict,
numericalFluxType,
TimeIntegrationClass,
massLumping,
reactionLumping,
options,
name,
reuse_trial_and_test_quadrature,
sd,
movingDomain)
#
#set the objects describing the method and boundary conditions
#
self.movingDomain=movingDomain
self.tLast_mesh=None
#
#cek todo clean up these flags in the optimized version
self.bcsTimeDependent=options.bcsTimeDependent
self.bcsSet=False
self.name=name
self.sd=sd
self.lowmem=True
self.timeTerm=True#allow turning off the time derivative
self.testIsTrial=True
self.phiTrialIsTrial=True
self.u = uDict
self.Hess=False
if isinstance(self.u[0].femSpace,C0_AffineQuadraticOnSimplexWithNodalBasis):
self.Hess=True
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 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.ebqe['x'] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,3),'d')
self.ebq_global[('totalFlux',0)] = numpy.zeros((self.mesh.nElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebq_global[('velocityAverage',0)] = numpy.zeros((self.mesh.nElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,self.nSpace_global),'d')
self.q[('u',1)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('u',2)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('u',3)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m',1)] = self.q[('u',1)]
self.q[('m',2)] = self.q[('u',2)]
self.q[('m',3)] = self.q[('u',3)]
self.q[('m_last',1)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m_last',2)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m_last',3)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m_tmp',1)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m_tmp',2)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('m_tmp',3)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('f',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element,self.nSpace_global),'d')
self.q[('velocity',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element,self.nSpace_global),'d')
self.q[('cfl',0)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('numDiff',1,1)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('numDiff',2,2)] = numpy.zeros((self.mesh.nElements_global,self.nQuadraturePoints_element),'d')
self.q[('numDiff',3,3)] = 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[('u',1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('u',2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('u',3)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('advectiveFlux_bc_flag',0)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('advectiveFlux_bc_flag',1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('advectiveFlux_bc_flag',2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('advectiveFlux_bc_flag',3)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('diffusiveFlux_bc_flag',1,1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('diffusiveFlux_bc_flag',2,2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('diffusiveFlux_bc_flag',3,3)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'i')
self.ebqe[('advectiveFlux_bc',0)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('advectiveFlux_bc',1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('advectiveFlux_bc',2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('advectiveFlux_bc',3)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('diffusiveFlux_bc',1,1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('penalty')] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('diffusiveFlux_bc',2,2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('diffusiveFlux_bc',3,3)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary),'d')
self.ebqe[('velocity',0)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,self.nSpace_global),'d')
self.ebqe[('velocity',1)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,self.nSpace_global),'d')
self.ebqe[('velocity',2)] = numpy.zeros((self.mesh.nExteriorElementBoundaries_global,self.nElementBoundaryQuadraturePoints_elementBoundary,self.nSpace_global),'d')
self.ebqe[('velocity',3)] = 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()
#
#show quadrature
#
log("Dumping quadrature shapes for model %s" % self.name,level=9)
log("Element quadrature array (q)", level=9)
for (k,v) in self.q.iteritems(): log(str((k,v.shape)),level=9)
log("Element boundary quadrature (ebq)",level=9)
for (k,v) in self.ebq.iteritems(): log(str((k,v.shape)),level=9)
log("Global element boundary quadrature (ebq_global)",level=9)
for (k,v) in self.ebq_global.iteritems(): log(str((k,v.shape)),level=9)
log("Exterior element boundary quadrature (ebqe)",level=9)
for (k,v) in self.ebqe.iteritems(): log(str((k,v.shape)),level=9)
log("Interpolation points for nonlinear diffusion potential (phi_ip)",level=9)
for (k,v) in self.phi_ip.iteritems(): log(str((k,v.shape)),level=9)
#
# allocate residual and Jacobian storage
#
#
# allocate residual and Jacobian storage
#
self.elementResidual = [numpy.zeros(
(self.mesh.nElements_global,
self.nDOF_test_element[ci]),
'd')]
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
log("Updating local to global mappings",2)
self.updateLocal2Global()
log("Building time integration object",2)
log(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)
log(memory("TimeIntegration","OneLevelTransport"),level=4)
log("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"
log(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
log(memory("numericalFlux","OneLevelTransport"),level=4)
self.elementEffectiveDiametersArray = self.mesh.elementInnerDiametersArray
#use post processing tools to get conservative fluxes, None by default
if self.postProcessing:
self.q[('v',0)] = self.tmpvt.q[('v',0)]
self.ebq[('v',0)] = self.tmpvt.ebq[('v',0)]
self.ebq[('w',0)] = self.tmpvt.ebq[('w',0)]
self.ebq['sqrt(det(g))'] = self.tmpvt.ebq['sqrt(det(g))']
self.ebq['n'] = self.tmpvt.ebq['n']
self.ebq[('dS_u',0)] = self.tmpvt.ebq[('dS_u',0)]
self.ebqe['dS'] = self.tmpvt.ebqe['dS']
self.ebqe['n'] = self.tmpvt.ebqe['n']
self.ebq_global['n'] = self.tmpvt.ebq_global['n']
self.ebq_global['x'] = self.tmpvt.ebq_global['x']
from proteus import PostProcessingTools
self.velocityPostProcessor = PostProcessingTools.VelocityPostProcessingChooser(self)
log(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()
for ci,fbcObject in self.fluxBoundaryConditionsObjectsDict.iteritems():
self.ebqe[('advectiveFlux_bc_flag',ci)] = numpy.zeros(self.ebqe[('advectiveFlux_bc',ci)].shape,'i')
for t,g in fbcObject.advectiveFluxBoundaryConditionsDict.iteritems():
if self.coefficients.advection.has_key(ci):
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
for ck,diffusiveFluxBoundaryConditionsDict in fbcObject.diffusiveFluxBoundaryConditionsDictDict.iteritems():
self.ebqe[('diffusiveFlux_bc_flag',ck,ci)] = numpy.zeros(self.ebqe[('diffusiveFlux_bc',ck,ci)].shape,'i')
for t,g in diffusiveFluxBoundaryConditionsDict.iteritems():
self.ebqe[('diffusiveFlux_bc',ck,ci)][t[0],t[1]] = g(self.ebqe[('x')][t[0],t[1]],self.timeIntegration.t)
self.ebqe[('diffusiveFlux_bc_flag',ck,ci)][t[0],t[1]] = 1
self.numericalFlux.setDirichletValues(self.ebqe)
if self.movingDomain:
self.MOVING_DOMAIN=1.0
else:
self.MOVING_DOMAIN=0.0
#cek hack
self.movingDomain=False
self.MOVING_DOMAIN=0.0
if self.mesh.nodeVelocityArray==None:
self.mesh.nodeVelocityArray = numpy.zeros(self.mesh.nodeArray.shape,'d')
#cek/ido todo replace python loops in modules with optimized code if possible/necessary
self.forceStrongConditions=False
self.dirichletConditionsForceDOF = {}
if self.forceStrongConditions:
for cj in range(self.nc):
self.dirichletConditionsForceDOF[cj] = DOFBoundaryConditions(self.u[cj].femSpace,dofBoundaryConditionsSetterDict[cj],weakDirichletConditions=False)
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.rans2p = cRANS3P_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)
def getResidual(self,u,r):
"""
Calculate the element residuals and add in to the global residual
"""
#Load the unknowns into the finite element dof
self.timeIntegration.calculateCoefs()
self.timeIntegration.calculateU(u)
self.setUnknowns(self.timeIntegration.u)
#cek todo put in logic to skip if BC's don't depend on t or u
#hack
if self.bcsTimeDependent or not self.bcsSet:
self.bcsSet=True
#Dirichlet boundary conditions
self.numericalFlux.setDirichletValues(self.ebqe)
#Flux boundary conditions
for ci,fbcObject in self.fluxBoundaryConditionsObjectsDict.iteritems():
for t,g in fbcObject.advectiveFluxBoundaryConditionsDict.iteritems():
if self.coefficients.advection.has_key(ci):
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
for ck,diffusiveFluxBoundaryConditionsDict in fbcObject.diffusiveFluxBoundaryConditionsDictDict.iteritems():
for t,g in diffusiveFluxBoundaryConditionsDict.iteritems():
self.ebqe[('diffusiveFlux_bc',ck,ci)][t[0],t[1]] = g(self.ebqe[('x')][t[0],t[1]],self.timeIntegration.t)
self.ebqe[('diffusiveFlux_bc_flag',ck,ci)][t[0],t[1]] = 1
r.fill(0.0)
self.Ct_sge = 4.0
self.Cd_sge = 144.0
if self.forceStrongConditions:
for cj in range(len(self.dirichletConditionsForceDOF)):
for dofN,g in self.dirichletConditionsForceDOF[cj].DOFBoundaryConditionsDict.iteritems():
self.u[cj].dof[dofN] = g(self.dirichletConditionsForceDOF[cj].DOFBoundaryPointDict[dofN],self.timeIntegration.t)
self.rans2p.calculateResidual(#element
self.u[0].femSpace.elementMaps.psi,
self.u[0].femSpace.elementMaps.grad_psi,
self.mesh.nodeArray,
self.mesh.nodeVelocityArray,
self.MOVING_DOMAIN,
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,
self.u[1].femSpace.psi,
self.u[1].femSpace.grad_psi,
self.u[1].femSpace.psi,
self.u[1].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[1].femSpace.psi_trace,
self.u[1].femSpace.grad_psi_trace,
self.u[1].femSpace.psi_trace,
self.u[1].femSpace.grad_psi_trace,
self.u[0].femSpace.elementMaps.boundaryNormals,
self.u[0].femSpace.elementMaps.boundaryJacobians,
#physics
self.elementDiameter,#mesh.elementDiametersArray,
self.stabilization.hFactor,
self.mesh.nElements_global,
self.coefficients.useRBLES,
self.coefficients.useMetrics,
self.timeIntegration.alpha_bdf,
self.coefficients.epsFact_density,
self.coefficients.epsFact,
self.coefficients.sigma,
self.coefficients.rho_0,
self.coefficients.nu_0,