def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.presinc.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.numericalFlux.isDOFBoundary[0],
self.ebqe[('diffusiveFlux_bc_flag', 0, 0)],
self.u[0].femSpace.dofMap.l2g,
self.u[0].dof,
self.coefficients.fluidModel.timeIntegration.alpha_bdf,
self.coefficients.fluidModel.q[('velocity', 0)],
self.coefficients.fluidModel.coefficients.q_velocity_solid,
self.coefficients.fluidModel.coefficients.q_vos,
self.coefficients.fluidModel.coefficients.rho_s,
self.coefficients.fluidModel.coefficients.q_rho,
self.coefficients.rho_s_min,
self.coefficients.rho_f_min,
self.coefficients.fluidModel.ebqe[('velocity', 0)],
self.coefficients.fluidModel.coefficients.ebqe_velocity_solid,
self.coefficients.fluidModel.coefficients.ebqe_vos,
self.coefficients.fluidModel.coefficients.ebqe_rho,
self.csrRowIndeces[(0, 0)], self.csrColumnOffsets[(0, 0)],
jacobian,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.csrColumnOffsets_eb[(0, 0)])
if self.coefficients.fixNullSpace:
dofN = 0
global_dofN = self.offset[0] + self.stride[0] * dofN
for i in range(self.rowptr[global_dofN], self.rowptr[global_dofN + 1]):
if (self.colind[i] == global_dofN):
self.nzval[i] = 1.0
else:
self.nzval[i] = 0.0
log("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.addedMass.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.u[0].femSpace.dofMap.l2g,
self.u[0].dof,
self.coefficients.q_rho,
self.csrRowIndeces[(0, 0)], self.csrColumnOffsets[(0, 0)],
jacobian,
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.csrColumnOffsets_eb[(0, 0)])
for dofN in self.dirichletConditionsForceDOF[0].DOFBoundaryConditionsDict.keys():
global_dofN = self.offset[0] + self.stride[0] * dofN
self.nzval[numpy.where(self.colind == global_dofN)] = 0.0 # column
self.nzval[self.rowptr[global_dofN]:self.rowptr[global_dofN + 1]] = 0.0 # row
zeroRow = True
for i in range(self.rowptr[global_dofN], self.rowptr[global_dofN + 1]): # row
if (self.colind[i] == global_dofN):
self.nzval[i] = 1.0
zeroRow = False
if zeroRow:
raise RuntimeError("Jacobian has a zero row because sparse matrix has no diagonal entry at row " +
`global_dofN`+". You probably need add diagonal mass or reaction term")
logEvent("Jacobian ", level=10, data=jacobian)
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.addedMass.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.u[0].femSpace.dofMap.l2g,
self.u[0].dof,
self.coefficients.q_rho,
self.csrRowIndeces[(0, 0)], self.csrColumnOffsets[(0, 0)],
jacobian.getCSRrepresentation()[2],
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.csrColumnOffsets_eb[(0, 0)])
for dofN in list(self.dirichletConditionsForceDOF[0].DOFBoundaryConditionsDict.keys()):
global_dofN = self.offset[0] + self.stride[0] * dofN
self.nzval[np.where(self.colind == global_dofN)] = 0.0 # column
self.nzval[self.rowptr[global_dofN]:self.rowptr[global_dofN + 1]] = 0.0 # row
zeroRow = True
for i in range(self.rowptr[global_dofN], self.rowptr[global_dofN + 1]): # row
if (self.colind[i] == global_dofN):
self.nzval[i] = 1.0
zeroRow = False
if zeroRow:
raise RuntimeError("Jacobian has a zero row because sparse matrix has no diagonal entry at row " +
repr(global_dofN)+". You probably need add diagonal mass or reaction term")
logEvent("Jacobian ", level=10, data=jacobian)
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
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["u_grad_test_ref"] = self.u[0].femSpace.grad_psi
argsDict["mesh_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.psi_trace
argsDict["mesh_grad_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.grad_psi_trace
argsDict["dS_ref"] = self.elementBoundaryQuadratureWeights[('u', 0)]
argsDict["u_trial_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["u_grad_trial_trace_ref"] = self.u[0].femSpace.grad_psi_trace
argsDict["u_test_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["u_grad_test_trace_ref"] = self.u[0].femSpace.grad_psi_trace
argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
argsDict["boundaryJac_ref"] = self.u[
0].femSpace.elementMaps.boundaryJacobians
argsDict["nElements_global"] = self.mesh.nElements_global
argsDict["useMetrics"] = self.coefficients.useMetrics
argsDict["epsFactHeaviside"] = self.coefficients.epsFactHeaviside
argsDict["epsFactDirac"] = self.coefficients.epsFactDirac
argsDict["epsFactDiffusion"] = self.coefficients.epsFactDiffusion
argsDict["u_l2g"] = self.u[0].femSpace.dofMap.l2g
argsDict["elementDiameter"] = self.elementDiameter
argsDict["nodeDiametersArray"] = self.mesh.nodeDiametersArray
argsDict["u_dof"] = self.u[0].dof
argsDict["q_phi"] = self.coefficients.q_u_ls
argsDict["q_normal_phi"] = self.coefficients.q_n_ls
argsDict["q_H"] = self.coefficients.q_H_vof
argsDict["q_vos"] = self.coefficients.q_vos
argsDict["csrRowIndeces_u_u"] = self.csrRowIndeces[(0, 0)]
argsDict["csrColumnOffsets_u_u"] = self.csrColumnOffsets[(0, 0)]
argsDict["globalJacobian"] = jacobian.getCSRrepresentation()[2]
self.presinit.calculateJacobian(argsDict)
log("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.presinit.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_vos,
self.csrRowIndeces[(0, 0)],
self.csrColumnOffsets[(0, 0)],
jacobian)
log("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.presinit.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_vos,
self.csrRowIndeces[(0, 0)], self.csrColumnOffsets[(0, 0)],
jacobian)
log("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
#import superluWrappers
#import numpy
import pdb
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.adr.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,
self.mesh.elementDiametersArray,
self.q[('cfl', 0)],
self.shockCapturing.shockCapturingFactor,
self.coefficients.sc_uref,
self.coefficients.sc_beta,
self.coefficients.useMetrics,
#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.u[0].femSpace.dofMap.l2g,
self.u[0].dof,
self.coefficients.sdInfo[(0, 0)][0],
self.coefficients.sdInfo[(0, 0)][1],
self.q[('a', 0, 0)],
self.q[('df', 0, 0)],
self.q[('r', 0)],
self.shockCapturing.lag,
self.shockCapturing.shockCapturingFactor,
self.shockCapturing.numDiff[0],
self.shockCapturing.numDiff_last[0],
self.csrRowIndeces[(0, 0)],
self.csrColumnOffsets[(0, 0)],
jacobian.getCSRrepresentation()[2],
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.ebqe[('a', 0, 0)],
self.ebqe[('df', 0, 0)],
self.numericalFlux.isDOFBoundary[0],
self.numericalFlux.ebqe[('u', 0)],
self.ebqe[('diffusiveFlux_bc_flag', 0, 0)],
self.ebqe[('advectiveFlux_bc_flag', 0)],
self.ebqe[('diffusiveFlux_bc', 0, 0)],
self.ebqe[('advectiveFlux_bc', 0)],
self.csrColumnOffsets_eb[(0, 0)],
self.ebqe['penalty'],
self.numericalFlux.boundaryAdjoint_sigma)
log("Jacobian ", level=10, data=jacobian)
#mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
if self.nSpace_global == 2:
self.csrRowIndeces[(0, 2)] = self.csrRowIndeces[(0, 1)]
self.csrColumnOffsets[(0, 2)] = self.csrColumnOffsets[(0, 1)]
self.csrRowIndeces[(1, 2)] = self.csrRowIndeces[(0, 1)]
self.csrColumnOffsets[(1, 2)] = self.csrColumnOffsets[(0, 1)]
self.csrRowIndeces[(2, 0)] = self.csrRowIndeces[(1, 0)]
self.csrColumnOffsets[(2, 0)] = self.csrColumnOffsets[(1, 0)]
self.csrRowIndeces[(2, 1)] = self.csrRowIndeces[(1, 0)]
self.csrColumnOffsets[(2, 1)] = self.csrColumnOffsets[(1, 0)]
self.csrRowIndeces[(2, 2)] = self.csrRowIndeces[(1, 0)]
self.csrColumnOffsets[(2, 2)] = self.csrColumnOffsets[(1, 0)]
self.csrColumnOffsets_eb[(0, 2)] = self.csrColumnOffsets[(0, 1)]
self.csrColumnOffsets_eb[(1, 2)] = self.csrColumnOffsets[(0, 1)]
self.csrColumnOffsets_eb[(2, 2)] = self.csrColumnOffsets[(0, 1)]
self.csrColumnOffsets_eb[(2, 0)] = self.csrColumnOffsets[(0, 1)]
self.csrColumnOffsets_eb[(2, 1)] = self.csrColumnOffsets[(0, 1)]
self.csrColumnOffsets_eb[(2, 2)] = self.csrColumnOffsets[(0, 1)]
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["disp_trial_ref"] = self.u[0].femSpace.psi
argsDict["disp_grad_trial_ref"] = self.u[0].femSpace.grad_psi
argsDict["disp_test_ref"] = self.u[0].femSpace.psi
argsDict["disp_grad_test_ref"] = self.u[0].femSpace.grad_psi
argsDict["mesh_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.psi_trace
argsDict["mesh_grad_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.grad_psi_trace
argsDict["dS_ref"] = self.elementBoundaryQuadratureWeights[('u', 0)]
argsDict["disp_trial_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["disp_grad_trial_trace_ref"] = self.u[
0].femSpace.grad_psi_trace
argsDict["disp_test_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["disp_grad_test_trace_ref"] = self.u[
0].femSpace.grad_psi_trace
argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
argsDict["boundaryJac_ref"] = self.u[
0].femSpace.elementMaps.boundaryJacobians
argsDict["nElements_global"] = self.mesh.nElements_global
argsDict["materialTypes"] = self.mesh.elementMaterialTypes
argsDict["nMaterialProperties"] = self.coefficients.nMaterialProperties
argsDict["materialProperties"] = self.coefficients.materialProperties
argsDict["disp_l2g"] = self.u[0].femSpace.dofMap.l2g
argsDict["u_dof"] = self.u[0].dof
argsDict["v_dof"] = self.u[1].dof
argsDict["w_dof"] = self.u[2].dof
argsDict["bodyForce"] = self.coefficients.bodyForce
argsDict["csrRowIndeces_u_u"] = self.csrRowIndeces[(0, 0)]
argsDict["csrColumnOffsets_u_u"] = self.csrColumnOffsets[(0, 0)]
argsDict["csrRowIndeces_u_v"] = self.csrRowIndeces[(0, 1)]
argsDict["csrColumnOffsets_u_v"] = self.csrColumnOffsets[(0, 1)]
argsDict["csrRowIndeces_u_w"] = self.csrRowIndeces[(0, 2)]
argsDict["csrColumnOffsets_u_w"] = self.csrColumnOffsets[(0, 2)]
argsDict["csrRowIndeces_v_u"] = self.csrRowIndeces[(1, 0)]
argsDict["csrColumnOffsets_v_u"] = self.csrColumnOffsets[(1, 0)]
argsDict["csrRowIndeces_v_v"] = self.csrRowIndeces[(1, 1)]
argsDict["csrColumnOffsets_v_v"] = self.csrColumnOffsets[(1, 1)]
argsDict["csrRowIndeces_v_w"] = self.csrRowIndeces[(1, 2)]
argsDict["csrColumnOffsets_v_w"] = self.csrColumnOffsets[(1, 2)]
argsDict["csrRowIndeces_w_u"] = self.csrRowIndeces[(2, 0)]
argsDict["csrColumnOffsets_w_u"] = self.csrColumnOffsets[(2, 0)]
argsDict["csrRowIndeces_w_v"] = self.csrRowIndeces[(2, 1)]
argsDict["csrColumnOffsets_w_v"] = self.csrColumnOffsets[(2, 1)]
argsDict["csrRowIndeces_w_w"] = self.csrRowIndeces[(2, 2)]
argsDict["csrColumnOffsets_w_w"] = self.csrColumnOffsets[(2, 2)]
argsDict["globalJacobian"] = jacobian.getCSRrepresentation()[2]
argsDict[
"nExteriorElementBoundaries_global"] = self.mesh.nExteriorElementBoundaries_global
argsDict[
"exteriorElementBoundariesArray"] = self.mesh.exteriorElementBoundariesArray
argsDict[
"elementBoundaryElementsArray"] = self.mesh.elementBoundaryElementsArray
argsDict[
"elementBoundaryLocalElementBoundariesArray"] = self.mesh.elementBoundaryLocalElementBoundariesArray
argsDict["isDOFBoundary_u"] = self.numericalFlux.isDOFBoundary[0]
argsDict["isDOFBoundary_v"] = self.numericalFlux.isDOFBoundary[1]
argsDict["isDOFBoundary_w"] = self.numericalFlux.isDOFBoundary[2]
argsDict["isStressFluxBoundary_u"] = self.ebqe[('stressFlux_bc_flag',
0)]
argsDict["isStressFluxBoundary_v"] = self.ebqe[('stressFlux_bc_flag',
1)]
argsDict["isStressFluxBoundary_w"] = self.ebqe[('stressFlux_bc_flag',
2)]
argsDict["csrColumnOffsets_eb_u_u"] = self.csrColumnOffsets_eb[(0, 0)]
argsDict["csrColumnOffsets_eb_u_v"] = self.csrColumnOffsets_eb[(0, 1)]
argsDict["csrColumnOffsets_eb_u_w"] = self.csrColumnOffsets_eb[(0, 2)]
argsDict["csrColumnOffsets_eb_v_u"] = self.csrColumnOffsets_eb[(1, 0)]
argsDict["csrColumnOffsets_eb_v_v"] = self.csrColumnOffsets_eb[(1, 1)]
argsDict["csrColumnOffsets_eb_v_w"] = self.csrColumnOffsets_eb[(1, 2)]
argsDict["csrColumnOffsets_eb_w_u"] = self.csrColumnOffsets_eb[(2, 0)]
argsDict["csrColumnOffsets_eb_w_v"] = self.csrColumnOffsets_eb[(2, 1)]
argsDict["csrColumnOffsets_eb_w_w"] = self.csrColumnOffsets_eb[(2, 2)]
self.moveMesh.calculateJacobian(argsDict)
# Load the Dirichlet conditions directly into residual
if self.forceStrongConditions:
scaling = 1.0 # probably want to add some scaling to match non-dirichlet diagonals in linear system
for cj in range(self.nc):
for dofN in list(self.dirichletConditionsForceDOF[cj].
DOFBoundaryConditionsDict.keys()):
global_dofN = self.offset[cj] + self.stride[cj] * dofN
for i in range(self.rowptr[global_dofN],
self.rowptr[global_dofN + 1]):
if (self.colind[i] == global_dofN):
self.nzval[i] = scaling
else:
self.nzval[i] = 0.0
logEvent("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
# jacobian.fwrite("jacobian_p"+`self.nonlinear_function_jacobian_evaluations`)
return jacobian
def getJacobian(self, jacobian):
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
self.presinc.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.numericalFlux.isDOFBoundary[0],
self.ebqe[('diffusiveFlux_bc_flag', 0, 0)],
self.u[0].femSpace.dofMap.l2g,
self.u[0].dof,
self.coefficients.fluidModel.timeIntegration.alpha_bdf,
self.coefficients.fluidModel.q[('velocity', 0)],
self.coefficients.fluidModel.coefficients.q_velocity_solid,
self.coefficients.fluidModel.coefficients.q_vos,
self.coefficients.fluidModel.coefficients.rho_s,
self.coefficients.fluidModel.coefficients.q_rho,
self.coefficients.rho_s_min,
self.coefficients.rho_f_min,
self.coefficients.fluidModel.ebqe[('velocity', 0)],
self.coefficients.fluidModel.coefficients.ebqe_velocity_solid,
self.coefficients.fluidModel.coefficients.ebqe_vos,
self.coefficients.fluidModel.coefficients.ebqe_rho,
self.csrRowIndeces[(0, 0)],
self.csrColumnOffsets[(0, 0)],
jacobian.getCSRrepresentation()[2],
self.mesh.nExteriorElementBoundaries_global,
self.mesh.exteriorElementBoundariesArray,
self.mesh.elementBoundaryElementsArray,
self.mesh.elementBoundaryLocalElementBoundariesArray,
self.csrColumnOffsets_eb[(0, 0)])
if self.coefficients.fixNullSpace and self.comm.rank() == 0:
dofN = 0
global_dofN = self.offset[0] + self.stride[0] * dofN
for i in range(self.rowptr[global_dofN],
self.rowptr[global_dofN + 1]):
if (self.colind[i] == global_dofN):
self.nzval[i] = 1.0
else:
self.nzval[i] = 0.0
log("Jacobian ", level=10, data=jacobian)
# mwf decide if this is reasonable for solver statistics
self.nonlinear_function_jacobian_evaluations += 1
return jacobian
def getJacobian(self, jacobian):
#import superluWrappers
#import numpy
import pdb
cfemIntegrals.zeroJacobian_CSR(self.nNonzerosInJacobian, jacobian)
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["u_grad_test_ref"] = self.u[0].femSpace.grad_psi
argsDict["elementDiameter"] = self.mesh.elementDiametersArray
argsDict["cfl"] = self.q[('cfl', 0)]
argsDict["Ct_sge"] = self.shockCapturing.shockCapturingFactor
argsDict["sc_uref"] = self.coefficients.sc_uref
argsDict["sc_alpha"] = self.coefficients.sc_beta
argsDict["useMetrics"] = self.coefficients.useMetrics
argsDict["mesh_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.psi_trace
argsDict["mesh_grad_trial_trace_ref"] = self.u[
0].femSpace.elementMaps.grad_psi_trace
argsDict["dS_ref"] = self.elementBoundaryQuadratureWeights[('u', 0)]
argsDict["u_trial_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["u_grad_trial_trace_ref"] = self.u[0].femSpace.grad_psi_trace
argsDict["u_test_trace_ref"] = self.u[0].femSpace.psi_trace
argsDict["u_grad_test_trace_ref"] = self.u[0].femSpace.grad_psi_trace
argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
argsDict["boundaryJac_ref"] = self.u[
0].femSpace.elementMaps.boundaryJacobians
argsDict["nElements_global"] = self.mesh.nElements_global
argsDict["u_l2g"] = self.u[0].femSpace.dofMap.l2g
argsDict["u_dof"] = self.u[0].dof
argsDict["sd_rowptr"] = self.coefficients.sdInfo[(0, 0)][0]
argsDict["sd_colind"] = self.coefficients.sdInfo[(0, 0)][1]
argsDict["q_a"] = self.q[('a', 0, 0)]
argsDict["q_v"] = self.q[('df', 0, 0)]
argsDict["q_r"] = self.q[('r', 0)]
argsDict["lag_shockCapturing"] = self.shockCapturing.lag
argsDict[
"shockCapturingDiffusion"] = self.shockCapturing.shockCapturingFactor
argsDict["q_numDiff_u"] = self.shockCapturing.numDiff[0]
argsDict["q_numDiff_u_last"] = self.shockCapturing.numDiff_last[0]
argsDict["csrRowIndeces_u_u"] = self.csrRowIndeces[(0, 0)]
argsDict["csrColumnOffsets_u_u"] = self.csrColumnOffsets[(0, 0)]
argsDict["globalJacobian"] = jacobian.getCSRrepresentation()[2]
argsDict[
"nExteriorElementBoundaries_global"] = self.mesh.nExteriorElementBoundaries_global
argsDict[
"exteriorElementBoundariesArray"] = self.mesh.exteriorElementBoundariesArray
argsDict[
"elementBoundaryElementsArray"] = self.mesh.elementBoundaryElementsArray
argsDict[
"elementBoundaryLocalElementBoundariesArray"] = self.mesh.elementBoundaryLocalElementBoundariesArray
argsDict["ebqe_a"] = self.ebqe[('a', 0, 0)]
argsDict["ebqe_v"] = self.ebqe[('df', 0, 0)]
argsDict["isDOFBoundary_u"] = self.numericalFlux.isDOFBoundary[0]
argsDict["ebqe_bc_u_ext"] = self.numericalFlux.ebqe[('u', 0)]
argsDict["isDiffusiveFluxBoundary_u"] = self.ebqe[(
'diffusiveFlux_bc_flag', 0, 0)]
argsDict["isAdvectiveFluxBoundary_u"] = self.ebqe[(
'advectiveFlux_bc_flag', 0)]
argsDict["ebqe_bc_flux_u_ext"] = self.ebqe[('diffusiveFlux_bc', 0, 0)]
argsDict["ebqe_bc_advectiveFlux_u_ext"] = self.ebqe[(
'advectiveFlux_bc', 0)]
argsDict["csrColumnOffsets_eb_u_u"] = self.csrColumnOffsets_eb[(0, 0)]
argsDict["ebqe_penalty_ext"] = self.ebqe['penalty']
argsDict["eb_adjoint_sigma"] = self.numericalFlux.boundaryAdjoint_sigma
argsDict["embeddedBoundary"] = self.coefficients.embeddedBoundary
argsDict[
"embeddedBoundary_penalty"] = self.coefficients.embeddedBoundary_penalty
argsDict[
"embeddedBoundary_ghost_penalty"] = self.coefficients.embeddedBoundary_ghost_penalty
argsDict[
"embeddedBoundary_sdf_nodes"] = self.coefficients.embeddedBoundary_sdf_nodes
argsDict["embeddedBoundary_sdf"] = self.q['embeddedBoundary_sdf']
argsDict["embeddedBoundary_normal"] = self.q['embeddedBoundary_normal']
argsDict["embeddedBoundary_u"] = self.q['embeddedBoundary_u']
argsDict["isActiveDOF"] = self.isActiveDOF
self.adr.calculateJacobian(argsDict)
log("Jacobian ", level=10, data=jacobian)
self.nonlinear_function_jacobian_evaluations += 1
for global_dofN_a in np.argwhere(self.isActiveDOF == 0.0):
global_dofN = global_dofN_a[0]
for i in range(self.rowptr[global_dofN],
self.rowptr[global_dofN + 1]):
if (self.colind[i] == global_dofN):
self.nzval[i] = 1.0
else:
self.nzval[i] = 0.0
return jacobian
