def updMassMatMS(self, elmLst, elmCompDiagMassMat, rho=1.0):
self.M = mfem.ParBilinearForm(self.fespace)
self.ro = mfem.ConstantCoefficient(rho)
self.M.AddDomainIntegrator(mfem.VectorMassIntegrator(self.ro))
print("in updateMass")
self.M.Assemble(0, elmLst, elmCompDiagMassMat, True, True)
self.M.EliminateEssentialBC(self.vess_bdr)
self.M.Finalize(0)
self.Mmat = self.M.ParallelAssemble()
self.M_solver.SetOperator(self.Mmat)
mu_func = mfem.PWConstCoefficient(mu)
ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max())
ess_bdr.Assign(0)
ess_bdr[0] = 1
a = mfem.ParBilinearForm(fespace)
a.AddDomainIntegrator(mfem.ElasticityIntegrator(lambda_func, mu_func))
if (myid == 0):
print("matrix ... ")
a.Assemble()
a.EliminateEssentialBCDiag(ess_bdr, 1.0)
a.Finalize()
m = mfem.ParBilinearForm(fespace)
m.AddDomainIntegrator(mfem.VectorMassIntegrator())
m.Assemble()
# shift the eigenvalue corresponding to eliminated dofs to a large value
m.EliminateEssentialBCDiag(ess_bdr, 3.0e-300)
m.Finalize()
if (myid == 0):
print("done. ")
A = a.ParallelAssemble()
M = m.ParallelAssemble()
# 9. Define and configure the LOBPCG eigensolver and the BoomerAMG
# preconditioner for A to be used within the solver. Set the matrices
# which define the generalized eigenproblem A x = lambda M x.
amg = mfem.HypreBoomerAMG(A)
def __init__(self, fespace, ess_bdr, visc, mu, K):
mfem.PyTimeDependentOperator.__init__(self, 2 * fespace.TrueVSize(),
0.0)
rel_tol = 1e-8
skip_zero_entries = 0
ref_density = 1.0
self.ess_tdof_list = intArray()
self.z = mfem.Vector(self.Height() // 2)
self.fespace = fespace
self.viscosity = visc
self.newton_solver = mfem.NewtonSolver(fespace.GetComm())
M = mfem.ParBilinearForm(fespace)
S = mfem.ParBilinearForm(fespace)
H = mfem.ParNonlinearForm(fespace)
self.M = M
self.H = H
self.S = S
rho = mfem.ConstantCoefficient(ref_density)
M.AddDomainIntegrator(mfem.VectorMassIntegrator(rho))
M.Assemble(skip_zero_entries)
M.EliminateEssentialBC(ess_bdr)
M.Finalize(skip_zero_entries)
self.Mmat = M.ParallelAssemble()
fespace.GetEssentialTrueDofs(ess_bdr, self.ess_tdof_list)
self.Mmat.EliminateRowsCols(self.ess_tdof_list)
M_solver = mfem.CGSolver(fespace.GetComm())
M_prec = mfem.HypreSmoother()
M_solver.iterative_mode = False
M_solver.SetRelTol(rel_tol)
M_solver.SetAbsTol(0.0)
M_solver.SetMaxIter(30)
M_solver.SetPrintLevel(0)
M_prec.SetType(mfem.HypreSmoother.Jacobi)
M_solver.SetPreconditioner(M_prec)
M_solver.SetOperator(self.Mmat)
self.M_solver = M_solver
self.M_prec = M_prec
model = mfem.NeoHookeanModel(mu, K)
H.AddDomainIntegrator(mfem.HyperelasticNLFIntegrator(model))
H.SetEssentialTrueDofs(self.ess_tdof_list)
self.model = model
visc_coeff = mfem.ConstantCoefficient(visc)
S.AddDomainIntegrator(mfem.VectorDiffusionIntegrator(visc_coeff))
S.Assemble(skip_zero_entries)
S.EliminateEssentialBC(ess_bdr)
S.Finalize(skip_zero_entries)
self.reduced_oper = ReducedSystemOperator(M, S, H, self.ess_tdof_list)
J_hypreSmoother = mfem.HypreSmoother()
J_hypreSmoother.SetType(mfem.HypreSmoother.l1Jacobi)
J_hypreSmoother.SetPositiveDiagonal(True)
J_prec = J_hypreSmoother
J_minres = mfem.MINRESSolver(fespace.GetComm())
J_minres.SetRelTol(rel_tol)
J_minres.SetAbsTol(0.0)
J_minres.SetMaxIter(300)
J_minres.SetPrintLevel(-1)
J_minres.SetPreconditioner(J_prec)
self.J_solver = J_minres
self.J_prec = J_prec
newton_solver = mfem.NewtonSolver(fespace.GetComm())
newton_solver.iterative_mode = False
newton_solver.SetSolver(self.J_solver)
newton_solver.SetOperator(self.reduced_oper)
newton_solver.SetPrintLevel(1)
#print Newton iterations
newton_solver.SetRelTol(rel_tol)
newton_solver.SetAbsTol(0.0)
newton_solver.SetMaxIter(10)
self.newton_solver = newton_solver
def __init__(self,
fespace,
lmbda=1.,
mu=1.,
rho=1.,
visc=0.0,
vess_tdof_list=None,
vess_bdr=None,
xess_tdof_list=None,
xess_bdr=None,
v_gfBdr=None,
x_gfBdr=None,
deform=None,
velo=None,
vx=None):
mfem.PyTimeDependentOperator.__init__(self, 2 * fespace.GetTrueVSize(),
0.0)
self.lmbda = lmbda
self.mu = mu
self.viscosity = visc
self.deform = deform
self.velo = velo
self.x_gfBdr = x_gfBdr
self.v_gfBdr = v_gfBdr
self.vx = vx
self.z = mfem.Vector(self.Height() / 2)
self.z.Assign(0.0)
self.w = mfem.Vector(self.Height() / 2)
self.w.Assign(0.0)
self.tmpVec = mfem.Vector(self.Height() / 2)
self.tmpVec.Assign(0.0)
self.fespace = fespace
self.xess_bdr = xess_bdr
self.vess_bdr = vess_bdr
self.xess_tdof_list = xess_tdof_list
self.vess_tdof_list = vess_tdof_list
# setting up linear form
cv = mfem.Vector(3)
cv.Assign(0.0)
#self.zero_coef = mfem.ConstantCoefficient(0.0)
self.zero_coef = mfem.VectorConstantCoefficient(cv)
self.bx = mfem.LinearForm(self.fespace)
self.bx.AddDomainIntegrator(
mfem.VectorBoundaryLFIntegrator(self.zero_coef))
self.bx.Assemble()
self.bv = mfem.LinearForm(self.fespace)
self.bv.AddDomainIntegrator(
mfem.VectorBoundaryLFIntegrator(self.zero_coef))
self.bv.Assemble()
self.Bx = mfem.Vector()
self.Bv = mfem.Vector()
# setting up bilinear forms
self.M = mfem.ParBilinearForm(self.fespace)
self.K = mfem.ParBilinearForm(self.fespace)
self.S = mfem.ParBilinearForm(self.fespace)
self.ro = mfem.ConstantCoefficient(rho)
self.M.AddDomainIntegrator(mfem.VectorMassIntegrator(self.ro))
self.M.Assemble(0)
self.M.EliminateEssentialBC(self.vess_bdr)
self.M.Finalize(0)
self.Mmat = self.M.ParallelAssemble()
self.M_solver = mfem.CGSolver(self.fespace.GetComm())
self.M_solver.iterative_mode = False
self.M_solver.SetRelTol(1e-8)
self.M_solver.SetAbsTol(0.0)
self.M_solver.SetMaxIter(30)
self.M_solver.SetPrintLevel(0)
self.M_prec = mfem.HypreSmoother()
self.M_prec.SetType(mfem.HypreSmoother.Jacobi)
self.M_solver.SetPreconditioner(self.M_prec)
self.M_solver.SetOperator(self.Mmat)
lambVec = mfem.Vector(self.fespace.GetMesh().attributes.Max())
print('Number of volume attributes : ' +
str(self.fespace.GetMesh().attributes.Max()))
lambVec.Assign(lmbda)
lambVec[0] = lambVec[1] * 1.0
lambda_func = mfem.PWConstCoefficient(lambVec)
muVec = mfem.Vector(self.fespace.GetMesh().attributes.Max())
muVec.Assign(mu)
muVec[0] = muVec[1] * 1.0
mu_func = mfem.PWConstCoefficient(muVec)
self.K.AddDomainIntegrator(
mfem.ElasticityIntegrator(lambda_func, mu_func))
self.K.Assemble(0)
# to set essential BC to zero value uncomment
#self.K.EliminateEssentialBC(self.xess_bdr)
#self.K.Finalize(0)
#self.Kmat = self.K.ParallelAssemble()
# to set essential BC to non-zero uncomment
self.Kmat = mfem.HypreParMatrix()
visc_coeff = mfem.ConstantCoefficient(visc)
self.S.AddDomainIntegrator(mfem.VectorDiffusionIntegrator(visc_coeff))
self.S.Assemble(0)
#self.S.EliminateEssentialBC(self.vess_bdr)
#self.S.Finalize(0)
#self.Smat = self.S.ParallelAssemble()
self.Smat = mfem.HypreParMatrix()
# VX solver for implicit time-stepping
self.VX_solver = mfem.CGSolver(self.fespace.GetComm())
self.VX_solver.iterative_mode = False
self.VX_solver.SetRelTol(1e-8)
self.VX_solver.SetAbsTol(0.0)
self.VX_solver.SetMaxIter(30)
self.VX_solver.SetPrintLevel(0)
self.VX_prec = mfem.HypreSmoother()
self.VX_prec.SetType(mfem.HypreSmoother.Jacobi)
self.VX_solver.SetPreconditioner(self.VX_prec)
# setting up operators
empty_tdof_list = intArray()
self.S.FormLinearSystem(empty_tdof_list, self.v_gfBdr, self.bv,
self.Smat, self.vx.GetBlock(0), self.Bv, 1)
self.K.FormLinearSystem(empty_tdof_list, self.x_gfBdr, self.bx,
self.Kmat, self.vx.GetBlock(1), self.Bx, 1)