def _create_smoother(name, mat):
if use_parallel:
smoother = mfem.HypreSmoother(mat)
smoother.SetType(getattr(mfem.HypreSmoother, name))
else:
cls = SparseSmootherCls[name][0]
arg = SparseSmootherCls[name][1]
smoother = cls(mat, arg)
smoother.iterative_mode = False
return smoother
def __init__(self, fespace, alpha, kappa, u):
mfem.PyTimeDependentOperator.__init__(self, fespace.GetTrueVSize(),
0.0)
rel_tol = 1e-8
self.alpha = alpha
self.kappa = kappa
self.T = None
self.K = None
self.M = None
self.fespace = fespace
self.ess_tdof_list = intArray()
self.Mmat = mfem.HypreParMatrix()
self.Kmat = mfem.HypreParMatrix()
self.M_solver = mfem.CGSolver(fespace.GetComm())
self.M_prec = mfem.HypreSmoother()
self.T_solver = mfem.CGSolver(fespace.GetComm())
self.T_prec = mfem.HypreSmoother()
self.z = mfem.Vector(self.Height())
self.M = mfem.ParBilinearForm(fespace)
self.M.AddDomainIntegrator(mfem.MassIntegrator())
self.M.Assemble()
self.M.FormSystemMatrix(self.ess_tdof_list, self.Mmat)
self.M_solver.iterative_mode = False
self.M_solver.SetRelTol(rel_tol)
self.M_solver.SetAbsTol(0.0)
self.M_solver.SetMaxIter(100)
self.M_solver.SetPrintLevel(0)
self.M_prec.SetType(mfem.HypreSmoother.Jacobi)
self.M_solver.SetPreconditioner(self.M_prec)
self.M_solver.SetOperator(self.Mmat)
self.T_solver.iterative_mode = False
self.T_solver.SetRelTol(rel_tol)
self.T_solver.SetAbsTol(0.0)
self.T_solver.SetMaxIter(100)
self.T_solver.SetPrintLevel(0)
self.T_solver.SetPreconditioner(self.T_prec)
self.SetParameters(u)
def mfem_smoother(name, **kwargs):
prc = kwargs.pop('prc')
blockname = kwargs.pop('blockname')
row = prc.get_row_by_name(blockname)
col = prc.get_col_by_name(blockname)
mat = prc.get_operator_block(row, col)
if use_parallel:
smoother = mfem.HypreSmoother(mat)
smoother.SetType(getattr(mfem.HypreSmoother, name))
else:
cls = SparseSmootherCls[name][0]
arg = SparseSmootherCls[name][1]
smoother = cls(mat, arg)
smoother.iterative_mode = False
return smoother
def __init__(self, M, K, b):
mfem.PyTimeDependentOperator.__init__(self, M.Height())
self.M_prec = mfem.HypreSmoother()
self.M_solver = mfem.CGSolver(M.GetComm())
self.z = mfem.Vector(M.Height())
self.K = K
self.M = M
self.b = b
self.M_prec.SetType(mfem.HypreSmoother.Jacobi)
self.M_solver.SetPreconditioner(self.M_prec)
self.M_solver.SetOperator(M)
self.M_solver.iterative_mode = False
self.M_solver.SetRelTol(1e-9)
self.M_solver.SetAbsTol(0.0)
self.M_solver.SetMaxIter(100)
self.M_solver.SetPrintLevel(0)
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 solve_parallel(self, A, b, x=None):
from mpi4py import MPI
myid = MPI.COMM_WORLD.rank
nproc = MPI.COMM_WORLD.size
from petram.helper.mpi_recipes import gather_vector
def get_block(Op, i, j):
try:
return Op._linked_op[(i, j)]
except KeyError:
return None
offset = A.RowOffsets()
rows = A.NumRowBlocks()
cols = A.NumColBlocks()
if self.gui.write_mat:
for i in range(cols):
for j in range(rows):
m = get_block(A, i, j)
if m is None: continue
m.Print('matrix_' + str(i) + '_' + str(j))
for i, bb in enumerate(b):
for j in range(rows):
v = bb.GetBlock(j)
v.Print('rhs_' + str(i) + '_' + str(j) + '.' + smyid)
if x is not None:
for j in range(rows):
xx = x.GetBlock(j)
xx.Print('x_' + str(i) + '_' + str(j) + '.' + smyid)
M = mfem.BlockDiagonalPreconditioner(offset)
prcs = dict(self.gui.preconditioners)
name = self.Aname
assert not self.gui.parent.is_complex(), "can not solve complex"
if self.gui.parent.is_converted_from_complex():
name = sum([[n, n] for n in name], [])
for k, n in enumerate(name):
prc = prcs[n][1]
if prc == "None": continue
name = "".join([tmp for tmp in prc if not tmp.isdigit()])
A0 = get_block(A, k, k)
if A0 is None and not name.startswith('schur'): continue
if hasattr(mfem.HypreSmoother, prc):
invA0 = mfem.HypreSmoother(A0)
invA0.SetType(getattr(mfem.HypreSmoother, prc))
elif prc == 'ams':
depvar = self.engine.r_dep_vars[k]
dprint1("setting up AMS for ", depvar)
prec_fespace = self.engine.fespaces[depvar]
invA0 = mfem.HypreAMS(A0, prec_fespace)
invA0.SetSingularProblem()
elif name == 'MUMPS':
cls = SparseSmootherCls[name][0]
invA0 = cls(A0, gui=self.gui[prc], engine=self.engine)
elif name.startswith('schur'):
args = name.split("(")[-1].split(")")[0].split(",")
dprint1("setting up schur for ", args)
if len(args) > 1:
assert False, "not yet supported"
for arg in args:
r1 = self.engine.dep_var_offset(arg.strip())
c1 = self.engine.r_dep_var_offset(arg.strip())
B = get_block(A, k, c1)
Bt = get_block(A, r1, k).Transpose()
Bt = Bt.Transpose()
B0 = get_block(A, r1, c1)
Md = mfem.HypreParVector(MPI.COMM_WORLD,
B0.GetGlobalNumRows(),
B0.GetColStarts())
B0.GetDiag(Md)
Bt.InvScaleRows(Md)
S = mfem.ParMult(B, Bt)
invA0 = mfem.HypreBoomerAMG(S)
invA0.iterative_mode = False
else:
cls = SparseSmootherCls[name][0]
invA0 = cls(A0, gui=self.gui[prc])
invA0.iterative_mode = False
M.SetDiagonalBlock(k, invA0)
'''
We should support Shur complement type preconditioner
if offset.Size() > 2:
B = get_block(A, 1, 0)
MinvBt = get_block(A, 0, 1)
#Md = mfem.HypreParVector(MPI.COMM_WORLD,
# A0.GetGlobalNumRows(),
# A0.GetRowStarts())
Md = mfem.Vector()
A0.GetDiag(Md)
MinvBt.InvScaleRows(Md)
S = mfem.ParMult(B, MinvBt)
invS = mfem.HypreBoomerAMG(S)
invS.iterative_mode = False
M.SetDiagonalBlock(1, invS)
'''
maxiter = int(self.maxiter)
atol = self.abstol
rtol = self.reltol
kdim = int(self.kdim)
printit = 1
sol = []
solver = mfem.GMRESSolver(MPI.COMM_WORLD)
solver.SetKDim(kdim)
#solver = mfem.MINRESSolver(MPI.COMM_WORLD)
#solver.SetOperator(A)
#solver = mfem.CGSolver(MPI.COMM_WORLD)
solver.SetOperator(A)
solver.SetAbsTol(atol)
solver.SetRelTol(rtol)
solver.SetMaxIter(maxiter)
solver.SetPreconditioner(M)
solver.SetPrintLevel(1)
# solve the problem and gather solution to head node...
# may not be the best approach
for bb in b:
rows = MPI.COMM_WORLD.allgather(np.int32(bb.Size()))
rowstarts = np.hstack((0, np.cumsum(rows)))
dprint1("rowstarts/offser", rowstarts, offset.ToList())
if x is None:
xx = mfem.BlockVector(offset)
xx.Assign(0.0)
else:
xx = x
#for j in range(cols):
# dprint1(x.GetBlock(j).Size())
# dprint1(x.GetBlock(j).GetDataArray())
#assert False, "must implement this"
solver.Mult(bb, xx)
s = []
for i in range(offset.Size() - 1):
v = xx.GetBlock(i).GetDataArray()
vv = gather_vector(v)
if myid == 0:
s.append(vv)
else:
pass
if myid == 0:
sol.append(np.hstack(s))
if myid == 0:
sol = np.transpose(np.vstack(sol))
return sol
else:
return None
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)