def apply_essential(self, engine, gf, real=False, kfes=0):
if kfes > 0:
return
c0 = self.vt.make_value_or_expression(self)[0]
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index), 'c0', c0)
else:
dprint1("Apply Ess.(imag)" + str(self._sel_index), 'c0', c0)
name = self.get_root_phys().dep_vars[0]
fes = engine.get_fes(self.get_root_phys(), name=name)
fec_name = fes.FEColl().Name()
mesh = engine.get_emesh(mm=self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0] * mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx - 1] = 1
ess_vdofs = mfem.intArray()
fes.GetEssentialVDofs(mfem.intArray(bdr_attr), ess_vdofs, 0)
vdofs = np.where(np.array(ess_vdofs.ToList()) == -1)[0]
dofs = mfem.intArray([fes.VDofToDof(i) for i in vdofs])
fes.BuildDofToArrays()
coeff1 = SCoeff(c0,
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
gf.ProjectCoefficient(coeff1, dofs, 0)
def apply_essential(self, engine, gf, real=False, kfes=0):
if kfes > 1: return
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index))
else:
dprint1("Apply Ess.(imag)" + str(self._sel_index))
Exyz = self.vt.make_value_or_expression(self)
mesh = engine.get_mesh(mm=self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0] * mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx - 1] = 1
if kfes == 0:
coeff1 = Exy(2,
Exyz,
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
gf.ProjectBdrCoefficientTangent(coeff1, mfem.intArray(bdr_attr))
elif kfes == 1:
coeff1 = Ez(Exyz,
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
gf.ProjectBdrCoefficient(coeff1, mfem.intArray(bdr_attr))
def make_inv_mat(self, idx, inv):
ro = np.hstack([0, np.cumsum(np.array(self.lsize)[idx])])
row = mfem.intArray(list(ro))
col = mfem.intArray(list(ro))
mat = mfem.BlockOperator(row, col)
for ii, i in enumerate(idx):
mat.SetBlock(ii, ii, inv[i])
return mat
def get_global_blkmat_interleave(self):
'''
This routine ordered unkonws in the following order
Re FFE1, Im FES1, ReFES2, Im FES2, ...
If self.complex is False, it assembles a nomal block
matrix FES1, FES2...
'''
roffsets, coffsets = self.get_local_partitioning(convert_real=True,
interleave=True)
dprint1("offsets", roffsets, coffsets)
ro = mfem.intArray(list(roffsets))
co = mfem.intArray(list(coffsets))
glcsr = mfem.BlockOperator(ro, co)
ii = 0
for i in range(self.shape[0]):
jj = 0
for j in range(self.shape[1]):
if self[i, j] is not None:
if use_parallel:
if isinstance(self[i, j], chypre.CHypreMat):
gcsr = self[i, j]
cp = self[i, j].GetColPartArray()
rp = self[i, j].GetRowPartArray()
s = self[i, j].shape
#if (cp == rp).all() and s[0] == s[1]:
if gcsr[0] is not None:
csr = ToScipyCoo(gcsr[0]).tocsr()
gcsr[0] = ToHypreParCSR(csr, col_starts=cp)
if gcsr[1] is not None:
csr = ToScipyCoo(gcsr[1]).tocsr()
gcsr[1] = ToHypreParCSR(csr, col_starts=cp)
gcsrm = ToHypreParCSR(-csr, col_starts=cp)
dprint2(i, j, s, rp, cp)
else:
assert False, "unsupported block element " + str(
type(self[i, j]))
else:
if isinstance(self[i, j], ScipyCoo):
gcsr = self[i, j].get_mfem_sparsemat()
if gcsr[1] is not None:
gcsrm = mfem.SparseMatrix(gcsr[1])
gcsrm *= -1.
else:
assert False, "unsupported block element " + type(
self[i, j])
glcsr.SetBlock(ii, jj, gcsr[0])
if self.complex:
glcsr.SetBlock(ii + 1, jj + 1, gcsr[0])
if gcsr[1] is not None:
glcsr.SetBlock(ii + 1, jj, gcsr[1])
glcsr.SetBlock(ii, jj + 1, gcsrm)
jj = jj + 2 if self.complex else jj + 1
ii = ii + 2 if self.complex else ii + 1
return glcsr
def make_sub_matrix(self, src_mat, roffset, coffset, row_idx, col_idx):
ro = mfem.intArray(list(roffset))
co = mfem.intArray(list(coffset))
mat = mfem.BlockOperator(ro, co)
for ii, i in enumerate(row_idx):
for jj, j in enumerate(col_idx):
m = get_block(src_mat, i, j)
if m is None: continue
mat.SetBlock(ii, jj, m)
return mat
def add_mesh_refined_level(self, name, engine, inc=1, refine_dom=None):
emesh_idx, old_refine, element, order, fecdim, vdim = self._dataset[
name][-1]
new_refine = old_refine + 1
if not (emesh_idx, new_refine) in self._refined_mesh_storage:
m = self._refined_mesh_storage[(emesh_idx, old_refine)]
m2 = self._owner.new_mesh_from_mesh(m)
for i in range(inc):
if refine_dom is None:
m2.UniformRefinement()
else:
attr = m2.GetAttributeArray()
idx = list(np.where(np.in1d(attr, refine_dom))[0])
idx0 = mfem.intArray(idx)
m2.GeneralRefinement(idx0) # this is parallel refinement
m2.GetEdgeVertexTable()
self._refined_mesh_storage[(emesh_idx, old_refine + inc)] = m2
else:
m2 = self._refined_mesh_storage[(emesh_idx, new_refine)]
fec = self.get_or_allocate_fec(element, order, fecdim)
key1 = (emesh_idx, old_refine, element, order, fecdim, vdim)
key2 = (emesh_idx, new_refine, element, order, fecdim, vdim)
fes1 = self.get_or_allocate_fes(*key1)
fes2 = self.get_or_allocate_fes(*key2)
P = self.get_or_allocate_transfer(name, key1, key2, engine)
h = self._hierarchies[name]
h.AddLevel(m2, fes2, P, False, False, False)
self._dataset[name].append(key2)
return len(self._dataset[name])
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 isinstance(mat, mfem.ComplexOperator):
conv = mat.GetConvention()
blockOffsets = mfem.intArray()
blockOffsets.SetSize(3)
blockOffsets[0] = 0
blockOffsets[1] = mat.Height() // 2
blockOffsets[2] = mat.Height() // 2
blockOffsets.PartialSum()
smoother = mfem.BlockDiagonalPreconditioner(blockOffsets)
m_r = mat._real_operator
#m_i = mat._imag_operator
pc_r = _create_smoother(name, m_r)
pc_i = mfem.ScaledOperator(
pc_r, 1 if conv == mfem.ComplexOperator.HERMITIAN else -1)
smoother.SetDiagonalBlock(0, pc_r)
smoother.SetDiagonalBlock(1, pc_i)
smoother._smoothers = (pc_r, pc_i)
else:
smoother = _create_smoother(name, mat)
return smoother
def test_course_to_file_map():
mesh_file = "../data/inline-quad.mesh"
device = mfem.Device('cpu')
mesh = mfem.Mesh(mesh_file, 1, 1)
refinements = mfem.RefinementArray()
refinements.Append(mfem.Refinement(0, 0b11))
refinements.Append(mfem.Refinement(1, 0b10))
refinements.Append(mfem.Refinement(2, 0b01))
mesh.GeneralRefinement(refinements)
cft = mesh.GetRefinementTransforms()
coarse_to_fine = mfem.Table()
coarse_to_ref_type = mfem.intArray()
ref_type_to_matrix = mfem.Table()
ref_type_to_geom = mfem.GeometryTypeArray()
cft.GetCoarseToFineMap(mesh,
coarse_to_fine,
coarse_to_ref_type,
ref_type_to_matrix,
ref_type_to_geom)
print("coarse_to_fine element number mapping:")
coarse_to_fine.Print()
print("ref_type_to_geom mapping:")
for i in range(ref_type_to_geom.Size()):
g = ref_type_to_geom[i]
print("ref_type: " + str(i) + "=> geom: " + str(g))
def gather_blkvec_merged(self, size_hint=None, symmetric=False):
'''
Construct MFEM::BlockVector
This routine ordered unkonws in the following order
(Re_FES1_node1, Im_FES1_node1, Re_FES1_node2, Im_FES1_node2, ...)
'''
assert self.complex, "this format is complex only"
roffsets = self.get_local_partitioning_v(size_hint=size_hint)
roffsets = np.sum(np.diff(roffsets).reshape(-1, 2), 1)
roffsets = np.hstack([0, np.cumsum(roffsets)])
dprint1("roffsets(vector)", roffsets)
offset = mfem.intArray(list(roffsets))
vec = mfem.BlockVector(offset)
vec._offsets = offset # in order to keep it from freed
data = []
ii = 0
jj = 0
# Here I don't like that I am copying the data between two vectors..
# But, avoiding this takes the large rearangement of program flow...
for i in range(self.shape[0]):
if self[i, 0] is not None:
if isinstance(self[i, 0], chypre.CHypreVec):
rr = self[i, 0][0].GetDataArray()
if self[i, 0][1] is not None:
if symmetric:
ii = -self[i, 0][1].GetDataArray()
else:
ii = self[i, 0][1].GetDataArray()
else:
ii = rr * 0
vv = np.hstack([rr, ii])
vec.GetBlock(i).Assign(vv)
elif isinstance(self[i, 0], ScipyCoo):
arr = np.atleast_1d(self[i, 0].toarray().squeeze())
if symmetric:
arr = np.hstack([np.real(arr), -np.imag(arr)])
else:
arr = np.hstack([np.real(arr), np.imag(arr)])
vec.GetBlock(i).Assign(arr)
else:
assert False, "not implemented, " + str(type(self[i, 0]))
else:
vec.GetBlock(i).Assign(0.0)
return vec
def apply_essential_1(self, method, real, c0, vdim, vvdim, bdr_attr):
if vdim == 1:
coeff1 = SCoeff(c0[0],
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
else:
coeff1 = VCoeff(vdim,
c0,
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
assert not (vvdim != -1
and vdim > 1), "Wrong setting...(vvdim != -1 and vdim > 1)"
#print vvdim, vdim, method, coeff1
if vvdim == -1:
method(coeff1, mfem.intArray(bdr_attr))
else:
for cp in vvdim:
method(coeff1, mfem.intArray(bdr_attr), cp)
def apply_essential(self, engine, gf, kfes, real=False, **kwargs):
mesh = engine.get_mesh(mm=self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0] * mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx - 1] = 1
if kfes == 0:
coeff1 = mfem.VectorArrayCoefficient(3)
coeff1.Set(0, mfem.ConstantCoefficient(0.0))
coeff1.Set(1, mfem.ConstantCoefficient(0.0))
coeff1.Set(2, mfem.ConstantCoefficient(0.0))
gf.ProjectBdrCoefficientTangent(coeff1, mfem.intArray(bdr_attr))
def FindPoints(self, pp, warn=True, inv_trans=None):
r"""count, element_id, integration_points = FindPoints(points, warn=True, int_trans=None)"""
import numpy as np
import mfem.par as mfem
pp = np.array(pp, copy=False, dtype=float).transpose()
M = mfem.DenseMatrix(pp.shape[0], pp.shape[1])
M.Assign(pp)
elem_ids = mfem.intArray()
int_points = mfem.IntegrationPointArray()
count = _mesh.Mesh_FindPoints(self, M, elem_ids, int_points, warn,
inv_trans)
elem_ids = elem_ids.ToList()
return count, elem_ids, int_points
def gather_blkvec_interleave(self, size_hint=None):
'''
Construct MFEM::BlockVector
This routine ordered unkonws in the following order
Re FFE1, Im FES1, ReFES2, Im FES2, ...
If self.complex is False, it assembles a nomal block
vector
This routine is used together with get_global_blkmat_interleave(self):
'''
roffsets = self.get_local_partitioning_v(convert_real=True,
interleave=True,
size_hint=size_hint)
dprint1("roffsets(vector)", roffsets)
offset = mfem.intArray(list(roffsets))
vec = mfem.BlockVector(offset)
vec._offsets = offset # in order to keep it from freed
data = []
ii = 0
jj = 0
# Here I don't like that I am copying the data between two vectors..
# But, avoiding this takes the large rearangement of program flow...
for i in range(self.shape[0]):
if self[i, 0] is not None:
if isinstance(self[i, 0], chypre.CHypreVec):
vec.GetBlock(ii).Assign(self[i, 0][0].GetDataArray())
if self.complex:
if self[i, 0][1] is not None:
vec.GetBlock(ii + 1).Assign(
self[i, 0][1].GetDataArray())
else:
vec.GetBlock(ii + 1).Assign(0.0)
elif isinstance(self[i, 0], ScipyCoo):
arr = np.atleast_1d(self[i, 0].toarray().squeeze())
vec.GetBlock(ii).Assign(np.real(arr))
if self.complex:
vec.GetBlock(ii + 1).Assign(np.imag(arr))
else:
assert False, "not implemented, " + str(type(self[i, 0]))
else:
vec.GetBlock(ii).Assign(0.0)
if self.complex:
vec.GetBlock(ii + 1).Assign(0.0)
ii = ii + 2 if self.complex else ii + 1
return vec
def apply_essential(self, engine, gf, real = False, kfes = 0):
if kfes > 1: return
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index))
else:
dprint1("Apply Ess.(imag)" + str(self._sel_index))
Erphiz = self.vt.make_value_or_expression(self)
mesh = engine.get_mesh(mm = self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0]*mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx-1] = 1
if kfes == 0:
coeff1 = mfem.VectorArrayCoefficient(2)
coeff1.Set(0, mfem.ConstantCoefficient(0.0))
coeff1.Set(1, mfem.ConstantCoefficient(0.0))
gf.ProjectBdrCoefficientTangent(coeff1,
mfem.intArray(bdr_attr))
elif kfes == 1:
coeff1 = mfem.ConstantCoefficient(0.0)
gf.ProjectBdrCoefficient(coeff1,
mfem.intArray(bdr_attr))
def do_findpoints(mesh, *args):
sdim = mesh.SpaceDimension()
shape = args[0].shape
size= len(args[0].flatten())
ptx = np.vstack([t.flatten() for t in args]).transpose().flatten()
ptx2 = mfem.Vector(ptx)
point_mat = mfem.DenseMatrix(ptx2.GetData(), size, sdim)
elem_id = mfem.intArray()
ips = mfem.IntegrationPointArray()
num_found = mesh.FindPoints(point_mat, elem_id, ips, True)
elem_id = np.array(elem_id.ToList())
return v, elem_id, ips
def apply_essential(self, engine, gf, real=False, kfes=0):
if kfes > 0: return
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index))
else:
dprint1("Apply Ess.(imag)" + str(self._sel_index))
mesh = engine.get_mesh(mm=self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0] * mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx - 1] = 1
coeff1 = mfem.ConstantCoefficient(0.0)
gf.ProjectBdrCoefficient(coeff1, mfem.intArray(bdr_attr))
def make_sub_vec(self, src_vec, idx, inv=False, nocopy=False):
if inv:
idx = [k for k in range(self.nb) if not k in idx]
size = [src_vec.BlockSize(i) for i in idx]
offset = np.hstack([0, np.cumsum(size, dtype=int)])
offset = mfem.intArray(list(offset))
sub_vec = mfem.BlockVector(offset)
sub_vec._offsets = offset # in order to keep it from freed
for k, i in enumerate(idx):
if nocopy:
sub_vec.GetBlock(k).Assign(0.0)
else:
sub_vec.GetBlock(k).Assign(src_vec.GetBlock(i).GetDataArray())
return sub_vec
def updStiffMatMS(self, elmLst, elmCompStiffMat):
self.K = mfem.ParBilinearForm(self.fespace)
lambVec = mfem.Vector(self.fespace.GetMesh().attributes.Max())
lambVec.Assign(self.lmbda)
lambVec[0] = lambVec[1]
lambda_func = mfem.PWConstCoefficient(lambVec)
muVec = mfem.Vector(self.fespace.GetMesh().attributes.Max())
muVec.Assign(self.mu)
muVec[0] = muVec[1]
mu_func = mfem.PWConstCoefficient(muVec)
self.K.AddDomainIntegrator(
mfem.ElasticityIntegrator(lambda_func, mu_func))
self.K.Assemble(0, elmLst, elmCompStiffMat, False, True)
self.Kmat = mfem.HypreParMatrix()
empty_tdof_list = intArray()
self.K.FormLinearSystem(empty_tdof_list, self.x_gfBdr, self.bx,
self.Kmat, self.vx.GetBlock(1), self.Bx, 1)
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 apply_essential(self, engine, gf, real = False, kfes = 0):
if kfes == 0: return
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index))
coeff = mfem.ConstantCoefficient(float(self.psi0))
else:
return
#dprint1("Apply Ess.(imag)" + str(self._sel_index))
#coeff = mfem.ConstantCoefficient(complex(self.psi0).imag)
coeff = self.restrict_coeff(coeff, engine)
mesh = engine.get_mesh(mm = self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0]*mesh.bdr_attributes.Max()
ess_bdr = self.get_essential_idx(1)
dprint1("Essential boundaries", ess_bdr)
for idx in ess_bdr:
bdr_attr[idx-1] = 1
gf.ProjectBdrCoefficient(coeff, mfem.intArray(bdr_attr))
def apply_essential(self, engine, gf, real=False, kfes=0):
if kfes != 0: return
if real:
dprint1("Apply Ess.(real)" + str(self._sel_index))
else:
dprint1("Apply Ess.(imag)" + str(self._sel_index))
f_name = self._make_f_name()
coeff1 = Et(3,
f_name,
self.get_root_phys().ind_vars,
self._local_ns,
self._global_ns,
real=real)
coeff1 = self.restrict_coeff(coeff1, engine, vec=True)
mesh = engine.get_mesh(mm=self)
ibdr = mesh.bdr_attributes.ToList()
bdr_attr = [0] * mesh.bdr_attributes.Max()
for idx in self._sel_index:
bdr_attr[idx - 1] = 1
gf.ProjectBdrCoefficientTangent(coeff1, mfem.intArray(bdr_attr))
# 7. Set up the linear form F(.) which corresponds to the right-hand side of # the FEM linear system, which in this case is (f,phi_i) where f=1.0 and # phi_i are the basis functions in the test finite element fespace. one = mfem.ConstantCoefficient(1.0) F = mfem.ParLinearForm(test_space) F.AddDomainIntegrator(mfem.DomainLFIntegrator(one)) F.Assemble() x0 = mfem.ParGridFunction(x0_space) x0.Assign(0.0) # 8. Set up the mixed bilinear form for the primal trial unknowns, B0, # the mixed bilinear form for the interfacial unknowns, Bhat, # the inverse stiffness matrix on the discontinuous test space, Sinv, # and the stiffness matrix on the continuous trial space, S0. ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max()) ess_bdr.Assign(1) ess_dof = mfem.intArray() x0_space.GetEssentialVDofs(ess_bdr, ess_dof) B0 = mfem.ParMixedBilinearForm(x0_space, test_space) B0.AddDomainIntegrator(mfem.DiffusionIntegrator(one)) B0.Assemble() B0.EliminateEssentialBCFromTrialDofs(ess_dof, x0, F) B0.Finalize() Bhat = mfem.ParMixedBilinearForm(xhat_space, test_space) Bhat.AddTraceFaceIntegrator(mfem.TraceJumpIntegrator()) Bhat.Assemble() Bhat.Finalize()
# corresponding to the Laplacian operator -Delta, by adding the Diffusion
# and Mass domain integrators.
a = mfem.ParBilinearForm(fespace)
a.AddDomainIntegrator(mfem.DiffusionIntegrator(one))
a.AddDomainIntegrator(mfem.MassIntegrator(one))
# 8. Assemble the linear system, apply conforming constraints, etc.
a.Assemble()
a.Finalize()
mat = a.ParallelAssemble()
mat.Print("parmatrix")
A = mfem.HypreParMatrix()
B = mfem.Vector()
X = mfem.Vector()
empty_tdof_list = mfem.intArray()
a.FormLinearSystem(empty_tdof_list, x, b, A, X, B)
amg = mfem.HypreBoomerAMG(A)
pcg = mfem.HyprePCG(A)
pcg.SetTol(1e-12)
pcg.SetMaxIter(200)
pcg.SetPrintLevel(2)
pcg.SetPreconditioner(amg)
pcg.Mult(B, X)
# 10. Recover the solution as a finite element grid function.
a.RecoverFEMSolution(X, b, x)
# 12. Compute and print the L^2 norm of the error.
l2_coll = mfem.L2_FECollection(order, dim)
R_space = mfem.ParFiniteElementSpace(pmesh, hdiv_coll)
W_space = mfem.ParFiniteElementSpace(pmesh, l2_coll)
dimR = R_space.GlobalTrueVSize()
dimW = W_space.GlobalTrueVSize()
if verbose:
print("***********************************************************")
print("dim(R) = " + str(dimR))
print("dim(W) = " + str(dimW))
print("dim(R+W) = " + str(dimR + dimW))
print("***********************************************************")
block_offsets = intArray([0, R_space.GetVSize(), W_space.GetVSize()])
block_offsets.PartialSum()
block_trueOffsets = intArray([0, R_space.TrueVSize(), W_space.TrueVSize()])
block_trueOffsets.PartialSum()
k = mfem.ConstantCoefficient(1.0)
fcoeff = fFunc(dim)
fnatcoeff = f_natural()
gcoeff = gFunc()
ucoeff = uFunc_ex(dim)
pcoeff = pFunc_ex()
x = mfem.BlockVector(block_offsets)
rhs = mfem.BlockVector(block_offsets)
def get_global_blkmat_merged(self, symmetric=False):
'''
This routine ordered unkonws in the following order
Re FFE1, Im FES1, ReFES2, Im FES2, ...
matrix FES1, FES2...
'''
assert self.complex, "this format is complex only"
roffsets, coffsets = self.get_local_partitioning()
roffsets = np.sum(np.diff(roffsets).reshape(-1, 2), 1)
coffsets = np.sum(np.diff(coffsets).reshape(-1, 2), 1)
roffsets = np.hstack([0, np.cumsum(roffsets)])
coffsets = np.hstack([0, np.cumsum(coffsets)])
dprint1("Generating MFEM BlockMatrix: shape = " +
str((len(roffsets) - 1, len(coffsets) - 1)))
dprint1("Generating MFEM BlockMatrix: roffset/coffset = ", roffsets,
coffsets)
ro = mfem.intArray(list(roffsets))
co = mfem.intArray(list(coffsets))
glcsr = mfem.BlockOperator(ro, co)
ii = 0
for j in range(self.shape[1]):
jfirst = True
for i in range(self.shape[0]):
if self[i, j] is not None:
if use_parallel:
if isinstance(self[i, j], chypre.CHypreMat):
gcsr = self[i, j]
cp = self[i, j].GetColPartArray()
rp = self[i, j].GetRowPartArray()
rsize_local = rp[1] - rp[0]
if jfirst:
csize_local = cp[1] - cp[0]
csize = allgather(csize_local)
cstarts = np.hstack([0, np.cumsum(csize)])
jfirst = False
s = self[i, j].shape
# if (cp == rp).all() and s[0] == s[1]:
'''
if gcsr[0] is not None:
csc = ToScipyCoo(gcsr[0]).tocsc()
csc1 = [csc[:,cstarts[k]:cstarts[k+1]] for k in range(len(cstarts)-1)]
if symmetric:
csc1m = [-csc[:,cstarts[k]:cstarts[k+1]] for k in range(len(cstarts)-1)]
else:
csc1 = [None]*len(csize)
csc1m = [None]*len(csize)
if gcsr[1] is not None:
csc = ToScipyCoo(gcsr[1]).tocsc()
if not symmetric:
csc2 = [ csc[:,cstarts[k]:cstarts[k+1]] for k in range(len(cstarts)-1)]
csc2m = [-csc[:,cstarts[k]:cstarts[k+1]] for k in range(len(cstarts)-1)]
else:
csc2 = [None]*len(csize)
csc2m = [None]*len(csize)
if symmetric:
csr = scipy.sparse.bmat([sum(zip(csc1, csc2m), ()),
sum(zip(csc2m, csc1m), ())]).tocsr()
else:
csr = scipy.sparse.bmat([sum(zip(csc1, csc2m), ()),
sum(zip(csc2, csc1), ())]).tocsr()
cp2 = [(cp*2)[0], (cp*2)[1], np.sum(csize)*2]
#gcsr[1] = ToHypreParCSR(csr, col_starts =cp)
gcsr = ToHypreParCSR(csr, col_starts =cp2)
'''
if gcsr[0] is None:
csr = scipy.sparse.csr_matrix(
(rsize_local, cstarts[-1]),
dtype=np.float64)
cp3 = [cp[0], cp[1], cstarts[-1]]
gcsa = ToHypreParCSR(csr, col_starts=cp3)
else:
gcsa = gcsr[0]
if gcsr[1] is None:
csr = scipy.sparse.csr_matrix(
(rsize_local, cstarts[-1]),
dtype=np.float64)
cp3 = [cp[0], cp[1], cstarts[-1]]
gcsb = ToHypreParCSR(csr, col_starts=cp3)
else:
gcsb = gcsr[1]
else:
assert False, "unsupported block element " + \
str(type(self[i, j]))
else:
if isinstance(self[i, j], ScipyCoo):
'''
if symmetric:
tmp = scipy.sparse.bmat([[ self[i, j].real, -self[i, j].imag],
[-self[i, j].imag, -self[i, j].real]])
else:
tmp = scipy.sparse.bmat([[self[i, j].real, -self[i, j].imag],
[self[i, j].imag, self[i, j].real]])
'''
csra = self[i, j].real.tocsr()
csrb = self[i, j].imag.tocsr()
csra.eliminate_zeros()
csrb.eliminate_zeros()
gcsa = mfem.SparseMatrix(csra)
gcsb = mfem.SparseMatrix(csrb)
else:
assert False, "unsupported block element " + \
type(self[i, j])
Hermitian = False if symmetric else True
gcsr = mfem.ComplexOperator(gcsa, gcsb, False, False,
Hermitian)
gcsr._real_operator = gcsa
gcsr._imag_operator = gcsb
glcsr.SetBlock(i, j, gcsr)
return glcsr
# needed on the right hand side of the generalized eigenvalue problem
# below. The boundary conditions are implemented by marking only boundary
# attribute 1 as essential. We use special values on the diagonal to
# shift the Dirichlet eigenvalues out of the computational range. After
# serial/parallel assembly we extract the corresponding parallel matrices
# A and M.
lamb = mfem.Vector(pmesh.attributes.Max())
lamb.Assign(1.0)
lamb[0] = lamb[1] * 50
lambda_func = mfem.PWConstCoefficient(lamb)
mu = mfem.Vector(pmesh.attributes.Max())
mu.Assign(1.0)
mu[0] = mu[1] * 50
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()
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
# 7. Define the parallel vector finite element spaces representing the mesh
# deformation x_gf, the velocity v_gf, and the initial configuration,
# x_ref. Define also the elastic energy density, w_gf, which is in a
# discontinuous higher-order space. Since x and v are integrated in time
# as a system, we group them together in block vector vx, on the unique
# parallel degrees of freedom, with offsets given by array true_offset.
fec = mfem.H1_FECollection(order, dim)
fespace = mfem.ParFiniteElementSpace(pmesh, fec, dim)
glob_size = fespace.GlobalTrueVSize()
if (myid == 0):
print('Number of velocity/deformation unknowns: ' + str(glob_size))
true_size = fespace.TrueVSize()
true_offset = mfem.intArray(3)
true_offset[0] = 0
true_offset[1] = true_size
true_offset[2] = 2 * true_size
vx = mfem.BlockVector(true_offset)
v_gf = mfem.ParGridFunction(fespace)
x_gf = mfem.ParGridFunction(fespace)
x_ref = mfem.ParGridFunction(fespace)
pmesh.GetNodes(x_ref)
w_fec = mfem.L2_FECollection(order + 1, dim)
w_fespace = mfem.ParFiniteElementSpace(pmesh, w_fec)
w_gf = mfem.ParGridFunction(w_fespace)
# 4. Project a NURBS mesh to a piecewise-quadratic curved mesh. Make sure
# that the mesh is non-conforming if it has quads or hexes and refine it
if (mesh.NURBSext):
mesh.UniformRefinement()
if ref_levels > 0: ref_levels = ref_levels - 1
mesh.SetCurvature(2)
mesh.EnsureNCMesh()
for l in range(ref_levels):
mesh.UniformRefinement()
# 5. Define a parallel mesh by partitioning the serial mesh. Once the
# parallel mesh is defined, the serial mesh can be deleted.
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max())
ess_bdr.Assign(1)
# 6. Define a finite element space on the mesh. The polynomial order is one
# (linear) by default, but this can be changed on the command line.
fec = mfem.H1_FECollection(order, dim)
fespace = mfem.ParFiniteElementSpace(pmesh, fec)
# 7. As in Example 1p, we set up bilinear and linear forms corresponding to
# the Laplace problem -\Delta u = 1. We don't assemble the discrete
# problem yet, this will be done in the inner loop.
a = mfem.ParBilinearForm(fespace)
b = mfem.ParLinearForm(fespace)
one = mfem.ConstantCoefficient(1.0)
bdr = BdrCoefficient()
def run(order = 1, static_cond = False,
meshfile = def_meshfile, visualization = False,
use_strumpack = False):
mesh = mfem.Mesh(meshfile, 1,1)
dim = mesh.Dimension()
ref_levels = int(np.floor(np.log(10000./mesh.GetNE())/np.log(2.)/dim))
for x in range(ref_levels):
mesh.UniformRefinement();
mesh.ReorientTetMesh();
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
par_ref_levels = 2
for l in range(par_ref_levels):
pmesh.UniformRefinement();
if order > 0:
fec = mfem.H1_FECollection(order, dim)
elif mesh.GetNodes():
fec = mesh.GetNodes().OwnFEC()
print( "Using isoparametric FEs: " + str(fec.Name()));
else:
order = 1
fec = mfem.H1_FECollection(order, dim)
fespace =mfem.ParFiniteElementSpace(pmesh, fec)
fe_size = fespace.GlobalTrueVSize()
if (myid == 0):
print('Number of finite element unknowns: '+ str(fe_size))
ess_tdof_list = mfem.intArray()
if pmesh.bdr_attributes.Size()>0:
ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max())
ess_bdr.Assign(1)
fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list)
# the basis functions in the finite element fespace.
b = mfem.ParLinearForm(fespace)
one = mfem.ConstantCoefficient(1.0)
b.AddDomainIntegrator(mfem.DomainLFIntegrator(one))
b.Assemble();
x = mfem.ParGridFunction(fespace);
x.Assign(0.0)
a = mfem.ParBilinearForm(fespace);
a.AddDomainIntegrator(mfem.DiffusionIntegrator(one))
if static_cond: a.EnableStaticCondensation()
a.Assemble();
A = mfem.HypreParMatrix()
B = mfem.Vector()
X = mfem.Vector()
a.FormLinearSystem(ess_tdof_list, x, b, A, X, B)
if (myid == 0):
print("Size of linear system: " + str(x.Size()))
print("Size of linear system: " + str(A.GetGlobalNumRows()))
if use_strumpack:
import mfem.par.strumpack as strmpk
Arow = strmpk.STRUMPACKRowLocMatrix(A)
args = ["--sp_hss_min_sep_size", "128", "--sp_enable_hss"]
strumpack = strmpk.STRUMPACKSolver(args, MPI.COMM_WORLD)
strumpack.SetPrintFactorStatistics(True)
strumpack.SetPrintSolveStatistics(False)
strumpack.SetKrylovSolver(strmpk.KrylovSolver_DIRECT);
strumpack.SetReorderingStrategy(strmpk.ReorderingStrategy_METIS)
strumpack.SetMC64Job(strmpk.MC64Job_NONE)
# strumpack.SetSymmetricPattern(True)
strumpack.SetOperator(Arow)
strumpack.SetFromCommandLine()
strumpack.Mult(B, X);
else:
amg = mfem.HypreBoomerAMG(A)
cg = mfem.CGSolver(MPI.COMM_WORLD)
cg.SetRelTol(1e-12)
cg.SetMaxIter(200)
cg.SetPrintLevel(1)
cg.SetPreconditioner(amg)
cg.SetOperator(A)
cg.Mult(B, X);
a.RecoverFEMSolution(X, b, x)
smyid = '{:0>6d}'.format(myid)
mesh_name = "mesh."+smyid
sol_name = "sol."+smyid
pmesh.Print(mesh_name, 8)
x.Save(sol_name, 8)