fform.Update(R_space, rhs.GetBlock(0), 0) fform.AddDomainIntegrator(mfem.VectorFEDomainLFIntegrator(fcoeff)) fform.AddBoundaryIntegrator(mfem.VectorFEBoundaryFluxLFIntegrator(fnatcoeff)) fform.Assemble() fform.ParallelAssemble(trueRhs.GetBlock(0)) gform = mfem.ParLinearForm() gform.Update(W_space, rhs.GetBlock(1), 0) gform.AddDomainIntegrator(mfem.DomainLFIntegrator(gcoeff)) gform.Assemble() gform.ParallelAssemble(trueRhs.GetBlock(1)) mVarf = mfem.ParBilinearForm(R_space) bVarf = mfem.ParMixedBilinearForm(R_space, W_space) mVarf.AddDomainIntegrator(mfem.VectorFEMassIntegrator(k)) mVarf.Assemble() mVarf.Finalize() M = mVarf.ParallelAssemble() bVarf.AddDomainIntegrator(mfem.VectorFEDivergenceIntegrator()) bVarf.Assemble() bVarf.Finalize() B = bVarf.ParallelAssemble() B *= -1 BT = B.Transpose() darcyOp = mfem.BlockOperator(block_trueOffsets) darcyOp.SetBlock(0, 0, M) darcyOp.SetBlock(0, 1, BT) darcyOp.SetBlock(1, 0, B)
if (myid == 0):
print("Number of unknowns: " + str(size))
one = mfem.ConstantCoefficient(1.0)
ess_bdr = intArray()
if (pmesh.bdr_attributes.Size() > 0):
ess_bdr.SetSize(pmesh.bdr_attributes.Max())
ess_bdr.Assign(1)
a = mfem.ParBilinearForm(fespace)
a.AddDomainIntegrator(mfem.CurlCurlIntegrator(one))
if (pmesh.bdr_attributes.Size() == 0):
# Add a mass term if the mesh has no boundary, e.g. periodic mesh or
# closed surface.
a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(one))
a.Assemble()
a.EliminateEssentialBCDiag(ess_bdr, 1.0)
a.Finalize()
m = mfem.ParBilinearForm(fespace)
m.AddDomainIntegrator(mfem.VectorFEMassIntegrator(one))
m.Assemble()
# shift the eigenvalue corresponding to eliminated dofs to a large value
m.EliminateEssentialBCDiag(ess_bdr, 2.3e-308)
m.Finalize()
A = a.ParallelAssemble()
M = m.ParallelAssemble()
def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
mesh = mfem.Mesh(3, 3, 3, "TETRAHEDRON")
mesh.ReorientTetMesh()
order = 1
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec1 = mfem.H1_FECollection(order, dim)
fespace1 = mfem.FiniteElementSpace(mesh, fec1, 1)
fec2 = mfem.ND_FECollection(order, dim)
fespace2 = mfem.FiniteElementSpace(mesh, fec2, 1)
print("Element order :", order)
print('Number of H1 finite element unknowns: ' +
str(fespace1.GetTrueVSize()))
print('Number of ND finite element unknowns: ' +
str(fespace2.GetTrueVSize()))
print("Checking scalar")
gf = mfem.GridFunction(fespace1)
c1 = mfem.NumbaFunction(s_func, sdim).GenerateCoefficient()
c2 = s_coeff()
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c1)
end = time.time()
data1 = gf.GetDataArray().copy()
print("Numba time (scalar)", end - start)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c2)
end = time.time()
data2 = gf.GetDataArray().copy()
print("Python time (scalar)", end - start)
check(data1, data2, "scalar coefficient does not agree with original")
print("Checking vector")
gf = mfem.GridFunction(fespace2)
c3 = mfem.VectorNumbaFunction(v_func, sdim, dim).GenerateCoefficient()
c4 = v_coeff(dim)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c3)
end = time.time()
data1 = gf.GetDataArray().copy()
print("Numba time (vector)", end - start)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c4)
end = time.time()
data2 = gf.GetDataArray().copy()
print("Python time (vector)", end - start)
check(data1, data2, "vector coefficient does not agree with original")
print("Checking matrix")
a1 = mfem.BilinearForm(fespace2)
a2 = mfem.BilinearForm(fespace2)
c4 = mfem.MatrixNumbaFunction(m_func, sdim, dim).GenerateCoefficient()
c5 = m_coeff(dim)
a1.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c4))
a2.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c5))
start = time.time()
a1.Assemble()
end = time.time()
a1.Finalize()
M1 = a1.SpMat()
print("Numba time (matrix)", end - start)
start = time.time()
a2.Assemble()
end = time.time()
a2.Finalize()
M2 = a2.SpMat()
print("Python time (matrix)", end - start)
#from mfem.commmon.sparse_utils import sparsemat_to_scipycsr
#csr1 = sparsemat_to_scipycsr(M1, float)
#csr2 = sparsemat_to_scipycsr(M2, float)
check(M1.GetDataArray(), M2.GetDataArray(),
"matrix coefficient does not agree with original")
check(M1.GetIArray(), M2.GetIArray(),
"matrix coefficient does not agree with original")
check(M1.GetJArray(), M2.GetJArray(),
"matrix coefficient does not agree with original")
print("PASSED")
# solution. Note that only values from the boundary faces will be used
# when eliminating the non-homogeneous boundary condition to modify the
# r.h.s. vector b.
x = mfem.ParGridFunction(fespace)
F = E_exact(sdim)
x.ProjectCoefficient(F)
# 10. Set up the parallel bilinear form corresponding to the H(div)
# diffusion operator grad alpha div + beta I, by adding the div-div and
# the mass domain integrators.
alpha = mfem.ConstantCoefficient(1.0)
beta = mfem.ConstantCoefficient(1.0)
a = mfem.ParBilinearForm(fespace)
a.AddDomainIntegrator(mfem.DivDivIntegrator(alpha))
a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(beta))
# 11. Assemble the parallel bilinear form and the corresponding linear
# system, applying any necessary transformations such as: parallel
# assembly, eliminating boundary conditions, applying conforming
# constraints for non-conforming AMR, static condensation,
# hybridization, etc.
if (static_cond): a.EnableStaticCondensation()
elif (hybridization):
hfec = mfem.DG_Interface_FECollection(order - 1, dim)
hfes = mfem.ParFiniteElementSpace(mesh, hfec)
a.EnableHybridization(hfes, mfem.NormalTraceJumpIntegrator(),
ess_tdof_list)
a.Assemble()
A = mfem.HypreParMatrix()
# when eliminating the non-homogeneous boundary condition to modify the
# r.h.s. vector b.
x = mfem.ParGridFunction(fespace)
E = E_exact()
x.ProjectCoefficient(E)
# 10. Set up the bilinear form corresponding to the EM diffusion operator
# curl muinv curl + sigma I, by adding the curl-curl and the mass domain
# integrators.
muinv = mfem.ConstantCoefficient(1.0)
sigma = mfem.ConstantCoefficient(1.0)
a = mfem.ParBilinearForm(fespace)
a.AddDomainIntegrator(mfem.CurlCurlIntegrator(muinv))
a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(sigma))
# 11. Assemble the bilinear form and the corresponding linear system,
# applying any necessary transformations such as: eliminating boundary
# conditions, applying conforming constraints for non-conforming AMR,
# static condensation, etc.
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 verbose:
print("Size of linear system: " + str(A.GetGlobalNumRows()))
