def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
meshfile = "../data/amr-quad.mesh"
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
print("write mesh to STDOUT")
mesh.Print(mfem.STDOUT)
print("creat VTK file to file")
mesh.PrintVTK('mesh.vtk', 1)
print("creat VTK to STDOUT")
mesh.PrintVTK(mfem.STDOUT, 1)
print("save GridFunction to file")
gf.Save('out_test_gridfunc.gf')
gf.SaveVTK(mfem.wFILE('out_test_gridfunc1.vtk'), 'data', 1)
print("save GridFunction to file in VTK format")
gf.SaveVTK('out_test_gridfunc2.vtk', 'data', 1)
print("Gridfunction to STDOUT")
gf.Save(mfem.STDOUT)
o = io.StringIO()
count = gf.Save(o)
count2 = gf.SaveVTK(o, 'data', 1)
print("length of data ", count, count2)
print('result: ', o.getvalue())
def run_test():
meshfile = expanduser(join(mfem_path, 'data', 'beam-tri.mesh'))
mesh = mfem.Mesh(meshfile, 1, 1)
fec = mfem.H1_FECollection(1, 1)
fespace = mfem.FiniteElementSpace(mesh, fec)
fespace.Save()
def run_test():
#meshfile =expanduser(join(mfem_path, 'data', 'beam-tri.mesh'))
meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
gf.Save('out_test_gridfunc.gf')
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()
rhs = RhsCoefficient()
integ = mfem.DiffusionIntegrator(one)
a.AddDomainIntegrator(integ)
b.AddDomainIntegrator(mfem.DomainLFIntegrator(rhs))
# degree may depend on the spatial dimension of the domain, the type of
# the mesh and the trial space order.
trial_order = order
trace_order = order - 1
test_order = order # reduced order, full order is (order + dim - 1)
if (dim == 2
and (order % 2 == 0 or (pmesh.MeshGenerator() & 2 and order > 1))):
test_order = test_order + 1
if (test_order < trial_order):
if myid == 0:
print(
"Warning, test space not enriched enough to handle primal trial space"
)
x0_fec = mfem.H1_FECollection(trial_order, dim)
xhat_fec = mfem.RT_Trace_FECollection(trace_order, dim)
test_fec = mfem.L2_FECollection(test_order, dim)
x0_space = mfem.ParFiniteElementSpace(pmesh, x0_fec)
xhat_space = mfem.ParFiniteElementSpace(pmesh, xhat_fec)
test_space = mfem.ParFiniteElementSpace(pmesh, test_fec)
glob_true_s0 = x0_space.GlobalTrueVSize()
glob_true_s1 = xhat_space.GlobalTrueVSize()
glob_true_s_test = test_space.GlobalTrueVSize()
if myid == 0:
print('\n'.join([
"nNumber of Unknowns", " Trial space, X0 : " +
str(glob_true_s0) + " (order " + str(trial_order) + ")",
mesh.AddTriangle(tri_e[j], j + 1)
mesh.FinalizeTriMesh(1, 1, True)
else:
quad_v = [[-1, -1, -1], [+1, -1, -1], [+1, +1, -1], [-1, +1, -1],
[-1, -1, +1], [+1, -1, +1], [+1, +1, +1], [-1, +1, +1]]
quad_e = [[3, 2, 1, 0], [0, 1, 5, 4], [1, 2, 6, 5], [2, 3, 7, 6],
[3, 0, 4, 7], [4, 5, 6, 7]]
for j in range(Nvert):
mesh.AddVertex(quad_v[j])
for j in range(Nelem):
mesh.AddQuad(quad_e[j], j + 1)
mesh.FinalizeQuadMesh(1, 1, True)
# Set the space for the high-order mesh nodes.
fec = mfem.H1_FECollection(order, mesh.Dimension())
nodal_fes = mfem.FiniteElementSpace(mesh, fec, mesh.SpaceDimension())
mesh.SetNodalFESpace(nodal_fes)
def SnapNodes(mesh):
nodes = mesh.GetNodes()
node = mfem.Vector(mesh.SpaceDimension())
for i in np.arange(nodes.FESpace().GetNDofs()):
for d in np.arange(mesh.SpaceDimension()):
node[d] = nodes[nodes.FESpace().DofToVDof(i, d)]
node /= node.Norml2()
for d in range(mesh.SpaceDimension()):
nodes[nodes.FESpace().DofToVDof(i, d)] = node[d]
# we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
# a command-line parameter.
for lev in range(ser_ref_levels):
mesh.UniformRefinement()
# 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
# this mesh further in parallel to increase the resolution. Once the
# parallel mesh is defined, the serial mesh can be deleted.
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
for x in range(par_ref_levels):
pmesh.UniformRefinement()
# 7. Define the vector finite element space representing the current and the
# initial temperature, u_ref.
fe_coll = mfem.H1_FECollection(order, dim)
fespace = mfem.ParFiniteElementSpace(pmesh, fe_coll)
fe_size = fespace.GlobalTrueVSize()
if myid == 0:
print("Number of temperature unknowns: " + str(fe_size))
u_gf = mfem.ParGridFunction(fespace)
# 8. Set the initial conditions for u. All boundaries are considered
# natural.
u_0 = InitialTemperature()
u_gf.ProjectCoefficient(u_0)
u = mfem.Vector()
u_gf.GetTrueDofs(u)
# 9. Initialize the conduction operator and the visualization.
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)
def ex19_main(args):
ser_ref_levels = args.refine_serial
par_ref_levels = args.refine_parallel
order = args.order
visualization = args.visualization
mu = args.shear_modulus
newton_rel_tol = args.relative_tolerance
newton_abs_tol = args.absolute_tolerance
newton_iter = args.newton_iterations
if myid == 0: parser.print_options(args)
meshfile = expanduser(join(path, 'data', args.mesh))
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
for lev in range(ser_ref_levels):
mesh.UniformRefinement()
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
for lev in range(par_ref_levels):
pmesh.UniformRefinement()
# 4. Define the shear modulus for the incompressible Neo-Hookean material
c_mu = mfem.ConstantCoefficient(mu)
# 5. Define the finite element spaces for displacement and pressure
# (Taylor-Hood elements). By default, the displacement (u/x) is a second
# order vector field, while the pressure (p) is a linear scalar function.
quad_coll = mfem.H1_FECollection(order, dim)
lin_coll = mfem.H1_FECollection(order - 1, dim)
R_space = mfem.ParFiniteElementSpace(pmesh, quad_coll, dim,
mfem.Ordering.byVDIM)
W_space = mfem.ParFiniteElementSpace(pmesh, lin_coll)
spaces = [R_space, W_space]
glob_R_size = R_space.GlobalTrueVSize()
glob_W_size = W_space.GlobalTrueVSize()
# 6. Define the Dirichlet conditions (set to boundary attribute 1 and 2)
ess_bdr_u = mfem.intArray(R_space.GetMesh().bdr_attributes.Max())
ess_bdr_p = mfem.intArray(W_space.GetMesh().bdr_attributes.Max())
ess_bdr_u.Assign(0)
ess_bdr_u[0] = 1
ess_bdr_u[1] = 1
ess_bdr_p.Assign(0)
ess_bdr = [ess_bdr_u, ess_bdr_p]
if myid == 0:
print("***********************************************************")
print("dim(u) = " + str(glob_R_size))
print("dim(p) = " + str(glob_W_size))
print("dim(u+p) = " + str(glob_R_size + glob_W_size))
print("***********************************************************")
block_offsets = intArray([0, R_space.TrueVSize(), W_space.TrueVSize()])
block_offsets.PartialSum()
xp = mfem.BlockVector(block_offsets)
# 9. Define grid functions for the current configuration, reference
# configuration, final deformation, and pressure
x_gf = mfem.ParGridFunction(R_space)
x_ref = mfem.ParGridFunction(R_space)
x_def = mfem.ParGridFunction(R_space)
p_gf = mfem.ParGridFunction(W_space)
#x_gf.MakeRef(R_space, xp.GetBlock(0), 0)
#p_gf.MakeRef(W_space, xp.GetBlock(1), 0)
deform = InitialDeformation(dim)
refconfig = ReferenceConfiguration(dim)
x_gf.ProjectCoefficient(deform)
x_ref.ProjectCoefficient(refconfig)
p_gf.Assign(0.0)
# 12. Set up the block solution vectors
x_gf.GetTrueDofs(xp.GetBlock(0))
p_gf.GetTrueDofs(xp.GetBlock(1))
# 13. Initialize the incompressible neo-Hookean operator
oper = RubberOperator(spaces, ess_bdr, block_offsets, newton_rel_tol,
newton_abs_tol, newton_iter, mu)
# 14. Solve the Newton system
oper.Solve(xp)
# 15. Distribute the shared degrees of freedom
x_gf.Distribute(xp.GetBlock(0))
p_gf.Distribute(xp.GetBlock(1))
# 16. Compute the final deformation
mfem.subtract_vector(x_gf, x_ref, x_def)
# 17. Visualize the results if requested
if (visualization):
vis_u = mfem.socketstream("localhost", 19916)
visualize(vis_u, pmesh, x_gf, x_def, "Deformation", True)
MPI.COMM_WORLD.Barrier()
vis_p = mfem.socketstream("localhost", 19916)
visualize(vis_p, pmesh, x_gf, p_gf, "Deformation", True)
# 14. Save the displaced mesh, the final deformation, and the pressure
nodes = x_gf
owns_nodes = 0
nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes)
smyid = '.' + '{:0>6d}'.format(myid)
pmesh.PrintToFile('deformed.mesh' + smyid, 8)
p_gf.SaveToFile('pressure.sol' + smyid, 8)
x_def.SaveToFile("deformation.sol" + smyid, 8)
def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
meshfile = "../data/amr-quad.mesh"
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
odata = gf.GetDataArray().copy()
gf.Save("out_test_gz.gf")
gf2 = mfem.GridFunction(mesh, "out_test_gz.gf")
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, "text file does not agree with original")
gf.Save("out_test_gz.gz")
gf2.Assign(0.0)
gf2 = mfem.GridFunction(mesh, "out_test_gz.gz")
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".gz file does not agree with original")
gf.Print("out_test_gz.dat")
gf2.Assign(0.0)
gf2.Load("out_test_gz.dat", gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".dat file does not agree with original")
gf.Print("out_test_gz.dat.gz")
gf2.Assign(0.0)
gf2.Load("out_test_gz.dat.gz", gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".dat file does not agree with original (gz)")
import gzip
import io
gf.Print("out_test_gz.dat2.gz")
with gzip.open("out_test_gz.dat2.gz", 'rt') as f:
sio = io.StringIO(f.read())
gf3 = mfem.GridFunction(fespace)
gf3.Load(sio, gf.Size())
odata3 = gf3.GetDataArray().copy()
check(odata, odata3, ".dat file does not agree with original(gz-io)")
c = mfem.ConstantCoefficient(2.0)
gf.ProjectCoefficient(c)
odata = gf.GetDataArray().copy()
o = io.StringIO()
gf.Print(o)
gf2.Load(o, gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, "StringIO does not agree with original")
print("GridFunction .gf, .gz .dat and StringIO agree with original")
mesh2 = mfem.Mesh()
mesh.Print("out_test_gz.mesh")
mesh2.Load("out_test_gz.mesh")
check_mesh(mesh, mesh2, ".mesh does not agree with original")
mesh2 = mfem.Mesh()
mesh.Print("out_test_gz.mesh.gz")
mesh2.Load("out_test_gz.mesh.gz")
check_mesh(mesh, mesh2, ".mesh.gz does not agree with original")
mesh3 = mfem.Mesh()
mesh.PrintGZ("out_test_gz3.mesh")
mesh3.Load("out_test_gz3.mesh")
check_mesh(mesh, mesh3,
".mesh (w/o .gz exntension) does not agree with original")
o = io.StringIO()
mesh2 = mfem.Mesh()
mesh.Print(o)
mesh2.Load(o)
check_mesh(mesh, mesh2, ".mesh.gz does not agree with original")
print("Mesh .mesh, .mesh.gz and StringIO agree with original")
print("PASSED")
def run(order = 1, static_cond = False,
meshfile = def_meshfile, visualization = 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()
prinr( "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()))
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);
a.RecoverFEMSolution(X, b, x)
smyid = '{:0>6d}'.format(myid)
mesh_name = "mesh."+smyid
sol_name = "sol."+smyid
pmesh.PrintToFile(mesh_name, 8)
x.SaveToFile(sol_name, 8)
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")
def initialize(self, inMeshObj=None, inMeshFile=None):
# 2. Problem initialization
self.parser = ArgParser(description='Based on MFEM Ex16p')
self.parser.add_argument('-m',
'--mesh',
default='beam-tet.mesh',
action='store',
type=str,
help='Mesh file to use.')
self.parser.add_argument('-rs',
'--refine-serial',
action='store',
default=1,
type=int,
help="Number of times to refine the mesh \
uniformly in serial")
self.parser.add_argument('-rp',
'--refine-parallel',
action='store',
default=0,
type=int,
help="Number of times to refine the mesh \
uniformly in parallel")
self.parser.add_argument('-o',
'--order',
action='store',
default=1,
type=int,
help="Finite element order (polynomial \
degree)")
self.parser.add_argument(
'-s',
'--ode-solver',
action='store',
default=3,
type=int,
help='\n'.join([
"ODE solver: 1 - Backward Euler, 2 - SDIRK2, \
3 - SDIRK3", "\t\t 11 - Forward Euler, \
12 - RK2, 13 - RK3 SSP, 14 - RK4."
]))
self.parser.add_argument('-t',
'--t-final',
action='store',
default=20.,
type=float,
help="Final time; start time is 0.")
self.parser.add_argument("-dt",
"--time-step",
action='store',
default=5e-3,
type=float,
help="Time step.")
self.parser.add_argument("-v",
"--viscosity",
action='store',
default=0.00,
type=float,
help="Viscosity coefficient.")
self.parser.add_argument('-L',
'--lmbda',
action='store',
default=1.e0,
type=float,
help='Lambda of Hooks law')
self.parser.add_argument('-mu',
'--shear-modulus',
action='store',
default=1.e0,
type=float,
help='Shear modulus for Hooks law')
self.parser.add_argument('-rho',
'--density',
action='store',
default=1.0,
type=float,
help='mass density')
self.parser.add_argument('-vis',
'--visualization',
action='store_true',
help='Enable GLVis visualization')
self.parser.add_argument('-vs',
'--visualization-steps',
action='store',
default=25,
type=int,
help="Visualize every n-th timestep.")
args = self.parser.parse_args()
self.ser_ref_levels = args.refine_serial
self.par_ref_levels = args.refine_parallel
self.order = args.order
self.dt = args.time_step
self.visc = args.viscosity
self.t_final = args.t_final
self.lmbda = args.lmbda
self.mu = args.shear_modulus
self.rho = args.density
self.visualization = args.visualization
self.ti = 1
self.vis_steps = args.visualization_steps
self.ode_solver_type = args.ode_solver
self.t = 0.0
self.last_step = False
if self.myId == 0: self.parser.print_options(args)
# 3. Reading mesh
if inMeshObj is None:
self.meshFile = inMeshFile
if self.meshFile is None:
self.meshFile = args.mesh
self.mesh = mfem.Mesh(self.meshFile, 1, 1)
else:
self.mesh = inMeshObj
self.dim = self.mesh.Dimension()
print("Mesh dimension: %d" % self.dim)
print("Number of vertices in the mesh: %d " % self.mesh.GetNV())
print("Number of elements in the mesh: %d " % self.mesh.GetNE())
# 4. Define the ODE solver used for time integration.
# Several implicit singly diagonal implicit
# Runge-Kutta (SDIRK) methods, as well as
# explicit Runge-Kutta methods are available.
if self.ode_solver_type == 1:
self.ode_solver = BackwardEulerSolver()
elif self.ode_solver_type == 2:
self.ode_solver = mfem.SDIRK23Solver(2)
elif self.ode_solver_type == 3:
self.ode_solver = mfem.SDIRK33Solver()
elif self.ode_solver_type == 11:
self.ode_solver = ForwardEulerSolver()
elif self.ode_solver_type == 12:
self.ode_solver = mfem.RK2Solver(0.5)
elif self.ode_solver_type == 13:
self.ode_solver = mfem.RK3SSPSolver()
elif self.ode_solver_type == 14:
self.ode_solver = mfem.RK4Solver()
elif self.ode_solver_type == 22:
self.ode_solver = mfem.ImplicitMidpointSolver()
elif self.ode_solver_type == 23:
self.ode_solver = mfem.SDIRK23Solver()
elif self.ode_solver_type == 24:
self.ode_solver = mfem.SDIRK34Solver()
else:
print("Unknown ODE solver type: " + str(self.ode_solver_type))
exit
# 5. Refine the mesh in serial to increase the
# resolution. In this example we do
# 'ser_ref_levels' of uniform refinement, where
# 'ser_ref_levels' is a command-line parameter.
for lev in range(self.ser_ref_levels):
self.mesh.UniformRefinement()
# 6. Define a parallel mesh by a partitioning of
# the serial mesh. Refine this mesh further
# in parallel to increase the resolution. Once the
# parallel mesh is defined, the serial mesh can
# be deleted.
self.pmesh = mfem.ParMesh(MPI.COMM_WORLD, self.mesh)
for lev in range(self.par_ref_levels):
self.pmesh.UniformRefinement()
# 7. Define the vector finite element space
# representing the current and the
# initial temperature, u_ref.
self.fe_coll = mfem.H1_FECollection(self.order, self.dim)
self.fespace = mfem.ParFiniteElementSpace(self.pmesh, self.fe_coll,
self.dim)
self.fe_size = self.fespace.GlobalTrueVSize()
if self.myId == 0:
print("FE Number of unknowns: " + str(self.fe_size))
true_size = self.fespace.TrueVSize()
self.true_offset = mfem.intArray(3)
self.true_offset[0] = 0
self.true_offset[1] = true_size
self.true_offset[2] = 2 * true_size
self.vx = mfem.BlockVector(self.true_offset)
self.v_gf = mfem.ParGridFunction(self.fespace)
self.v_gfbnd = mfem.ParGridFunction(self.fespace)
self.x_gf = mfem.ParGridFunction(self.fespace)
self.x_gfbnd = mfem.ParGridFunction(self.fespace)
self.x_ref = mfem.ParGridFunction(self.fespace)
self.pmesh.GetNodes(self.x_ref)
# 8. Set the initial conditions for u.
#self.velo = InitialVelocity(self.dim)
self.velo = velBCs(self.dim)
#self.deform = InitialDeformation(self.dim)
self.deform = defBCs(self.dim)
self.v_gf.ProjectCoefficient(self.velo)
self.v_gfbnd.ProjectCoefficient(self.velo)
self.x_gf.ProjectCoefficient(self.deform)
self.x_gfbnd.ProjectCoefficient(self.deform)
#self.v_gf.GetTrueDofs(self.vx.GetBlock(0));
#self.x_gf.GetTrueDofs(self.vx.GetBlock(1));
# setup boundary-conditions
self.xess_bdr = mfem.intArray(
self.fespace.GetMesh().bdr_attributes.Max())
self.xess_bdr.Assign(0)
self.xess_bdr[0] = 1
self.xess_bdr[1] = 1
self.xess_tdof_list = intArray()
self.fespace.GetEssentialTrueDofs(self.xess_bdr, self.xess_tdof_list)
#print('True x essential BCs are')
#self.xess_tdof_list.Print()
self.vess_bdr = mfem.intArray(
self.fespace.GetMesh().bdr_attributes.Max())
self.vess_bdr.Assign(0)
self.vess_bdr[0] = 1
self.vess_bdr[1] = 1
self.vess_tdof_list = intArray()
self.fespace.GetEssentialTrueDofs(self.vess_bdr, self.vess_tdof_list)
#print('True v essential BCs are')
#self.vess_tdof_list.Print()
# 9. Initialize the stiffness operator
self.oper = StiffnessOperator(self.fespace, self.lmbda, self.mu,
self.rho, self.visc, self.vess_tdof_list,
self.vess_bdr, self.xess_tdof_list,
self.xess_bdr, self.v_gfbnd,
self.x_gfbnd, self.deform, self.velo,
self.vx)
# 10. Setting up file output
self.smyid = '{:0>2d}'.format(self.myId)
# initializing ode solver
self.ode_solver.Init(self.oper)
def run_test():
print("Test complex_operator module")
Nvert = 6
Nelem = 8
Nbelem = 2
mesh = mfem.Mesh(2, Nvert, Nelem, 2, 3)
tri_v = [[1., 0., 0.], [0., 1., 0.], [-1., 0., 0.], [0., -1., 0.],
[0., 0., 1.], [0., 0., -1.]]
tri_e = [[0, 1, 4], [1, 2, 4], [2, 3, 4], [3, 0, 4], [1, 0, 5], [2, 1, 5],
[3, 2, 5], [0, 3, 5]]
tri_l = [[1, 4], [1, 2]]
for j in range(Nvert):
mesh.AddVertex(tri_v[j])
for j in range(Nelem):
mesh.AddTriangle(tri_e[j], 1)
for j in range(Nbelem):
mesh.AddBdrSegment(tri_l[j], 1)
mesh.FinalizeTriMesh(1, 1, True)
dim = mesh.Dimension()
order = 1
fec = mfem.H1_FECollection(order, dim)
if use_parallel:
mesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
fes = mfem.ParFiniteElementSpace(mesh, fec)
a1 = mfem.ParBilinearForm(fes)
a2 = mfem.ParBilinearForm(fes)
else:
fes = mfem.FiniteElementSpace(mesh, fec)
a1 = mfem.BilinearForm(fes)
a2 = mfem.BilinearForm(fes)
one = mfem.ConstantCoefficient(1.0)
a1.AddDomainIntegrator(mfem.DiffusionIntegrator(one))
a1.Assemble()
a1.Finalize()
a2.AddDomainIntegrator(mfem.DiffusionIntegrator(one))
a2.Assemble()
a2.Finalize()
if use_parallel:
M1 = a1.ParallelAssemble()
M2 = a2.ParallelAssemble()
M1.Print('M1')
width = fes.GetTrueVSize()
#X = mfem.HypreParVector(fes)
#Y = mfem.HypreParVector(fes)
#X.SetSize(fes.TrueVSize())
#Y.SetSize(fes.TrueVSize())
#from mfem.common.parcsr_extra import ToScipyCoo
#MM1 = ToScipyCoo(M1)
#print(MM1.toarray())
#print(MM1.dot(np.ones(6)))
else:
M1 = a1.SpMat()
M2 = a2.SpMat()
M1.Print('M1')
width = fes.GetVSize()
#X = mfem.Vector()
#Y = mfem.Vector()
#X.SetSize(M1.Width())
#Y.SetSize(M1.Height())
#from mfem.common.sparse_utils import sparsemat_to_scipycsr
#MM1 = sparsemat_to_scipycsr(M1, np.float)
#print(MM1.toarray())
#print(MM1.dot(np.ones(6)))
#X.Assign(0.0)
#X[0] = 1.0
#M1.Mult(X, Y)
#print(Y.GetDataArray())
Mc = mfem.ComplexOperator(M1, M2, hermitan=True)
offsets = mfem.intArray([0, width, width])
offsets.PartialSum()
x = mfem.BlockVector(offsets)
y = mfem.BlockVector(offsets)
x.GetBlock(0).Assign(0)
if myid == 0:
x.GetBlock(0)[0] = 1.0
x.GetBlock(1).Assign(0)
if myid == 0:
x.GetBlock(1)[0] = 1.0
Mc.Mult(x, y)
print("x", x.GetDataArray())
print("y", y.GetDataArray())
if myid == 0:
x.GetBlock(1)[0] = -1.0
x.Print()
Mc.Mult(x, y)
print("x", x.GetDataArray())
print("y", y.GetDataArray())
def do_integration(expr, solvars, phys, mesh, kind, attrs,
order, num):
from petram.helper.variables import (Variable,
var_g,
NativeCoefficientGenBase,
CoefficientVariable)
from petram.phys.coefficient import SCoeff
st = parser.expr(expr)
code= st.compile('<string>')
names = code.co_names
g = {}
#print solvars.keys()
for key in phys._global_ns.keys():
g[key] = phys._global_ns[key]
for key in solvars.keys():
g[key] = solvars[key]
l = var_g.copy()
ind_vars = ','.join(phys.get_independent_variables())
if kind == 'Domain':
size = max(max(mesh.attributes.ToList()), max(attrs))
else:
size = max(max(mesh.bdr_attributes.ToList()), max(attrs))
arr = [0]*(size)
for k in attrs:
arr[k-1] = 1
flag = mfem.intArray(arr)
s = SCoeff(expr, ind_vars, l, g, return_complex=False)
## note L2 does not work for boundary....:D
if kind == 'Domain':
fec = mfem.L2_FECollection(order, mesh.Dimension())
else:
fec = mfem.H1_FECollection(order, mesh.Dimension())
fes = mfem.FiniteElementSpace(mesh, fec)
one = mfem.ConstantCoefficient(1)
gf = mfem.GridFunction(fes)
gf.Assign(0.0)
if kind == 'Domain':
gf.ProjectCoefficient(mfem.RestrictedCoefficient(s, flag))
else:
gf.ProjectBdrCoefficient(mfem.RestrictedCoefficient(s, flag), flag)
b = mfem.LinearForm(fes)
one = mfem.ConstantCoefficient(1)
if kind == 'Domain':
itg = mfem.DomainLFIntegrator(one)
b.AddDomainIntegrator(itg)
else:
itg = mfem.BoundaryLFIntegrator(one)
b.AddBoundaryIntegrator(itg)
b.Assemble()
from petram.engine import SerialEngine
en = SerialEngine()
ans = mfem.InnerProduct(en.x2X(gf), en.b2B(b))
if not np.isfinite(ans):
print("not finite", ans, arr)
print(size, mesh.bdr_attributes.ToList())
from mfem.common.chypre import LF2PyVec, PyVec2PyMat, Array2PyVec, IdentityPyMat
#print(list(gf.GetDataArray()))
print(len(gf.GetDataArray()), np.sum(gf.GetDataArray()))
print(np.sum(list(b.GetDataArray())))
return ans
