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', '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 surface_weight(refine, gtype):
if (refine, gtype) in globals()['weight']:
return globals()['weight'][(refine, gtype)]
quad_v = [[0, 0], [1, 0], [1, 1], [0, 3]]
quad_e = [[0, 1, 2, 3]]
tri_v = [[0, 0], [1, 0], [0, 1]]
tri_e = [[0, 1, 2,]]
seg_v = [[0,], [1, ],]
seg_e = [[0, 1,]]
if gtype == mfem.Geometry.TRIANGLE:
mesh = mfem.Mesh(2, 3, 1, 0, 2)
for j in range(3):
mesh.AddVertex(tri_v[j])
for j in range(1):
mesh.AddTri(tri_e[j], 11)
mesh.FinalizeTriMesh(1,1, True)
elif gtype == mfem.Geometry.SQUARE:
mesh = mfem.Mesh(2, 4, 1, 0, 2)
for j in range(4):
mesh.AddVertex(quad_v[j])
for j in range(1):
mesh.AddQuad(quad_e[j], 11)
mesh.FinalizeQuadMesh(1,1, True)
elif gtype == mfem.Geometry.SEGMENT:
mesh = mfem.Mesh(1, 2, 1, 0, 1)
for j in range(2):
mesh.AddVertex(seg_v[j])
for j in range(1):
seg = mfem.Segment(seg_e[j], j+1)
mesh.AddElement(seg)
seg.thisown = False
mesh.FinalizeTopology()
mesh.Finalize(False, False)
fec_type = mfem.H1_FECollection
fe_coll = fec_type(1, 2)
fes = mfem.FiniteElementSpace(mesh, fe_coll, 2)
el = fes.GetFE(0)
npt = Geom.GetVertices(gtype).GetNPoints()
RefG = GR.Refine(gtype, refine)
shape = mfem.Vector(el.GetDof())
ir = RefG.RefPts
shapes =[]
for i in range(ir.GetNPoints()):
el.CalcShape(ir.IntPoint(i), shape)
shapes.append(shape.GetDataArray().copy())
w = np.vstack(shapes)
globals()['weight'][(refine, gtype)] = w
return w
def save_scaled_jacobian(filename, mesh, sd=-1):
sj = get_scaled_jacobian(mesh, sd=sd)
fec = mfem.L2_FECollection(0, mesh.Dimension())
fes = mfem.FiniteElementSpace(mesh, fec)
vec = mfem.Vector(sj)
gf = mfem.GridFunction(fes, vec.GetData())
gf.Save(filename)
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.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]
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 volume(mesh, in_attr, filename='', precision=8):
'''
make a new mesh which contains only spedified attributes.
note:
1) boundary elements are also copied and bdr_attributes
are maintained
2) in parallel, new mesh must be geometrically continuous.
this routine does not check it
mesh must have sdim == 3:
in_attr : domain attribute
filename : an option to save the file
return new volume mesh
'''
in_attr = np.atleast_1d(in_attr)
sdim = mesh.SpaceDimension()
dim = mesh.Dimension()
Nodal = mesh.GetNodalFESpace()
hasNodal = (Nodal is not None)
if sdim != 3: assert False, "sdim must be three for volume mesh"
if dim != 3: assert False, "sdim must be three for volume mesh"
idx, attrs, ivert, nverts, base = _collect_data(in_attr, mesh, 'dom')
v2s = mesh.extended_connectivity['vol2surf']
in_battr = np.unique(np.hstack([v2s[k]
for k in in_attr])).astype(int, copy=False)
if isParMesh(mesh):
in_battr = np.unique(allgather_vector(in_battr))
bidx, battrs, bivert, nbverts, bbase = _collect_data(in_battr, mesh, 'bdr')
iface = np.array([mesh.GetBdrElementEdgeIndex(i) for i in bidx], dtype=int)
# note u is sorted unique
u, indices = np.unique(np.hstack((ivert, bivert)), return_inverse=True)
kbelem = np.array([True] * len(bidx), dtype=bool)
u_own = u
if isParMesh(mesh):
shared_info = distribute_shared_entity(mesh)
u_own, ivert, bivert = _gather_shared_vertex(mesh, u, shared_info,
ivert, bivert)
if len(u_own) > 0:
vtx = np.vstack([mesh.GetVertexArray(i) for i in u_own])
else:
vtx = np.array([]).reshape((-1, sdim))
if isParMesh(mesh):
#
# distribute vertex/element data
#
base = allgather_vector(base)
nverts = allgather_vector(nverts)
attrs = allgather_vector(attrs)
ivert = allgather_vector(ivert)
bivert = allgather_vector(bivert)
vtx = allgather_vector(vtx.flatten()).reshape(-1, sdim)
u, indices = np.unique(np.hstack([ivert, bivert]), return_inverse=True)
#
# take care of shared boundary (face)
#
# 2018.11.28
# skip_adding is on. This basically skip shared_element
# processing. Check em3d_TEwg7 if you need to remov this.
#
kbelem, battrs, nbverts, bbase, bivert = (_gather_shared_element(
mesh,
'face',
shared_info,
iface,
kbelem,
battrs,
nbverts,
bbase,
bivert,
skip_adding=True))
#indices0 = np.array([np.where(u == biv)[0][0] for biv in ivert])
#bindices0 = np.array([np.where(u == biv)[0][0] for biv in bivert])
iv, ivi = np.unique(ivert, return_inverse=True)
tmp = np.where(np.in1d(u, ivert, assume_unique=True))[0]
indices = tmp[ivi]
iv, ivi = np.unique(bivert, return_inverse=True)
tmp = np.where(np.in1d(u, bivert, assume_unique=True))[0]
bindices = tmp[ivi]
#print('check', np.sum(np.abs(indices - indices0)))
Nvert = len(vtx)
Nelem = len(attrs)
Nbelem = np.sum(kbelem) #len(battrs)
if myid == 0:
print("NV, NBE, NE: " +
",".join([str(x) for x in (Nvert, Nbelem, Nelem)]))
omesh = mfem.Mesh(3, Nvert, Nelem, Nbelem, sdim)
#omesh = mfem.Mesh(3, Nvert, Nelem, 0, sdim)
_fill_mesh_elements(omesh, vtx, indices, nverts, attrs, base)
_fill_mesh_bdr_elements(omesh, vtx, bindices, nbverts, battrs, bbase,
kbelem)
omesh.FinalizeTopology()
omesh.Finalize(refine=True, fix_orientation=True)
if hasNodal:
odim = omesh.Dimension()
fec = Nodal.FEColl()
dNodal = mfem.FiniteElementSpace(omesh, fec, sdim)
omesh.SetNodalFESpace(dNodal)
omesh._nodal = dNodal
GetXDofs = Nodal.GetElementDofs
GetNX = Nodal.GetNE
dGetXDofs = dNodal.GetElementDofs
dGetNX = dNodal.GetNE
DofToVDof = Nodal.DofToVDof
dDofToVDof = dNodal.DofToVDof
#nicePrint(dGetNX(),',', GetNX())
nodes = mesh.GetNodes()
node_ptx1 = nodes.GetDataArray()
onodes = omesh.GetNodes()
node_ptx2 = onodes.GetDataArray()
#nicePrint(len(idx), idx)
if len(idx) > 0:
dof1_idx = np.hstack([[DofToVDof(i, d) for d in range(sdim)]
for j in idx for i in GetXDofs(j)])
data = node_ptx1[dof1_idx]
else:
dof1_idx = np.array([])
data = np.array([])
if isParMesh(mesh): data = allgather_vector(data)
if isParMesh(mesh): idx = allgather_vector(idx)
#nicePrint(len(data), ',', len(idx))
dof2_idx = np.hstack([[dDofToVDof(i, d) for d in range(sdim)]
for j in range(len(idx)) for i in dGetXDofs(j)])
node_ptx2[dof2_idx] = data
#nicePrint(len(dof2_idx))
if isParMesh(mesh):
omesh = mfem.ParMesh(comm, omesh)
if filename != '':
if isParMesh(mesh):
smyid = '{:0>6d}'.format(myid)
filename = filename + '.' + smyid
omesh.PrintToFile(filename, precision)
return omesh
def surface(mesh, in_attr, filename='', precision=8):
'''
mesh must be
if sdim == 3:
a domain of 2D mesh
a boundary of 3D mesh
if sdim == 2:
a domain in 2D mesh
in_attr : eihter
filename : an option to save the file
return new surface mesh
'''
sdim = mesh.SpaceDimension()
dim = mesh.Dimension()
Nodal = mesh.GetNodalFESpace()
hasNodal = (Nodal is not None)
if sdim == 3 and dim == 3:
mode = 'bdr', 'edge'
elif sdim == 3 and dim == 2:
mode = 'dom', 'bdr'
elif sdim == 2 and dim == 2:
mode = 'dom', 'bdr'
else:
assert False, "unsupported mdoe"
idx, attrs, ivert, nverts, base = _collect_data(in_attr, mesh, mode[0])
s2l = mesh.extended_connectivity['surf2line']
in_eattr = np.unique(np.hstack([s2l[k]
for k in in_attr])).astype(int, copy=False)
if isParMesh(mesh):
in_eattr = np.unique(allgather_vector(in_eattr))
eidx, eattrs, eivert, neverts, ebase = _collect_data(
in_eattr, mesh, mode[1])
u, indices = np.unique(np.hstack((ivert, eivert)), return_inverse=True)
keelem = np.array([True] * len(eidx), dtype=bool)
u_own = u
if isParMesh(mesh):
shared_info = distribute_shared_entity(mesh)
u_own, ivert, eivert = _gather_shared_vertex(mesh, u, shared_info,
ivert, eivert)
Nvert = len(u)
if len(u_own) > 0:
vtx = np.vstack([mesh.GetVertexArray(i) for i in u_own])
else:
vtx = np.array([]).reshape((-1, sdim))
if isParMesh(mesh):
#
# distribute vertex/element data
#
base = allgather_vector(base)
nverts = allgather_vector(nverts)
attrs = allgather_vector(attrs)
ivert = allgather_vector(ivert)
eivert = allgather_vector(eivert)
vtx = allgather_vector(vtx.flatten()).reshape(-1, sdim)
u, indices = np.unique(np.hstack([ivert, eivert]), return_inverse=True)
#
# take care of shared boundary (edge)
#
keelem, eattrs, neverts, ebase, eivert = (_gather_shared_element(
mesh,
'edge',
shared_info,
eidx,
keelem,
eattrs,
neverts,
ebase,
eivert,
skip_adding=True))
#indices = np.array([np.where(u == biv)[0][0] for biv in ivert])
#eindices = np.array([np.where(u == biv)[0][0] for biv in eivert])
iv, ivi = np.unique(ivert, return_inverse=True)
tmp = np.where(np.in1d(u, ivert, assume_unique=True))[0]
indices = tmp[ivi]
iv, ivi = np.unique(eivert, return_inverse=True)
tmp = np.where(np.in1d(u, eivert, assume_unique=True))[0]
eindices = tmp[ivi]
Nvert = len(vtx)
Nelem = len(attrs)
Nbelem = len(eattrs)
if myid == 0:
print("NV, NBE, NE: " +
",".join([str(x) for x in (Nvert, Nbelem, Nelem)]))
omesh = mfem.Mesh(2, Nvert, Nelem, Nbelem, sdim)
_fill_mesh_elements(omesh, vtx, indices, nverts, attrs, base)
_fill_mesh_bdr_elements(omesh, vtx, eindices, neverts, eattrs, ebase,
keelem)
omesh.FinalizeTopology()
omesh.Finalize(refine=True, fix_orientation=True)
if hasNodal:
odim = omesh.Dimension()
print("odim, dim, sdim", odim, " ", dim, " ", sdim)
fec = Nodal.FEColl()
dNodal = mfem.FiniteElementSpace(omesh, fec, sdim)
omesh.SetNodalFESpace(dNodal)
omesh._nodal = dNodal
if sdim == 3:
if dim == 3:
GetXDofs = Nodal.GetBdrElementDofs
GetNX = Nodal.GetNBE
elif dim == 2:
GetXDofs = Nodal.GetElementDofs
GetNX = Nodal.GetNE
else:
assert False, "not supported ndim 1"
if odim == 3:
dGetXDofs = dNodal.GetBdrElementDofs
dGetNX = dNodal.GetNBE
elif odim == 2:
dGetXDofs = dNodal.GetElementDofs
dGetNX = dNodal.GetNE
else:
assert False, "not supported ndim (3->1)"
elif sdim == 2:
GetNX = Nodal.GetNE
dGetNX = dNodal.GetNE
GetXDofs = Nodal.GetElementDofs
dGetXDofs = dNodal.GetElementDofs
DofToVDof = Nodal.DofToVDof
dDofToVDof = dNodal.DofToVDof
#nicePrint(dGetNX(),',', GetNX())
nodes = mesh.GetNodes()
node_ptx1 = nodes.GetDataArray()
onodes = omesh.GetNodes()
node_ptx2 = onodes.GetDataArray()
#nicePrint(len(idx), idx)
if len(idx) > 0:
dof1_idx = np.hstack([[DofToVDof(i, d) for d in range(sdim)]
for j in idx for i in GetXDofs(j)])
data = node_ptx1[dof1_idx]
else:
dof1_idx = np.array([])
data = np.array([])
if isParMesh(mesh): data = allgather_vector(data)
if isParMesh(mesh): idx = allgather_vector(idx)
#nicePrint(len(data), ',', len(idx))
dof2_idx = np.hstack([[dDofToVDof(i, d) for d in range(sdim)]
for j in range(len(idx)) for i in dGetXDofs(j)])
node_ptx2[dof2_idx] = data
#nicePrint(len(dof2_idx))
if isParMesh(mesh):
omesh = mfem.ParMesh(comm, omesh)
if filename != '':
if isParMesh(mesh):
smyid = '{:0>6d}'.format(myid)
filename = filename + '.' + smyid
omesh.PrintToFile(filename, precision)
return omesh
def eval_shape(order = 1, refine = 5, elem_type = 0,
fec = 'ND'):
if fec == 'ND':
fec_type = mfem.ND_FECollection
if order < 1: assert False, "ND order is 1 and above"
elif fec == 'RT':
fec_type = mfem.RT_FECollection
elif fec == 'H1':
fec_type = mfem.H1_FECollection
if order < 1: assert False, "H1 order is 1 and above"
elif fec == 'L2':
fec_type = mfem.L2_FECollection
else:
assert False, "unknown basis"
if elem_type == 0:
Nvert = 3; Nelem = 1; spaceDim = 2
elif elem_type == 1:
Nvert = 4; Nelem = 1; spaceDim = 2
mesh = mfem.Mesh(2, Nvert, Nelem, 0, spaceDim)
if elem_type == 0:
tri_v = [[1., 0.3 ], [0., 1.,], [0, 0]]
tri_e = [[0, 1, 2], ]
for j in range(Nvert):
mesh.AddVertex(tri_v[j])
for j in range(Nelem):
mesh.AddTriangle(tri_e[j], j+1)
mesh.FinalizeTriMesh(1,1, True)
else:
quad_v = [[-1, -1.3, ], [+1, -1, ], [+1, +1, ], [-1, +1,]]
quad_e = [[0, 1, 2, 3]]
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)
#mesh.PrintToFile('plot_basis.mesh', 8)
fe_coll = fec_type(order, spaceDim)
fespace = mfem.FiniteElementSpace(mesh, fe_coll)
x = mfem.GridFunction(fespace)
x.Assign(0.0)
x[0] = 1.0
idx = 0
geom = mesh.GetElementBaseGeometry(idx)
T = mesh.GetElementTransformation(idx)
fe = fespace.GetFE(idx)
fe_nd = fe.GetDof()
ir = fe.GetNodes()
npt = ir.GetNPoints()
dof = np.vstack([T.Transform(ir.IntPoint(i)) for i in range(npt)])
RefG = mfem.GlobGeometryRefiner.Refine(geom, refine, 1);
ir = RefG.RefPts
npt = ir.GetNPoints()
ptx = np.vstack([T.Transform(ir.IntPoint(i)) for i in range(npt)])
shape = []
if fec == 'ND' or fec == 'RT':
mat = mfem.DenseMatrix(fe_nd, spaceDim)
shape_func = fe.CalcVShape
for i in range(npt):
ip = ir.IntPoint(i)
T.SetIntPoint(ip)
fe.CalcVShape(T, mat)
shape.append(mat.GetDataArray().copy())
else:
vec = mfem.Vector(fe_nd)
for i in range(npt):
ip = ir.IntPoint(i)
fe.CalcShape(ip, vec)
shape.append(vec.GetDataArray().copy())
return dof, ptx, np.stack(shape)
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 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 edge(mesh, in_attr, filename='', precision=8):
'''
make a new mesh which contains only spedified edges.
in_attr : eihter
filename : an option to save the file
return new surface mesh
'''
sdim = mesh.SpaceDimension()
dim = mesh.Dimension()
Nodal = mesh.GetNodalFESpace()
hasNodal = (Nodal is not None)
if sdim == 3 and dim == 3:
mode = 'edge', 'vertex'
elif sdim == 3 and dim == 2:
mode = 'bdr', 'vertex'
elif sdim == 2 and dim == 2:
mode = 'bdr', 'vertex'
elif sdim == 2 and dim == 1:
mode = 'dom', 'vertex'
else:
assert False, "unsupported mdoe"
idx, attrs, ivert, nverts, base = _collect_data(in_attr, mesh, mode[0])
l2v = mesh.extended_connectivity['line2vert']
in_eattr = np.unique(np.hstack([l2v[k]
for k in in_attr])).astype(int, copy=False)
if isParMesh(mesh):
in_eattr = np.unique(allgather_vector(in_eattr))
eidx, eattrs, eivert, neverts, ebase = _collect_data(
in_eattr, mesh, mode[1])
u, indices = np.unique(np.hstack((ivert, eivert)), return_inverse=True)
keelem = np.array([True] * len(eidx), dtype=bool)
u_own = u
if isParMesh(mesh):
shared_info = distribute_shared_entity(mesh)
u_own, ivert, eivert = _gather_shared_vertex(mesh, u, shared_info,
ivert, eivert)
Nvert = len(u)
if len(u_own) > 0:
vtx = np.vstack([mesh.GetVertexArray(i) for i in u_own])
else:
vtx = np.array([]).reshape((-1, sdim))
if isParMesh(mesh):
#
# distribute vertex/element data
#
base = allgather_vector(base)
nverts = allgather_vector(nverts)
attrs = allgather_vector(attrs)
ivert = allgather_vector(ivert)
eivert = allgather_vector(eivert)
vtx = allgather_vector(vtx.flatten()).reshape(-1, sdim)
u, indices = np.unique(np.hstack([ivert, eivert]), return_inverse=True)
#
# take care of shared boundary (edge)
#
keelem, eattrs, neverts, ebase, eivert = (_gather_shared_element(
mesh, 'vertex', shared_info, eidx, keelem, eattrs, neverts, ebase,
eivert))
indices = np.array([np.where(u == biv)[0][0] for biv in ivert])
eindices = np.array([np.where(u == biv)[0][0] for biv in eivert])
Nvert = len(vtx)
Nelem = len(attrs)
Nbelem = len(eattrs)
dprint1("NV, NBE, NE: " +
",".join([str(x) for x in (Nvert, Nbelem, Nelem)]))
omesh = mfem.Mesh(1, Nvert, Nelem, Nbelem, sdim)
_fill_mesh_elements(omesh, vtx, indices, nverts, attrs, base)
_fill_mesh_bdr_elements(omesh, vtx, eindices, neverts, eattrs, ebase,
keelem)
omesh.FinalizeTopology()
if hasNodal:
odim = omesh.Dimension()
dprint1("odim, dim, sdim", odim, " ", dim, " ", sdim)
fec = Nodal.FEColl()
dNodal = mfem.FiniteElementSpace(omesh, fec, sdim)
omesh.SetNodalFESpace(dNodal)
omesh._nodal = dNodal
GetXDofs = Nodal.GetElementDofs
if dim == 3:
GetXDofs = Nodal.GetEdgeDofs
elif dim == 2:
GetXDofs = Nodal.GetBdrElementDofs
elif dim == 1:
GetXDofs = Nodal.GetElementDofs
dGetXDofs = dNodal.GetElementDofs
DofToVDof = Nodal.DofToVDof
dDofToVDof = dNodal.DofToVDof
#nicePrint(dGetNX(),',', GetNX())
nodes = mesh.GetNodes()
node_ptx1 = nodes.GetDataArray()
onodes = omesh.GetNodes()
node_ptx2 = onodes.GetDataArray()
#nicePrint(len(idx), idx)
if len(idx) > 0:
dof1_idx = np.hstack([[DofToVDof(i, d) for d in range(sdim)]
for j in idx for i in GetXDofs(j)])
data = node_ptx1[dof1_idx]
else:
dof1_idx = np.array([])
data = np.array([])
if isParMesh(mesh): data = allgather_vector(data)
if isParMesh(mesh): idx = allgather_vector(idx)
#nicePrint(len(data), ',', len(idx))
dof2_idx = np.hstack([[dDofToVDof(i, d) for d in range(sdim)]
for j in range(len(idx)) for i in dGetXDofs(j)])
node_ptx2[dof2_idx] = data
#nicePrint(len(dof2_idx))
# this should be after setting HO nodals...
omesh.Finalize(refine=True, fix_orientation=True)
if isParMesh(mesh):
if omesh.GetNE() < nprc * 3:
parts = omesh.GeneratePartitioning(1, 1)
else:
parts = None
omesh = mfem.ParMesh(comm, omesh, parts)
if filename != '':
if isParMesh(mesh):
smyid = '{:0>6d}'.format(myid)
filename = filename + '.' + smyid
omesh.PrintToFile(filename, precision)
return omesh
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