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MFEMReader.py
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import numpy as np
from paraview.util.vtkAlgorithm import (
VTKPythonAlgorithmBase,
smdomain,
smhint,
smproperty,
smproxy,
)
from vtkmodules.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
import vtk
__author__ = "Benjamin F. Zwick"
__email__ = "benzwick@gmail.com"
__copyright__ = "Copyright (c) 2021 {} <{}>".format(__author__, __email__)
__license__ = "License :: OSI Approved :: BSD-3-Clause License"
__version__ = "0.1.0"
extensions = [
# MFEM collection
"mfem_root",
# MFEM mesh format
"mesh",
"mesh.gz",
# Other meshes supported by MFEM
"msh", # Gmsh
"vtk", # VTK
# TODO: Add more mesh formats
]
file_description = "MFEM files"
# VTK element type based on MFEM geometry and nodes FE space order
# MFEM: - https://github.com/mfem/mfem/blob/master/fem/geom.hpp
# - https://github.com/mfem/mfem/blob/master/mesh/vtk.cpp
# VTK: - https://vtk.org/doc/nightly/html/vtkCellType_8h_source.html
# NOTE: Linear elements load much faster than arbitrary order Lagrange elements
VTKGeometry_Map = [ # MFEM:
vtk.VTK_VERTEX, # POINT
vtk.VTK_LINE, # SEGMENT
vtk.VTK_TRIANGLE, # TRIANGLE
vtk.VTK_QUAD, # SQUARE
vtk.VTK_TETRA, # TETRAHEDRON
vtk.VTK_HEXAHEDRON, # CUBE
vtk.VTK_WEDGE] # PRISM
VTKGeometry_QuadraticMap = [ # MFEM:
vtk.VTK_VERTEX, # POINT
vtk.VTK_QUADRATIC_EDGE, # SEGMENT
vtk.VTK_QUADRATIC_TRIANGLE, # TRIANGLE
vtk.VTK_BIQUADRATIC_QUAD, # SQUARE
vtk.VTK_QUADRATIC_TETRA, # TETRAHEDRON
vtk.VTK_TRIQUADRATIC_HEXAHEDRON, # CUBE
vtk.VTK_BIQUADRATIC_QUADRATIC_WEDGE] # PRISM
VTKGeometry_HighOrderMap = [ # MFEM:
vtk.VTK_VERTEX, # POINT
vtk.VTK_LAGRANGE_CURVE, # SEGMENT
vtk.VTK_LAGRANGE_TRIANGLE, # TRIANGLE
vtk.VTK_LAGRANGE_QUADRILATERAL, # SQUARE
vtk.VTK_LAGRANGE_TETRAHEDRON, # TETRAHEDRON
vtk.VTK_LAGRANGE_HEXAHEDRON, # CUBE
vtk.VTK_LAGRANGE_WEDGE] # PRISM
VTKGeometry_PrismMap = [0, 2, 1, 3, 5, 4]
VTKGeometry_VertexPermutation = [
None, None, None, None, None, None, VTKGeometry_PrismMap]
# https://github.com/mfem/mfem/blob/master/mesh/mesh_readers.cpp
Mesh_vtk_quadratic_tet = [
0, 1, 2, 3, 4, 7, 5, 6, 8, 9]
Mesh_vtk_quadratic_wedge = [
0, 2, 1, 3, 5, 4, 8, 7, 6, 11, 10, 9, 12, 14, 13, 17, 16, 15]
Mesh_vtk_quadratic_hex = [
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
24, 22, 21, 23, 20, 25, 26]
VTKGeometry_QuadraticVertexPermutation = [
None, None, None, None,
Mesh_vtk_quadratic_tet,
Mesh_vtk_quadratic_hex,
Mesh_vtk_quadratic_wedge]
@smproxy.reader(
label="MFEM reader",
extensions=extensions,
file_description=file_description)
class MFEMReader(VTKPythonAlgorithmBase):
def __init__(self):
VTKPythonAlgorithmBase.__init__(
self, nInputPorts=0, nOutputPorts=1,
outputType="vtkUnstructuredGrid")
self._filename = None
@smproperty.stringvector(name="FileName")
@smdomain.filelist()
@smhint.filechooser(extensions=extensions,
file_description=file_description)
def SetFileName(self, filename):
if self._filename != filename:
self._filename = filename
self.Modified()
def RequestData(self, request, inInfo, outInfo):
output = dsa.WrapDataObject(vtkUnstructuredGrid.GetData(outInfo))
import os
import json
import mfem.ser as mfem
_, ext = os.path.splitext(self._filename)
cwd = os.path.dirname(self._filename)
if ext == ".mfem_root":
with open(self._filename) as f:
root = json.load(f)
cycle = int(root['dsets']['main']['cycle'])
mesh_filename = root['dsets']['main']['mesh']['path']
mesh_filename = format(mesh_filename % cycle)
mesh_filename = os.path.join(cwd, mesh_filename)
else:
mesh_filename = self._filename
mesh = mfem.Mesh(mesh_filename)
dim = mesh.SpaceDimension()
nelem = mesh.GetNE()
# Points
mesh_fes = mesh.GetNodalFESpace()
nodes = mesh.GetNodes()
if nodes is None:
nnode = mesh.GetNV()
points = np.array(mesh.GetVertexArray())
else:
nnode = mesh.GetNodes().Size() // dim
points = np.array(mesh.GetNodes().GetDataArray())
if mesh_fes.GetOrdering() == 0:
points = points.reshape((dim, nnode)).T
elif mesh_fes.GetOrdering() == 1:
points = points.reshape((nnode, dim))
else:
raise NotImplementedError
if dim == 1:
points = np.hstack([points, np.zeros((nnode, 2))])
elif dim == 2:
points = np.hstack([points, np.zeros((nnode, 1))])
output.SetPoints(points)
# Cells
cell_attributes = np.empty((nelem), dtype=int)
cell_types = np.empty((nelem), dtype=np.ubyte)
cell_offsets = np.empty((nelem), dtype=int)
cell_conn = []
offset = 0
if nodes is None:
for i in range(nelem):
v = mesh.GetElementVertices(i)
geom = mesh.GetElementBaseGeometry(i)
perm = VTKGeometry_VertexPermutation[geom]
if perm: v = [v[i] for i in perm]
cell_types[i] = VTKGeometry_Map[geom]
cell_offsets[i] = offset
offset += len(v) + 1
cell_conn.append(len(v))
cell_conn.extend(v)
else:
for i in range(nelem):
v = mesh_fes.GetElementDofs(i)
geom = mesh.GetElementBaseGeometry(i)
order = mesh_fes.GetOrder(i)
if order == 1:
perm = VTKGeometry_VertexPermutation[geom]
cell_types[i] = VTKGeometry_Map[geom]
elif order == 2:
perm = VTKGeometry_QuadraticVertexPermutation[geom]
cell_types[i] = VTKGeometry_QuadraticMap[geom]
else:
# FIXME: this needs more work...
# See CreateVTKMesh for reading VTK Lagrange elements and
# invert that process to create VTK Lagrange elements.
# https://github.com/mfem/mfem/blob/master/mesh/mesh_readers.cpp
parray = mfem.intArray()
mfem.CreateVTKElementConnectivity(parray, geom, order)
perm = parray.ToList()
cell_types[i] = VTKGeometry_HighOrderMap[geom]
if perm: v = [v[i] for i in perm]
cell_offsets[i] = offset
offset += len(v) + 1
cell_conn.append(len(v))
cell_conn.extend(v)
output.SetCells(cell_types, cell_offsets, cell_conn)
# Attributes
for i in range(nelem):
cell_attributes[i] = mesh.GetAttribute(i)
output.CellData.append(cell_attributes, "attribute")
# Read fields
if ext == ".mfem_root":
fields = root['dsets']['main']['fields']
for name, prop in fields.items():
filename = prop['path']
filename = format(filename % cycle)
filename = os.path.join(cwd, filename)
gf = mfem.GridFunction(mesh, filename)
gf_fes = gf.FESpace()
gf_vdim = gf.VectorDim()
gf_nnode = gf_fes.GetNDofs() // gf_vdim
gf_nelem = gf_fes.GetNBE()
data = np.array(gf.GetDataArray())
if prop['tags']['assoc'] == 'nodes':
assert gf_nnode == nnode, "Mesh and grid function have different number of nodes"
if gf_fes.GetOrdering() == 0:
data = data.reshape((gf_vdim, gf_nnode)).T
elif gf_fes.GetOrdering() == 1:
data = data.reshape((gf_nnode, gf_vdim))
else:
raise NotImplementedError
output.PointData.append(data, name)
elif prop['tags']['assoc'] == 'elements':
assert gf_nelem == nelem, "Mesh and grid function have different number of elements"
if gf_fes.GetOrdering() == 0:
data = data.reshape((gf_vdim, gf_nelem)).T
elif gf_fes.GetOrdering() == 1:
data = data.reshape((gf_nelem, gf_vdim))
else:
raise NotImplementedError
output.CellData.append(data, name)
else:
raise NotImplementedError("assoc: '{}'".format(prop['tags']['assoc']))
return 1