def convert(msh_file, h5_file):
'''Temporary version of convert from msh to h5'''
root, _ = os.path.splitext(msh_file)
assert os.path.splitext(msh_file)[1] == '.msh'
assert os.path.splitext(h5_file)[1] == '.h5'
# Get the xml mesh
xml_file = '.'.join([root, 'xml'])
subprocess.call(['dolfin-convert %s %s' % (msh_file, xml_file)], shell=True)
# Success?
assert os.path.exists(xml_file)
mesh = Mesh(xml_file)
out = HDF5File(mesh.mpi_comm(), h5_file, 'w')
out.write(mesh, 'mesh')
info('Mesh has %d cells' % mesh.num_cells())
info('Mesh size %g %g' % (mesh.hmin(), mesh.hmax()))
outputs = [mesh]
# Save ALL data as facet_functions
names = ('surfaces', 'volumes')
for name, region in zip(names, ('facet_region.xml', 'physical_region.xml')):
r_xml_file = '_'.join([root, region])
f = MeshFunction('size_t', mesh, r_xml_file)
out.write(f, name)
outputs.append(f)
return outputs
def convert(msh_file, h5_file, save_mvc=False):
'''Temporary version of convertin from msh to h5'''
root, _ = os.path.splitext(msh_file)
assert os.path.splitext(msh_file)[1] == '.msh'
assert os.path.splitext(h5_file)[1] == '.h5'
# Get the xml mesh
xml_file = '.'.join([root, 'xml'])
subprocess.call(['dolfin-convert %s %s' % (msh_file, xml_file)], shell=True)
# Success?
assert os.path.exists(xml_file)
mesh = Mesh(xml_file)
out = HDF5File(mesh.mpi_comm(), h5_file, 'w')
out.write(mesh, 'mesh')
print('Mesh has %d cells' % mesh.num_cells())
print('Mesh size %g %g' % (mesh.hmin(), mesh.hmax()))
# Save ALL data as facet_functions
names = ('surfaces', 'volumes')
if not save_mvc:
for name, region in zip(names, ('facet_region.xml', 'physical_region.xml')):
r_xml_file = '_'.join([root, region])
f = MeshFunction('size_t', mesh, r_xml_file)
print('%d %s with 1' % (sum(1 for _ in SubsetIterator(f, 1)), name))
out.write(f, name)
return True
for name, region in zip(names, ('facet_region.xml', 'physical_region.xml')):
r_xml_file = '_'.join([root, region])
f = MeshFunction('size_t', mesh, r_xml_file)
# With mesh value collection we only store nonzero tags
mvc = MeshValueCollection('size_t', mesh, f.dim())
# Fill
fill_mvc_from_mf(f, mvc)
# And save
out.write(mvc, name)
return True
args = parser.parse_args()
h5_file = convert(args.input)
# VTK visualize tags
if args.save_pvd or args.mesh_size:
h5 = HDF5File(mpi_comm_world(), h5_file, 'r')
mesh = Mesh()
h5.read(mesh, 'mesh', False)
info('Mesh has %d cells' % mesh.num_cells())
info('Mesh has %d vertices' % mesh.num_vertices())
info('Box size %s' %
(mesh.coordinates().max(axis=0) - mesh.coordinates().min(axis=0)))
hmin, hmax = mesh.hmin(), mesh.hmax()
info('Mesh has sizes %g %g' % (hmin, hmax))
root = os.path.splitext(args.input)[0]
tdim = mesh.topology().dim()
data_sets = ('curves', 'surfaces', 'volumes')
dims = (1, tdim - 1, tdim)
for ds, dim in zip(data_sets, dims):
if h5.has_dataset(ds):
f = MeshFunction('size_t', mesh, dim, 0)
h5.read(f, ds)
if args.save_pvd:
File('%s_%s.pvd' % (root, ds)) << f