Exemplo n.º 1
0
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
Exemplo n.º 2
0
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
Exemplo n.º 3
0
    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