def test_base_functions_delta(self): """ Test :math:`\delta` property of base functions evaluated in the reference element nodes. """ from sfepy.base.base import ordered_iteritems from sfepy.fem.poly_spaces import PolySpace ok = True for key, gel in ordered_iteritems(self.gels): for order in range(11): ps = PolySpace.any_from_args('aux', gel, order, base='lagrange', force_bubble=False) bf = ps.eval_base(ps.node_coors) _ok = nm.allclose(nm.eye(ps.n_nod), bf.squeeze(), rtol=0.0, atol=(order + 1) * 1e-14) self.report('%s order %d (n_nod: %d): %s' % (key, order, ps.n_nod, _ok)) if not _ok: import pdb pdb.set_trace() ok = ok and _ok return ok
def test_base_functions_delta(self): """ Test :math:`\delta` property of base functions evaluated in the reference element nodes. """ from sfepy.base.base import ordered_iteritems from sfepy.fem.poly_spaces import PolySpace ok = True for key, gel in ordered_iteritems(self.gels): for order in range(11): ps = PolySpace.any_from_args('aux', gel, order, base='lagrange', force_bubble=False) bf = ps.eval_base(ps.node_coors) _ok = nm.allclose(nm.eye(ps.n_nod), bf.squeeze(), rtol=0.0, atol=(order + 1) * 1e-14) self.report('%s order %d (n_nod: %d): %s' % (key, order, ps.n_nod, _ok)) if not _ok: import pdb; pdb.set_trace() ok = ok and _ok return ok
def test_normals(self): """ Check orientations of surface normals on the reference elements. """ import sfepy from sfepy.fem import Mesh, Domain, Integral from sfepy.fem.poly_spaces import PolySpace from sfepy.fem.mappings import SurfaceMapping from sfepy.linalg import normalize_vectors ok = True for geom in ['2_3', '2_4', '3_4', '3_8']: mesh = Mesh.from_file('meshes/elements/%s_1.mesh' % geom, prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) surface = domain.create_region('Surface', 'vertices of surface', 'facet') domain.create_surface_group(surface) sd = domain.surface_groups[0][surface.name] coors = domain.get_mesh_coors() gel = domain.geom_els[geom].surface_facet ps = PolySpace.any_from_args('aux', gel, 1) mapping = SurfaceMapping(coors, sd.get_connectivity(), ps) integral = Integral('i', order=1) vals, weights = integral.get_qp(gel.name) # Evaluate just in the first quadrature point... geo = mapping.get_mapping(vals[:1], weights[:1]) expected = expected_normals[geom].copy() normalize_vectors(expected) _ok = nm.allclose(expected, geo.normal[:, 0, :, 0], rtol=0.0, atol=1e-14) self.report('%s: %s' % (geom, _ok)) if not _ok: self.report('expected:') self.report(expected) self.report('actual:') self.report(geo.normal[:, 0, :, 0]) ok = ok and _ok return ok
def __init__(self, coors, conn, poly_space=None, gel=None, order=1): self.coors = coors self.conn = conn self.n_el, self.n_ep = conn.shape self.dim = self.coors.shape[1] if poly_space is None: poly_space = PolySpace.any_from_args(None, gel, order, base='lagrange', force_bubble=False) self.poly_space = poly_space
def test_normals(self): """ Check orientations of surface normals on the reference elements. """ import sfepy from sfepy.fem import Mesh, Domain, Integral from sfepy.fem.poly_spaces import PolySpace from sfepy.fem.mappings import SurfaceMapping from sfepy.linalg import normalize_vectors ok = True for geom in ['2_3', '2_4', '3_4', '3_8']: mesh = Mesh.from_file('meshes/elements/%s_1.mesh' % geom, prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) surface = domain.create_region('Surface', 'nodes of surface') domain.create_surface_group(surface) sd = domain.surface_groups[0][surface.name] coors = domain.get_mesh_coors() gel = domain.geom_els[geom].surface_facet ps = PolySpace.any_from_args('aux', gel, 1) mapping = SurfaceMapping(coors, sd.get_connectivity(), ps) integral = Integral('i', order=1) vals, weights = integral.get_qp(gel.name) # Evaluate just in the first quadrature point... geo = mapping.get_mapping(vals[:1], weights[:1]) expected = expected_normals[geom].copy() normalize_vectors(expected) _ok = nm.allclose(expected, geo.normal[:, 0, :, 0], rtol=0.0, atol=1e-14) self.report('%s: %s' % (geom, _ok)) if not _ok: self.report('expected:') self.report(expected) self.report('actual:') self.report(geo.normal[:, 0, :, 0]) ok = ok and _ok return ok
def describe_geometry(ig, field, region, integral): """ Describe membrane geometry in a given region. Parameters ---------- ig : int The element group index. field : Field instance The field defining the FE approximation. region : Region instance The surface region to describe. integral : Integral instance The integral defining the quadrature points. Returns ------- mtx_t : array The transposed transformation matrix :math:`T`, see :func:`create_transformation_matrix`. membrane_geo : CVolumeMapping instance The mapping from transformed elements to a reference elements. """ # Coordinates of element vertices. sg, _ = field.get_mapping(ig, region, integral, "surface") sd = field.aps[ig].surface_data[region.name] coors = field.coors[sd.econn[:, : sg.n_fp]] # Coordinate transformation matrix (transposed!). mtx_t = create_transformation_matrix(coors) # Transform coordinates to the local coordinate system. coors_loc = dot_sequences((coors - coors[:, 0:1, :]), mtx_t) # Mapping from transformed elements to reference elements. gel = field.gel.surface_facet vm = create_mapping(coors_loc, gel, 1) qp = integral.get_qp(gel.name) ps = PolySpace.any_from_args(None, gel, field.approx_order) membrane_geo = vm.get_mapping(qp[0], qp[1], poly_space=ps) return mtx_t, membrane_geo
def describe_geometry(ig, field, region, integral): """ Describe membrane geometry in a given region. Parameters ---------- ig : int The element group index. field : Field instance The field defining the FE approximation. region : Region instance The surface region to describe. integral : Integral instance The integral defining the quadrature points. Returns ------- mtx_t : array The transposed transformation matrix :math:`T`, see :func:`create_transformation_matrix`. membrane_geo : CVolumeMapping instance The mapping from transformed elements to a reference elements. """ # Coordinates of element vertices. sg, _ = field.get_mapping(ig, region, integral, 'surface') sd = field.aps[ig].surface_data[region.name] coors = field.coors[sd.econn[:, :sg.n_fp]] # Coordinate transformation matrix (transposed!). mtx_t = create_transformation_matrix(coors) # Transform coordinates to the local coordinate system. coors_loc = dot_sequences((coors - coors[:, 0:1, :]), mtx_t) # Mapping from transformed elements to reference elements. gel = field.gel.surface_facet vm = create_mapping(coors_loc, gel, 1) qp = integral.get_qp(gel.name) ps = PolySpace.any_from_args(None, gel, field.approx_order) membrane_geo = vm.get_mapping(qp[0], qp[1], poly_space=ps) return mtx_t, membrane_geo
def __init__(self, coors, conn, poly_space=None, gel=None, order=1): self.coors = coors self.conn = conn try: self.coors[self.conn] except IndexError: output("coordinates shape: %s" % list(coors.shape)) output("connectivity: min: %d, max: %d" % (conn.min(), conn.max())) msg = "incompatible connectivity and coordinates (see above)" raise IndexError(msg) self.n_el, self.n_ep = conn.shape self.dim = self.coors.shape[1] if poly_space is None: poly_space = PolySpace.any_from_args(None, gel, order, base="lagrange", force_bubble=False) self.poly_space = poly_space
def describe_membrane_geometry(self, ig, field, sg, sd): # Coordinates of element vertices. coors = field.coors[sd.econn[:, :sg.n_fp]] # Coordinate transformation matrix (transposed!). self.mtx_t[ig] = membranes.create_transformation_matrix(coors) # Transform coordinates to the local coordinate system. coors_loc = dot_sequences((coors - coors[:, 0:1, :]), self.mtx_t[ig]) # Mapping from transformed element to reference element. gel = field.gel.surface_facet vm = membranes.create_mapping(coors_loc, gel, 1) qp = self.integral.get_qp(gel.name) ps = PolySpace.any_from_args(None, gel, field.approx_order) self.membrane_geo[ig] = vm.get_mapping(qp[0], qp[1], poly_space=ps) # Transformed base function gradient w.r.t. material coordinates # in quadrature points. self.bfg[ig] = self.membrane_geo[ig].bfg
def test_base_functions_values(self): """ Compare base function values and their gradients with correct data. Also test that sum of values over all element nodes gives one. """ from sfepy.base.base import ordered_iteritems from sfepy.fem.poly_spaces import PolySpace ok = True for key, val in ordered_iteritems(test_bases): gel = self.gels[key[:3]] diff = key[-4:] == 'grad' order = int(key[5]) force_bubble = key[6:7] == 'B' ps = PolySpace.any_from_args('aux', gel, order, base='lagrange', force_bubble=force_bubble) dim = ps.geometry.dim coors = nm.r_[ps.geometry.coors, [[0.2] * dim]] bf = ps.eval_base(coors, diff=diff) _ok = nm.allclose(val, bf, rtol=0.0, atol=1e-14) ## if not _ok: ## nm.set_printoptions(threshold=1000000, linewidth=65) ## print bf.__repr__() if not diff: _ok = _ok and nm.allclose( bf.sum(axis=2), 1.0, rtol=0.0, atol=1e-14) self.report('%s: %s' % (key, _ok)) ok = ok and _ok return ok
def __init__(self, coors, conn, poly_space=None, gel=None, order=1): self.coors = coors self.conn = conn try: nm.take(self.coors, self.conn) except IndexError: output('coordinates shape: %s' % list(coors.shape)) output('connectivity: min: %d, max: %d' % (conn.min(), conn.max())) msg = 'incompatible connectivity and coordinates (see above)' raise IndexError(msg) self.n_el, self.n_ep = conn.shape self.dim = self.coors.shape[1] if poly_space is None: poly_space = PolySpace.any_from_args(None, gel, order, base='lagrange', force_bubble=False) self.poly_space = poly_space
def test_base_functions_values(self): """ Compare base function values and their gradients with correct data. Also test that sum of values over all element nodes gives one. """ from sfepy.base.base import ordered_iteritems from sfepy.fem.poly_spaces import PolySpace ok = True for key, val in ordered_iteritems(test_bases): gel = self.gels[key[:3]] diff = key[-4:] == 'grad' order = int(key[5]) force_bubble = key[6:7] == 'B' ps = PolySpace.any_from_args('aux', gel, order, base='lagrange', force_bubble=force_bubble) dim = ps.geometry.dim coors = nm.r_[ps.geometry.coors, [[0.2] * dim]] bf = ps.eval_base(coors, diff=diff) _ok = nm.allclose(val, bf, rtol=0.0, atol=1e-14) ## if not _ok: ## nm.set_printoptions(threshold=1000000, linewidth=65) ## print bf.__repr__() if not diff: _ok = _ok and nm.allclose(bf.sum(axis=2), 1.0, rtol=0.0, atol=1e-14) self.report('%s: %s' % (key, _ok)) ok = ok and _ok return ok
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-d', '--derivative', metavar='d', type=int, action='store', dest='derivative', default=0, help=help['derivative']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=2, help=help['max_order']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) parser.add_option('-m', '--mesh', metavar='mesh', action='store', dest='mesh', default=None, help=help['mesh']) parser.add_option('', '--permutations', metavar='permutations', action='store', dest='permutations', default=None, help=help['permutations']) parser.add_option('', '--dofs', metavar='dofs', action='store', dest='dofs', default=None, help=help['dofs']) parser.add_option('-l', '--lin-options', metavar='options', action='store', dest='lin_options', default='min_level=2,max_level=5,eps=1e-3', help=help['lin_options']) parser.add_option('', '--plot-dofs', action='store_true', dest='plot_dofs', default=False, help=help['plot_dofs']) options, args = parser.parse_args() if len(args) == 1: output_dir = args[0] else: parser.print_help(), return output('polynomial space:', options.basis) output('max. order:', options.max_order) lin = Struct(kind='adaptive', min_level=2, max_level=5, eps=1e-3) for opt in options.lin_options.split(','): key, val = opt.split('=') setattr(lin, key, eval(val)) if options.mesh is None: dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) gel = GeometryElement(options.geometry) gps = PolySpace.any_from_args(None, gel, 1, base=options.basis) ps = PolySpace.any_from_args(None, gel, options.max_order, base=options.basis) n_digit, _format = get_print_info(ps.n_nod, fill='0') name_template = os.path.join(output_dir, 'bf_%s.vtk' % _format) for ip in get_dofs(options.dofs, ps.n_nod): output('shape function %d...' % ip) def eval_dofs(iels, rx): if options.derivative == 0: bf = ps.eval_base(rx).squeeze() rvals = bf[None, :, ip:ip+1] else: bfg = ps.eval_base(rx, diff=True) rvals = bfg[None, ..., ip] return rvals def eval_coors(iels, rx): bf = gps.eval_base(rx).squeeze() coors = nm.dot(bf, gel.coors)[None, ...] return coors (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, 1, ps, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) out = { 'bf' : Struct(name='output_data', mode='vertex', data=vdofs, var_name='bf', dofs=None) } mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids], [options.geometry]) name = name_template % ip mesh.write(name, out=out) output('...done (%s)' % name) else: mesh = Mesh.from_file(options.mesh) output('mesh geometry:') output(' dimension: %d, vertices: %d, elements: %d' % (mesh.dim, mesh.n_nod, mesh.n_el)) domain = Domain('domain', mesh) if options.permutations: permutations = [int(ii) for ii in options.permutations.split(',')] output('using connectivity permutations:', permutations) for group in domain.iter_groups(): perms = group.gel.get_conn_permutations()[permutations] offsets = nm.arange(group.shape.n_el) * group.shape.n_ep group.conn[:] = group.conn.take(perms + offsets[:, None]) domain.setup_facets() omega = domain.create_region('Omega', 'all') field = Field.from_args('f', nm.float64, shape=1, region=omega, approx_order=options.max_order, poly_space_base=options.basis) var = FieldVariable('u', 'unknown', field, 1) if options.plot_dofs: import sfepy.postprocess.plot_dofs as pd group = domain.groups[0] ax = pd.plot_mesh(None, mesh.coors, mesh.conns[0], group.gel.edges) ax = pd.plot_global_dofs(ax, field.get_coor(), field.aps[0].econn) ax = pd.plot_local_dofs(ax, field.get_coor(), field.aps[0].econn) pd.plt.show() output('dofs: %d' % var.n_dof) vec = nm.empty(var.n_dof, dtype=var.dtype) n_digit, _format = get_print_info(var.n_dof, fill='0') name_template = os.path.join(output_dir, 'dof_%s.vtk' % _format) for ip in get_dofs(options.dofs, var.n_dof): output('dof %d...' % ip) vec.fill(0.0) vec[ip] = 1.0 var.data_from_any(vec) if options.derivative == 0: out = var.create_output(vec, linearization=lin) else: out = create_expression_output('ev_grad.ie.Elements(u)', 'u', 'f', {'f' : field}, None, Variables([var]), mode='qp', verbose=False, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) name = name_template % ip out['u'].mesh.write(name, out=out) output('...done (%s)' % name)
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-d', '--derivative', metavar='d', type=int, action='store', dest='derivative', default=0, help=help['derivative']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=2, help=help['max_order']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) parser.add_option('-m', '--mesh', metavar='mesh', action='store', dest='mesh', default=None, help=help['mesh']) parser.add_option('', '--permutations', metavar='permutations', action='store', dest='permutations', default=None, help=help['permutations']) parser.add_option('', '--dofs', metavar='dofs', action='store', dest='dofs', default=None, help=help['dofs']) parser.add_option('-l', '--lin-options', metavar='options', action='store', dest='lin_options', default='min_level=2,max_level=5,eps=1e-3', help=help['lin_options']) parser.add_option('', '--plot-dofs', action='store_true', dest='plot_dofs', default=False, help=help['plot_dofs']) options, args = parser.parse_args() if len(args) == 1: output_dir = args[0] else: parser.print_help(), return output('polynomial space:', options.basis) output('max. order:', options.max_order) lin = Struct(kind='adaptive', min_level=2, max_level=5, eps=1e-3) for opt in options.lin_options.split(','): key, val = opt.split('=') setattr(lin, key, eval(val)) if options.mesh is None: dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) gel = GeometryElement(options.geometry) gps = PolySpace.any_from_args(None, gel, 1, base=options.basis) ps = PolySpace.any_from_args(None, gel, options.max_order, base=options.basis) n_digit, _format = get_print_info(ps.n_nod, fill='0') name_template = os.path.join(output_dir, 'bf_%s.vtk' % _format) for ip in get_dofs(options.dofs, ps.n_nod): output('shape function %d...' % ip) def eval_dofs(iels, rx): if options.derivative == 0: bf = ps.eval_base(rx).squeeze() rvals = bf[None, :, ip:ip + 1] else: bfg = ps.eval_base(rx, diff=True) rvals = bfg[None, ..., ip] return rvals def eval_coors(iels, rx): bf = gps.eval_base(rx).squeeze() coors = nm.dot(bf, gel.coors)[None, ...] return coors (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, 1, ps, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) out = { 'bf': Struct(name='output_data', mode='vertex', data=vdofs, var_name='bf', dofs=None) } mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids], [options.geometry]) name = name_template % ip ensure_path(name) mesh.write(name, out=out) output('...done (%s)' % name) else: mesh = Mesh.from_file(options.mesh) output('mesh geometry:') output(' dimension: %d, vertices: %d, elements: %d' % (mesh.dim, mesh.n_nod, mesh.n_el)) if options.permutations: if options.permutations == 'all': from sfepy.linalg import cycle gel = GeometryElement(mesh.descs[0]) n_perms = gel.get_conn_permutations().shape[0] all_permutations = [ii for ii in cycle(mesh.n_el * [n_perms])] else: all_permutations = [ int(ii) for ii in options.permutations.split(',') ] all_permutations = nm.array(all_permutations) np = len(all_permutations) all_permutations.shape = (np / mesh.n_el, mesh.n_el) output('using connectivity permutations:\n', all_permutations) else: all_permutations = [None] for ip, permutations in enumerate(all_permutations): if permutations is None: suffix = '' else: suffix = '_' + '_'.join('%d' % ii for ii in permutations) save_basis_on_mesh(mesh, options, output_dir, lin, permutations, suffix)
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-d', '--derivative', metavar='d', type=int, action='store', dest='derivative', default=0, help=help['derivative']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=2, help=help['max_order']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) parser.add_option('-m', '--mesh', metavar='mesh', action='store', dest='mesh', default=None, help=help['mesh']) parser.add_option('', '--permutations', metavar='permutations', action='store', dest='permutations', default=None, help=help['permutations']) parser.add_option('', '--dofs', metavar='dofs', action='store', dest='dofs', default=None, help=help['dofs']) parser.add_option('-l', '--lin-options', metavar='options', action='store', dest='lin_options', default='min_level=2,max_level=5,eps=1e-3', help=help['lin_options']) parser.add_option('', '--plot-dofs', action='store_true', dest='plot_dofs', default=False, help=help['plot_dofs']) options, args = parser.parse_args() if len(args) == 1: output_dir = args[0] else: parser.print_help(), return output('polynomial space:', options.basis) output('max. order:', options.max_order) lin = Struct(kind='adaptive', min_level=2, max_level=5, eps=1e-3) for opt in options.lin_options.split(','): key, val = opt.split('=') setattr(lin, key, eval(val)) if options.mesh is None: dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) gel = GeometryElement(options.geometry) gps = PolySpace.any_from_args(None, gel, 1, base=options.basis) ps = PolySpace.any_from_args(None, gel, options.max_order, base=options.basis) n_digit, _format = get_print_info(ps.n_nod, fill='0') name_template = os.path.join(output_dir, 'bf_%s.vtk' % _format) for ip in get_dofs(options.dofs, ps.n_nod): output('shape function %d...' % ip) def eval_dofs(iels, rx): if options.derivative == 0: bf = ps.eval_base(rx).squeeze() rvals = bf[None, :, ip:ip+1] else: bfg = ps.eval_base(rx, diff=True) rvals = bfg[None, ..., ip] return rvals def eval_coors(iels, rx): bf = gps.eval_base(rx).squeeze() coors = nm.dot(bf, gel.coors)[None, ...] return coors (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, 1, ps, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) out = { 'bf' : Struct(name='output_data', mode='vertex', data=vdofs, var_name='bf', dofs=None) } mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids], [options.geometry]) name = name_template % ip ensure_path(name) mesh.write(name, out=out) output('...done (%s)' % name) else: mesh = Mesh.from_file(options.mesh) output('mesh geometry:') output(' dimension: %d, vertices: %d, elements: %d' % (mesh.dim, mesh.n_nod, mesh.n_el)) if options.permutations: if options.permutations == 'all': from sfepy.linalg import cycle gel = GeometryElement(mesh.descs[0]) n_perms = gel.get_conn_permutations().shape[0] all_permutations = [ii for ii in cycle(mesh.n_el * [n_perms])] else: all_permutations = [int(ii) for ii in options.permutations.split(',')] all_permutations = nm.array(all_permutations) np = len(all_permutations) all_permutations.shape = (np / mesh.n_el, mesh.n_el) output('using connectivity permutations:\n', all_permutations) else: all_permutations = [None] for ip, permutations in enumerate(all_permutations): if permutations is None: suffix = '' else: suffix = '_' + '_'.join('%d' % ii for ii in permutations) save_basis_on_mesh(mesh, options, output_dir, lin, permutations, suffix)
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-d', '--derivative', metavar='d', type=int, action='store', dest='derivative', default=0, help=help['derivative']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=2, help=help['max_order']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) parser.add_option('-m', '--mesh', metavar='mesh', action='store', dest='mesh', default=None, help=help['mesh']) parser.add_option('', '--permutations', metavar='permutations', action='store', dest='permutations', default=None, help=help['permutations']) parser.add_option('', '--dofs', metavar='dofs', action='store', dest='dofs', default=None, help=help['dofs']) parser.add_option('-l', '--lin-options', metavar='options', action='store', dest='lin_options', default='min_level=2,max_level=5,eps=1e-3', help=help['lin_options']) parser.add_option('', '--plot-dofs', action='store_true', dest='plot_dofs', default=False, help=help['plot_dofs']) options, args = parser.parse_args() if len(args) == 1: output_dir = args[0] else: parser.print_help(), return output('polynomial space:', options.basis) output('max. order:', options.max_order) lin = Struct(kind='adaptive', min_level=2, max_level=5, eps=1e-3) for opt in options.lin_options.split(','): key, val = opt.split('=') setattr(lin, key, eval(val)) if options.mesh is None: dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) gel = GeometryElement(options.geometry) gps = PolySpace.any_from_args(None, gel, 1, base=options.basis) ps = PolySpace.any_from_args(None, gel, options.max_order, base=options.basis) n_digit, _format = get_print_info(ps.n_nod, fill='0') name_template = os.path.join(output_dir, 'bf_%s.vtk' % _format) for ip in get_dofs(options.dofs, ps.n_nod): output('shape function %d...' % ip) def eval_dofs(iels, rx): if options.derivative == 0: bf = ps.eval_base(rx).squeeze() rvals = bf[None, :, ip:ip + 1] else: bfg = ps.eval_base(rx, diff=True) rvals = bfg[None, ..., ip] return rvals def eval_coors(iels, rx): bf = gps.eval_base(rx).squeeze() coors = nm.dot(bf, gel.coors)[None, ...] return coors (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, 1, ps, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) out = { 'bf': Struct(name='output_data', mode='vertex', data=vdofs, var_name='bf', dofs=None) } mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids], [options.geometry]) name = name_template % ip mesh.write(name, out=out) output('...done (%s)' % name) else: mesh = Mesh.from_file(options.mesh) output('mesh geometry:') output(' dimension: %d, vertices: %d, elements: %d' % (mesh.dim, mesh.n_nod, mesh.n_el)) domain = Domain('domain', mesh) if options.permutations: permutations = [int(ii) for ii in options.permutations.split(',')] output('using connectivity permutations:', permutations) for group in domain.iter_groups(): perms = group.gel.get_conn_permutations()[permutations] offsets = nm.arange(group.shape.n_el) * group.shape.n_ep group.conn[:] = group.conn.take(perms + offsets[:, None]) domain.setup_facets() omega = domain.create_region('Omega', 'all') field = Field.from_args('f', nm.float64, shape=1, region=omega, approx_order=options.max_order, poly_space_base=options.basis) var = FieldVariable('u', 'unknown', field, 1) if options.plot_dofs: import sfepy.postprocess.plot_dofs as pd group = domain.groups[0] ax = pd.plot_mesh(None, mesh.coors, mesh.conns[0], group.gel.edges) ax = pd.plot_global_dofs(ax, field.get_coor(), field.aps[0].econn) ax = pd.plot_local_dofs(ax, field.get_coor(), field.aps[0].econn) if options.dofs is not None: ax = pd.plot_nodes(ax, field.get_coor(), field.aps[0].econn, field.aps[0].interp.poly_spaces['v'].nodes, get_dofs(options.dofs, var.n_dof)) pd.plt.show() output('dofs: %d' % var.n_dof) vec = nm.empty(var.n_dof, dtype=var.dtype) n_digit, _format = get_print_info(var.n_dof, fill='0') name_template = os.path.join(output_dir, 'dof_%s.vtk' % _format) for ip in get_dofs(options.dofs, var.n_dof): output('dof %d...' % ip) vec.fill(0.0) vec[ip] = 1.0 var.set_data(vec) if options.derivative == 0: out = var.create_output(vec, linearization=lin) else: out = create_expression_output('ev_grad.ie.Elements(u)', 'u', 'f', {'f': field}, None, Variables([var]), mode='qp', verbose=False, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) name = name_template % ip out['u'].mesh.write(name, out=out) output('...done (%s)' % name)
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-d', '--derivative', metavar='d', type=int, action='store', dest='derivative', default=0, help=help['derivative']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=2, help=help['max_order']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) options, args = parser.parse_args() dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) output('polynomial space:', options.basis) output('max. order:', options.max_order) gel = GeometryElement(options.geometry) gps = PolySpace.any_from_args(None, gel, 1, base=options.basis) ps = PolySpace.any_from_args(None, gel, options.max_order, base=options.basis) n_digit, _format = get_print_info(ps.n_nod, fill='0') name_template = 'bf_%s.vtk' % _format for ip in range(ps.n_nod): output('shape function %d...' % ip) def eval_dofs(iels, rx, bf): if options.derivative == 0: rvals = bf[None, :, ip:ip+1] else: bfg = ps.eval_base(rx, diff=True) rvals = bfg[None, ..., ip] return rvals def eval_coors(iels, rx): bf = gps.eval_base(rx).squeeze() coors = nm.dot(bf, gel.coors)[None, ...] return coors (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, 1, ps, min_level=2, max_level=5, eps=1e-3) out = { 'bf' : Struct(name='output_data', mode='vertex', data=vdofs, var_name='bf', dofs=None) } mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids], [options.geometry]) name = name_template % ip mesh.write(name, out=out) output('...done (%s)' % name)