class Domain(Struct): def __init__(self, name, mesh=None, nurbs=None, bmesh=None, regions=None, verbose=False): Struct.__init__(self, name=name, mesh=mesh, nurbs=nurbs, bmesh=bmesh, regions=regions, verbose=verbose) def get_centroids(self, dim): """ Return the coordinates of centroids of mesh entities with dimension `dim`. """ return self.cmesh.get_centroids(dim) def has_faces(self): return self.shape.tdim == 3 def reset_regions(self): """ Reset the list of regions associated with the domain. """ self.regions = OneTypeList(Region) self._region_stack = [] self._bnf = create_bnf(self._region_stack) def create_region(self, name, select, kind='cell', parent=None, check_parents=True, functions=None, add_to_regions=True, allow_empty=False): """ Region factory constructor. Append the new region to self.regions list. """ if check_parents: parents = get_parents(select) for p in parents: if p not in [region.name for region in self.regions]: msg = 'parent region %s of %s not found!' % (p, name) raise ValueError(msg) stack = self._region_stack try: self._bnf.parseString(select) except ParseException: print 'parsing failed:', select raise region = visit_stack(stack, region_op, region_leaf(self, self.regions, select, functions)) region.name = name region.definition = select region.set_kind(kind) region.finalize(allow_empty=allow_empty) region.parent = parent region.update_shape() if add_to_regions: self.regions.append(region) return region def create_regions(self, region_defs, functions=None): output('creating regions...') tt = time.clock() self.reset_regions() ## # Sort region definitions by dependencies. graph, name_to_sort_name = get_dependency_graph(region_defs) sorted_regions = sort_by_dependency(graph) ## # Define regions. for name in sorted_regions: sort_name = name_to_sort_name[name] rdef = region_defs[sort_name] region = self.create_region(name, rdef.select, kind=rdef.get('kind', 'cell'), parent=rdef.get('parent', None), check_parents=False, functions=functions) output(' ', region.name) output('...done in %.2f s' % (time.clock() - tt)) return self.regions def save_regions(self, filename, region_names=None): """ Save regions as individual meshes. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ import os if region_names is None: region_names = self.regions.get_names() trunk, suffix = os.path.splitext(filename) output('saving regions...') for name in region_names: region = self.regions[name] output(name) aux = self.mesh.from_region(region, self.mesh) aux.write('%s_%s%s' % (trunk, region.name, suffix), io='auto') output('...done') def save_regions_as_groups(self, filename, region_names=None): """ Save regions in a single mesh but mark them by using different element/node group numbers. If regions overlap, the result is undetermined, with exception of the whole domain region, which is marked by group id 0. Region masks are also saved as scalar point data for output formats that support this. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ output('saving regions as groups...') aux = self.mesh.copy() n_ig = c_ig = 0 n_nod = self.shape.n_nod # The whole domain region should go first. names = (region_names if region_names is not None else self.regions.get_names()) for name in names: region = self.regions[name] if region.vertices.shape[0] == n_nod: names.remove(region.name) names = [region.name] + names break out = {} for name in names: region = self.regions[name] output(region.name) aux.cmesh.vertex_groups[region.vertices] = n_ig n_ig += 1 mask = nm.zeros((n_nod, 1), dtype=nm.float64) mask[region.vertices] = 1.0 out[name] = Struct(name='region', mode='vertex', data=mask, var_name=name, dofs=None) if region.has_cells(): ii = region.get_cells() aux.cmesh.cell_groups[ii] = c_ig c_ig += 1 aux.write(filename, io='auto', out=out) output('...done')
class Domain(Struct): """ Domain is divided into groups, whose purpose is to have homogeneous data shapes. """ def __init__(self, name, mesh, verbose=False): """Create a Domain. Parameters ---------- name : str Object name. mesh : Mesh A mesh defining the domain. """ geom_els = {} for ig, desc in enumerate(mesh.descs): gel = GeometryElement(desc) # Create geometry elements of dimension - 1. gel.create_surface_facet() geom_els[desc] = gel interps = {} for gel in geom_els.itervalues(): key = gel.get_interpolation_name() gel.interp = interps.setdefault(key, fea.Interpolant(key, gel)) gel = gel.surface_facet if gel is not None: key = gel.get_interpolation_name() gel.interp = interps.setdefault(key, fea.Interpolant(key, gel)) Struct.__init__(self, name=name, mesh=mesh, geom_els=geom_els, geom_interps=interps) self.mat_ids_to_i_gs = {} for ig, mat_id in enumerate(mesh.mat_ids): self.mat_ids_to_i_gs[mat_id[0]] = ig self.setup_groups() self.fix_element_orientation() self.reset_regions() self.clear_surface_groups() from sfepy.fem.geometry_element import create_geometry_elements from sfepy.fem.extmods.cmesh import CMesh self.cmesh = CMesh.from_mesh(mesh) gels = create_geometry_elements() self.cmesh.set_local_entities(gels) self.cmesh.setup_entities() self.shape.tdim = self.cmesh.tdim def setup_groups(self): n_nod, dim = self.mesh.coors.shape self.shape = Struct(n_gr=len(self.mesh.conns), n_el=0, n_nod=n_nod, dim=dim) self.groups = {} for ii in range(self.shape.n_gr): gel = self.geom_els[self.mesh.descs[ii]] # Shortcut. conn = self.mesh.conns[ii] vertices = nm.unique(conn) n_vertex = vertices.shape[0] n_el, n_ep = conn.shape n_edge = gel.n_edge n_edge_total = n_edge * n_el if gel.dim == 3: n_face = gel.n_face n_face_total = n_face * n_el else: n_face = n_face_total = 0 shape = Struct(n_vertex=n_vertex, n_el=n_el, n_ep=n_ep, n_edge=n_edge, n_edge_total=n_edge_total, n_face=n_face, n_face_total=n_face_total, dim=self.mesh.dims[ii]) self.groups[ii] = Struct(ig=ii, vertices=vertices, conn=conn, gel=gel, shape=shape) self.shape.n_el += n_el def iter_groups(self, igs=None): if igs is None: for ig in xrange(self.shape.n_gr): # sorted by ig. yield self.groups[ig] else: for ig in igs: yield ig, self.groups[ig] def get_cell_offsets(self): offs = {} off = 0 for group in self.iter_groups(): ig = group.ig offs[ig] = off off += group.shape.n_el return offs def get_mesh_coors(self, actual=False): """ Return the coordinates of the underlying mesh vertices. """ if actual and hasattr(self.mesh, 'coors_act'): return self.mesh.coors_act else: return self.mesh.coors def get_centroids(self, dim): """ Return the coordinates of centroids of mesh entities with dimension `dim`. """ return self.cmesh.get_centroids(dim) def get_mesh_bounding_box(self): """ Return the bounding box of the underlying mesh. Returns ------- bbox : ndarray (2, dim) The bounding box with min. values in the first row and max. values in the second row. """ return self.mesh.get_bounding_box() def get_diameter(self): """ Return the diameter of the domain. Notes ----- The diameter corresponds to the Friedrichs constant. """ bbox = self.get_mesh_bounding_box() return (bbox[1,:] - bbox[0,:]).max() def get_conns(self): """ Return the element connectivity groups of the underlying mesh. """ return self.mesh.conns def fix_element_orientation(self): """ Ensure element nodes ordering giving positive element volume. The groups with elements of lower dimension than the space dimension are skipped. """ from extmods.cmesh import orient_elements coors = self.mesh.coors for ii, group in self.groups.iteritems(): if group.shape.dim < self.shape.dim: continue ori, conn = group.gel.orientation, group.conn itry = 0 while itry < 2: flag = -nm.ones(conn.shape[0], dtype=nm.int32) # Changes orientation if it is wrong according to swap*! # Changes are indicated by positive flag. orient_elements(flag, conn, coors, ori.roots, ori.vecs, ori.swap_from, ori.swap_to) if nm.alltrue(flag == 0): if itry > 0: output('...corrected') itry = -1 break output('warning: bad element orientation, trying to correct...') itry += 1 if itry == 2 and flag[0] != -1: raise RuntimeError('elements cannot be oriented! (%d, %s)' % (ii, self.mesh.descs[ii])) elif flag[0] == -1: output('warning: element orienation not checked') def has_faces(self): return sum([group.shape.n_face for group in self.iter_groups()]) > 0 def reset_regions(self): """ Reset the list of regions associated with the domain. """ self.regions = OneTypeList(Region) self._region_stack = [] self._bnf = create_bnf(self._region_stack) def create_region(self, name, select, kind='cell', parent=None, check_parents=True, functions=None, add_to_regions=True): """ Region factory constructor. Append the new region to self.regions list. """ if check_parents: parents = get_parents(select) for p in parents: if p not in [region.name for region in self.regions]: msg = 'parent region %s of %s not found!' % (p, name) raise ValueError(msg) stack = self._region_stack try: self._bnf.parseString(select) except ParseException: print 'parsing failed:', select raise region = visit_stack(stack, region_op, region_leaf(self, self.regions, select, functions)) region.name = name region.definition = select region.set_kind(kind) region.parent = parent region.update_shape() if add_to_regions: self.regions.append(region) return region def create_regions(self, region_defs, functions=None): output('creating regions...') tt = time.clock() self.reset_regions() ## # Sort region definitions by dependencies. graph, name_to_sort_name = get_dependency_graph(region_defs) sorted_regions = sort_by_dependency(graph) ## # Define regions. for name in sorted_regions: sort_name = name_to_sort_name[name] rdef = region_defs[sort_name] region = self.create_region(name, rdef.select, kind=rdef.get('kind', 'cell'), parent=rdef.get('parent', None), check_parents=False, functions=functions) output(' ', region.name) output('...done in %.2f s' % (time.clock() - tt)) return self.regions def save_regions(self, filename, region_names=None): """ Save regions as individual meshes. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ import os if region_names is None: region_names = self.regions.get_names() trunk, suffix = os.path.splitext(filename) output('saving regions...') for name in region_names: region = self.regions[name] output(name) aux = self.mesh.from_region(region, self.mesh) aux.write('%s_%s%s' % (trunk, region.name, suffix), io='auto') output('...done') def save_regions_as_groups(self, filename, region_names=None): """ Save regions in a single mesh but mark them by using different element/node group numbers. If regions overlap, the result is undetermined, with exception of the whole domain region, which is marked by group id 0. Region masks are also saved as scalar point data for output formats that support this. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ output('saving regions as groups...') aux = self.mesh.copy() n_ig = c_ig = 0 n_nod = self.shape.n_nod # The whole domain region should go first. names = (region_names if region_names is not None else self.regions.get_names()) for name in names: region = self.regions[name] if region.vertices.shape[0] == n_nod: names.remove(region.name) names = [region.name] + names break out = {} for name in names: region = self.regions[name] output(region.name) aux.ngroups[region.vertices] = n_ig n_ig += 1 mask = nm.zeros((n_nod, 1), dtype=nm.float64) mask[region.vertices] = 1.0 out[name] = Struct(name='region', mode='vertex', data=mask, var_name=name, dofs=None) if region.has_cells(): for ig in region.igs: ii = region.get_cells(ig) aux.mat_ids[ig][ii] = c_ig c_ig += 1 aux.write(filename, io='auto', out=out) output('...done') def get_element_diameters(self, ig, cells, vg, mode, square=True): group = self.groups[ig] diameters = nm.empty((len(cells), 1, 1, 1), dtype=nm.float64) if vg is None: diameters.fill(1.0) else: vg.get_element_diameters(diameters, group.gel.edges, self.get_mesh_coors().copy(), group.conn, cells.astype(nm.int32), mode) if square: out = diameters.squeeze() else: out = nm.sqrt(diameters.squeeze()) return out def clear_surface_groups(self): """ Remove surface group data. """ self.surface_groups = {} def create_surface_group(self, region): """ Create a new surface group corresponding to `region` if it does not exist yet. Notes ----- Surface groups define surface facet connectivity that is needed for :class:`sfepy.fem.mappings.SurfaceMapping`. """ for ig in region.igs: groups = self.surface_groups.setdefault(ig, {}) if region.name not in groups: group = self.groups[ig] gel_faces = group.gel.get_surface_entities() name = 'surface_group_%s_%d' % (region.name, ig) surface_group = FESurface(name, region, gel_faces, group.conn, ig) groups[region.name] = surface_group def refine(self): """ Uniformly refine the domain mesh. Returns ------- domain : Domain instance The new domain with the refined mesh. Notes ----- Works only for meshes with single element type! Does not preserve node groups! """ names = set() for group in self.groups.itervalues(): names.add(group.gel.name) if len(names) != 1: msg = 'refine() works only for meshes with single element type!' raise NotImplementedError(msg) el_type = names.pop() if el_type == '2_3': mesh = refine_2_3(self.mesh, self.cmesh) elif el_type == '2_4': mesh = refine_2_4(self.mesh, self.cmesh) elif el_type == '3_4': mesh = refine_3_4(self.mesh, self.cmesh) elif el_type == '3_8': mesh = refine_3_8(self.mesh, self.cmesh) else: msg = 'unsupported element type! (%s)' % el_type raise NotImplementedError(msg) domain = Domain(self.name + '_r', mesh) return domain
class Domain(Struct): def __init__(self, name, mesh=None, nurbs=None, bmesh=None, regions=None, verbose=False): Struct.__init__(self, name=name, mesh=mesh, nurbs=nurbs, bmesh=bmesh, regions=regions, verbose=verbose) def get_centroids(self, dim): """ Return the coordinates of centroids of mesh entities with dimension `dim`. """ return self.cmesh.get_centroids(dim) def has_faces(self): return self.shape.tdim == 3 def reset_regions(self): """ Reset the list of regions associated with the domain. """ self.regions = OneTypeList(Region) self._region_stack = [] self._bnf = create_bnf(self._region_stack) def create_region(self, name, select, kind='cell', parent=None, check_parents=True, functions=None, add_to_regions=True, allow_empty=False): """ Region factory constructor. Append the new region to self.regions list. """ if check_parents: parents = get_parents(select) for p in parents: if p not in [region.name for region in self.regions]: msg = 'parent region %s of %s not found!' % (p, name) raise ValueError(msg) stack = self._region_stack try: self._bnf.parseString(select) except ParseException: print('parsing failed:', select) raise region = visit_stack( stack, region_op, region_leaf(self, self.regions, select, functions)) region.name = name region.definition = select region.set_kind(kind) region.finalize(allow_empty=allow_empty) region.parent = parent region.update_shape() if add_to_regions: self.regions.append(region) return region def create_regions(self, region_defs, functions=None): output('creating regions...') tt = time.clock() self.reset_regions() ## # Sort region definitions by dependencies. graph, name_to_sort_name = get_dependency_graph(region_defs) sorted_regions = sort_by_dependency(graph) ## # Define regions. for name in sorted_regions: sort_name = name_to_sort_name[name] rdef = region_defs[sort_name] region = self.create_region(name, rdef.select, kind=rdef.get('kind', 'cell'), parent=rdef.get('parent', None), check_parents=False, functions=functions) output(' ', region.name) output('...done in %.2f s' % (time.clock() - tt)) return self.regions def save_regions(self, filename, region_names=None): """ Save regions as individual meshes. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ import os if region_names is None: region_names = self.regions.get_names() trunk, suffix = os.path.splitext(filename) output('saving regions...') for name in region_names: region = self.regions[name] output(name) aux = self.mesh.from_region(region, self.mesh) aux.write('%s_%s%s' % (trunk, region.name, suffix), io='auto') output('...done') def save_regions_as_groups(self, filename, region_names=None): """ Save regions in a single mesh but mark them by using different element/node group numbers. If regions overlap, the result is undetermined, with exception of the whole domain region, which is marked by group id 0. Region masks are also saved as scalar point data for output formats that support this. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ output('saving regions as groups...') aux = self.mesh.copy() n_ig = c_ig = 0 n_nod = self.shape.n_nod # The whole domain region should go first. names = (region_names if region_names is not None else self.regions.get_names()) for name in names: region = self.regions[name] if region.vertices.shape[0] == n_nod: names.remove(region.name) names = [region.name] + names break out = {} for name in names: region = self.regions[name] output(region.name) aux.cmesh.vertex_groups[region.vertices] = n_ig n_ig += 1 mask = nm.zeros((n_nod, 1), dtype=nm.float64) mask[region.vertices] = 1.0 out[name] = Struct(name='region', mode='vertex', data=mask, var_name=name, dofs=None) if region.has_cells(): ii = region.get_cells() aux.cmesh.cell_groups[ii] = c_ig c_ig += 1 aux.write(filename, io='auto', out=out) output('...done')
class Domain(Struct): """ Domain is divided into groups, whose purpose is to have homogeneous data shapes. """ def __init__(self, name, mesh, verbose=False): """Create a Domain. Parameters ---------- name : str Object name. mesh : Mesh A mesh defining the domain. """ geom_els = {} for ig, desc in enumerate(mesh.descs): gel = GeometryElement(desc) # Create geometry elements of dimension - 1. gel.create_surface_facet() geom_els[desc] = gel interps = {} for gel in geom_els.itervalues(): key = gel.get_interpolation_name() gel.interp = interps.setdefault(key, fea.Interpolant(key, gel)) gel = gel.surface_facet if gel is not None: key = gel.get_interpolation_name() gel.interp = interps.setdefault(key, fea.Interpolant(key, gel)) Struct.__init__(self, name=name, mesh=mesh, geom_els=geom_els, geom_interps=interps) self.mat_ids_to_i_gs = {} for ig, mat_id in enumerate(mesh.mat_ids): self.mat_ids_to_i_gs[mat_id[0]] = ig self.setup_groups() self.fix_element_orientation() self.reset_regions() self.clear_surface_groups() from sfepy.fem.geometry_element import create_geometry_elements from sfepy.fem.extmods.cmesh import CMesh self.cmesh = CMesh.from_mesh(mesh) gels = create_geometry_elements() self.cmesh.set_local_entities(gels) self.cmesh.setup_entities() self.shape.tdim = self.cmesh.tdim def setup_groups(self): n_nod, dim = self.mesh.coors.shape self.shape = Struct(n_gr=len(self.mesh.conns), n_el=0, n_nod=n_nod, dim=dim) self.groups = {} for ii in range(self.shape.n_gr): gel = self.geom_els[self.mesh.descs[ii]] # Shortcut. conn = self.mesh.conns[ii] vertices = nm.unique(conn) n_vertex = vertices.shape[0] n_el, n_ep = conn.shape n_edge = gel.n_edge n_edge_total = n_edge * n_el if gel.dim == 3: n_face = gel.n_face n_face_total = n_face * n_el else: n_face = n_face_total = 0 shape = Struct(n_vertex=n_vertex, n_el=n_el, n_ep=n_ep, n_edge=n_edge, n_edge_total=n_edge_total, n_face=n_face, n_face_total=n_face_total, dim=self.mesh.dims[ii]) self.groups[ii] = Struct(ig=ii, vertices=vertices, conn=conn, gel=gel, shape=shape) self.shape.n_el += n_el def iter_groups(self, igs=None): if igs is None: for ig in xrange(self.shape.n_gr): # sorted by ig. yield self.groups[ig] else: for ig in igs: yield ig, self.groups[ig] def get_cell_offsets(self): offs = {} off = 0 for group in self.iter_groups(): ig = group.ig offs[ig] = off off += group.shape.n_el return offs def get_mesh_coors(self, actual=False): """ Return the coordinates of the underlying mesh vertices. """ if actual and hasattr(self.mesh, 'coors_act'): return self.mesh.coors_act else: return self.mesh.coors def get_centroids(self, dim): """ Return the coordinates of centroids of mesh entities with dimension `dim`. """ return self.cmesh.get_centroids(dim) def get_mesh_bounding_box(self): """ Return the bounding box of the underlying mesh. Returns ------- bbox : ndarray (2, dim) The bounding box with min. values in the first row and max. values in the second row. """ return self.mesh.get_bounding_box() def get_diameter(self): """ Return the diameter of the domain. Notes ----- The diameter corresponds to the Friedrichs constant. """ bbox = self.get_mesh_bounding_box() return (bbox[1, :] - bbox[0, :]).max() def get_conns(self): """ Return the element connectivity groups of the underlying mesh. """ return self.mesh.conns def fix_element_orientation(self): """ Ensure element nodes ordering giving positive element volume. The groups with elements of lower dimension than the space dimension are skipped. """ from extmods.cmesh import orient_elements coors = self.mesh.coors for ii, group in self.groups.iteritems(): if group.shape.dim < self.shape.dim: continue ori, conn = group.gel.orientation, group.conn itry = 0 while itry < 2: flag = -nm.ones(conn.shape[0], dtype=nm.int32) # Changes orientation if it is wrong according to swap*! # Changes are indicated by positive flag. orient_elements(flag, conn, coors, ori.roots, ori.vecs, ori.swap_from, ori.swap_to) if nm.alltrue(flag == 0): if itry > 0: output('...corrected') itry = -1 break output( 'warning: bad element orientation, trying to correct...') itry += 1 if itry == 2 and flag[0] != -1: raise RuntimeError('elements cannot be oriented! (%d, %s)' % (ii, self.mesh.descs[ii])) elif flag[0] == -1: output('warning: element orienation not checked') def has_faces(self): return sum([group.shape.n_face for group in self.iter_groups()]) > 0 def reset_regions(self): """ Reset the list of regions associated with the domain. """ self.regions = OneTypeList(Region) self._region_stack = [] self._bnf = create_bnf(self._region_stack) def create_region(self, name, select, kind='cell', parent=None, check_parents=True, functions=None, add_to_regions=True): """ Region factory constructor. Append the new region to self.regions list. """ if check_parents: parents = get_parents(select) for p in parents: if p not in [region.name for region in self.regions]: msg = 'parent region %s of %s not found!' % (p, name) raise ValueError(msg) stack = self._region_stack try: self._bnf.parseString(select) except ParseException: print 'parsing failed:', select raise region = visit_stack( stack, region_op, region_leaf(self, self.regions, select, functions)) region.name = name region.definition = select region.set_kind(kind) region.parent = parent region.update_shape() if add_to_regions: self.regions.append(region) return region def create_regions(self, region_defs, functions=None): output('creating regions...') tt = time.clock() self.reset_regions() ## # Sort region definitions by dependencies. graph, name_to_sort_name = get_dependency_graph(region_defs) sorted_regions = sort_by_dependency(graph) ## # Define regions. for name in sorted_regions: sort_name = name_to_sort_name[name] rdef = region_defs[sort_name] region = self.create_region(name, rdef.select, kind=rdef.get('kind', 'cell'), parent=rdef.get('parent', None), check_parents=False, functions=functions) output(' ', region.name) output('...done in %.2f s' % (time.clock() - tt)) return self.regions def save_regions(self, filename, region_names=None): """ Save regions as individual meshes. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ import os if region_names is None: region_names = self.regions.get_names() trunk, suffix = os.path.splitext(filename) output('saving regions...') for name in region_names: region = self.regions[name] output(name) aux = self.mesh.from_region(region, self.mesh) aux.write('%s_%s%s' % (trunk, region.name, suffix), io='auto') output('...done') def save_regions_as_groups(self, filename, region_names=None): """ Save regions in a single mesh but mark them by using different element/node group numbers. If regions overlap, the result is undetermined, with exception of the whole domain region, which is marked by group id 0. Region masks are also saved as scalar point data for output formats that support this. Parameters ---------- filename : str The output filename. region_names : list, optional If given, only the listed regions are saved. """ output('saving regions as groups...') aux = self.mesh.copy() n_ig = c_ig = 0 n_nod = self.shape.n_nod # The whole domain region should go first. names = (region_names if region_names is not None else self.regions.get_names()) for name in names: region = self.regions[name] if region.vertices.shape[0] == n_nod: names.remove(region.name) names = [region.name] + names break out = {} for name in names: region = self.regions[name] output(region.name) aux.ngroups[region.vertices] = n_ig n_ig += 1 mask = nm.zeros((n_nod, 1), dtype=nm.float64) mask[region.vertices] = 1.0 out[name] = Struct(name='region', mode='vertex', data=mask, var_name=name, dofs=None) if region.has_cells(): for ig in region.igs: ii = region.get_cells(ig) aux.mat_ids[ig][ii] = c_ig c_ig += 1 aux.write(filename, io='auto', out=out) output('...done') def get_element_diameters(self, ig, cells, vg, mode, square=True): group = self.groups[ig] diameters = nm.empty((len(cells), 1, 1, 1), dtype=nm.float64) if vg is None: diameters.fill(1.0) else: vg.get_element_diameters(diameters, group.gel.edges, self.get_mesh_coors().copy(), group.conn, cells.astype(nm.int32), mode) if square: out = diameters.squeeze() else: out = nm.sqrt(diameters.squeeze()) return out def clear_surface_groups(self): """ Remove surface group data. """ self.surface_groups = {} def create_surface_group(self, region): """ Create a new surface group corresponding to `region` if it does not exist yet. Notes ----- Surface groups define surface facet connectivity that is needed for :class:`sfepy.fem.mappings.SurfaceMapping`. """ for ig in region.igs: groups = self.surface_groups.setdefault(ig, {}) if region.name not in groups: group = self.groups[ig] gel_faces = group.gel.get_surface_entities() name = 'surface_group_%s_%d' % (region.name, ig) surface_group = FESurface(name, region, gel_faces, group.conn, ig) groups[region.name] = surface_group def refine(self): """ Uniformly refine the domain mesh. Returns ------- domain : Domain instance The new domain with the refined mesh. Notes ----- Works only for meshes with single element type! Does not preserve node groups! """ names = set() for group in self.groups.itervalues(): names.add(group.gel.name) if len(names) != 1: msg = 'refine() works only for meshes with single element type!' raise NotImplementedError(msg) el_type = names.pop() if el_type == '2_3': mesh = refine_2_3(self.mesh, self.cmesh) elif el_type == '2_4': mesh = refine_2_4(self.mesh, self.cmesh) elif el_type == '3_4': mesh = refine_3_4(self.mesh, self.cmesh) elif el_type == '3_8': mesh = refine_3_8(self.mesh, self.cmesh) else: msg = 'unsupported element type! (%s)' % el_type raise NotImplementedError(msg) domain = Domain(self.name + '_r', mesh) return domain