Source code for sfepy.discrete.common.domain

from __future__ import print_function

import numpy as nm

from sfepy.base.base import output, assert_, OneTypeList, Struct
from sfepy.base.timing import Timer
from sfepy.discrete.common.region import (Region, get_dependency_graph,
                                          sort_by_dependency, get_parents)
from sfepy.discrete.parse_regions import create_bnf, visit_stack, ParseException

[docs]def region_leaf(domain, regions, rdef, functions, tdim): """ Create/setup a region instance according to rdef. """ n_coor = domain.shape.n_nod dim = domain.shape.dim cmesh = domain.cmesh_tdim[tdim] def _region_leaf(level, op): token, details = op['token'], op['orig'] if token != 'KW_Region': parse_def = token + '<' + ' '.join(details) + '>' if token != 'E_COG': region = Region('leaf', rdef, domain, parse_def=parse_def, tdim=tdim) if token == 'KW_Region': details = details[1][2:] aux = regions.find(details) if not aux: raise ValueError('region %s does not exist' % details) else: if rdef[:4] == 'copy': region = aux.copy() else: region = aux elif token == 'KW_All': region.vertices = nm.arange(n_coor, dtype=nm.uint32) elif token == 'E_VIR': where = details[2] if where[0] == '[': vertices = nm.array(eval(where), dtype=nm.uint32) assert_(nm.amin(vertices) >= 0) assert_(nm.amax(vertices) < n_coor) else: coors = cmesh.coors y = z = None x = coors[:,0] if dim > 1: y = coors[:,1] if dim > 2: z = coors[:,2] coor_dict = {'x' : x, 'y' : y, 'z': z} vertices = nm.where(eval(where, {}, coor_dict))[0] region.vertices = vertices elif token == 'E_VOS': facets = cmesh.get_surface_facets() region.set_kind('facet') region.facets = facets elif token == 'E_VBF': where = details[2] coors = cmesh.coors fun = functions[where] vertices = fun(coors, domain=domain) region.vertices = vertices elif token == 'E_CBF': where = details[2] coors = domain.get_centroids(dim) fun = functions[where] cells = fun(coors, domain=domain) region.cells = cells elif token == 'E_COG': group = int(details[3]) td = 0 for k in range(4): if domain.cmesh_tdim[k] is not None: cg = domain.cmesh_tdim[k].cell_groups if nm.any(cg == group): td = k break if td == 0: raise ValueError('cell group %s does not exist' % group) region = Region('leaf', rdef, domain, parse_def=parse_def, tdim=td) region.cells = \ nm.where(domain.cmesh_tdim[td].cell_groups == group)[0] elif token == 'E_COSET': raise NotImplementedError('element sets not implemented!') elif token == 'E_VOG': group = int(details[3]) region.vertices = nm.where(cmesh.vertex_groups == group)[0] elif token == 'E_VOSET': try: vertices = domain.vertex_set_bcs[details[3]] except KeyError: msg = 'undefined vertex set! (%s)' % details[3] raise ValueError(msg) region.vertices = vertices elif token == 'E_OVIR': aux = regions[details[3][2:]] region.vertices = aux.vertices[0:1] elif token == 'E_VI': region.vertices = nm.array([int(ii) for ii in details[1:]], dtype=nm.uint32) elif token == 'E_CI': region.cells = nm.array([int(ii) for ii in details[1:]], dtype=nm.uint32) else: output('token "%s" unkown - check regions!' % token) raise NotImplementedError return region return _region_leaf
[docs]def region_op(level, op_code, item1, item2): token = op_code['token'] op = {'S' : '-', 'A' : '+', 'I' : '*'}[token[3]] if token[-1] == 'V': return item1.eval_op_vertices(item2, op) elif token[-1] == 'E': return item1.eval_op_edges(item2, op) elif token[-1] == 'F': return item1.eval_op_faces(item2, op) elif token[-1] == 'S': return item1.eval_op_facets(item2, op) elif token[-1] == 'C': return item1.eval_op_cells(item2, op) else: raise ValueError('unknown region operator token! (%s)' % token)
[docs]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)
[docs] def get_centroids(self, dim): """ Return the coordinates of centroids of mesh entities with dimension `dim`. """ return self.cmesh.get_centroids(dim)
[docs] def has_faces(self): return self.shape.tdim == 3
[docs] 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)
[docs] def create_extra_tdim_region(self, region, functions, tdim): from sfepy.discrete.fem.geometry_element import (GeometryElement, create_geometry_elements) from sfepy.discrete import PolySpace """ Create a new region which has its own cmesh with topological dimension tdim. """ mesh = self.mesh if mesh.cmesh_tdim[tdim] is not None: raise ValueError(f'cmesh of dimension {tdim} already exists!') aux = mesh.from_region(region, mesh, tdim=tdim) cmesh = aux.cmesh new_mat_id = nm.max([nm.max(k.cell_groups) for k in mesh.cmesh_tdim if k is not None]) + 1 cmesh.cell_groups[:] = new_mat_id mesh.cmesh_tdim[tdim] = cmesh mesh.descs += aux.descs mesh.dims += aux.dims mesh.n_el += aux.n_el cmesh.set_local_entities(create_geometry_elements()) cmesh.setup_entities() gel = GeometryElement(aux.descs[0]) if gel.dim > 0: gel.create_surface_facet() new_gel_entry = {aux.descs[0]: gel} self.geom_els.update(new_gel_entry) self.fix_element_orientation(geom_els=new_gel_entry, force_check=True) key = gel.get_interpolation_name() gel.poly_space = PolySpace.any_from_args(key, gel, 1) gel = gel.surface_facet if gel is not None: key = gel.get_interpolation_name() gel.poly_space = PolySpace.any_from_args(key, gel, 1) select = f'cells of group {new_mat_id}' self._bnf.parseString(select) region = visit_stack(self._region_stack, region_op, region_leaf(self, self.regions, select, functions, tdim)) region.field_dim = tdim return region
[docs] def create_region(self, name, select, kind='cell', parent=None, check_parents=True, extra_options=None, 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 [ 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 eopts = extra_options tdim = self.shape.tdim if parent is None else self.regions[parent].tdim if eopts is not None: tdim = eopts.get('cell_tdim', tdim) region = visit_stack(stack, region_op, region_leaf(self, self.regions, select, functions, tdim)) finalize = True if eopts is not None: if 'mesh_dim' in eopts: region = self.create_extra_tdim_region(region, functions, eopts['mesh_dim']) if not(eopts.get('finalize', True)): finalize = False if 'vertices_from' in eopts: vreg = eopts['vertices_from'] region.entities[0] = self.regions[vreg].vertices.copy() finalize = False = name region.definition = select region.set_kind(kind) if finalize: region.finalize(allow_empty=allow_empty) region.parent = parent region.extra_options = extra_options region.update_shape() if add_to_regions: self.regions.append(region) return region
[docs] def create_regions(self, region_defs, functions=None, allow_empty=False): output('creating regions...') timer = Timer(start=True) 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,, kind=rdef.get('kind', 'cell'), parent=rdef.get('parent', None), check_parents=False, extra_options=rdef.get('extra_options', None), functions=functions, allow_empty=allow_empty) output(' ', output('...done in %.2f s' % timer.stop()) return self.regions
[docs] 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) dim = region.tdim is_surf = not region.can[dim] and region.can[dim - 1] aux = self.mesh.from_region(region, self.mesh, is_surface=is_surf) aux.write('%s_%s%s' % (trunk,, suffix), io='auto') output('...done')
[docs] 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( names = [] + names break out = {} for name in names: region = self.regions[name] output( 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')