Source code for sfepy.discrete.fem.domain

Computational domain, consisting of the mesh and regions.
from __future__ import absolute_import
import numpy as nm

from sfepy.base.base import output, Struct
from .geometry_element import GeometryElement
from sfepy.discrete import Domain, PolySpace
from sfepy.discrete.fem.refine import refine_2_3, refine_2_4, refine_3_4, \
    refine_3_8, refine_1_2
from sfepy.discrete.fem.fe_surface import FESurface
import six

[docs]class FEDomain(Domain): """ Domain is divided into groups, whose purpose is to have homogeneous data shapes. """ def __init__(self, name, mesh, verbose=False, **kwargs): """Create a Domain. Parameters ---------- name : str Object name. mesh : Mesh A mesh defining the domain. """ Domain.__init__(self, name, mesh=mesh, verbose=verbose, **kwargs) if len(mesh.descs) > 1: msg = 'meshes with several cell kinds are not supported!' raise NotImplementedError(msg) self.geom_els = geom_els = {} for ig, desc in enumerate(mesh.descs): gel = GeometryElement(desc) if gel.dim > 0: # Create geometry elements of dimension - 1. gel.create_surface_facet() geom_els[desc] = gel for gel in six.itervalues(geom_els): 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) self.vertex_set_bcs = self.mesh.nodal_bcs self.cmesh = self.mesh.cmesh # Must be before creating derived connectivities. self.fix_element_orientation() from sfepy.discrete.fem.geometry_element import create_geometry_elements gels = create_geometry_elements() self.cmesh.set_local_entities(gels) self.cmesh.setup_entities() n_nod, dim = self.mesh.coors.shape self.shape = Struct(n_nod=n_nod, dim=dim, tdim=self.cmesh.tdim, n_el=self.cmesh.n_el, n_gr=len(self.geom_els)) self.reset_regions() self.clear_surface_groups()
[docs] 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
[docs] 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()
[docs] 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()
[docs] def fix_element_orientation(self): """ Ensure element vertices ordering giving positive cell volumes. """ from sfepy.discrete.common.extmods.cmesh import orient_elements if self.cmesh.tdim != self.cmesh.dim: output('warning: mesh with topological dimension %d lower than' ' space dimension %d' % (self.cmesh.tdim, self.cmesh.dim)) output('- element orientation not checked!') return cmesh = self.cmesh for key, gel in six.iteritems(self.geom_els): ori = gel.orientation cells = nm.where(cmesh.cell_types == cmesh.key_to_index[]) cells = cells[0].astype(nm.uint32) itry = 0 while itry < 2: flag = -nm.ones(self.cmesh.n_el, dtype=nm.int32) # Changes orientation if it is wrong according to swap*! # Changes are indicated by positive flag. orient_elements(flag, self.cmesh, cells, gel.dim, 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! (%s)' % key) elif flag[0] == -1: output('warning: element orienation not checked')
[docs] def get_conn(self, ret_gel=False): """ Get the cell-vertex connectivity and, if `ret_gel` is True, also the corresponding reference geometry element. """ conn = self.cmesh.get_conn(self.cmesh.tdim, 0).indices conn = conn.reshape((self.cmesh.n_el, -1)).astype(nm.int32) if ret_gel: gel = list(self.geom_els.values())[0] return conn, gel else: return conn
[docs] def get_element_diameters(self, cells, vg, mode, square=True): diameters = nm.empty((len(cells), 1, 1, 1), dtype=nm.float64) if vg is None: diameters.fill(1.0) else: conn, gel = self.get_conn(ret_gel=True) vg.get_element_diameters(diameters, gel.edges, self.get_mesh_coors().copy(), conn, cells.astype(nm.int32), mode) if square: out = diameters.squeeze() else: out = nm.sqrt(diameters.squeeze()) return out
[docs] def clear_surface_groups(self): """ Remove surface group data. """ self.surface_groups = {}
[docs] 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.discrete.fem.mappings.SurfaceMapping`. """ groups = self.surface_groups if not in groups: conn, gel = self.get_conn(ret_gel=True) gel_faces = gel.get_surface_entities() name = 'surface_group_%s' % ( surface_group = FESurface(name, region, gel_faces, conn) groups[] = surface_group
[docs] def refine(self): """ Uniformly refine the domain mesh. Returns ------- domain : FEDomain instance The new domain with the refined mesh. Notes ----- Works only for meshes with single element type! Does not preserve node groups! """ if len(self.geom_els) != 1: msg = 'refine() works only for meshes with single element type!' raise NotImplementedError(msg) el_type = list(self.geom_els.values())[0].name if el_type == '1_2': mesh = refine_1_2(self.mesh) elif el_type == '2_3': mesh = refine_2_3(self.mesh) elif el_type == '2_4': mesh = refine_2_4(self.mesh) elif el_type == '3_4': mesh = refine_3_4(self.mesh) elif el_type == '3_8': mesh = refine_3_8(self.mesh) else: msg = 'unsupported element type! (%s)' % el_type raise NotImplementedError(msg) domain = FEDomain( + '_r', mesh) return domain