Source code for sfepy.discrete.fem.fields_base


Important attributes of continuous (order > 0) :class:`Field` and
:class:`SurfaceField` instances:

- `vertex_remap` : `econn[:, :n_vertex] = vertex_remap[conn]`
- `vertex_remap_i` : `conn = vertex_remap_i[econn[:, :n_vertex]]`

where `conn` is the mesh vertex connectivity, `econn` is the
region-local field connectivity.
from __future__ import absolute_import
import numpy as nm

from sfepy.base.base import output, get_default, assert_
from sfepy.base.base import Struct
from sfepy.base.timing import Timer
from sfepy.discrete.common.fields import parse_shape, Field
from sfepy.discrete import PolySpace
from sfepy.discrete.fem.mesh import Mesh
from sfepy.discrete.fem.meshio import convert_complex_output
from sfepy.discrete.fem.utils import (extend_cell_data, prepare_remap,
                                      invert_remap, get_min_value)
from sfepy.discrete.fem.mappings import FEMapping
from sfepy.discrete.fem.fe_surface import FESurface, FEPhantomSurface
from sfepy.discrete.integrals import Integral
from sfepy.discrete.fem.linearizer import (get_eval_dofs, get_eval_coors,

def _find_geometry(region):
    cmesh = region.cmesh
    if region.kind == 'cell':
        ct = cmesh.cell_types
        for _gel in region.domain.geom_els.values():
            if (ct[region.cells] == cmesh.key_to_index[]).all():
                gel = _gel
            raise ValueError(f'region {} of contains multiple'
                             ' reference geometries!')

        is_surface = False

    elif region.kind == 'facet':
        for _gel in region.domain.geom_els.values():
            gel = _gel.surface_facet

        if gel is None:
            raise ValueError('cells with no surface!')

        is_surface = True

        raise ValueError('cannot find geometry element for region'
                         f' {} of kind {region.kind}, '
                         f'"region.kind" must be "cell" or "facet"!')

    return gel, is_surface

[docs] def set_mesh_coors(domain, fields, coors, update_fields=False, actual=False, clear_all=True, extra_dofs=False): if actual: if not hasattr(domain.mesh, 'coors_act'): domain.mesh.coors_act = nm.zeros_like(domain.mesh.coors) domain.mesh.coors_act[:] = coors[:domain.mesh.n_nod] else: domain.cmesh.coors[:] = coors[:domain.mesh.n_nod] if update_fields: for field in fields.values(): field.set_coors(coors, extra_dofs=extra_dofs) field.clear_mappings(clear_all=clear_all)
[docs] def eval_nodal_coors(coors, mesh_coors, region, poly_space, geom_poly_space, econn, only_extra=True): """ Compute coordinates of nodes corresponding to `poly_space`, given mesh coordinates and `geom_poly_space`. """ if only_extra: iex = (poly_space.nts[:, 0] > 0).nonzero()[0] if iex.shape[0] == 0: return qp_coors = poly_space.node_coors[iex, :] econn = econn[:, iex].copy() else: qp_coors = poly_space.node_coors ## # Evaluate geometry interpolation base functions in (extra) nodes. bf = geom_poly_space.eval_base(qp_coors) bf = bf[:, 0, :].copy() ## # Evaluate extra coordinates with 'bf'. cmesh = region.cmesh conn = cmesh.get_incident(0, region.cells, region.tdim) conn.shape = (econn.shape[0], -1) ecoors =, mesh_coors[conn]) coors[econn] = nm.swapaxes(ecoors, 0, 1)
def _interp_to_faces(vertex_vals, bfs, faces): dim = vertex_vals.shape[1] n_face = faces.shape[0] n_qp = bfs.shape[0] faces_vals = nm.zeros((n_face, n_qp, dim), nm.float64) for ii, face in enumerate(faces): vals = vertex_vals[face, :dim] faces_vals[ii, :, :] =[:, 0, :], vals) return(faces_vals)
[docs] def get_eval_expression(expression, fields, materials, variables, functions=None, mode='eval', term_mode=None, extra_args=None, verbose=True, kwargs=None): """ Get the function for evaluating an expression given a list of elements, and reference element coordinates. """ from sfepy.discrete.evaluate import eval_in_els_and_qp def _eval(iels, coors): val = eval_in_els_and_qp(expression, iels, coors, fields, materials, variables, functions=functions, mode=mode, term_mode=term_mode, extra_args=extra_args, verbose=verbose, kwargs=kwargs) return val[..., 0] return _eval
[docs] def create_expression_output(expression, name, primary_field_name, fields, materials, variables, functions=None, mode='eval', term_mode=None, extra_args=None, verbose=True, kwargs=None, min_level=0, max_level=1, eps=1e-4): """ Create output mesh and data for the expression using the adaptive linearizer. Parameters ---------- expression : str The expression to evaluate. name : str The name of the data. primary_field_name : str The name of field that defines the element groups and polynomial spaces. fields : dict The dictionary of fields used in `variables`. materials : Materials instance The materials used in the expression. variables : Variables instance The variables used in the expression. functions : Functions instance, optional The user functions for materials etc. mode : one of 'eval', 'el_avg', 'qp' The evaluation mode - 'qp' requests the values in quadrature points, 'el_avg' element averages and 'eval' means integration over each term region. term_mode : str The term call mode - some terms support different call modes and depending on the call mode different values are returned. extra_args : dict, optional Extra arguments to be passed to terms in the expression. verbose : bool If False, reduce verbosity. kwargs : dict, optional The variables (dictionary of (variable name) : (Variable instance)) to be used in the expression. min_level : int The minimum required level of mesh refinement. max_level : int The maximum level of mesh refinement. eps : float The relative tolerance parameter of mesh adaptivity. Returns ------- out : dict The output dictionary. """ field = fields[primary_field_name] vertex_coors = field.coors[:field.n_vertex_dof, :] ps = field.poly_space gps = field.gel.poly_space vertex_conn = field.econn[:, :field.gel.n_vertex] eval_dofs = get_eval_expression(expression, fields, materials, variables, functions=functions, mode=mode, extra_args=extra_args, verbose=verbose, kwargs=kwargs) eval_coors = get_eval_coors(vertex_coors, vertex_conn, gps) (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, vertex_conn.shape[0], ps, min_level=min_level, max_level=max_level, eps=eps) mesh = Mesh.from_data('linearized_mesh', coors, None, [conn], [mat_ids], field.domain.mesh.descs) out = {} out[name] = Struct(name='output_data', mode='vertex', data=vdofs, var_name=name, dofs=None, mesh=mesh, level=level) out = convert_complex_output(out) return out
[docs] class FEField(Field): """ Base class for finite element fields. Notes ----- - interps and hence node_descs are per region (must have single geometry!) Field shape information: - ``shape`` - the shape of the base functions in a point - ``n_components`` - the number of DOFs per FE node - ``val_shape`` - the shape of field value (the product of DOFs and base functions) in a point """ def __init__(self, name, dtype, shape, region, approx_order=1): """ Create a finite element field. Parameters ---------- name : str The field name. dtype : numpy.dtype The field data type: float64 or complex128. shape : int/tuple/str The field shape: 1 or (1,) or 'scalar', space dimension (2, or (2,) or 3 or (3,)) or 'vector', or a tuple. The field shape determines the shape of the FE base functions and is related to the number of components of variables and to the DOF per node count, depending on the field kind. region : Region The region where the field is defined. approx_order : int or tuple The FE approximation order. The tuple form is (order, has_bubble), e.g. (1, True) means order 1 with a bubble function. Notes ----- Assumes one cell type for the whole region! """ field_dim = region.field_dim if hasattr(region, 'field_dim')\ else region.domain.shape.dim shape = parse_shape(shape, field_dim) Struct.__init__(self, name=name, dtype=dtype, shape=shape, region=region) self.domain = self.region.domain self.cmesh = self.region.cmesh self._set_approx_order(approx_order) self.gel, self.is_surface = _find_geometry(self.region) self._setup_kind() self._setup_shape() self.extra_data = {} self.ori = None self._create_interpolant() self._setup_global_base() self.setup_coors() self.clear_mappings(clear_all=True) self.clear_qp_base() self.basis_transform = None self.econn0 = None self.unused_dofs = None self.stored_subs = None def _set_approx_order(self, approx_order): """ Set a uniform approximation order. """ if isinstance(approx_order, tuple): self.approx_order = approx_order[0] self.force_bubble = approx_order[1] else: self.approx_order = approx_order self.force_bubble = False def _create_interpolant(self): name = '%s_%s_%s_%d%s' % (,, self.poly_space_base, self.approx_order, 'B' * self.force_bubble) ps = PolySpace.any_from_args(name, self.gel, self.approx_order, base=self.poly_space_base, force_bubble=self.force_bubble) self.poly_space = ps
[docs] def get_true_order(self): """ Get the true approximation order depending on the reference element geometry. For example, for P1 (linear) approximation the true order is 1, while for Q1 (bilinear) approximation in 2D the true order is 2. """ gel = self.gel if (gel.dim + 1) == gel.n_vertex: order = self.approx_order else: order = gel.dim * self.approx_order if self.force_bubble: bubble_order = gel.dim + 1 order = max(order, bubble_order) return order
[docs] def is_higher_order(self): """ Return True, if the field's approximation order is greater than one. """ return self.force_bubble or (self.approx_order > 1)
def _setup_global_base(self): """ Setup global DOF/base functions, their indices and connectivity of the field. Called methods implemented in subclasses. """ self._setup_facet_orientations() self._init_econn() self.n_vertex_dof, self.vertex_remap = self._setup_vertex_dofs() self.vertex_remap_i = invert_remap(self.vertex_remap) aux = self._setup_edge_dofs() self.n_edge_dof, self.edge_dofs, self.edge_remap = aux aux = self._setup_face_dofs() self.n_face_dof, self.face_dofs, self.face_remap = aux aux = self._setup_bubble_dofs() self.n_bubble_dof, self.bubble_dofs, self.bubble_remap = aux self.n_nod = (self.n_vertex_dof + self.n_edge_dof + self.n_face_dof + self.n_bubble_dof) self._setup_esurface() def _init_econn(self): """ Initialize the extended DOF connectivity. """ n_ep = self.poly_space.n_nod n_cell = self.region.get_n_cells(is_surface=self.is_surface) self.econn = nm.zeros((n_cell, n_ep), nm.int32) def _setup_vertex_dofs(self): """ Setup vertex DOF connectivity. """ if self.node_desc.vertex is None: return 0, None region = self.region remap = prepare_remap(region.vertices, region.n_v_max) n_dof = region.vertices.shape[0] # Remap vertex node connectivity to field-local numbering. if self.is_surface: aux = FESurface.from_region('aux', region) self.econn[:, :aux.n_fp] = aux.leconn self.extra_data[f'sd_{}'] = aux else: conn = self.domain.get_conn(tdim=region.tdim, cells=region.cells) self.econn[:, :conn.shape[1]] = nm.take(remap, conn) return n_dof, remap def _setup_esurface(self): """ Setup extended surface entities (edges in 2D, faces in 3D), i.e. indices of surface entities into the extended connectivity. """ node_desc = self.node_desc gel = self.gel self.efaces = gel.get_surface_entities().copy() nd = node_desc.edge if nd is not None: efs = [] for eof in gel.get_edges_per_face(): efs.append(nm.concatenate([nd[ie] for ie in eof])) efs = nm.array(efs).squeeze() if efs.ndim < 2: efs = efs[:, nm.newaxis] self.efaces = nm.hstack((self.efaces, efs)) efs = node_desc.face if efs is not None: efs = nm.array(efs).squeeze() if efs.ndim < 2: efs = efs[:, nm.newaxis] self.efaces = nm.hstack((self.efaces, efs)) if gel.dim == 3: self.eedges = gel.edges.copy() efs = node_desc.edge if efs is not None: efs = nm.array(efs).squeeze() if efs.ndim < 2: efs = efs[:, nm.newaxis] self.eedges = nm.hstack((self.eedges, efs))
[docs] def set_coors(self, coors, extra_dofs=False): """ Set coordinates of field nodes. """ # Mesh vertex nodes. if self.n_vertex_dof: indx = self.vertex_remap_i self.coors[:self.n_vertex_dof] = nm.take(coors, indx.astype(nm.int32), axis=0) n_ex_dof = self.n_bubble_dof + self.n_edge_dof + self.n_face_dof # extra nodes if n_ex_dof: if extra_dofs: if self.n_nod != coors.shape[0]: raise NotImplementedError self.coors[:] = coors else: gps = self.gel.poly_space ps = self.poly_space eval_nodal_coors(self.coors, coors, self.region, ps, gps, self.econn)
[docs] def setup_coors(self): """ Setup coordinates of field nodes. """ mesh = self.domain.mesh self.coors = nm.empty((self.n_nod, mesh.dim), nm.float64) self.set_coors(mesh.coors)
[docs] def get_vertices(self): """ Return indices of vertices belonging to the field region. """ return self.vertex_remap_i
def _get_facet_dofs(self, rfacets, remap, dofs): facets = remap[rfacets] return dofs[facets[facets >= 0]].ravel()
[docs] def get_data_shape(self, integral, integration='cell', region_name=None): """ Get element data dimensions. Parameters ---------- integral : Integral instance The integral describing used numerical quadrature. integration : 'cell', 'facet', 'facet_extra', 'point' or 'custom' The term integration mode. region_name : str The name of the region of the integral. Returns ------- data_shape : 4 ints The `(n_el, n_qp, dim, n_en)` for volume shape kind, `(n_fa, n_qp, dim, n_fn)` for surface shape kind and `(n_nod, 0, 0, 1)` for point shape kind. Notes ----- Integration modes: - 'cell': integration over cells/elements - 'facet': integration over cell facets (faces, edges) - 'facet_extra': same as 'facet' but also the normal derivatives are evaluated - 'point': point integration - 'custom': user defined integration Dimensions: - `n_el`, `n_fa` = number of elements/facets - `n_qp` = number of quadrature points per element/facet - `dim` = spatial dimension - `n_en`, `n_fn` = number of element/facet nodes - `n_nod` = number of element nodes """ region = self.domain.regions[region_name] shape = region.shape dim = region.field_dim if hasattr(region, 'field_dim') else region.dim if integration is None: integration == region.kind if 'facet' in integration: name = f'sd_{region_name}' if name not in self.extra_data: reg = self.domain.regions[region_name] self.domain.create_surface_group(reg) self.setup_surface_data(reg, None) sd = self.extra_data[name] # This works also for surface fields. key = sd.face_type weights = self.get_qp(key, integral).weights n_qp = weights.shape[0] if integration == 'facet_extra': data_shape = (sd.n_fa, n_qp, dim, self.econn.shape[1]) else: data_shape = (sd.n_fa, n_qp, dim, sd.n_fp) elif (integration == 'cell' and self.region.tdim > 1 and region.tdim == 1): data_shape = (shape.n_cell, 0, dim, 2) # bar elements elif integration in ('cell', 'custom'): _, weights = integral.get_qp( n_qp = weights.shape[0] data_shape = (shape.n_cell, n_qp, dim, self.econn.shape[1]) elif integration == 'point': dofs = self.get_dofs_in_region(region, merge=True) data_shape = (dofs.shape[0], 0, 0, 1) else: raise NotImplementedError('unsupported integration type! (%s)' % integration) return data_shape
[docs] def get_dofs_in_region(self, region, merge=True): """ Return indices of DOFs that belong to the given region. """ node_desc = self.node_desc dofs = [] vdofs = nm.empty((0,), dtype=nm.int32) if node_desc.vertex is not None: vdofs = self.vertex_remap[region.vertices] vdofs = vdofs[vdofs >= 0] dofs.append(vdofs) edofs = nm.empty((0,), dtype=nm.int32) if node_desc.edge is not None: edofs = self._get_facet_dofs(region.edges, self.edge_remap, self.edge_dofs) dofs.append(edofs) fdofs = nm.empty((0,), dtype=nm.int32) if node_desc.face is not None: fdofs = self._get_facet_dofs(region.faces, self.face_remap, self.face_dofs) dofs.append(fdofs) bdofs = nm.empty((0,), dtype=nm.int32) if (node_desc.bubble is not None) and region.has_cells(): els = self.bubble_remap[region.cells] bdofs = self.bubble_dofs[els[els >= 0]].ravel() dofs.append(bdofs) if merge: dofs = nm.concatenate(dofs) return dofs
[docs] def clear_qp_base(self): """ Remove cached quadrature points and base functions. """ self.qp_coors = {} = {}
[docs] def get_qp(self, key, integral): """ Get quadrature points and weights corresponding to the given key and integral. The key is 'v', 's#' or 'b#', where # is the number of face vertices. For 'b#', the quadrature must already be created by calling :func:`FEField.create_bqp()`, usually through :func:`FEField.create_mapping()`. """ qpkey = (integral.order, key) if qpkey not in self.qp_coors: if key[0] == 'b': raise ValueError(f'the quadrature "{qpkey}" does not exist!') if (key[0] == 's') and not self.is_surface: dim = self.gel.dim - 1 if isinstance(self.gel.surface_facet, dict): n_fp = int(key[1:]) else: n_fp = self.gel.surface_facet.n_vertex geometry = '%d_%d' % (dim, n_fp) else: geometry = vals, weights = integral.get_qp(geometry) self.qp_coors[qpkey] = Struct(vals=vals, weights=weights) return self.qp_coors[qpkey]
[docs] def substitute_dofs(self, subs, restore=False): """ Perform facet DOF substitutions according to `subs`. Modifies `self.econn` in-place and sets `self.econn0`, `self.unused_dofs` and `self.basis_transform`. """ if restore and (self.stored_subs is not None): self.econn0 = self.econn self.econn, self.unused_dofs, basis_transform = self.stored_subs else: if subs is None: self.econn0 = self.econn return else: self.econn0 = self.econn.copy() self._substitute_dofs(subs) self.unused_dofs = nm.setdiff1d(self.econn0, self.econn) basis_transform = self._eval_basis_transform(subs) self.set_basis_transform(basis_transform)
[docs] def restore_dofs(self, store=False): """ Undoes the effect of :func:`FEField.substitute_dofs()`. """ if self.econn0 is None: raise ValueError('no original DOFs to restore!') if store: self.stored_subs = (self.econn, self.unused_dofs, self.basis_transform) else: self.stored_subs = None self.econn = self.econn0 self.econn0 = None self.unused_dofs = None self.basis_transform = None
[docs] def set_basis_transform(self, transform): """ Set local element basis transformation. The basis transformation is applied in :func:`FEField.get_base()` and :func:`FEField.create_mapping()`. Parameters ---------- transform : array, shape `(n_cell, n_ep, n_ep)` The array with `(n_ep, n_ep)` transformation matrices for each cell in the field's region, where `n_ep` is the number of element DOFs. """ self.basis_transform = transform
[docs] def restore_substituted(self, vec): """ Restore values of the unused DOFs using the transpose of the applied basis transformation. """ if (self.econn0 is None) or (self.basis_transform is None): raise ValueError('no original DOF values to restore!!') vec = vec.reshape((self.n_nod, self.n_components)).copy() evec = vec[self.econn] vec[self.econn0] = nm.einsum('cji,cjk->cik', self.basis_transform, evec, optimize=True) return vec.ravel()
[docs] def get_base(self, key, derivative, integral, iels=None, from_geometry=False, base_only=True): qp = self.get_qp(key, integral) if from_geometry: ps = self.gel.poly_space else: ps = self.poly_space _key = key if not from_geometry else 'g' + key bf_key = (integral.order, _key, derivative) if bf_key not in ori = self.ori[bf_key] = ps.eval_base(qp.vals, diff=derivative, ori=ori, transform=self.basis_transform) bf =[bf_key] if iels is not None and bf.ndim == 4: bf = bf[iels] if base_only: return bf else: return bf, qp.weights
[docs] def create_bqp(self, region_name, integral): gel = self.gel sd = self.extra_data[f'sd_{region_name}'] bqpkey = (integral.order, sd.bkey) if bqpkey not in self.qp_coors: qp = self.get_qp(sd.face_type, integral) ps_s = self.gel.surface_facet.poly_space bf_s = ps_s.eval_base(qp.vals) coors, faces = gel.coors, gel.get_surface_entities() vals = _interp_to_faces(coors, bf_s, faces) self.qp_coors[bqpkey] = Struct(name='BQP_%s' % sd.bkey, vals=vals, weights=qp.weights)
[docs] def create_bqp_key(self, integral, bkey): gel = self.gel sd_bkey, face_type = f'b{bkey}', f's{bkey}' bqpkey = (integral.order, sd_bkey) if bqpkey not in self.qp_coors: qp = self.get_qp(face_type, integral) ps_s = self.gel.surface_facet[bkey].poly_space bf_s = ps_s.eval_base(qp.vals) coors, faces = gel.coors, gel.get_surface_entities() vals = _interp_to_faces(coors, bf_s, faces[:, :bf_s.shape[-1]]) self.qp_coors[bqpkey] = Struct(name=f'BQP_{sd_bkey}', vals=vals, weights=qp.weights)
[docs] def extend_dofs(self, dofs, fill_value=None): """ Extend DOFs to the whole domain using the `fill_value`, or the smallest value in `dofs` if `fill_value` is None. """ if fill_value is None: if nm.isrealobj(dofs): fill_value = get_min_value(dofs) else: # Complex values - treat real and imaginary parts separately. fill_value = get_min_value(dofs.real) fill_value += 1j * get_min_value(dofs.imag) if self.approx_order != 0: indx = self.get_vertices() n_nod = self.domain.shape.n_nod new_dofs = nm.empty((n_nod, dofs.shape[1]), dtype=self.dtype) new_dofs.fill(fill_value) new_dofs[indx] = dofs[:indx.size] else: new_dofs = extend_cell_data(dofs, self.domain, self.region, val=fill_value) return new_dofs
[docs] def remove_extra_dofs(self, dofs): """ Remove DOFs defined in higher order nodes (order > 1). """ if self.approx_order != 0: new_dofs = dofs[:self.n_vertex_dof] else: new_dofs = dofs return new_dofs
[docs] def linearize(self, dofs, min_level=0, max_level=1, eps=1e-4): """ Linearize the solution for post-processing. Parameters ---------- dofs : array, shape (n_nod, n_component) The array of DOFs reshaped so that each column corresponds to one component. min_level : int The minimum required level of mesh refinement. max_level : int The maximum level of mesh refinement. eps : float The relative tolerance parameter of mesh adaptivity. Returns ------- mesh : Mesh instance The adapted, nonconforming, mesh. vdofs : array The DOFs defined in vertices of `mesh`. levels : array of ints The refinement level used for each element group. """ assert_(dofs.ndim == 2) n_nod, dpn = dofs.shape assert_(n_nod == self.n_nod) assert_(dpn == self.shape[0]) vertex_coors = self.coors[:self.n_vertex_dof, :] ps = self.poly_space gps = self.gel.poly_space vertex_conn = self.econn[:, :self.gel.n_vertex] eval_dofs = get_eval_dofs(dofs, self.econn, ps, ori=self.ori) eval_coors = get_eval_coors(vertex_coors, vertex_conn, gps) (level, coors, conn, vdofs, mat_ids) = create_output(eval_dofs, eval_coors, vertex_conn.shape[0], ps, min_level=min_level, max_level=max_level, eps=eps) mesh = Mesh.from_data('linearized_mesh', coors, None, [conn], [mat_ids], self.domain.mesh.descs) return mesh, vdofs, level
[docs] def get_output_approx_order(self): """ Get the approximation order used in the output file. """ return min(self.approx_order, 1)
[docs] def create_output(self, dofs, var_name, dof_names=None, key=None, extend=True, fill_value=None, linearization=None): """ Convert the DOFs corresponding to the field to a dictionary of output data usable by Mesh.write(). Parameters ---------- dofs : array, shape (n_nod, n_component) The array of DOFs reshaped so that each column corresponds to one component. var_name : str The variable name corresponding to `dofs`. dof_names : tuple of str The names of DOF components. key : str, optional The key to be used in the output dictionary instead of the variable name. extend : bool Extend the DOF values to cover the whole domain. fill_value : float or complex The value used to fill the missing DOF values if `extend` is True. linearization : Struct or None The linearization configuration for higher order approximations. Returns ------- out : dict The output dictionary. """ linearization = get_default(linearization, Struct(kind='strip')) out = {} reg_name = if linearization.kind is None: out[key] = Struct(name='output_data', mode='full', data=dofs, var_name=var_name, region_name=reg_name, dofs=dof_names, elif linearization.kind == 'strip': if extend: ext = self.extend_dofs(dofs, fill_value) else: ext = self.remove_extra_dofs(dofs) if ext is not None: approx_order = self.get_output_approx_order() if approx_order != 0: # Has vertex data. out[key] = Struct(name='output_data', mode='vertex', data=ext, var_name=var_name, dofs=dof_names, region_name=reg_name) else: ext.shape = (ext.shape[0], 1, ext.shape[1], 1) out[key] = Struct(name='output_data', mode='cell', data=ext, var_name=var_name, dofs=dof_names, region_name=reg_name) else: mesh, vdofs, levels = self.linearize(dofs, linearization.min_level, linearization.max_level, linearization.eps) out[key] = Struct(name='output_data', mode='vertex', data=vdofs, var_name=var_name, dofs=dof_names, mesh=mesh, levels=levels, region_name=reg_name) out = convert_complex_output(out) return out
[docs] def create_mesh(self, extra_nodes=True): """ Create a mesh from the field region, optionally including the field extra nodes. """ mesh = self.domain.mesh if self.approx_order != 0: if extra_nodes: conn = self.econn else: conn = self.econn[:, :self.gel.n_vertex] conns = [conn] mat_ids = [self.cmesh.cell_groups] tdim = self.cmesh.tdim descs = f'{tdim}_{conn.shape[1]}' if descs not in mesh.descs: msg = f'element type {descs} not in mesh! ({mesh.descs})' raise ValueError(msg) if extra_nodes: coors = self.coors else: coors = self.coors[:self.n_vertex_dof] mesh = Mesh.from_data(, coors[:, :tdim], None, conns, mat_ids, [descs]) return mesh
[docs] def get_evaluate_cache(self, cache=None, share_geometry=False, verbose=False): """ Get the evaluate cache for :func:`Variable.evaluate_at() <sfepy.discrete.variables.Variable.evaluate_at()>`. Parameters ---------- cache : Struct instance, optional Optionally, use the provided instance to store the cache data. share_geometry : bool Set to True to indicate that all the evaluations will work on the same region. Certain data are then computed only for the first probe and cached. verbose : bool If False, reduce verbosity. Returns ------- cache : Struct instance The evaluate cache. """ try: from scipy.spatial import cKDTree as KDTree except ImportError: from scipy.spatial import KDTree from sfepy.discrete.fem.geometry_element import \ create_geometry_elements if cache is None: cache = Struct(name='evaluate_cache') timer = Timer(start=True) if (cache.get('cmesh', None) is None) or not share_geometry: mesh = self.create_mesh(extra_nodes=False) cache.cmesh = cmesh = self.cmesh gels = create_geometry_elements() cmesh.set_local_entities(gels) cmesh.setup_entities() cache.centroids = cmesh.get_centroids(cmesh.tdim) if != '3_8': cache.normals0 = cmesh.get_facet_normals() cache.normals1 = None else: cache.normals0 = cmesh.get_facet_normals(0) cache.normals1 = cmesh.get_facet_normals(1) output('cmesh setup: %f s' % timer.stop(), verbose=verbose) timer.start() if (cache.get('kdtree', None) is None) or not share_geometry: cache.kdtree = KDTree(cmesh.coors) output('kdtree: %f s' % timer.stop(), verbose=verbose) return cache
[docs] def interp_to_qp(self, dofs): """ Interpolate DOFs into quadrature points. The quadrature order is given by the field approximation order. Parameters ---------- dofs : array The array of DOF values of shape `(n_nod, n_component)`. Returns ------- data_qp : array The values interpolated into the quadrature points. integral : Integral The corresponding integral defining the quadrature points. """ integral = Integral('i', order=self.approx_order) bf = self.get_base('v', False, integral) bf = bf[:, 0, :].copy() data_qp =, dofs[self.econn]) data_qp = nm.swapaxes(data_qp, 0, 1) data_qp.shape = data_qp.shape + (1,) return data_qp, integral
[docs] def get_coor(self, nods=None): """ Get coordinates of the field nodes. Parameters ---------- nods : array, optional The indices of the required nodes. If not given, the coordinates of all the nodes are returned. """ if nods is None: return self.coors else: return self.coors[nods]
[docs] def get_econn(self, conn_type, region, trace_region=None, local=False): """ Get extended connectivity of the given type in the given region. Parameters ---------- conn_type: tuple or string DOF connectivity type, eg. ('cell', 3) or 'cell'. If the topological dimension not specified, it is taken from region.tdim. region: sfepy.discrete.common.region.Region The region for which the connectivity is required. trace_region: None or string If not None, return mirror connectivity according to `local`. local: bool If True, return local connectivity w.r.t. facet nodes, otherwise return global connectivity w.r.t. all mesh nodes. Returns ------- econn: numpy.ndarray The extended connectivity array. """ if isinstance(conn_type, tuple): integration, tdim = conn_type else: integration, tdim = conn_type, region.tdim if integration == 'cell' and tdim == 1 and self.region.tdim > 1: # bar elements conn = self.extra_data[f'bars_{}'] elif (integration in ('cell', 'custom')) and (trace_region is None): if == conn = self.econn else: tco = region.kind == 'cell' cells = region.get_cells(true_cells_only=tco) ii = self.region.get_cell_indices(cells, true_cells_only=tco) conn = nm.take(self.econn, ii, axis=0) elif integration == 'cell' and trace_region is not None: name = f'sd_{}' sd = self.extra_data[name] # FEPhantomSurface conn = sd.get_connectivity(local=local, trace_region=trace_region) elif integration == 'facet': name = f'sd_{}' if name not in self.extra_data: self.domain.create_surface_group(region) self.setup_surface_data(region) if self.is_surface: local = True sd = self.extra_data[name] conn = sd.get_connectivity(local=local, trace_region=trace_region) elif integration == 'point': conn = self.extra_data[f'pd_{}'] else: raise ValueError(f'unknown integration type! ({integration})') return conn
[docs] def setup_extra_data(self, info): for dct, tdim in set(info.dof_conn_types.values()): if dct == 'facet': reg = info.get_region() mreg_name = info.get_region_name(can_trace=False) mreg_name = None if == mreg_name else mreg_name self.domain.create_surface_group(reg) self.setup_surface_data(reg, mreg_name) elif dct == 'edge': raise NotImplementedError('dof connectivity type %s' % dct) elif dct == 'point': self.setup_point_data(self, info.region) elif dct == 'cell' and tdim == 1 and self.region.tdim > 1: # bar elements self.setup_bar_data(self, info.region) elif dct not in ('cell', 'custom'): raise ValueError('unknown dof connectivity type! (%s)' % dct)
[docs] def setup_surface_data(self, region, trace_region=None): """nodes[leconn] == econn""" """nodes are sorted by node number -> same order as region.vertices""" name = f'sd_{}' if name not in self.extra_data: if trace_region is not None and region.tdim == (region.dim - 1): sd = FEPhantomSurface(name, region, self.econn) else: sd = FESurface(name, region, self.efaces, self.econn, self.region) self.extra_data[name] = sd if name in self.extra_data and trace_region is not None: sd = self.extra_data[name] sd.setup_mirror_connectivity(region, trace_region)
[docs] def setup_point_data(self, field, region): name = f'pd_{}' if name not in self.extra_data: conn = field.get_dofs_in_region(region, merge=True) conn.shape += (1,) self.extra_data[name] = conn
[docs] def setup_bar_data(self, field, region): name = f'bars_{}' if name not in self.extra_data: conn = region.domain.get_conn(tdim=1)[region.cells] self.extra_data[name] = conn
[docs] def create_mapping(self, region, integral, integration, return_mapping=True): """ Create a new reference mapping. Compute jacobians, element volumes and base function derivatives for Volume-type geometries (volume mappings), and jacobians, normals and base function derivatives for Surface-type geometries (surface mappings). Notes ----- - surface mappings are defined on the surface region - surface mappings require field order to be > 0 """ domain = self.domain coors = domain.get_mesh_coors(actual=True) iels = region.get_cells(true_cells_only=(region.kind == 'cell')) transform = (self.basis_transform[iels] if self.basis_transform is not None else None) geo_ps = self.gel.poly_space ps = self.poly_space if region.kind == 'cell': qp = self.get_qp('v', integral) bf = self.get_base('v', 0, integral, iels=iels) dconn = domain.get_conn(tdim=region.tdim, cells=iels) mapping = FEMapping(coors, dconn, poly_space=geo_ps) out = mapping.get_mapping(qp.vals, qp.weights, bf, poly_space=ps, ori=self.ori, transform=transform) elif region.kind == 'facet': assert_(self.approx_order > 0) if self.ori is not None: msg = 'surface integrals do not work yet with the' \ ' hierarchical basis!' raise ValueError(msg) if self.basis_transform is not None: msg = 'surface integrals do not work with the' \ ' basis transform!' raise ValueError(msg) sd = domain.surface_groups[] esd = self.extra_data[f'sd_{}'] face_indices = region.get_facet_indices() cells = face_indices[:, 0] dconn = domain.get_conn(tdim=region.tdim, cells=cells) conn = sd.get_connectivity() mapping = FEMapping(coors, conn, poly_space=geo_ps) if not self.is_surface: if isinstance(ps.geometry.surface_facet, dict): if integration == 'facet_extra': msg = ('facet integration not supported for ' f'element type {}!') raise ValueError(msg) nfc, dim = self.gel.n_face, self.gel.coors.shape[1] bkeys = list(ps.geometry.surface_facet.keys()) for bkey in bkeys: self.create_bqp_key(integral, bkey) nqp = nm.max([integral.qps[f'{dim - 1}_{bkey}'].n_point for bkey in bkeys]) flag = ''.join(str(k) for k in bkeys) qp = Struct( name=f'BQP_b{flag}', vals=nm.zeros((nfc, nqp, dim), dtype=nm.float64), weights=nm.zeros((nfc, nqp), dtype=nm.float64) ) efc_map = nm.count_nonzero( nm.diff(nm.sort(self.gel.faces)), axis=1) + 1 indxs = {} fcaxes = {} ffcidxs = [] fc_map = efc_map[sd.fis[:, 1]] * (-1) for ikey, bkey in enumerate(bkeys): idx = efc_map == bkey qp0 = self.qp_coors[(integral.order, f'b{bkey}')] nqp0 = qp0.vals.shape[1] qp.vals[idx, :nqp0, :] = qp0.vals[idx] qp.weights[idx, :nqp0] = qp0.weights if qp0.weights.shape[0] < qp.weights.shape[1]: qp.weights[idx, qp0.weights.shape[0]:] = 0 ffcidx = nm.where(efc_map == bkey)[0][0] ffcidxs.append(ffcidx) indx = self.efaces[ffcidx] indx = nm.roll(indx[:bkey], -1)[::-1] indxs[ikey] = indx fcco = ps.geometry.coors[indx] fcax = [nm.where((fcco[1] - fcco[0]) == 1)[0][0], nm.where((fcco[-1] - fcco[0]) == 1)[0][0]] fcaxes[ikey] = fcax fc_map[fc_map == -bkey] = ikey abf = ps.eval_base(qp.vals, transform=transform) bf = nm.zeros((nfc, nqp, 1, max(bkeys)), dtype=nm.float64) for ifc, efc in enumerate(self.efaces): bkey = efc_map[ifc] bf[ifc, ..., :bkey] = abf[ifc, ...][..., efc[:bkey]] mapping.set_basis_indices(indxs) weights = nm.ascontiguousarray(qp.weights[ffcidxs][fc_map]) bf = nm.ascontiguousarray(bf[ffcidxs][fc_map]) out = mapping.get_mapping(qp.vals[ffcidxs], weights, bf, extra=(None, None, None), is_face=True, fc_bf_map=(fc_map, fcaxes)) else: self.create_bqp(, integral) qp = self.qp_coors[(integral.order, esd.bkey)] abf = ps.eval_base(qp.vals[0], transform=transform) bf = abf[..., self.efaces[0]] indx = self.gel.get_surface_entities()[0] # Fix geometry element's 1st facet orientation for gradients. indx = nm.roll(indx, -1)[::-1] mapping.set_basis_indices(indx) if integration == 'facet_extra': se_bf_bg = geo_ps.eval_base(qp.vals, diff=True) se_bf_bg = se_bf_bg[sd.fis[:, 1]] se_ebf_bg = self.get_base(esd.bkey, 1, integral) se_ebf_bg = se_ebf_bg[sd.fis[:, 1]] remap = prepare_remap(cells, cells.max() + 1) se_conn = dconn[remap[sd.fis[:, 0]], :] else: se_bf_bg, se_ebf_bg, se_conn = None, None, None out = mapping.get_mapping(qp.vals[0], qp.weights, bf, extra=(se_conn, se_bf_bg, se_ebf_bg), is_face=True) else: # Do not use BQP for surface fields. qp = self.get_qp(sd.face_type, integral) bf = ps.eval_base(qp.vals, transform=transform) out = mapping.get_mapping(qp.vals, qp.weights, bf, is_face=True) else: out = mapping = None if out is not None: # Store the integral used. out.integral = integral out.qp = qp = ps if return_mapping: out = (out, mapping) return out
[docs] def average_qp_to_vertices(self, data_qp, integral): r""" Average data given in quadrature points in region elements into region vertices. .. math:: u_n = \sum_e (u_{e,avg} * area_e) / \sum_e area_e = \sum_e \int_{area_e} u / \sum area_e """ region = self.region n_cells = region.get_n_cells(is_surface=self.is_surface) if n_cells != data_qp.shape[0]: msg = 'incomatible shape! (%d == %d)' % (n_cells, data_qp.shape[0]) raise ValueError(msg) n_vertex = self.n_vertex_dof nc = data_qp.shape[2] nod_vol = nm.zeros((n_vertex,), dtype=nm.float64) data_vertex = nm.zeros((n_vertex, nc), dtype=nm.float64) rg = self.get_mapping(self.region, integral, region.kind)[0] area = nm.squeeze(rg.volume) iels = self.region.get_cells() data_e = nm.zeros((area.shape[0], 1, nc, 1), dtype=nm.float64) rg.integrate(data_e, data_qp[iels]) ir = nm.arange(nc, dtype=nm.int32) if region.kind == 'cell': conn = self.econn[:, :self.gel.n_vertex] elif region.kind == 'facet': sd = self.domain.surface_groups[] # Should be vertex connectivity! conn = sd.get_connectivity(local=True) for ii, cc in enumerate(conn): # Assumes unique nodes in cc! ind2, ind1 = nm.meshgrid(ir, cc) data_vertex[ind1, ind2] += data_e[iels[ii], 0, :, 0] nod_vol[cc] += area[ii] data_vertex /= nod_vol[:, nm.newaxis] return data_vertex
def _setup_bubble_dofs(self): """ Setup bubble DOF connectivity for surface field. """ if self.is_surface: return 0, None, None
[docs] class H1Mixin(Struct): """ Methods of fields specific to H1 space. """ def _setup_shape(self): """ Setup the field's shape-related attributes, see :class:`Field`. """ self.n_components = self.val_shape = self.shape