def _setup_vertex_dofs(self):
"""
Setup vertex DOF connectivity.
"""
if self.node_desc.vertex is None:
return 0, None
region = self.region
cmesh = self.domain.cmesh
conn, offsets = cmesh.get_incident(0,
region.cells,
region.tdim,
ret_offsets=True)
vertices = nm.unique(conn)
remap = prepare_remap(vertices, region.n_v_max)
n_dof = vertices.shape[0]
aux = nm.unique(nm.diff(offsets))
assert_(len(aux) == 1, 'region with multiple reference geometries!')
offset = aux[0]
# Remap vertex node connectivity to field-local numbering.
aux = conn.reshape((-1, offset)).astype(nm.int32)
self.econn[:, :offset] = nm.take(remap, aux)
return n_dof, remap
def _setup_global_base(self):
"""
Setup global DOF/base function indices and connectivity of the field.
"""
self._setup_facet_orientations()
self._init_econn()
ii = self.region.get_cells()
self.bubble_remap = prepare_remap(ii, self.domain.cmesh.n_el)
n_dof = nm.prod(self.econn.shape)
all_dofs = nm.arange(n_dof, dtype=nm.int32)
all_dofs.shape = self.econn.shape
self.econn[:] = all_dofs
self.n_nod = n_dof
self.n_bubble_dof = n_dof
self.bubble_dofs = all_dofs
self.n_vertex_dof = self.n_edge_dof = self.n_face_dof = 0
self._setup_esurface()
def _setup_vertex_dofs(self):
"""
Setup vertex DOF connectivity.
"""
if self.node_desc.vertex is None:
return 0, None
region = self.region
vertices = region.get_vertices_of_cells()
remap = prepare_remap(vertices, region.n_v_max)
n_dof = vertices.shape[0]
##
# Remap vertex node connectivity to field-local numbering.
for ig, ap in self.aps.iteritems():
group = self.domain.groups[ig]
offset = group.shape.n_ep
cells = region.get_cells(ig)
ap.econn[:,:offset] = nm.take(remap,
nm.take(group.conn,
cells.astype(nm.int32),
axis=0))
return n_dof, remap
def _setup_vertex_dofs(self):
"""
Setup vertex DOF connectivity.
"""
if self.node_desc.vertex is None:
return 0, None
region = self.region
vertices = region.get_vertices_of_cells()
remap = prepare_remap(vertices, region.n_v_max)
n_dof = vertices.shape[0]
##
# Remap vertex node connectivity to field-local numbering.
for ig, ap in self.aps.iteritems():
group = self.domain.groups[ig]
offset = group.shape.n_ep
cells = region.get_cells(ig)
ap.econn[:,:offset] = nm.take(remap,
nm.take(group.conn,
cells.astype(nm.int32),
axis=0))
return n_dof, remap
def _setup_bubble_dofs(self):
"""
Setup bubble DOF connectivity.
"""
if self.node_desc.bubble is None:
return 0, None, None
offset = self.n_vertex_dof + self.n_edge_dof + self.n_face_dof
n_dof = 0
n_dof_per_cell = self.node_desc.bubble.shape[0]
all_dofs = {}
remaps = {}
for ig, ap in self.aps.iteritems():
ii = self.region.get_cells(ig)
n_cell = ii.shape[0]
nd = n_dof_per_cell * n_cell
group = self.domain.groups[ig]
remaps[ig] = prepare_remap(ii, group.shape.n_el)
aux = nm.arange(offset + n_dof, offset + n_dof + nd,
dtype=nm.int32)
aux.shape = (n_cell, n_dof_per_cell)
iep = self.node_desc.bubble[0]
ap.econn[:,iep:] = aux
all_dofs[ig] = aux
n_dof += nd
return n_dof, all_dofs, remaps
def _setup_global_base(self):
"""
Setup global DOF/base function indices and connectivity of the field.
"""
self._setup_facet_orientations()
self._init_econn()
ii = self.region.get_cells()
self.bubble_remap = prepare_remap(ii, self.domain.cmesh.n_el)
n_dof = nm.prod(self.econn.shape)
all_dofs = nm.arange(n_dof, dtype=nm.int32)
all_dofs.shape = self.econn.shape
self.econn[:] = all_dofs
self.n_nod = n_dof
self.n_bubble_dof = n_dof
self.bubble_dofs = all_dofs
self.n_vertex_dof = self.n_edge_dof = self.n_face_dof = 0
self._setup_esurface()
def _setup_bubble_dofs(self):
"""
Setup bubble DOF connectivity.
"""
if self.node_desc.bubble is None:
return 0, None, None
offset = self.n_vertex_dof + self.n_edge_dof + self.n_face_dof
n_dof = 0
n_dof_per_cell = self.node_desc.bubble.shape[0]
all_dofs = {}
remaps = {}
for ig, ap in self.aps.iteritems():
ii = self.region.get_cells(ig)
n_cell = ii.shape[0]
nd = n_dof_per_cell * n_cell
group = self.domain.groups[ig]
remaps[ig] = prepare_remap(ii, group.shape.n_el)
aux = nm.arange(offset + n_dof,
offset + n_dof + nd,
dtype=nm.int32)
aux.shape = (n_cell, n_dof_per_cell)
iep = self.node_desc.bubble[0]
ap.econn[:, iep:] = aux
all_dofs[ig] = aux
n_dof += nd
return n_dof, all_dofs, remaps
def _setup_global_base( self ):
"""
Setup global DOF/base function indices and connectivity of the field.
"""
self._setup_facet_orientations()
self._init_econn()
n_dof = 0
all_dofs = {}
remaps = {}
for ig, ap in self.aps.iteritems():
ii = self.region.get_cells(ig)
nd = nm.prod(ap.econn.shape)
group = self.domain.groups[ig]
remaps[ig] = prepare_remap(ii, group.shape.n_el)
aux = nm.arange(n_dof, n_dof + nd, dtype=nm.int32)
aux.shape = ap.econn.shape
ap.econn[:] = aux
all_dofs[ig] = aux
n_dof += nd
self.n_nod = n_dof
self.n_bubble_dof = n_dof
self.bubble_dofs = all_dofs
self.bubble_remaps = remaps
self.n_vertex_dof = self.n_edge_dof = self.n_face_dof = 0
self._setup_esurface()
def _setup_vertex_dofs(self):
"""
Setup vertex DOF connectivity.
"""
if self.node_desc.vertex is None:
return 0, None
region = self.region
cmesh = self.domain.cmesh
conn, offsets = cmesh.get_incident(0, region.cells, region.tdim,
ret_offsets=True)
vertices = nm.unique(conn)
remap = prepare_remap(vertices, region.n_v_max)
n_dof = vertices.shape[0]
aux = nm.unique(nm.diff(offsets))
assert_(len(aux) == 1, 'region with multiple reference geometries!')
offset = aux[0]
# Remap vertex node connectivity to field-local numbering.
aux = conn.reshape((-1, offset)).astype(nm.int32)
self.econn[:, :offset] = nm.take(remap, aux)
return n_dof, remap
def _setup_global_base(self):
"""
Setup global DOF/base function indices and connectivity of the field.
"""
self._setup_facet_orientations()
self._init_econn()
n_dof = 0
all_dofs = {}
remaps = {}
for ig, ap in self.aps.iteritems():
ii = self.region.get_cells(ig)
nd = nm.prod(ap.econn.shape)
group = self.domain.groups[ig]
remaps[ig] = prepare_remap(ii, group.shape.n_el)
aux = nm.arange(n_dof, n_dof + nd, dtype=nm.int32)
aux.shape = ap.econn.shape
ap.econn[:] = aux
all_dofs[ig] = aux
n_dof += nd
self.n_nod = n_dof
self.n_bubble_dof = n_dof
self.bubble_dofs = all_dofs
self.bubble_remaps = remaps
self.n_vertex_dof = self.n_edge_dof = self.n_face_dof = 0
self._setup_esurface()
def __init__(self, name, nurbs, bmesh, regions=None, **kwargs):
"""
Create an IGA domain.
Parameters
----------
name : str
The domain name.
"""
Domain.__init__(self, name, nurbs=nurbs, bmesh=bmesh, regions=regions,
**kwargs)
from sfepy.discrete.fem.geometry_element import create_geometry_elements
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.extmods.cmesh import CMesh
from sfepy.discrete.fem.utils import prepare_remap
ac = nm.ascontiguousarray
self.nurbs.cs = [ac(nm.array(cc, dtype=nm.float64)[:, None, ...])
for cc in self.nurbs.cs]
self.nurbs.degrees = self.nurbs.degrees.astype(nm.int32)
self.facets = iga.get_bezier_element_entities(nurbs.degrees)
tconn = iga.get_bezier_topology(bmesh.conn, nurbs.degrees)
itc = nm.unique(tconn)
remap = prepare_remap(itc, bmesh.conn.max() + 1)
ltcoors = bmesh.cps[itc]
ltconn = remap[tconn]
n_nod, dim = ltcoors.shape
n_el = ltconn.shape[0]
self.shape = Struct(n_nod=n_nod, dim=dim, tdim=0, n_el=n_el, n_gr=1)
desc = '%d_%d' % (dim, 2**dim)
mat_id = nm.zeros(ltconn.shape[0], dtype=nm.int32)
self.mesh = Mesh.from_data(self.name + '_topo', ltcoors, None, [ltconn],
[mat_id], [desc])
self.cmesh = CMesh.from_mesh(self.mesh)
gels = create_geometry_elements()
self.cmesh.set_local_entities(gels)
self.cmesh.setup_entities()
self.shape.tdim = self.cmesh.tdim
self.gel = gels[desc]
if regions is not None:
self.vertex_set_bcs = {}
for key, val in self.regions.iteritems():
self.vertex_set_bcs[key] = remap[val]
self.cell_offsets = {0 : 0}
self.reset_regions()
def __init__(self, name, region, efaces, volume_econn, volume_region=None):
"""nodes[leconn] == econn"""
"""nodes are sorted by node number -> same order as region.vertices"""
self.name = get_default(name, 'surface_data_%s' % region.name)
face_indices = region.get_facet_indices()
faces = efaces[face_indices[:,1]]
if faces.size == 0 and not region.is_empty:
raise ValueError('region with no faces! (%s)' % region.name)
if volume_region is None:
ii = face_indices[:, 0]
else:
ii = volume_region.get_cell_indices(face_indices[:, 0])
try:
ee = volume_econn[ii]
except:
raise ValueError('missing region face indices! (%s)'
% region.name)
econn = nm.empty(faces.shape, dtype=nm.int32)
for ir, face in enumerate( faces ):
econn[ir] = ee[ir,face]
nodes = nm.unique(econn)
if len(nodes):
remap = prepare_remap(nodes, nodes.max() + 1)
leconn = remap[econn].copy()
else:
leconn = econn.copy()
n_fa, n_fp = face_indices.shape[0], faces.shape[1]
face_type = 's%d' % n_fp
# Store bkey in SurfaceData, so that base function can be
# queried later.
bkey = 'b%s' % face_type[1:]
self.econn = econn
self.fis = nm.ascontiguousarray(face_indices.astype(nm.int32))
self.n_fa, self.n_fp = n_fa, n_fp
self.nodes = nodes
self.leconn = leconn
self.face_type = face_type
self.bkey = bkey
self.meconn = self.mleconn = None
if self.n_fp <= 4:
self.ori_map, _, _ = build_orientation_map(self.n_fp)
else:
self.ori_map = None
def __init__(self, name, nurbs, bmesh, regions=None, **kwargs):
"""
Create an IGA domain.
Parameters
----------
name : str
The domain name.
"""
Domain.__init__(self,
name,
nurbs=nurbs,
bmesh=bmesh,
regions=regions,
**kwargs)
from sfepy.discrete.fem.geometry_element import create_geometry_elements
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.utils import prepare_remap
tconn = iga.get_bezier_topology(bmesh.conn, nurbs.degrees)
itc = nm.unique(tconn)
remap = prepare_remap(itc, bmesh.conn.max() + 1)
ltcoors = bmesh.cps[itc]
ltconn = remap[tconn]
n_nod, dim = ltcoors.shape
n_el = ltconn.shape[0]
self.shape = Struct(n_nod=n_nod, dim=dim, tdim=0, n_el=n_el)
desc = '%d_%d' % (dim, bmesh.conn.shape[1])
mat_id = nm.zeros(bmesh.conn.shape[0], dtype=nm.int32)
eval_mesh = Mesh.from_data(self.name + '_eval', nurbs.cps, None,
[nurbs.conn], [mat_id], [desc])
self.eval_mesh = eval_mesh
desc = '%d_%d' % (dim, 2**dim)
mat_id = nm.zeros(ltconn.shape[0], dtype=nm.int32)
self.mesh = Mesh.from_data(self.name + '_topo', ltcoors, None,
[ltconn], [mat_id], [desc])
self.cmesh = self.mesh.cmesh
gels = create_geometry_elements()
self.cmesh.set_local_entities(gels)
self.cmesh.setup_entities()
self.shape.tdim = self.cmesh.tdim
self.gel = gels[desc]
if regions is not None:
self.vertex_set_bcs = {}
for key, val in six.iteritems(self.regions):
self.vertex_set_bcs[key] = remap[val]
self.reset_regions()
def _setup_facet_dofs(self, dim, facet_desc, facet_perms, offset):
"""
Helper function to setup facet DOF connectivity, works for both
edges and faces.
"""
facet_desc = nm.array(facet_desc)
n_dof_per_facet = facet_desc.shape[1]
cmesh = self.domain.cmesh
facets = self.region.entities[dim]
ii = nm.arange(facets.shape[0], dtype=nm.int32)
all_dofs = offset + expand_nodes_to_dofs(ii, n_dof_per_facet)
# Prepare global facet id remapping to field-local numbering.
remap = prepare_remap(facets, cmesh.num[dim])
cconn = self.region.domain.cmesh.get_conn(self.region.tdim, dim)
offs = cconn.offsets
n_f = self.gel.edges.shape[0] if dim == 1 else self.gel.faces.shape[0]
oris = cmesh.get_orientations(dim)
gcells = self.region.get_cells()
n_el = gcells.shape[0]
# Elements of facets.
iel = nm.arange(n_el, dtype=nm.int32).repeat(n_f)
ies = nm.tile(nm.arange(n_f, dtype=nm.int32), n_el)
aux = offs[gcells][:, None] + ies.reshape((n_el, n_f))
indices = cconn.indices[aux]
facets_of_cells = remap[indices].ravel()
ori = oris[aux].ravel()
perms = facet_perms[ori]
# Define global facet dof numbers.
gdofs = offset + expand_nodes_to_dofs(facets_of_cells,
n_dof_per_facet)
# DOF columns in econn for each facet.
iep = facet_desc[ies]
iaux = nm.arange(gdofs.shape[0], dtype=nm.int32)
self.econn[iel[:, None], iep] = gdofs[iaux[:, None], perms]
n_dof = n_dof_per_facet * facets.shape[0]
assert_(n_dof == nm.prod(all_dofs.shape))
return n_dof, all_dofs, remap
def _setup_facet_dofs(self, dim, facet_desc, facet_perms, offset):
"""
Helper function to setup facet DOF connectivity, works for both
edges and faces.
"""
facet_desc = nm.array(facet_desc)
n_dof_per_facet = facet_desc.shape[1]
cmesh = self.domain.cmesh
facets = self.region.entities[dim]
ii = nm.arange(facets.shape[0], dtype=nm.int32)
all_dofs = offset + expand_nodes_to_dofs(ii, n_dof_per_facet)
# Prepare global facet id remapping to field-local numbering.
remap = prepare_remap(facets, cmesh.num[dim])
cconn = self.region.domain.cmesh.get_conn(self.region.tdim, dim)
offs = cconn.offsets
n_f = self.gel.edges.shape[0] if dim == 1 else self.gel.faces.shape[0]
oris = cmesh.get_orientations(dim)
gcells = self.region.get_cells()
n_el = gcells.shape[0]
# Elements of facets.
iel = nm.arange(n_el, dtype=nm.int32).repeat(n_f)
ies = nm.tile(nm.arange(n_f, dtype=nm.int32), n_el)
aux = offs[gcells][:, None] + ies.reshape((n_el, n_f))
indices = cconn.indices[aux]
facets_of_cells = remap[indices].ravel()
ori = oris[aux].ravel()
perms = facet_perms[ori]
# Define global facet dof numbers.
gdofs = offset + expand_nodes_to_dofs(facets_of_cells,
n_dof_per_facet)
# DOF columns in econn for each facet.
iep = facet_desc[ies]
iaux = nm.arange(gdofs.shape[0], dtype=nm.int32)
self.ap.econn[iel[:, None], iep] = gdofs[iaux[:, None], perms]
n_dof = n_dof_per_facet * facets.shape[0]
assert_(n_dof == nm.prod(all_dofs.shape))
return n_dof, all_dofs, remap
def __init__(self, name, nurbs, bmesh, regions=None, **kwargs):
"""
Create an IGA domain.
Parameters
----------
name : str
The domain name.
"""
Domain.__init__(self, name, nurbs=nurbs, bmesh=bmesh, regions=regions,
**kwargs)
from sfepy.discrete.fem.geometry_element import create_geometry_elements
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.utils import prepare_remap
tconn = iga.get_bezier_topology(bmesh.conn, nurbs.degrees)
itc = nm.unique(tconn)
remap = prepare_remap(itc, bmesh.conn.max() + 1)
ltcoors = bmesh.cps[itc]
ltconn = remap[tconn]
n_nod, dim = ltcoors.shape
n_el = ltconn.shape[0]
self.shape = Struct(n_nod=n_nod, dim=dim, tdim=0, n_el=n_el)
desc = '%d_%d' % (dim, bmesh.conn.shape[1])
mat_id = nm.zeros(bmesh.conn.shape[0], dtype=nm.int32)
eval_mesh = Mesh.from_data(self.name + '_eval', nurbs.cps, None,
[nurbs.conn], [mat_id], [desc])
self.eval_mesh = eval_mesh
desc = '%d_%d' % (dim, 2**dim)
mat_id = nm.zeros(ltconn.shape[0], dtype=nm.int32)
self.mesh = Mesh.from_data(self.name + '_topo', ltcoors, None, [ltconn],
[mat_id], [desc])
self.cmesh = self.mesh.cmesh
gels = create_geometry_elements()
self.cmesh.set_local_entities(gels)
self.cmesh.setup_entities()
self.shape.tdim = self.cmesh.tdim
self.gel = gels[desc]
if regions is not None:
self.vertex_set_bcs = {}
for key, val in self.regions.iteritems():
self.vertex_set_bcs[key] = remap[val]
self.reset_regions()
def setup_mirror_connectivity(self, region, mirror_name):
"""
Setup mirror surface connectivity required to integrate over a
mirror region.
1. Get orientation of the faces:
a) for own elements -> ooris
b) for mirror elements -> moris
2. orientation -> permutation.
"""
mregion = region.get_mirror_region(mirror_name)
oo = self.ori_map
ori_map = nm.zeros((nm.max(list(oo.keys())) + 1, self.n_fp),
dtype=nm.int32)
ori_map[list(oo.keys())] = nm.array([ii[1] for ii in oo.values()])
conn = region.domain.cmesh.get_conn_as_graph(region.dim,
region.dim - 1)
oris = region.domain.cmesh.facet_oris
econn = self.econn
ofis = region.get_facet_indices()
if mirror_name in region.mirror_maps\
and region.mirror_maps[mirror_name] is not None:
mirror_map = region.mirror_maps[mirror_name]
ofis = ofis[mirror_map]
econn = econn[mirror_map]
ooris = oris[conn.indptr[ofis[:, 0]] + ofis[:, 1]]
mfis = mregion.get_facet_indices()
moris = oris[conn.indptr[mfis[:, 0]] + mfis[:, 1]]
omap = ori_map[ooris]
mmap = ori_map[moris]
n_el, n_ep = self.econn.shape
ii = nm.repeat(nm.arange(n_el)[:, None], n_ep, 1)
self.meconn = nm.empty_like(self.econn)
self.meconn[ii, omap] = econn[ii, mmap]
nodes = nm.unique(self.meconn)
remap = prepare_remap(nodes, nodes.max() + 1)
self.mleconn = remap[self.meconn].copy()
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.
conn, gel = self.domain.get_conn(ret_gel=True)
faces = gel.get_surface_entities()
aux = FESurface('aux', region, faces, conn)
self.econn[:, :aux.n_fp] = aux.leconn
self.surface_data[region.name] = aux
return n_dof, remap
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.
conn, gel = self.domain.get_conn(ret_gel=True)
faces = gel.get_surface_entities()
aux = FESurface('aux', region, faces, conn)
self.econn[:, :aux.n_fp] = aux.leconn
self.surface_data[region.name] = aux
return n_dof, remap
def get_econn(self,
conn_type,
region,
is_trace=False,
integration=None,
local=False):
"""
Get DOF connectivity of the given type in the given region.
"""
ct = conn_type.type if isinstance(conn_type, Struct) else conn_type
nconn = self.nurbs.conn
if ct == 'volume':
if region.name == self.region.name:
conn = nconn
else:
cells = region.get_cells(true_cells_only=True)
conn = nm.take(nconn, cells.astype(nm.int32), axis=0)
elif ct == 'surface':
fis = region.get_facet_indices()
tdim = region.kind_tdim
facets = self._get_facets(tdim)
conn = []
for ii, fi in enumerate(fis):
conn.append(nconn[fi[0], facets[fi[1]]])
if local:
from sfepy.discrete.fem.utils import prepare_remap
nods = nm.unique(conn)
remap = prepare_remap(nods, nods.max() + 1)
conn = [remap[ii] for ii in conn]
else:
raise ValueError('unsupported connectivity type! (%s)' % ct)
return conn
def _setup_bubble_dofs(self):
"""
Setup bubble DOF connectivity.
"""
if self.node_desc.bubble is None:
return 0, None, None
offset = self.n_vertex_dof + self.n_edge_dof + self.n_face_dof
n_dof_per_cell = self.node_desc.bubble.shape[0]
ii = self.region.get_cells()
remap = prepare_remap(ii, self.domain.cmesh.n_el)
n_cell = ii.shape[0]
n_dof = n_dof_per_cell * n_cell
all_dofs = nm.arange(offset, offset + n_dof, dtype=nm.int32)
all_dofs.shape = (n_cell, n_dof_per_cell)
iep = self.node_desc.bubble[0]
self.econn[:,iep:] = all_dofs
return n_dof, all_dofs, remap
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.
for ig, ap in self.aps.iteritems():
group = self.domain.groups[ig]
faces = group.gel.get_surface_entities()
aux = FESurface('aux', region, faces, group.conn, ig)
ap.econn[:,:aux.n_fp] = aux.leconn
ap.surface_data[region.name] = aux
return n_dof, remap
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.
for ig, ap in self.aps.iteritems():
group = self.domain.groups[ig]
faces = group.gel.get_surface_entities()
aux = FESurface('aux', region, faces, group.conn, ig)
ap.econn[:,:aux.n_fp] = aux.leconn
ap.surface_data[region.name] = aux
return n_dof, remap
def _setup_bubble_dofs(self):
"""
Setup bubble DOF connectivity.
"""
if self.node_desc.bubble is None:
return 0, None, None
offset = self.n_vertex_dof + self.n_edge_dof + self.n_face_dof
n_dof_per_cell = self.node_desc.bubble.shape[0]
ii = self.region.get_cells()
remap = prepare_remap(ii, self.domain.cmesh.n_el)
n_cell = ii.shape[0]
n_dof = n_dof_per_cell * n_cell
all_dofs = nm.arange(offset, offset + n_dof, dtype=nm.int32)
all_dofs.shape = (n_cell, n_dof_per_cell)
iep = self.node_desc.bubble[0]
self.econn[:, iep:] = all_dofs
return n_dof, all_dofs, remap
def setup_mirror_connectivity(self, region):
"""
Setup mirror surface connectivity required to integrate over a
mirror region.
1. Get orientation of the faces:
a) for elements in group ig -> ooris (own)
b) for elements in group mig -> moris (mirror)
2. orientation -> permutation.
"""
mregion, ig_map, ig_map_i = region.get_mirror_region()
mig = ig_map_i[self.ig]
oo = self.ori_map
ori_map = nm.zeros((nm.max(oo.keys()) + 1, self.n_fp), dtype=nm.int32)
ori_map[oo.keys()] = nm.array([ii[1] for ii in oo.values()])
conn = region.domain.cmesh.get_conn_as_graph(region.dim,
region.dim - 1)
oris = region.domain.cmesh.facet_oris
ofis = region.get_facet_indices(self.ig, offset=False)
ooris = oris[conn.indptr[ofis[:, 0]] + ofis[:, 1]]
mfis = mregion.get_facet_indices(mig, offset=False)
moris = oris[conn.indptr[mfis[:, 0]] + mfis[:, 1]]
omap = ori_map[ooris]
mmap = ori_map[moris]
n_el, n_ep = self.econn.shape
ii = nm.repeat(nm.arange(n_el)[:, None], n_ep, 1)
self.meconn = nm.empty_like(self.econn)
self.meconn[ii, omap] = self.econn[ii, mmap]
nodes = nm.unique(self.meconn)
remap = prepare_remap(nodes, nodes.max() + 1)
self.mleconn = remap[self.meconn].copy()
def setup_mirror_connectivity(self, region):
"""
Setup mirror surface connectivity required to integrate over a
mirror region.
1. Get orientation of the faces:
a) for elements in group ig -> ooris (own)
b) for elements in group mig -> moris (mirror)
2. orientation -> permutation.
"""
mregion, ig_map, ig_map_i = region.get_mirror_region()
mig = ig_map_i[self.ig]
oo = self.ori_map
ori_map = nm.zeros((nm.max(oo.keys()) + 1, self.n_fp), dtype=nm.int32)
ori_map[oo.keys()] = nm.array([ii[1] for ii in oo.values()])
conn = region.domain.cmesh.get_conn_as_graph(region.dim, region.dim - 1)
oris = region.domain.cmesh.facet_oris
ofis = region.get_facet_indices(self.ig, offset=False)
ooris = oris[conn.indptr[ofis[:, 0]] + ofis[:, 1]]
mfis = mregion.get_facet_indices(mig, offset=False)
moris = oris[conn.indptr[mfis[:, 0]] + mfis[:, 1]]
omap = ori_map[ooris]
mmap = ori_map[moris]
n_el, n_ep = self.econn.shape
ii = nm.repeat(nm.arange(n_el)[:, None], n_ep, 1)
self.meconn = nm.empty_like(self.econn)
self.meconn[ii, omap] = self.econn[ii, mmap]
nodes = nm.unique(self.meconn)
remap = prepare_remap(nodes, nodes.max() + 1)
self.mleconn = remap[self.meconn].copy()
def _setup_facet_dofs(self, dim, facet_desc, offset):
"""
Helper function to setup facet DOF connectivity, works for both
edges and faces.
"""
facet_desc = nm.array(facet_desc)
n_dof_per_facet = facet_desc.shape[1]
cmesh = self.domain.cmesh
facets = self.region.entities[dim]
ii = nm.arange(facets.shape[0], dtype=nm.int32)
all_dofs = offset + expand_nodes_to_dofs(ii, n_dof_per_facet)
# Prepare global facet id remapping to field-local numbering.
remap = prepare_remap(facets, cmesh.num[dim])
cconn = self.region.domain.cmesh.get_conn(self.region.tdim, dim)
offs = cconn.offsets
n_f = self.gel.edges.shape[0] if dim == 1 else self.gel.faces.shape[0]
n_fp = 2 if dim == 1 else self.gel.surface_facet.n_vertex
oris = cmesh.get_orientations(dim)
ap = self.ap
gcells = self.region.get_cells()
n_el = gcells.shape[0]
# Elements of facets.
iel = nm.arange(n_el, dtype=nm.int32).repeat(n_f)
ies = nm.tile(nm.arange(n_f, dtype=nm.int32), n_el)
aux = offs[gcells][:, None] + ies.reshape((n_el, n_f))
indices = cconn.indices[aux]
facets_of_cells = remap[indices].ravel()
# Define global facet dof numbers.
gdofs = offset + expand_nodes_to_dofs(facets_of_cells,
n_dof_per_facet)
# DOF columns in econn for each facet (repeating same values for
# each element.
iep = facet_desc[ies]
ap.econn[iel[:, None], iep] = gdofs
ori = oris[aux].ravel()
if (n_fp == 2) and (ap.interp.gel.name in ['2_4', '3_8']):
tp_edges = ap.interp.gel.edges
ecs = ap.interp.gel.coors[tp_edges]
# True = positive, False = negative edge orientation w.r.t.
# reference tensor product axes.
tp_edge_ori = (nm.diff(ecs, axis=1).sum(axis=2) > 0).squeeze()
aux = nm.tile(tp_edge_ori, n_el)
ori = nm.where(aux, ori, 1 - ori)
if n_fp == 2: # Edges.
# ori == 1 means the basis has to be multiplied by -1.
ps = ap.interp.poly_spaces['v']
orders = ps.node_orders
eori = nm.repeat(ori[:, None], n_dof_per_facet, 1)
eoo = orders[iep] % 2 # Odd orders.
ap.ori[iel[:, None], iep] = eori * eoo
elif n_fp == 3: # Triangular faces.
raise NotImplementedError
else: # Quadrilateral faces.
# ori encoding in 3 bits:
# 0: axis swap, 1: axis 1 sign, 2: axis 2 sign
# 0 = + or False, 1 = - or True
# 63 -> 000 = 0
# 0 -> 001 = 1
# 30 -> 010 = 2
# 33 -> 011 = 3
# 11 -> 100 = 4
# 7 -> 101 = 5
# 52 -> 110 = 6
# 56 -> 111 = 7
# Special cases:
# Both orders same and even -> 000
# Both orders same and odd -> 0??
# Bits 1, 2 are multiplied by (swapped) axial order % 2.
new = nm.repeat(nm.arange(8, dtype=nm.int32), 3)
translate = prepare_translate([31, 59, 63,
0, 1, 4,
22, 30, 62,
32, 33, 41,
11, 15, 43,
3, 6, 7,
20, 52, 60,
48, 56, 57], new)
ori = translate[ori]
eori = nm.repeat(ori[:, None], n_dof_per_facet, 1)
ps = ap.interp.poly_spaces['v']
orders = ps.face_axes_nodes[iep - ps.face_indx[0]]
eoo = orders % 2
eoo0, eoo1 = eoo[..., 0], eoo[..., 1]
i0 = nm.where(eori < 4)
i1 = nm.where(eori >= 4)
eori[i0] = nm.bitwise_and(eori[i0], 2*eoo0[i0] + 5)
eori[i0] = nm.bitwise_and(eori[i0], eoo1[i0] + 6)
eori[i1] = nm.bitwise_and(eori[i1], eoo0[i1] + 6)
eori[i1] = nm.bitwise_and(eori[i1], 2*eoo1[i1] + 5)
ap.ori[iel[:, None], iep] = eori
n_dof = n_dof_per_facet * facets.shape[0]
assert_(n_dof == nm.prod(all_dofs.shape))
return n_dof, all_dofs, remap
def set_dofs(self, fun=0.0, region=None, dpn=None, warn=None):
"""
Set the values of DOFs given by the `region` using a function of space
coordinates or value `fun`.
If `fun` is a function, the l2 projection that is global for all region
facets is used to set the DOFs.
If `dpn > 1`, and `fun` is a function, it has to return the values
DOF-by-DOF, i.e. a single one-dimensional vector with all values of the
first component, then of the second one etc. concatenated
together.
Parameters
----------
fun : float or array of length dpn or callable
The DOF values.
region : Region
The region containing the DOFs.
dpn : int, optional
The DOF-per-node count. If not given, the number of field
components is used.
warn : str, optional
The warning message printed when the region selects no DOFs.
Returns
-------
nods : array, shape (n_dof,)
The field DOFs (or node indices) given by the region.
vals : array, shape (dpn, n_dof)
The values of the DOFs, DOF-by-DOF when raveled in C (row-major)
order.
"""
if region is None:
region = self.region
if dpn is None:
dpn = self.n_components
nods = []
vals = []
aux = self.get_dofs_in_region(region)
nods = nm.unique(nm.hstack(aux))
if nm.isscalar(fun):
vals = nm.repeat([fun], nods.shape[0] * dpn)
elif isinstance(fun, nm.ndarray):
assert_(len(fun) == dpn)
vals = nm.repeat(fun, nods.shape[0])
elif callable(fun):
import scipy.sparse as sps
from sfepy.solvers.ls import solve
from sfepy.discrete.integrals import Integral
from sfepy.discrete.fem.utils import prepare_remap
import sfepy.discrete.iga as iga
from sfepy.discrete.iga.extmods.igac import eval_mapping_data_in_qp
nurbs = self.nurbs
facets = self._get_facets(region.kind_tdim)
# Region facet connectivity.
rconn = self.get_econn('surface', region)
# Local connectivity.
remap = prepare_remap(nods, nods.max() + 1)
lconn = [remap[ii] for ii in rconn]
# Cell and face(cell) ids for each facet.
fis = region.get_facet_indices()
# Integral given by max. NURBS surface degree.
fdegrees = iga.get_surface_degrees(nurbs.degrees)
order = fdegrees.max()
integral = Integral('i', order=2 * order)
vals, weights = integral.get_qp(self.domain.gel.surface_facet_name)
# Boundary QP - use tensor product structure.
bvals = iga.create_boundary_qp(vals, region.tdim)
# Compute facet basis, jacobians and physical BQP.
n_dof = len(nods)
rhs = nm.zeros((dpn, n_dof), dtype=nm.float64)
rows, cols, mvals = [], [], []
all_qp = []
all_fbfs = []
all_dets = []
for ii, (ie, ifa) in enumerate(fis):
qp_coors = bvals[ifa]
bfs, _, dets = eval_mapping_data_in_qp(qp_coors, nurbs.cps,
nurbs.weights,
nurbs.degrees, nurbs.cs,
nurbs.conn,
nm.array([ie]))
# Facet basis.
fbfs = bfs[..., facets[ifa]][0, :, 0, :]
# Weight Jacobians by quadrature point weights.
dets = nm.abs(dets) * weights[None, :, None, None]
dets = dets[0, :, 0, :]
# Physical BQP.
fcps = nurbs.cps[nurbs.conn[ie, facets[ifa]]]
qp = nm.dot(fbfs, fcps)
all_qp.append(qp)
all_fbfs.append(fbfs)
all_dets.append(dets)
# DOF values in the physical BQP.
qps = nm.concatenate(all_qp)
vals = nm.asarray(fun(qps))
vals.shape = (dpn, qps.shape[0])
n_qp_face = len(bvals[0])
# Assemble l2 projection system.
for ii, (ie, ifa) in enumerate(fis):
# Assembling indices.
elc = lconn[ii]
fvals = vals[:, n_qp_face * ii:n_qp_face * (ii + 1)]
fbfs = all_fbfs[ii]
dets = all_dets[ii]
# Local projection system.
for idof in range(dpn):
lrhs = (fbfs * (fvals[idof, :, None] * dets)).sum(0)
rhs[idof, elc] += lrhs
lmtx = ((fbfs[..., None] * fbfs[:, None, :]) *
dets[..., None]).sum(0)
er, ec = nm.meshgrid(elc, elc)
rows.append(er.ravel())
cols.append(ec.ravel())
mvals.append(lmtx.ravel())
rows = nm.concatenate(rows)
cols = nm.concatenate(cols)
mvals = nm.concatenate(mvals)
mtx = sps.coo_matrix((mvals, (rows, cols)), shape=(n_dof, n_dof))
vals = nm.zeros((dpn, n_dof), dtype=nm.float64)
# Solve l2 projection system.
for idof in range(dpn):
dofs = solve(mtx, rhs[idof, :])
vals[idof, remap[nods]] = dofs
else:
raise ValueError('unknown function/value type! (%s)' % type(fun))
return nods, vals
def set_dofs(self, fun=0.0, region=None, dpn=None, warn=None):
"""
Set the values of DOFs given by the `region` using a function of space
coordinates or value `fun`.
If `fun` is a function, the l2 projection that is global for all region
facets is used to set the DOFs.
If `dpn > 1`, and `fun` is a function, it has to return the values
DOF-by-DOF, i.e. a single one-dimensional vector with all values of the
first component, then of the second one etc. concatenated
together.
Parameters
----------
fun : float or array of length dpn or callable
The DOF values.
region : Region
The region containing the DOFs.
dpn : int, optional
The DOF-per-node count. If not given, the number of field
components is used.
warn : str, optional
The warning message printed when the region selects no DOFs.
Returns
-------
nods : array, shape (n_dof,)
The field DOFs (or node indices) given by the region.
vals : array, shape (dpn, n_dof)
The values of the DOFs, DOF-by-DOF when raveled in C (row-major)
order.
"""
if region is None:
region = self.region
if dpn is None:
dpn = self.n_components
nods = []
vals = []
aux = self.get_dofs_in_region(region)
nods = nm.unique(nm.hstack(aux))
if nm.isscalar(fun):
vals = nm.repeat([fun], nods.shape[0] * dpn)
elif isinstance(fun, nm.ndarray):
assert_(len(fun) == dpn)
vals = nm.repeat(fun, nods.shape[0])
elif callable(fun):
import scipy.sparse as sps
from sfepy.solvers.ls import solve
from sfepy.discrete.integrals import Integral
from sfepy.discrete.fem.utils import prepare_remap
import sfepy.discrete.iga as iga
from sfepy.discrete.iga.extmods.igac import eval_mapping_data_in_qp
nurbs = self.nurbs
facets = self._get_facets(region.kind_tdim)
# Region facet connectivity.
rconn = self.get_econn('surface', region)
# Local connectivity.
remap = prepare_remap(nods, nods.max() + 1)
lconn = [remap[ii] for ii in rconn]
# Cell and face(cell) ids for each facet.
fis = region.get_facet_indices()
# Integral given by max. NURBS surface degree.
fdegrees = iga.get_surface_degrees(nurbs.degrees)
order = fdegrees.max()
integral = Integral('i', order=2*order)
vals, weights = integral.get_qp(self.domain.gel.surface_facet_name)
# Boundary QP - use tensor product structure.
bvals = iga.create_boundary_qp(vals, region.tdim)
# Compute facet basis, jacobians and physical BQP.
n_dof = len(nods)
rhs = nm.zeros((dpn, n_dof), dtype=nm.float64)
rows, cols, mvals = [], [], []
all_qp = []
all_fbfs = []
all_dets = []
for ii, (ie, ifa) in enumerate(fis):
qp_coors = bvals[ifa]
bfs, _, dets = eval_mapping_data_in_qp(qp_coors, nurbs.cps,
nurbs.weights,
nurbs.degrees,
nurbs.cs,
nurbs.conn,
nm.array([ie]))
# Facet basis.
fbfs = bfs[..., facets[ifa]][0, :, 0, :]
# Weight Jacobians by quadrature point weights.
dets = nm.abs(dets) * weights[None, :, None, None]
dets = dets[0, :, 0, :]
# Physical BQP.
fcps = nurbs.cps[nurbs.conn[ie, facets[ifa]]]
qp = nm.dot(fbfs, fcps)
all_qp.append(qp)
all_fbfs.append(fbfs)
all_dets.append(dets)
# DOF values in the physical BQP.
qps = nm.concatenate(all_qp)
vals = nm.asarray(fun(qps))
vals.shape = (dpn, qps.shape[0])
n_qp_face = len(bvals[0])
# Assemble l2 projection system.
for ii, (ie, ifa) in enumerate(fis):
# Assembling indices.
elc = lconn[ii]
fvals = vals[:, n_qp_face * ii : n_qp_face * (ii + 1)]
fbfs = all_fbfs[ii]
dets = all_dets[ii]
# Local projection system.
for idof in xrange(dpn):
lrhs = (fbfs * (fvals[idof, :, None] * dets)).sum(0)
rhs[idof, elc] += lrhs
lmtx = ((fbfs[..., None] * fbfs[:, None, :])
* dets[..., None]).sum(0)
er, ec = nm.meshgrid(elc, elc)
rows.append(er.ravel())
cols.append(ec.ravel())
mvals.append(lmtx.ravel())
rows = nm.concatenate(rows)
cols = nm.concatenate(cols)
mvals = nm.concatenate(mvals)
mtx = sps.coo_matrix((mvals, (rows, cols)), shape=(n_dof, n_dof))
vals = nm.zeros((dpn, n_dof), dtype=nm.float64)
# Solve l2 projection system.
for idof in xrange(dpn):
dofs = solve(mtx, rhs[idof, :])
vals[idof, remap[nods]] = dofs
else:
raise ValueError('unknown function/value type! (%s)' % type(fun))
return nods, vals
def _setup_facet_dofs(self, dim, facet_desc, offset):
"""
Helper function to setup facet DOF connectivity, works for both
edges and faces.
"""
facet_desc = nm.array(facet_desc)
n_dof_per_facet = facet_desc.shape[1]
cmesh = self.domain.cmesh
facets = self.region.entities[dim]
ii = nm.arange(facets.shape[0], dtype=nm.int32)
all_dofs = offset + expand_nodes_to_dofs(ii, n_dof_per_facet)
# Prepare global facet id remapping to field-local numbering.
remap = prepare_remap(facets, cmesh.num[dim])
cconn = self.region.domain.cmesh.get_conn(self.region.tdim, dim)
offs = cconn.offsets
n_f = self.gel.edges.shape[0] if dim == 1 else self.gel.faces.shape[0]
n_fp = 2 if dim == 1 else self.gel.surface_facet.n_vertex
oris = cmesh.get_orientations(dim)
ap = self.ap
gcells = self.region.get_cells()
n_el = gcells.shape[0]
# Elements of facets.
iel = nm.arange(n_el, dtype=nm.int32).repeat(n_f)
ies = nm.tile(nm.arange(n_f, dtype=nm.int32), n_el)
aux = offs[gcells][:, None] + ies.reshape((n_el, n_f))
indices = cconn.indices[aux]
facets_of_cells = remap[indices].ravel()
# Define global facet dof numbers.
gdofs = offset + expand_nodes_to_dofs(facets_of_cells, n_dof_per_facet)
# DOF columns in econn for each facet (repeating same values for
# each element.
iep = facet_desc[ies]
ap.econn[iel[:, None], iep] = gdofs
ori = oris[aux].ravel()
if (n_fp == 2) and (ap.interp.gel.name in ['2_4', '3_8']):
tp_edges = ap.interp.gel.edges
ecs = ap.interp.gel.coors[tp_edges]
# True = positive, False = negative edge orientation w.r.t.
# reference tensor product axes.
tp_edge_ori = (nm.diff(ecs, axis=1).sum(axis=2) > 0).squeeze()
aux = nm.tile(tp_edge_ori, n_el)
ori = nm.where(aux, ori, 1 - ori)
if n_fp == 2: # Edges.
# ori == 1 means the basis has to be multiplied by -1.
ps = ap.interp.poly_spaces['v']
orders = ps.node_orders
eori = nm.repeat(ori[:, None], n_dof_per_facet, 1)
eoo = orders[iep] % 2 # Odd orders.
ap.ori[iel[:, None], iep] = eori * eoo
elif n_fp == 3: # Triangular faces.
raise NotImplementedError
else: # Quadrilateral faces.
# ori encoding in 3 bits:
# 0: axis swap, 1: axis 1 sign, 2: axis 2 sign
# 0 = + or False, 1 = - or True
# 63 -> 000 = 0
# 0 -> 001 = 1
# 30 -> 010 = 2
# 33 -> 011 = 3
# 11 -> 100 = 4
# 7 -> 101 = 5
# 52 -> 110 = 6
# 56 -> 111 = 7
# Special cases:
# Both orders same and even -> 000
# Both orders same and odd -> 0??
# Bits 1, 2 are multiplied by (swapped) axial order % 2.
new = nm.repeat(nm.arange(8, dtype=nm.int32), 3)
translate = prepare_translate([
31, 59, 63, 0, 1, 4, 22, 30, 62, 32, 33, 41, 11, 15, 43, 3, 6,
7, 20, 52, 60, 48, 56, 57
], new)
ori = translate[ori]
eori = nm.repeat(ori[:, None], n_dof_per_facet, 1)
ps = ap.interp.poly_spaces['v']
orders = ps.face_axes_nodes[iep - ps.face_indx[0]]
eoo = orders % 2
eoo0, eoo1 = eoo[..., 0], eoo[..., 1]
i0 = nm.where(eori < 4)
i1 = nm.where(eori >= 4)
eori[i0] = nm.bitwise_and(eori[i0], 2 * eoo0[i0] + 5)
eori[i0] = nm.bitwise_and(eori[i0], eoo1[i0] + 6)
eori[i1] = nm.bitwise_and(eori[i1], eoo0[i1] + 6)
eori[i1] = nm.bitwise_and(eori[i1], 2 * eoo1[i1] + 5)
ap.ori[iel[:, None], iep] = eori
n_dof = n_dof_per_facet * facets.shape[0]
assert_(n_dof == nm.prod(all_dofs.shape))
return n_dof, all_dofs, remap
