def make_solvars(self, solsets, g=None):
from petram.mesh.mesh_utils import (get_extended_connectivity,
get_reverse_connectivity)
from petram.helper.variables import Variable
from petram.helper.variables import add_scalar
solvars = [None] * len(solsets)
if g is None:
g = {}
for k, v in enumerate(solsets):
mesh, soldict = v
get_extended_connectivity(mesh[0])
get_reverse_connectivity(mesh[0])
solvar = g.copy()
for phys in self.iter_enabled():
phys.soldict_to_solvars(soldict, solvar)
for var in solvar.values():
if isinstance(var, Variable):
var.add_topological_info(mesh[0])
solvars[k] = solvar
if 'minSJac_' + str(k) in soldict:
add_scalar(solvar, "minSJac", "", ['x', 'y', 'z'],
soldict['minSJac_' + str(k)][0], None)
# print "solvars", solvars
return solvars
def populate_plotdata(mesh, table, cells, cell_data):
from petram.mesh.mesh_utils import get_extended_connectivity
if not hasattr(mesh, 'extended_connectivity'):
get_extended_connectivity(mesh)
ndim = mesh.Dimension()
ec = mesh.extended_connectivity
cell_data['line'] = {}
cell_data['vertex'] = {}
l2e = ec['line2edge']
v2v = ec['vert2vert']
kedge = []
if mesh.Dimension() >= 2:
method = mesh.GetEdgeVertices
else:
method = mesh.GetElementVertices
if len(l2e) > 0:
#kedge = np.array(sum([[key]*len(l2e[key]) for key in l2e], [])).astype(int)
kedge = np.hstack([[key] * len(l2e[key])
for key in l2e]).astype(int, copy=False)
iverts = np.vstack([method(ie) for key in l2e for ie in l2e[key]])
else:
iverts = np.atleast_1d([]).astype(int)
cells['line'] = table[iverts]
cell_data['line']['physical'] = np.array(kedge)
kvert = np.array([key for key in v2v]).astype(int, copy=False)
iverts = np.array([v2v[key] for key in v2v]).astype(int, copy=False)
cells['vertex'] = table[iverts]
cell_data['vertex']['physical'] = kvert
if ndim == 3:
l_s_loop = [ec['surf2line'], ec['vol2surf']]
elif ndim == 2:
l_s_loop = [ec['surf2line'], None]
else:
l_s_loop = [None, None]
iedge2bb = None # is it used?
return l_s_loop
def extract_mesh_data_1D(mesh):
nv = mesh.GetNV()
X = np.vstack([mesh.GetVertexArray(k) for k in range(nv)])
if X.shape[1] == 2:
X = np.hstack((X, np.zeros((X.shape[0], 1))))
elif X.shape[1] == 1:
X = np.hstack((X, np.zeros((X.shape[0], 2))))
cells = {}
cell_data = {}
attrs = mesh.GetAttributeArray()
lverts = []
lattr = []
for attr in np.unique(attrs):
idx = np.where(attrs == attr)[0]
for i in idx:
lverts.append(mesh.GetElementVertices(i))
lattr.extend([attr] * len(idx))
cells['line'] = np.array(lverts)
cell_data['line'] = {}
cell_data['line']['physical'] = np.array(lattr).flatten()
vverts = []
vattr = []
for ibe in range(mesh.GetNBE()):
battr = mesh.GetBdrAttribute(ibe)
vattr.append(battr)
vverts.append(mesh.GetBdrElementVertices(ibe))
cells['vertex'] = np.array(vverts)
cell_data['vertex'] = {}
cell_data['vertex']['physical'] = np.array(vattr).flatten()
from petram.mesh.mesh_utils import get_extended_connectivity
if not hasattr(mesh, 'extended_connectivity'):
get_extended_connectivity(mesh)
return X, cells, cell_data, [None, None], None
def postprocess(self, caller, gf=None, edges=None):
from petram.helper.mpi_recipes import safe_flatstack
from mfem.common.mpi_debug import nicePrint
if edges is None: return
print("postprocess is called")
gfr, gfi = gf
print(caller, gfr)
try:
fes = gfr.ParFESpace()
mesh = fes.GetParMesh()
except:
fes = gfr.FESpace()
mesh = fes.GetMesh()
from petram.mesh.mesh_utils import get_extended_connectivity
if not hasattr(mesh, 'extended_connectivity'):
get_extended_connectivity(mesh)
l2e = mesh.extended_connectivity['line2edge']
idx = safe_flatstack([l2e[e] for e in edges])
if len(idx) > 0:
dofs = safe_flatstack([fes.GetEdgeDofs(i) for i in idx])
size = dofs.size // idx.size
w = []
for i in idx:
# don't put this Tr outside the loop....
Tr = mesh.GetEdgeTransformation(i)
w.extend([Tr.Weight()] * size)
w = np.array(w)
data = gfr.GetDataArray()[dofs] + 1j * gfi.GetDataArray()[dofs]
field = data / w
else:
w = np.array([])
field = np.array([])
nicePrint(w)
nicePrint(field)
def preprocess_geometry(self, attrs, emesh_idx=0):
self.vertices = None
self.knowns = WKD()
mesh = self.mesh()[emesh_idx]
self.iverts = []
self.attrs = attrs
if attrs[0] == 'all':
eattrs = 'all'
else:
eattrs = attrs
if mesh.Dimension() == 3:
'''
from petram.mesh.find_edges import find_edges
edges, bb_edges = find_edges(mesh)
bb_bdrs = bb_edges.keys()
iverts = []
for bb_bdr in bb_bdrs:
if eattrs != 'all':
check = [sorted(tuple(eattr)) == sorted(bb_bdr) for eattr in eattrs]
if not any(check): continue
iedges = bb_edges[bb_bdr]
iverts.extend([mesh.GetEdgeVertices(ie) for ie in iedges])
print iverts
'''
from petram.mesh.mesh_utils import get_extended_connectivity
if not hasattr(mesh, 'extended_connectivity'):
get_extended_connectivity(mesh)
l2e = mesh.extended_connectivity['line2edge']
keys = l2e.keys() if eattrs == 'all' else list(
np.atleast_1d(eattrs).flatten())
iedges = list(set(sum([l2e[k] for k in keys if k in l2e], [])))
iverts = [mesh.GetEdgeVertices(ie) for ie in iedges]
self.ibeles = None # can not use boundary variable in this evaulator
elif mesh.Dimension() == 2:
kbdr = mesh.GetBdrAttributeArray()
if eattrs == 'all': eattrs = np.unique(kbdr)
iverts = []
#d = defaultdict(list)
for i in range(mesh.GetNBE()):
attr = mesh.GetBdrAttribute(i)
if attr in eattrs:
iverts.append(
list(mesh.GetBdrElement(i).GetVerticesArray()))
x = np.unique([mesh.GetBdrArray(e)
for e in eattrs]).astype(int, copy=False)
self.ibeles = x
#d[attr].extend(mesh.GetBdrElement(i).GetVerticesArray())
elif mesh.Dimension() == 1:
kbdr = mesh.GetAttributeArray()
if eattrs == 'all': eattrs = np.unique(kbdr)
iverts = []
#d = defaultdict(list)
for i in range(mesh.GetNE()):
attr = mesh.GetAttribute(i)
if attr in eattrs:
iverts.append(list(mesh.GetElement(i).GetVerticesArray()))
#d[attr].extend(mesh.GetBdrElement(i).GetVerticesArray())
x = np.unique([mesh.GetDomainArray(e)
for e in eattrs]).astype(int, copy=False)
self.ibeles = x
else:
assert False, "Unsupported dim"
self.emesh_idx = emesh_idx
if len(iverts) == 0: return
iverts = np.stack(iverts)
self.iverts = iverts
if len(self.iverts) == 0: return
data = process_iverts2nodals(mesh, iverts)
for k in six.iterkeys(data):
setattr(self, k, data[k])
import sys
import petram
use_parallel = False
filename = 'circle.mesh'
for param in sys.argv[1:]:
if param == '-p':
use_parallel = True
else:
filename = param
from petram.helper.load_mfem import load
mfem, MPI = load(use_parallel)
print("use_parallel", use_parallel)
from petram.mesh.partial_mesh import edge
from petram.mesh.mesh_utils import get_extended_connectivity
mesh0 = mfem.Mesh(filename)
if use_parallel:
mesh = mfem.ParMesh(MPI.COMM_WORLD, mesh0)
else:
mesh = mesh0
get_extended_connectivity(mesh)
out_file = filename.split('.')[0] + "_edge.mesh"
edge(mesh, [1, 2, 3, 4, 5], filename=out_file, precision=8)
def merge_domain_3d(mesh, domain_list, reorder_dom=True):
if not hasattr(mesh, 'extended_connectivity'):
from petram.mesh.mesh_utils import get_extended_connectivity
get_extended_connectivity(mesh)
ec = mesh.extended_connectivity
v2s = ec['vol2surf']
s2l = ec['surf2line']
from petram.mesh.mesh_utils import vol2line, line2surf, line2vol
v2l = vol2line(v2s, s2l)
l2v = line2vol(v2l)
l2s = line2surf(s2l)
# find surfaces to remove
# find edge to remove
remove_surf = []
remove_edge = Set()
merge_vol = {}
for d in domain_list:
merge_vol[d] = 0
touched_dom = []
for i, j in combinations(domain_list, 2):
iscts = np.intersect1d(v2s[i], v2s[j])
if len(iscts) != 0: touched_dom.append((i, j))
remove_surf.append(iscts)
remove_surf = list(np.hstack(remove_surf).astype(int))
for s in remove_surf:
for l in s2l[s]:
for v in v2l:
if l in v2l[v] and not v in domain_list:
break
else:
remove_edge.add(l)
for l in s2l[s]:
connected_surf = [s for s in l2s[l] if not s in remove_surf]
if len(connected_surf) != 2: continue
v1 = [
v for v in v2s
if not v in domain_list and connected_surf[0] in v2s[v]
]
v2 = [
v for v in v2s
if not v in domain_list and connected_surf[1] in v2s[v]
]
if len(Set(v1 + v2)) == 1:
remove_edge.add(l)
remove_edge = list(remove_edge)
# check merging to one domain
if len(touched_dom) == 0:
assert False, "domains are not connected"
c = list(touched_dom[0])
for i in range(len(touched_dom)):
for j in range(i, len(touched_dom)):
if touched_dom[j][0] in c and not touched_dom[j][1] in c:
c.append(touched_dom[j][1])
if touched_dom[j][1] in c and not touched_dom[j][0] in c:
c.append(touched_dom[j][0])
print("touched_domain", c)
if len(c) != len(domain_list):
assert False, "domains are not connected"
# collect faces to merge
merge_face0 = []
for k, l in enumerate(remove_edge):
for f in merge_face0:
if np.intersect1d(list(f), l2s[l]).size != 0:
for s in l2s[l]:
if not s in remove_surf: f.add(s)
break
else:
sss = [s for s in l2s[l] if not s in remove_surf]
merge_face0.append(Set(sss))
print(merge_face0)
merge_face = {}
for k, ss in enumerate(merge_face0):
for s in ss:
merge_face[s] = k
# mapping of bdr (face) attributes
idx = 1
bdrattr_map = {}
for s in s2l:
if s in remove_surf: continue
if not s in merge_face:
bdrattr_map[s] = idx
idx = idx + 1
for s, k in merge_face.items():
if s in remove_surf: continue
bdrattr_map[s] = k + idx
# mapping of domaon attributes
if reorder_dom:
idx = 1
domattr_map = {}
for v in v2s:
if not v in merge_vol:
domattr_map[v] = idx
idx = idx + 1
for v, k in merge_vol.items():
domattr_map[v] = k + idx
else:
domattr_map = {}
for v in v2s:
if not v in merge_vol:
domattr_map[v] = v
idx = max(v2s.keys()) + 1
for v, k in merge_vol.tems():
domattr_map[v] = k + idx
print("merge_vol", merge_vol)
print("merge_surf", merge_face)
print("remove_edge", remove_edge)
print("remove_surf", remove_surf)
print("domattr_map", domattr_map)
print("bdrattr_map", bdrattr_map)
# check if edge can be removed...
NV = mesh.GetNV()
NE = mesh.GetNE()
NBE = mesh.GetNBE()
bdrattr = mesh.GetBdrAttributeArray()
domattr = mesh.GetAttributeArray()
Nbelem = np.sum([x in bdrattr_map for x in bdrattr])
print("NV, NE, NBE", NV, NE, Nbelem)
import sys
if 'mfem.par' in sys.modules:
import mfem.par as mfem
else:
import mfem.par as mfem
omesh = mfem.Mesh(3, NV, NE, Nbelem, 3)
for k in range(NV):
v = mesh.GetVertexArray(k)
omesh.AddVertex(list(v))
for k in range(NE):
iv = mesh.GetElementVertices(k)
a = domattr_map[domattr[k]]
if len(iv) == 4:
omesh.AddTet(list(iv), a)
if len(iv) == 8:
omesh.AddHex(list(iv), a)
for k in range(NBE):
iv = mesh.GetBdrElementVertices(k)
if not bdrattr[k] in bdrattr_map: continue
a = bdrattr_map[bdrattr[k]]
if len(iv) == 3:
omesh.AddBdrTriangle(list(iv), a)
if len(iv) == 4:
omesh.AddBdrQuad(list(iv), a)
omesh.FinalizeTopology()
omesh.Finalize(refine=True, fix_orientation=True)
return omesh