def set_point(self, T, ip, g, l, t=None):
self.x = T.Transform(ip)
self.t = t
T.SetIntPoint(ip)
nor = mfem.Vector(self.sdim)
mfem.CalcOrtho(T.Jacobian(), nor)
self.nor = nor.GetDataArray().copy()
def ncface_values(self,
ifaces=None,
irs=None,
gtypes=None,
locs=None,
mesh=None,
**kwargs):
size = len(locs)
ret = np.zeros((size, self.sdim))
if ifaces is None: return
nor = mfem.Vector(self.sdim)
if mesh.Dimension() == 3:
m = mesh.GetFaceTransformation
elif mesh.Dimension() == 2:
m = mesh.GetElementTransformation
idx = 0
for i, gtype, in zip(ifaces, gtypes):
ir = irs[gtype]
nv = ir.GetNPoints()
T = m(i)
for j in range(nv):
T.SetIntPoint(ir.IntPoint(i))
mfem.CalcOrtho(T.Jacobian(), nor)
ret[idx, :] = nor.GetDataArray().copy()
idx = idx + 1
from petram.helper.right_broadcast import div
ret = div(ret, np.sqrt(np.sum(ret**2, -1)))
if self.comp == -1: return ret
return ret[:, self.comp - 1]
def nodal_values(self, ibele=None, mesh=None, iverts_f=None, **kwargs):
# iele = None, elattr = None, el2v = None,
# wverts = None, locs = None, g = None
g = mfem.Geometry()
size = len(iverts_f)
#wverts = np.zeros(size)
ret = np.zeros((size, self.sdim))
if ibele is None: return
ibe = ibele[0]
el = mesh.GetBdrElement(ibe)
rule = g.GetVertices(el.GetGeometryType())
nv = rule.GetNPoints()
for ibe in ibele:
T = mesh.GetBdrElementTransformation(ibe)
bverts = mesh.GetBdrElement(ibe).GetVerticesArray()
for i in range(nv):
nor = mfem.Vector(self.sdim)
T.SetIntPoint(rule.IntPoint(i))
mfem.CalcOrtho(T.Jacobian(), nor)
idx = np.searchsorted(iverts_f, bverts[i])
ret[idx, :] += nor.GetDataArray().copy()
#wverts[idx] = wverts[idx] + 1
#for i in range(self.sdim): ret[:,i] /= wvert
# normalize to length one.
ret = ret / np.sqrt(np.sum(ret**2, 1)).reshape(-1, 1)
if self.comp == -1: return ret
return ret[:, self.comp - 1]
def preprocess_params(self, engine):
### find normal (outward) vector...
mesh = engine.get_emesh(mm=self)
fespace = engine.fespaces[self.get_root_phys().dep_vars[0]]
nbe = mesh.GetNBE()
ibe = np.array([
i for i in range(nbe)
if mesh.GetBdrElement(i).GetAttribute() == self._sel_index[0]
])
dprint1("idb", ibe)
el = mesh.GetBdrElement(ibe[0])
Tr = fespace.GetBdrElementTransformation(ibe[0])
rules = mfem.IntegrationRules()
ir = rules.Get(el.GetGeometryType(), 1)
Tr.SetIntPoint(ir.IntPoint(0))
nor = mfem.Vector(2)
mfem.CalcOrtho(Tr.Jacobian(), nor)
self.norm = nor.GetDataArray().copy()
self.norm = self.norm / np.sqrt(np.sum(self.norm**2))
dprint1("Normal Vector " + list(self.norm).__repr__())
### find rectangular shape
edges = np.array([mesh.GetBdrElementEdges(i)[0]
for i in ibe]).flatten()
d = {}
for x in edges:
d[x] = x in d
edges = [x for x in d.keys() if not d[x]]
ivert = [mesh.GetEdgeVertices(x) for x in edges]
ivert = connect_pairs2(ivert)[0]
vv = np.vstack([mesh.GetVertexArray(i) for i in ivert])
self.ctr = (vv[0] + vv[-1]) / 2.0
dprint1("Center " + list(self.ctr).__repr__())
### rectangular port
self.a_vec = (vv[0] - vv[-1])
self.a = np.sqrt(np.sum(self.a_vec**2))
self.a_vec /= self.a
self.c = vv[-1]
dprint1("Cornor " + self.c.__repr__())
dprint1("Edge " + self.a.__repr__())
dprint1("Edge Vec." + list(self.a_vec).__repr__())
Erz, Ephi = self.get_e_coeff_cls()
Hrz, Hphi = self.get_h_coeff_cls()
if self.mode == 'TE':
dprint1("E field pattern")
c1 = Ephi(self, real=True)
c2 = Hphi(0.0, self, real=False)
for p in vv:
dprint1(p.__repr__() + ' : ' + c1.EvalValue(p).__repr__())
dprint1("H field pattern")
for p in vv:
dprint1(p.__repr__() + ' : ' + c2.EvalValue(p).__repr__())
def hcurln(fes1,
fes2,
coeff,
is_complex=False,
bdr='all',
orderinc=1,
verbose=False):
mat, rstart = get_empty_map(fes2, fes1, is_complex=is_complex)
mat2, rstart = get_empty_map(fes2, fes1, is_complex=is_complex)
from petram.helper.element_map import map_element
name_fes1 = fes1.FEColl().Name()[:2]
name_fes2 = fes2.FEColl().Name()[:2]
if verbose:
if myid == 0:
dprint1("fes", name_fes1, name_fes2)
mesh1 = fes1.GetMesh()
mesh2 = fes2.GetMesh()
mesh2.Print("/home/shiraiwa/part.mesh")
if verbose:
if myid == 0:
dprint1("NE", mesh1.GetNE(), mesh2.GetNE())
elmap, elmap_r = map_element(mesh1, mesh2, bdr, map_bdr=True)
sdim1 = mesh1.SpaceDimension()
sdim2 = mesh1.SpaceDimension()
dim1 = mesh1.Dimension()
dim2 = mesh2.Dimension()
shape1 = mfem.DenseMatrix()
shape2 = mfem.Vector()
ip = mfem.IntegrationPoint()
nor = mfem.Vector(sdim1)
if USE_PARALLEL:
# this is global TrueDoF (offset is not subtracted)
P = fes1.Dof_TrueDof_Matrix()
P1mat = ToScipyCoo(P).tocsr()
#VDoFtoGTDoF1 = P.indices
#P = fes2.Dof_TrueDof_Matrix()
#P = ToScipyCoo(P).tocsr()
#VDoFtoGTDoF2 = P.indices
#P2mat = P
vdofs1_senddata = []
shared_data = []
el2_2_node = {}
el2_2_el1 = {}
for d in elmap_r:
for x in list(elmap_r[d]):
el2_2_node[x] = d
for x in list(elmap_r[d]):
el2_2_el1[x] = elmap_r[d][x]
# working for fes2
# find boundary element on mesh1 using mesh2 boundary
el2_arr = [list() for x in range(nprc)]
el1_arr = [list() for x in range(nprc)]
fe2o_arr = [list() for x in range(nprc)]
for i_el in range(fes2.GetNE()):
attr = fes2.GetAttribute(i_el)
if bdr != 'all' and not attr in bdr:
continue
el1_arr[el2_2_node[i_el]].append(el2_2_el1[i_el])
el2_arr[el2_2_node[i_el]].append(i_el)
fe2 = fes2.GetFE(i_el)
fe2o_arr[el2_2_node[i_el]].append(fe2.GetOrder())
if USE_PARALLEL:
el1_arr = alltoall_vector(el1_arr, int) # transfer to mesh1 owners
# working for fes1
# find elemet order on mesh1
fe1o_arr = [list() for x in range(nprc)]
i_fe1_arr = [list() for x in range(nprc)]
rank = 0
for rank, i_bdrs in enumerate(el1_arr):
for i_bdr in i_bdrs:
iface = mesh1.GetBdrElementEdgeIndex(i_bdr)
transs = mesh1.GetFaceElementTransformations(iface)
i_el1 = transs.Elem1No
assert transs.Elem2No == -1, "boundary must be exterior for this operator"
fe1 = fes1.GetFE(i_el1)
fe1o_arr[rank].append(fe1.GetOrder())
i_fe1_arr[rank].append(i_el1)
rank = rank + 1
if USE_PARALLEL:
fe1o_arr = alltoall_vector(fe1o_arr, int) # transfer to mesh2
# working for fes2
locnor_arr = [list() for x in range(nprc)]
data2_arr = [list() for x in range(nprc)]
verbose1 = verbose
for rank, i_el2s in enumerate(el2_arr):
for i_el2, fe1o in zip(i_el2s, fe1o_arr[rank]):
eltrans = fes2.GetElementTransformation(i_el2)
fe2 = fes2.GetFE(i_el2)
nd2 = fe2.GetDof()
ir = get_rule(fe1o,
fe2,
eltrans,
orderinc=orderinc,
verbose=verbose1)
verbose1 = False
shape2.SetSize(nd2)
data2 = []
locnors = []
for jj in range(ir.GetNPoints()):
ip1 = ir.IntPoint(jj)
eltrans.SetIntPoint(ip1)
w = eltrans.Weight() * ip1.weight
mfem.CalcOrtho(eltrans.Jacobian(), nor)
nor2 = nor.GetDataArray() / np.linalg.norm(nor.GetDataArray())
fe2.CalcShape(ip1, shape2)
if dim2 == 1:
d = np.array([ip1.x] + list(eltrans.Transform(ip1)) +
list(nor2))
locnors.append(d)
elif dim2 == 2:
d = np.array([ip1.x, ip1.y] +
list(eltrans.Transform(ip1)) + list(nor2))
locnors.append(d)
else:
assert False, "boundary mesh must be dim=1 or 2"
data2.append(w * shape2.GetDataArray().copy())
# np.vstack(locnors).shape = (#Npoints, dim2+sdim2*2)
# np.vstack(data2).shape = (#Npoints, #NDoF2)
#print("size here", np.vstack(locnors).shape, np.vstack(data2).shape)
locnor_arr[rank].append(np.vstack(locnors))
data2_arr[rank].append(np.vstack(data2))
if USE_PARALLEL:
locnor_arr = alltoall_vectorv(locnor_arr, float) # transfer to mesh1
ll = dim2 + 2 * sdim2
vdofs1_arr = [list() for x in range(nprc)]
data1_arr = [list() for x in range(nprc)]
# space to compute the coefficient
MV = [mfem.Vector(sdim1), mfem.DenseMatrix(sdim1, sdim1)]
max_misalignment = -np.inf
for rank, i_fe1s in enumerate(i_fe1_arr):
locnorss = locnor_arr[rank]
sign_dict = {}
for k, i_fe1 in enumerate(i_fe1s):
fe1 = fes1.GetFE(i_fe1)
nd1 = fe1.GetDof()
eltrans = fes1.GetElementTransformation(i_fe1)
doftrans = fes1.GetElementDofTransformation(i_fe1)
#ctr = eval_element_center(fe1, eltrans)
locnors2 = locnorss[k]
shape1.SetSize(nd1, sdim1)
vdofs1 = fes1.GetElementVDofs(i_fe1)
dof_sign1 = np.array([
[1 if vv >= 0 else -1 for vv in vdofs1],
])
vdofs1 = [-1 - x if x < 0 else x for x in vdofs1]
mat_doftrans = get_inv_doftrans(doftrans, dof_sign1)
if USE_PARALLEL:
# After DofTransformation is introduced we can not use GetGlobalTDofNumber, because
# element local DoF could be linked with two TrueDoFs in neighber processes
# We construct submatrix of Prolongation to construct element matrix
# in TrueDof space
vv1 = [
P1mat.indices[P1mat.indptr[ii]:P1mat.indptr[ii + 1]]
for ii in vdofs1
]
vv3 = [
P1mat.data[P1mat.indptr[ii]:P1mat.indptr[ii + 1]]
for ii in vdofs1
]
ngtof = np.sum([len(x) for x in vv3])
sub_p = np.zeros((nd1, ngtof))
k1 = 0
k2 = 0
for gtofs, weights in zip(vv1, vv3):
for g, w in zip(gtofs, weights):
sub_p[k1, k2] = w
k2 = k2 + 1
k1 = k1 + 1
vdofs1 = np.hstack(vv1).flatten()
mat_doftrans = mat_doftrans.dot(sub_p)
res, misalignment = map_ir(fe1, eltrans, coeff, shape1, dim2,
sdim2, locnors2, dof_sign1,
mat_doftrans, MV)
vdofs1_arr[rank].append(np.array(vdofs1))
data1_arr[rank].append(res)
max_misalignment = np.max([max_misalignment, np.max(misalignment)])
# res.shape = (#Npoints, #DoF1)
if USE_PARALLEL:
vdofs1_arr = alltoall_vectorv(vdofs1_arr, int) # transfer to mesh2
if is_complex:
data1_arr = alltoall_vectorv(data1_arr,
complex) # transfer to mesh2
else:
data1_arr = alltoall_vectorv(data1_arr, float) # transfer to mesh2
max_misalignment = np.max(
MPI.COMM_WORLD.gather(max_misalignment, root=0))
dprint1("Max misalignment: ", max_misalignment)
shared_data = []
for rank, i_el2s in enumerate(el2_arr):
for k, i_el2 in enumerate(i_el2s):
vdofs1 = vdofs1_arr[rank][k]
fe2 = fes2.GetFE(i_el2)
eltrans2 = fes2.GetElementTransformation(i_el2)
vdofs2 = fes2.GetElementVDofs(i_el2)
vdofs2 = [-1 - x if x < 0 else x for x in vdofs2]
d1 = data1_arr[rank][k]
d2 = data2_arr[rank][k]
mm = d2.transpose().dot(d1)
if USE_PARALLEL:
# prepare data for not-owned DoFs, which will be shared later
vdofs22 = [fes2.GetLocalTDofNumber(ii) for ii in vdofs2]
vdofs22g = [fes2.GetGlobalTDofNumber(ii) for ii in vdofs2]
kkk = 0
for v2, v2g in zip(vdofs22, vdofs22g):
if v2 < 0:
shared_data.append([v2g, mm[kkk, :], vdofs1])
kkk = kkk + 1
else:
vdofs22 = vdofs2
for i, ltdof2 in enumerate(vdofs22):
if ltdof2 < 0:
continue
for j, gtdof1 in enumerate(vdofs1):
mat[ltdof2, gtdof1] = mat[ltdof2, gtdof1] + mm[i, j]
if USE_PARALLEL:
#nicePrint("shared data", shared_data)
for source_id in range(nprc):
data = comm.bcast(shared_data, root=source_id)
myoffset = fes2.GetMyTDofOffset()
for v2g, elmat, vdofs1 in data:
if v2g >= myoffset and v2g < myoffset + mat.shape[0]:
i = v2g - myoffset
for j, gtdof1 in enumerate(vdofs1):
mat[i, gtdof1] = mat[i, gtdof1] + elmat[j]
#mat[i, vdofs1] = mat[i, vdofs1] + elmat
from scipy.sparse import coo_matrix, csr_matrix
if USE_PARALLEL:
if is_complex:
m1 = csr_matrix(mat.real, dtype=float)
m2 = csr_matrix(mat.imag, dtype=float)
else:
m1 = csr_matrix(mat.real, dtype=float)
m2 = None
from mfem.common.chypre import CHypreMat
start_col = fes1.GetMyTDofOffset()
end_col = fes1.GetMyTDofOffset() + fes1.GetTrueVSize()
col_starts = [start_col, end_col, mat.shape[1]]
M = CHypreMat(m1, m2, col_starts=col_starts)
else:
from petram.helper.block_matrix import convert_to_ScipyCoo
M = convert_to_ScipyCoo(coo_matrix(mat, dtype=mat.dtype))
return M
def set_point(self, T, ip, g, l, t=None):
nor = mfem.Vector(self.sdim)
mfem.CalcOrtho(T.Jacobian(), nor)
self.nor = nor.GetDataArray().copy()
def preprocess_params(self, engine):
### find normal (outward) vector...
mesh = engine.get_emesh(mm=self) ###
fespace = engine.fespaces[self.get_root_phys().dep_vars[0]]
nbe = mesh.GetNBE()
ibe = np.array([
i for i in range(nbe)
if mesh.GetBdrElement(i).GetAttribute() == self._sel_index[0]
])
dprint1("idb", ibe)
el = mesh.GetBdrElement(ibe[0])
Tr = fespace.GetBdrElementTransformation(ibe[0])
rules = mfem.IntegrationRules()
ir = rules.Get(el.GetGeometryType(), 1)
Tr.SetIntPoint(ir.IntPoint(0))
nor = mfem.Vector(3)
mfem.CalcOrtho(Tr.Jacobian(), nor)
self.norm = nor.GetDataArray().copy()
self.norm = self.norm / np.sqrt(np.sum(self.norm**2))
#freq = self._global_ns["freq"]
#self.omega = freq * 2 * np.pi
#dprint1("Frequency " + (freq).__repr__())
dprint1("Normal Vector " + list(self.norm).__repr__())
### find rectangular shape
if str(self.mode).upper().strip() in ['TE', 'TM', 'TEM']:
edges = np.array([mesh.GetBdrElementEdges(i)[0]
for i in ibe]).flatten()
d = {}
for x in edges:
d[x] = x in d
edges = [x for x in d.keys() if not d[x]]
ivert = [mesh.GetEdgeVertices(x) for x in edges]
ivert = connect_pairs(ivert)
vv = np.vstack([mesh.GetVertexArray(i) for i in ivert])
self.ctr = (np.max(vv, 0) + np.min(vv, 0)) / 2.0
dprint1("Center " + list(self.ctr).__repr__())
### rectangular port
#idx = np.argsort(np.sqrt(np.sum((vv - self.ctr)**2,1)))
#corners = vv[idx[-4:],:]
# since vv is cyclic I need to omit last one element here..
idx = np.argsort(np.sqrt(np.sum((vv[:-1] - self.ctr)**2, 1)))
corners = vv[:-1][idx[-4:], :]
for i in range(4):
dprint1("Corner " + list(corners[i]).__repr__())
tmp = np.sort(np.sqrt(np.sum((corners - corners[0, :])**2, 1)))
self.b = tmp[1]
self.a = tmp[2]
tmp = np.argsort(np.sqrt(np.sum((corners - corners[0, :])**2, 1)))
self.c = corners[0] # corner
self.b_vec = corners[tmp[1]] - corners[0]
self.a_vec = np.cross(self.b_vec, self.norm)
# self.a_vec = corners[tmp[2]]-corners[0]
self.b_vec = self.b_vec / np.sqrt(np.sum(self.b_vec**2))
self.a_vec = self.a_vec / np.sqrt(np.sum(self.a_vec**2))
if np.sum(np.cross(self.a_vec, self.b_vec) * self.norm) > 0:
self.a_vec = -self.a_vec
if self.mode == 'TEM':
'''
special handling
set a vector along PEC-like edge, regardless the actual
length of edges
'''
for i in range(nbe):
if (edges[0] in mesh.GetBdrElementEdges(i)[0]
and self._sel_index[0] != mesh.GetBdrAttribute(i)):
dprint1("Checking surface :", mesh.GetBdrAttribute(i))
attr = mesh.GetBdrAttribute(i)
break
for node in self.get_root_phys().walk():
if not isinstance(node, Bdry): continue
if not node.enabled: continue
if attr in node._sel_index:
break
from petram.model import Pair
ivert = mesh.GetEdgeVertices(edges[0])
vect = mesh.GetVertexArray(ivert[0]) - mesh.GetVertexArray(
ivert[1])
vect = vect / np.sqrt(np.sum(vect**2))
do_swap = False
if (isinstance(node, Pair)
and np.abs(np.sum(self.a_vec * vect)) > 0.9):
do_swap = True
if (not isinstance(node, Pair)
and np.abs(np.sum(self.a_vec * vect)) < 0.001):
do_swap = True
if do_swap:
dprint1("swapping port edges")
tmp = self.a_vec
self.a_vec = -self.b_vec
self.b_vec = tmp
# - sign is to keep a \times b direction.
tmp = self.a
self.a = self.b
self.b = tmp
if self.a_vec[np.argmax(np.abs(self.a_vec))] < 0:
self.a_vec = -self.a_vec
self.b_vec = -self.b_vec
dprint1("Long Edge " + self.a.__repr__())
dprint1("Long Edge Vec." + list(self.a_vec).__repr__())
dprint1("Short Edge " + self.b.__repr__())
dprint1("Short Edge Vec." + list(self.b_vec).__repr__())
elif self.mode == 'Coax(TEM)':
edges = np.array([mesh.GetBdrElementEdges(i)[0]
for i in ibe]).flatten()
d = {}
for x in edges:
d[x] = x in d
edges = [x for x in d.keys() if not d[x]]
ivert = [mesh.GetEdgeVertices(x) for x in edges]
iv1, iv2 = connect_pairs(ivert) # index of outer/inner circles
vv1 = np.vstack([mesh.GetVertexArray(i) for i in iv1])
vv2 = np.vstack([mesh.GetVertexArray(i) for i in iv2])
ctr1, a1 = find_circle_center_radius(vv1, self.norm)
ctr2, b1 = find_circle_center_radius(vv2, self.norm)
self.ctr = np.mean((ctr1, ctr2), 0)
self.a = a1 if a1 < b1 else b1
self.b = a1 if a1 > b1 else b1
dprint1("Big R: " + self.b.__repr__())
dprint1("Small R: " + self.a.__repr__())
dprint1("Center: " + self.ctr.__repr__())
vv = vv1
C_Et, C_jwHt = self.get_coeff_cls()
self.vt.preprocess_params(self)
inc_amp, inc_phase, eps, mur = self.vt.make_value_or_expression(self)
dprint1("E field pattern", eps, mur)
Et = C_Et(3, self, real=True, eps=eps, mur=mur)
for p in vv:
dprint1(p.__repr__() + ' : ' + Et.EvalValue(p).__repr__())
dprint1("H field pattern")
Ht = C_jwHt(3, 0.0, self, real=False, eps=eps, mur=mur)
for p in vv:
dprint1(p.__repr__() + ' : ' + Ht.EvalValue(p).__repr__())