def load_state_1D_vtk(name):
"""Load one VTK file containing state in time
Parameters
----------
name : str
Returns
-------
coors : ndarray
u : ndarray
"""
from sfepy.discrete.fem.meshio import MeshioLibIO
io = MeshioLibIO(name)
coors = io.read(Mesh()).coors[:, 0, None]
data = io.read_data(step=0)
var_name = head([k for k in data.keys() if "_modal" in k])[:-1]
if var_name is None:
print("File {} does not contain modal data.".format(name))
return
porder = len([k for k in data.keys() if var_name in k])
u = nm.zeros((porder, coors.shape[0] - 1, 1, 1))
for ii in range(porder):
u[ii, :, 0, 0] = data[var_name+'{}'.format(ii)].data
return coors, u
def load_1D_vtks(fold, name):
"""Reads series of .vtk files and crunches them into form
suitable for plot10_DG_sol.
Attempts to read modal cell data for variable mod_data. i.e.
``?_modal{i}``, where i is number of modal DOF
Resulting solution data have shape:
``(order, nspace_steps, ntime_steps, 1)``
Parameters
----------
fold :
folder where to look for files
name :
used in ``{name}.i.vtk, i = 0,1, ... tns - 1``
Returns
-------
coors : ndarray
mod_data : ndarray
solution data
"""
files = glob(pjoin(fold, name) + ".[0-9]*")
if len(files) == 0: # no multiple time steps, try loading single file
print("No files {} found in {}".format(pjoin(fold, name) + ".[0-9]*", fold))
print("Trying {}".format(pjoin(fold, name) + ".vtk"))
files = glob(pjoin(fold, name) + ".vtk")
if files:
return load_state_1D_vtk(files[0])
else:
print("Nothing found.")
return
io = MeshioLibIO(files[0])
coors = io.read(Mesh()).coors[:, 0, None]
data = io.read_data(step=0)
var_name = head([k for k in data.keys() if "_modal" in k])[:-1]
if var_name is None:
print("File {} does not contain modal data.".format(files[0]))
return
porder = len([k for k in data.keys() if var_name in k])
tn = len(files)
nts = sorted([int(f.split(".")[-2]) for f in files])
digs = len(files[0].split(".")[-2])
full_name_form = ".".join((pjoin(fold, name), ("{:0" + str(digs) + "d}"), "vtk"))
mod_data = nm.zeros((porder, coors.shape[0] - 1, tn, 1))
for i, nt in enumerate(nts):
io = MeshioLibIO(full_name_form.format(nt))
# parameter "step" does nothing, but is obligatory
data = io.read_data(step=0)
for ii in range(porder):
mod_data[ii, :, i, 0] = data[var_name+'{}'.format(ii)].data
return coors, mod_data
def gen_mesh_from_poly(filename, verbose=True):
"""
Import mesh generated by tetgen or triangle.
Parameters
----------
filename : string
file name
Returns
-------
mesh : Mesh instance
triangular or tetrahedral mesh
"""
def getnodes(fnods, up):
f = file(fnods)
l = [int(x) for x in f.readline().split()]
npoints, dim, nattrib, nbound = l
if verbose: up.init(npoints)
nodes = []
for line in f:
if line[0] == "#": continue
l = [float(x) for x in line.split()]
l = l[:(dim + 1)]
l[0] = int(l[0])
nodes.append(tuple(l))
assert l[0] == len(nodes)
assert npoints == len(nodes)
return nodes
def getele(fele, up):
f = file(fele)
l = [int(x) for x in f.readline().split()]
nele, nnod, nattrib = l
#we have either linear or quadratic tetrahedra:
if nnod in [4, 10]:
elem = 'tetra'
linear = (nnod == 4)
if nnod in [3, 7]:
elem = 'tri'
linear = (nnod == 3)
# if nattrib!=1:
# raise "tetgen didn't assign an entity number to each element (option -A)"
els = []
regions = {}
for line in f:
if line[0] == "#": continue
l = [int(x) for x in line.split()]
if elem == 'tri':
if linear:
assert (len(l) - 1 - nattrib) == 3
els.append((l[0], l[1], l[2], l[3]))
regionnum = l[5]
else:
assert len(l) - 2 == 10
els.append((l[0], 54, l[1], l[2], l[3], l[4], l[5], l[6],
l[7], l[8], l[9], l[10]))
regionnum = l[11]
if elem == 'tetra':
if linear:
assert len(l) - 2 == 4
els.append((l[0], 54, l[1], l[2], l[3], l[4]))
regionnum = l[5]
else:
assert len(l) - 2 == 10
els.append((l[0], 54, l[1], l[2], l[3], l[4], l[5], l[6],
l[7], l[8], l[9], l[10]))
regionnum = l[11]
if regionnum == 0:
print "see %s, element # %d" % (fele, l[0])
raise "there are elements not belonging to any physical entity"
if regions.has_key(regionnum):
regions[regionnum].append(l[0])
else:
regions[regionnum] = [l[0]]
assert l[0] == len(els)
if verbose: up.update(l[0])
return els, regions, linear
def getBCfaces(ffaces, up):
f = file(ffaces)
l = [int(x) for x in f.readline().split()]
nfaces, nattrib = l
if nattrib != 1:
raise "tetgen didn't assign an entity number to each face \
(option -A)"
if verbose: up.init(nfaces)
faces = {}
for line in f:
if line[0] == "#": continue
l = [int(x) for x in line.split()]
assert len(l) == 5
regionnum = l[4]
if regionnum == 0: continue
if faces.has_key(regionnum):
faces[regionnum].append((l[1], l[2], l[3]))
else:
faces[regionnum] = [(l[1], l[2], l[3])]
if verbose: up.update(l[0])
return faces
def calculatexyz(nodes, els):
"""Calculate the missing xyz values in place"""
def avg(i, j, n4, nodes):
a = nodes[n4[i - 1] - 1]
b = nodes[n4[j - 1] - 1]
return (a[1] + b[1]) / 2, (a[2] + b[2]) / 2, (a[3] + b[3]) / 2
def getxyz(i, n4, nodes):
if i + 5 == 5: return avg(1, 2, n4, nodes)
if i + 5 == 6: return avg(2, 3, n4, nodes)
if i + 5 == 7: return avg(1, 3, n4, nodes)
if i + 5 == 8: return avg(1, 4, n4, nodes)
if i + 5 == 9: return avg(2, 4, n4, nodes)
if i + 5 == 10: return avg(3, 4, n4, nodes)
raise "wrong topology"
for e in els:
n4 = e[2:2 + 4]
n6 = e[2 + 4:2 + 4 + 10]
for i, n in enumerate(n6):
x, y, z = getxyz(i, n4, nodes)
nodes[n - 1] = (n, x, y, z)
if verbose: print "Reading geometry from poly file..."
m = Mesh()
m.nodes = getnodes(filename + ".node")
m.elements, m.regions, lin = getele(filename + ".ele")
if not lin:
#tetgen doesn't compute xyz coordinates of the aditional 6 nodes
#(only of the 4 corner nodes) in tetrahedra.
calculatexyz(m.nodes, m.elements)
m.faces = getBCfaces(filename + ".face")
return m
