def saveMeshPoisson(self):
nNodes = cubit.get_node_count()
nTets = cubit.get_tet_count()
meshFile = open(folder+"meshPoisson.xml", 'w')
meshFile.write('<mesh celltype="tetrahedron" dim="3">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
meshFile.write(' <elements size="%d">\n' % (nTets))
for x in range(0, nTets):
nodes = cubit.get_connectivity("tet", x+1)
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d" v3="%d"/>\n' % (x,nodes[0]-1,nodes[1]-1,nodes[2]-1,nodes[3]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <boundary celltype="triangle" dim="2">\n')
surfs = cubit.get_relatives("volume", self.vol, "surface")
ec = 0
for x in range(0, 2):
tris = cubit.get_surface_tris(surfs[x])
for y in range(0, len(tris)):
nodes = cubit.get_connectivity("tri", tris[y])
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
ec = ec+1
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec,x,element[0],element[1],element[2]))
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec+1,2,element[0],element[1],element[2]))
meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
meshFile.write(' <node id="0" marker="0" value="-1.0" />\n')
meshFile.write(' <node id="1" marker="1" value="1.0" />\n')
meshFile.write(' </neumann>\n')
meshFile.write(' <dirichlet>\n')
meshFile.write(' <node id="2" marker="2" value="0.0" />\n')
meshFile.write(' </dirichlet>\n')
meshFile.write('</poisson>\n')
meshFile.close()
def saveMesh2D2(self):
cubit.cmd("create surface rectangle width 5000 height 5000 zplane")
cubit.cmd("create surface rectangle width 1000 height 1000 zplane")
cubit.cmd("subtract body 2 from body 1")
surfID = cubit.get_last_id("surface")
cubit.cmd("surface all size auto factor 4")
cubit.cmd("surface all scheme TriMesh")
cubit.cmd("mesh surface all")
nNodes = cubit.get_node_count()
meshFile = open(folder+"mesh2D2.xml", 'w')
meshFile.write('<mesh celltype="triangle" dim="2">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
tris = cubit.get_surface_tris(surfID)
meshFile.write(' <elements size="%d">\n' % (len(tris)))
for x in range(0, len(tris)):
nd = cubit.get_connectivity("tri", tris[x])
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d"/>\n' % (x,nd[0]-1,nd[1]-1,nd[2]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, len(tris)):
meshFile.write(' <element id="%d">\n' %(x))
meshFile.write(' <fiber>1.000000,0.000000,0.000000</fiber>\n')
meshFile.write(' </element>\n')
meshFile.write(' </element_data>\n')
meshFile.write(' <boundary celltype="line" dim="1">\n')
eds = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
ec = 1
surf = cubit.surface(surfID)
for y in range(0, len(eds)):
nodes = cubit.get_connectivity("edge", eds[y])
element = [nodes[0]-1, nodes[1]-1]
#cp = cubit.get_center_point("edge", eds[y])
#norm = surf.normal_at([cp[0],cp[1],cp[2]])
#cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" % (cp[0],cp[1],cp[2], norm[0], norm[1], norm[2], 200))
#ec = ec+1
#meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1,element[0],element[1], norm[0], norm[1], norm[2]))
#meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec+1,2,element[0],element[1],element[2]))
meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
meshFile.write(' <node id="1" marker="1" value="1.0" />\n')
meshFile.write(' </neumann>\n')
#meshFile.write(' <dirichlet>\n')
#meshFile.write(' <node id="2" marker="2" value="0.0" />\n')
#meshFile.write(' </dirichlet>\n')
meshFile.write('</poisson>\n')
meshFile.write('<electrophysiology>\n')
meshFile.write(' <stimuli number="1">\n')
bb = cubit.get_bounding_box("surface", surfID)
x0 = bb[0]
x1 = 0.8*x0 + 0.2*bb[1]
y0 = bb[3]
y1 = 0.8*y0 + 0.2*bb[4]
#z0 = bb[6]
#z1 = 0.8*z0 + 0.2*bb[7]
meshFile.write(' <stim start="0.00" duration="4.00" value="-35.7140" x0="%f" x1="%f" y0="%f" y1="%f" />\n' % (x0,x1,y0,y1))
meshFile.write(' </stimuli>\n')
meshFile.write('</electrophysiology>\n')
meshFile.close()
def saveMesh3D(self):
cubit.cmd("brick x 5000 y 5000 z 5000")
cubit.cmd("create cylinder height 4000 radius 500")
cubit.cmd("subtract body 2 from body 1")
volID = cubit.get_last_id("volume")
self.vol = volID
self.mesh()
nNodes = cubit.get_node_count()
meshFile = open(folder+"mesh3D2.xml", 'w')
meshFile.write('<mesh celltype="tetrahedron" dim="3">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
nTets = cubit.get_tet_count()
meshFile.write(' <elements size="%d">\n' % (nTets))
for x in range(0, nTets):
nodes = cubit.get_connectivity("tet", x+1)
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d" v3="%d"/>\n' % (x,nodes[0]-1,nodes[1]-1,nodes[2]-1,nodes[3]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, nTets):
meshFile.write(' <element id="%d">\n' %(x))
meshFile.write(' <fiber>1.000000,0.000000,0.000000</fiber>\n')
meshFile.write(' </element>\n')
meshFile.write(' </element_data>\n')
meshFile.write(' <boundary celltype="triangle" dim="2">\n')
bsurfs = [10, 11, 12]
ec = 0
for x in range(0, len(bsurfs)):
tris = cubit.get_surface_tris(bsurfs[x])
surf = cubit.surface(bsurfs[x])
for y in range(0, len(tris)):
cp = cubit.get_center_point("tri", tris[y])
norm = surf.normal_at([cp[0],cp[1],cp[2]])
#cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" % (cp[0],cp[1],cp[2],norm[0],norm[1],norm[2],200))
nodes = cubit.get_connectivity("tri", tris[y])
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1.0,element[0],element[1],element[2],norm[0],norm[1],norm[2]))
ec = ec+1
meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
meshFile.write(' <node id="1" marker="1" value="0.5" />\n')
meshFile.write(' </neumann>\n')
meshFile.write('</poisson>\n')
#meshFile.write('<electrophysiology>\n')
#meshFile.write(' <stimuli number="1">\n')
#bb = cubit.get_bounding_box("volume", self.vol)
#x0 = bb[0]
#x1 = 0.8*x0 + 0.2*bb[1]
#y0 = bb[3]
#y1 = 0.8*y0 + 0.2*bb[4]
#z0 = bb[6]
#z1 = 0.8*z0 + 0.2*bb[7]
#meshFile.write(' <stim start="0.00" duration="4.00" value="-35.7140" x0="%f" x1="%f" y0="%f" y1="%f" z0="%f" z1="%f" />\n' % (x0,x1,y0,y1,z0,z1))
#meshFile.write(' </stimuli>\n')
#meshFile.write('</electrophysiology>\n')
meshFile.close()
def saveMesh(self):
nNodes = cubit.get_node_count()
nTets = cubit.get_tet_count()
meshFile = open(folder+"Cubo.xml", 'w')
meshFile.write('<mesh celltype="tetrahedron" dim="3">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
meshFile.write(' <elements size="%d">\n' % (nTets))
for x in range(0, nTets):
nodes = cubit.get_connectivity("tet", x+1)
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d" v3="%d"/>\n' % (x,nodes[0]-1,nodes[1]-1,nodes[2]-1,nodes[3]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, nTets):
meshFile.write(' <element id="%d">\n' %(x))
meshFile.write(' <fiber>1.000000,0.000000,0.000000</fiber>\n')
meshFile.write(' </element>\n')
meshFile.write(' </element_data>\n')
meshFile.write(' <boundary celltype="triangle" dim="2">\n')
bsurfs = cubit.get_relatives("volume", self.vol, "surface")
ec = 0
for x in range(0, len(bsurfs)):
#for x in range(6, len(bsurfs)):
#if x is not 16 and x is not 14:
tris = cubit.get_surface_tris(bsurfs[x])
surf = cubit.surface(bsurfs[x])
for y in range(0, len(tris)):
cp = cubit.get_center_point("tri", tris[y])
norm = surf.normal_at([cp[0],cp[1],cp[2]])
#cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" % (cp[0],cp[1],cp[2],norm[0],norm[1],norm[2],200))
nodes = cubit.get_connectivity("tri", tris[y])
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1.0,element[0],element[1],element[2],norm[0],norm[1],norm[2]))
ec = ec+1
meshFile.write(' </boundary>\n')
#meshFile.write(' <boundary celltype="triangle" dim="2">\n')
#surfs = cubit.get_relatives("volume", self.vol, "surface")
#ec = 0
#for x in range(0, 2):
# tris = cubit.get_surface_tris(surfs[x])
# for y in range(0, len(tris)):
# nodes = cubit.get_connectivity("tri", tris[y])
# element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
# ec = ec+1
# meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec,x,element[0],element[1],element[2]))
#meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec+1,2,element[0],element[1],element[2]))
#meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
#meshFile.write(' <node id="0" marker="0" value="-1.0" />\n')
meshFile.write(' <node id="1" marker="1" value="0.05"/>\n')
meshFile.write(' </neumann>\n')
#meshFile.write(' <dirichlet>\n')
#meshFile.write(' <node id="2" marker="2" value="0.0" />\n')
#meshFile.write(' </dirichlet>\n')
meshFile.write('</poisson>\n')
#meshFile.write('<electrophysiology>\n')
#meshFile.write(' <stimuli number="1">\n')
#bb = cubit.get_bounding_box("volume", self.vol)
#x0 = bb[0]
#x1 = 0.8*x0 + 0.2*bb[1]
#y0 = bb[3]
#y1 = 0.8*y0 + 0.2*bb[4]
#z0 = bb[6]
#z1 = 0.8*z0 + 0.2*bb[7]
#meshFile.write(' <stim start="0.00" duration="4.00" value="-35.7140" x0="%f" x1="%f" y0="%f" y1="%f" z0="%f" z1="%f" />\n' % (x0,x1,y0,y1,z0,z1))
#meshFile.write(' </stimuli>\n')
#meshFile.write('</electrophysiology>\n')
meshFile.close()
def savemesh(mpiflag, iproc=0, filename=None):
import start as start
cfg = start.start_cfg(filename=filename)
mpiflag, iproc, numproc, mpi = start.start_mpi()
def runsave(meshfile, iproc, filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag = 0
ner = cubit.get_error_count()
cubitcommand = 'save as "' + cfg.output_dir + \
'/' + meshfile + '.cub' + '" overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
cubitcommand = 'export mesh "' + cfg.output_dir + '/' + \
meshfile + '.e' + '" dimension 3 block all overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
flag = 1
return flag
meshfile = 'mesh_vol_' + str(iproc)
flagsaved = 0
infosave = (iproc, flagsaved)
mpi.barrier()
total_saved = mpi.allgather(flagsaved)
if isinstance(total_saved, int):
total_saved = [total_saved]
ind = 0
saving = True
while saving:
if len(total_saved) != sum(total_saved):
#
if not flagsaved:
flagsaved = runsave(meshfile, iproc, filename=filename)
if flagsaved:
infosave = (iproc, flagsaved)
if numproc > 1:
f = open('mesh_saved' + str(iproc), 'w')
f.close()
mpi.barrier()
total_saved = mpi.allgather(flagsaved)
if isinstance(total_saved, int):
total_saved = [total_saved]
ind = ind + 1
else:
saving = False
if ind > len(total_saved) + 10:
saving = False
print sum(total_saved), '/', len(total_saved), ' saved'
info_total_saved = mpi.allgather(infosave)
if isinstance(info_total_saved, int):
info_total_saved = [info_total_saved]
if iproc == 0:
f = open('mesh_saving.log', 'w')
f.write('\n'.join(str(x) for x in info_total_saved))
f.close()
f = open(cfg.output_dir + '/' + 'blocks_' + str(iproc).zfill(5), 'w')
blocks = cubit.get_block_id_list()
for block in blocks:
name = cubit.get_exodus_entity_name('block', block)
element_count = cubit.get_exodus_element_count(block, "block")
nattrib = cubit.get_block_attribute_count(block)
attr = [cubit.get_block_attribute_value(
block, x) for x in range(0, nattrib)]
ty = cubit.get_block_element_type(block)
f.write(str(block) + ' ; ' + name + ' ; nattr ' + str(nattrib) +
' ; ' + ' '.join(str(x) for x in attr) + ' ; ' + ty + ' ' +
str(element_count) + '\n')
f.close()
import quality_log
f = open(cfg.output_dir + '/' + 'quality_' + str(iproc).zfill(5), 'w')
max_skewness, min_length = quality_log.quality_log(f)
f.close()
count_hex = [cubit.get_hex_count()]
count_node = [cubit.get_node_count()]
max_skew = [(iproc, max_skewness)]
min_l = [(iproc, min_length)]
mpi.barrier()
total_min_l = mpi.gather(min_l)
total_hex = mpi.gather(count_hex)
total_node = mpi.gather(count_node)
total_max_skew = mpi.gather(max_skew)
mpi.barrier()
if iproc == 0:
min_total_min_l = min([ms[1] for ms in total_min_l])
max_total_max_skew = max([ms[1] for ms in total_max_skew])
sum_total_node = sum(total_node)
sum_total_hex = sum(total_hex)
totstat_file = open(cfg.output_dir + '/totstat.log', 'w')
text = 'hex total number,node total number,max skew, min length\n'
totstat_file.write(text)
text = str(sum_total_hex) + ' , ' + str(sum_total_node) + ' , ' + \
str(max_total_max_skew) + ' , ' + str(min_total_min_l) + '\n'
totstat_file.write(text)
totstat_file.write(str(total_max_skew))
totstat_file.close()
print 'meshing process end... proc ', iproc
def savemesh(mpiflag, iproc=0, filename=None):
import start as start
cfg = start.start_cfg(filename=filename)
mpiflag, iproc, numproc, mpi = start.start_mpi()
def runsave(meshfile, iproc, filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag = 0
ner = cubit.get_error_count()
cubitcommand = 'save as "' + cfg.output_dir + '/' + meshfile + '.cub' + '" overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
cubitcommand = 'export mesh "' + cfg.output_dir + '/' + meshfile + '.e' + '" dimension 3 block all overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
flag = 1
return flag
meshfile = 'mesh_vol_' + str(iproc)
flagsaved = 0
infosave = (iproc, flagsaved)
mpi.barrier()
total_saved = mpi.allgather(flagsaved)
if isinstance(total_saved, int): total_saved = [total_saved]
ind = 0
saving = True
while saving:
if len(total_saved) != sum(total_saved):
#
if not flagsaved:
flagsaved = runsave(meshfile, iproc, filename=filename)
if flagsaved:
infosave = (iproc, flagsaved)
if numproc > 1:
f = open('mesh_saved' + str(iproc), 'w')
f.close()
mpi.barrier()
total_saved = mpi.allgather(flagsaved)
if isinstance(total_saved, int): total_saved = [total_saved]
ind = ind + 1
else:
saving = False
if ind > len(total_saved) + 10: saving = False
print sum(total_saved), '/', len(total_saved), ' saved'
info_total_saved = mpi.allgather(infosave)
if isinstance(info_total_saved, int): info_total_saved = [info_total_saved]
if iproc == 0:
f = open('mesh_saving.log', 'w')
f.write('\n'.join(str(x) for x in info_total_saved))
f.close()
f = open(cfg.output_dir + '/' + 'blocks_' + str(iproc).zfill(5), 'w')
blocks = cubit.get_block_id_list()
for block in blocks:
name = cubit.get_exodus_entity_name('block', block)
element_count = cubit.get_exodus_element_count(block, "block")
nattrib = cubit.get_block_attribute_count(block)
attr = [
cubit.get_block_attribute_value(block, x)
for x in range(0, nattrib)
]
ty = cubit.get_block_element_type(block)
f.write(
str(block) + ' ; ' + name + ' ; nattr ' + str(nattrib) + ' ; ' +
' '.join(str(x) for x in attr) + ' ; ' + ty + ' ' +
str(element_count) + '\n')
f.close()
import quality_log
f = open(cfg.output_dir + '/' + 'quality_' + str(iproc).zfill(5), 'w')
max_skewness, min_length = quality_log.quality_log(f)
f.close()
count_hex = [cubit.get_hex_count()]
count_node = [cubit.get_node_count()]
max_skew = [(iproc, max_skewness)]
min_l = [(iproc, min_length)]
mpi.barrier()
total_min_l = mpi.gather(min_l)
total_hex = mpi.gather(count_hex)
total_node = mpi.gather(count_node)
total_max_skew = mpi.gather(max_skew)
mpi.barrier()
if iproc == 0:
min_total_min_l = min([ms[1] for ms in total_min_l])
max_total_max_skew = max([ms[1] for ms in total_max_skew])
sum_total_node = sum(total_node)
sum_total_hex = sum(total_hex)
totstat_file = open(cfg.output_dir + '/totstat.log', 'w')
text = 'hex total number,node total number,max skew, min length\n'
totstat_file.write(text)
text = str(sum_total_hex) + ' , ' + str(sum_total_node) + ' , ' + str(
max_total_max_skew) + ' , ' + str(min_total_min_l) + '\n'
totstat_file.write(text)
totstat_file.write(str(total_max_skew))
totstat_file.close()
print 'meshing process end... proc ', iproc
side = 5
elif set(nodes).issubset(set(np.array(nodes_hx)[[4, 5, 6,
7]])):
side = 6
trac_el.append([hx, side])
mat_typ[hx - 1] = 2
mat = [[
3.0E10, 0.25, 1.0E25, 1.0, 3000, 1.0E-12, 0.9664429530201342, 0.0, 2.2E9
], [3.0E10, 0.25, 1.0E25, 1.0, 3000, 1.0E-12, 0.9664429530201342, 0.0, 2.2E9]]
trac_bc = np.zeros(shape=[len(trac_el), 6])
trac_bc[:, 2] = -1E6
coord = np.empty(shape=[0, 3], dtype=np.float16)
hx_node = np.empty(shape=[0, 8], dtype=np.uint16)
for node in range(cubit.get_node_count()):
coord = np.vstack((coord, cubit.get_nodal_coordinates(node + 1)))
bcy_nodes = cubit.get_nodeset_nodes_inclusive(1)
bcx_nodes = cubit.get_nodeset_nodes_inclusive(2)
bcz_nodes = cubit.get_nodeset_nodes_inclusive(3)
bcp_nodes = cubit.get_nodeset_nodes_inclusive(4)
bc_typ = np.ones((cubit.get_node_count(), 4), dtype=np.int8)
for node in bcx_nodes:
bc_typ[node - 1, 0] = 0
for node in bcy_nodes:
bc_typ[node - 1, 1] = 0
for node in bcz_nodes:
bc_typ[node - 1, 2] = 0
for node in bcp_nodes: