def __init__(self):
self.filename_nodes = 'node_coordinates'
self.filename_hex8 = 'cell_connectivity_hex8'
self.filename_tet4 = 'cell_connectivity_tet4'
#
self.hex8 = []
self.tet4 = []
#
print "number of volumes = " + str(cubit.get_volume_count())
print "number of hexes in entire mesh: cubit.get_hex_count = " + str(
cubit.get_hex_count())
print "number of tets in entire mesh: cubit.get_tet_count = " + str(
cubit.get_tet_count())
#
for volume in cubit.get_entities("volume"):
print "VOLUME " + str(volume) + ":"
print " number of elements: " + str(
cubit.get_volume_element_count(volume))
hex8_list = cubit.get_volume_hexes(volume)
self.hex8 += hex8_list
print " number of hexes: " + str(len(hex8_list))
tet4_list = cubit.get_volume_tets(volume)
self.tet4 += tet4_list
print " number of tets: " + str(len(tet4_list))
#
print "number of hexes found while iterating over all volumes: " + str(
len(self.hex8))
print "number of tets found while iterating over all volumes: " + str(
len(self.tet4))
def mesh_write(self,mesh_name):
meshfile=open(mesh_name,'w')
print 'Writing '+mesh_name+'.....'
num_elems=cubit.get_hex_count()
print ' total number of elements:',str(num_elems)
meshfile.write(str(num_elems)+'\n')
for block,flag in zip(self.block_mat,self.block_flag):
hexes=cubit.get_block_hexes(block)
print 'block ',block,' hexes ',len(hexes)
for hexa in hexes:
txt=self.create_hexnode_string(hexa)
meshfile.write(txt)
meshfile.close()
def mesh_write(self, mesh_name):
meshfile = open(mesh_name, 'w')
print 'Writing ' + mesh_name + '.....'
num_elems = cubit.get_hex_count()
print ' total number of elements:', str(num_elems)
meshfile.write(str(num_elems) + '\n')
for block, flag in zip(self.block_mat, self.block_flag):
hexes = cubit.get_block_hexes(block)
print 'block ', block, ' hexes ', len(hexes)
for hexa in hexes:
txt = self.create_hexnode_string(hexa)
meshfile.write(txt)
meshfile.close()
def main():
cubit.init([''])
cubit.cmd('## Cubit Version 11.0')
cubit.cmd('## -warning = On')
cubit.cmd('## -information = On')
cubit.cmd('reset')
#
cubit.cmd('brick x 10 y 10 z 10')
cubit.cmd('volume 1 size auto factor 4')
cubit.cmd('mesh volume 1')
cubit.cmd('sideset 1 surface 4')
cubit.cmd('sideset 2 surface 6')
#
hexs = cubit.get_hex_count()
for i in xrange(1, hexs+1):
cubit.cmd('block ' + str(i) + ' hex ' + str(i))
#
cubit.cmd('export genesis "large_sub_cube.e" dimension 3 overwrite')
def mesh_write(self, mesh_name):
meshfile = open(mesh_name, "w")
print "Writing " + mesh_name + "....."
num_elems = cubit.get_hex_count()
print " number of elements:", str(num_elems)
meshfile.write(str(num_elems) + "\n")
num_write = 0
for block, flag in zip(self.block_mat, self.block_flag):
# print block,flag
hexes = cubit.get_block_hexes(block)
# print len(hexes)
for hexa in hexes:
# print hexa
nodes = cubit.get_connectivity("Hex", hexa)
# nodes=self.jac_check(nodes) #is it valid for 3D? TODO
txt = ("%10i ") % hexa
txt = txt + ("%10i %10i %10i %10i %10i %10i %10i %10i\n") % nodes[:]
meshfile.write(txt)
meshfile.close()
print "Ok"
def mesh_write(self,mesh_name):
meshfile=open(mesh_name,'w')
print 'Writing '+mesh_name+'.....'
num_elems=cubit.get_hex_count()
print ' number of elements:',str(num_elems)
meshfile.write(str(num_elems)+'\n')
num_write=0
for block,flag in zip(self.block_mat,self.block_flag):
#print block,flag
hexes=cubit.get_block_hexes(block)
#print len(hexes)
for hexa in hexes:
#print hexa
nodes=cubit.get_connectivity('Hex',hexa)
#nodes=self.jac_check(nodes) #is it valid for 3D? TODO
txt=('%10i ')% hexa
txt=txt+('%10i %10i %10i %10i %10i %10i %10i %10i\n')% nodes[:]
meshfile.write(txt)
meshfile.close()
print 'Ok'
def mesh_write(self, mesh_name):
meshfile = open(mesh_name, 'w')
print 'Writing ' + mesh_name + '.....'
num_elems = cubit.get_hex_count()
print ' number of elements:', str(num_elems)
meshfile.write(str(num_elems) + '\n')
num_write = 0
for block, flag in zip(self.block_mat, self.block_flag):
#print block,flag
hexes = cubit.get_block_hexes(block)
#print len(hexes)
for hexa in hexes:
#print hexa
nodes = cubit.get_connectivity('Hex', hexa)
#nodes=self.jac_check(nodes) #is it valid for 3D? TODO
txt = ('%10i ') % hexa
txt = txt + (
'%10i %10i %10i %10i %10i %10i %10i %10i\n') % nodes[:]
meshfile.write(txt)
meshfile.close()
print 'Ok'
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
cubit.cmd('Block ' + str(b) + ' name "face_abs_ymin"')
b = b + 1
for i in side_xmax:
cmd = 'block ' + str(b) + ' face in surface ' + str(i)
cubit.cmd(cmd)
cubit.cmd('Block ' + str(b) + ' name "face_abs_xmax"')
b = b + 1
for i in side_ymax:
cmd = 'block ' + str(b) + ' face in surface ' + str(i)
cubit.cmd(cmd)
cubit.cmd('Block ' + str(b) + ' name "face_abs_ymax"')
b = b + 1
for i in side_zmin:
cmd = 'block ' + str(b) + ' face in surface ' + str(i)
cubit.cmd(cmd)
cubit.cmd('Block ' + str(b) + ' name "face_abs_bottom"')
b = b + 1
cubit.cmd('Block ' + str(b) + ' face in surface ' + str(s[0]))
cubit.cmd('Block ' + str(b) + ' name "face_topo"')
print '##total number of hex: ', cubit.get_hex_count(), ' ##'
os.system('mkdir -p MESH')
#### Export to SESAME format using cubit2specfem3d.py of GEOCUBIT
cubit2specfem3d.export2SESAME('MESH')
import cubit, os, sys
cubit.init([''])
cubit.cmd("reset")
cubit.cmd("playback 'Mandel3D_msh.jou'")
cubit.cmd("reset")
cubit.cmd(
"import mesh geometry './Mandel3D.exo' block all use nodeset sideset")
surf_list = cubit.get_sideset_surfaces(1)
quad_list = [
cubit.get_surface_quads(surf_list[i]) for i in range(len(surf_list))
]
vol_list = cubit.get_block_volumes(1)
hex_list = [cubit.get_volume_hexes(vol_list[i]) for i in range(len(vol_list))]
trac_el = []
mat_typ = np.ones(shape=(cubit.get_hex_count(), 1), dtype=np.uint8)
for quadset, hexset in zip(quad_list, hex_list):
for quad in quadset:
nodes = cubit.get_connectivity("quad", quad)
for hx in hexset:
nodes_hx = cubit.get_connectivity("hex", hx)
if set(nodes).issubset(set(nodes_hx)):
if set(nodes).issubset(set(np.array(nodes_hx)[[0, 1, 5, 4]])):
side = 1
elif set(nodes).issubset(set(np.array(nodes_hx)[[1, 2, 6,
6]])):
side = 2
elif set(nodes).issubset(set(np.array(nodes_hx)[[2, 3, 7,
7]])):
side = 3
elif set(nodes).issubset(set(np.array(nodes_hx)[[3, 2, 6,
