def collect_old(cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1,cubfiles=False,ckbound_method1=False,ckbound_method2=False,merge_tolerance=None,curverefining=False,outfilename='totalmesh_merged',qlog=False,export2SPECFEM3D=False,listblock=None,listflag=None,outdir='.',add_sea=False,decimate=False,cpml=False,cpml_size=False,top_absorbing=False,hex27=False):
#
cubit.cmd('set journal error off')
cubit.cmd('set verbose error off')
collecting_merging(cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy,cubfiles=cubfiles,ckbound_method1=ckbound_method1,ckbound_method2=ckbound_method2,merge_tolerance=merge_tolerance,decimate=decimate)
cubit.cmd('set journal error on')
cubit.cmd('set verbose error on')
#
if curverefining:
block=1001 #topography
refine_closecurve(block,curverefining,acis=True)
#
#
if add_sea:
block=1001
add_sea_layer(block=block)
outdir2='/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2=outdir+'/'
else:
outdir2=outdir+'/'+outdir2+'/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command="export mesh '"+outdir2+outfilename+".e' block all overwrite xml '"+outdir2+outfilename+".xml'"
cubit.cmd(command)
f=open(outdir2+'blocks.dat','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()
#
#
cubit.cmd('set info echo journ off')
cmd='del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
command = "save as '"+outdir2+outfilename+".cub' overwrite"
cubit.cmd(command)
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq=open(outdir2+outfilename+'.quality','w')
max_skewness,min_length=quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,listblock=listblock,listflag=listflag,outdir=outdir,cpml=cpml,cpml_size=cpml_size,top_absorbing=top_absorbing,hex27=hex27)
def collect_new(cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1,cubfiles=False,ckbound_method1=False,ckbound_method2=False,merge_tolerance=None,curverefining=False,outfilename='totalmesh_merged',qlog=False,export2SPECFEM3D=False,listblock=None,listflag=None,outdir='.',add_sea=False,decimate=False,cpml=False,cpml_size=False,top_absorbing=False,hex27=False,save_cubfile=True,check_merging=False):
#
cubit.cmd('set info off')
cubit.cmd('set echo off')
cubit.cmd('set journal off')
#cubit.cmd('set error off')
version_cubit=get_cubit_version()
if decimate:
if version_cubit >= 14.0:
raise VersionException('check cubit version, decimate capability has been tested only with cubit <= 12.2')
if version_cubit <= 12.2:
collecting_merging(cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy,cubfiles=cubfiles,ckbound_method1=ckbound_method1,ckbound_method2=ckbound_method2,merge_tolerance=merge_tolerance,decimate=decimate)
elif version_cubit >= 14:
collecting_merging_new(cpuxmin,cpuxmax+1,cpuymin,cpuymax+1,cpux,cpuy,cubfiles=cubfiles,check_merging=check_merging)
else:
raise VersionException('check cubit version, parallel capability of geocubit is working with cubit/trelis 14+ (or cubit 12.2)')
cubit.cmd('set info on')
cubit.cmd('set echo on')
cubit.cmd('set journal on')
#cubit.cmd('set error on')
#
if curverefining:
if version_cubit <= 12.2:
block=1001 #topography
refine_closecurve(block,curverefining,acis=True)
else:
raise VersionException('check cubit version, refine curve capability has been tested only with cubit <= 12.2')
#
#
if add_sea:
if version_cubit <= 12.2:
block=1001
add_sea_layer(block=block)
else:
raise VersionException('check cubit version, sea capability has been tested only with cubit <= 12.2')
outdir2='/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2=outdir+'/'
else:
outdir2=outdir+'/'+outdir2+'/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command="export mesh '"+outdir2+outfilename+".e' block all overwrite xml '"+outdir2+outfilename+".xml'"
cubit.cmd(command)
f=open(outdir2+'blocks.dat','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()
#
#
cubit.cmd('set info echo journ off')
cmd='del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq=open(outdir2+outfilename+'.quality','w')
max_skewness,min_length=quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,listblock=listblock,listflag=listflag,outdir=outdir,cpml=cpml,cpml_size=cpml_size,top_absorbing=top_absorbing,hex27=hex27)
if save_cubfile:
vol_blocks=[x for x in blocks if x <=1000]
cubit.cmd("create mesh geometry block "+' '.join(str(x) for x in vol_blocks)+" feature_angle 135.0")
command = "save as '"+outdir2+outfilename+".cub' overwrite"
print command
cubit.cmd(command)
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 collect(cpuxmin=0,
cpuxmax=1,
cpuymin=0,
cpuymax=1,
cpux=1,
cpuy=1,
cubfiles=False,
ckbound_method1=False,
ckbound_method2=False,
merge_tolerance=None,
curverefining=False,
outfilename='totalmesh_merged',
qlog=False,
export2SPECFEM3D=False,
listblock=None,
listflag=None,
outdir='.',
add_sea=False,
decimate=False,
cpml=False,
cpml_size=False,
top_absorbing=False,
hex27=False):
#
cubit.cmd('set journal error off')
cubit.cmd('set verbose error off')
collecting_merging(cpuxmin,
cpuxmax,
cpuymin,
cpuymax,
cpux,
cpuy,
cubfiles=cubfiles,
ckbound_method1=ckbound_method1,
ckbound_method2=ckbound_method2,
merge_tolerance=merge_tolerance,
decimate=decimate)
cubit.cmd('set journal error on')
cubit.cmd('set verbose error on')
#
if curverefining:
block = 1001 #topography
refine_closecurve(block, curverefining, acis=True)
#
#
if add_sea:
block = 1001
add_sea_layer(block=block)
outdir2 = '/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2 = outdir + '/'
else:
outdir2 = outdir + '/' + outdir2 + '/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command = "export mesh '" + outdir2 + outfilename + ".e' block all overwrite xml '" + outdir2 + outfilename + ".xml'"
cubit.cmd(command)
f = open(outdir2 + 'blocks.dat', '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()
#
#
cubit.cmd('set info echo journ off')
cmd = 'del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
command = "save as '" + outdir2 + outfilename + ".cub' overwrite"
cubit.cmd(command)
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq = open(outdir2 + outfilename + '.quality', 'w')
max_skewness, min_length = quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,
listblock=listblock,
listflag=listflag,
outdir=outdir,
cpml=cpml,
cpml_size=cpml_size,
top_absorbing=top_absorbing,
hex27=hex27)
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
