def start_cubit(init=False):
"""
start cubit, it return the cubit object
init argument set the monitotr files
"""
import sys,os
try:
cubit.silent_cmd('comment')
except:
try:
import cubit
import utilities
cubit.init([""])
except:
print 'error importing cubit'
sys.exit()
try:
if init:
from start import start_cfg,start_mpi
cfg=start_cfg()
mpiflag,iproc,numproc,mpi = start_mpi()
cubit.cmd('set logging on file "'+cfg.working_dir+'/cubit_proc_'+str(iproc)+'.log"')
cubit.cmd("set echo off")
cubit.cmd("set info off")
if iproc == cfg.monitored_cpu:
cubit.cmd("record '"+cfg.working_dir+"/monitor_"+str(cfg.monitored_cpu)+".jou'")
cubit.cmd("set journal on")
cubit.cmd("journal error on")
d=cfg.__dict__
ks=d.keys()
ks.sort()
for k in ks:
if '__' not in k and '<' not in str(d[k]) and d[k] is not None:
txt=str(k)+' -----> '+str(d[k])
txt=txt.replace("'","").replace('"','')
cubit.cmd('comment "'+txt+'"')
else:
cubit.cmd("set journal "+cfg.jou_info)
cubit.cmd("journal error "+cfg.jer_info)
d=cfg.__dict__
ks=d.keys()
ks.sort()
for k in ks:
if '__' not in k and '<' not in str(d[k]) and d[k] is not None:
txt=str(k)+' -----> '+str(d[k])
txt=txt.replace("'","").replace('"','')
cubit.cmd('comment "'+txt+'"')
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set info "+cfg.cubit_info)
version_cubit=utilities.get_cubit_version()
if version_cubit > 13 and version_cubit < 15:
print 'VERSION CUBIT ',version_cubit
print 'VERSIONs of CUBIT > 13 have bugs with merge node commands and equivalence'
print 'the merge option is not operative with this version, please download CUBIT 13'
else:
print 'VERSION CUBIT ',version_cubit
except:
print 'error start cubit'
sys.exit()
return cubit
def build_block(vol_list, name, id_0=1, top_surf=None, optionsea=False):
#
from sets import Set
if optionsea:
sea = optionsea['sea']
seaup = optionsea['seaup']
sealevel = optionsea['sealevel']
seathres = optionsea['seathres']
else:
sea = False
seaup = False
sealevel = False
seathres = False
#
block_list = cubit.get_block_id_list()
if len(block_list) > 0:
id_block = max(max(block_list), 2) + id_0
else:
id_block = 2 + id_0
for v, n in zip(vol_list, name):
id_block += 1
v_other = Set(vol_list) - Set([v])
if sea and v == vol_list[-1]:
cubit.cmd('set duplicate block elements off')
tsurf_string = " ".join(str(x) for x in top_surf)
# sea
command = 'block ' + str(id_block) + ' hex in node in surf ' + \
tsurf_string + ' with Z_coord < ' + str(seathres)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'sea" + n + "'"
cubit.cmd(command)
if not seaup:
id_block += 1
command = 'block ' + str(id_block) + ' hex in node in surf ' +\
tsurf_string + ' with (Z_coord > ' + str(seathres) +\
' and Z_coord < ' + str(sealevel)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'shwater" + n + "'"
cubit.cmd(command)
id_block += 1
command = 'block ' + str(id_block) + ' hex in node in surf ' + \
tsurf_string + ' with Z_coord >= ' + str(sealevel)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'continent" + n + "'"
cubit.cmd(command)
else:
version_cubit = get_cubit_version()
if version_cubit >= 15:
command = 'block ' + str(id_block) + ' hex in vol ' + \
str(v)
else:
command = 'block ' + str(id_block) + ' hex in vol ' + \
str(v) + ' except hex in vol ' + str(list(v_other))
print command
command = command.replace("[", " ").replace("]", " ")
cubit.cmd(command)
command = "block " + str(id_block) + " name '" + n + "'"
cubit.cmd(command)
def __init__(self,
hex27=False,
cpml=False,
cpml_size=False,
top_absorbing=False):
super(mesh, self).__init__()
self.mesh_name = 'mesh_file'
self.nodecoord_name = 'nodes_coords_file'
self.material_name = 'materials_file'
self.nummaterial_name = 'nummaterial_velocity_file'
self.absname = 'absorbing_surface_file'
self.cpmlname = 'absorbing_cpml_file'
self.freename = 'free_or_absorbing_surface_file_zmax'
self.recname = 'STATIONS'
version_cubit = get_cubit_version()
if version_cubit >= 12:
self.face = 'SHELL4'
else:
self.face = 'QUAD4'
self.hex = 'HEX'
if version_cubit <= 13:
if hex27:
print "ATTENTION **********************\n\nCubit <= 12.2 doesn't support HEX27\nassuming HEX8 .....\n\n"
self.hex27 = False
else:
self.hex27 = hex27
self.edge = 'BAR2'
self.topo = 'face_topo'
self.topography = None
self.free = None
self.freetxt = 'free'
self.rec = 'receivers'
self.cpml = cpml
if cpml:
if cpml_size:
self.size = cpml_size
else:
print 'please specify cmpl size if you want to use cpml'
self.top_absorbing = top_absorbing
if hex27:
cubit.cmd(
'block all except block 1001 1002 1003 1004 1005 1006 element type hex27'
)
self.block_definition()
self.ngll = 5
self.percent_gll = 0.172
self.point_wavelength = 5
self.xmin = False
self.ymin = False
self.zmin = False
self.xmax = False
self.ymax = False
self.zmax = False
cubit.cmd('compress all')
def __init__(self,hex27=False,cpml=False,cpml_size=False,top_absorbing=False):
super(mesh, self).__init__()
self.mesh_name='mesh_file'
self.nodecoord_name='nodes_coords_file'
self.material_name='materials_file'
self.nummaterial_name='nummaterial_velocity_file'
self.absname='absorbing_surface_file'
self.cpmlname='absorbing_cpml_file'
self.freename='free_or_absorbing_surface_file_zmax'
self.recname='STATIONS'
version_cubit=get_cubit_version()
if version_cubit >= 15:
self.face='SHELL'
elif version_cubit >= 12:
self.face='SHELL4'
else:
self.face='QUAD4'
self.hex='HEX'
if version_cubit <= 13:
if hex27:
print "ATTENTION **********************\n\nCubit <= 12.2 doesn't support HEX27\nassuming HEX8 .....\n\n"
self.hex27=False
else:
self.hex27=hex27
self.edge='BAR2'
self.topo='face_topo'
self.topography=None
self.free=None
self.freetxt='free'
self.rec='receivers'
self.cpml=cpml
if cpml:
if cpml_size:
self.size=cpml_size
else:
print 'please specify cmpl size if you want to use cpml'
self.top_absorbing=top_absorbing
if hex27: cubit.cmd('block all except block 1001 1002 1003 1004 1005 1006 element type hex27')
self.block_definition()
self.ngll=5
self.percent_gll=0.172
self.point_wavelength=5
self.xmin=False
self.ymin=False
self.zmin=False
self.xmax=False
self.ymax=False
self.zmax=False
cubit.cmd('compress all')
def start_cubit(init=False):
"""
start cubit, it return the cubit object
init argument set the monitotr files
"""
import sys
try:
cubit.silent_cmd('comment')
except:
try:
import cubit
import utilities
cubit.init([""])
except:
print('error importing cubit')
sys.exit()
try:
if init:
from start import start_cfg, start_mpi
cfg = start_cfg()
mpiflag, iproc, numproc, mpi = start_mpi()
version_cubit = utilities.get_cubit_version()
cubit.cmd('set logging on file "' + cfg.working_dir +
'/cubit_proc_' + str(iproc) + '.log"')
cubit.cmd("set echo off")
cubit.cmd("set info off")
if iproc == cfg.monitored_cpu:
cubit.cmd("record '" + cfg.working_dir +
"/monitor_" + str(cfg.monitored_cpu) + ".jou'")
cubit.cmd("set journal on")
if version_cubit < 16:
cubit.cmd("journal error on")
d = cfg.__dict__
ks = d.keys()
ks.sort()
for k in ks:
if '__' not in k and '<' not in str(d[k]):
if d[k] is not None:
txt = str(k) + ' -----> ' + str(d[k])
txt = txt.replace("'", "").replace('"', '')
cubit.cmd('comment "' + txt + '"')
else:
cubit.cmd("set journal " + cfg.jou_info)
if version_cubit < 16:
cubit.cmd("journal error " + cfg.jer_info)
d = cfg.__dict__
ks = d.keys()
ks.sort()
for k in ks:
if '__' not in k and '<' not in str(d[k]):
if d[k] is not None:
txt = str(k) + ' -----> ' + str(d[k])
txt = txt.replace("'", "").replace('"', '')
cubit.cmd('comment "' + txt + '"')
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set info " + cfg.cubit_info)
if version_cubit > 13 and version_cubit < 15:
print('VERSION CUBIT ', version_cubit)
print('VERSIONs of CUBIT > 13 have bugs with merge node')
print('the merge option is not operative with this version')
print('please download CUBIT 15+')
else:
print('VERSION CUBIT ', version_cubit)
except:
print('error start cubit')
sys.exit()
return cubit
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)
cpuymax = None
curverefining = False
add_sea = False
decimate = False
cpml = False
cpml_size = False
top_absorbing = False
qlog = False
hex27 = False
check_merging = False
save_cubfile = False
cubit_version = get_cubit_version()
if opts:
for o, value in opts:
if o in ('--starting_tolerance'):
starting_tolerance = float(value)
# print o, value
if o in ('--save_cubfile'):
save_cubfile = True
if o in ('--step_tolerance'):
step_tolerance = float(value)
if o in ('--hex27'):
hex27 = True
if o in ('--cpml'):
cpuymax = None
curverefining = False
add_sea = False
decimate = False
cpml = False
cpml_size = False
top_absorbing = False
qlog = False
hex27 = False
check_merging = False
save_cubfile = False
cubit_version = get_cubit_version()
if opts:
for o, value in opts:
if o in ('--starting_tolerance'):
starting_tolerance = float(value)
# print o, value
if o in ('--save_cubfile'):
save_cubfile = True
if o in ('--step_tolerance'):
step_tolerance = float(value)
if o in ('--hex27'):
hex27 = True
if o in ('--cpml'):
cpml = True
def build_block(vol_list, name, id_0=1, top_surf=None, optionsea=False):
#
from sets import Set
if optionsea:
sea = optionsea['sea']
seaup = optionsea['seaup']
sealevel = optionsea['sealevel']
seathres = optionsea['seathres']
else:
sea = False
seaup = False
sealevel = False
seathres = False
#
print 'build blocks'
block_list = cubit.get_block_id_list()
print block_list, vol_list
if len(block_list) > 0:
id_block = max(max(block_list), 2) + id_0
else:
# id_block = 2 + id_0
id_block = 0
for v, n in zip(vol_list, name):
id_block += 1
v_other = Set(vol_list) - Set([v])
if sea and v == vol_list[-1]:
cubit.cmd('set duplicate block elements off')
tsurf_string = " ".join(str(x) for x in top_surf)
# sea
command = 'block ' + str(id_block) + ' hex in node in surf ' + \
tsurf_string + ' with Z_coord < ' + str(seathres)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'sea" + n + "'"
cubit.cmd(command)
if not seaup:
id_block += 1
command = 'block ' + str(id_block) + ' hex in node in surf ' +\
tsurf_string + ' with (Z_coord > ' + str(seathres) +\
' and Z_coord < ' + str(sealevel)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'shwater" + n + "'"
cubit.cmd(command)
id_block += 1
command = 'block ' + str(id_block) + ' hex in node in surf ' + \
tsurf_string + ' with Z_coord >= ' + str(sealevel)
cubit.cmd(command)
command = "block " + str(id_block) + " name 'continent" + n + "'"
cubit.cmd(command)
else:
version_cubit = get_cubit_version()
if version_cubit >= 15:
command = 'block ' + str(id_block) + ' hex in vol ' + \
str(v)
print command
else:
command = 'block ' + str(id_block) + ' hex in vol ' + \
str(v) + ' except hex in vol ' + str(list(v_other))
print command
command = command.replace("[", " ").replace("]", " ")
cubit.cmd(command)
command = "block " + str(id_block) + " name '" + n + "'"
cubit.cmd(command)
def mesh_layercake_regularmap(filename=None):
import start as start
mpiflag, iproc, numproc, mpi = start.start_mpi()
from utilities import importgeometry, savemesh, get_v_h_list
from utilities import cubit_command_check, get_cubit_version
#
# numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
# from math import sqrt
from sets import Set
version_cubit = get_cubit_version()
list_vol = cubit.parse_cubit_list("volume", "all")
if len(list_vol) != 0:
pass
else:
geometryfile = 'geometry_vol_' + str(iproc) + '.cub'
importgeometry(geometryfile, iproc=iproc)
command = 'composite create curve all'
cubit.cmd(command)
print('###"No valid composites can be created from the specified curves." \
is NOT a critical ERROR.')
#
command = "compress all"
cubit.cmd(command)
list_vol = cubit.parse_cubit_list("volume", "all")
nvol = len(list_vol)
vol = []
for id_vol in list_vol:
p = cubit.get_center_point("volume", id_vol)
vol.append(cubitvolume(id_vol, 1, p[2], 0))
vol.sort(by_z)
#
for id_vol in range(0, nvol):
vol[id_vol].intervalv = cfg.iv_interval[id_vol]
#
#
surf_vertical = []
surf_or = []
# top_surface = 0
# top_surface_add = ''
# bottom_surface = 0
# #
# zmin_box = cubit.get_total_bounding_box("volume", list_vol)[6]
# xmin_box = cubit.get_total_bounding_box("volume", list_vol)[0]
# xmax_box = cubit.get_total_bounding_box("volume", list_vol)[1]
# ymin_box = cubit.get_total_bounding_box("volume", list_vol)[3]
# ymax_box = cubit.get_total_bounding_box("volume", list_vol)[4]
#
#
# interval assignement
surf_or, surf_vertical, list_curve_or, list_curve_vertical, \
bottom, top = get_v_h_list(list_vol, chktop=cfg.chktop)
print('vertical surfaces: ', surf_vertical)
for k in surf_vertical:
command = "surface " + str(k) + " scheme submap"
cubit.cmd(command)
for k in surf_or:
command = "surface " + str(k) + " scheme " + cfg.or_mesh_scheme
cubit.cmd(command)
#
ucurve, vcurve = get_uv_curve(list_curve_or)
schemepave = False
#
ucurve_interval = {}
for k in ucurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
ucurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(ucurve_interval.values()) != min(ucurve_interval.values()):
schemepave = True
print('mesh scheme is set to pave')
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
vcurve_interval = {}
for k in vcurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
vcurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(vcurve_interval.values()) != min(vcurve_interval.values()):
print('mesh scheme is set to pave')
schemepave = True
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
for s in surf_vertical:
lcurve = cubit.get_relatives("surface", s, "curve")
interval_store = []
for k in lcurve:
interval_curve = cubit.get_mesh_intervals('curve', k)
if k in list_curve_vertical:
volume_id = cubit.get_owning_volume("curve", k)
for idv in range(0, nvol):
if vol[idv].ID == volume_id:
int_v = vol[idv].intervalv
command = "curve " + str(k) + " interval " + str(int_v)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
else:
interval_store.append((k, interval_curve))
if len(interval_store) != 0:
interval_min = min([iv[1] for iv in interval_store])
str_interval = [str(iv[0]) for iv in interval_store]
cmd = "curve " + ' '.join(str_interval) + \
" interval " + str(interval_min)
cubit.cmd(cmd)
command = "curve " + \
' '.join(str(iv[0])
for iv in interval_store) + " scheme equal"
cubit.cmd(command)
command = "surface " + str(s) + " scheme submap"
cubit.cmd(command)
# meshing
if cfg.or_mesh_scheme == 'pave' or schemepave:
command = 'mesh surf ' + ' '.join(str(t) for t in top)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
elif cfg.or_mesh_scheme == 'map':
command = 'mesh surf ' + ' '.join(str(t) for t in bottom)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
for id_volume in range(nvol - 1, -1, -1):
command = "mesh vol " + str(vol[id_volume].ID)
status = cubit_command_check(iproc, command, stop=False)
if not status:
for s in surf_vertical:
command_surf = "mesh surf " + str(s)
cubit.cmd(command_surf)
if version_cubit < 16:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
volume all sweep smooth Auto
'''
else:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
'''
status2 = cubit_command_check(
iproc, command_set_meshvol, stop=False)
status2 = cubit_command_check(iproc, command, stop=False)
if not status2:
_surf = cubit.get_relatives(
'volume', vol[id_volume].ID, 'surface')
local_o_surf = [x for x in _surf if x in surf_or]
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' redistribute nodes off')
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' scheme Sweep source surface ' +
' '.join(str(x) for x in local_o_surf[0:-1]) +
' target surface ' + str(local_o_surf[-1]))
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' autosmooth_target off')
status = cubit_command_check(iproc, command, stop=True)
#
# smoothing
print(iproc, 'untangling...')
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
if cfg.smoothing:
print('smoothing .... ' + str(cfg.smoothing))
cubitcommand = 'surf all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth surf all'
cubit.cmd(cubitcommand)
#
cubitcommand = 'vol all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth vol all'
cubit.cmd(cubitcommand)
#
#
# vertical refinement
# for nvol = 3
##
# ___________________________ interface 4
##
# vol 2
# ___________________________ interface 3
##
# vol 1
# ___________________________ interface 2
##
# vol 0
# ___________________________ interface 1
##
refinement(nvol, vol, filename=filename)
#
# top layer vertical coarsening
print('coarsening top layer... ', cfg.coarsening_top_layer)
if cfg.coarsening_top_layer:
cubitcommand = 'del mesh vol ' + str(vol[-1].ID) + ' propagate'
cubit.cmd(cubitcommand)
s1 = Set(list_curve_vertical)
command = "group 'list_curve_tmp' add curve " + \
"in vol " + str(vol[-1].ID)
cubit.cmd(command)
group = cubit.get_id_from_name("list_curve_tmp")
list_curve_tmp = cubit.get_group_curves(group)
command = "delete group " + str(group)
cubit.cmd(command)
s2 = Set(list_curve_tmp)
lc = list(s1 & s2)
#
cubitcommand = 'curve ' + \
' '.join(str(x) for x in lc) + ' interval ' + \
str(cfg.actual_vertical_interval_top_layer)
cubit.cmd(cubitcommand)
cubitcommand = 'mesh vol ' + str(vol[-1].ID)
cubit.cmd(cubitcommand)
#
n = cubit.get_sideset_id_list()
if len(n) != 0:
command = "del sideset all"
cubit.cmd(command)
n = cubit.get_block_id_list()
if len(n) != 0:
command = "del block all"
cubit.cmd(command)
#
import boundary_definition
entities = ['face']
print(iproc, 'hex block definition...')
boundary_definition.define_bc(entities, parallel=True,
cpux=cfg.cpux, cpuy=cfg.cpuy,
cpuxmin=0, cpuymin=0, optionsea=False)
# save mesh
print(iproc, 'untangling...')
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
print(iproc, 'saving...')
savemesh(mpiflag, iproc=iproc, filename=filename)
def readcfg(filename=None,importmenu=False,mpiflag=False):
"""
read the configuration file, filename is defined in the command line arguments (see menu.py)
"""
if importmenu:
import menu as menu
cfgname=menu.cfg_name
id_proc=menu.id_proc
create_plane=menu.create_plane
menusurface=menu.surface
single=menu.single
elif filename:
cfgname=filename
id_proc=0
menu=False
create_plane=False
menusurface=False
single=False
else:
print 'error: no configuration file'
import sys
sys.exit()
#
from utilities import geo2utm,get_cubit_version #here I can use pyproj but I prefere to include a function in pure python in order to avoid an additional installation
#
#
import ConfigParser
config = ConfigParser.ConfigParser()
#
#
def converter(s):
if s == 'True':
value=True
elif s == 'False':
value=False
elif s == 'None':
value= None
else:
if s.count(',') != 0:
value=s.split(',')
while value.count(''):
value.remove('')
else:
value=s
try:
if type(value).__name__ == 'str':
if str(value).count('.') != 0:
value=float(value)
else:
value=int(value)
else:
if str(value).count('.') != 0:
value=map(float,value)
else:
value=map(int,value)
except:
pass
return value
#
def section_dict(section):
dict_o = {}
options = config.options(section)
for option in options:
try:
value=converter(config.get(section, option))
dict_o[option] = value
except:
dict_o[option] = None
return dict_o
class attrdict(dict):
def __init__(self, *args, **kwargs):
dict.__init__(self, *args, **kwargs)
self.__dict__ = self
def __str__(self):
names=[]
values=[]
for name,value in self.items():
names.append(name)
values.append(value)
print names,values
a=zip(names,values)
a.sort()
arc=''
for o in a:
if o[0][0] != arc: print
print o[0],' -> ',o[1]
arc=o[0][0]
return '____'
#
dcfg={}
#
#CONSTANTS
dcfg['osystem'] = 'linux'
dcfg['debug_cfg']=False
dcfg['version_cubit']=get_cubit_version()
dcfg['checkbound']=False
dcfg['top_partitioner'] = 10000
dcfg['tres']=0.3 #if n is the vertical component of the normal at a surface pointing horizontally, when -tres < n < tres then the surface is vertical
dcfg['precision'] =0.02 #precision for the boundary check (0.02 m)
#
#INIT
dcfg['debug']=True
dcfg['cubit_info']="on"
dcfg['echo_info']="on"
dcfg['jou_info']="on"
dcfg['jer_info']="on"
dcfg['monitored_cpu']=0
dcfg['parallel_import']=True
dcfg['save_geometry_cubit']=True
dcfg['save_surface_cubit']=False
dcfg['save_geometry_paraview'] = False #not implemented
dcfg['save_geometry_ACIS'] = False #not implemented
dcfg['export_exodus_mesh']=False
dcfg['manual_adj'] =False
dcfg['play_adj'] =False
dcfg['no_adj'] =False
dcfg['nx']=False
dcfg['ny']=False
dcfg['nstep']=False
dcfg['localdir_is_globaldir']=True
dcfg['refinement_depth']=[]
dcfg['scratchdir']=None
dcfg['map_meshing_type']='regularmap'
dcfg['4sideparallel']=True
dcfg["outlinebasin_curve"]=False
dcfg["transition_curve"]=False
dcfg["faulttrace_curve"]=False
dcfg['geological_imprint']=False
dcfg['number_processor_xi']=1
dcfg['number_processor_eta']=1
dcfg['filename']=None
dcfg['actual_vertical_interval_top_layer']=1
dcfg['coarsening_top_layer']=False
dcfg['refineinsidevol']=False
dcfg['sea']=False
dcfg['seaup']=False
dcfg['sea_level']=False
dcfg['sea_threshold']=False
dcfg['subduction']=True
dcfg['subduction_thres']=500
dcfg['debugsurface']=False #if true it creates only the surface not the lofted volumes
dcfg['lat_orientation']=False
dcfg['irregulargridded_surf']=False
dcfg['chktop']=False
dcfg['smoothing']=False
dcfg['ntripl']=0
dcfg['debug_geometry']=False
if float(dcfg['version_cubit']) >= 13.1:
dcfg['volumecreation_method']=None
else:
dcfg['volumecreation_method']='loft'
dcfg['nsurf'] = None
if cfgname:
config.read(cfgname)
sections=['cubit.options','simulation.cpu_parameters','geometry.surfaces','geometry.volumes','geometry.volumes.layercake','geometry.volumes.flatcake','geometry.volumes.partitioner','geometry.partitioner','meshing']
for section in sections:
try:
d=section_dict(section)
dcfg.update(d)
except:
pass
if dcfg['nsurf']:
surface_name=[]
num_x=[]
num_y=[]
xstep=[]
ystep=[]
step=[]
directionx=[]
directiony=[]
unit2=[]
surf_type=[]
delimiter=[]
nsurf=int(dcfg['nsurf'])
for i in range(1,nsurf+1):
section='surface'+str(i)+'.parameters'
d=section_dict(section)
surface_name.append(d['name'])
surf_type.append(d['surf_type'])
unit2.append(d['unit_surf'])
if d['surf_type'] == 'regular_grid':
xstep.append(d['step_along_x'])
ystep.append(d['step_along_y'])
num_x.append(d['number_point_along_x'])
num_y.append(d['number_point_along_y'])
elif d['surf_type'] == 'skin':
step.append(d['step'])
try:
delimiter.append(d['delimiter'])
except:
pass
directionx.append(d['directionx'])
directiony.append(d['directiony'])
dcfg['surface_name']=surface_name
dcfg['num_x']=num_x
dcfg['num_y']=num_y
dcfg['xstep']=xstep
dcfg['ystep']=ystep
dcfg['step']=step
dcfg['directionx']=directionx
dcfg['directiony']=directiony
dcfg['unit2']=unit2
dcfg['surf_type']=surf_type
dcfg['delimiter']=delimiter
try:
tres=0
xmin,ymin=geo2utm(dcfg['longitude_min'],dcfg['latitude_min'],dcfg['unit'])
xmax,ymax=geo2utm(dcfg['longitude_max'],dcfg['latitude_max'],dcfg['unit'])
dcfg['xmin']=xmin
dcfg['ymin']=ymin
dcfg['xmax']=xmax
dcfg['ymax']=ymax
x1,y1=geo2utm(dcfg['longitude_min'],dcfg['latitude_min'],dcfg['unit'])
x2,y2=geo2utm(dcfg['longitude_max'],dcfg['latitude_min'],dcfg['unit'])
x3,y3=geo2utm(dcfg['longitude_max'],dcfg['latitude_max'],dcfg['unit'])
x4,y4=geo2utm(dcfg['longitude_min'],dcfg['latitude_max'],dcfg['unit'])
dcfg['x1_box']=x1
dcfg['y1_box']=y1
dcfg['x2_box']=x2
dcfg['y2_box']=y2
dcfg['x3_box']=x3
dcfg['y3_box']=y3
dcfg['x4_box']=x4
dcfg['y4_box']=y4
dcfg['tres_boundarydetection']=tres
except:
pass
if dcfg['sea']:
if not dcfg['sea_level']: dcfg['sea_level']=0
if not dcfg['sea_threshold']: dcfg['sea_threshold']=-200
dcfg['actual_vertical_interval_top_layer']=1
dcfg['coarsening_top_layer']=True
dcfg['optionsea']={'sea':dcfg['sea'],'seaup':dcfg['seaup'],'sealevel':dcfg['sea_level'],'seathres':dcfg['sea_threshold']}
cfg=attrdict(dcfg)
if menu:
try:
if cfg.working_dir[-1] == '/': cfg.working_dir=cfg.working_dir[:-1]
if cfg.working_dir[0] != '/': cfg.working_dir='./'+cfg.working_dir
except:
cfg.working_dir=os.getcwd()
try:
if cfg.output_dir[-1] == '/': cfg.output_dir=cfg.output_dir[:-1]
if cfg.output_dir[0] != '/': cfg.output_dir='./'+cfg.output_dir
except:
cfg.output_dir=os.getcwd()
try:
if cfg.SPECFEM3D_output_dir[-1] == '/': cfg.SPECFEM3D_output_dir=cfg.SPECFEM3D_output_dir[:-1]
if cfg.SPECFEM3D_output_dir[0] != '/': cfg.SPECFEM3D_output_dir='./'+cfg.SPECFEM3D_output_dir
except:
cfg.SPECFEM3D_output_dir=os.getcwd()
cfg.single=single
if menusurface:
cfg.nsurf=1
cfg.name=[menu.surface_name]
cfg.num_x=[menu.num_x]
cfg.num_y=[menu.num_x]
cfg.unit=[menu.unit]
cfg.surf_type=[menu.surf_type]
try:
cfg.delimiter=[menu.delimiter]
except:
cfg.delimiter=[' ']
cfg.directionx=[menu.directionx]
cfg.directiony=[menu.directiony]
else:
cfg.SPECFEM3D_output_dir=os.getcwd()
if not cfg.number_processor_eta and cfg.nodes:
cfg.number_processor_xi,cfg.number_processor_eta=split(cfg.nodes)
if isinstance(cfg.filename,str): cfg.filename=[cfg.filename]
try:
cfg.nproc_eta=cfg.number_processor_eta
cfg.nproc_xi=cfg.number_processor_xi
cfg.cpuy=cfg.number_processor_eta
cfg.cpux=cfg.number_processor_xi
except:
pass
if create_plane:
cfg.x1=map(float,menu.x1.split(','))
cfg.x2=map(float,menu.x2.split(','))
cfg.x3=map(float,menu.x3.split(','))
cfg.x4=map(float,menu.x4.split(','))
cfg.unit=menu.unit
#
if menu:
cfg.id_proc=menu.id_proc
else:
cfg.id_proc=id_proc
#
try:
if isinstance(cfg.tripl,int): cfg.tripl=[cfg.tripl]
except:
pass
try:
if isinstance(cfg.iv_interval,int): cfg.iv_interval=[cfg.iv_interval]
except:
pass
try:
if isinstance(cfg.refinement_depth,int): cfg.refinement_depth=[cfg.refinement_depth]
except:
pass
return cfg
def mesh_layercake_regularmap(filename=None):
import start as start
mpiflag, iproc, numproc, mpi = start.start_mpi()
from utilities import importgeometry, savemesh, get_v_h_list
from utilities import cubit_command_check, get_cubit_version
#
# numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
# from math import sqrt
from sets import Set
version_cubit = get_cubit_version()
list_vol = cubit.parse_cubit_list("volume", "all")
if len(list_vol) != 0:
pass
else:
geometryfile = 'geometry_vol_' + str(iproc) + '.cub'
importgeometry(geometryfile, iproc=iproc)
command = 'composite create curve all'
cubit.cmd(command)
print '###"No valid composites can be created from the specified curves." \
is NOT a critical ERROR.'
#
command = "compress all"
cubit.cmd(command)
list_vol = cubit.parse_cubit_list("volume", "all")
nvol = len(list_vol)
vol = []
for id_vol in list_vol:
p = cubit.get_center_point("volume", id_vol)
vol.append(cubitvolume(id_vol, 1, p[2], 0))
vol.sort(by_z)
#
for id_vol in range(0, nvol):
vol[id_vol].intervalv = cfg.iv_interval[id_vol]
#
#
surf_vertical = []
surf_or = []
# top_surface = 0
# top_surface_add = ''
# bottom_surface = 0
# #
# zmin_box = cubit.get_total_bounding_box("volume", list_vol)[6]
# xmin_box = cubit.get_total_bounding_box("volume", list_vol)[0]
# xmax_box = cubit.get_total_bounding_box("volume", list_vol)[1]
# ymin_box = cubit.get_total_bounding_box("volume", list_vol)[3]
# ymax_box = cubit.get_total_bounding_box("volume", list_vol)[4]
#
#
# interval assignement
surf_or, surf_vertical, list_curve_or, list_curve_vertical, \
bottom, top = get_v_h_list(list_vol, chktop=cfg.chktop)
print 'vertical surfaces: ', surf_vertical
for k in surf_vertical:
command = "surface " + str(k) + " scheme submap"
cubit.cmd(command)
for k in surf_or:
command = "surface " + str(k) + " scheme " + cfg.or_mesh_scheme
cubit.cmd(command)
#
ucurve, vcurve = get_uv_curve(list_curve_or)
schemepave = False
#
ucurve_interval = {}
for k in ucurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
ucurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(ucurve_interval.values()) != min(ucurve_interval.values()):
schemepave = True
print 'mesh scheme is set to pave'
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
vcurve_interval = {}
for k in vcurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
vcurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(vcurve_interval.values()) != min(vcurve_interval.values()):
print 'mesh scheme is set to pave'
schemepave = True
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
for s in surf_vertical:
lcurve = cubit.get_relatives("surface", s, "curve")
interval_store = []
for k in lcurve:
interval_curve = cubit.get_mesh_intervals('curve', k)
if k in list_curve_vertical:
volume_id = cubit.get_owning_volume("curve", k)
for idv in range(0, nvol):
if vol[idv].ID == volume_id:
int_v = vol[idv].intervalv
command = "curve " + str(k) + " interval " + str(int_v)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
else:
interval_store.append((k, interval_curve))
if len(interval_store) != 0:
interval_min = min([iv[1] for iv in interval_store])
str_interval = [str(iv[0]) for iv in interval_store]
cmd = "curve " + ' '.join(str_interval) + \
" interval " + str(interval_min)
cubit.cmd(cmd)
command = "curve " + \
' '.join(str(iv[0])
for iv in interval_store) + " scheme equal"
cubit.cmd(command)
command = "surface " + str(s) + " scheme submap"
cubit.cmd(command)
# meshing
if cfg.or_mesh_scheme == 'pave' or schemepave:
command = 'mesh surf ' + ' '.join(str(t) for t in top)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
elif cfg.or_mesh_scheme == 'map':
command = 'mesh surf ' + ' '.join(str(t) for t in bottom)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
for id_volume in range(nvol - 1, -1, -1):
command = "mesh vol " + str(vol[id_volume].ID)
status = cubit_command_check(iproc, command, stop=False)
if not status:
for s in surf_vertical:
command_surf = "mesh surf " + str(s)
cubit.cmd(command_surf)
if version_cubit < 16:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
volume all sweep smooth Auto
'''
else:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
'''
status2 = cubit_command_check(
iproc, command_set_meshvol, stop=False)
status2 = cubit_command_check(iproc, command, stop=False)
if not status2:
_surf = cubit.get_relatives(
'volume', vol[id_volume].ID, 'surface')
local_o_surf = [x for x in _surf if x in surf_or]
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' redistribute nodes off')
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' scheme Sweep source surface ' +
' '.join(str(x) for x in local_o_surf[0:-1]) +
' target surface ' + str(local_o_surf[-1]))
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' autosmooth_target off')
status = cubit_command_check(iproc, command, stop=True)
#
# smoothing
print iproc, 'untangling...'
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
if cfg.smoothing:
print 'smoothing .... ' + str(cfg.smoothing)
cubitcommand = 'surf all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth surf all'
cubit.cmd(cubitcommand)
#
cubitcommand = 'vol all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth vol all'
cubit.cmd(cubitcommand)
#
#
# vertical refinement
# for nvol = 3
##
# ___________________________ interface 4
##
# vol 2
# ___________________________ interface 3
##
# vol 1
# ___________________________ interface 2
##
# vol 0
# ___________________________ interface 1
##
refinement(nvol, vol, filename=filename)
#
# top layer vertical coarsening
print 'coarsening top layer... ', cfg.coarsening_top_layer
if cfg.coarsening_top_layer:
cubitcommand = 'del mesh vol ' + str(vol[-1].ID) + ' propagate'
cubit.cmd(cubitcommand)
s1 = Set(list_curve_vertical)
command = "group 'list_curve_tmp' add curve " + \
"in vol " + str(vol[-1].ID)
cubit.cmd(command)
group = cubit.get_id_from_name("list_curve_tmp")
list_curve_tmp = cubit.get_group_curves(group)
command = "delete group " + str(group)
cubit.cmd(command)
s2 = Set(list_curve_tmp)
lc = list(s1 & s2)
#
cubitcommand = 'curve ' + \
' '.join(str(x) for x in lc) + ' interval ' + \
str(cfg.actual_vertical_interval_top_layer)
cubit.cmd(cubitcommand)
cubitcommand = 'mesh vol ' + str(vol[-1].ID)
cubit.cmd(cubitcommand)
#
n = cubit.get_sideset_id_list()
if len(n) != 0:
command = "del sideset all"
cubit.cmd(command)
n = cubit.get_block_id_list()
if len(n) != 0:
command = "del block all"
cubit.cmd(command)
#
import boundary_definition
entities = ['face']
print iproc, 'hex block definition...'
boundary_definition.define_bc(entities, parallel=True,
cpux=cfg.cpux, cpuy=cfg.cpuy,
cpuxmin=0, cpuymin=0, optionsea=False)
# save mesh
print iproc, 'untangling...'
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
print iproc, 'saving...'
savemesh(mpiflag, iproc=iproc, filename=filename)
def readcfg(filename=None, importmenu=False, mpiflag=False):
"""
read the configuration file, filename is defined in the command line arguments (see menu.py)
"""
if importmenu:
import menu as menu
cfgname = menu.cfg_name
id_proc = menu.id_proc
create_plane = menu.create_plane
menusurface = menu.surface
single = menu.single
elif filename:
cfgname = filename
id_proc = 0
menu = False
create_plane = False
menusurface = False
single = False
else:
print "error: no configuration file"
import sys
sys.exit()
#
from utilities import (
geo2utm,
get_cubit_version,
) # here I can use pyproj but I prefere to include a function in pure python in order to avoid an additional installation
#
#
import ConfigParser
config = ConfigParser.ConfigParser()
#
#
def converter(s):
if s == "True":
value = True
elif s == "False":
value = False
elif s == "None":
value = None
else:
if s.count(",") != 0:
value = s.split(",")
while value.count(""):
value.remove("")
else:
value = s
try:
if type(value).__name__ == "str":
if str(value).count(".") != 0:
value = float(value)
else:
value = int(value)
else:
if str(value).count(".") != 0:
value = map(float, value)
else:
value = map(int, value)
except:
pass
return value
#
def section_dict(section):
dict_o = {}
options = config.options(section)
for option in options:
try:
value = converter(config.get(section, option))
dict_o[option] = value
except:
dict_o[option] = None
return dict_o
class attrdict(dict):
def __init__(self, *args, **kwargs):
dict.__init__(self, *args, **kwargs)
self.__dict__ = self
def __str__(self):
names = []
values = []
for name, value in self.items():
names.append(name)
values.append(value)
print names, values
a = zip(names, values)
a.sort()
arc = ""
for o in a:
if o[0][0] != arc:
print
print o[0], " -> ", o[1]
arc = o[0][0]
print __name__
return "____"
#
dcfg = {}
#
# CONSTANTS
dcfg["osystem"] = "linux"
dcfg["debug_cfg"] = False
dcfg["version_cubit"] = get_cubit_version()
dcfg["checkbound"] = False
dcfg["top_partitioner"] = 10000
dcfg[
"tres"
] = (
0.3
) # if n is the vertical component of the normal at a surface pointing horizontally, when -tres < n < tres then the surface is vertical
dcfg["precision"] = 0.02 # precision for the boundary check (0.02 m)
#
# INIT
dcfg["debug"] = True
dcfg["cubit_info"] = "on"
dcfg["echo_info"] = "on"
dcfg["jou_info"] = "on"
dcfg["jer_info"] = "on"
dcfg["monitored_cpu"] = 0
dcfg["parallel_import"] = True
dcfg["save_geometry_cubit"] = True
dcfg["save_surface_cubit"] = False
dcfg["save_geometry_paraview"] = False # not implemented
dcfg["save_geometry_ACIS"] = False # not implemented
dcfg["export_exodus_mesh"] = False
dcfg["manual_adj"] = False
dcfg["play_adj"] = False
dcfg["no_adj"] = False
dcfg["nx"] = False
dcfg["ny"] = False
dcfg["nstep"] = False
dcfg["localdir_is_globaldir"] = True
dcfg["refinement_depth"] = []
dcfg["scratchdir"] = None
dcfg["map_meshing_type"] = "regularmap"
dcfg["4sideparallel"] = True
dcfg["outlinebasin_curve"] = False
dcfg["transition_curve"] = False
dcfg["faulttrace_curve"] = False
dcfg["geological_imprint"] = False
dcfg["number_processor_xi"] = 1
dcfg["number_processor_eta"] = 1
dcfg["filename"] = None
dcfg["actual_vertical_interval_top_layer"] = 1
dcfg["coarsening_top_layer"] = False
dcfg["refineinsidevol"] = False
dcfg["sea"] = False
dcfg["seaup"] = False
dcfg["sea_level"] = False
dcfg["sea_threshold"] = False
dcfg["subduction"] = False
dcfg["subduction_thres"] = 500
dcfg["debugsurface"] = False # if true it creates only the surface not the lofted volumes
dcfg["lat_orientation"] = False
dcfg["irregulargridded_surf"] = False
dcfg["chktop"] = False
dcfg["smoothing"] = False
dcfg["ntripl"] = 0
dcfg["debug_geometry"] = False
dcfg["topflat"] = False
if float(dcfg["version_cubit"]) >= 13.1:
dcfg["volumecreation_method"] = None
else:
dcfg["volumecreation_method"] = "loft"
dcfg["nsurf"] = None
if cfgname:
config.read(cfgname)
sections = [
"cubit.options",
"simulation.cpu_parameters",
"geometry.surfaces",
"geometry.volumes",
"geometry.volumes.layercake",
"geometry.volumes.flatcake",
"geometry.volumes.partitioner",
"geometry.partitioner",
"meshing",
]
for section in sections:
try:
d = section_dict(section)
dcfg.update(d)
except:
pass
# print dcfg
if dcfg["nsurf"]:
surface_name = []
num_x = []
num_y = []
xstep = []
ystep = []
step = []
directionx = []
directiony = []
unit2 = []
surf_type = []
delimiter = []
nsurf = int(dcfg["nsurf"])
for i in range(1, nsurf + 1):
section = "surface" + str(i) + ".parameters"
d = section_dict(section)
surface_name.append(d["name"])
surf_type.append(d["surf_type"])
unit2.append(d["unit_surf"])
if d["surf_type"] == "regular_grid":
xstep.append(d["step_along_x"])
ystep.append(d["step_along_y"])
num_x.append(d["number_point_along_x"])
num_y.append(d["number_point_along_y"])
elif d["surf_type"] == "skin":
step.append(d["step"])
try:
delimiter.append(d["delimiter"])
except:
pass
directionx.append(d["directionx"])
directiony.append(d["directiony"])
dcfg["surface_name"] = surface_name
dcfg["num_x"] = num_x
dcfg["num_y"] = num_y
dcfg["xstep"] = xstep
dcfg["ystep"] = ystep
dcfg["step"] = step
dcfg["directionx"] = directionx
dcfg["directiony"] = directiony
dcfg["unit2"] = unit2
dcfg["surf_type"] = surf_type
dcfg["delimiter"] = delimiter
try:
tres = 0
xmin, ymin = geo2utm(dcfg["longitude_min"], dcfg["latitude_min"], dcfg["unit"])
xmax, ymax = geo2utm(dcfg["longitude_max"], dcfg["latitude_max"], dcfg["unit"])
dcfg["xmin"] = xmin
dcfg["ymin"] = ymin
dcfg["xmax"] = xmax
dcfg["ymax"] = ymax
x1, y1 = geo2utm(dcfg["longitude_min"], dcfg["latitude_min"], dcfg["unit"])
x2, y2 = geo2utm(dcfg["longitude_max"], dcfg["latitude_min"], dcfg["unit"])
x3, y3 = geo2utm(dcfg["longitude_max"], dcfg["latitude_max"], dcfg["unit"])
x4, y4 = geo2utm(dcfg["longitude_min"], dcfg["latitude_max"], dcfg["unit"])
dcfg["x1_box"] = x1
dcfg["y1_box"] = y1
dcfg["x2_box"] = x2
dcfg["y2_box"] = y2
dcfg["x3_box"] = x3
dcfg["y3_box"] = y3
dcfg["x4_box"] = x4
dcfg["y4_box"] = y4
dcfg["tres_boundarydetection"] = tres
except:
pass
if dcfg["irregulargridded_surf"]:
print "test"
dcfg["xmin"] = dcfg["longitude_min"]
dcfg["ymin"] = dcfg["latitude_min"]
dcfg["xmax"] = dcfg["longitude_max"]
dcfg["ymax"] = dcfg["latitude_max"]
if dcfg["sea"]:
if not dcfg["sea_level"]:
dcfg["sea_level"] = 0
if not dcfg["sea_threshold"]:
dcfg["sea_threshold"] = -200
dcfg["actual_vertical_interval_top_layer"] = 1
dcfg["coarsening_top_layer"] = True
dcfg["optionsea"] = {
"sea": dcfg["sea"],
"seaup": dcfg["seaup"],
"sealevel": dcfg["sea_level"],
"seathres": dcfg["sea_threshold"],
}
cfg = attrdict(dcfg)
if menu:
try:
if cfg.working_dir[-1] == "/":
cfg.working_dir = cfg.working_dir[:-1]
if cfg.working_dir[0] != "/":
cfg.working_dir = "./" + cfg.working_dir
except:
cfg.working_dir = os.getcwd()
try:
if cfg.output_dir[-1] == "/":
cfg.output_dir = cfg.output_dir[:-1]
if cfg.output_dir[0] != "/":
cfg.output_dir = "./" + cfg.output_dir
except:
cfg.output_dir = os.getcwd()
try:
if cfg.SPECFEM3D_output_dir[-1] == "/":
cfg.SPECFEM3D_output_dir = cfg.SPECFEM3D_output_dir[:-1]
if cfg.SPECFEM3D_output_dir[0] != "/":
cfg.SPECFEM3D_output_dir = "./" + cfg.SPECFEM3D_output_dir
except:
cfg.SPECFEM3D_output_dir = os.getcwd()
cfg.single = single
if menusurface:
cfg.nsurf = 1
cfg.name = [menu.surface_name]
cfg.num_x = [menu.num_x]
cfg.num_y = [menu.num_x]
cfg.unit = [menu.unit]
cfg.surf_type = [menu.surf_type]
try:
cfg.delimiter = [menu.delimiter]
except:
cfg.delimiter = [" "]
cfg.directionx = [menu.directionx]
cfg.directiony = [menu.directiony]
else:
cfg.SPECFEM3D_output_dir = os.getcwd()
if not cfg.number_processor_eta and cfg.nodes:
cfg.number_processor_xi, cfg.number_processor_eta = split(cfg.nodes)
if isinstance(cfg.filename, str):
cfg.filename = [cfg.filename]
try:
cfg.nproc_eta = cfg.number_processor_eta
cfg.nproc_xi = cfg.number_processor_xi
cfg.cpuy = cfg.number_processor_eta
cfg.cpux = cfg.number_processor_xi
except:
pass
if create_plane:
cfg.x1 = map(float, menu.x1.split(","))
cfg.x2 = map(float, menu.x2.split(","))
cfg.x3 = map(float, menu.x3.split(","))
cfg.x4 = map(float, menu.x4.split(","))
cfg.unit = menu.unit
#
if menu:
cfg.id_proc = menu.id_proc
else:
cfg.id_proc = id_proc
#
try:
if isinstance(cfg.tripl, int):
cfg.tripl = [cfg.tripl]
except:
pass
try:
if isinstance(cfg.iv_interval, int):
cfg.iv_interval = [cfg.iv_interval]
except:
pass
try:
if isinstance(cfg.refinement_depth, int):
cfg.refinement_depth = [cfg.refinement_depth]
except:
pass
return cfg
