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code cleaning & cubit script updates #1711

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Jul 8, 2024
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code cleaning & cubit script updates #1711

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b3611fc
fixes output comment
danielpeter Jul 5, 2024
6fd1993
updates script cubit2specfem3d.py (fixes issue w/ optional surfaces a…
danielpeter Jul 8, 2024
8ddfdda
updates ordering of imprint & merge commands in cubit scripts (first …
danielpeter Jul 8, 2024
b17f716
code cleaning
danielpeter Jul 8, 2024
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96 changes: 46 additions & 50 deletions CUBIT_GEOCUBIT/geocubitlib/cubit2specfem3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -652,14 +652,16 @@ def block_definition(self):
self.bc = bc
print('HEX Blocks:')
for m, f in zip(self.block_mat, self.block_flag):
print('block ', m, 'material flag ', f)
print(' block ', m, 'material flag ', f)
print('Absorbing Boundary Conditions:')
for m, f in zip(self.block_bc, self.block_bc_flag):
print('bc ', m, 'bc flag ', f)
print('Topography (free surface)')
print(self.topography)
print('Free surface')
print(self.free)
print(' bc ', m, 'bc flag ', f)
if self.topography:
print('Topography (free surface):')
print(' ',self.topography)
if self.free:
print('Free surface:')
print(' ',self.free)
except:
print('****************************************')
print('sorry, no blocks or blocks not properly defined')
Expand Down Expand Up @@ -765,7 +767,7 @@ def mat_parameter(self, properties):
else:
raise RuntimeError('Error: material id must be strictly positive or negative, but not equal to 0')
# info output
print("material: ",txt)
print(" material: ",txt)
return txt

def nummaterial_write(self, nummaterial_name, placeholder=True):
Expand Down Expand Up @@ -853,8 +855,7 @@ def create_hexnode_string(self, hexa, hexnode_string=True):
else:
map(int, txt.split())

def create_facenode_string(self, hexa, face, normal=None, cknormal=True,
facenode_string=True):
def create_facenode_string(self, hexa, face, normal=None, cknormal=True, facenode_string=True):
nodes = self.get_face_connectivity(face)
if cknormal:
nodes_ok = self.normal_check(nodes[0:4], normal)
Expand Down Expand Up @@ -886,7 +887,7 @@ def mesh_write(self, mesh_name):
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))
print(' block ', block, ' hexes ', len(hexes))
for hexa in hexes:
txt = self.create_hexnode_string(hexa)
meshfile.write(txt)
Expand All @@ -897,7 +898,7 @@ def material_write(self, mat_name):
mat = open(mat_name, 'w')
print('Writing ' + mat_name + '.....')
for block, flag in zip(self.block_mat, self.block_flag):
print('block ', block, 'flag ', flag)
print(' block ', block, 'flag ', flag)
hexes = cubit.get_block_hexes(block)
for hexa in hexes:
mat.write(('%10i %10i\n') % (hexa, flag))
Expand Down Expand Up @@ -949,8 +950,7 @@ def free_write(self, freename=None):
for block, flag in zip(self.block_bc, self.block_bc_flag):
if block == self.topography:
name = cubit.get_exodus_entity_name('block', block)
print('free surface (topography) block name:', \
name, 'id:', block)
print(' free surface (topography): block name:', name, 'id:', block)
quads_all = cubit.get_block_faces(block)
print(' number of faces = ', len(quads_all))
dic_quads_all = dict(zip(quads_all, quads_all))
Expand All @@ -968,13 +968,13 @@ def free_write(self, freename=None):
faces = cubit.get_sub_elements('hex', h, 2)
for f in faces:
if f in s:
txt = self.create_facenode_string(
h, f, normal, cknormal=True)
# topography surface: checks face orientation against vertical normal (0,0,1)
txt = self.create_facenode_string(h, f, normal, cknormal=True)
freehex.write(txt)
print(' 100 %')
elif block == self.free:
name = cubit.get_exodus_entity_name('block', block)
print('free surface block name:', name, 'id:', block)
print(' free surface: block name:', name, 'id:', block)
quads_all = cubit.get_block_faces(block)
print(' number of faces = ', len(quads_all))
dic_quads_all = dict(zip(quads_all, quads_all))
Expand All @@ -992,8 +992,8 @@ def free_write(self, freename=None):
faces = cubit.get_sub_elements('hex', h, 2)
for f in faces:
if f in s:
txt = self.create_facenode_string(
h, f, normal, cknormal=False)
# free surface: no face orientation check against vertical normal
txt = self.create_facenode_string(h, f, normal, cknormal=False)
freehex.write(txt)
print(' 100 %')
freehex.close()
Expand Down Expand Up @@ -1122,60 +1122,60 @@ def abs_write(self, absname=None):
# loops through all block definitions
list_hex = cubit.parse_cubit_list('hex', 'all')
for block, flag in zip(self.block_bc, self.block_bc_flag):
if block != self.topography:
if block != self.topography and block != self.free:
name = cubit.get_exodus_entity_name('block', block)
print(' block name:', name, 'id:', block)
cknormal = True
abshex_local = False
# opens file
if re.search('xmin', name):
print("xmin")
print(" xmin")
abshex_local = open(absname + '_xmin', 'w')
normal = (-1, 0, 0)
elif re.search('xmax', name):
print("xmax")
print(" xmax")
abshex_local = open(absname + '_xmax', 'w')
normal = (1, 0, 0)
elif re.search('ymin', name):
print("ymin")
print(" ymin")
abshex_local = open(absname + '_ymin', 'w')
normal = (0, -1, 0)
elif re.search('ymax', name):
print("ymax")
print(" ymax")
abshex_local = open(absname + '_ymax', 'w')
normal = (0, 1, 0)
elif re.search('bottom', name):
print("bottom")
print(" bottom")
abshex_local = open(absname + '_bottom', 'w')
normal = (0, 0, -1)
elif re.search('abs', name):
print("abs all - experimental, check the output")
print(" abs all - experimental, check the output")
cknormal = False
abshex_local = open(absname, 'w')
normal = None
else:
if block == 1003:
print("xmin")
print(" xmin")
abshex_local = open(absname + '_xmin', 'w')
normal = (-1, 0, 0)
elif block == 1004:
print("ymin")
print(" ymin")
abshex_local = open(absname + '_ymin', 'w')
normal = (0, -1, 0)
elif block == 1005:
print("xmax")
print(" xmax")
abshex_local = open(absname + '_xmax', 'w')
normal = (1, 0, 0)
elif block == 1006:
print("ymax")
print(" ymax")
abshex_local = open(absname + '_ymax', 'w')
normal = (0, 1, 0)
elif block == 1002:
print("bottom")
print(" bottom")
abshex_local = open(absname + '_bottom', 'w')
normal = (0, 0, -1)
elif block == 1000:
print("custom")
print(" custom")
abshex_local = open(absname, 'w')
cknormal = False
normal = None
Expand All @@ -1199,8 +1199,7 @@ def abs_write(self, absname=None):
faces = cubit.get_sub_elements('hex', h, 2)
for f in faces:
if f in s:
txt = self.create_facenode_string(
h, f, normal=normal, cknormal=cknormal)
txt = self.create_facenode_string(h, f, normal=normal, cknormal=cknormal)
abshex_local.write(txt)
abshex_local.close()
print(' 100 %')
Expand All @@ -1215,19 +1214,23 @@ def surface_write(self, pathdir=None):
# > block 10 name 'moho_surface'
import re
for block in self.block_bc:
if block != self.topography:
if block != self.topography and block != self.free:
name = cubit.get_exodus_entity_name('block', block)
# skips block names like face_abs**, face_topo**
# skips block names like face_abs**, face_topo**, face_free**
if re.search('abs', name):
continue
elif re.search('topo', name):
continue
elif re.search('free', name):
continue
elif re.search('surface', name):
# e.g. moho_surface
filename = pathdir + name + '_file'
else:
continue
# gets face elements
print(' surface block name: ', name, 'id: ', block)
print('Optional surface:')
print(' surface: block name: ', name, 'id: ', block)
quads_all = cubit.get_block_faces(block)
print(' face = ', len(quads_all))
if len(quads_all) == 0:
Expand All @@ -1243,17 +1246,16 @@ def surface_write(self, pathdir=None):
Nhex = len(list_hex)
# Create a set to speed up "if f in dic_quads_all.keys()" big time
s = set(dic_quads_all.keys())
percentageDone = -1
for h in list_hex:
lastDisplayed = -1
for ih, h in enumerate(list_hex):
percentageDone = float(ih)/Nhex*100.0
if int(percentageDone)%10 == 0 and lastDisplayed != int(percentageDone):
print(' ', int(percentageDone), '%')
lastDisplayed = int(percentageDone)
faces = cubit.get_sub_elements('hex', h, 2)
for f in faces:
if f in s:
txt = self.create_facenode_string(
h, f, cknormal=False)
txt = self.create_facenode_string(h, f, cknormal=False)
surfhex_local.write(txt)
# closes file
surfhex_local.close()
Expand Down Expand Up @@ -1388,7 +1390,7 @@ def _get_bc_flag(self, block):
normal = (0, 0, -1)
elif re.search('abs', name):
label = "all"
print("abs all - experimental, check the output")
print(" abs all - experimental, check the output")
cknormal = False
else:
if block == 1003:
Expand Down Expand Up @@ -1424,9 +1426,7 @@ def _get_bc_flag(self, block):
# faces = cubit.get_sub_elements('hex', h, 2)
# for f in faces:
# if dic_quads_all.has_key(f):
# abs_array.append(self.create_facenode_string(
# h, f, normal=normal, cknormal=cknormal,
# facenode_string=False))
# abs_array.append(self.create_facenode_string(h, f, normal=normal, cknormal=cknormal, facenode_string=False))
# print('Ok')
# cubit.cd('set info on')
# cubit.cmd('set echo on')
Expand Down Expand Up @@ -1474,9 +1474,7 @@ def _get_bc_flag(self, block):
# for f in faces:
# if dic_quads_all.has_key(f):
# # print(f)
# free_array.append(self.create_facenode_string(
# h, f, normal, cknormal=True,
# facenode_string=False))
# free_array.append(self.create_facenode_string(h, f, normal, cknormal=True, facenode_string=False))
# elif block == self.free:
# name = cubit.get_exodus_entity_name('block', block)
# print('free surface block name:', name, 'id:', block)
Expand All @@ -1488,9 +1486,7 @@ def _get_bc_flag(self, block):
# faces = cubit.get_sub_elements('hex', h, 2)
# for f in faces:
# if dic_quads_all.has_key(f):
# free_array.append(self.create_facenode_string(
# h, f, normal, cknormal=False,
# facenode_string=False))
# free_array.append(self.create_facenode_string(h, f, normal, cknormal=False, facenode_string=False))
# print('Ok')
# cubit.cmd('set info on')
# cubit.cmd('set echo on')
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/Mount_StHelens/mesh_mount.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,8 +158,8 @@
else:
print("#" + time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime()))
print("# imprinting volume, this will take around 1 min, please be patience...")
cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# exports only surfaces which will create single volume
cubit.cmd('export acis "topo_2.acis" surface 3 10 12 14 15 9 ascii overwrite')
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/Mount_StHelens/mesh_mount_stl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@
# imprints topography surfaces into brick volume, creates connected surfaces
# note: this is a develop feature
cubit.cmd('imprint all')

cubit.cmd('merge all')

cubit.cmd('version')

Expand Down
1 change: 1 addition & 0 deletions EXAMPLES/applications/fault_examples/tpv5/TPV5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,7 @@

cubit.cmd("imprint all")
cubit.cmd("merge all")

cubit.cmd("surface 1 size "+str(elementsize))
cubit.cmd("volume 1 size "+str(elementsize))
cubit.cmd("surface 1 scheme pave")
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/layered_halfspace/2lay_mesh_boundary_fig8-nodoubling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,8 @@

cubit.cmd('delete volume 2 4')

cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

cubit.cmd('volume 3 size '+str(elementsize))
cubit.cmd('mesh volume 3')
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/layered_halfspace/2lay_mesh_boundary_fig8.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,8 @@

cubit.cmd('delete volume 2 4')

cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# Meshing the volumes
## middle volume
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/waterlayered_halfspace/make_mesh_waterlayer-default.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,8 @@

cubit.cmd('delete volume 2 4')

cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# Meshing the volumes
cubit.cmd('volume 3 size '+str(elementsize))
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,8 @@

cubit.cmd('delete volume 2 4')

cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# Meshing the volumes
cubit.cmd('volume 3 size 3589.2')
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/waterlayered_halfspace/waterlayer_only-nodoubling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,8 +64,8 @@

cubit.cmd('delete volume 2 4')

cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# Meshing the volumes
#elementsize = 1196.4 #hi-resolution
Expand Down
2 changes: 1 addition & 1 deletion EXAMPLES/applications/waterlayered_poroelastic/create_mesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,8 +95,8 @@
cubit.cmd('delete volume 4')

# merges surfaces
cubit.cmd('merge all')
cubit.cmd('imprint all')
cubit.cmd('merge all')

# resets numbering
cubit.cmd('compress all')
Expand Down
4 changes: 2 additions & 2 deletions src/decompose_mesh/part_decompose_mesh.F90
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Expand Up @@ -620,7 +620,7 @@ subroutine write_wavefield_discontinuity_database(iproc, outputpath_name, &
implicit none
integer, intent(in) :: iproc
integer, intent(in) :: nspec
integer, intent(in) :: nb_wd
integer, intent(in) :: nb_wd
integer, dimension(:), pointer :: glob2loc_elmnts
integer, dimension(1:nspec) :: part
integer, dimension(1:nb_wd), intent(in) :: boundary_to_ispec_wd, side_wd
Expand All @@ -632,7 +632,7 @@ subroutine write_wavefield_discontinuity_database(iproc, outputpath_name, &
character(len=MAX_STRING_LEN) :: prname
write(prname, "('proc',i6.6,'_')") iproc
open(unit=IFILE_WAVEFIELD_DISCONTINUITY, &
file=trim(outputpath_name)//'/'//trim(prname)//&
file = trim(outputpath_name)//'/'//trim(prname)//&
trim(FNAME_WAVEFIELD_DISCONTINUITY_MESH), &
form='unformatted', action='write')
local_nb_wd = 0
Expand Down
4 changes: 2 additions & 2 deletions src/decompose_mesh/read_mesh_files.F90
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Expand Up @@ -39,7 +39,7 @@ subroutine read_mesh_files()
use fault_scotch, only: ANY_FAULT,read_fault_files,save_nodes_coords,close_faults

use constants, only: FNAME_WAVEFIELD_DISCONTINUITY_INTERFACE

implicit none

! local parameters
Expand Down Expand Up @@ -592,7 +592,7 @@ subroutine read_mesh_files()
read(IIN_DB, *, iostat=ier) boundary_to_ispec_wd(ib), side_wd(ib)
enddo
close(IIN_DB)
endif
endif

! reads in absorbing boundary files
open(unit=IIN_DB, file=localpath_name(1:len_trim(localpath_name))//'/absorbing_surface_file_xmin', &
Expand Down
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