liaohaiyang1534 commented 1 year ago

Hi,

I'm going to create a model with a hole in it, I put seven blocks together, the middle block adds the materiall property of the hole. The python code runs successfully, but it doesn't seem to generate the mesh_file and materials_file.

Here is a picture of the model, which looks alright

Here is a small portion of the output of python code:

In case you need more detailed code information, here is the python code:

#!/usr/bin/env python

from __future__ import print_function

import os
import sys

# Add the PATH of Cubit-associated DLL files to path
dll_path = r"E:\coreform cubit\coreform cubit 2022.11\bin"
path = os.environ.get('PATH', '')
if dll_path not in path.split(';'):
    new_path = path + ';' + dll_path if path else dll_path
    os.environ['PATH'] = new_path

sys.path.append("E:\\coreforum cubit\\coreform cubit 2022.11\\bin")
sys.path.append("E:\\coreforum cubit\\coreform cubit 2022.11\\bin\\_cubit3.pyd")

# Add cubit path to PYTHONPATH
cubit_path = r"E:\coreform cubit\coreform cubit 2022.11\bin"
python_path = os.environ.get('PYTHONPATH', '')
if cubit_path not in python_path.split(';'):
    new_python_path = python_path + ';' + cubit_path if python_path else cubit_path
    os.environ['PYTHONPATH'] = new_python_path

sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT/geocubitlib")
sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT")

elementsize = 1

SEMoutput='MESH'
CUBIToutput='MESH_GEOCUBIT'

os.system('mkdir -p '+ SEMoutput)
os.system('mkdir -p '+ CUBIToutput)

import cubit
try:
    cubit.init(["-noecho","-nojournal"])
except:
    pass

version = cubit.get_version()
version_major = int(version.split(".")[0])
version_minor = int(version.split(".")[1])
print("cubit version: ",version)

cubit.cmd('reset')

# create a hole
cubit.cmd('brick x 3 y 3 z 3')
cubit.cmd('volume 1 move x 0 y 0 z -4')

# create the top volume of the hole
cubit.cmd('brick x 100 y 16 z 13.5')
cubit.cmd('volume 2 move x 0 y 0 z 4.25')

# create the bottom volume of the hole 
cubit.cmd('brick x 100 y 16 z 13.5')
cubit.cmd('volume 3 move x 0 y 0 z -12.25')

# create the front volume of the hole 
cubit.cmd('brick x 48.5 y 16 z 3')
cubit.cmd('volume 4 move x 25.75 y 0 z -4')

# create the back volume of the hole 
cubit.cmd('brick x 48.5 y 16 z 3')
cubit.cmd('volume 5 move x -25.75 y 0 z -4')

# create the left volume of the hole 
cubit.cmd('brick x 3 y 6.5 z 3')
cubit.cmd('volume 6 move x 0 y 4.75 z -4')

# create the right volume of the hole 
cubit.cmd('brick x 3 y 6.5 z 3')
cubit.cmd('volume 7 move x 0 y -4.75 z -4')

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

cubit.cmd('volume all size 1')
cubit.cmd('mesh volume all')

cubit.cmd('block 1 volume 1')
cubit.cmd('block 1 name "elastic 1"')
cubit.cmd('block 1 attribute count 7')
cubit.cmd('block 1 attribute index 1 1')
cubit.cmd('block 1 attribute index 2 340')
cubit.cmd('block 1 attribute index 3 17')
cubit.cmd('block 1 attribute index 4 500')
cubit.cmd('block 1 attribute index 5 9999')
cubit.cmd('block 1 attribute index 6 9999')
cubit.cmd('block 1 attribute index 7 0')

cubit.cmd('block 2 volume 2')
cubit.cmd('block 2 name "elastic 2"')
cubit.cmd('block 2 attribute count 7')
cubit.cmd('block 2 attribute index 1 2')
cubit.cmd('block 2 attribute index 2 475')
cubit.cmd('block 2 attribute index 3 230')
cubit.cmd('block 2 attribute index 4 2000')
cubit.cmd('block 2 attribute index 5 9999')
cubit.cmd('block 2 attribute index 6 9999')
cubit.cmd('block 2 attribute index 7 0')

cubit.cmd('block 3 volume 3')
cubit.cmd('block 3 name "elastic 2"')
cubit.cmd('block 3 attribute count 7')
cubit.cmd('block 3 attribute index 1 3')
cubit.cmd('block 3 attribute index 2 475')
cubit.cmd('block 3 attribute index 3 230')
cubit.cmd('block 3 attribute index 4 2000')
cubit.cmd('block 3 attribute index 5 9999')
cubit.cmd('block 3 attribute index 6 9999')
cubit.cmd('block 3 attribute index 7 0')

cubit.cmd('block 4 volume 4')
cubit.cmd('block 4 name "elastic 2"')
cubit.cmd('block 4 attribute count 7')
cubit.cmd('block 4 attribute index 1 4')
cubit.cmd('block 4 attribute index 2 475')
cubit.cmd('block 4 attribute index 3 230')
cubit.cmd('block 4 attribute index 4 2000')
cubit.cmd('block 4 attribute index 5 9999')
cubit.cmd('block 4 attribute index 6 9999')
cubit.cmd('block 4 attribute index 7 0')

cubit.cmd('block 5 volume 5')
cubit.cmd('block 5 name "elastic 2"')
cubit.cmd('block 5 attribute count 7')
cubit.cmd('block 5 attribute index 1 5')
cubit.cmd('block 5 attribute index 2 475')
cubit.cmd('block 5 attribute index 3 230')
cubit.cmd('block 5 attribute index 4 2000')
cubit.cmd('block 5 attribute index 5 9999')
cubit.cmd('block 5 attribute index 6 9999')
cubit.cmd('block 5 attribute index 7 0')

cubit.cmd('block 6 volume 6')
cubit.cmd('block 6 name "elastic 2"')
cubit.cmd('block 6 attribute count 7')
cubit.cmd('block 6 attribute index 1 6')
cubit.cmd('block 6 attribute index 2 475')
cubit.cmd('block 6 attribute index 3 230')
cubit.cmd('block 6 attribute index 4 2000')
cubit.cmd('block 6 attribute index 5 9999')
cubit.cmd('block 6 attribute index 6 9999')
cubit.cmd('block 6 attribute index 7 0')

cubit.cmd('block 7 volume 7')
cubit.cmd('block 7 name "elastic 2"')
cubit.cmd('block 7 attribute count 7')
cubit.cmd('block 7 attribute index 1 7')
cubit.cmd('block 7 attribute index 2 475')
cubit.cmd('block 7 attribute index 3 230')
cubit.cmd('block 7 attribute index 4 2000')
cubit.cmd('block 7 attribute index 5 9999')
cubit.cmd('block 7 attribute index 6 9999')
cubit.cmd('block 7 attribute index 7 0')

cubit.cmd('export mesh MESH_GEOCUBIT/top.e dimension 3 overwrite')
cubit.cmd('save as MESH_GEOCUBIT/top.cub overwrite')

cubit2specfem3d.export2SPECFEM3D(SEMoutput)

if version_major >= 16 and version_minor >= 4:
    cubit.cmd('view top')
    cubit.cmd('hardcopy "' + CUBIToutput + '/waterlayered.png" png')

I'm very appreciated to have any advice and suggestions for this. (If you need any more clarifications, please let me know)

Regards

Haiyang Liao haiyangliao@smail.nju.edu.cn

homnath commented 1 year ago

Hi Haiyang Liao,

There may be an issue with voids.

Alternatively, you can define the sidesets within the Cubit, and use the exodus2specfem3d application in MeshAssist package (https://github.com/homnath/MeshAssist). It generally works in any complex models including voids. https://github.com/homnath/MeshAssist Check section 4.6 of the documentation https://github.com/homnath/MeshAssist/blob/master/doc/manual_MeshAssist.pdf

Best, Hom Nath

From: liaohaiyang1534 @.> Sent: Wednesday, June 28, 2023 9:20 AM To: SPECFEM/specfem3d @.> Cc: Subscribed @.***> Subject: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620)

Hi,

I'm going to create a model with a hole in it, I put seven blocks together, the middle block adds the materiall property of the hole. The python code runs successfully, but it doesn't seem to generate the mesh_file and materials_file.

Here is a picture of the model, which looks alright

[image]https://user-images.githubusercontent.com/104192749/249480543-17edb8bb-e8bd-4cb2-b7c5-7f4cbc86c53c.png

Here is a small portion of the output of python code:

[image]https://user-images.githubusercontent.com/104192749/249481018-af69c3e3-7a1b-4045-8b03-1598e4f7b36a.png

In case you need more detailed code information, here is the python code:

!/usr/bin/env python

from future import print_function

import os import sys

Add the PATH of Cubit-associated DLL files to path

dll_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" path = os.environ.get('PATH', '') if dll_path not in path.split(';'): new_path = path + ';' + dll_path if path else dll_path os.environ['PATH'] = new_path

sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin") sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin\_cubit3.pyd")

Add cubit path to PYTHONPATH

cubit_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" python_path = os.environ.get('PYTHONPATH', '') if cubit_path not in python_path.split(';'): new_python_path = python_path + ';' + cubit_path if python_path else cubit_path os.environ['PYTHONPATH'] = new_python_path

sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT/geocubitlib") sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT")

elementsize = 1

SEMoutput='MESH' CUBIToutput='MESH_GEOCUBIT'

os.system('mkdir -p '+ SEMoutput) os.system('mkdir -p '+ CUBIToutput)

import cubit try: cubit.init(["-noecho","-nojournal"]) except: pass

version = cubit.get_version() version_major = int(version.split(".")[0]) version_minor = int(version.split(".")[1]) print("cubit version: ",version)

cubit.cmd('reset')

create a hole

cubit.cmd('brick x 3 y 3 z 3') cubit.cmd('volume 1 move x 0 y 0 z -4')

create the top volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 2 move x 0 y 0 z 4.25')

create the bottom volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 3 move x 0 y 0 z -12.25')

create the front volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 4 move x 25.75 y 0 z -4')

create the back volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 5 move x -25.75 y 0 z -4')

create the left volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 6 move x 0 y 4.75 z -4')

create the right volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 7 move x 0 y -4.75 z -4')

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

cubit.cmd('volume all size 1') cubit.cmd('mesh volume all')

cubit.cmd('block 1 volume 1') cubit.cmd('block 1 name "elastic 1"') cubit.cmd('block 1 attribute count 7') cubit.cmd('block 1 attribute index 1 1') cubit.cmd('block 1 attribute index 2 340') cubit.cmd('block 1 attribute index 3 17') cubit.cmd('block 1 attribute index 4 500') cubit.cmd('block 1 attribute index 5 9999') cubit.cmd('block 1 attribute index 6 9999') cubit.cmd('block 1 attribute index 7 0')

cubit.cmd('block 2 volume 2') cubit.cmd('block 2 name "elastic 2"') cubit.cmd('block 2 attribute count 7') cubit.cmd('block 2 attribute index 1 2') cubit.cmd('block 2 attribute index 2 475') cubit.cmd('block 2 attribute index 3 230') cubit.cmd('block 2 attribute index 4 2000') cubit.cmd('block 2 attribute index 5 9999') cubit.cmd('block 2 attribute index 6 9999') cubit.cmd('block 2 attribute index 7 0')

cubit.cmd('block 3 volume 3') cubit.cmd('block 3 name "elastic 2"') cubit.cmd('block 3 attribute count 7') cubit.cmd('block 3 attribute index 1 3') cubit.cmd('block 3 attribute index 2 475') cubit.cmd('block 3 attribute index 3 230') cubit.cmd('block 3 attribute index 4 2000') cubit.cmd('block 3 attribute index 5 9999') cubit.cmd('block 3 attribute index 6 9999') cubit.cmd('block 3 attribute index 7 0')

cubit.cmd('block 4 volume 4') cubit.cmd('block 4 name "elastic 2"') cubit.cmd('block 4 attribute count 7') cubit.cmd('block 4 attribute index 1 4') cubit.cmd('block 4 attribute index 2 475') cubit.cmd('block 4 attribute index 3 230') cubit.cmd('block 4 attribute index 4 2000') cubit.cmd('block 4 attribute index 5 9999') cubit.cmd('block 4 attribute index 6 9999') cubit.cmd('block 4 attribute index 7 0')

cubit.cmd('block 5 volume 5') cubit.cmd('block 5 name "elastic 2"') cubit.cmd('block 5 attribute count 7') cubit.cmd('block 5 attribute index 1 5') cubit.cmd('block 5 attribute index 2 475') cubit.cmd('block 5 attribute index 3 230') cubit.cmd('block 5 attribute index 4 2000') cubit.cmd('block 5 attribute index 5 9999') cubit.cmd('block 5 attribute index 6 9999') cubit.cmd('block 5 attribute index 7 0')

cubit.cmd('block 6 volume 6') cubit.cmd('block 6 name "elastic 2"') cubit.cmd('block 6 attribute count 7') cubit.cmd('block 6 attribute index 1 6') cubit.cmd('block 6 attribute index 2 475') cubit.cmd('block 6 attribute index 3 230') cubit.cmd('block 6 attribute index 4 2000') cubit.cmd('block 6 attribute index 5 9999') cubit.cmd('block 6 attribute index 6 9999') cubit.cmd('block 6 attribute index 7 0')

cubit.cmd('block 7 volume 7') cubit.cmd('block 7 name "elastic 2"') cubit.cmd('block 7 attribute count 7') cubit.cmd('block 7 attribute index 1 7') cubit.cmd('block 7 attribute index 2 475') cubit.cmd('block 7 attribute index 3 230') cubit.cmd('block 7 attribute index 4 2000') cubit.cmd('block 7 attribute index 5 9999') cubit.cmd('block 7 attribute index 6 9999') cubit.cmd('block 7 attribute index 7 0')

cubit.cmd('export mesh MESH_GEOCUBIT/top.e dimension 3 overwrite') cubit.cmd('save as MESH_GEOCUBIT/top.cub overwrite')

cubit2specfem3d.export2SPECFEM3D(SEMoutput)

if version_major >= 16 and version_minor >= 4: cubit.cmd('view top') cubit.cmd('hardcopy "' + CUBIToutput + '/waterlayered.png" png')

I'm very appreciated to have any advice and suggestions for this. (If you need any more clarifications, please let me know)

Regards

Haiyang Liao @.**@.>

— Reply to this email directly, view it on GitHubhttps://github.com/SPECFEM/specfem3d/issues/1620, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABMCQ4UDWOEO3QNYOBJZKDLXNQVTJANCNFSM6AAAAAAZXD6IUA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

casarotti commented 1 year ago

could you try with a small different definition of the blocks?

for example

cubit.cmd('block 4 hex in volume 4')

instead of

cubit.cmd('block 4 volume 4')

On Thu, Jun 29, 2023 at 6:11 AM Hom Nath Gharti @.***> wrote:

Hi Haiyang Liao,

There may be an issue with voids.

Alternatively, you can define the sidesets within the Cubit, and use the exodus2specfem3d application in MeshAssist package ( https://github.com/homnath/MeshAssist). It generally works in any complex models including voids. https://github.com/homnath/MeshAssist Check section 4.6 of the documentation https://github.com/homnath/MeshAssist/blob/master/doc/manual_MeshAssist.pdf

Best, Hom Nath

From: liaohaiyang1534 @.> Sent: Wednesday, June 28, 2023 9:20 AM To: SPECFEM/specfem3d @.> Cc: Subscribed @.***> Subject: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620)

Hi,

I'm going to create a model with a hole in it, I put seven blocks together, the middle block adds the materiall property of the hole. The python code runs successfully, but it doesn't seem to generate the mesh_file and materials_file.

Here is a picture of the model, which looks alright

[image]< https://user-images.githubusercontent.com/104192749/249480543-17edb8bb-e8bd-4cb2-b7c5-7f4cbc86c53c.png>

Here is a small portion of the output of python code:

[image]< https://user-images.githubusercontent.com/104192749/249481018-af69c3e3-7a1b-4045-8b03-1598e4f7b36a.png>

In case you need more detailed code information, here is the python code:

!/usr/bin/env python

from future import print_function

import os import sys

Add the PATH of Cubit-associated DLL files to path

dll_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" path = os.environ.get('PATH', '') if dll_path not in path.split(';'): new_path = path + ';' + dll_path if path else dll_path os.environ['PATH'] = new_path

sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin") sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin\_cubit3.pyd")

Add cubit path to PYTHONPATH

cubit_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" python_path = os.environ.get('PYTHONPATH', '') if cubit_path not in python_path.split(';'): new_python_path = python_path + ';' + cubit_path if python_path else cubit_path os.environ['PYTHONPATH'] = new_python_path

sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT/geocubitlib") sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT")

elementsize = 1

SEMoutput='MESH' CUBIToutput='MESH_GEOCUBIT'

os.system('mkdir -p '+ SEMoutput) os.system('mkdir -p '+ CUBIToutput)

import cubit try: cubit.init(["-noecho","-nojournal"]) except: pass

version = cubit.get_version() version_major = int(version.split(".")[0]) version_minor = int(version.split(".")[1]) print("cubit version: ",version)

cubit.cmd('reset')

create a hole

cubit.cmd('brick x 3 y 3 z 3') cubit.cmd('volume 1 move x 0 y 0 z -4')

create the top volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 2 move x 0 y 0 z 4.25')

create the bottom volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 3 move x 0 y 0 z -12.25')

create the front volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 4 move x 25.75 y 0 z -4')

create the back volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 5 move x -25.75 y 0 z -4')

create the left volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 6 move x 0 y 4.75 z -4')

create the right volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 7 move x 0 y -4.75 z -4')

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

cubit.cmd('volume all size 1') cubit.cmd('mesh volume all')

cubit.cmd('block 1 volume 1') cubit.cmd('block 1 name "elastic 1"') cubit.cmd('block 1 attribute count 7') cubit.cmd('block 1 attribute index 1 1') cubit.cmd('block 1 attribute index 2 340') cubit.cmd('block 1 attribute index 3 17') cubit.cmd('block 1 attribute index 4 500') cubit.cmd('block 1 attribute index 5 9999') cubit.cmd('block 1 attribute index 6 9999') cubit.cmd('block 1 attribute index 7 0')

cubit.cmd('block 2 volume 2') cubit.cmd('block 2 name "elastic 2"') cubit.cmd('block 2 attribute count 7') cubit.cmd('block 2 attribute index 1 2') cubit.cmd('block 2 attribute index 2 475') cubit.cmd('block 2 attribute index 3 230') cubit.cmd('block 2 attribute index 4 2000') cubit.cmd('block 2 attribute index 5 9999') cubit.cmd('block 2 attribute index 6 9999') cubit.cmd('block 2 attribute index 7 0')

cubit.cmd('block 3 volume 3') cubit.cmd('block 3 name "elastic 2"') cubit.cmd('block 3 attribute count 7') cubit.cmd('block 3 attribute index 1 3') cubit.cmd('block 3 attribute index 2 475') cubit.cmd('block 3 attribute index 3 230') cubit.cmd('block 3 attribute index 4 2000') cubit.cmd('block 3 attribute index 5 9999') cubit.cmd('block 3 attribute index 6 9999') cubit.cmd('block 3 attribute index 7 0')

cubit.cmd('block 4 volume 4') cubit.cmd('block 4 name "elastic 2"') cubit.cmd('block 4 attribute count 7') cubit.cmd('block 4 attribute index 1 4') cubit.cmd('block 4 attribute index 2 475') cubit.cmd('block 4 attribute index 3 230') cubit.cmd('block 4 attribute index 4 2000') cubit.cmd('block 4 attribute index 5 9999') cubit.cmd('block 4 attribute index 6 9999') cubit.cmd('block 4 attribute index 7 0')

cubit.cmd('block 5 volume 5') cubit.cmd('block 5 name "elastic 2"') cubit.cmd('block 5 attribute count 7') cubit.cmd('block 5 attribute index 1 5') cubit.cmd('block 5 attribute index 2 475') cubit.cmd('block 5 attribute index 3 230') cubit.cmd('block 5 attribute index 4 2000') cubit.cmd('block 5 attribute index 5 9999') cubit.cmd('block 5 attribute index 6 9999') cubit.cmd('block 5 attribute index 7 0')

cubit.cmd('block 6 volume 6') cubit.cmd('block 6 name "elastic 2"') cubit.cmd('block 6 attribute count 7') cubit.cmd('block 6 attribute index 1 6') cubit.cmd('block 6 attribute index 2 475') cubit.cmd('block 6 attribute index 3 230') cubit.cmd('block 6 attribute index 4 2000') cubit.cmd('block 6 attribute index 5 9999') cubit.cmd('block 6 attribute index 6 9999') cubit.cmd('block 6 attribute index 7 0')

cubit.cmd('block 7 volume 7') cubit.cmd('block 7 name "elastic 2"') cubit.cmd('block 7 attribute count 7') cubit.cmd('block 7 attribute index 1 7') cubit.cmd('block 7 attribute index 2 475') cubit.cmd('block 7 attribute index 3 230') cubit.cmd('block 7 attribute index 4 2000') cubit.cmd('block 7 attribute index 5 9999') cubit.cmd('block 7 attribute index 6 9999') cubit.cmd('block 7 attribute index 7 0')

cubit.cmd('export mesh MESH_GEOCUBIT/top.e dimension 3 overwrite') cubit.cmd('save as MESH_GEOCUBIT/top.cub overwrite')

cubit2specfem3d.export2SPECFEM3D(SEMoutput)

if version_major >= 16 and version_minor >= 4: cubit.cmd('view top') cubit.cmd('hardcopy "' + CUBIToutput + '/waterlayered.png" png')

I'm very appreciated to have any advice and suggestions for this. (If you need any more clarifications, please let me know)

Regards

Haiyang Liao @.**@.>

— Reply to this email directly, view it on GitHub< https://github.com/SPECFEM/specfem3d/issues/1620>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABMCQ4UDWOEO3QNYOBJZKDLXNQVTJANCNFSM6AAAAAAZXD6IUA>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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liaohaiyang1534 commented 1 year ago

Hi, casarotti

it really works! thanks a lot! i really appreciate that

liaohaiyang1534 commented 1 year ago

Hi, Hom Nath

Thanks for your suggestion, I'll take a closer look

Best

liaohaiyang1534 commented 1 year ago

could you try with a small different definition of the blocks? for example cubit.cmd('block 4 hex in volume 4') instead of cubit.cmd('block 4 volume 4') … On Thu, Jun 29, 2023 at 6:11 AM Hom Nath Gharti @.> wrote: Hi Haiyang Liao, There may be an issue with voids. Alternatively, you can define the sidesets within the Cubit, and use the exodus2specfem3d application in MeshAssist package ( https://github.com/homnath/MeshAssist). It generally works in any complex models including voids. https://github.com/homnath/MeshAssist Check section 4.6 of the documentation https://github.com/homnath/MeshAssist/blob/master/doc/manual_MeshAssist.pdf Best, Hom Nath ____ From: liaohaiyang1534 @.> Sent: Wednesday, June 28, 2023 9:20 AM To: SPECFEM/specfem3d @.> Cc: Subscribed @.> Subject: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620) Hi, I'm going to create a model with a hole in it, I put seven blocks together, the middle block adds the materiall property of the hole. The python code runs successfully, but it doesn't seem to generate the mesh_file and materials_file. Here is a picture of the model, which looks alright [image]< https://user-images.githubusercontent.com/104192749/249480543-17edb8bb-e8bd-4cb2-b7c5-7f4cbc86c53c.png> Here is a small portion of the output of python code: [image]< https://user-images.githubusercontent.com/104192749/249481018-af69c3e3-7a1b-4045-8b03-1598e4f7b36a.png> In case you need more detailed code information, here is the python code: #!/usr/bin/env python from future import print_function import os import sys # Add the PATH of Cubit-associated DLL files to path dll_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" path = os.environ.get('PATH', '') if dll_path not in path.split(';'): new_path = path + ';' + dll_path if path else dll_path os.environ['PATH'] = new_path sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin") sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin\_cubit3.pyd") # Add cubit path to PYTHONPATH cubit_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" python_path = os.environ.get('PYTHONPATH', '') if cubit_path not in python_path.split(';'): new_python_path = python_path + ';' + cubit_path if python_path else cubit_path os.environ['PYTHONPATH'] = new_python_path sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT/geocubitlib") sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT") elementsize = 1 SEMoutput='MESH' CUBIToutput='MESH_GEOCUBIT' os.system('mkdir -p '+ SEMoutput) os.system('mkdir -p '+ CUBIToutput) import cubit try: cubit.init(["-noecho","-nojournal"]) except: pass version = cubit.get_version() version_major = int(version.split(".")[0]) version_minor = int(version.split(".")[1]) print("cubit version: ",version) cubit.cmd('reset') # create a hole cubit.cmd('brick x 3 y 3 z 3') cubit.cmd('volume 1 move x 0 y 0 z -4') # create the top volume of the hole cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 2 move x 0 y 0 z 4.25') # create the bottom volume of the hole cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 3 move x 0 y 0 z -12.25') # create the front volume of the hole cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 4 move x 25.75 y 0 z -4') # create the back volume of the hole cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 5 move x -25.75 y 0 z -4') # create the left volume of the hole cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 6 move x 0 y 4.75 z -4') # create the right volume of the hole cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 7 move x 0 y -4.75 z -4') cubit.cmd('merge all') cubit.cmd('imprint all') cubit.cmd('volume all size 1') cubit.cmd('mesh volume all') cubit.cmd('block 1 volume 1') cubit.cmd('block 1 name "elastic 1"') cubit.cmd('block 1 attribute count 7') cubit.cmd('block 1 attribute index 1 1') cubit.cmd('block 1 attribute index 2 340') cubit.cmd('block 1 attribute index 3 17') cubit.cmd('block 1 attribute index 4 500') cubit.cmd('block 1 attribute index 5 9999') cubit.cmd('block 1 attribute index 6 9999') cubit.cmd('block 1 attribute index 7 0') cubit.cmd('block 2 volume 2') cubit.cmd('block 2 name "elastic 2"') cubit.cmd('block 2 attribute count 7') cubit.cmd('block 2 attribute index 1 2') cubit.cmd('block 2 attribute index 2 475') cubit.cmd('block 2 attribute index 3 230') cubit.cmd('block 2 attribute index 4 2000') cubit.cmd('block 2 attribute index 5 9999') cubit.cmd('block 2 attribute index 6 9999') cubit.cmd('block 2 attribute index 7 0') cubit.cmd('block 3 volume 3') cubit.cmd('block 3 name "elastic 2"') cubit.cmd('block 3 attribute count 7') cubit.cmd('block 3 attribute index 1 3') cubit.cmd('block 3 attribute index 2 475') cubit.cmd('block 3 attribute index 3 230') cubit.cmd('block 3 attribute index 4 2000') cubit.cmd('block 3 attribute index 5 9999') cubit.cmd('block 3 attribute index 6 9999') cubit.cmd('block 3 attribute index 7 0') cubit.cmd('block 4 volume 4') cubit.cmd('block 4 name "elastic 2"') cubit.cmd('block 4 attribute count 7') cubit.cmd('block 4 attribute index 1 4') cubit.cmd('block 4 attribute index 2 475') cubit.cmd('block 4 attribute index 3 230') cubit.cmd('block 4 attribute index 4 2000') cubit.cmd('block 4 attribute index 5 9999') cubit.cmd('block 4 attribute index 6 9999') cubit.cmd('block 4 attribute index 7 0') cubit.cmd('block 5 volume 5') cubit.cmd('block 5 name "elastic 2"') cubit.cmd('block 5 attribute count 7') cubit.cmd('block 5 attribute index 1 5') cubit.cmd('block 5 attribute index 2 475') cubit.cmd('block 5 attribute index 3 230') cubit.cmd('block 5 attribute index 4 2000') cubit.cmd('block 5 attribute index 5 9999') cubit.cmd('block 5 attribute index 6 9999') cubit.cmd('block 5 attribute index 7 0') cubit.cmd('block 6 volume 6') cubit.cmd('block 6 name "elastic 2"') cubit.cmd('block 6 attribute count 7') cubit.cmd('block 6 attribute index 1 6') cubit.cmd('block 6 attribute index 2 475') cubit.cmd('block 6 attribute index 3 230') cubit.cmd('block 6 attribute index 4 2000') cubit.cmd('block 6 attribute index 5 9999') cubit.cmd('block 6 attribute index 6 9999') cubit.cmd('block 6 attribute index 7 0') cubit.cmd('block 7 volume 7') cubit.cmd('block 7 name "elastic 2"') cubit.cmd('block 7 attribute count 7') cubit.cmd('block 7 attribute index 1 7') cubit.cmd('block 7 attribute index 2 475') cubit.cmd('block 7 attribute index 3 230') cubit.cmd('block 7 attribute index 4 2000') cubit.cmd('block 7 attribute index 5 9999') cubit.cmd('block 7 attribute index 6 9999') cubit.cmd('block 7 attribute index 7 0') cubit.cmd('export mesh MESH_GEOCUBIT/top.e dimension 3 overwrite') cubit.cmd('save as MESH_GEOCUBIT/top.cub overwrite') cubit2specfem3d.export2SPECFEM3D(SEMoutput) if version_major >= 16 and version_minor >= 4: cubit.cmd('view top') cubit.cmd('hardcopy "' + CUBIToutput + '/waterlayered.png" png') I'm very appreciated to have any advice and suggestions for this. (If you need any more clarifications, please let me know) Regards Haiyang Liao @.**@.> — Reply to this email directly, view it on GitHub< #1620>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABMCQ4UDWOEO3QNYOBJZKDLXNQVTJANCNFSM6AAAAAAZXD6IUA>. You are receiving this because you are subscribed to this thread.Message ID: @.> — Reply to this email directly, view it on GitHub <#1620 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAQG2CNXH2KFEJJX2IGUVDXNT6ALANCNFSM6AAAAAAZXD6IUA . You are receiving this because you are subscribed to this thread.Message ID: @.>

Hi casarotti,

You gave me a suggestion last time, which worked, but then I encountered a problem, which has not been resolved until now. The problem is that an error occurs when running this line of command: cubit2specfem3d.export2SPECFEM3D(SEMoutput) An error occurred while generating the boundary conditions:

Although this error is due to adding boundary conditions, and I can add better CPML in specfem3d, maybe I can ignore this error. But I later found that there may be a problem inside the grid, so I wonder if it is related to the error here. I haven't been able to solve this error for days.

Do you have any other suggestions? I will be very grateful!

In case you need more detailed information, here is the python code and error information: TypeError 'NoneType' object is not iterable.txt

zuoxuan-de commented 3 months ago

@liaohaiyang1534 I've been working on this model building issue recently as well, did you finally fix it，Have you ever tried treating the hole with a free surface instead of treating it as air?

liaohaiyang1534 commented 3 months ago

I haven't done simulations for a long time, and the issue wasn't resolved last time. I plan to continue with noise simulations in the future. Please let me know if there are any updates. Recently, I have been working on noise imaging.

	廖海洋

@. | ---- Replied Message ---- | From | @.> | | Date | 7/2/2024 11:17 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620) |

@liaohaiyang1534 I've been working on this model building issue recently as well, did you finally fix it

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

liaohaiyang1534 commented 3 months ago

Yes, I clearly remember trying that, but it didn't work either. I don't quite remember the specific error.

Any suggestions are welcome at any time~

	廖海洋

@. | ---- Replied Message ---- | From | emanuele @.> | | Date | 6/29/2023 12:31 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620) |

could you try with a small different definition of the blocks?

for example

cubit.cmd('block 4 hex in volume 4')

instead of

cubit.cmd('block 4 volume 4')

On Thu, Jun 29, 2023 at 6:11 AM Hom Nath Gharti @.***> wrote:

Hi Haiyang Liao,

There may be an issue with voids.

Alternatively, you can define the sidesets within the Cubit, and use the exodus2specfem3d application in MeshAssist package ( https://github.com/homnath/MeshAssist). It generally works in any complex models including voids. https://github.com/homnath/MeshAssist Check section 4.6 of the documentation https://github.com/homnath/MeshAssist/blob/master/doc/manual_MeshAssist.pdf

Best, Hom Nath

From: liaohaiyang1534 @.> Sent: Wednesday, June 28, 2023 9:20 AM To: SPECFEM/specfem3d @.> Cc: Subscribed @.***> Subject: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620)

Hi,

I'm going to create a model with a hole in it, I put seven blocks together, the middle block adds the materiall property of the hole. The python code runs successfully, but it doesn't seem to generate the mesh_file and materials_file.

Here is a picture of the model, which looks alright

[image]< https://user-images.githubusercontent.com/104192749/249480543-17edb8bb-e8bd-4cb2-b7c5-7f4cbc86c53c.png>

Here is a small portion of the output of python code:

[image]< https://user-images.githubusercontent.com/104192749/249481018-af69c3e3-7a1b-4045-8b03-1598e4f7b36a.png>

In case you need more detailed code information, here is the python code:

!/usr/bin/env python

from future import print_function

import os import sys

Add the PATH of Cubit-associated DLL files to path

dll_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" path = os.environ.get('PATH', '') if dll_path not in path.split(';'): new_path = path + ';' + dll_path if path else dll_path os.environ['PATH'] = new_path

sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin") sys.path.append("E:\coreforum cubit\coreform cubit 2022.11\bin\_cubit3.pyd")

Add cubit path to PYTHONPATH

cubit_path = r"E:\coreform cubit\coreform cubit 2022.11\bin" python_path = os.environ.get('PYTHONPATH', '') if cubit_path not in python_path.split(';'): new_python_path = python_path + ';' + cubit_path if python_path else cubit_path os.environ['PYTHONPATH'] = new_python_path

sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT/geocubitlib") sys.path.append("../../specfem3d-master/CUBIT_GEOCUBIT")

elementsize = 1

SEMoutput='MESH' CUBIToutput='MESH_GEOCUBIT'

os.system('mkdir -p '+ SEMoutput) os.system('mkdir -p '+ CUBIToutput)

import cubit try: cubit.init(["-noecho","-nojournal"]) except: pass

version = cubit.get_version() version_major = int(version.split(".")[0]) version_minor = int(version.split(".")[1]) print("cubit version: ",version)

cubit.cmd('reset')

create a hole

cubit.cmd('brick x 3 y 3 z 3') cubit.cmd('volume 1 move x 0 y 0 z -4')

create the top volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 2 move x 0 y 0 z 4.25')

create the bottom volume of the hole

cubit.cmd('brick x 100 y 16 z 13.5') cubit.cmd('volume 3 move x 0 y 0 z -12.25')

create the front volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 4 move x 25.75 y 0 z -4')

create the back volume of the hole

cubit.cmd('brick x 48.5 y 16 z 3') cubit.cmd('volume 5 move x -25.75 y 0 z -4')

create the left volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 6 move x 0 y 4.75 z -4')

create the right volume of the hole

cubit.cmd('brick x 3 y 6.5 z 3') cubit.cmd('volume 7 move x 0 y -4.75 z -4')

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

cubit.cmd('volume all size 1') cubit.cmd('mesh volume all')

cubit.cmd('block 1 volume 1') cubit.cmd('block 1 name "elastic 1"') cubit.cmd('block 1 attribute count 7') cubit.cmd('block 1 attribute index 1 1') cubit.cmd('block 1 attribute index 2 340') cubit.cmd('block 1 attribute index 3 17') cubit.cmd('block 1 attribute index 4 500') cubit.cmd('block 1 attribute index 5 9999') cubit.cmd('block 1 attribute index 6 9999') cubit.cmd('block 1 attribute index 7 0')

cubit.cmd('block 2 volume 2') cubit.cmd('block 2 name "elastic 2"') cubit.cmd('block 2 attribute count 7') cubit.cmd('block 2 attribute index 1 2') cubit.cmd('block 2 attribute index 2 475') cubit.cmd('block 2 attribute index 3 230') cubit.cmd('block 2 attribute index 4 2000') cubit.cmd('block 2 attribute index 5 9999') cubit.cmd('block 2 attribute index 6 9999') cubit.cmd('block 2 attribute index 7 0')

cubit.cmd('block 3 volume 3') cubit.cmd('block 3 name "elastic 2"') cubit.cmd('block 3 attribute count 7') cubit.cmd('block 3 attribute index 1 3') cubit.cmd('block 3 attribute index 2 475') cubit.cmd('block 3 attribute index 3 230') cubit.cmd('block 3 attribute index 4 2000') cubit.cmd('block 3 attribute index 5 9999') cubit.cmd('block 3 attribute index 6 9999') cubit.cmd('block 3 attribute index 7 0')

cubit.cmd('block 4 volume 4') cubit.cmd('block 4 name "elastic 2"') cubit.cmd('block 4 attribute count 7') cubit.cmd('block 4 attribute index 1 4') cubit.cmd('block 4 attribute index 2 475') cubit.cmd('block 4 attribute index 3 230') cubit.cmd('block 4 attribute index 4 2000') cubit.cmd('block 4 attribute index 5 9999') cubit.cmd('block 4 attribute index 6 9999') cubit.cmd('block 4 attribute index 7 0')

cubit.cmd('block 5 volume 5') cubit.cmd('block 5 name "elastic 2"') cubit.cmd('block 5 attribute count 7') cubit.cmd('block 5 attribute index 1 5') cubit.cmd('block 5 attribute index 2 475') cubit.cmd('block 5 attribute index 3 230') cubit.cmd('block 5 attribute index 4 2000') cubit.cmd('block 5 attribute index 5 9999') cubit.cmd('block 5 attribute index 6 9999') cubit.cmd('block 5 attribute index 7 0')

cubit.cmd('block 6 volume 6') cubit.cmd('block 6 name "elastic 2"') cubit.cmd('block 6 attribute count 7') cubit.cmd('block 6 attribute index 1 6') cubit.cmd('block 6 attribute index 2 475') cubit.cmd('block 6 attribute index 3 230') cubit.cmd('block 6 attribute index 4 2000') cubit.cmd('block 6 attribute index 5 9999') cubit.cmd('block 6 attribute index 6 9999') cubit.cmd('block 6 attribute index 7 0')

cubit.cmd('block 7 volume 7') cubit.cmd('block 7 name "elastic 2"') cubit.cmd('block 7 attribute count 7') cubit.cmd('block 7 attribute index 1 7') cubit.cmd('block 7 attribute index 2 475') cubit.cmd('block 7 attribute index 3 230') cubit.cmd('block 7 attribute index 4 2000') cubit.cmd('block 7 attribute index 5 9999') cubit.cmd('block 7 attribute index 6 9999') cubit.cmd('block 7 attribute index 7 0')

cubit.cmd('export mesh MESH_GEOCUBIT/top.e dimension 3 overwrite') cubit.cmd('save as MESH_GEOCUBIT/top.cub overwrite')

cubit2specfem3d.export2SPECFEM3D(SEMoutput)

if version_major >= 16 and version_minor >= 4: cubit.cmd('view top') cubit.cmd('hardcopy "' + CUBIToutput + '/waterlayered.png" png')

I'm very appreciated to have any advice and suggestions for this. (If you need any more clarifications, please let me know)

Regards

Haiyang Liao @.**@.>

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liaohaiyang1534 commented 3 months ago

Thank you, I have used this before. Thanks for this library, I should try it again later.

I hope this cavity simulation will be more convenient in the future.

By the way, do you have any recommended software for ambient noise simulation?

	廖海洋

@. | ---- Replied Message ---- | From | Hom Nath @.> | | Date | 6/29/2023 12:11 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [SPECFEM/specfem3d] error when creating a model with a hole (Issue #1620) |