homnath
commented
3 weeks ago I manually set the material blocks and surface files (See the Cubit file) and used MeshAssist to convert the Exodus file to SPECFEM3D files. Here I define three blocks, because you have three layers. You still need to create nummaterial_velocity_file. For the top surface, you have option within the Par_file whether to set it free or absorbing surface.
Best, Hom Nath
Hom Nath Gharti, PhD Assistant Professor | Digital Earth Scientist https://www.digitalearthscience.com/ Department of Geological Sciences and Geological Engineering Miller Hall 314, 36 Union St Queen’s University Kingston, ON K7L 3N6, Canada
Queen’s University is situated on traditional Anishinaabe and Haudenosaunee Territory.https://www.queensu.ca/encyclopedia/t/traditional-territories
From: zuoxuan-de @.> Sent: Thursday, July 4, 2024 4:32 AM To: SPECFEM/specfem3d @.> Cc: Hom Nath Gharti @.>; Mention @.> Subject: [SPECFEM/specfem3d] Question about creating external models with cubit, can't generate absorption boundary files (Issue #1710)
Hello guys, I'm creating a three-layer model containing an alleyway, where the alleyway is located in the middle layer, in addition, I manually set his free surface and other absorbing surfaces. But when I run cubit2SPECFEM3D, I have a problem with my absorbing_surface_file_bottom,free_or_absorbing_surface_file_zmax,absorbing_surface_file_ymin and other similar absorbing surface files are all empty. I saw your replies related to this in my previous question, I hope you can be generous with your suggestions, thanks a lot! @casarottihttps://github.com/casarotti @homnathhttps://github.com/homnath image.png (view on web)https://github.com/SPECFEM/specfem3d/assets/129966017/51e27655-b6ab-4dd6-b1d0-494a1dd681e2 This is the specific case of the lane in the second layer, which is empty in the center, without any medium, and has all free surfaces. image.png (view on web)https://github.com/SPECFEM/specfem3d/assets/129966017/16f66f0c-e2f5-4d8a-8304-b5e1cb31a673 This is the free surface of the lane I set manually. image.png (view on web)https://github.com/SPECFEM/specfem3d/assets/129966017/8324b787-823f-4efb-9919-db3e1a37c567 In order to set the absorbing layer on the upper surface, I set both the upper and lower interfaces (zmax,zmin) to face_bottom again.
Next is my specific python script：
!/usr/bin/env python
import cubit import cubit2specfem3d
import os import sys
SEMoutput='MESH03' CUBIToutput='MESH_GEOCUBIT03'
os.system('mkdir -p '+ SEMoutput) os.system('mkdir -p '+ CUBIToutput)
Simulating a coal seam with a roadway This geological structure is mainly divided into three layers, the upper and lower peripheral rocks and the coal seam, which contains two roadways, of which the roadway portion is not defined by any medium and is all free surface
cubit.cmd('reset')
underlying rock
cubit.cmd('brick x 50 y 40 z 10') cubit.cmd('vol 1 move x 25 y 20 z 5')
################################################# intermediate seam ##############################################
Leftmost part of the coal seam in the y-direction, also the left wall of the left roadway
cubit.cmd('brick x 50 y 15 z 5') cubit.cmd('vol 2 move x 25 y 7.5 z -2.5')
Rightmost part of the coal seam in the y-direction, also the right wall of the right roadway
cubit.cmd('brick x 50 y 15 z 5') cubit.cmd('volume 3 move x 25 y 32.5 z -2.5')
The top of the lane in the y-direction
cubit.cmd('brick x 5 y 10 z 5') cubit.cmd('volume 4 move x 2.5 y 20 z -2.5')
The end of the lane in the y-direction
cubit.cmd('brick x 5 y 10 z 5') cubit.cmd('volume 5 move x 47.5 y 20 z -2.5')
#################################################### end ####################################################
top layer of surrounding rock
cubit.cmd('brick x 50 y 40 z 10') cubit.cmd('volume 6 move x 25 y 20 z -10')
cubit.cmd('merge all') cubit.cmd('imprint all')
Meshing the volumes
elementsize = 1.0
cubit.cmd('volume all size 1') cubit.cmd('mesh volume all')
cubit.cmd('block 1001 add surface 24 28 38 42 46 49 ') cubit.cmd('block 1001 name "face_topo"')
cubit.cmd('block 1002 add surface 1 32 ') cubit.cmd('block 1002 name "face_bottom"')
cubit.cmd('block 1003 add surface 4 10 16 22 34 ') cubit.cmd('block 1003 name "face_abs_xmin"')
cubit.cmd('block 1004 add surface 3 9 33') cubit.cmd('block 1004 name "face_abs_ymin"')
cubit.cmd('block 1005 add surface 6 12 18 36 30 ') cubit.cmd('block 1005 name "face_abs_xmax"')
cubit.cmd('block 1006 add surface 5 17 35') cubit.cmd('block 1006 name "face_abs_ymax"')
from geocubitlib import cubit2specfem3d
Define material properties for the 3 volumes
cubit.cmd('#### DEFINE MATERIAL PROPERTIES #######################') cubit.cmd('block 1 hex in volume 1') cubit.cmd('block 1 name "elastic 1" ') # elastic material region cubit.cmd('block 1 attribute count 7') cubit.cmd('block 1 attribute index 1 1') # flag for material: 1 for 1. material cubit.cmd('block 1 attribute index 2 3500') # vp cubit.cmd('block 1 attribute index 3 2000') # vs cubit.cmd('block 1 attribute index 4 2400') # rho cubit.cmd('block 1 attribute index 5 9999.0') # Q_kappa cubit.cmd('block 1 attribute index 6 9999.0') # Qmu cubit.cmd('block 1 attribute index 7 0 ') # anisotropy_flag
cubit.cmd('block 2 hex in volume 2') cubit.cmd('block 2 name "elastic 2" ') # elastic material region cubit.cmd('block 2 attribute count 7') cubit.cmd('block 2 attribute index 1 2') # flag for material: 1 for 1. material cubit.cmd('block 2 attribute index 2 1900') # vp cubit.cmd('block 2 attribute index 3 1100') # vs cubit.cmd('block 2 attribute index 4 1300') # rho cubit.cmd('block 2 attribute index 5 9999.0') # Q_mu cubit.cmd('block 2 attribute index 6 9999.0') # Qmu cubit.cmd('block 2 attribute index 7 0 ') # anisotropy_flag
cubit.cmd('block 3 hex in volume 3') cubit.cmd('block 3 name "elastic 3"') cubit.cmd('block 3 attribute count 7') cubit.cmd('block 3 attribute index 1 3 ') cubit.cmd('block 3 attribute index 2 1900 ') cubit.cmd('block 3 attribute index 3 1100 ') cubit.cmd('block 3 attribute index 4 1300 ') 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 hex in volume 4') cubit.cmd('block 4 name "elastic 4"') cubit.cmd('block 4 attribute count 7') cubit.cmd('block 4 attribute index 1 4 ') cubit.cmd('block 4 attribute index 2 1900 ') cubit.cmd('block 4 attribute index 3 1100 ') cubit.cmd('block 4 attribute index 4 1300 ') 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 hex in volume 5') cubit.cmd('block 5 name "elastic 5"') cubit.cmd('block 5 attribute count 7') cubit.cmd('block 5 attribute index 1 5 ') cubit.cmd('block 5 attribute index 2 1900 ') cubit.cmd('block 5 attribute index 3 1100 ') cubit.cmd('block 5 attribute index 4 1300 ') 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 hex in volume 6') cubit.cmd('block 6 name "elastic 6"') cubit.cmd('block 6 attribute count 7') cubit.cmd('block 6 attribute index 1 6 ') cubit.cmd('block 6 attribute index 2 3500 ') cubit.cmd('block 6 attribute index 3 2000 ') cubit.cmd('block 6 attribute index 4 2400 ') 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('export mesh "top.e" dimension 3 overwrite') cubit.cmd('save as "meshing.cub" overwrite')
Export to SPECFEM3D format using cubit2specfem3d.py of GEOCUBIT
os.system('mkdir -p MESH0703') cubit2specfem3d.export2SPECFEM3D('MESH0703')
all files needed by SCOTCH are now in directory MESH
One last question, can cubit determine the dimensions of the three dimensions of a hexahedral cell, similar to 110.5, instead of a square with side lengths of 1. Thank you again and I hope to hear back from you all sooner rather than later!
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danielpeter
Hello guys, I'm creating a three-layer model containing an alleyway, where the alleyway is located in the middle layer, in addition, I manually set his free surface and other absorbing surfaces. But when I run cubit2SPECFEM3D, I have a problem with my absorbing_surface_file_bottom,free_or_absorbing_surface_file_zmax,absorbing_surface_file_ymin and other similar absorbing surface files are all empty. I saw your replies related to this in my previous question, I hope you can be generous with your suggestions, thanks a lot! @casarotti @homnath
This is the specific case of the lane in the second layer, which is empty in the center, without any medium, and has all free surfaces.
This is the free surface of the lane I set manually.
In order to set the absorbing layer on the upper surface, I set both the upper and lower interfaces (zmax,zmin) to face_bottom again.
Next is my specific python script：
One last question, can cubit determine the dimensions of the three dimensions of a hexahedral cell, similar to 110.5, instead of a square with side lengths of 1. Thank you again and I hope to hear back from you all sooner rather than later!