casarotti
commented
9 years ago Hi! do you run the last version of specfem3d? and did "make_mesh.sh" work for you?
Emanuele
On Fri Dec 19 2014 at 06:21:17 specfem3d-zhang-ksu notifications@github.com wrote:
the boundary_definition does not work properly to define the block and later to assign material properties to the block. Here is a history file by running the EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py. This run is on Trelis 15.01, and my python version is 2.6.6. I have not run this script on other Trelis or cubit but I was told from csimsoft.com that same thing happens on Trelis 15.1. Running other examples gets the same problem.
****** Now playing /home/chzhang_ksu/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py
Trelis>#!/usr/bin/env python Trelis>
Trelis>########################################################################### Trelis>#### TNM: This is the mesh generation, adapted from a journal file Trelis>#### specific to the settings of Komatitsch and Tromp 1999, Fig.8 Trelis>#### Aug 2009
Trelis>########################################################################### Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis>reset Default CUBIT model file is '/home/chzhang_ksu/specfem3d/EXAMPLES/layered_halfspace/cubit01.cub'
Finished Command: reset
Trelis>brick x 134000 y 134000 z 60000 Successfully created brick volume 1 Finished Command: brick x 134000 y 134000 z 60000
Trelis> Trelis># This seems to conflict with boundary_definition.py Trelis># ....which leaves the model space at e.g. x=[-67,67] km Trelis>volume 1 move x 67000 y 67000 z -30000 Finished Command: volume 1 move x 67000 y 67000 z -30000
Trelis> Trelis># create vertices for discontinuity Trelis> Trelis>split curve 9 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 9 distance 3000
Trelis>split curve 10 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 10 distance 3000
Trelis>split curve 11 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 11 distance 3000
Trelis>split curve 12 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 12 distance 3000
Trelis> Trelis># create surface for interface Trelis># surface at 3 km depth Trelis>create surface vertex 9 10 12 11
Creation of Surface 7 (Surface 7) Successful. This is sheet body 2 (Body 2) Finished Command: create surface vertex 9 10 12 11
Trelis> Trelis>section volume 1 with surface 7 keep normal Created volume(s): 3 SECTION successfully completed Created volume 3 Finished Command: section volume 1 with surface 7 keep normal
Trelis>section volume 1 with surface 7 reverse Preserving undo information...done Updated volume(s): 1 SECTION successfully completed Created volume 1 Finished Command: section volume 1 with surface 7 reverse
Trelis> Trelis># create vertices for auxiliary interface to allow for refinement Trelis>#distance = 9000 Trelis># to have a surface at 25050 m depth, such that point force source can be located exactly Trelis># on a GLL point at that depth as in Komatitsch et al. (1999) Trelis> Trelis>split curve 29 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 29 distance 22050
Trelis>split curve 31 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 31 distance 22050
Trelis>split curve 32 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 32 distance 22050
Trelis>split curve 36 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 36 distance 22050
Trelis> Trelis> Trelis># create surface for buffer interface to refine BELOW the discontinuity Trelis># surface at 3 km depth Trelis>create surface vertex 25 26 28 27
Creation of Surface 19 (Surface 19) Successful. This is sheet body 4 (Body 4) Finished Command: create surface vertex 25 26 28 27
Trelis> Trelis>section volume 3 with surface 19 keep normal Created volume(s): 5 SECTION successfully completed Created volume 5 Finished Command: section volume 3 with surface 19 keep normal
Trelis>section volume 3 with surface 19 reverse Preserving undo information...done Updated volume(s): 3 SECTION successfully completed Created volume 3 Finished Command: section volume 3 with surface 19 reverse
Trelis> Trelis>delete volume 2 4 Preserving undo information...done Deleted volume 2 Deleted volume 4 Finished Command: delete volume 2 4
Trelis> Trelis>merge all
...Merging all features in the model
...Merging all Surfaces in the model Consolidated 2 pairs of surfaces
...Merging all Curves in the model Consolidated 0 pair of curves
...Merging all Vertices in the model Consolidated 0 pairs of vertices All detected matches successfully merged Finished Command: merge all
Trelis>imprint all Preserving undo information...done Group imprint finished. IMPRINT completed. Finished Command: imprint all
Trelis> Trelis># Meshing the volumes Trelis>## middle volume Trelis>#cubit.cmd('volume 3 size 3589.2') Trelis>volume 3 size 4500. Finished Command: volume 3 size 4500
Trelis>mesh volume 3 Volume 3 (Volume 3) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 3 (Volume 3) Generated 900 faces for Surface 20 (Surface 20). Generated 150 faces for Surface 27 (Surface 27). Generated 150 faces for Surface 28 (Surface 28). Generated 900 faces for Surface 8 (Surface 8). Generated 150 faces for Surface 29 (Surface 29). Generated 150 faces for Surface 30 (Surface 30). Generated 4500 hexes for Volume 3 (Volume 3). Volume 3 (Volume 3) meshing completed using scheme: submap
Meshing time: 0.160000 Finished Command: mesh volume 3
Trelis> Trelis># refine boundary surface between top and middle volume Trelis># this will create a tripling layer from the bottom to the top in the middle volume Trelis>refine surface 8 numsplit 1 bias 1.0 depth 1 Finished Command: refine surface 8 numsplit 1 bias 1 depth 1
Trelis> Trelis>#cubit.cmd('pause') Trelis> Trelis>## top volume Trelis>#cubit.cmd('volume 1 size 1196.4') Trelis>volume 1 size 1000.0 Finished Command: volume 1 size 1000
Trelis>mesh volume 1 Volume 1 (Volume 1) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 1 (Volume 1) Generated 270 faces for Surface 15 (Surface 15). Generated 270 faces for Surface 16 (Surface 16). Generated 8100 faces for Surface 1 (Surface 1). Generated 270 faces for Surface 17 (Surface 17). Generated 270 faces for Surface 18 (Surface 18). Generated 24300 hexes for Volume 1 (Volume 1). Volume 1 (Volume 1) meshing completed using scheme: submap
Meshing time: 0.360000 Finished Command: mesh volume 1
Trelis> Trelis>#cubit.cmd('pause') Trelis> Trelis>## bottom volume Trelis>#cubit.cmd('volume 5 size 4785.71') Trelis>volume 5 size 4500. Finished Command: volume 5 size 4500
Trelis>mesh volume 5 Volume 5 (Volume 5) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 5 (Volume 5) Generated 240 faces for Surface 21 (Surface 21). Generated 240 faces for Surface 22 (Surface 22). Generated 240 faces for Surface 23 (Surface 23). Generated 240 faces for Surface 24 (Surface 24). Generated 900 faces for Surface 25 (Surface 25). Generated 7200 hexes for Volume 5 (Volume 5). Volume 5 (Volume 5) meshing completed using scheme: submap
Meshing time: 0.150000 Finished Command: mesh volume 5
Trelis> Trelis># draw/update mesh lines for visualization Trelis># this will draw also the tripling layer mesh lines Trelis>draw volume all Trelis> Trelis>#### End of meshing Trelis> Trelis>###### This is boundary_definition.py of GEOCUBIT Trelis>#..... which extracts the bounding faces and defines them into blocks Trelis> Trelis> proc 0 is has absorbing boundary xmin proc 0 is has absorbing boundary ymin proc 0 is has absorbing boundary xmax proc 0 is has absorbing boundary ymax block 4 hex in vol 1 except hex in vol [3, 5] WARNING: No entity with ID 4 was found Finished Command: block 4 hex in volume 1 except hex in volume 3 5
Finished Command: block 4 name "vol1"
block 5 hex in vol 3 except hex in vol [1, 5] WARNING: No entity with ID 5 was found Finished Command: block 5 hex in volume 3 except hex in volume 1 5
Finished Command: block 5 name "vol3"
block 6 hex in vol 5 except hex in vol [1, 3] WARNING: No entity with ID 6 was found Finished Command: block 6 hex in volume 5 except hex in volume 1 3
Finished Command: block 6 name "vol5"
Trelis> Trelis>#### Define material properties for the 3 volumes ################ Trelis>#### DEFINE MATERIAL PROPERTIES ####################### Trelis>block 1 name "elastic 1" WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (98) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (98) No entities specified. Trelis>block 1 attribute count 6 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (99) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (99) No entities specified. Trelis>block 1 attribute index 1 1 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (100) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (100) No entities specified. Trelis>block 1 attribute index 2 2800 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (101) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (101) No entities specified. Trelis>block 1 attribute index 3 1500 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (102) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (102) No entities specified. Trelis>block 1 attribute index 4 2300 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (103) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (103) No entities specified. Trelis>block 1 attribute index 5 9000.0 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (104) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (104) No entities specified. Trelis>block 1 attribute index 6 0 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (105) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (105) No entities specified. Trelis> Trelis>block 2 name "elastic 2" WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (107) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (107) No entities specified. Trelis>block 2 attribute count 6 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (108) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (108) No entities specified. Trelis>block 2 attribute index 1 2 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (109) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (109) No entities specified. Trelis>block 2 attribute index 2 7500 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (110) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (110) No entities specified. Trelis>block 2 attribute index 3 4300 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (111) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (111) No entities specified. Trelis>block 2 attribute index 4 3200 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (112) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (112) No entities specified. Trelis>block 2 attribute index 5 9000.0 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (113) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (113) No entities specified. Trelis>block 2 attribute index 6 0 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (114) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (114) No entities specified. Trelis> Trelis>block 3 name "elastic 3" WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (116) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (116) No entities specified. Trelis>block 3 attribute count 6 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (117) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (117) No entities specified. Trelis>block 3 attribute index 1 3 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (118) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (118) No entities specified. Trelis>block 3 attribute index 2 7500 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (119) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (119) No entities specified. Trelis>block 3 attribute index 3 4300 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (120) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (120) No entities specified. Trelis>block 3 attribute index 4 3200 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (121) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (121) No entities specified. Trelis>block 3 attribute index 5 9000.0 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (122) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (122) No entities specified. Trelis>block 3 attribute index 6 0 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (123) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (123) No entities specified. Trelis> Trelis>export mesh "top.e" dimension 3 overwrite
Using ExodusII API version 4.98 and DB version 4.98 to export "top.e".
Executive Exodus summary: Number of dimensions = 3 Number of element blocks = 3 Number of sidesets = 0 Number of nodesets = 0 Number of bc sets = 1 Number of elements = 70200 Number of nodes = 76819
Finished writing top.e Finished Command: export mesh "top.e" dimension 3 overwrite
Trelis>save as "meshing.cub" overwrite
Exported: 3 Volumes
Successfully saved CUBIT file 'meshing.cub' Finished Command: save as "meshing.cub" overwrite
Trelis> Trelis>#### Export to SPECFEM3D format using cubit2specfem3d.py of GEOCUBIT Trelis> Trelis> Trelis> HEX Blocks: block 4 material flag 4 block 5 material flag 5 block 6 material flag 6 Absorbing Boundary Conditions: Topography (free surface) None Free surface None Preserving undo information...done Finished Command: compress all
Turning informational messages off. Writing MESH/mesh_file..... total number of elements: 70200 block 4 hexes 24300 block 5 hexes 38700 block 6 hexes 7200 Writing MESH/materials_file..... block 4 flag 4 block 5 flag 5 block 6 flag 6 Writing MESH/nodes_coords_file..... number of nodes: 76819 Writing MESH/free_or_absorbing_surface_file_zmax..... Echoing has been turned ON Finished Command: set echo on
Turning informational messages off. Echoing has been turned ON Finished Command: set echo on
Writing MESH/nummaterial_velocity_file..... Turning informational messages on. Finished Command: set info on
Echoing has been turned ON Finished Command: set echo on
END SPECFEM3D exporting process...... Trelis> Trelis># all files needed by SCOTCH are now in directory MESH Trelis> Trelis>
— Reply to this email directly or view it on GitHub https://github.com/geodynamics/specfem3d/issues/330.
specfem3d-zhang-ksu
komatits
the boundary_definition does not work properly to define the block and later to assign material properties to the block. Here is a history file by running the EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py. This run is on Trelis 15.01, and my python version is 2.6.6. I have not run this script on other Trelis or cubit but I was told from csimsoft.com that same thing happens on Trelis 15.1. Running other examples gets the same problem.
\ Now playing /home/chzhang_ksu/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py **
Trelis>#!/usr/bin/env python Trelis> Trelis>########################################################################### Trelis>#### TNM: This is the mesh generation, adapted from a journal file Trelis>#### specific to the settings of Komatitsch and Tromp 1999, Fig.8 Trelis>#### Aug 2009 Trelis>########################################################################### Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis> Trelis>reset Default CUBIT model file is '/home/chzhang_ksu/specfem3d/EXAMPLES/layered_halfspace/cubit01.cub'
Finished Command: reset
Trelis>brick x 134000 y 134000 z 60000 Successfully created brick volume 1 Finished Command: brick x 134000 y 134000 z 60000
Trelis> Trelis># This seems to conflict with boundary_definition.py Trelis># ....which leaves the model space at e.g. x=[-67,67] km Trelis>volume 1 move x 67000 y 67000 z -30000 Finished Command: volume 1 move x 67000 y 67000 z -30000
Trelis> Trelis># create vertices for discontinuity Trelis> Trelis>split curve 9 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 9 distance 3000
Trelis>split curve 10 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 10 distance 3000
Trelis>split curve 11 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 11 distance 3000
Trelis>split curve 12 distance '+str(distance)) Preserving undo information...done Updated volume(s): 1 Finished Command: split curve 12 distance 3000
Trelis> Trelis># create surface for interface Trelis># surface at 3 km depth Trelis>create surface vertex 9 10 12 11
Creation of Surface 7 (Surface 7) Successful. This is sheet body 2 (Body 2) Finished Command: create surface vertex 9 10 12 11
Trelis> Trelis>section volume 1 with surface 7 keep normal Created volume(s): 3 SECTION successfully completed Created volume 3 Finished Command: section volume 1 with surface 7 keep normal
Trelis>section volume 1 with surface 7 reverse Preserving undo information...done Updated volume(s): 1 SECTION successfully completed Created volume 1 Finished Command: section volume 1 with surface 7 reverse
Trelis> Trelis># create vertices for auxiliary interface to allow for refinement Trelis>#distance = 9000 Trelis># to have a surface at 25050 m depth, such that point force source can be located exactly Trelis># on a GLL point at that depth as in Komatitsch et al. (1999) Trelis> Trelis>split curve 29 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 29 distance 22050
Trelis>split curve 31 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 31 distance 22050
Trelis>split curve 32 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 32 distance 22050
Trelis>split curve 36 distance '+str(distance)) Preserving undo information...done Updated volume(s): 3 Finished Command: split curve 36 distance 22050
Trelis> Trelis> Trelis># create surface for buffer interface to refine BELOW the discontinuity Trelis># surface at 3 km depth Trelis>create surface vertex 25 26 28 27
Creation of Surface 19 (Surface 19) Successful. This is sheet body 4 (Body 4) Finished Command: create surface vertex 25 26 28 27
Trelis> Trelis>section volume 3 with surface 19 keep normal Created volume(s): 5 SECTION successfully completed Created volume 5 Finished Command: section volume 3 with surface 19 keep normal
Trelis>section volume 3 with surface 19 reverse Preserving undo information...done Updated volume(s): 3 SECTION successfully completed Created volume 3 Finished Command: section volume 3 with surface 19 reverse
Trelis> Trelis>delete volume 2 4 Preserving undo information...done Deleted volume 2 Deleted volume 4 Finished Command: delete volume 2 4
Trelis> Trelis>merge all
...Merging all features in the model
...Merging all Surfaces in the model Consolidated 2 pairs of surfaces
...Merging all Curves in the model Consolidated 0 pair of curves
...Merging all Vertices in the model Consolidated 0 pairs of vertices All detected matches successfully merged Finished Command: merge all
Trelis>imprint all Preserving undo information...done Group imprint finished. IMPRINT completed. Finished Command: imprint all
Trelis> Trelis># Meshing the volumes Trelis>## middle volume Trelis>#cubit.cmd('volume 3 size 3589.2') Trelis>volume 3 size 4500. Finished Command: volume 3 size 4500
Trelis>mesh volume 3 Volume 3 (Volume 3) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 3 (Volume 3) Generated 900 faces for Surface 20 (Surface 20). Generated 150 faces for Surface 27 (Surface 27). Generated 150 faces for Surface 28 (Surface 28). Generated 900 faces for Surface 8 (Surface 8). Generated 150 faces for Surface 29 (Surface 29). Generated 150 faces for Surface 30 (Surface 30). Generated 4500 hexes for Volume 3 (Volume 3). Volume 3 (Volume 3) meshing completed using scheme: submap
Meshing time: 0.160000 Finished Command: mesh volume 3
Trelis> Trelis># refine boundary surface between top and middle volume Trelis># this will create a tripling layer from the bottom to the top in the middle volume Trelis>refine surface 8 numsplit 1 bias 1.0 depth 1 Finished Command: refine surface 8 numsplit 1 bias 1 depth 1
Trelis> Trelis>#cubit.cmd('pause') Trelis> Trelis>## top volume Trelis>#cubit.cmd('volume 1 size 1196.4') Trelis>volume 1 size 1000.0 Finished Command: volume 1 size 1000
Trelis>mesh volume 1 Volume 1 (Volume 1) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 1 (Volume 1) Generated 270 faces for Surface 15 (Surface 15). Generated 270 faces for Surface 16 (Surface 16). Generated 8100 faces for Surface 1 (Surface 1). Generated 270 faces for Surface 17 (Surface 17). Generated 270 faces for Surface 18 (Surface 18). Generated 24300 hexes for Volume 1 (Volume 1). Volume 1 (Volume 1) meshing completed using scheme: submap
Meshing time: 0.360000 Finished Command: mesh volume 1
Trelis> Trelis>#cubit.cmd('pause') Trelis> Trelis>## bottom volume Trelis>#cubit.cmd('volume 5 size 4785.71') Trelis>volume 5 size 4500. Finished Command: volume 5 size 4500
Trelis>mesh volume 5 Volume 5 (Volume 5) meshing scheme automatically set to submap. Matching intervals successful. Meshing Volume 5 (Volume 5) Generated 240 faces for Surface 21 (Surface 21). Generated 240 faces for Surface 22 (Surface 22). Generated 240 faces for Surface 23 (Surface 23). Generated 240 faces for Surface 24 (Surface 24). Generated 900 faces for Surface 25 (Surface 25). Generated 7200 hexes for Volume 5 (Volume 5). Volume 5 (Volume 5) meshing completed using scheme: submap
Meshing time: 0.150000 Finished Command: mesh volume 5
Trelis> Trelis># draw/update mesh lines for visualization Trelis># this will draw also the tripling layer mesh lines Trelis>draw volume all Trelis> Trelis>#### End of meshing Trelis> Trelis>###### This is boundary_definition.py of GEOCUBIT Trelis>#..... which extracts the bounding faces and defines them into blocks Trelis> Trelis> proc 0 is has absorbing boundary xmin proc 0 is has absorbing boundary ymin proc 0 is has absorbing boundary xmax proc 0 is has absorbing boundary ymax block 4 hex in vol 1 except hex in vol [3, 5] WARNING: No entity with ID 4 was found Finished Command: block 4 hex in volume 1 except hex in volume 3 5
Finished Command: block 4 name "vol1"
block 5 hex in vol 3 except hex in vol [1, 5] WARNING: No entity with ID 5 was found Finished Command: block 5 hex in volume 3 except hex in volume 1 5
Finished Command: block 5 name "vol3"
block 6 hex in vol 5 except hex in vol [1, 3] WARNING: No entity with ID 6 was found Finished Command: block 6 hex in volume 5 except hex in volume 1 3
Finished Command: block 6 name "vol5"
Trelis> Trelis>#### Define material properties for the 3 volumes ################ Trelis>#### DEFINE MATERIAL PROPERTIES ####################### Trelis>block 1 name "elastic 1" WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (98) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (98) No entities specified. Trelis>block 1 attribute count 6 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (99) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (99) No entities specified. Trelis>block 1 attribute index 1 1 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (100) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (100) No entities specified. Trelis>block 1 attribute index 2 2800 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (101) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (101) No entities specified. Trelis>block 1 attribute index 3 1500 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (102) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (102) No entities specified. Trelis>block 1 attribute index 4 2300 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (103) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (103) No entities specified. Trelis>block 1 attribute index 5 9000.0 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (104) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (104) No entities specified. Trelis>block 1 attribute index 6 0 WARNING: No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (105) No entity with ID 1 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (105) No entities specified. Trelis> Trelis>block 2 name "elastic 2" WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (107) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (107) No entities specified. Trelis>block 2 attribute count 6 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (108) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (108) No entities specified. Trelis>block 2 attribute index 1 2 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (109) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (109) No entities specified. Trelis>block 2 attribute index 2 7500 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (110) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (110) No entities specified. Trelis>block 2 attribute index 3 4300 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (111) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (111) No entities specified. Trelis>block 2 attribute index 4 3200 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (112) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (112) No entities specified. Trelis>block 2 attribute index 5 9000.0 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (113) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (113) No entities specified. Trelis>block 2 attribute index 6 0 WARNING: No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (114) No entity with ID 2 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (114) No entities specified. Trelis> Trelis>block 3 name "elastic 3" WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (116) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (116) No entities specified. Trelis>block 3 attribute count 6 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (117) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (117) No entities specified. Trelis>block 3 attribute index 1 3 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (118) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (118) No entities specified. Trelis>block 3 attribute index 2 7500 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (119) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (119) No entities specified. Trelis>block 3 attribute index 3 4300 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (120) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (120) No entities specified. Trelis>block 3 attribute index 4 3200 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (121) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (121) No entities specified. Trelis>block 3 attribute index 5 9000.0 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (122) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (122) No entities specified. Trelis>block 3 attribute index 6 0 WARNING: No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (123) No entity with ID 3 was found ERROR: /home/chzhang/specfem3d/EXAMPLES/layered_halfspace/2lay_mesh_boundary_fig8.py (123) No entities specified. Trelis> Trelis>export mesh "top.e" dimension 3 overwrite
Using ExodusII API version 4.98 and DB version 4.98 to export "top.e".
Executive Exodus summary: Number of dimensions = 3 Number of element blocks = 3 Number of sidesets = 0 Number of nodesets = 0 Number of bc sets = 1 Number of elements = 70200 Number of nodes = 76819
Finished writing top.e Finished Command: export mesh "top.e" dimension 3 overwrite
Trelis>save as "meshing.cub" overwrite
Exported: 3 Volumes
Successfully saved CUBIT file 'meshing.cub' Finished Command: save as "meshing.cub" overwrite
Trelis> Trelis>#### Export to SPECFEM3D format using cubit2specfem3d.py of GEOCUBIT Trelis> Trelis> Trelis> HEX Blocks: block 4 material flag 4 block 5 material flag 5 block 6 material flag 6 Absorbing Boundary Conditions: Topography (free surface) None Free surface None Preserving undo information...done Finished Command: compress all
Turning informational messages off. Writing MESH/mesh_file..... total number of elements: 70200 block 4 hexes 24300 block 5 hexes 38700 block 6 hexes 7200 Writing MESH/materials_file..... block 4 flag 4 block 5 flag 5 block 6 flag 6 Writing MESH/nodes_coords_file..... number of nodes: 76819 Writing MESH/free_or_absorbing_surface_file_zmax..... Echoing has been turned ON Finished Command: set echo on
Turning informational messages off. Echoing has been turned ON Finished Command: set echo on
Writing MESH/nummaterial_velocity_file..... Turning informational messages on. Finished Command: set info on
Echoing has been turned ON Finished Command: set echo on
END SPECFEM3D exporting process...... Trelis> Trelis># all files needed by SCOTCH are now in directory MESH Trelis> Trelis>