[CIG-SEISMO] module boundary_definition wouldn't work on Trelis
Dimitri Komatitsch
komatitsch at lma.cnrs-mrs.fr
Tue Nov 11 13:11:40 PST 2014
Hi Emanuele and Chang-hua, Hi all,
Emanuele is right, that is likely the reason; I have merged the devel
branch into the master branch a few minutes ago. Thus please type "git
pull" and try again, and let us know if the problem remains.
Thanks,
Best regards,
Dimitri.
On 11/11/2014 10:44 AM, emanuele casarotti wrote:
> Hi Chang-hua,
>
> thanks of your feedback.
>
> First a quick check....
> Are you looking at the examples in the master version of github? you
> need to switch to the devel branch.
>
> Emanuele
>
>
> On Tue, Nov 11, 2014 at 12:03 AM, Changhua Zhang <chhzhang011 at gmail.com
> <mailto:chhzhang011 at gmail.com>> wrote:
>
>
> I install Trelis on a Centos 6 linux machine, and try to build the
> 2-layer half-space model in EXAMPLE directory. My python version is
> 2.6.6.
> When I run the script, 2lay_mesh_boundary_fig8.py, it is OK before
> the comment line ### End of meshing. But it has a problem when it
> reaches
>
> ###### This is boundary_definition.py of GEOCUBIT
> #..... which extracts the bounding faces and defines them into blocks
> boundary_definition.entities=['face']
> boundary_definition.define_bc(boundary_definition.entities,parallel=True)
>
> I attached the whole history below. As we can see from the history,
> I get a lot of
> WARNING: No entity with ID 4 was found
> WARNING: No entity with ID 5 was found
> WARNING: No entity with ID 6 was found
>
> etc. and this causes the execution of of defining the material
> properties fail.
>
> Can someone take a look and tell me how to fix it? Many thanks!
>
> Best Regards,
> Chang-hua
>
>
>
> ********** Now playing
> /home/chzhang/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/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>
>
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>
>
>
>
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>
--
Dimitri Komatitsch
CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics,
UPR 7051, Marseille, France http://komatitsch.free.fr
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