[CIG-SEISMO] problem with block names in examples?

Wed Feb 25 12:06:43 PST 2015

Hi,

I just recently downloaded specfem from the devel branch and am having a
problem running the "layered_halfspace" and "waterlayered_halfspace"
examples (using Trelis 15.1).

The error seems to occur in the "DEFINE MATERIAL PROPERTIES" section (see
output, below). "waterlayer_mesh_boundary_fig8.py" seems to be looking for
blocks with IDs 1-3, but mine are always ID 4-6. (See output below)

Any advice would be appreciated!

Erin

********** Now playing
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_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

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>split curve 9 distance 3000

Preserving undo information...done

Updated volume(s): 1

Finished Command: split curve 9 distance 3000

Trelis>split curve 10 distance 3000

Preserving undo information...done

Updated volume(s): 1

Finished Command: split curve 10 distance 3000

Trelis>split curve 11 distance 3000

Preserving undo information...done

Updated volume(s): 1

Finished Command: split curve 11 distance 3000

Trelis>split curve 12 distance 3000

Preserving undo information...done

Updated volume(s): 1

Finished Command: split curve 12 distance 3000

Trelis>

Trelis># create surface for interface

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>split curve 29 distance 9000

Preserving undo information...done

Updated volume(s): 3

Finished Command: split curve 29 distance 9000

Trelis>split curve 31 distance 9000

Preserving undo information...done

Updated volume(s): 3

Finished Command: split curve 31 distance 9000

Trelis>split curve 32 distance 9000

Preserving undo information...done

Updated volume(s): 3

Finished Command: split curve 32 distance 9000

Trelis>split curve 36 distance 9000

Preserving undo information...done

Updated volume(s): 3

Finished Command: split curve 36 distance 9000

Trelis>

Trelis># create surface for buffer interface to refine BELOW the
discontinuity

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>volume 3 size 3589.2

Finished Command: volume 3 size 3589.2

Trelis>mesh volume 3

Volume 3 (Volume 3) meshing scheme automatically set to submap.

Matching intervals successful.

Meshing Volume 3 (Volume 3)

Generated 1369 faces for Surface 20 (Surface 20).

Generated 111 faces for Surface 27 (Surface 27).

Generated 111 faces for Surface 28 (Surface 28).

Generated 1369 faces for Surface 8 (Surface 8).

Generated 111 faces for Surface 29 (Surface 29).

Generated 111 faces for Surface 30 (Surface 30).

Generated 4107 hexes for Volume 3 (Volume 3).

Volume 3 (Volume 3) meshing completed using scheme: submap

Meshing time: 0.074372

Finished Command: mesh volume 3

Trelis>

Trelis>refine surface 8 numsplit 1 bias 1.0 depth 1

Finished Command: refine surface 8 numsplit 1 bias 1 depth 1

Trelis>

Trelis>volume 1 size 1196.4

Finished Command: volume 1 size 1196.4

Trelis>mesh volume 1

Volume 1 (Volume 1) meshing scheme automatically set to submap.

Matching intervals successful.

Meshing Volume 1 (Volume 1)

Generated 333 faces for Surface 15 (Surface 15).

Generated 333 faces for Surface 16 (Surface 16).

Generated 12321 faces for Surface 1 (Surface 1).

Generated 333 faces for Surface 17 (Surface 17).

Generated 333 faces for Surface 18 (Surface 18).

Generated 36963 hexes for Volume 1 (Volume 1).

Volume 1 (Volume 1) meshing completed using scheme: submap

Meshing time: 0.385749

Finished Command: mesh volume 1

Trelis>

Trelis>volume 5 size 4785.71

Finished Command: volume 5 size 4785.71

Trelis>mesh volume 5

Volume 5 (Volume 5) meshing scheme automatically set to submap.

Matching intervals successful.

Meshing Volume 5 (Volume 5)

Generated 370 faces for Surface 21 (Surface 21).

Generated 370 faces for Surface 22 (Surface 22).

Generated 370 faces for Surface 23 (Surface 23).

Generated 370 faces for Surface 24 (Surface 24).

Generated 1369 faces for Surface 25 (Surface 25).

Generated 13690 hexes for Volume 5 (Volume 5).

Volume 5 (Volume 5) meshing completed using scheme: submap

Meshing time: 0.079905

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]

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]

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]

Finished Command: block 6 hex in volume 5 except hex in volume 1 3

Finished Command: block 6 name "vol5"

['face']

##entity: face

Finished Command: block 1001 face in surface 1

Finished Command: block 1001 name "face_topo"

Finished Command: block 1003 face in surface 30 22 15

Finished Command: block 1003 name "face_abs_xmin"

Finished Command: block 1005 face in surface 24 18 27

Finished Command: block 1005 name "face_abs_xmax"

Finished Command: block 1004 face in surface 16 29 21

Finished Command: block 1004 name "face_abs_ymin"

Finished Command: block 1006 face in surface 17 28 23

Finished Command: block 1006 name "face_abs_ymax"

Finished Command: block 1002 face in surface 25

Finished Command: block 1002 name "face_abs_bottom"

Trelis>

Trelis>#### Define material properties for the 3 volumes ################

Trelis>#### DEFINE MATERIAL PROPERTIES #######################

Trelis>block 1 name "acoustic 1"

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(78)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(78)

No entities specified.

Trelis>block 1 attribute count 4

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(79)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(79)

No entities specified.

Trelis>block 1 attribute index 1 1

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(80)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(80)

No entities specified.

Trelis>block 1 attribute index 2 1480

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(81)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(81)

No entities specified.

Trelis>block 1 attribute index 3 0

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(82)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(82)

No entities specified.

Trelis>block 1 attribute index 4 1028

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(83)

No entity with ID 1 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(83)

No entities specified.

Trelis>#cubit.cmd('block 1 attribute index 5 0 ') # Q_flag

Trelis>#cubit.cmd('block 1 attribute index 6 0 ') # anisotropy_flag

Trelis>

Trelis>block 2 name "elastic 1"

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(87)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(87)

No entities specified.

Trelis>block 2 attribute count 6

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(88)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(88)

No entities specified.

Trelis>block 2 attribute index 1 2

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(89)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(89)

No entities specified.

Trelis>block 2 attribute index 2 7500

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(90)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(90)

No entities specified.

Trelis>block 2 attribute index 3 4300

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(91)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(91)

No entities specified.

Trelis>block 2 attribute index 4 3200

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(92)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(92)

No entities specified.

Trelis>block 2 attribute index 5 9000.0

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(93)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(93)

No entities specified.

Trelis>block 2 attribute index 6 0

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(94)

No entity with ID 2 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(94)

No entities specified.

Trelis>

Trelis>block 3 name "elastic 2"

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(96)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(96)

No entities specified.

Trelis>block 3 attribute count 6

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(97)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(97)

No entities specified.

Trelis>block 3 attribute index 1 3

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(98)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(98)

No entities specified.

Trelis>block 3 attribute index 2 7500

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(99)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(99)

No entities specified.

Trelis>block 3 attribute index 3 4300

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(100)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(100)

No entities specified.

Trelis>block 3 attribute index 4 3200

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(101)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(101)

No entities specified.

Trelis>block 3 attribute index 5 9000.0

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(102)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(102)

No entities specified.

Trelis>block 3 attribute index 6 0

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(103)

No entity with ID 3 was found

ERROR:
/Applications/specfem3d/EXAMPLES/waterlayered_halfspace/waterlayer_mesh_boundary_fig8.py
(103)

No entities specified.

Trelis>

Trelis>export mesh "top.e" dimension 3 overwrite

Using ExodusII API version 6.05 and DB version 6.05 to export "top.e".

Executive Exodus summary:

Number of dimensions = 3

Number of element blocks = 9

Number of sidesets = 0

Number of nodesets = 0

Number of bc sets = 1

Number of elements = 125356

Number of nodes = 116236

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:

bc 1001 bc flag 4

bc 1002 bc flag 4

bc 1003 bc flag 4

bc 1004 bc flag 4

bc 1005 bc flag 4

bc 1006 bc flag 4

Topography (free surface)

1001

Free surface

None

Preserving undo information...done

Finished Command: compress all

Turning informational messages off.

Writing MESH/mesh_file.....

total number of elements: 106782

block 4 hexes 36963

block 5 hexes 56129

block 6 hexes 13690

Ok

Writing MESH/materials_file.....

block 4 flag 4

block 5 flag 5

block 6 flag 6

Ok

Writing MESH/nodes_coords_file.....

number of nodes: 116236

Ok

Writing MESH/free_or_absorbing_surface_file_zmax.....

free surface (topography) block name: face_topo id: 1001

number of faces = 12321

Ok

Echoing has been turned ON

Finished Command: set echo on

Turning informational messages off.

block name: face_abs_bottom id: 1002

bottom

number of faces = 1369

Ok

block name: face_abs_xmin id: 1003

xmin

number of faces = 1221

Ok

block name: face_abs_ymin id: 1004

ymin

number of faces = 1221

Ok

block name: face_abs_xmax id: 1005

xmax

number of faces = 1221

Ok

block name: face_abs_ymax id: 1006

ymax

number of faces = 1221

Ok

Echoing has been turned ON

Finished Command: set echo on

Writing MESH/nummaterial_velocity_file.....

number of material: 4

number of material: 5

number of material: 6

Ok

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>

Trelis>

Trelis>

Trelis>

Current entity is Volume 3.

Trelis>
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