[CIG-SEISMO] Cubit Import Error

Mon Feb 24 19:17:30 PST 2014

Dear All,

I have started working with development version. I am following the long version of step-by-step tutorial.

The tutorial says:

If successful, this will generate the files in src/shared/: Makefile, constants.h, and precision.h, among others
I can find constant.h, precision.h but not Makefile.h. This was also the case in the older version 2.1. Is this something to worry about?

When I reach to making mesh, i receive cubit import error: (details available in attachment)

user:~/specfem3d/examples/homogeneous_halfspace$ ./make_mesh.sh
[('--build_volume', ''), ('--mesh', ''), ('--cfg', 'homogeneous_halfspace.cfg')] []
None None
1 1
error importing cubit
error importing cubit, check if cubit is installed
error importing cubit
[('--collect', ''), ('--meshfiles', 'MESH_GEOCUBIT/mesh_vol_0.e'), ('--export2SPECFEM3D', ''), ('--SEMoutput', 'MESH')] []
None None
1 1
error importing cubit

There are few thing I am not sure about (highlighted in the attached doc). I don't know whether they are responsible for it? Do I need to set paths manually?
Is there any example script like 'block_mesh.py' in version2.1 for development version? Because I also tried making mesh with same type of script but boundary_deffinition.py and cubit2specfem3d.py are not working for it.

Thanks in advace.

Best regards,
Saad Khan

________________________________________
From: cig-seismo-bounces at geodynamics.org [cig-seismo-bounces at geodynamics.org] on behalf of emanuele casarotti [emanuele.casarotti at gmail.com]
Sent: Tuesday, January 14, 2014 4:34 PM
To: cig-seismo at geodynamics.org
Subject: Re: [CIG-SEISMO] cubit2specfem3d export

OK so this is the old version.

1) I will take a look next week, but I suggest **strongly** to update
specfem3d (https://github.com/geodynamics/specfem3d)

2) The cone_1 has a lot of very deformed hexa with negative jacobian.
You need that all the jacobians are positive.

here the step to create a a good mesh for a conical intrusion

brick x 10
create frustum height 3 radius 3 top 0
graphics silhouette off
rotate Volume 2 angle 180 about X include_merged
align Volume 2 surface 8 with surface 1
subtract volume 2 from volume 1 keep
delete Volume 1 2

create Cylinder height 20 radius 4
chop volume 3 with volume 4

webcut volume all with plane xplane offset 0 preview
webcut volume all with plane xplane offset 0 noimprint nomerge
webcut volume all with plane yplane offset 0 noimprint nomerge
unite volume 9 11 7 5
webcut volume 9 sweep curve 97 vector 0 0 -1 through_all preview
webcut volume 9 sweep curve 97 vector 0 0 -1 through_all
unite volume 6 10 12 8
webcut volume all with plane yplane offset 0 preview
webcut volume all with plane yplane offset 0 noimprint nomerge
webcut volume all with plane xplane offset 0 noimprint nomerge
merge vol all
volume 19 13 16 22 size .5
mesh volume 19 13 16 22
volume 18 9 15 21 scheme Auto
mesh volume 18 9 15 21
surface 137 135 162 169 scheme pave
surface 137 135 162 169 size .5
mesh surface 137 135 162 169
volume 17 6 20 14 scheme Auto
mesh volume 17 6 20 14

block 1 volume all
create mesh geometry Block 1 feature_angle 100.0

On Tue, Jan 14, 2014 at 2:15 PM, <s.khan-1 at utwente.nl> wrote:
> Dear Emanuele,
>
>
>
> Please find the scripts and the volume in attachment. I use block_mesh.py
> after making some modification to it. I am using Cubit 13.0.
>
>
>
> Thanks
>
> Best regards,
> Saad Khan
>
>
>
> From: cig-seismo-bounces at geodynamics.org
> [mailto:cig-seismo-bounces at geodynamics.org] On Behalf Of emanuele casarotti
> Sent: Monday, January 13, 2014 8:51 PM
> To: cig-seismo at geodynamics.org
> Subject: Re: [CIG-SEISMO] cubit2specfem3d export
>
>
>
> Hi
>
> Can you share the scripta and the volumes?
>
> And the version of cubit...
>
>
>
>
> Emanuele
>
>
> Il giorno 13/gen/2014, alle ore 19:47, "s.khan-1 at utwente.nl"
> <s.khan-1 at utwente.nl> ha scritto:
>
> Dear All,
>
>
>
> The boundary_definition.py script does not catch my topographic surface. I
> have to define it manually after running the script
> (boundary_definition.py). Then I export the mesh with
> run_cubit2specfem3d.py, which says
>
> :
>
> Writing MESH/free_surface_file.....
>
> block name: face_topo id: 2
>
> number of faces = 0
>
> :
>
> :
>
> # all files needed by SCOTCH are now in directory MESH
>
>
>
> Rest of the process goes smoothly and I also get result in the OUTPUT. The
> question is, what does “number of face=0” mean any does it affect the
> results?
>
>
>
> Another thing, when I use very fine mesh (e.g. mesh interval 3000) the
> result (in seismograms) produces a lot of NaNs and at some places
> Infinities. Why is it so?
>
>
>
> Note: The topo surface has been modified while the rest of geo model is the
> same as given in homogeneous_halfspace example. The topo surface is made of
> several surfaces which are combined to one using simplify option in cubit. I
> am using SPECFEM3D_Cartesian 2.1.
>
>
>
> Thanks in advance.
>
>
>
> Best regards,
>
> Saad Khan
>
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> CIG-SEISMO at geodynamics.org
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>
>
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