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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Emanuele,
<div><br>
</div>
<div>I can successfully run cubit from command line. And I was using it with the older specfem version. I had no problem with older version except export of topo surface (previous discussion down below), for which you suggested update.</div>
<div><br>
</div>
<div>I am getting this message from python command line:</div>
<div>
<div>>>> import cubit</div>
<div>Traceback (most recent call last):</div>
<div> File "<stdin>", line 1, in <module></div>
<div>ImportError: No module named cubit</div>
<div>>>></div>
<div><br>
</div>
<div>I don't have "cubit.py".</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Saad Khan</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF700410" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> cig-seismo-bounces@geodynamics.org [cig-seismo-bounces@geodynamics.org] on behalf of emanuele casarotti [emanuele.casarotti@gmail.com]<br>
<b>Sent:</b> Tuesday, February 25, 2014 11:17 AM<br>
<b>To:</b> cig-seismo@geodynamics.org<br>
<b>Subject:</b> Re: [CIG-SEISMO] Cubit Import Error<br>
</font><br>
</div>
<div></div>
<div>
<div>It looks like that your cubit pythonpath is not set correctly</div>
<div><br>
</div>
<div>Can you run cubit with the command "cubit" (or "claro") from command line?</div>
<div><br>
</div>
<div>Can you successfully run "import cubit" from the python command line?</div>
<div><br>
</div>
<div>You should have in your pythonpath the directory containing "cubit.py" from the base of cubit (not geocubit).<br>
<br>
Emanuele</div>
<div><br>
Il giorno 25/feb/2014, alle ore 04:44, "<a href="mailto:s.khan@utwente.nl" target="_blank">s.khan@utwente.nl</a>" <<a href="mailto:s.khan@utwente.nl" target="_blank">s.khan@utwente.nl</a>> ha scritto:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear All,<br>
<br>
I have started working with development version. I am following the long version of step-by-step tutorial.
<br>
<br>
The tutorial says:
<div><br>
<i>If successful, this will generate the files in src/shared/: Makefile, constants.h, and precision.h, among others</i><br>
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?</div>
<div><br>
</div>
<div>When I reach to making mesh, i receive cubit import error: (details available in attachment)</div>
<div><br>
</div>
<div>
<div><b>user:~/specfem3d/examples/homogeneous_halfspace$ ./make_mesh.sh</b></div>
<div>[('--build_volume', ''), ('--mesh', ''), ('--cfg', 'homogeneous_halfspace.cfg')] []</div>
<div>None None</div>
<div>1 1</div>
<div>error importing cubit</div>
<div>error importing cubit, check if cubit is installed</div>
<div>error importing cubit</div>
<div>[('--collect', ''), ('--meshfiles', 'MESH_GEOCUBIT/mesh_vol_0.e'), ('--export2SPECFEM3D', ''), ('--SEMoutput', 'MESH')] []</div>
<div>None None</div>
<div>1 1</div>
<div>error importing cubit</div>
</div>
<div><br>
</div>
<div>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?</div>
<div>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.</div>
<div><br>
</div>
<div>Thanks in advace.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Saad Khan</div>
<div><br>
________________________________________<br>
From: <a href="mailto:cig-seismo-bounces@geodynamics.org" target="_blank">cig-seismo-bounces@geodynamics.org</a> [<a href="mailto:cig-seismo-bounces@geodynamics.org" target="_blank">cig-seismo-bounces@geodynamics.org</a>] on behalf of emanuele casarotti [<a href="mailto:emanuele.casarotti@gmail.com" target="_blank">emanuele.casarotti@gmail.com</a>]<br>
Sent: Tuesday, January 14, 2014 4:34 PM<br>
To: <a href="mailto:cig-seismo@geodynamics.org" target="_blank">cig-seismo@geodynamics.org</a><br>
Subject: Re: [CIG-SEISMO] cubit2specfem3d export<br>
<br>
OK so this is the old version.<br>
<br>
1) I will take a look next week, but I suggest **strongly** to update<br>
specfem3d (<a href="https://github.com/geodynamics/specfem3d" target="_blank">https://github.com/geodynamics/specfem3d</a>)<br>
<br>
2) The cone_1 has a lot of very deformed hexa with negative jacobian.<br>
You need that all the jacobians are positive.<br>
<br>
here the step to create a a good mesh for a conical intrusion<br>
<br>
brick x 10<br>
create frustum height 3 radius 3 top 0<br>
graphics silhouette off<br>
rotate Volume 2 angle 180 about X include_merged<br>
align Volume 2 surface 8 with surface 1<br>
subtract volume 2 from volume 1 keep<br>
delete Volume 1 2<br>
<br>
create Cylinder height 20 radius 4<br>
chop volume 3 with volume 4<br>
<br>
webcut volume all with plane xplane offset 0 preview<br>
webcut volume all with plane xplane offset 0 noimprint nomerge<br>
webcut volume all with plane yplane offset 0 noimprint nomerge<br>
unite volume 9 11 7 5<br>
webcut volume 9 sweep curve 97 vector 0 0 -1 through_all preview<br>
webcut volume 9 sweep curve 97 vector 0 0 -1 through_all<br>
unite volume 6 10 12 8<br>
webcut volume all with plane yplane offset 0 preview<br>
webcut volume all with plane yplane offset 0 noimprint nomerge<br>
webcut volume all with plane xplane offset 0 noimprint nomerge<br>
merge vol all<br>
volume 19 13 16 22 size .5<br>
mesh volume 19 13 16 22<br>
volume 18 9 15 21 scheme Auto<br>
mesh volume 18 9 15 21<br>
surface 137 135 162 169 scheme pave<br>
surface 137 135 162 169 size .5<br>
mesh surface 137 135 162 169<br>
volume 17 6 20 14 scheme Auto<br>
mesh volume 17 6 20 14<br>
<br>
block 1 volume all<br>
create mesh geometry Block 1 feature_angle 100.0<br>
<br>
<br>
<br>
<br>
<br>
On Tue, Jan 14, 2014 at 2:15 PM, <<a href="mailto:s.khan-1@utwente.nl" target="_blank">s.khan-1@utwente.nl</a>> wrote:<br>
> Dear Emanuele,<br>
><br>
><br>
><br>
> Please find the scripts and the volume in attachment. I use block_mesh.py<br>
> after making some modification to it. I am using Cubit 13.0.<br>
><br>
><br>
><br>
> Thanks<br>
><br>
> Best regards,<br>
> Saad Khan<br>
><br>
><br>
><br>
> From: <a href="mailto:cig-seismo-bounces@geodynamics.org" target="_blank">cig-seismo-bounces@geodynamics.org</a><br>
> [<a href="mailto:cig-seismo-bounces@geodynamics.org" target="_blank">mailto:cig-seismo-bounces@geodynamics.org</a>] On Behalf Of emanuele casarotti<br>
> Sent: Monday, January 13, 2014 8:51 PM<br>
> To: <a href="mailto:cig-seismo@geodynamics.org" target="_blank">cig-seismo@geodynamics.org</a><br>
> Subject: Re: [CIG-SEISMO] cubit2specfem3d export<br>
><br>
><br>
><br>
> Hi<br>
><br>
> Can you share the scripta and the volumes?<br>
><br>
> And the version of cubit...<br>
><br>
><br>
><br>
><br>
> Emanuele<br>
><br>
><br>
> Il giorno 13/gen/2014, alle ore 19:47, "<a href="mailto:s.khan-1@utwente.nl" target="_blank">s.khan-1@utwente.nl</a>"<br>
> <<a href="mailto:s.khan-1@utwente.nl" target="_blank">s.khan-1@utwente.nl</a>> ha scritto:<br>
><br>
> Dear All,<br>
><br>
><br>
><br>
> The boundary_definition.py script does not catch my topographic surface. I<br>
> have to define it manually after running the script<br>
> (boundary_definition.py). Then I export the mesh with<br>
> run_cubit2specfem3d.py, which says<br>
><br>
> :<br>
><br>
> Writing MESH/free_surface_file.....<br>
><br>
> block name: face_topo id: 2<br>
><br>
> number of faces = 0<br>
><br>
> :<br>
><br>
> :<br>
><br>
> # all files needed by SCOTCH are now in directory MESH<br>
><br>
><br>
><br>
> Rest of the process goes smoothly and I also get result in the OUTPUT. The<br>
> question is, what does “number of face=0” mean any does it affect the<br>
> results?<br>
><br>
><br>
><br>
> Another thing, when I use very fine mesh (e.g. mesh interval 3000) the<br>
> result (in seismograms) produces a lot of NaNs and at some places<br>
> Infinities. Why is it so?<br>
><br>
><br>
><br>
> Note: The topo surface has been modified while the rest of geo model is the<br>
> same as given in homogeneous_halfspace example. The topo surface is made of<br>
> several surfaces which are combined to one using simplify option in cubit. I<br>
> am using SPECFEM3D_Cartesian 2.1.<br>
><br>
><br>
><br>
> Thanks in advance.<br>
><br>
><br>
><br>
> Best regards,<br>
><br>
> Saad Khan<br>
><br>
> _______________________________________________<br>
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http://geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo</a><br>
><br>
><br>
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</blockquote>
<blockquote type="cite">
<div><Cubit import error.docx></div>
</blockquote>
<blockquote type="cite">
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