[CIG-SEISMO] SPECFEM3D - test case for meshfem3D "simple model"

[Camille Mazoyer-Kervazo]

Thanks a lot for this answer!
Indeed, you are right, I thought my run was wrong whereas it perfectly run! I didn't understand the histogram of skewness. Now, it's clear as crystal!
I am now trying to set the variable MOVIE_VOLUME to .true., as I would like to see what happens in a vertical slice (eg. x,z) of the model. I will be usefull for our next model for observing submarine seismic propagation into the water column.

In the simple_model example, when I set MOVIE_VOLUME to true (and MOVIE_SURFACE to false), I've got a floating invalid error. I don't really understand what I should do to avoid this. The Dt step of the simulation is DT   = 0.03, and NSTEP = 2000. In the output_mesher.txt file, I was told to have a dt <= 0.04293954 to be below the CFL condition.
The output_mesher.txt says:
" that value is below the upper CFL limit of   0.480000000000000
 therefore the run should be stable"

Could you please advice me what should I take care of? 

Thanks a lot,

Camille Mazoyer

> 
> ps. and if you want to contribute your own setup as a new future example, please let me know as well. it's always great to provide more useful examples :)
> 

I'll have to ask the team I work with if they are willling to share their setup. As for me, I would be glad to give you my setup configurations, when they will be working.




Le 9 mars 2011 à 18:03, daniel peter a écrit :

> Salut Camille,
> 
> thanks for giving SPECFEM3D a try :) i was reading your mail below and it sounded like the example didn't run for you. however, the output you attached is the correct one. it seems that you are actually doing everything all right and the xmeshfem3D is working just fine for the example as well.
> 
> maybe you are just misinterpreting the skewness table:
> ...
> histogram of skewness (0. good - 1. bad):
> 
>  0.0000000E+00  -   5.0000001E-02       27648     81.81818      %
>  5.0000001E-02  -   0.1000000               0    0.0000000E+00  %
> ...
> 
> 
> the first line means that you have 27648 elements with a skewness value between 0 and 0.05 (which means the element is basically not skewed, just plain regular hexahedral element). the total number of elements you have in this mesh is (see in the output_mesher.txt file a bit further down):
> ...
> total number of elements in entire mesh:        33792
> ...
> 
> which gives you that:  27648 / 33792 ~ 81.8 % of all elements are not skewed, i.e. regular elements. a fantastic value :)
> 
> the histogram lists for this mesh also some stronger skewed elements, for example the worst ones belong to:
> ...
> 0.6000000      -   0.6500000            2048     6.060606      %
> ...
> 
> about 6 % of all elements have distortions with a skewness value between 0.6 and 0.65. the skewness values give you a hint of how good your mesh is. in an ideal world, you would want to have no distortions, just like the 81% from above. those elements give you the best approximate values by the GLL quadrature used in the spectral-element method. however, having weakly distorted elements is still fine and the solutions are still accurate enough. so empirically, values up to around 0.7 are tolerable, above that you should consider remeshing...
> 
> to give you an idea why some of the elements are distorted, i'll attach here a figure of the mesh you obtain in this example. you will see that the mesh contains a doubling layer, where we stitch elements together such that the size of two elements will transition to the size of one element (very useful to keep the ratio of wavespeed / element_size about constant). those elements in this doubling layer have higher skewness values and make up those 6 % in the histogram.
> 
> 
> <mesh_vp.jpg>
> 
> 
> about your concern, just try to continue the example (you might want to run >svn update to get the latest version of SPECFEM3D with an updated README for this simple_model/ example). then look at the mesh files generated in in_out_files/DATABASES_MPI/ after you run the xgenerate_databases executable (step 3 in the README, make sure you have set SAVE_MESH_FILES to .true. in the Par_file as it comes from the example). then you could use paraview (www.paraview.org) to load the proc****_vp.vtk files and compare them to the figure attached here. they should look the same.
> 
> i found this example better than the the second one for the internal mesher. the many_interfaces/ example is using a setup with many cpus (81), generates a huge mesh (~415 GB) and the forward simulation takes about 5h without too much of nice looking seismograms. i think, we will have to change that second example in future to make it somewhat easier to run...
> 
> maybe, in your case the example waterlayered_halfspace/ might be interesting as well. it explains how to set up a model with acoustic and elastic parts. however, that example works together with CUBIT (http://cubit.sandia.gov/), an external mesher which needs to be purchased (?~$200). especially for more complicated setups, accounting for complex bathymetry and subsurface structure, meshing with CUBIT becomes more and more powerful.
> 
> anyway, in case you encounter some more problems with the example, just let me know.
> 
> best wishes from Princeton,
> daniel
> 
> 
> ps. and if you want to contribute your own setup as a new future example, please let me know as well. it's always great to provide more useful examples :)
> 
> 
> --
> Daniel Peter
> Department of Geosciences
> 318 Guyot Hall
> Princeton University
> Princeton, NJ 08540, USA
> 
> Tel: +1 (609) 258-5031
> url: http://www.princeton.edu/~dpeter
> 
> 
> 
> On Mar 8, 2011, at 6:26 PM, Camille Mazoyer wrote:
> 
>> Hello,
>> 
>> I'm an engineer in scientific computing at Institut Universitaire Européen de la Mer (IUEM), Brest, France. One of the team with whom I work with would like to use SPECFEM3D in order to study submarine seisms and their  Hydroacoustic propagation.
>> 
>> Therefore, I'm learning how to use your software for helping this team. I started with the example of mesh generation called "simple model" found in examples/meshfem3D_examples/simple_model.Unfortunately, I didn't manage to make this example work. I probably forgot to do something but I can't see where: I just copied the files in in_data_files/meshfem3D_files as it is explained in the README of the example. And I didn't modify any of the files.
>> After executing xmeshfem3D, I've got elements with skewness of 81%, which is not correct. I send you in an attached file the output_mesher.txt. I hope this file will help you find what I missed in my simulation.
>> 
>> Thanks a lot for your help.
>> I am looking forward to work with this software which seems very accomplished.
>> 
>> Camille Mazoyer
>> <output_mesher.txt>_______________________________________________
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>> CIG-SEISMO at geodynamics.org
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> 

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