[CIG-LONG] tracking sedimentary layers during deformation
Tristan Salles-Taing
sallestaing at gmail.com
Sun Jan 3 17:43:45 PST 2010
*
Hope you had a good Xmas and New Year Eve break.
Attached is the minor changes I made in the SurfaceAdaptor files. The surface is
supposed to be defined on a regular square grid.
To use it in the xml input file you need to proceed like before except
that you must add
the number of points in x,z directions.
<struct name="surfaceAdaptor">
<param name="Type">SurfaceAdaptor</param>
<param name="mesh">mesh-linear</param>
<param name="sourceGenerator">linearMesh-generator</param>
<param name="surfaceType">topo_data</param>
<param name="surfaceName">test.topo</param>
<param name="nx">32</param>
<param name="ny">12</param>
</struct>
I've also attached the topography file to show the format (simply x,z,y).
I was thinking the PolygonShape was only for 2D simulation. The
SurfaceShape is made for
defining 3D shape. It consists in giving for each shape 2 surfaces
that represent its envelop.
It helps me to import easily our simulated sedimentary layers in Gale.
I have attached as well as the files
2 snapshots to give you a better idea. To make it work in Gale few
changes need to be done in the following files:
Init.c, SConscript, Shape.h, types.h
mainly to add the new shape type and the headers of the new file.
Considering the particle tracers it seems that it is exactly what I'm
looking for.
I had a try with the ManualParticleLayout but there are some problems
when the number of particle is 'large'.
Here is the kind of problem I have:
In func Materials_Register_AssignParticleProperties(): for swarm
"passiveTracerSwarm"
Assigning initial particle properties to the 101 global particles
done 10% (11 particles)...
done 20% (21 particles)...
done 30% (31 particles)...
done 40% (41 particles)...
done 50% (51 particles)...
done 60% (61 particles)...
done 70% (71 particles)...
done 80% (81 particles)...
done 90% (91 particles)...
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple
to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 11, Thu Mar 27
09:16:38 CDT 2008 HG revision:
0a79e1469a317b0468b3b3310524bf13867c66f5
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: /Users/sal116/workspace/Gale/bin/Gale on a underworl
named matris-kf.per.dpr.csiro.au by sal116 Mon Jan 4 09:40:42 2010
[0]PETSC ERROR: Libraries linked from /usr/local/lib/underworld
[0]PETSC ERROR: Configure run at Fri Oct 23 13:33:43 2009
[0]PETSC ERROR: Configure options CFLAGS=-Wl,-flat_namespace
--with-shared=1 --with-debugging=0 --with-fortran=0
--with-blas-lapack-dir=/usr/
--with-mpi-dir=/usr/local/mpich2-optimised --prefix=/usr/local
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
I don't know if you have any idea on how to solve this problem of memory access.
Cheers
Tristan
*
------------------------------
Tristan Salles-Taing <sallestaing at gmail.com
<http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long>> wrote:
>* For the moment Gale is not able to restart from a considered time step such*>* as Underworld so the material characteristics are lost between two starts*>* but Guillaume Duclaux (CSIRO such as me)*>* said that it will maybe be available in the next release. *
Restarting from a checkpoint will definitely be available in the next release.
>* Then I will have*>* to see how I can restart a Gale simulation with additional materials*>* (consisting of Sedsim stacked sedimentary layers)...anyway*>* that's not the purpose of my mail.*>* *>* First of all, if you are interested in the modifications I made how can I*>* send them to you (I suppose you want to check them so is it ok if I use*>* subversion) ?*
I am very interested in the modifications to SurfaceAdaptor. I always
had such a fix in the back of my mind. As for SurfaceShape, I do not
quite see how it differs from a regular polygon shape. If you just
send me the files, then I would probably have a better idea.
>* Secondly, I still have some issues when I try to export the modified*>* sedimentary layers from Gale. I already lost a lot of precision when I*>* import the SurfaceShape from Sedsim to Gale due to the fact that*>* Gale is distributing the swarm particle randomly inside a cell. So there*>* isn't a perfect match between my SurfaceShape coordinates and the swarm*>* particles. Then at the end of Gale run, I am computing*>* new surfaces which delimitate the different particles layers after*>* deformation. These surfaces are used to find the new sedimentary layers*>* thicknesses. However the surface tracking is really poor mainly*>* because it relies on randomly located particles.*>* *>* Is there a way of forcing a particle two be at a specific location (X,Y,Z)*>* and can I track this particle during Gale run ?*
You can add tracers at particular points that are then advected along
with the other particles. I am still not 100% confident about how
well they work, so I have not documented them. There is an example of
how to use them in
input/examples/tibet.xml
Cheers,
Walter Landrywalter at geodynamics.org
<http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long>
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