[CIG-SHORT] Pylith - Variable mesh resolution in a CUBIT volume with a cavity

Sun Sep 18 05:44:40 PDT 2016

Hi Brad

thanks for your quick reply. As far as I am aware, I have done so.

I have had another look over the weekend. The background mesh (from the
geometry.jou and mesh_cellsize.jou) appears to have the fn variable
incorporated correctly (I viewed this in ParaView - see attachment) at the
nodes.

However, I still observe the same messages in the command window (see
attachment) when I try to run the mesh_size_analyticfn.jou.

I have noticed that in the original example, that when I execute the lines

*volume all sizing function type exodus*

*surface all sizing function type exodus*

the command window reports

*Mesh was assigned to the following entities and their sub-entities:The 3
volume ids are: 1 to 3.*

However, when I run my modified geometry, the same lines now report

*Mesh was assigned to the following entities and their sub-entities:The 7
surface ids are: 1 to 7.*

The final mesh will still be created, but only on the outside surface of
the model. I am guessing that the new volume (final mesh) is not being
imported or meshed properly?

I am not sure if that helps.

Thanks again

Lucas

On 17 September 2016 at 01:08, Brad Aagaard <baagaard at usgs.gov> wrote:

> Lucas,
>
> Did you generate the background mesh with the exact same geometry (all
> exterior and interior vertices, edges, surfaces, and volumes) as your
> "final" mesh? In other words, does the background mesh that you use to
> generate the sizing function have the spherical cavity?
>
> Regards,
> Brad
>
>
> On 09/16/2016 06:24 AM, Lucas Holden wrote:
>
>> Hi
>>
>> I am hoping to get some advice on the use of variable mesh resolution
>> when the volume (block) has a spherical cavity within it (e.g.
>> representing a magma chamber or dike). I have been using the
>> meshing/cubit_cellsize example provided. The example runs successfully
>> using the provided geometry.jou, and py files etc for the surface fault
>> scenario.
>>
>> I am stumbling when I try to insert a spherical cavity at the centre of
>> the block to represent a magma chamber. My edited geometry file is shown
>> below. I have not altered the provided mesh_cellsize.jou,
>> exodus_add_properties.py, matprops.spatialdb or mesh_size_analyticfn.jou
>> files (as yet).
>>
>> When I compile the mesh_size_analyticfn.jou file in CUBIT, the software
>> lists the following errors.
>>
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> //////////////////
>>
>> //home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1
>> .0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (9)/
>>
>> //
>>
>> /Command: volume all sizing function type exodus/
>>
>> //
>>
>> /ERROR:
>> /home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1.
>> 0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (9)/
>>
>> //
>>
>> /nodal sizing data population failed - no storage mesh present./
>>
>> //
>>
>> /ERROR:
>> /home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1.
>> 0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (9)/
>>
>> //
>>
>> /Unable to assign an Exodus sizing function./
>>
>> //
>>
>> /
>> /
>>
>> ////
>>
>> //home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1
>> .0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (10)/
>>
>> //
>>
>> /Command: surface all sizing function type exodus/
>>
>> //
>>
>> /ERROR:
>> /home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1.
>> 0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (10)/
>>
>> //
>>
>> /nodal sizing data population failed - no storage mesh present./
>>
>> //
>>
>> /ERROR:
>> /home/lucas/PyLith/pylith-2.1.0-linux-x86_64/src/pylith-2.1.
>> 0/examples/meshing/edited_cubit_cellsize/mesh_size_analyticfn.jou
>> (10)/
>>
>> //
>>
>> /Unable to assign an Exodus sizing function./
>>
>>
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> //////////////////
>>
>> I have watched the relevant CIG workshop youtube videos (2013,2014) on
>> variable meshing etc, however have not been able to find a solution. Is
>> this related to there being no 'nodes' in the chamber for which to
>> calculate the distance to for the analytical function etc or something
>> simpler in my geometry.jou setup?
>>
>> I am grateful for any advice.
>>
>> Thanks
>>
>> Lucas
>>
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> //////////////////
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Set units to SI./
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /${Units('si')}/
>>
>> //
>>
>> /#/
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Reset geometry./
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /reset/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# Make sure undo is off to prevent errors in stitching volumes./
>>
>> //
>>
>> /undo off/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Create block/
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Block is 100 km x 100 km x 50 km/
>>
>> //
>>
>> /${blockLength=100.0*km}/
>>
>> //
>>
>> /${blockWidth=100.0*km}/
>>
>> //
>>
>> /${blockHeight=50.0*km}/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /brick x {blockLength} y {blockWidth} z {blockHeight}/
>>
>> //
>>
>> /# Translate block so the top is at z=0/
>>
>> //
>>
>> /volume 1 move x {domain_x} y {domain_y} z {-0.5*blockHeight}/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Create magma chamber./
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /#{chamber_center_x=domain_x}/
>>
>> //
>>
>> /#{chamber_center_y=domain_y}/
>>
>> //
>>
>> /#{chamber_center_z=-10.0*km}/
>>
>> //
>>
>> /#{chamber_radius=4*km}/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /create sphere radius {chamber_radius}/
>>
>> //
>>
>> /volume 2 move x {chamber_center_x} y {chamber_center_y} z
>> {chamber_center_z}/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Chop cylinder with sphere, then delete sphere./
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /chop volume 1 with volume 2/
>>
>> //
>>
>> /delete volume 3/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /# Imprint all volumes, merging surfaces/
>>
>> //
>>
>> /# ------------------------------------------------------------
>> ----------/
>>
>> //
>>
>> /imprint all/
>>
>> //
>>
>> /merge all/
>>
>> //
>>
>> /compress ids all/
>>
>> //
>>
>> /
>> /
>>
>> //
>>
>> /# End of file/
>>
>>
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////
>> //////////////////
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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