[CIG-SHORT] Pylith - Variable mesh resolution in a CUBIT volume with a cavity
Brad Aagaard
baagaard at usgs.gov
Mon Sep 19 10:45:29 PDT 2016
Lucas,
I suspect there is something wrong with your geometry or meshing journal
files such that something is not matching between the background
geometry/mesh and the final geometry.
Can you create a zip or tarball of your journal files AND the python
script you are running and send it to me? I will try to replicate the issue.
Brad
On 09/18/2016 05:44 AM, Lucas Holden wrote:
> 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
> <mailto: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 <mailto:CIG-SHORT at geodynamics.org>
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> <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
>
More information about the CIG-SHORT
mailing list