[CIG-SHORT] Question about accuracy in Pylith
Demian Gomez
demiang at gmail.com
Sun Oct 16 13:56:08 PDT 2016
Hi Charles,
Thanks for your help. I've been using an analytic function to have a graded
tetmesh (as in the example in the meshing directory). I also tried
smoothing the mesh using the iterative approach in the examples:
${condnum=2.0}
${loop(4)}
volume all smooth scheme condition number beta {condnum} cpu 2
smooth volume all
${condnum=condnum-0.1}
${endloop}
I've noticed that while the smoothing reduces the number of elements with
distorted shapes, it also tends to make a few of them worse. For example, I
start with a mesh where the maximum condition number is, say, 4. I apply
smoothing and after the process is over, the maximum condition number is
now 7. It seems that this problem occurs near the intersection of the fault
plane and each of the layers of my model (see figure; meshed surfaces are
the fault interface). Since the fault dip angle is ~ 18 degrees, I have a
sort of wedge where the elements tend to have larger condition numbers.
I already tried to refine the mesh around the curve where the fault plane
intersects the surface and the layer and then apply smoothing, but that
didn't help much. I did multiple experiments and, at these locations, I
can't make the condition number < ~3 no matter what I do.
I also obtained a stress profile and the mesh quality on that same profile,
as suggested by Brad. The mesh condition number is actually very decent at
the location of the profile (never exceeds 1.5), but the stress shows lots
of kinks (see attached plots; no axis labels, sorry, but X is distance from
some reference in the Paraview profile and Y either stress or quality). I
also checked that the condition number is < 2 around the location where I
take the profiles. Therefore, I am assuming that the high condition numbers
at the fault are distorting my results everywhere.
Do you have any suggestions on how can I solve this problem? It seems that
I must be doing something wrong since I haven't seen anybody with this type
of problems.
Thanks,
Demián
PS: Regarding Tabrez' comment, my solution is always converging.
--
*Dr. Demián D. Gómez*
Postdoctoral Researcher
The Ohio State University - School of Earth Sciences
275 Mendenhall Laboratory
125 South Oval Mall
Columbus, Ohio 43210
Cell: +1 (901) 900-7324
email: gomez.124 at osu.edu
On Fri, Oct 14, 2016 at 4:18 PM, Charles Williams <willic3 at gmail.com> wrote:
> Hi Demian,
>
> Ideally, you would like all condition numbers to be less than 2.0. Also,
> the gradients in cell size may also influence your solution. It might be
> worthwhile to make use of sizing functions to provide a more nicely graded
> mesh. There are several examples in the meshing directory.
>
> Cheers,
> Charles
>
>
> > On 15/10/2016, at 8:05 AM, Brad Aagaard <baagaard at usgs.gov> wrote:
> >
> > Demian,
> >
> > For a quasi-static problem the global accuracy of the solution should
> not be controlled by the worse cells. You should aim for a condition number
> of about 2.0 or less. I strongly recommend using ParaView to see if there
> is a correlation between condition number (or aspect ratio) and the local
> fluctuations in stress/strain that you see. If there is a correlation, this
> should tell you what condition number to aim for.
> >
> > Regards,
> > Brad
> >
> >
> > On 10/14/2016 11:58 AM, Demian Gomez wrote:
> >> Hi Brad,
> >>
> >> Thanks. Here's the output for the mesh quality:
> >>
> >> Tet quality, 3297540 elements:
> >>
> >> Condition No. ranges from 1.000e+00 to 4.650e+00 (3297540 entities)
> >>
> >> Red ranges from 4.128e+00 to 4.650e+00 (3 entities)
> >>
> >> Magenta ranges from 3.607e+00 to 4.128e+00 (69 entities)
> >>
> >> DkYellow ranges from 3.086e+00 to 3.607e+00 (196 entities)
> >>
> >> Yellow ranges from 2.564e+00 to 3.086e+00 (862 entities)
> >>
> >> Green ranges from 2.043e+00 to 2.564e+00 (4427 entities)
> >>
> >> Cyan ranges from 1.521e+00 to 2.043e+00 (75597 entities)
> >>
> >> Blue ranges from 1.000e+00 to 1.521e+00 (3216386 entities)
> >>
> >>
> >> The highest Co. number is 4.65 and there are only 3 elements, mostly on
> >> the edges. Can this distort all the solution? Also, although we want all
> >> the elements to be as close to 1 as possible, is there an acceptable
> >> range limit?
> >>
> >>
> >> Thank you,
> >>
> >> Demián
> >>
> >>
> >> --
> >> *Dr. Demián D. Gómez*
> >> Postdoctoral Researcher
> >> The Ohio State University - School of Earth Sciences
> >> 275 Mendenhall Laboratory
> >> 125 South Oval Mall
> >> Columbus, Ohio 43210
> >> Cell: +1 (901) 900-7324
> >> email: gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> >>
> >>
> >> On Fri, Oct 14, 2016 at 2:28 PM, Brad Aagaard <baagaard at usgs.gov
> >> <mailto:baagaard at usgs.gov>> wrote:
> >>
> >> Demian,
> >>
> >> Have you looked at mesh quality (aspect and condition numbers close
> >> to 1.0)? Distorted cells (slivers, squashed tets, etc) will be
> >> stiffer and may cause local stress/strain concentrations. My guess
> >> is that your 2-D mesh has better quality. Look to see if there is a
> >> correlation between condition number or aspect ratio and the kinks,
> >> etc in your stress field (you can do this in ParaView). If so, then
> >> spend some time playing with the bias value, cell size, and
> >> smoothing to improve the mesh quality.
> >>
> >> Regards,
> >> Brad
> >>
> >>
> >>
> >> On 10/14/2016 11:17 AM, Demian Gomez wrote:
> >>
> >> Dear Brad, Matt and Charles,
> >>
> >> I have a question regarding the accuracy of the solution using
> >> tets. I
> >> have a model with a biased tet mesh (4 km at the fault and 160
> >> km at the
> >> edges, ~2200 km away) from which I am trying to get the strain
> and
> >> stress on some depth profiles at ~ 400 km from the fault. I am
> >> running
> >> Pylith with the refiner on (only one level) to refine my mesh and
> >> improve the resolution.
> >>
> >> The problem I'm having is that when I plot the strains and
> >> stresses, the
> >> plots are very "noisy" (see profiles_70.png). The displacement
> >> looks ok,
> >> maybe a few bumps and kinks here and there, but acceptable. I
> think
> >> these small displacement kinks are translating into the "noise"
> and
> >> larger kinks in strain and stress. I did tests in 2D (on a cross
> >> section
> >> of my 3D model) to figure out the best discretization size, and
> >> if I use
> >> a mesh with constant element size (say, 1 km), then everything
> >> is smooth
> >> and nice (see profiles_70_2D.png). However, a 3D model of the
> >> size that
> >> I need meshed with 1 km elements is huge and very impractical.
> >> Moreover,
> >> there shouldn't be any problems with using a biased mesh since
> >> there are
> >> examples within Pylith were you guys use this type of mesh.
> >>
> >> I know that I can improve the accuracy by using hexes, but
> >> unfortunately
> >> I've been trying to mesh my model with hexes (in Trelis) without
> any
> >> success. The model has the shape of a spherical cap and
> >> apparently there
> >> is something that Trelis doesn't like about this geometry. No
> >> matter how
> >> I divide and subdivide the model to help the mesher, there is
> >> always one
> >> volume that I cannot mesh. With tets, however, it works fine.
> >>
> >> Do you have any suggestions on what can I try to improve these
> >> results,
> >> without increasing the number of elements? I am at the limit of
> >> resources in terms of the model size (right now I'm at 125 GB of
> >> required memory to run my model). I could start using the HPC
> but it
> >> seems that there should be another way to solve this problem
> >> other than
> >> "brute force", i.e. making the model larger and using a bigger
> >> computer.
> >> You may also have suggestions regarding the meshing process. I
> would
> >> appreciate any advise that can help me to solve my problem. Let
> >> me know
> >> if there is any additional information you may need that I did
> >> not include.
> >>
> >> Cheers,
> >> Demián
> >>
> >> PS: I've attached the cfg files, just in case you want to see
> >> how I'm
> >> running the problem.
> >>
> >> --
> >> *Dr. Demián D. Gómez*
> >> Postdoctoral Researcher
> >> The Ohio State University - School of Earth Sciences
> >> 275 Mendenhall Laboratory
> >> 125 South Oval Mall
> >> Columbus, Ohio 43210
> >> Cell: +1 (901) 900-7324 <tel:%2B1%20%28901%29%20900-7324>
> >> email: gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> >> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> >>
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
> Charles A. Williams
> Scientist
> GNS Science
> 1 Fairway Drive, Avalon
> PO Box 30368
> Lower Hutt 5040
> New Zealand
> ph (office): 0064-4570-4566
> fax (office): 0064-4570-4600
> C.Williams at gns.cri.nz
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20161016/4b9c6229/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: quality_profile.eps
Type: application/postscript
Size: 7728 bytes
Desc: not available
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20161016/4b9c6229/attachment-0003.eps>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: stress_profile.eps
Type: application/postscript
Size: 7705 bytes
Desc: not available
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20161016/4b9c6229/attachment-0004.eps>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: geometry.eps
Type: application/postscript
Size: 2100334 bytes
Desc: not available
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20161016/4b9c6229/attachment-0005.eps>
More information about the CIG-SHORT
mailing list