[CIG-SHORT] PyLith: Stresses not transmitted throughout the domain from Drichlet BCs on CUBIT Mesh
Matthew Knepley
knepley at mcs.anl.gov
Thu Oct 15 16:35:31 PDT 2015
On Thu, Oct 15, 2015 at 6:07 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:
> Dear Matt,
>
> I have tried with pc_type = lu, which shows zero pivots in the matrices.
> Did not realize that before setting pc_type = lu. Thanks a lot for telling
> me that. Then I have tried with pc_type = cholesky, which seems to be
> working now resulting in convergence of my problem.
> Thanks to you and Charles again for guiding me in the right direction to
> investigate the problem further.
>
If you have zero pivots, that means your problem is under-constrained, and
you need to fix the model.
Thanks,
Matt
> On Thu, Oct 15, 2015 at 3:11 PM, Matthew Knepley <knepley at mcs.anl.gov>
> wrote:
>
>> On Thu, Oct 15, 2015 at 4:26 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:
>>
>>> Charles,
>>>
>>> Thanks again for your suggestion. I have reproduced the geometry and
>>> improved the mesh quality by checking with 'Allmetrics' in Cubit (attached
>>> below). Condition number is below 2 (1.606) and maximum aspect ratio is 3.
>>> Still I am getting the same convergence errors. I have also tried the tips
>>> found in the threads that Brad answered in the CIG-SHORT:
>>>
>>
>> Run with LU until you understand the system: --petsc.pc_type=lu
>>
>> There is an entire tutorial on the solvers which tells you to do this
>> first.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> http://lists.geodynamics.org/pipermail/cig-short/2014-October/001885.html
>>>
>>> http://lists.geodynamics.org/pipermail/cig-short/2012-September/001129.html
>>>
>>>
>>> Hex quality, 810 elements:
>>>
>>> ------------------------------------
>>>
>>> Function Name Average Std Dev Minimum (id) Maximum (id)
>>>
>>> ----------------- --------- --------- --------------
>>> -------------
>>>
>>> Aspect Ratio 1.222e+00 6.289e-01 1.000e+00 (1) 3.000e+00 (724)
>>>
>>> Skew 8.104e-16 8.536e-16 0.000e+00 (10) 6.821e-15 (733)
>>>
>>> Taper 8.561e-16 8.748e-16 0.000e+00 (3) 6.845e-15 (736)
>>>
>>> Element Volume 2.500e+07 5.660e+06 9.000e+06 (733) 2.700e+07 (505)
>>>
>>> Stretch 9.330e-01 1.895e-01 3.974e-01 (782) 1.000e+00 (10)
>>>
>>> Diagonal Ratio 1.000e+00 4.591e-08 1.000e+00 (372) 1.000e+00 (10)
>>>
>>> Dimension 1.640e+02 2.602e+01 9.045e+01 (809) 1.732e+02 (315)
>>>
>>> Condition No. 1.067e+00 1.907e-01 1.000e+00 (3) 1.606e+00 (737)
>>>
>>> Jacobian 2.500e+07 5.660e+06 9.000e+06 (763) 2.700e+07 (315)
>>>
>>> Scaled Jacobian 1.000e+00 0.000e+00 1.000e+00 (248) 1.000e+00 (1)
>>>
>>> Shear 1.000e+00 0.000e+00 1.000e+00 (248) 1.000e+00 (1)
>>>
>>> Shape 9.648e-01 9.963e-02 6.832e-01 (737) 1.000e+00 (1)
>>>
>>> Relative Size 7.765e-01 2.288e-01 1.296e-01 (733) 8.573e-01 (487)
>>>
>>> Shear And Size 7.765e-01 2.288e-01 1.296e-01 (733) 8.573e-01 (487)
>>>
>>> Shape And Size 7.719e-01 2.418e-01 8.854e-02 (733) 8.573e-01 (487)
>>>
>>> Distortion 1.000e+00 5.167e-08 1.000e+00 (367) 1.000e+00 (11)
>>>
>>>
>>>
>>> Not sure what else I should try next. Please also see the attached files.
>>>
>>> Thanks,
>>> Mamun
>>>
>>>
>>> On Wed, Oct 14, 2015 at 11:11 AM, Charles Williams <willic3 at gmail.com>
>>> wrote:
>>>
>>>> Dear Mamun,
>>>>
>>>> Your linear convergence looks very slow. You could increase the number
>>>> of iterations, but I’m not sure if that would solve your problem. I would
>>>> start with a higher quality mesh. Ideally, you would like to have a mesh
>>>> where the condition number quality measure is less than 2 for the entire
>>>> mesh, particularly for problems involving fault friction. If this is too
>>>> difficult to achieve using hexahedral elements, you might need to try
>>>> tetrahedral elements.
>>>>
>>>> Cheers,
>>>> Charles
>>>>
>>>>
>>>> On 15/10/2015, at 6:09 am, Mamun Miah <mmiah at go.olemiss.edu> wrote:
>>>>
>>>> Thanks, Charles. Your comments are very helpful. I have been going
>>>> through each of your comments and discovered that both KSPSolve and
>>>> SNESSolve do not converge when I uncommented corresponding flag options. So
>>>> I figured the problem is with the mesh creation. Also set the the
>>>> normalizer according to the smallest mesh dimension. Attached here is the
>>>> log file in case you want to see.
>>>>
>>>> Thanks again,
>>>> Mamun
>>>>
>>>> On Tue, Oct 13, 2015 at 12:37 PM, Charles Williams <willic3 at gmail.com>
>>>> wrote:
>>>>
>>>>> Dear Mamun,
>>>>>
>>>>> It is a bit difficult to diagnose your problem without more
>>>>> information. However, here are several potential problems:
>>>>>
>>>>>
>>>>> 1. First of all, the mesh you’re using is not of very high quality.
>>>>> The method you’ve used for refinement is pretty crude, and will never
>>>>> result in high quality elements. Trelis/Cubit has a number of more powerful
>>>>> methods for creating a high quality mesh, and I would take advantage of
>>>>> those.
>>>>> 2. It is unclear why you have set the normalization length scale to 1
>>>>> m, since I believe this is much smaller than your smallest element.
>>>>> 3. There is no indication of whether the linear and nonlinear
>>>>> solutions are converging, since you have turned off all the solution
>>>>> monitoring options, including the journal options. You should never do
>>>>> this, as there is then no way to tell what has happened with your solution.
>>>>>
>>>>> You should try running your problem again with all the solution
>>>>> monitoring options turned back on, and save the results to a log file.
>>>>> This will help us diagnose your problem further. I would also try
>>>>> improving your mesh quality and selecting a normalization length scale that
>>>>> is appropriate for your mesh (~equal to the smallest cell dimension).
>>>>>
>>>>> Cheers,
>>>>> Charles
>>>>>
>>>>>
>>>>> On 14/10/2015, at 6:26 am, Mamun Miah <mmiah at go.olemiss.edu> wrote:
>>>>>
>>>>> Hello Developers,
>>>>>
>>>>> I have created the attached geometry (5kmx5kmx4.1km) in CUBIT. It has
>>>>> three layer of materials (2000m+100m+200m) and a vertical fault (along Z
>>>>> axis) 1000m to the left from the positive X-plane boundary. The exported
>>>>> Exodus mesh is then used to run a PyLith simulation with Dirichlet
>>>>> displacement and displacement rate BCs (e.g. PyLith Tutorial 'step12.cfg')
>>>>> on +x and -x sides. The simulation runs fine but even after running for 100
>>>>> years I don't see any stress being transmitted to the interior domain. All
>>>>> I can see is the stress changes in the boundary elements where the
>>>>> Dirichlet BCs are applied. I am not sure if it is caused by improper
>>>>> meshing or boundary conditions.
>>>>>
>>>>> Attached also are the .cfg files, geometry journal file, and stress
>>>>> output file from simulation. I would highly appreciate any help.
>>>>>
>>>>> --
>>>>> Thanks & Best Regards,
>>>>>
>>>>> Mamun Miah
>>>>> Graduate Research Assistant
>>>>> Department of Civil Engineering
>>>>> The University of Mississippi
>>>>> Oxford, MS 38655
>>>>> Phone: (662)-801-1904
>>>>> Website: http://www.linkedin.com/pub/mamun-miah-eit/21/53/339
>>>>> <geometry.jpg><application.cfg><pylithapp.cfg><visit0000.png>
>>>>> <application.jou>_______________________________________________
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Thanks & Best Regards,
>>>>
>>>> Mamun Miah
>>>> Graduate Research Assistant
>>>> Department of Civil Engineering
>>>> The University of Mississippi
>>>> Oxford, MS 38655
>>>> Phone: (662)-801-1904
>>>> Website: http://www.linkedin.com/pub/mamun-miah-eit/21/53/339
>>>> <log>_______________________________________________
>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> Thanks & Best Regards,
>>>
>>> Mamun Miah
>>> Graduate Research Assistant
>>> Department of Civil Engineering
>>> The University of Mississippi
>>> Oxford, MS 38655
>>> Phone: (662)-801-1904
>>> Website: http://www.linkedin.com/pub/mamun-miah-eit/21/53/339
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
>
>
> --
> Thanks & Best Regards,
>
> Mamun Miah
> Graduate Research Assistant
> Department of Civil Engineering
> The University of Mississippi
> Oxford, MS 38655
> Phone: (662)-801-1904
> Website: http://www.linkedin.com/pub/mamun-miah-eit/21/53/339
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20151015/dacfb5bc/attachment-0001.html>
More information about the CIG-SHORT
mailing list