[CIG-SHORT] PyLith: Stresses not transmitted throughout the domain from Drichlet BCs on CUBIT Mesh

Thu Oct 15 16:07:17 PDT 2015

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.

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
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>>>>
>>>>
>>>> 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
>>>>
>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> 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
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>> 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
>
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-- 
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
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