[CIG-SHORT] PyLith: Stresses not transmitted throughout the domain from Drichlet BCs on CUBIT Mesh
Mamun Miah
mmiah at go.olemiss.edu
Thu Oct 15 17:14:03 PDT 2015
Thanks, Matt for the clarification of the zero pivots related to fault.
Yep, setting fieldslpit option along with pc_type = lu results in the
convergence of the solution. Will make use of the 2015 tutorial like you
suggested. Really appreciate Charles's, Matt's, and your help.
On Thu, Oct 15, 2015 at 4:48 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> If you tried to use lu with a fault, you will get zero pivots because the
> Lagrange multiplier constraints have zero entries on the diagonal. Using
> the fieldsplit settings (see examples/3d/tet4/step04.cfg) will remedy this
> problem.
>
> I strongly recommend that you make use of the PyLith tutorial information
> posted at https://wiki.geodynamics.org/software:pylith:start. We have a
> lot of hints on how to check your solution and debug. From the 2015
> tutorial, you will likely find the slides from Session I and the
> presentations for Sessions III and IV most useful.
>
> Regards,
> Brad
>
>
>
> On 10/15/2015 04:35 PM, Matthew Knepley wrote:
>
>> 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
>>>>
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>>>> CIG-SHORT mailing list
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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
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>>
>>
>>
>>
>>
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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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