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

Thu Oct 15 16:48:38 PDT 2015

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