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

Tue Oct 20 10:29:59 PDT 2015

Hello Brad et al,

Following your tips I was able to run my simulation smoothly for 10 years.
Now when I increased the same problem for a simulation time of 100 years, I
am getting SNESSolve convergence error: 'Nonlinear solve did not converge
due to DIVERGED_MAX_IT iterations 100.' After searching the log file I have
found the following; not sure if that's the root of this issue.

"Line search: Cubic step no good, shrinking lambda, current gnorm
9.815191568334e-05 lambda=1.3655042609323631e-01"

I have tried your tips in the following threads:
http://lists.geodynamics.org/pipermail/cig-short/2012-September/001129.html
http://lists.geodynamics.org/pipermail/cig-short/2014-October/001881.html
http://lists.geodynamics.org/pipermail/cig-short/2015-July/002174.html

Also, like Matt suggested in this link:
http://lists.geodynamics.org/pipermail/cig-short/2013-December/001555.html,
that using a

fs_fieldsplit_0_pc_factor_shift_type nonzero

for Lagrange multipliers weakens the preconditioner. Could it be an issue?

Finally, I have tried various PETSc options from 2015 tutorial but in vain.
I end up with the same SNESSolve error. I would really appreciate any hints
or suggestions in this regard.

Attached are the relevant files.

On Thu, Oct 15, 2015 at 5:14 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:

> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
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>>>
>>>
>> _______________________________________________
>> 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
>

-- 
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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