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

Tue Oct 20 14:54:07 PDT 2015

On Tue, Oct 20, 2015 at 1:35 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:

> Please find attached.
>

Can you rerun without the -snes_view (and -ksp_view if you have it). That
is a lot of noise here.

It looks like the friction solver is not converging. That is pretty tricky
and we have no theory for
when it should work and fail. I will have to talk to Brad about this one.

  Thanks,

    Matt

> Thanks,
> Mamun
>
> On Tue, Oct 20, 2015 at 11:14 AM, Matthew Knepley <knepley at mcs.anl.gov>
> wrote:
>
>> On Tue, Oct 20, 2015 at 12:29 PM, Mamun Miah <mmiah at go.olemiss.edu>
>> wrote:
>>
>>> 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"
>>>
>>
>> For any convergence question I need to see the output from
>>
>>   -snes_view -snes_monitor -ksp_monitor_true_residual
>> -snes_converged_reason -ksp_converged_reason -snes_linesearch_monitor
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> 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
>>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _______________________________________________
>>> 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/20151020/00d32851/attachment-0001.html>