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

Thu Oct 15 15:11:30 PDT 2015

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>_______________________________________________
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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
>
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> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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