[CIG-SHORT] UNCHECKED Re: Applying Gravitational Forces with Pylith

Thu Aug 16 01:05:37 PDT 2018

Thanks. I will continue checking the mesh and will get back to you in case
I could not figure it out.

Thanks,
Niloufar

On Tue, Aug 14, 2018 at 11:30 PM, Charles Williams <willic3 at gmail.com>
wrote:

> Hi Niloufar,
>
> If you are using Trelis or Cubit to create your mesh, there is a simple
> way to check the quality.  Otherwise, if you have a VTK file, you can use
> Paraview to check the quality.  There is a mesh quality filter.  For hexes,
> I think you should probably use the condition number criterion.
>
> Cheers,
> Charles
>
>
> On 15/08/2018, at 5:50 PM, Niloufar Abolfathian <
> niloufar.abolfathian at gmail.com> wrote:
>
> Thanks, Charles. You should be right. I am using hexahedral cells. The
> model is a very simple vertical strike-slip fault. But gravity and finite
> deformation may destort the cells. I have to run the model again to save
> the vtk files in order to check the paraview. Also now I am trying to check
> some finer cell sizes and tetrahedral mesh to see how they will affect the
> results. Thanks for the suggestion.
>
> I am still not sure how to check the quality of the mesh! Is there any
> simple way to do that or any resources I can read from?
>
> Best,
> Niloufar
>
>
>
> On Tue, Aug 14, 2018 at 10:02 PM, Charles Williams <willic3 at gmail.com>
> wrote:
>
>> Hi Niloufar,
>>
>> I can’t run your problem since I don’t have your mesh; however, it
>> appears that this problem is bombing at about 7300 years.  You have given
>> it a total_time of 30000 years, which is quite a long time.  I would see
>> what the solution looks like running for 7300 years or so (so it doesn’t
>> diverge).  One useful thing would be to look at the deformed mesh (I
>> believe this is called something like ‘warp mesh’ in Paraview).  Use a
>> magnification factor of 1 and see if the mesh is getting too deformed.  It
>> might also be useful to look at the behavior of the solution with time to
>> see if you can detect anything unusual.
>>
>> Cheers,
>> Charles
>>
>> p.s.  Have you checked the quality of your mesh?
>>
>>
>> On 15/08/2018, at 3:55 PM, Niloufar Abolfathian <
>> niloufar.abolfathian at gmail.com> wrote:
>>
>> Hi,
>>
>> I followed the 2D gravity example and I could run my models with gravity
>> and add initial stresses. But in models including finite strain, the
>> nonlinear solver could not converge. I have tried running the model with
>> gravitation on and off, applying depth dependent initial stress and no
>> initial stress, applying multigrid preconditioner and also not applying the
>> preconditioner and also modifying the linear and nonlinear tolerances, but
>> could not converge the model. I have attached the setting when setting when
>> I am using the gravity on, applying initial stress and using
>> preconditioning, I am wondering why it is always giving the error after
>> 6000 years. I really appreciate all your help solving these issues.
>>
>> Thanks,
>> Niloufar
>>
>>
>>
>> On Thu, Aug 2, 2018 at 8:43 AM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>
>>> Is this the gravity only problem to compute the initial stresses? If so,
>>> then you should remove the fault.
>>>
>>> On 08/01/2018 08:59 PM, Niloufar Abolfathian wrote:
>>>
>>>> Thanks, Charles.
>>>>
>>>> My error is due to the convergence of the nonlinear solver. I have made
>>>> some modifications but not sure if it is a good idea to decrease my
>>>> residual norms.
>>>>
>>>> Best,
>>>> Niloufar
>>>>
>>>>
>>>> This is the setting I am using:
>>>>
>>>>
>>>> [pylithapp.timedependent]
>>>> formulation =pylith.problems.ImplicitLgDeform
>>>>
>>>>
>>>> [pylithapp.timedependent.formulation]
>>>> output =[domain,subdomain]
>>>> output.subdomain =pylith.meshio.OutputSolnSubset
>>>> solver =pylith.problems.SolverNonlinear
>>>>
>>>> [pylithapp.timedependent.formulation.time_step]
>>>> total_time =50000.0*year
>>>> dt =2.0*year
>>>>
>>>> [pylithapp.timedependent.interfaces]
>>>> fault =pylith.faults.FaultCohesiveDyn
>>>>
>>>> [pylithapp.timedependent.interfaces.fault]
>>>> label =fault
>>>> edge =fault_edge
>>>> zero_tolerance =1.0e-11
>>>>
>>>> # Use the slip-weakening friction model.
>>>> friction.db_properties =spatialdata.spatialdb.UniformDB
>>>> friction.db_properties.label =Slip weakening
>>>> friction.db_properties.values =[static-coefficient,dynamic-c
>>>> oefficient,slip-weakening-parameter,cohesion]
>>>>
>>>> friction.db_properties.data =[0.6,0.4,0.2*m,0.0*Pa]
>>>>
>>>> # ------------------------------------------------------------
>>>> ----------
>>>> # PETSc settings
>>>> # ------------------------------------------------------------
>>>> ----------
>>>> [pylithapp.petsc]
>>>> malloc_dump =
>>>>
>>>> # Preconditioner settings.
>>>> pc_type =asm
>>>> sub_pc_factor_shift_type =nonzero
>>>>
>>>
>>> When you encounter convergence errors, a good strategy is to revert to
>>> the direct solver. Note that this only works when you don't have a fault.
>>>
>>> pc_type = lu
>>>
>>>
>>> For most real applications (after you have debugged the setup)l, we
>>> recommend using the multigrid preconditioner. See
>>> solver_algebraicmultigrid.cfg (no fault) and solver_fieldsplit.cfg )with
>>> fault) in examples/3d/subduction.
>>>
>>>
>>>> # Friction sensitivity solve used to compute the increment in slip
>>>> # associated with changes in the Lagrange multiplier imposed by the
>>>> # fault constitutive model.
>>>> friction_pc_type =asm
>>>> friction_sub_pc_factor_shift_type =nonzero
>>>> friction_ksp_max_it =50
>>>> friction_ksp_gmres_restart =30
>>>>
>>>> # Uncomment to view details of friction sensitivity solve.
>>>> #friction_ksp_monitor = true
>>>> #friction_ksp_view = true
>>>> friction_ksp_converged_reason =true
>>>>
>>>> # Reduce convergence tolerances.
>>>> ksp_rtol =1.0e-16
>>>> ksp_atol =1.0e-12
>>>> ksp_max_it =4000
>>>> ksp_gmres_restart =100
>>>>
>>>> snes_rtol =1.0e-9
>>>> snes_atol =1.0e-8
>>>> snes_max_it =4000
>>>>
>>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>
>> <error_files.zip>_______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
>>
>> *Charles Williams I Geodynamic ModelerGNS Science **I** Te Pῡ Ao*
>> 1 Fairway Drive, Avalon 5010, PO Box 30368, Lower Hutt 5040, New Zealand
>> *Ph* 0064-4-570-4566 I *Mob* 0064-22-350-7326 I *Fax* 0064-4-570-4600
>> *http://www.gns.cri.nz/* <http://www.gns.cri.nz/> *I* *Email: *
>> *C.Williams at gns.cri.nz* <your.email at gns.cri.nz>
>>
>>
>> _______________________________________________
>> 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
>
>
>
> *Charles Williams I Geodynamic ModelerGNS Science **I** Te Pῡ Ao*
> 1 Fairway Drive, Avalon 5010, PO Box 30368, Lower Hutt 5040, New Zealand
> *Ph* 0064-4-570-4566 I *Mob* 0064-22-350-7326 I *Fax* 0064-4-570-4600
> *http://www.gns.cri.nz/* <http://www.gns.cri.nz/> *I* *Email: *
> *C.Williams at gns.cri.nz* <your.email at gns.cri.nz>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20180816/f6ef755a/attachment.html>

[CIG-SHORT] ***UNCHECKED*** Re: Applying Gravitational Forces with Pylith

[CIG-SHORT] UNCHECKED Re: Applying Gravitational Forces with Pylith