[CIG-SHORT] Question about normal slip of points along the fault
Charles Williams
willic3 at gmail.com
Tue Aug 22 21:54:58 PDT 2017
Hi Teng,
If you’re sure there aren’t any PETSc settings in pylithapp.cfg, you definitely need to include a number of settings. I can’t think of a good example to point you to, but have a look in the manual. You might also get some ideas from the friction examples in examples/3d/hex8.
Cheers,
Charles
> On 23/08/2017, at 4:46 PM, Li, Teng <tengli2 at illinois.edu> wrote:
>
> Hi Charles,
>
> This is the only line in the PETSc settings. It seems that I need to add more arguments in PETSc settings. I am wondering whether I can just use the default value?
>
> Best,
> Teng
>
> Teng Li
>
> Master Candidate in Structures
>
> Department of Civil and Environmental Engineering
>
> University of Illinois at Urbana-Champaign
>
> 205 North Mathews Ave, Urbana, IL. 61801
>
> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>
>
> From: CIG-SHORT [cig-short-bounces at geodynamics.org <mailto:cig-short-bounces at geodynamics.org>] on behalf of Charles Williams [willic3 at gmail.com <mailto:willic3 at gmail.com>]
> Sent: Tuesday, August 22, 2017 11:24 PM
> To: cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
> Subject: Re: [CIG-SHORT] Question about normal slip of points along the fault
>
> Hi Teng,
>
> I don’t see any PETSc settings in here other than log_summary. Where are all your solver/convergence settings?
>
> Cheers,
> Charles
>
>
>> On 23/08/2017, at 4:17 PM, Li, Teng <tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>> wrote:
>>
>> Hi Charles,
>>
>> Please see the attached .cfg file.
>>
>> Best,
>> Teng
>>
>>
>> Teng Li
>>
>> Master Candidate in Structures
>>
>> Department of Civil and Environmental Engineering
>>
>> University of Illinois at Urbana-Champaign
>>
>> 205 North Mathews Ave, Urbana, IL. 61801
>>
>> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>
>>
>> From: CIG-SHORT [cig-short-bounces at geodynamics.org <mailto:cig-short-bounces at geodynamics.org>] on behalf of Charles Williams [willic3 at gmail.com <mailto:willic3 at gmail.com>]
>> Sent: Tuesday, August 22, 2017 11:12 PM
>> To: cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
>> Subject: Re: [CIG-SHORT] Question about normal slip of points along the fault
>>
>> Hi Teng,
>>
>> You had sent it before, I just forgot. Also, could you send the .cfg files with your PETSc settings?
>>
>> Cheers,
>> Charles
>>
>>
>>> On 23/08/2017, at 3:33 PM, Li, Teng <tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>> wrote:
>>>
>>> Dear Charles,
>>>
>>> Thanks!
>>>
>>> I remember I sent the .json file in a previous email. Maybe there is something wrong. Please find the attachment for the .json file.
>>>
>>> And actually, in the same position, I find both shear traction and normal traction become zero after time step 69. If there is no normal slip, can I assume there is no damage in this region?
>>>
>>> Best,
>>> Teng
>>>
>>> Teng Li
>>>
>>> Master Candidate in Structures
>>>
>>> Department of Civil and Environmental Engineering
>>>
>>> University of Illinois at Urbana-Champaign
>>>
>>> 205 North Mathews Ave, Urbana, IL. 61801
>>>
>>> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>>
>>>
>>> From: CIG-SHORT [cig-short-bounces at geodynamics.org <mailto:cig-short-bounces at geodynamics.org>] on behalf of Charles Williams [willic3 at gmail.com <mailto:willic3 at gmail.com>]
>>> Sent: Tuesday, August 22, 2017 10:14 PM
>>> To: cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
>>> Subject: Re: [CIG-SHORT] Question about normal slip of points along the fault
>>>
>>> Dear Teng,
>>>
>>> You are correct that the normal slip doesn’t seem to show up in Paraview. I believe this must be a rounding issue. When I look at the HDF5 file, it appears that opening slip with absolute values greater than 1.0e-5 occurs for time steps 69 and greater, on nodes 1804-1807. These nodes are not quite at the center of your mesh (slightly to the right), and we have the following:
>>>
>>> >>> coords[1804:1808,:]
>>> array([[ 0. , 2575.51243781],
>>> [ 0. , 2563.00995025],
>>> [ 0. , 2550.50746269],
>>> [ 0. , 2538.00497512]])
>>> >>> slip[68:70,1804:1808,:]
>>> array([[[ 6.89918509e-01, 5.03786406e-04],
>>> [ 6.84512853e-01, 2.90598425e-03],
>>> [ 6.76231093e-01, 4.27721576e-03],
>>> [ 6.65871813e-01, 1.48424451e-03]],
>>>
>>> [[ 8.21537711e-01, -6.18814173e-03],
>>> [ 8.20121053e-01, -6.61874706e-03],
>>> [ 8.16053970e-01, -5.52545028e-03],
>>> [ 8.08475567e-01, -5.13870352e-03]]])
>>>
>>> slip[106:110,1804:1808,:]
>>> array([[[ 3.22609558, -0.00405558],
>>> [ 3.2170178 , -0.00427933],
>>> [ 3.2045508 , -0.00417583],
>>> [ 3.1879853 , -0.00531141]],
>>>
>>> [[ 3.27816325, -0.0040641 ],
>>> [ 3.26907165, -0.00429604],
>>> [ 3.25659285, -0.00419845],
>>> [ 3.24001916, -0.00533315]],
>>>
>>> [[ 3.33065722, -0.00405906],
>>> [ 3.32156487, -0.00428167],
>>> [ 3.30908228, -0.00417447],
>>> [ 3.29249541, -0.00530886]],
>>>
>>> [[ 3.38360076, -0.00405536],
>>> [ 3.37449161, -0.00428148],
>>> [ 3.3619885 , -0.00418184],
>>> [ 3.34538406, -0.0053216 ]]])
>>>
>>> I’ve just printed out a few time steps as an example. It appears that the ratio of normal slip to shear slip decreases with time. I’m actually not sure what a reasonable amount of normal slip would be — maybe Brad knows. Can you send the .json file that Brad mentioned? That will tell us the settings you’ve been using.
>>>
>>> Cheers,
>>> Charles
>>>
>>>
>>>> On 23/08/2017, at 2:33 PM, Li, Teng <tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> Please find the attachments. The first file is xmf file which can be viewed in Paraview. However, I don't see any slip y value in Paraview in all time steps. And I use Matlab to postprocess fault.h5 file and obtain the results. Please find the two pictures for details. As we can see, four points have normal slip.
>>>>
>>>> Here are the Matlab code to find the slip:
>>>>
>>>> hinfoh=hdf5info('/Desktop/fault.h5');
>>>> coords=hdf5read(hinfoh.GroupHierarchy.Groups(1).Datasets(1));
>>>> slip=hdf5read(hinfoh.GroupHierarchy.Groups(3).Datasets(1));
>>>>
>>>> After opening the variable slip, I find normal slip in columns 1805 - 1808 after time step 69. I am wondering why we have value here in fault.h5 file and we can not see the normal slip in fault.xmf file in Paraview? And I used pylith --nodes=2 to run the .cfg file in my personal Macbook. I am wondering whether this can cause some wrong datas in the output fault.h5 file?
>>>>
>>>> Best,
>>>> Teng
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Teng Li
>>>>
>>>> Master Candidate in Structures
>>>>
>>>> Department of Civil and Environmental Engineering
>>>>
>>>> University of Illinois at Urbana-Champaign
>>>>
>>>> 205 North Mathews Ave, Urbana, IL. 61801
>>>>
>>>> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>>>
>>>>
>>>>
>>>> ________________________________________
>>>> From: CIG-SHORT [cig-short-bounces at geodynamics.org <mailto:cig-short-bounces at geodynamics.org>] on behalf of Brad Aagaard [baagaard at usgs.gov <mailto:baagaard at usgs.gov>]
>>>> Sent: Tuesday, August 22, 2017 3:22 PM
>>>> To: cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
>>>> Subject: Re: [CIG-SHORT] Question about normal slip of points along the fault
>>>>
>>>> Teng,
>>>>
>>>> Is this a quasi-static simulation? If so, is the solution converging at
>>>> every time step?
>>>>
>>>> If you are using PyLith v2.2.0, please send the JSON parameters file
>>>> that is generated during the run.
>>>>
>>>> Regards,
>>>> Brad
>>>>
>>>>
>>>> On 8/22/17 12:52 PM, Li, Teng wrote:
>>>>> Dear Charles,
>>>>>
>>>>> We have a 2d model in my problem. And in this region, where I have
>>>>> normal slip, both normal traction and shear traction become zero. In the
>>>>> beginning, all the points in this region have positive normal slip, and
>>>>> the maximum slip is 0.004. Then, the points have negative normal slip,
>>>>> the values are between -0.006 to -0.003.
>>>>>
>>>>> And I will use Paraview to see the possible normal slip of the points
>>>>> along the fault.
>>>>>
>>>>> Best,
>>>>> Teng
>>>>>
>>>>> Teng Li
>>>>>
>>>>> Master Candidate in Structures
>>>>>
>>>>> Department of Civil and Environmental Engineering
>>>>>
>>>>> University of Illinois at Urbana-Champaign
>>>>>
>>>>> 205 North Mathews Ave, Urbana, IL. 61801
>>>>>
>>>>> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org <mailto:cig-short-bounces at geodynamics.org>] on behalf of
>>>>> Charles Williams [willic3 at gmail.com <mailto:willic3 at gmail.com>]
>>>>> *Sent:* Monday, August 21, 2017 11:04 PM
>>>>> *To:* cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
>>>>> *Subject:* Re: [CIG-SHORT] Question about normal slip of points along
>>>>> the fault
>>>>>
>>>>> Dear Teng,
>>>>>
>>>>> Is this a 2D or 3D problem? If it’s 2D then slip(:,2) should be the
>>>>> normal slip. If it’s 3D I think it should be slip(:,3) (I’m not a
>>>>> Matlab user, but I believe it uses 1-based indexing). If there is
>>>>> actually normal slip, how large is it?
>>>>>
>>>>> You should be able to look at the VTK files in Paraview. Just open the
>>>>> fault VTK file and view ‘slip’. Then select the component you want to view.
>>>>>
>>>>> Cheers,
>>>>> Charles
>>>>>
>>>>>
>>>>>> On 22/08/2017, at 3:02 PM, Li, Teng <tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>>>>> <mailto:tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have some questions about the normal slip of the points along the
>>>>>> fault. Please find the attachments.
>>>>>>
>>>>>> I output the slip(:,2) in matlab to obtain the normal slip of all the
>>>>>> points along the fault in my model. And I use open_free_surface=False
>>>>>> to make sure the initial traction still exists when the fault opens.
>>>>>> However, I find certain points have normal slip. In some time steps,
>>>>>> they have positive normal slip, while in some other times, they have
>>>>>> negative normal slip. I am wondering why they have the normal slip in
>>>>>> 2 different directions?
>>>>>>
>>>>>> And the second picture is the slip convention in pylith-2.2.0 manual.
>>>>>> It is in the page 119/268. I think the meaning is that the positive
>>>>>> normal slip is the fault opening direction.
>>>>>>
>>>>>> And in the third picture, I see negative values of fault opening
>>>>>> implys penetration.
>>>>>>
>>>>>> Since the penetration is never allowed, I wonder why we have both
>>>>>> positive and negative slip results? Is it due to the incomplete or
>>>>>> wrong .vtk output?
>>>>>>
>>>>>> And is there a way to see the fault opening using Paraview? I think
>>>>>> using Paraview to visualize those points can help me figure out the
>>>>>> meaning of their normal slips.
>>>>>>
>>>>>> Hope for your reply!
>>>>>>
>>>>>> Best,
>>>>>> Teng
>>>>>>
>>>>>>
>>>>>>
>>>>>> Teng Li
>>>>>>
>>>>>> Master Candidate in Structures
>>>>>>
>>>>>> Department of Civil and Environmental Engineering
>>>>>>
>>>>>> University of Illinois at Urbana-Champaign
>>>>>>
>>>>>> 205 North Mathews Ave, Urbana, IL. 61801
>>>>>>
>>>>>> Phone:(217)8196210, Email: tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>
>>>>>> <mailto:tengli2 at illinois.edu <mailto:tengli2 at illinois.edu>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> <Positive_values.png><Negative.png>_______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org> <mailto:CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>>
>>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>>>>
>>>>> *Charles Williams I Geodynamic Modeler
>>>>> GNS 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 <mailto:C.Williams at gns.cri.nz>*
>>>>> <mailto:your.email at gns.cri.nz <mailto:your.email at gns.cri.nz>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>>> <fault.xmf><Normal_slip_Time_69.jpg><Normal_slip_Time_70.jpg><fault.h5>_______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>> Charles Williams I Geodynamic Modeler
>>> GNS 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 <mailto:your.email at gns.cri.nz>
>>> <pylith_parameters.json>_______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>> Charles Williams I Geodynamic Modeler
>> GNS 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 <mailto:your.email at gns.cri.nz>
>> <secondary_fault.cfg>_______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
> Charles Williams I Geodynamic Modeler
> GNS 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 <mailto:your.email at gns.cri.nz>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
Charles Williams I Geodynamic Modeler
GNS 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 <mailto:your.email at gns.cri.nz>
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