[CIG-SHORT] Question about normal slip of points along the fault
Matthew Knepley
knepley at rice.edu
Tue Aug 22 22:43:36 PDT 2017
On Wed, Aug 23, 2017 at 12:57 AM, Li, Teng <tengli2 at illinois.edu> wrote:
> Hi Charles,
>
> Thanks! I will read the manual and have a look at this example.
>
At least give --petsc.ksp_converged_reason in order to get one line about
solver convergence, and --petsc.ksp_view to see what solver was used.
Thanks,
Matt
> 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ------------------------------
> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of
> Charles Williams [willic3 at gmail.com]
> *Sent:* Tuesday, August 22, 2017 11:54 PM
>
> *To:* cig-short at geodynamics.org
> *Subject:* Re: [CIG-SHORT] Question about normal slip of points along the
> fault
>
> 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ------------------------------
> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of
> Charles Williams [willic3 at gmail.com]
> *Sent:* Tuesday, August 22, 2017 11:24 PM
> *To:* 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> 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ------------------------------
> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of
> Charles Williams [willic3 at gmail.com]
> *Sent:* Tuesday, August 22, 2017 11:12 PM
> *To:* 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> 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ------------------------------
> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of
> Charles Williams [willic3 at gmail.com]
> *Sent:* Tuesday, August 22, 2017 10:14 PM
> *To:* 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> 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ________________________________________
> From: CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of Brad
> Aagaard [baagaard at usgs.gov]
> Sent: Tuesday, August 22, 2017 3:22 PM
> To: 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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
>
>
>
> ------------------------------------------------------------------------
> *From:* CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of
> Charles Williams [willic3 at gmail.com]
> *Sent:* Monday, August 21, 2017 11:04 PM
> *To:* 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 <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 <(217)%20819-6210>, Email: tengli2 at illinois.edu
> <mailto:tengli2 at illinois.edu <tengli2 at illinois.edu>>
>
>
>
> <Positive_values.png><Negative.png>_________________
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>
> *Charles Williams I Geodynamic Modeler
> GNS Science **I** Te Pῡ Ao*
> 1 Fairway Drive, Avalon 5010, PO Box 30368, Lower Hutt 5040, New Zealand
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> <fault.xmf><Normal_slip_Time_69.jpg><Normal_slip_Time_70.jpg><fault.h5>
> _______________________________________________
> CIG-SHORT mailing list
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>
>
> *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* <your.email at gns.cri.nz>
>
> <pylith_parameters.json>_______________________________________________
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>
>
> *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* <your.email at gns.cri.nz>
>
> <secondary_fault.cfg>_______________________________________________
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>
>
> *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* <your.email at gns.cri.nz>
>
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>
>
> *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: *
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