request from RR main #78

rrezakhani · 2021-05-25T17:58:04Z

pull request to add several material and kernel source files as well as a benchmark problem for pressurized fracture.

hugary1995 · 2021-07-18T00:16:46Z

Hi Roozbeh, I can finally work on this now -- sorry for taking so long. If you can give me write access to this branch, I can directly work on it.

hugary1995 · 2021-07-27T11:24:56Z

You can see why the tests are failing by clicking on "details". For example, the Precheck fails because some files contain trailing white spaces. I think if you enforce the .clang-format in the root directory they should be gone. Although I'm not sure how to set it up in spy. There is also one file containing banned keywords.

rrezakhani · 2021-07-27T14:05:05Z

Thanks, I will work on it today. ************************************************************************ Roozbeh Rezakhani, PhD Postdoctoral Researcher Department of Mechanical Engineering and Material Science Duke University Durham, NC, USA Email: ***@***.*** Cell: +1 224 204 4500 ************************************************************************

…

On Tue, Jul 27, 2021 at 7:25 AM Gary (Tianchen) Hu ***@***.***> wrote: You can see why the tests are failing by clicking on "details". For example, the Precheck fails because some files contain trailing white spaces. I think if you enforce the .clang-format in the root directory they should be gone. Although I'm not sure how to set it up in spy. There is also one file containing banned keywords. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#78 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKK4RAOIH2XZP4UI3MZ2JCDTZ2JRFANCNFSM45P4RHMQ> .

hugary1995

Thanks Roozbeh, looks pretty good overall. I have done the first round review - mostly some formatting issues.

Most of the comments are notes to myself. But if you can go through them and stick to the formatting guideline in future PRs, that'll be really helpful.

.directory

benchmarks/hydraulic_fracture/fracture.i

benchmarks/hydraulic_fracture/run.sh

benchmarks/mode1_geometric_notch_fatigue/fracture.i

src/kernels/ADAnisotropicDiffusion.C

src/kernels/ADMaterialDerivativeTestKernel.C

src/kernels/ADSPFPressureTimeDerivative.C

src/kernels/ADValueKernelCoupled.C

src/kernels/ValueKernelCoupled.C

hugary1995

Some more questions...

doc/content/source/kernels/ADAnisotropicDiffusion.md

doc/content/source/kernels/ADMaterialDerivativeTestKernel.md

doc/content/source/kernels/ADValueKernelCoupled.md

doc/content/source/kernels/ValueKernel.md

doc/content/source/materials/ADComputeFluidMobility.md

doc/content/source/materials/ADComputePorosity.md

doc/content/source/materials/ComputePorosity.md

doc/content/source/materials/FatigueMobility.md

doc/content/source/kernels/ADAnisotropicDiffusion.md

doc/content/source/kernels/ADMaterialDerivativeTestKernel.md

src/kernels/ADPorousFlowTimeDerivative.C

doc/content/source/kernels/ADValueKernelCoupled.md

doc/content/source/kernels/ValueKernel.md

doc/content/source/kernels/ValueKernelCoupled.md

include/materials/ADComputeFluidMobility.h

hugary1995 · 2021-09-20T07:38:31Z

Hi @rrezakhani, could you please remind me where we were on this? Are you just waiting for my changes? If so, let me know and I'll work on this. I would like to get this PR in soon so that I can start preparing that SoftwareX paper.

- benchmark pressurized fracture added - fatigue benchmark problem added - documentation files added hugary1995#98 - tutorial example for hydraulic fracturing is ready

hugary1995 · 2021-10-13T10:23:40Z

Hey Roozbeh, are you sure the gold file in your tutorial is correct? I ran the test but it is giving me diff.

tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: ERROR: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    *****************************************************************
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               EXODIFF	(Version: 2.90) Modified: 2018-02-15
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               Authors:  Richard Drake, rrdrake@sandia.gov           
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:                         Greg Sjaardema, gdsjaar@sandia.gov          
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               Run on    2021/10/13   18:21:58 CST
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    *****************************************************************
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Reading first file ... 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Reading second file ... 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:   FILE 1: /home/gary/projects/raccoon/tutorials/hydraulic_fracturing_SPF/gold/results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    Title: results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Dim = 2, Blocks = 1, Nodes = 1681, Elements = 1600, Nodesets = 4, Sidesets = 4
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Vars: Global = 4, Nodal = 5, Element = 29, Nodeset = 0, Sideset = 0, Times = 2
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:   FILE 2: /home/gary/projects/raccoon/tutorials/hydraulic_fracturing_SPF/results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    Title: results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Dim = 2, Blocks = 1, Nodes = 441, Elements = 400, Nodesets = 4, Sidesets = 4
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Vars: Global = 4, Nodal = 5, Element = 29, Nodeset = 0, Sideset = 0, Times = 2
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: ERROR: .. Number of nodes doesn't agree.
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: ERROR: .. Number of elements doesn't agree.
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: Files are different
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:  
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: ################################################################################
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Tester failed, reason: EXODIFF
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture ............................ [FINISHED] FAILED (EXODIFF)

rrezakhani · 2021-10-13T14:29:22Z

Hey Roozbeh, are you sure the gold file in your tutorial is correct? I ran the test but it is giving me diff.

tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: ERROR: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    *****************************************************************
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               EXODIFF	(Version: 2.90) Modified: 2018-02-15
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               Authors:  Richard Drake, rrdrake@sandia.gov           
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:                         Greg Sjaardema, gdsjaar@sandia.gov          
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:               Run on    2021/10/13   18:21:58 CST
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    *****************************************************************
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Reading first file ... 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Reading second file ... 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:   FILE 1: /home/gary/projects/raccoon/tutorials/hydraulic_fracturing_SPF/gold/results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    Title: results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Dim = 2, Blocks = 1, Nodes = 1681, Elements = 1600, Nodesets = 4, Sidesets = 4
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Vars: Global = 4, Nodal = 5, Element = 29, Nodeset = 0, Sideset = 0, Times = 2
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:   FILE 2: /home/gary/projects/raccoon/tutorials/hydraulic_fracturing_SPF/results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:    Title: results.e
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Dim = 2, Blocks = 1, Nodes = 441, Elements = 400, Nodesets = 4, Sidesets = 4
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:           Vars: Global = 4, Nodal = 5, Element = 29, Nodeset = 0, Sideset = 0, Times = 2
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: ERROR: .. Number of nodes doesn't agree.
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: ERROR: .. Number of elements doesn't agree.
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: exodiff: Files are different
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture:  
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: ################################################################################
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: Tester failed, reason: EXODIFF
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture: 
tutorials/hydraulic_fracturing_SPF.hydraulic_fracture ............................ [FINISHED] FAILED (EXODIFF)

Sorry my bad, it is fixed. It passes the test here.

hugary1995 · 2021-10-14T11:34:25Z

The ADPorousFlowTimederivative kernel isn't used anywhere.

hugary1995 · 2021-10-16T00:54:57Z

  [biot_coefficient]
    type = ADDerivativeParsedMaterial
    f_name = alpha
    material_property_names = 'alpha0'
    args = 'd'
    function = 'alpha0'
    derivative_order = 1
  []

Just wanted to make sure this is what you meant: is your biot coefficient always the same as the intact biot coefficient?

hugary1995 · 2021-10-16T00:57:07Z

doc/content/source/kernels/ADPorousFlowTimeDerivative.md

@@ -0,0 +1,11 @@
+# ADPorousFlowTimeDerivative


This object isn't being used anywhere.

hugary1995 · 2021-10-16T00:57:37Z

doc/content/source/materials/ADComputePorosity.md

@@ -0,0 +1,20 @@
+# ADComputePorosity


This object isn't being used anywhere.

hugary1995 · 2021-10-16T00:59:41Z

include/diracKernel/DiracSource.h

@@ -0,0 +1,42 @@
+//* This file is part of the RACCOON application


This object isn't being used anywhere.

hugary1995 · 2021-10-16T00:59:58Z

include/ics/PhasefieldShapes.h

@@ -0,0 +1,28 @@
+//* This file is part of the RACCOON application


This object isn't being used anywhere.

hugary1995 · 2021-10-16T01:11:29Z

I think I've made most of the changes I want. Just two more questions:

Do you still need the four classes I mentioned above that aren't being used anywhere? If you need them, we'll have to think of test cases for them. Otherwise, I'll remove them.
It seems that you've removed all the fatigue stuff. Did you hand them over to Yuanchen? Or do you want to make them into another PR?

rrezakhani · 2021-10-19T15:03:25Z

I think I've made most of the changes I want. Just two more questions:

Do you still need the four classes I mentioned above that aren't being used anywhere? If you need them, we'll have to think of test cases for them. Otherwise, I'll remove them.

It seems that you've removed all the fatigue stuff. Did you hand them over to Yuanchen? Or do you want to make them into another PR?

Those classes are used for two-phase flow simulations. I wanted to add them in the next pull request. I missed to remove those classes. Please remove them from this pull request.
I wanted to add fatigue to next pull request as well, but I can actually do it for this one. I will add that with the relevant test and tutorial today.

rrezakhani · 2021-10-28T02:51:16Z

Gary, I removed those unnecessary source files and tried to push, but it says there are things that have been done on github:
To github.com:rrezakhani/raccoon.git
! [rejected] RRmain -> RRmain (fetch first)
error: failed to push some refs to 'git@github.com:rrezakhani/raccoon.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Have you done some modifications?

rrezakhani · 2021-10-28T02:52:41Z

  [biot_coefficient]
    type = ADDerivativeParsedMaterial
    f_name = alpha
    material_property_names = 'alpha0'
    args = 'd'
    function = 'alpha0'
    derivative_order = 1
  []

Just wanted to make sure this is what you meant: is your biot coefficient always the same as the intact biot coefficient?

In this specific simulation, biot coefficient is not changing. But it can be a function of damage in general. So I decided to keep this format. We can define a simple parameter for this specific example if you want.

rrezakhani · 2021-10-28T02:53:21Z

Gary, I will add fatigue and multiphase flow files in the next PR. Let's finalize this one.

hugary1995 · 2021-11-09T10:07:04Z

Gary, I removed those unnecessary source files and tried to push, but it says there are things that have been done on github: To github.com:rrezakhani/raccoon.git ! [rejected] RRmain -> RRmain (fetch first) error: failed to push some refs to 'git@github.com:rrezakhani/raccoon.git' hint: Updates were rejected because the remote contains work that you do hint: not have locally. This is usually caused by another repository pushing hint: to the same ref. You may want to first integrate the remote changes hint: (e.g., 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Have you done some modifications?

Yes, I have made several modifications. Can you do a git fetch then rebase your work on top of the remote head?

hugary1995 · 2021-11-09T10:07:40Z

Sorry for the late reply -- I was taking vacation for the last two weeks.

hugary1995 · 2021-11-09T10:10:06Z

I suspect that you may encounter several conflicts when trying to do the rebase. If you want we can meet via zoom and look at it together.

rrezakhani force-pushed the RRmain branch 2 times, most recently from 8e07ff8 to db2f5b0 Compare July 29, 2021 22:46

hugary1995 requested changes Jul 29, 2021

View reviewed changes

hugary1995 requested changes Jul 30, 2021

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hugary1995 reviewed Aug 1, 2021

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Fatigue, porous flow, multi-phase flow, and more

9d15280

- benchmark pressurized fracture added - fatigue benchmark problem added - documentation files added hugary1995#98 - tutorial example for hydraulic fracturing is ready

hugary1995 force-pushed the RRmain branch from 70faa17 to 9d15280 Compare October 13, 2021 10:05

hugary1995 changed the base branch from master to devel October 13, 2021 10:07

hugary1995 added 2 commits October 13, 2021 18:08

Remove soil desiccation

163cef1

remove run.sh

0a59f1f

hugary1995 added 5 commits October 15, 2021 07:40

Edit ADAnisotropicDiffusion

c6d7dcc

Edit several kernels

91bc2fd

Fix tutorial regression test

47f6395

Edit(rename) ADComputeCrackOpening

8b79d30

AD/regular bug

62c9841

hugary1995 added 2 commits October 16, 2021 08:55

Renamed a bunch of parameters

3beee99

Remove DegradationBase, remove test.i

a3ae6f6

hugary1995 requested changes Oct 16, 2021

View reviewed changes

Clang-format

43fc0cb

clang-format DiracSource.h

d3766fc

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request from RR main #78

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		@@ -0,0 +1,42 @@
		//* This file is part of the RACCOON application

		@@ -0,0 +1,28 @@
		//* This file is part of the RACCOON application

request from RR main #78

Are you sure you want to change the base?

request from RR main #78

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