Phase-field model for fracture using MPI and AMR

[WasimNiyazMunshi]

This pull request adds a phase-field solver for fracture to the code gallery. The fracture model uses the MPI and Adaptive Mesh Refinement (AMR) capabilities of deal.II to solve large scale problems in 3D.

[bangerth]

@WasimNiyazMunshi is a visiting student in my lab, and I've contributed to this program. I would appreciate if someone else would handle this PR!

[marcfehling]

Nice work. The code looks fine! I did not check the formulas in the code, as they overstep my expertise. According to your manuscript, you validated your code against literature data, which suffices for me.

The following two points are more suggestions than requirements for being merged. Please apply according to your own assessment :)

• If you'd like, you can run a code indentation tool like clang-format over your source file, which further improves readability.
• If you are feeling fancy: Consider collecting all parameters in a parameter class or multiple classes, and use the ParameterHandler.

[blaisb]

Just a few comments there and there. Very cool work!

[WasimNiyazMunshi]

@blaisb, @Rombur and @marcfehling.
Thank you all for taking the time to review my code. I have worked on addressing most of your comments and suggestions. The only pending items are the two blocks of commented-out code that @marcfehling suggested removing. May I kindly request you to review the code once more, so we can proceed with adding it to the code gallery soon? :-)
Best regards
Wasim

[bangerth]

As for the commented-out code blocks: @WasimNiyazMunshi suggests to leave them in there because many benchmarks are described with traction boundary conditions rather than displacements, and the commented out code is what you will need if you want to use the code for a traction-based modification. That seems reasonable to me.

[WasimNiyazMunshi]

Yes. Also, the other block of commented out code is used to describe any pre-existing cracks. This is very common in most of the benchmark problems in fracture, so I suggest to keep that as well.

…

On Sun, 15 Dec, 2024, 16:44 Wolfgang Bangerth, ***@***.***> wrote: As for the commented-out code blocks: @WasimNiyazMunshi <https://github.com/WasimNiyazMunshi> suggests to leave them in there because many benchmarks are described with traction boundary conditions rather than displacements, and the commented out code is what you will need if you want to use the code for a traction-based modification. That seems reasonable to me. — Reply to this email directly, view it on GitHub <#203 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLC5F7EQ5LVU43GAL5AR3GT2FYH55AVCNFSM6AAAAABQCLWRZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBUGE4TCNBVGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[marcfehling]

The only pending items are the two blocks of commented-out code that @marcfehling suggested removing.

I'm fine with leaving the commented blocks of code in the patch. The comments you placed in front of the code blocks are helpful for context.

[marcfehling]

You now have a name conflict: The name PF was already used in petsc. Your namespace PF only contains the PhaseField class -- I would suggest to remove your namespace. @WasimNiyazMunshi @bangerth -- What do you think?

[ 50%] Building CXX object CMakeFiles/phase_field.dir/phase_field.cc.o
/__w/code-gallery/code-gallery/Phase_field_fracture_model_in_3D/phase_field.cc:60:11: error: ‘namespace PF { }’ redeclared as different kind of entity
   60 | namespace PF
      |           ^~
In file included from /usr/include/petsc/petscdmda.h:6,
                 from /usr/include/petsc/petsc.h:14,
                 from /usr/local/include/deal.II/fe/fe_values.h:53,
                 from /__w/code-gallery/code-gallery/Phase_field_fracture_model_in_3D/phase_field.cc:40:
/usr/include/petsc/petscpf.h:36:23: note: previous declaration ‘typedef struct _p_PF* PF’
   36 | typedef struct _p_PF* PF;
      |                       ^~
/__w/code-gallery/code-gallery/Phase_field_fracture_model_in_3D/phase_field.cc: In function ‘int main(int, char**)’:
/__w/code-gallery/code-gallery/Phase_field_fracture_model_in_3D/phase_field.cc:1437:23: error: ‘PF’ is not a namespace-name
 1437 |       using namespace PF;
      |                       ^~
make[2]: *** [CMakeFiles/phase_field.dir/build.make:76: CMakeFiles/phase_field.dir/phase_field.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:90: CMakeFiles/phase_field.dir/all] Error 2
make: *** [Makefile:91: all] Error 2

[bangerth]

We use namespaces in all tutorial programs. Perhaps keep it the same here? Maybe just rename it to namespace FracturePropagation or some such?

[WasimNiyazMunshi]

I agree with you, Wolfgang. I'll make the necessary changes and rename the namespace. Thanks Wasim

…

On Wed, 8 Jan, 2025, 09:05 Wolfgang Bangerth, ***@***.***> wrote: We use namespaces in all tutorial programs. Perhaps keep it the same here? Maybe just rename it to namespace FracturePropagation or some such? — Reply to this email directly, view it on GitHub <#203 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLC5F7DDBSU2G6JK7HMVKRD2JVEDJAVCNFSM6AAAAABQCLWRZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNZYGA2DQNBZGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[WasimNiyazMunshi]

Dear All, It seems that the code has now been merged into the master. Thank you, everyone, for reviewing the code and providing your valuable feedback. Best regards Wasim

…

On Thu, 9 Jan, 2025, 07:23 Marc Fehling, ***@***.***> wrote: Merged #203 <#203> into master. — Reply to this email directly, view it on GitHub <#203 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLC5F7D77AACSH3WGIXCWVT2J2A55AVCNFSM6AAAAABQCLWRZWVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJVHA3DQNZUGUZDENY> . You are receiving this because you were mentioned.Message ID: ***@***.***>