Add hard coded patched for tests

[danieljvickers]

User description

Description

The primary intent of this PR is to remove hardcoded patches from the test suite, preventing the need to recompile them and saving time during testing. In doing so, I also refactored the geometries because we had no existing support for creating hard-coded patches on any geometries other than line segments, rectangles, and cuboids. Now we can generate hard-coded patches on almost any geometries except for the airfoil geometries (I left a TODO about this) and the model (STL) geometry (this will require it's own dedicated refactor). I also changed every test that used analytic patches to use new hard coded patches, added comments to some code in the toolchain, and updated the docs to note that the old analytic geometry patches are deprecated. I left a print statement warning that those geometries are deprecated, and we should delete them after some time. For now, I had then call subroutines that recreated their original functionality.

TODO :: After this PR, we should go back and add the analytic patches as examples that will be skipped so that they are present for external reference.

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)
• Something else

Scope

• This PR comprises a set of related changes with a common goal

If you cannot check the above box, please split your PR into multiple PRs that each have a common goal.

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

• This was tested on the full test suite. (./mfc.sh test -j $(nproc))

Test Configuration:

All of my testing was done locally on Ubuntu with the intel and non-intel compilers.

Checklist

• I have added comments for the new code
• I added Doxygen docstrings to the new code
• I have made corresponding changes to the documentation (docs/)
• I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
• I have added example cases in examples/ that demonstrate my new feature performing as expected.
  They run to completion and demonstrate "interesting physics"
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

If your code changes any code source files (anything in src/simulation)

To make sure the code is performing as expected on GPU devices, I have:

• Checked that the code compiles using NVHPC compilers
• Checked that the code compiles using CRAY compilers
• Ran the code on either V100, A100, or H100 GPUs and ensured the new feature performed as expected (the GPU results match the CPU results)
• Ran the code on MI200+ GPUs and ensure the new features performed as expected (the GPU results match the CPU results)
• Enclosed the new feature via nvtx ranges so that they can be identified in profiles
• Ran a Nsight Systems profile using ./mfc.sh run XXXX --gpu -t simulation --nsys, and have attached the output file (.nsys-rep) and plain text results to this PR
• Ran a Rocprof Systems profile using ./mfc.sh run XXXX --gpu -t simulation --rsys --hip-trace, and have attached the output file and plain text results to this PR.
• Ran my code using various numbers of different GPUs (1, 2, and 8, for example) in parallel and made sure that the results scale similarly to what happens if you run without the new code/feature

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PR Type

Enhancement, Tests

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Description

• Replace analytical patches with hardcoded patches for test optimization

• Add hardcoded patch support to all geometry types

• Deprecate old analytical patch geometries (7, 13, 15)

• Update test cases to use new hardcoded patch system

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Changes diagram

flowchart LR
  A["Analytical Patches"] --> B["Hardcoded Patches"]
  B --> C["Test Cases Updated"]
  B --> D["Geometry Support Added"]
  E["Old Geometries"] --> F["Deprecated"]

Loading

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Changes walkthrough 📝

	Relevant files
Enhancement	4 files 1dHardcodedIC.fpp Add 1D hardcoded patch cases 180-181                                          +12/-1    2dHardcodedIC.fpp Add 2D hardcoded patch cases 280-282                                          +32/-1    3dHardcodedIC.fpp Add 3D hardcoded patch case 380                                                    +10/-0    m_patches.fpp Integrate hardcoded patches into geometry functions            +115/-183
Tests	11 files case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 180                            +2/-1      case.py Replace analytical with hardcoded patch 181                            +2/-1      case.py Replace analytical with hardcoded patch 281                            +3/-2      case.py Replace analytical with hardcoded patch 280                            +5/-4      case.py Replace analytical with hardcoded patch 282                            +5/-4      case.py Replace analytical with hardcoded patch 380                            +4/-3
Documentation	2 files case.py Add comments to analytical patch generation                            +13/-1    case.md Update patch documentation and deprecation notes                  +7/-6
Configuration changes	1 files intel.yml Add Intel compiler CI workflow                                                      +32/-0

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⚡ Recommended focus areas for review Debug Statement A debug print statement was left in the code that will output to console during execution. This should be removed before merging to production. print *, "DEBUG: patch_id=", patch_id, " hcid=", patch_icpp(patch_id)%hcid Code Duplication The hardcoded patch implementations contain very similar mathematical expressions with hardcoded constants. Consider extracting common patterns or using parameterized functions to reduce duplication and improve maintainability. case (280) ! This is patch is hard-coded for test suite optimization used in the ! 2D_isentropicvortex case: ! This analytic patch uses geometry 2 if (patch_id == 1) then q_prim_vf(E_idx)%sf(i, j, 0) = 1d0*(1d0 - (1d0/1d0)*(5d0/(2d0*3.141592653589793))*(5d0/(8d0*1d0*(1.4 + 1d0)*3.141592653589793))*exp(2d0*1d0*(1d0 - (x_cc(i) - patch_icpp(1)%x_centroid)**2d0 - (y_cc(j) - patch_icpp(1)%y_centroid)**2d0)))**(1.4 + 1d0) q_prim_vf(contxb + 0)%sf(i, j, 0) = 1d0*(1d0 - (1d0/1d0)*(5d0/(2d0*3.141592653589793))*(5d0/(8d0*1d0*(1.4 + 1d0)*3.141592653589793))*exp(2d0*1d0*(1d0 - (x_cc(i) - patch_icpp(1)%x_centroid)**2d0 - (y_cc(j) - patch_icpp(1)%y_centroid)**2d0)))**1.4 q_prim_vf(momxb + 0)%sf(i, j, 0) = 0d0 + (y_cc(j) - patch_icpp(1)%y_centroid)*(5d0/(2d0*3.141592653589793))*exp(1d0*(1d0 - (x_cc(i) - patch_icpp(1)%x_centroid)**2d0 - (y_cc(j) - patch_icpp(1)%y_centroid)**2d0)) q_prim_vf(momxb + 1)%sf(i, j, 0) = 0d0 - (x_cc(i) - patch_icpp(1)%x_centroid)*(5d0/(2d0*3.141592653589793))*exp(1d0*(1d0 - (x_cc(i) - patch_icpp(1)%x_centroid)**2d0 - (y_cc(j) - patch_icpp(1)%y_centroid)**2d0)) end if case (281) ! This is patch is hard-coded for test suite optimization used in the ! 2D_acoustic_pulse case: ! This analytic patch uses geometry 2 if (patch_id == 2) then q_prim_vf(E_idx)%sf(i, j, 0) = 101325*(1 - 0.5*(1.4 - 1)*(0.4)**2*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))))**(1.4/(1.4 - 1)) q_prim_vf(contxb + 0)%sf(i, j, 0) = 1*(1 - 0.5*(1.4 - 1)*(0.4)**2*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))))**(1/(1.4 - 1)) end if case (282) ! This is patch is hard-coded for test suite optimization used in the ! 2D_zero_circ_vortex case: ! This analytic patch uses geometry 2 if (patch_id == 2) then q_prim_vf(E_idx)%sf(i, j, 0) = 101325*(1 - 0.5*(1.4 - 1)*(0.1/0.3)**2*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))))**(1.4/(1.4 - 1)) q_prim_vf(contxb + 0)%sf(i, j, 0) = 1*(1 - 0.5*(1.4 - 1)*(0.1/0.3)**2*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))))**(1/(1.4 - 1)) q_prim_vf(momxb + 0)%sf(i, j, 0) = 112.99092883944267*(1 - (0.1/0.3))*y_cc(j)*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))) q_prim_vf(momxb + 1)%sf(i, j, 0) = 112.99092883944267*((0.1/0.3))*x_cc(i)*exp(0.5*(1 - sqrt(x_cc(i)**2 + y_cc(j)**2))) end if Possible Issue Variable assignments like j = 0.0_wp and k = 0.0_wp are assigning floating point values to integer variables, which may cause compilation errors or unexpected behavior. j = 0.0_wp k = 0.0_wp

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	✅ Remove debug print statement Suggestion Impact: The debug print statement was removed from line 5 of the diff, exactly as suggested code diff: - print *, "DEBUG: patch_id=", patch_id, " hcid=", patch_icpp(patch_id)%hcid Remove debug print statement from production code. Debug output should not be included in the final codebase as it can clutter logs and impact performance. src/pre_process/include/2dHardcodedIC.fpp [12] -print *, "DEBUG: patch_id=", patch_id, " hcid=", patch_icpp(patch_id)%hcid +! Debug print removed Suggestion importance[1-10]: 5 __ Why: The suggestion correctly identifies a debug print statement that should be removed from the final code to avoid cluttering logs and potential performance impacts.	Low
Update

[codecov]

Codecov Report

Attention: Patch coverage is 11.11111% with 64 lines in your changes missing coverage. Please review.

Project coverage is 44.07%. Comparing base (293557c) to head (03622a1).

Files with missing lines	Patch %	Lines
src/pre_process/m_patches.fpp	11.59%	47 Missing and 14 partials ⚠️
src/pre_process/m_check_patches.fpp	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #942      +/-   ##
==========================================
+ Coverage   43.76%   44.07%   +0.30%     
==========================================
  Files          68       68              
  Lines       18378    18227     -151     
  Branches     2292     2289       -3     
==========================================
- Hits         8044     8033      -11     
+ Misses       8945     8829     -116     
+ Partials     1389     1365      -24     

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[sbryngelson]

added several comments. also, some of these hardcoded examples are important. it would be useful to somehow check that you didn't break the case when you switched from analytical to hardcoded.

also probably won't merge this until analytical examples are added (but skipped in the test suite). Presumably, we only need a few of these.