(Atomic) Boundary Condition Patches (pt. 1/2)

[henryleberre]

This part (pt. 1)

• Removes (net) ~4k LOC by abstracting the iteration over the buffer region and making more code common between the three MFC targets.
• Adds (opt-in) "Boundary Condition Patches" (cuboid & spheroid).
• Adds --dry-run to testing so that CI can build all necessary versions of MFC before submitting jobs for testing to a queue system.
• Fixes an IBM method bug for slip-walls (credit @anshgupta1234).
• Fixes a CheMFC bug that prevented the use of analytically defined patches.

Checklist for getting out of the "draft" stage

• Check GPU performance.
• Verify the boundary patches still work with any number of ranks.
• Support parallel_io=T.
• Add spheroid boundary patch code back.
• Fix the three test cases that fail (some variations of cylindrical coordinates).
• Documentation.

Next part (pt. 2)

• All edge cases addressed. That is, bc_[x,y,z] should no longer be used anywhere in the code. One example of such an oversight in pt. 1 is the lack of support for CBCs.

Why two parts?

> 8k LOC changes is a lot to carry around in one atomic commit.

[sbryngelson]

@henryleberre GCBCs from @anandrdbz have been merged #698

[sbryngelson]

Removes (net) ~4k LOC by abstracting the iteration over the buffer region and making more code common between the three MFC targets.

A true beauty.

[sbryngelson]

Add to test suite 2D and 3D tests that have square and circle patches on at least one side.

[codecov]

Codecov Report

Attention: Patch coverage is 56.44444% with 196 lines in your changes missing coverage. Please review.

Project coverage is 44.37%. Comparing base (d1b8028) to head (7912215).

Files with missing lines	Patch %	Lines
src/common/m_mpi_common.fpp	53.23%	71 Missing and 23 partials ⚠️
src/common/m_boundary_conditions_common.fpp	68.96%	21 Missing and 6 partials ⚠️
src/simulation/m_mpi_proxy.fpp	40.90%	23 Missing and 3 partials ⚠️
src/simulation/m_cbc.fpp	41.66%	8 Missing and 6 partials ⚠️
src/common/m_helper.fpp	22.22%	7 Missing ⚠️
src/simulation/m_start_up.fpp	62.50%	6 Missing ⚠️
src/common/m_checker_common.fpp	16.66%	5 Missing ⚠️
src/simulation/m_viscous.fpp	0.00%	2 Missing and 2 partials ⚠️
src/post_process/m_data_input.fpp	40.00%	3 Missing ⚠️
src/simulation/m_ibm.fpp	25.00%	3 Missing ⚠️
... and 5 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #737      +/-   ##
==========================================
+ Coverage   43.63%   44.37%   +0.73%     
==========================================
  Files          61       63       +2     
  Lines       16893    15320    -1573     
  Branches     1948     1798     -150     
==========================================
- Hits         7372     6798     -574     
+ Misses       8404     7469     -935     
+ Partials     1117     1053      -64     

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