Update AD code structure

[ewu63]

Purpose

I updated the entire AD code structure:

• created a new adjoint directory where AD-related code is located in
• updated Tapenade build process by creating a temporary directory for pre-processed files, such that they are no longer located in the original directory. This fixes some weird <something>.F90_b.f90 filename issue with 3.16.

Type of change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (non-backwards-compatible fix or feature)
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no API changes)
• Documentation update
• Maintenance update
• Other (please describe)

Testing

This PR just changes the AD build process. Existing tests should pass.

Checklist

• I have run flake8 and black to make sure the code adheres to PEP-8 and is consistently formatted
• I have run unit and regression tests which pass locally with my changes
• I have added new tests that prove my fix is effective or that my feature works
• I have added necessary documentation

[codecov]

Codecov Report

Merging #62 (35b5b2b) into master (055874b) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #62   +/-   ##
=======================================
  Coverage   45.80%   45.80%           
=======================================
  Files           6        6           
  Lines         751      751           
=======================================
  Hits          344      344           
  Misses        407      407           

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[bernardopacini]

I left two broader comments about the PR. I think the changes are fine, but since we are refactoring things now it may be worth making these small changes too while we are here.

Since I worked with you (@nwu63) on this, we should have at least one more person who knows about Tapenade review this.

[anilyil]

The changes look good, but then again, I am no expert on any of the files that have changes. My only broad comment would be to be careful about a possible parallel make. I am not sure if tapenade makefiles even do that, but just something that can cause race conditions with the addition and removal of temp files. If what I am saying is completely unrelated, then this PR is probably good to go for me.

[bernardopacini]

The changes look good, but then again, I am no expert on any of the files that have changes. My only broad comment would be to be careful about a possible parallel make. I am not sure if tapenade makefiles even do that, but just something that can cause race conditions with the addition and removal of temp files. If what I am saying is completely unrelated, then this PR is probably good to go for me.

As far as I know, Tapenade does not support that kind of parallelism and we do not use it anywhere even if it does. I don't think we have to worry about this, Tapenade handles IO itself and our preprocessing is serial in the makefile. Tapenade is realistically pretty quick so I think that we should avoid parallelism in the future even if it does exist -- not worth the extra effort. If Tapenade is parallel within the executable that's fine, it shouldn't change anything for our makefile.

[anilyil]

Okay, then it looks good on my end. We need 2 approvals to merge I think.