Doxygen marked source - PR3

[MatthewMasarik-NOAA]

Pull Request Summary

Collection of doxygen marked files.

Description

The following list of files has been marked with doxygen tags for documentation:

• mod_xnl4v5.f90
• mod_fileio.f90
• mod_constants.f90
• constants.F90
• w3src2md.F90
• w3src1md.F90
• w3src0md.F90
• w3swldmd.F90
• w3uno2md.F90
• w3uqckmd.F90
• w3wavemd.F90
• w3wavset.F90
• w3wdatmd.F90
• w3wdasmd.F90
• w3str2md.F90
• w3str1md.F90

Is a change of answers expected from this PR?
No. Documentation only added. However, there is one small change described below.

Please also include the following information:

• Mention any labels that should be added: documentation.
• Are answer changes expected from this PR? No.

Issue(s) addressed

• addresses, though does not close Add doxygen marked-down source #586

Commit Message

Doxygen documentation - marked source PR 3
Co-author: @JessicaMeixner-NOAA

Check list

• Branch is up to date with the authoritative repository (NOAA-EMC) develop branch.
• Checked the checklist for a developer submitting to develop.
• If a version number update is required, checked the updating version number checklist.
• If a new feature was added, a regression test for testing the new feature is added.

Testing

• How were these changes tested?

  • By running the matrix of regression tests against develop.
  • Running doxygen for the new files and removing all errors and warnings for the additions (this is true with the exception of two warnings related to an #ifdef block. The block toggles optional input to a subroutine call in w3wavemd.F90 and may be difficult to remove entirely.)
  • Checking HTTP output for formatting and correctness of all files added with mark-up.

• Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
  No. The changes are only documentation. Documentation is not tested.

• Have the matrix regression tests been run (if yes, please note HPC and compiler)?
  Yes. Hera / Intel.

• Please indicate the expected changes in the regression test output, (Note the list of known non-identical tests.)
  No expected changes except for the known non-identical tests and unstructured grid mod_defs. That said, there is one change to a text log file mentioned below.

• Please provide the summary output of matrix.comp (matrix.Diff.txt, matrixCompFull.txt and matrixCompSummary.txt):

  Note: the file OUTPUT_TOY.txt in the test ww3_tp2.14/./work_OASICM below differs by one line of text, APPLE partitioning. The repo under review contains this line as shown in the screenshot below, whereas the same file in the develop branch does not have it at this location. Both files do have the same line appearing lower down in the file. This is the third time matrix has been run, and each time the same result.

**********************************************************************
********************* non-identical cases ****************************
**********************************************************************
mww3_test_03/./work_PR2_UNO_MPI_d2                     (12 files differ)
mww3_test_03/./work_PR1_MPI_d2                     (17 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2_c                     (15 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2_c                     (15 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2                     (14 files differ)
mww3_test_03/./work_PR2_UQ_MPI_d2                     (15 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2                     (15 files differ)
ww3_ta1/./work_UPD0F_U                     (0 files differ)
ww3_tp2.10/./work_MPI_OMPH                     (7 files differ)
ww3_tp2.14/./work_OASICM                     (1 files differ)
ww3_tp2.16/./work_MPI_OMPH                     (4 files differ)
ww3_tp2.17/./work_a                     (1 files differ)
ww3_tp2.17/./work_c                     (1 files differ)
ww3_tp2.17/./work_b                     (1 files differ)
ww3_tp2.6/./work_ST0                     (1 files differ)
ww3_tp2.6/./work_ST4                     (1 files differ)
ww3_tp2.6/./work_pdlib                     (1 files differ)
ww3_ufs1.3/./work_a                     (1 files differ)
 
**********************************************************************
************************ identical cases *****************************
**********************************************************************

matrixDiff.txt
matrixCompSummary.txt
matrixCompFull.txt

new.OUTPUT_TOY.txt
dev.OUTPUT_TOY.txt

[aliabdolali]

@ukmo-ccbunney @mickaelaccensi We are seeing differences in the file OUTPUT_TOY.txt in test ww3_tp2.14/./work_OASICM below differs by one line of text, APPLE partitioning. Could you take a look and let us know if you know why it happens? This PR is for deoxygenizing the modules and routines.

[aliabdolali]

I ran the regtests twice and did not encounter the same issue @MatthewMasarik-NOAA have seen, so I approve this PR and proceed with the merge.
List of pre-know non-identical cases:

**********************************************************************
********************* non-identical cases ****************************
**********************************************************************
mww3_test_03/./work_PR2_UQ_MPI_d2                     (12 files differ)
mww3_test_03/./work_PR2_UNO_MPI_d2                     (15 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2_c                     (15 files differ)
mww3_test_03/./work_PR1_MPI_d2                     (17 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2_c                     (15 files differ)
mww3_test_03/./work_PR3_UNO_MPI_d2                     (17 files differ)
mww3_test_03/./work_PR3_UQ_MPI_d2                     (15 files differ)
ww3_tp2.10/./work_MPI_OMPH                     (7 files differ)
ww3_tp2.16/./work_MPI_OMPH                     (4 files differ)
ww3_tp2.6/./work_ST4                     (1 files differ)
ww3_tp2.6/./work_ST0                     (1 files differ)
ww3_ufs1.3/./work_a                     (1 files differ)

matrixCompFull.txt
matrixCompSummary.txt
matrixDiff.txt