Add support for kpp format #497

rs028 · 2023-05-17T11:35:46Z

This will let the model use chemical mechanisms in KPP format (issue #304).

Also includes minor and cosmetic changes to the Python scripts in build/ and tools/ (checked using pylint) and to some bash scripts.

This also changes the version number back to development towards the 1.3 release (1.3-dev).

codecov · 2023-05-17T11:38:20Z

Codecov Report

Merging #497 (25cd946) into master (457b3e4) will not change coverage.
Report is 2 commits behind head on master.
The diff coverage is 100.00%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #497   +/-   ##
=======================================
  Coverage   66.66%   66.66%           
=======================================
  Files          17       17           
  Lines        2049     2049           
=======================================
  Hits         1366     1366           
  Misses        683      683

Flag	Coverage Δ
build	`52.70% <100.00%> (ø)`
tests	`66.83% <100.00%> (ø)`
unittests	`54.78% <100.00%> (ø)`

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Files Changed	Coverage Δ
src/atchem2.f90	`87.68% <100.00%> (ø)`

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rs028 · 2023-08-10T12:19:09Z

tools/fix_indent.py

-                  or re.match('^\s*select\s*', to_output, flags=re.IGNORECASE) \
-                  or re.match('^\s*case\s*', to_output, flags=re.IGNORECASE) \
-                  or re.match('^\s*type\s+', to_output, flags=re.IGNORECASE):
+                if re.search(r'\s*if.+then', to_output, flags=re.IGNORECASE) \


I changed this because the fix_style.py script changes IF-THEN-ELSE to lowercase, but it shouldn't make a difference given the IGNORECASE flag.

Makes sense

rs028 · 2023-08-10T12:33:38Z

build/mech_converter.py

+    # at the top of mechanism.f90 for each errant species.
+    #
+    # TODO: This will break the expected format when mechanism.f90 is
+    #       replaced by a parsable format


This TODO comment was added with PR #347. I think it refers to the implementation of the function parser which then was abandoned in favor of the shared .so file (?)
If so, it's probably not something "to do" anymore?

I think so - fine to delete.

codecov · 2023-09-14T13:23:36Z

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (4373dc9) 52.00% compared to head (7d1fdc1) 52.05%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #497      +/-   ##
==========================================
+ Coverage   52.00%   52.05%   +0.04%     
==========================================
  Files          17       17              
  Lines        2096     2096              
  Branches      166      166              
==========================================
+ Hits         1090     1091       +1     
+ Misses        934      933       -1     
  Partials       72       72

Files	Coverage Δ
src/atchem2.f90	`78.53% <100.00%> (ø)`

... and 1 file with indirect coverage changes

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rs028 · 2023-09-26T12:51:51Z

The procedure involves a new script kpp_conversion.py which converts the mechanism in KPP format to a .fac file, which is then processed as usual. Possibly not the most efficient way to do it, but the easiest to implement.

This only works for the KPP files created by the MCM website. There is a large variability in the possible format of kpp files so it is hard to do better without specific examples.

Two new tests are also added to verify that the conversion is correct: a reference test with a normal fac mechanism and an identical (ie using same config) test using a kpp mechanism. They give the same results.

spco · 2023-11-07T21:32:24Z

tools/fix_indent.py

-                  or re.match('^\s*select\s*', to_output, flags=re.IGNORECASE) \
-                  or re.match('^\s*case\s*', to_output, flags=re.IGNORECASE) \
-                  or re.match('^\s*type\s+', to_output, flags=re.IGNORECASE):
+                if re.search(r'\s*if.+then', to_output, flags=re.IGNORECASE) \


Makes sense

spco · 2023-11-07T21:55:32Z

build/mech_converter.py

+    # at the top of mechanism.f90 for each errant species.
+    #
+    # TODO: This will break the expected format when mechanism.f90 is
+    #       replaced by a parsable format


I think so - fine to delete.

spco · 2023-11-07T22:00:10Z

I think this all makes sense. On formatting and style, I have thoughts we should use existing external tools rather than rolling our own if possible - will create a separate issue.

rs028 · 2023-11-10T02:36:05Z

@spco thanks a lot!

rs028 commented Aug 10, 2023

View reviewed changes

rs028 added 14 commits September 13, 2023 09:58

Set up to support KPP formats

87412d5

Tidy build py scripts

78d3690

Rename some variables for clarity

989ed41

Tidy build scripts

8c4c3d6

Further tidying

7216a79

Remove logfile printout

db3c397

Reset version number to dev status

ee061d0

Tidy mech_converter.py script

1b2f9bf

Cosmetic changes to sh scripts

16af6b3

Check python scripts with pylint

4e22272

Check with pylint; move kpp conversion

9633e63

Skeleton convert_kpp.py and other small fixes

015774c

Functional conversion script

89e0d57

Amend mcm/ and .fac info

cf3e601

rs028 force-pushed the add_kpp_format branch from 25cd946 to cf3e601 Compare September 13, 2023 10:14

Tidy comments py scripts

61c8289

rs028 added 5 commits September 22, 2023 12:55

Links for the badges

004cebd

Call kpp cpnversion script froom mech_converter

151588e

Set path of the kpp file

4911676

Model test for the KPP conversion

ba7381e

cmp files for the new model tests

5c59051

rs028 requested a review from spco September 26, 2023 12:52

rs028 added 3 commits September 26, 2023 13:52

Remove extra fac file

e60558b

Fix compilation of model in kpp test

dbca873

Upload coverage only if tests are run

635966c

Compile manual

7d1fdc1

spco approved these changes Nov 7, 2023

View reviewed changes

spco mentioned this pull request Nov 7, 2023

Use external tools for formatting and style #509

Open

rs028 merged commit d3ce21b into AtChem:master Nov 10, 2023

rs028 deleted the add_kpp_format branch November 10, 2023 02:36

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Add support for kpp format #497

Add support for kpp format #497

rs028 commented May 17, 2023 •

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rs028 Aug 10, 2023 •

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spco Nov 7, 2023

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rs028 commented Sep 26, 2023

spco Nov 7, 2023

spco Nov 7, 2023

spco commented Nov 7, 2023

rs028 commented Nov 10, 2023

Add support for kpp format #497

Add support for kpp format #497

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