cti2yaml: fix issues with composition strings and kinetics model of "None" #1127

ischoegl · 2021-10-22T16:20:04Z

Changes proposed in this pull request

Handle transport/kinetics models specified as None consistently
Allow for spaces in CTI composition definition (e.g. N2: 0.9 rather than N2:0.9)
Allow for specification of exact reaction id's

If applicable, fill in the issue number this pull request is fixing

Closes #1009

If applicable, provide an example illustrating new features this pull request is introducing

see conversion of Mayur-ISSP.cti atttached to #1009. The result after applying this fix is Mayur-ISSP.yaml.txt

Checklist

The pull request includes a clear description of this code change
Commit messages have short titles and reference relevant issues
Build passes (scons build & scons test) and unit tests address code coverage
Style & formatting of contributed code follows contributing guidelines
The pull request is ready for review

This change allows for composition specifications that include a whitespace after a separating colon (example: "N2: 0.9, O2: 0.1" rather than "N2:0.9, O2:0.1")

…cation

ischoegl · 2021-10-26T03:50:45Z

@speth / @bryanwweber ... I dropped the 'fix' for #1132 from here (per @speth's comment this will resolve itself).

speth

Thanks, @ischoegl. The first two changes look fine to me.

I'm not sure about the change to "allow for specification of exact reaction id's", though. If I'm reading this correctly, it only supports the case where a single reaction id is given (which I don't think is frequently used), correct? As currently implemented, this has the side-effect of obscuring the warning that was in place to let users know that cti2yaml does not support the range notation that CTI used (which I think was also rarely used).

speth · 2021-10-29T02:48:05Z

interfaces/cython/cantera/cti2yaml.py

-                        " files not supported ({}: {})".format(datasrc, rnum))
-            else:
-                _printerr("WARNING: Reaction specification"
-                          " '{}' not supported".format(rnum))


Changing this set of allowed reaction specifications to be permissive means that certain cases that we know are not handled, like n005 to n008 are passed through without raising a warning, and the resulting error when importing the mechanism is not easy to diagnose as it no longer mentions the unsupported user input.

If I'm reading this correctly, it only supports the case where a single reaction id is given

this is correct. I didn’t see a way around replacing the warnings as I had assumed that correct cti conversion was most important.

Could you be more specific about n005 to n008?

Actually, there's always the option to still produce a warning while leaving the same in place. ~~I added this as a separate commit, but can squash if necessary. As is, the conversion works, but produces a warning, i.e.~~

$ cti2yaml Mayur-ISSP.cti WARNING: Conversion of reaction specification 'rxn-SEI-comp' may not be supported

Edit: I ended up changing things, so this is obsolete

Take a look at some of the examples given here: https://cantera.org/tutorials/cti/phases.html#declaring-the-reactions

Admittedly, I've never seen this construct used in the wild, which is why I didn't worry about it for cti2yaml in the first place. But I've also the reaction selection used to pick just a single reaction, either.

@speth ... thanks! I think it's possible to add the conversion of n005 to n008 if it ever comes up. As it stands, the single reaction already came up, so I'd suggest to update the warning message and leave the import in place.

~~Edit: I added a separate error for anything containing to, and tweaked the warning message.~~

PS: found a better way by catching exceptions at a later point

codecov · 2021-10-29T04:11:24Z

Codecov Report

Merging #1127 (a37e3d0) into main (861377d) will increase coverage by 0.04%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1127      +/-   ##
==========================================
+ Coverage   73.45%   73.49%   +0.04%     
==========================================
  Files         365      365              
  Lines       47912    48187     +275     
==========================================
+ Hits        35194    35417     +223     
- Misses      12718    12770      +52

Impacted Files	Coverage Δ
src/oneD/IonFlow.cpp	`52.38% <0.00%> (-1.47%)`	⬇️
src/oneD/Boundary1D.cpp	`53.22% <0.00%> (-0.21%)`	⬇️
include/cantera/base/AnyMap.h	`100.00% <0.00%> (ø)`
include/cantera/oneD/OneDim.h	`52.45% <0.00%> (ø)`
include/cantera/oneD/StFlow.h	`99.04% <0.00%> (ø)`
include/cantera/oneD/IonFlow.h	`84.61% <0.00%> (ø)`
include/cantera/oneD/Domain1D.h	`85.57% <0.00%> (ø)`
include/cantera/oneD/Boundary1D.h	`50.00% <0.00%> (ø)`
src/base/AnyMap.cpp	`89.75% <0.00%> (+0.24%)`	⬆️
src/oneD/StFlow.cpp	`90.44% <0.00%> (+0.35%)`	⬆️
... and 4 more

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ischoegl · 2021-10-29T14:01:35Z

@speth ... thank you for the comment. I believe I found a good solution by raising exceptions when things get parsed at a later point. As an example, the unimplemented n005 to n008 input will produce the following warning:

$ cti2yaml test.cti 
WARNING: Unable to generate field 'test_not_implemented-reactions'
from reaction specification 'n005 to n008'

The specification of a single reaction works, and will not raise a confusing warning message (the test_not_implemented above points to the CTI phase definition that attempts to add those reactions).

speth

Thanks, @ischoegl. This looks good to me.

[cti2yaml] Consistent handling of kinetics/transport='None'

eea4afd

ischoegl added the Input Input parsing and conversion (for example, ck2yaml) label Oct 22, 2021

ischoegl requested review from a team and removed request for a team October 22, 2021 16:22

ischoegl marked this pull request as draft October 22, 2021 16:31

ischoegl force-pushed the fix-1009 branch from 1ead9f1 to e905e4b Compare October 23, 2021 00:16

ischoegl marked this pull request as ready for review October 23, 2021 00:38

ischoegl requested a review from a team October 23, 2021 00:38

ischoegl added 2 commits October 23, 2021 07:44

[cti2yaml] Allow for spaces after colon in CTI composition input

10f411f

This change allows for composition specifications that include a whitespace after a separating colon (example: "N2: 0.9, O2: 0.1" rather than "N2:0.9, O2:0.1")

[cti2yaml] Allow for selection of exact reaction ids in phase specifi…

01a17c0

…cation

ischoegl force-pushed the fix-1009 branch from e905e4b to 01a17c0 Compare October 23, 2021 12:45

This was referenced Oct 24, 2021

Broken example CI runs #1132

Closed

Improve YAML output formatting #1128

Closed

ischoegl force-pushed the fix-1009 branch from 6f75029 to 01a17c0 Compare October 26, 2021 03:49

speth reviewed Oct 29, 2021

View reviewed changes

ischoegl force-pushed the fix-1009 branch from 6702687 to 35b6bbd Compare October 29, 2021 03:34

ischoegl requested a review from speth October 29, 2021 03:45

ischoegl force-pushed the fix-1009 branch from 35b6bbd to e17bec1 Compare October 29, 2021 04:03

ischoegl force-pushed the fix-1009 branch from e17bec1 to e183c36 Compare October 29, 2021 13:53

[cti2yaml] Do not let ambiguous reaction specification pass silently

a37e3d0

ischoegl force-pushed the fix-1009 branch from e183c36 to a37e3d0 Compare October 29, 2021 14:04

speth approved these changes Nov 18, 2021

View reviewed changes

speth merged commit 032de5e into Cantera:main Nov 18, 2021

ischoegl deleted the fix-1009 branch November 22, 2021 18:16

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cti2yaml: fix issues with composition strings and kinetics model of "None" #1127

cti2yaml: fix issues with composition strings and kinetics model of "None" #1127

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cti2yaml: fix issues with composition strings and kinetics model of "None" #1127

cti2yaml: fix issues with composition strings and kinetics model of "None" #1127

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