Update to `cantera` 3.x #2751

JacksonBurns · 2025-01-22T18:20:56Z

This upgrade is needed for multiple reasons:

We use 2.6 which is deprecated
Resolve We should replace cantera.Species.fromCti() calls with cantera.Species.from_yaml() calls #2676
Using Cantera 3.x will allow using more modern Python versions, namely 3.11 needed to add ChemProp v2 to RMG (and thus unblock Status Tracking: chemprop and ML Thermochemistry Prediction #2559)

These squashed commits contain all of the initial efforts by HWP to switch from pythoncall to JuliaCall

These were the first commits to change to Python 3.9, and they do not work on their own but instead open the door to finding issues to make the rest of the changes

here are all the solutions that were implemented: - in a couple places we were implicitly casting a double to a numpy float, now need to explicitly grad the _real_ part of the double - Cython does not allow nested function declaration inside cpdef functions, move all of these outside of their parent functions or redefine them to be purely functional where practical - similar to the above, lambda function are no longer allowed - get the same treatment. what's different here is that usually we are using lambda in sorting calls, so we can replace these with operator.itemgetter or attrgetter, where relevant. this also involves re-writing a couple reduce calls, which also used lambda - modern cython does not allow re-declaring existing Cython variables (in previous versions this was a warning I think), so I just remove these where needed. (btw Cython is super cool, actually points out both of the declaration so that you can delete one) i made these fixes while listening to The Metal by Tenacious D, Talk Too Much by Renee Rapp, BEST INTEREST by Tyler, The Creator (love the bass line), mos thoser by food house, and Doritos & Fritos by 100 Gecs

as requested in: #2687 (comment)

These commits are the second (and final) round of attempting JuliaCall debugging by HWP

These commits reflect the initial effort by XD to re-implement the MILP for Clar optimization in SciPy. They were unsuccessful because at the time RMG could not actually run a required version of Python to install SciPy with MILP.

These commits rescued some abandoned work from another branch

This is a collection of largely unordered commits which implement all of the changes discussed in the commit name

…lopment, gone on main

JacksonBurns · 2025-01-22T18:45:10Z

I am using this script to change our CTI blocks into YAML:

from cantera.cti2yaml import convert

convert(text="""species(name=u'Ar',
        atoms='Ar:1',
        thermo=(NASA([200.00, 1000.00],
                     [ 2.50000000E+00,  0.00000000E+00,  0.00000000E+00,
                       0.00000000E+00,  0.00000000E+00, -7.45375000E+02,
                       4.37967000E+00]),
                NASA([1000.00, 6000.00],
                     [ 2.50000000E+00,  0.00000000E+00,  0.00000000E+00,
                       0.00000000E+00,  0.00000000E+00, -7.45375000E+02,
                       4.37967000E+00])),
        transport=gas_transport(geom='atom',
                                diam=3.33,
                                well_depth=136.501,
                                dipole=2.0,
                                polar=1.0,
                                rot_relax=15.0))""",
                                output_name="temp_yaml.yaml"
         )

JacksonBurns · 2025-01-22T21:32:12Z

Here are the other errors which must be resolved:

 FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_pdep_arrhenius - AttributeError: 'cantera.reaction.Reaction' object has no attribute 'rates'
FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_multi_pdep_arrhenius - AttributeError: 'cantera.reaction.Reaction' object has no attribute 'rates'
FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_falloff - AttributeError: module 'cantera' has no attribute 'FalloffReaction'
FAILED test/rmgpy/speciesTest.py::TestSpecies::test_cantera - cantera._utils.CanteraError: 
*******************************************************************************
InputFileError thrown by AnyMap::operator[]:
Error on line 1 of input string:
Key 'composition' not found.
Existing keys: species, date, generator, cantera-version, description
|  Line |
>     1 > 
          ^
|     2 | description: |-
|     3 |   Argon
|     4 | 
*******************************************************************************
FAILED test/rmgpy/transportDataTest.py::TestTransportData::test_to_cantera - AttributeError: type object 'cantera.thermo.Species' has no attribute 'fromCti'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_species_conversion - AttributeError: module 'cantera' has no attribute 'FalloffReaction'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_reaction_conversion - AttributeError: module 'cantera' has no attribute 'FalloffReaction'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_surface_species_conversion - AttributeError: module 'cantera' has no attribute 'FalloffReaction'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_surface_reaction_conversion - AttributeError: module 'cantera' has no attribute 'FalloffReaction'

JacksonBurns · 2025-01-22T21:34:37Z

FalloffReaction has been merged with Reaction: https://cantera.org/3.0/doxygen/html/da/d58/deprecated.html#_deprecated000043

- CI updates: run CI on all platforms with and without RMS, split regression tests into separate job after that so that regression is only checked on one platform - installation updates: make RMG-Py actually `pip`-installable as `reactionmechanismgenerator` to avoid having to set the `PYTHONPATH` variable, which breaks `juliacall`, add a convenience script for installing RMS - code changes: fix some small bugs in the new optional-rms setup (one missed `requires_rms` and one incorrect rebase)

…nstantTLiquidSurfaceReactor

passing an empty dict for third_body results in the attribute being None, but we need it to just be an unpopulated ThirdBody to indicate that the Reaction is a third body reaction

it seems that Cantera 3 seems to be a little bit pickier about the syntax for chemkin files

JacksonBurns · 2025-01-28T20:06:54Z

SITE specification: http://www.cvd.louisville.edu/Course/Chemical%20Vapour%20Deposition/Manuals/chemkin/chemkin11surfacechemkin.pdf page 52

- cantera3 can only read if there is a name - rmg can't read if there is a name - update rmg to ignore the name

JacksonBurns · 2025-05-29T19:42:56Z

TODO: rebase onto main after Python 3.9 is merged in main

hwpang and others added 16 commits January 14, 2025 11:49

HWP Initial JuliaCall efforts

0e2f7f2

These squashed commits contain all of the initial efforts by HWP to switch from pythoncall to JuliaCall

JWB initial increase to Python 3.9

a40cd0a

These were the first commits to change to Python 3.9, and they do not work on their own but instead open the door to finding issues to make the rest of the changes

make muq optional (like the docs say!) and add a helpful msg if missing

15c2828

add newly defined functions to pxd files

9f854ca

as requested in: #2687 (comment)

HWP Additional JulicaCall Debugging

363b0dc

These commits are the second (and final) round of attempting JuliaCall debugging by HWP

XD Initial MILP Re-implementation

e3a8bed

These commits reflect the initial effort by XD to re-implement the MILP for Clar optimization in SciPy. They were unsuccessful because at the time RMG could not actually run a required version of Python to install SciPy with MILP.

HWP Isodesmic Improvements

26f3d1f

These commits rescued some abandoned work from another branch

JWB Python 3.9 and Cython Debugging, Optional RMS, fix Clar

d758ef0

This is a collection of largely unordered commits which implement all of the changes discussed in the commit name

dont install juliacall by default

a9b56b3

np.bool is deprecated, bool

1530ada

re-bury the julia imports that got shuffled around

0fa7895

remove initial species add - was carried over by accident during deve…

2b27f4b

…lopment, gone on main

fix call to get_reaction_matches (should match other test)

0a13902

make the m1 mac run in x86 compat mode

b774dec

split the python-only test into separate CI to simplify reg test logic

24f140f

JacksonBurns mentioned this pull request Jan 22, 2025

Fix Python 3.9 julia Overhaul #2749

Closed

JacksonBurns linked an issue Jan 22, 2025 that may be closed by this pull request

We should replace cantera.Species.fromCti() calls with cantera.Species.from_yaml() calls #2676

Open

2 tasks

JacksonBurns force-pushed the py39/cantera3 branch 2 times, most recently from fddd38d to 206d426 Compare January 23, 2025 16:41

JacksonBurns changed the base branch from feat/py39_rebase-julia_fix to py39/juliacall-fix January 25, 2025 21:53

JacksonBurns force-pushed the py39/cantera3 branch from 845f13c to 558e48e Compare January 25, 2025 21:57

JacksonBurns added 2 commits January 25, 2025 20:29

docker build should wait for regression test

0e33bf3

JacksonBurns force-pushed the py39/juliacall-fix branch from 6d03db1 to 0e33bf3 Compare January 26, 2025 01:30

JacksonBurns force-pushed the py39/cantera3 branch 2 times, most recently from ee73300 to 33bd6f2 Compare January 26, 2025 02:20

jonwzheng and others added 5 commits January 27, 2025 17:01

change liquid initial conditions to surface initial conditions for Co…

80bb62f

…nstantTLiquidSurfaceReactor

run build-and-test on ARM Mac natively

5c549e0

cantera 3 updates

343b65a

collider is never None - must change test (See ext)

1ef5f94

passing an empty dict for third_body results in the attribute being None, but we need it to just be an unpopulated ThirdBody to indicate that the Reaction is a third body reaction

efficiencies attribute has moved

8464e20

JacksonBurns force-pushed the py39/cantera3 branch from 426c55e to 8464e20 Compare January 28, 2025 17:51

JacksonBurns added 2 commits January 28, 2025 14:14

no space between SITE and SDEN

f8819ef

it seems that Cantera 3 seems to be a little bit pickier about the syntax for chemkin files

exactly one space (?)

39f3124

sit emust have name, cantera 3 bug

bee42fa

JacksonBurns mentioned this pull request Jan 29, 2025

ck2yaml in v3 can't convert the same files as v2 Cantera/cantera#1845

Closed

possible workaround

ea0b252

- cantera3 can only read if there is a name - rmg can't read if there is a name - update rmg to ignore the name

JacksonBurns mentioned this pull request Feb 25, 2025

Py39/cantera26 arm #2765

Merged

Base automatically changed from py39/juliacall-fix to feat/py39_rebase February 25, 2025 21:55

JacksonBurns force-pushed the feat/py39_rebase branch from 4381db7 to f89c483 Compare February 25, 2025 22:01

JacksonBurns force-pushed the feat/py39_rebase branch from 74932d8 to 73deea4 Compare April 12, 2025 20:40

JacksonBurns force-pushed the feat/py39_rebase branch from f2f26f3 to 60c4125 Compare May 22, 2025 15:01

JacksonBurns mentioned this pull request May 25, 2025

Use rdkit for SSSR and RCs (bug fix + Python upgrade) #2796

Draft

JacksonBurns changed the base branch from feat/py39_rebase to main May 29, 2025 19:40

JacksonBurns changed the title ~~update cantera version to remove need for x86 emulation on arm mac~~ Update to cantera 3.x May 29, 2025

JacksonBurns marked this pull request as draft May 29, 2025 19:42

JacksonBurns assigned JacksonBurns and KnathanM May 29, 2025

JacksonBurns mentioned this pull request May 29, 2025

Add optional ML-based solvation correction pathway #2798

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