RMG-Py v4.0.0 `stable`#2981

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JacksonBurns merged 781 commits into

Jun 9, 2026

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Merge pull request #2932 from sevyharris/uncertainty_covariance
sevyharris
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passing extension_iter_item_cap to make_tree_nodes even if cascade algo isn't used

Nora-Khalil
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rwest
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Merge pull request #2941 to tweak SIDT tree generation
rwest
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Commits on May 11, 2026

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Harden get_reverse_reaction and the coverage-dependence reaction flip

rwest
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claude
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Apply kinetic coverage_dependence correction in the SurfaceReactor Jacobian

rwest
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claude
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get_reverse_reaction can handle missing kinetics.
rwest
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Cython declare Reaction.copy
rwest
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adjust flipping routine

bjkreitz
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rwest
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remove get_reverse_reaction

bjkreitz
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rwest
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remove TODO comment in generate_rate_coefficient

bjkreitz
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rwest
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remove import copy

bjkreitz
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add info for flipped reaction

bjkreitz
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change logging.debug to logging.info

bjkreitz
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rwest
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Restructure coverage-dependence reaction flip logic
rwest
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Merge pull request #2975 to fix coverage-dependent thermo
rwest
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add extra check in case ADS source is empty to avoid crashing

sevyharris
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add surface uncertainty demo notebook

sevyharris
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bugfix: surface UQ make sure X has 0 uncertainty

sevyharris
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UQ: read covariance from .csv instead of .npy

sevyharris
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Add example using covariance matrices to sample in Cantera

sevyharris
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rwest
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Merge pull request #2959 from sevyharris/surface_uncertainty_demo_notebook
rwest
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Fix Cantera 3.2 ReactorSurface syncState warning

rwest
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claude
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Use non-deprecated Cantera phase model names

rwest
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claude
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Commits on Jun 5, 2026

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Merge pull request #2968 from sevyharris/add_uq_assign_intermediate_tests
JacksonBurns
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draw vdW bond, the same way we do H bonds

bjkreitz
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JacksonBurns
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Adjust remove vdW bond, using new has_covalent_surface_bond function

bjkreitz
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JacksonBurns
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Make has_covalent_surface_bond more efficient.

rwest
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JacksonBurns
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Add test_has_covalent_surface_bond to test has_covalent_surface_bond.

rwest
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JacksonBurns
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Simplify remove_van_der_waals_bonds

rwest
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Accelerate is_multidentate.

rwest
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change is_molecule_forbidden

bjkreitz
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adding find_formate_delocalization_paths to pathfinder

bjkreitz
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Fix some Cython declarations in pathfinder.py

rwest
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add resonance structure generation for formate to resonance.py

bjkreitz
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add label for vdW bond in get_desorbed_molecules

bjkreitz
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add more constraints to formate path in resonance.py

bjkreitz
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clean up pathfinder and add constraints

bjkreitz
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add features for N species

bjkreitz
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Consider generate_formate_resonance_structures when no features specified.

rwest
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Rename generate_formate_resonance_structures to generate_adsorbate_formate_resonance_structures

rwest
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Test the new remove_van_der_waals_bonds behaviour.

rwest
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Add comments describing current implementation of is_molecule_forbidden

rwest
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Refactor is_molecule_forbidden checks in reaction family.

rwest
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Add has_vdw_surface_bond method on Molecule.

rwest
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Fix bug and add tests: unbonded X gives True for has_vdw_surface_bond

rwest
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Avoid calling fails_species_constraints() twice in a row.

rwest
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restructure is_molecule_forbbiden

bjkreitz
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restructure is_molecule_forbidden to check for vdWBidentate in family name

bjkreitz
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TEMPORARY: set RMG_DATABASE_BRANCH: formate_families

rwest
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Improve diagnostics for "Family had N reactants?" kinetics test failure

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Revert "TEMPORARY: set RMG_DATABASE_BRANCH: formate_families"
JacksonBurns
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Merge pull request #2706 from ReactionMechanismGenerator/vdW_bonds
JacksonBurns
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increment version
JacksonBurns
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add release notes
JacksonBurns
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Update documentation/source/users/rmg/installation/anacondaUser.rst

JacksonBurns
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rwest
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review comment from @sevyharris
JacksonBurns
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split 'and' bullet into two
JacksonBurns
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