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ReactionMechanismGenerator / ARC Public

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Implement the molecule module internally#789

Merged

kfir4444 merged 107 commits intomainReactionMechanismGenerator/ARC:mainfrom

moleculeReactionMechanismGenerator/ARC:moleculeCopy head branch name to clipboard

Aug 24, 2025

Conversation Commits107 (107)Checks Files changed

Merged

Implement the molecule module internally#789
kfir4444 merged 107 commits intomainfrom
molecule

Commits

Commits on Aug 24, 2025

Minor: Style modifications to converter
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Minor: modifications to conformers
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Minor: Adapted scheduler to NMD check
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Removed Fix.txt
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Modified .gitignore
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Updated gh-pages.uml

kfir4444
authored and
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Removed Conformer functions from converter
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Removed RMG Reaction object from ARCReaction
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Remove RMGDatabase() loading from restart test
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Updated devtool shell scripts
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Deleted bettercodehub
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Update CodeQL actions to version 3 for improved functionality and security

calvinp0
authored and
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Updated environment and requirements
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Updated CI
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Update Makefile
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Update docs Makefile
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Updated .coveragerc
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Updated code of conduct
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Updated the readme
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Added the molecule module
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Implement the new molecule module
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Modified external paths in settings
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Added RMG_PATH to settings
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Added element mass functionality to common
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Tests: common get_element_mass()
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Removed qcel, use internal element data
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Relaxed tols of coords checks
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Tests: Adaptations to converter tests
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committed
Tests: is_obj_of_rmg_species_type
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Added the constants module
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Updated exceptions
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Added setup and utilities
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Docs: Updated ARC's documentation (missing - complete and add new installation instructions)
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Added the parser module with adapters
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Tests: parser module
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Implement the new parser module
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Modified the Arkane statmech module
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Tests: arkane
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Implement Arkane modifications in main
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Let molecule deal with symmetry
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Fix job adapter imports
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Call generate_resonance_structures_safely()
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Added is_xyz_linear() to common, added Species is_linear property
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Removed the three_params option
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committed
Relocated StatmechEnum from main to statmech adapter
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committed
Minor logic improvement in DOF count in tani
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committed
Fix RDKit import in converter
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committed
Fixes to converter check_isomorphism()
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Relax tols in vector tests
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Implement ThermoData and TransportData classes in species
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Implement rmg_mol_from_dict_repr() in species
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Tests: RMG mol dict repr
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Tests: Modifications to conformers tests
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Tests: Modifications to checks ts_test
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Updated tani script
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Tests: Updated job adapter tests
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Fixed Arkane call in check ts for E0
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committed
Tests: Modifications to trsh tests
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Tests: Modifications to main tests
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committed
Tests: Modifications to scheduler tests
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committed
Tests: Removed test symmetry from species tests
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committed
Modifications to engine and driver mapping
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Tests: Adaptations to mapping tests
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Tests: Added mol_list tests for species
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committed
Rehaul of the xyz perception module
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Tests: Perceive
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Adaptation to new perception module
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Relocated distance_matrix() from converter to common
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Modified species mol_list treatment
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Improved common.get_bonds_from_dmat()
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Tests: updated test_get_bonds_from_dmat()
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Tests: Adaptations to family test
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committed
Tests: Adaptations to zmat tests
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committed
Modified ZMat functions
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Tests: Updated zmat converter tests
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committed
Updated conformers determine_well_width_tolerance()
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Tests: Modifications to reaction tests
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committed
Improved product_dicts definition in family
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Tests: Fixed species definition in multispecies plotter tests
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Added the NMD checks module
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Tests: checks NMD tests
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Added bond functions to reactions
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Tests: Scheduler tests adaptation
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Added get_bonds() to species
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Tests: species get_bonds()
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Added is_equal_family_product_dicts() to common
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Fix multiplicity report in Reaction
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Improved the is_isomorphic() check in species
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Make product_dicts a property of ARCReaction
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Added signed_angular_diff() to common
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Tests: test_signed_angular_diff()
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Updated the Heuristics TS adapter for H Abstraction
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Tests: Updated heuristics tests
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Added eq and hash to ARCSpecies
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Tests: ARCSpecies eq and hash
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Updated processor
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Modified rotor scan in trsh
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Updated plotter
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Unify environment activation for conda/micromamba in incore_commands
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Minor modification to vectors get_dihedral()
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Added error handling for failed Sella runs in xTB job adapter
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Updated processor
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Added save_arkane_thermo script
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committed
Modified common calculate_arrhenius_rate_coefficient()
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Tests: common calculate_arrhenius_rate_coefficient()
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Updated RMG libraries handling in plotter
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Tests: Updated functional tests
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committed

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