RMG-Py Version 3.1.0
Date: April 23, 2021
We recommend creating a new conda environment using the latest environment.yml
as many dependencies have changed, and upgrading an existing environment is
always troublesome.
-
RMG-Py
- Added support for Bromine
- Added improved method to calculate temperature dependent solvation free energy
- Made Rank 1 accuracy correspond to 0.2 kcal/mol instead of 0 kcal/mol
- Improvements to Group Additivity comments, in particular adding missing group comments
- Added support for trimolecular units in ArrheniusBM fits
- Improvements to profiling
- Use kekulized structures for transport estimation
- Automatic tree generation script improvements
- Properly short circuit is_isomorphic when strict=False
- Added block for specifying species tuples to react when starting an RMG run
- Improve ArrheniusBM fitting to a single reaction
- Improvements in bidentate thermochemistry estimation
- Added new surface attributes for metals and facets
- Added support for Phosphorus
- Enable use LSRs to scale thermo from different metals and enable proper
use of training reactions from different metals - Added maximumSurfaceSites constraint
-
Arkane
- Added frequency scaling factors for apfd/deef2tzvp and wb97xd/def2svp
- Kinetics and pdep sensitivities additionally saved in YAML format
- Enable automatic isodesmic reaction generation
- AECs, BACs and frequency scaling factors moved from Arkane to RMG-database
- Added functionality for Petersson and Melius BAC fitting using Arkane and
the reference database - Enabled two parameter Arrhenius fit option
- Added functionality for fitting AECs
- Added classes to standardize model chemistry definitions
- Use adjlists instead of smiles when saving
-
Bugfixes
- QMTP updated to work with g16 executable
- Fixed various Sticking Coefficient bugs
- Fixed issues with Surface Arrhenius reactions written in the reverse being converted
to ArrheniusEP instead of SurfaceArrheniusBEP - Fixed NaN handling in the explorer tool's steady state solve
- Fixed determine_qm_software for Orca
- Fixed bug where elementary_high_p library reactions with more than the maximum number of atoms for pdep
never entered the edge - Fixed bug related to pdep networks having sources not contained in the core
- Fixed various profiling bugs
- Fixed issue with indexing when merging models
- Fixed bug with ranged liquid reactors
- Fixed bug with loading of autogenerated trees in Arkane
- Fixed bug related to collision limit violation checks in LiquidReactor
- Fixed bug related to Pmin and Pmax definition in SurfaceReactor
- Fixed bugs in global uncertainty analysis for LiquidReactor
- Fixed bug related to the units of reverse rate constants for reactions involving surface species
- Fixed bug in Molecule isomorphism where it would simply assume the given initial map was correct
- Remove deprecated matplotlib warn keyword
- Fixed bug related to reading Chebyshev forms in Chemkin files
- Fixed reference concentration for surface species when calculating Kc
- Fixed issue with the reaction generation using the reversee of Surface_ElleyRideal_Addition_MultipleBond
- Fixed bug with adjlist multiplicitly line being mistaken as the species name
- Fixed bug with the library to training notebook
- Remove temporary seed mechanisms if they exist from a previous run
-
Miscellaneous
- Modified find_parameter_sources_and_assign_uncertainties to regenerate chem.inp as needed
- Added option to save atom order when labeling template reactions
- Added option to ignore atom type errors when creating molecule objects
- Enable use of critical_distance_factor in from_xyz
- Improved SIGINT handling when calling lpsolve
- Enable H-bond drawing
- Improvements to debug messages
- Updated dependencies cclib and OpenBabel
Note that the upgrade to OpenBabel v3+ will change the interpretation
of some ambiguous SMILES strings that use the lower-case aromatics notation.
Although we think the new interpretation is not wrong, it might be different
from previous versions, so take care.