Reactionmechanismgenerator

- New features:
- New ring membership attribute added to atoms. Can be specified in group adjacency lists in order to enforce ring membership of atoms during subgraph matching.
- Reactors now support specification of T, P, X ranges. Different conditions are sampled on each iteration to optimally capture the full parameter space.
- New termination type! Termination rate ratio stops the simulation when the characteristic rate falls to the specified fraction of the maximum characteristic rate. Currently not recommended for systems with two-stage ignition.
- New resonance transitions implemented for species with lone pairs (particularly N and S containing species). A filtration algorithm was also added to select only the most representative structures.
- Formal support for trimolecular reaction families.
- New isotopes module allows post-processing of RMG mechanisms to generate a mechanism with isotopic labeling.

- Changes:
- Library reactions can now be integrated into RMG pdep networks if the new elementary_high_p attribute is True
- Library reactions may be duplicated by pdep reactions if the new allow_pdep_route attribute is True
- Jupyter notebook for adding new training reactions has been revamped and is now located at ipython/kinetics_library_to_training.ipynb
- Syntax for recommended families has changed to set notation instead of dictionaries, old style still compatible
- Ranking system for database entries expanded to new 0-11 system from the old 0-5 system
- Collision limit checking has been added for database entries

- Cantherm:
- Improved support for MolPro output files
- Added iodine support
- Automatically read spin multiplicity from quantum output
- Automatically assign frequency scale factor for supported model chemistries
- Plot calculated rates and thermo by default
- New sensitivity analysis feature analyzes sensitivity of reaction rates to isomer/TS energies in pdep networks

- Fixes:
- Properly update charges when creating product templates in reaction families
- Excessive duplicate reactions from different resonance structures has been fixed (bug introduced in 2.1.3)
- Fixed rate calculation for MultiPdepArrhenius objects when member rates have different plists

- A more formal deprecation process is now being trialed. Deprecation warnings have been added to functions to be removed in version 2.3.0:
- All methods related to saving or reading RMG-Java databases and old-style adjacency lists
- The group additivity method for kinetics estimation (unrelated to thermo group additivity)
- The saveRestartPeriod option and the old method of saving restart files

- Cantherm:
- Atom counts are no longer necessary in input files and are automatically determined from geometries
- Custom atom energies can now be specified in input files
- Removed atom energies for a few ambiguous model chemistries
- Add atom energies for B3LYP/6-311+g(3df,2p)

- Changes:
- Refactored molecule.parser and molecule.generator modules into molecule.converter and molecule.translator to improve code organization
- SMILES generation now outputs canonical SMILES
- Molecule.sortAtoms method restored for deterministic atom order
- PDep reactions which match an existing library reaction are no longer added to the model

- Fixes:
- Fix issue with reaction filter initiation when using seed mechanisms

- New features:
- Chlorine and iodine atom types have been added, bringing support for these elements to RMG-database
- Forbidden structures now support Molecule and Species definitions in addition to Group definitions

- Changes:
- Reaction pair generation will now fall back to generic method instead of raising an exception
- Removed sensitivity.py script since it was effectively a duplicate of simulate.py
- Thermo jobs in Cantherm now output a species dictionary
- Fitted atom energy corrections added for B3LYP/6-31g**
- Initial framework added for hydrogen bonding
- Renamed molepro module and associated classes to molpro (MolPro) to match actual spelling of the program
- Chemkin module is now cythonized to improve performance

- Fixes:
- Allow delocalization of triradicals to prevent hysteresis in resonance structure generation
- Fix reaction comment parsing issue with uncertainty analysis
- Fix numerical issue causing a number of pressure dependent RMG jobs to crash
- Template reactions from seed mechanisms are now loaded as library reactions if the original family is not loaded
- Fix issues with degeneracy calculation for identical reactants

- Charged atom types:
- Atom types now have a charge attribute to cover a wider range of species
- New atom types added for nitrogen and sulfur groups
- Carbon and oxygen atom types renamed following new valence based naming scheme

- Ring perception:
- Ring perception methods in the Graph class now use RingDecomposerLib
- This includes the getSmallestSetOfSmallestRings methods and a newly added getRelevantCycles method
- The set of relevant cycles is unique and generally more useful for chemical graphs
- This also fixes inaccuracies with the original SSSR method

- Other changes:
- Automatically load reaction libraries when using a seed mechanism
- Default kinetics estimator has been changed to rate rules instead of group additivity
- Kinetics families can now be set to be irreversible
- Model enlargement now occurs after each reactor simulation rather than after all of them
- Updated bond additivity corrections for CBS-QB3 in Cantherm

- Fixes:
- Do not print SMILES when raising AtomTypeError to avoid further exceptions
- Do not recalculate thermo if a species already has it
- Fixes to parsing of family names in seed mechanisms

- Model resurrection:
- Automatically attempts to save simulation after encountering a DASPK error
- Adds species and reactions in order to modify model dynamics and fix the error

- New features:
- Add functionality to read RCCSD(T)-F12 energies from MolPro log files
- Add liquidReactor support to flux diagram generation

- Other changes:
- Removed rmgpy.rmg.model.Species class and merged functionality into main rmgpy.species.Species class
- Refactored parsing of RMG-generated kinetics comments from Chemkin files and fixed related issues
- Refactored framework for generating reactions to reduce code duplication
- Resonance methods renamed from generateResonanceIsomers to generate_resonance_structures across all modules
- Raise CpInf to Cphigh for entropy calculations to prevent invalid results

- Fixes:
- Update sensitivity analysis to use ModelSettings and SimulatorSettings classes introduced in v2.1.5
- Fixed generate_reactions methods in KineticsDatabase to be directly usable again
- Fixed issues with aromaticity perception and generation of aromatic resonance structures

- New bicyclic formula:
- Estimates polycyclic corrections for unsaturated bicyclics by adjusting the correction for the saturated version
- Can provide a decent estimate in many cases where there is not an exact match

- Other changes:
- Refactored simulation algorithm to properly add multiple objects per iteration
- Print equilibrium constant and reverse rate coefficient values when using Cantherm to calculate kinetics
- Speed up degeneracy calculation by reducing unnecessary operations

- Fixes:
- Loosen tolerance for bond order identification to account for floating point error
- Fixed uncertainty analysis to allow floats as bond orders
- Fixed some comment parsing issues in uncertainty analysis
- Added product structure atom relabeling for families added in RMG-database v2.1.5
- Fixed issue with automatic debugging of kinetics errors due to forbidden structures