Reactionmechanismgenerator

====================
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.

This release represents a major milestone in RMG development and includes many backwards-incompatible changes, most notably Python 3 compatibility and major API changes. Users switching to RMG 3 will need to create new conda environments and update any scripts which access the API. We recommend using the `futurize` script from python-future for updating scripts for Python 3 and the provided `rmg2to3.py` script for updating scripts for RMG 3.

Python 3 1724
- RMG is now compatible with Python 3.7 and newer
- RMG v2.x versions will no longer be supported
- API changes
- Method, function, and argument names have been standardized to use snake_case across RMG and Arkane
- Input file related code was not changed, in order to continue support for existing syntax
- Conversion script has been provided to aid transition (scripts/rmg2to3.py)
- Standardized submodule names in the rmgpy.tools module 1794
- Accompanying changes
- Reduction and scoop_framework modules have been removed
- New/updated hash and comparison methods for Species/Molecule/Atom/Bond classes
- DDE thermochemistry estimator has been replaced by chemprop
- Update example IPython notebooks 1735
- Update global uncertainty module to work with MUQ 2 and Python 3 1738
- Miscellaneous clean up and bug fixes following transition 1741, 1744, 1752, 1759, 1785, 1802, 1798, 1799, 1808

Arkane
- Improvements and refactoring of job output file creation and content 1607
- Fix kinetics fitting bug 1672
- Improvements to automatic network exploration tool 1647
- Support for ND classical and semi-classical rotor calculations 1640, 1849
- Support for 2D quantum mechanical rotor calculations using Q2DTor 1640
- Support for providing absolute file paths 1685
- Output RMG-style libraries 1769
- Check for error termination in Gaussian log files 1766
- Support for parsing Orca log files 1749
- Support for parsing MP2, double hybrid DFT, CCSD, and CCSD(T) energies from Gaussian log files 1815
- Support for TeraChem log files 1788
- Miscellaneous bug fixes 1810

New features and other additions
- Additional options for heterocycles in MLEstimator 1621
- Automatic tree generation algorithm implementation completed 1486, 1675, 1848
- New simulation restart approach using seed mechanisms (old pickle-based method removed) 1641
- Added new MBSampledReactor type for simulating molecular beam experiments (does not support model generation) 1669
- Improvements to group additivity thermo estimates for aromatics and sulfur species 1731, 1751
- Improvements to solvation correction determination with multiple resonance structures 1832
- Add support for reading and writing extended element syntax in Chemkin NASA polynomials 1636
- Add support for fitting negative Arrhenius rates (found in MultiArrhenius data) 1834

Bug fixes
- Fix numpy rcond usage to restore support for older numpy versions 1670
- Fix bug with duplicate library reactions when using RMG generated seed mechanisms 1676
- Move parse_command_line_arguments to facilitate importing in binary package 1717
- Fix issues with is_identical_to methods of kinetics models 1705
- Fix cython issue with make_object definitions 1817
- Fix issue with estimating solvation corrections for radicals 1773
- Fix parsing of certain types of RMG generated reaction comments 1842
- Fix identifier generation for surface species using OpenBabel 1842
- Fix mole fraction normalization for SimpleReactor 1809
- Fix permissions error when writing seed mechanisms in WSL 1796
- Fix issue with restarting from job without reaction filters 1847

Other
- Improvements to mergeModels.py script 1649
- Miscellaneous performance improvements 1677, 1765,
- Raise errors when NaN is encountered in solver 1679
- Allow sulfur species to have valence 12 in resonance algorithm 1751
- Add support for maxproc argument to generate_reactions module 1780
- Display atom index when drawing groups 1758
- Update sensitivity example 1805
- Update commented input file 1806
- Generate reverse reaction recipes in reverse order of the forward recipe 1829
- Add iodine to Chemkin elements list 1825
- Remove unnecessary duplicate checking for seed mechanisms 1824
- Organize examples for running RMG scripts 1840
- Increase RDKit version requirement to avoid memory leak 1851
- Logging changes 1721, 1755
- Documentation updates 1680, 1709, 1767, 1781, 1784, 1807, 1845

Thanks to all contributors: ajocher, alongd, amarkpayne, cgrambow, dranasinghe, hwpang, kspieks, goldmanm, mazeau, mjohnson541, mliu49, oscarwumit, rwest, rgillis8, sarakha, sudoursa, xiaoruiDong, yunsiechung, zjburas

- Bugfixes
- Improve error handling in NASA as_dict method 1630
- Fixes to Fluorine atomtypes 1656
- Fix pressure dependent network generation 1658
- Add support for reversing PDepArrhenius with MultiArrhenius rates 1659

- Arkane
- Implement ZPE scaling factor 1619
- Refactor infrastructure for bond additivity corrections 1605
- Add frequency scale factors for wb97xd/def2tzvp and apfd/def2tzvpp 1653
- Fix frequency scale factors in example files 1657
- Get element counts from conformers 1651

- Miscellaneous
- Update conda environment files 1623, 1644
- Output RMS (Reaction Mechanism Simulator) format mechanism files 1629
- Properly clean up files after running tests 1645
- Documentation fixes 1650
- Improve as_dict and make_object by making them recursive 1643

- Heterogeneous catalysis!
- RMG-cat fork has been merged 1573
- Introduce SurfaceReactor
- Thermo estimation for adsorbed species
- Surface reaction generation and kinetics estimation
- Introduce Van der Waals bonds (order 0) and quadruple bonds (order 4) 1542
- Arkane
- Automatically detect rotor symmetry 1526
- Introduce new YAML files for storing and loading species statmech data 1402, 1551
- Don't create species dictionary file if there are no structures 1528
- Improvements to network explorer tool 1545
- Improved class inheritance for quantum log file classes 1571
- Automatic determination of optical isomers and symmetry using `symmetry` package 1571
- Parse CCSD(T) energies from Molpro output 1592
- Automatically determine molecule linearity 1601
- Determine frequency scaling factor based on geom/freq method rather than sp method 1612
- Improve logging related to energy barriers 1575
- Ensure that translational mode is calculated for atoms 1620
- Miscellaneous features
- New `enumerate_bonds` method of Molecule to generate dictionary of bond types 1525
- Introduce `RMGObject` parent class to support YAML dumping and loading 1402, 1540
- Add support for fluorine atomtypes 1543
- Introduce `ArrheniusBM` class for Blower-Masel kinetics 1461
- Allow defining and using co-solvents for solvent libraries 1558
- Introduce `strict` option to perform isomorphism between species/molecules while ignoring electrons and bond orders 1329
- Molecule and Species objects can be instantiated by providing `SMILES` or `InChI` argument directly, and the identifiers can be accessed via the `SMILES` and `InChI` attributes 1329
- Parallelization has been completely refactored using Python multiprocessing module in replacement of scoop, currently supports parallel reaction generation and QMTP 1459
- Improvements to usability of uncertainty analysis functionality 1593
- Bug fixes
- Various fixes for supporting mono-atomic molecules in Arkane 1513, 1521
- Ensure `keras_backend` is set consistently 1535
- Fix handling of disconnected graphs in VF2 isomorphism algorithm 1538
- Ignore hydrogen bonds when converting to RDKit molecule 1552
- Other miscellaneous bugs 1546, 1556, 1593, 1600, 1622
- Backward incompatible changes
- Hydrogen bonds are now order 0.1 (instead of 0) 1542
- New dependencies
- pyyaml (required) 1402
- scikit-learn (required) 1461
- textgenrnn (optional) 1573
- Other
- Windows binaries are no longer officially supported. The new recommended way to use RMG on Windows computers is via a virtual machine or through the Linux subsystem. See documentation for updated installation instructions. 1531, 1534
- Documentation updates 1544, 1567
- Logging/exception improvements 1538, 1562
- PEP-8 improvements 1566, 1592, 1596
- Solver output files (png/csv) now report moles instead of mole fractions 1542
- Replace global RMGDatabase object if the database is reloaded 1565
- Print ML generated quote upon completion of RMG jobs 1573
- Infrastructure for automatically generated reaction rate trees 1461
- Testing related changes 1597, 1599
- Updates to example Jupyter notebooks 1541, 1593

- Arkane (formerly CanTherm):
- CanTherm has been renamed to Arkane (Automated Reaction Kinetics And Network Exploration)
- New network exploration functionality using RMG-database
- Support for all elements has been added for reading quantum output files
- New supporting information output file with rotational constants and frequencies
- Known thermo and kinetics can be provided in addition to quantum information
- Improve general user experience and error handling

- New machine learning thermo estimator
- Estimate species thermochemistry using a graph convolutional neural network
- Estimator trained on quantum calculations at B3LYP and CCSD(T)-F12 levels
- Currently supports C/H/O/N, with an emphasis on cyclic molecules

- Resonance:
- New pathways added for lone-pair multiple-bond resonance, replacing
two pathways which were more specific
- New pathways added for aryne resonance
- Aromatic resonance pathways simplified and refactored to use filtration
- Kekule structures are now considered unreactive structures

- Miscellaneous changes:
- Isotope support added for reading and writing InChI strings
- New branching algorithm for picking up feedback loops implemented (beta)
- Global forbidden structure checking is now only done for core species for
efficiency, which may lead to forbidden species existing in the edge
- Minor improvements to symmetry algorithm to fix a few incorrect cases

- Bug fixes:
- Fixed issue where react flags were being reset when filterReactions was
used with multiple reactors, resulting in no reactions generated
- File paths for collision violators log changed to output directory
- Fixed bug in local uncertainty introduced by ranged reactor changes
- Fixed bug with diffusion limitation calculations for multi-molecular reactions
- Various other minor fixes

This release is minor patch which fixes a number of issues discovered after 2.2.0.

- Collision limit checking:
- RMG will now output a list of collision limit violations for the generated model

- Fixes:
- Ambiguous chemical formulas in SMILES lookup leading to incorrect SMILES generation
- Fixed issue with reading geometries from QChem output files
- React flags for reaction filter were not properly updated on each iteration
- Fixed issue with inconsistent symmetry number calculation