add v3.2.0 release notes for RMG-Py and RMG-database

Author: sevyharris

documentation/source/users/rmg/releaseNotes.rst

@@ -3,6 +3,312 @@
 *************
 Release Notes
 *************
+
+RMG-Py Version 3.2.0
+====================
+Date: August 2, 2023
+
+- RMG-Py
+    - Transport: Added halogens transport corrections to boiling point when estimating critical properties using group additivity
+    - Updated solvation thermo GAV method to use more groups
+    - Made it optional to generate_resonance_structures when loading species dicts
+    - Added filter so radical/lone pair/formal charge is not added to surface site when generating resonance structures
+    - Forbid surface bidentate vdW species
+    - Add Transitory Edge Analysis species selection algorithm
+    - Added get_react_thermo function to avoid deepcopy
+    - Added decay framework for handling species RMG templates think exist, but really aren't wells
+    - Added check to prevent multiple surface bonds from forming through a single adatom
+    - Added multidentate adsorption correction for thermo estimation
+    - Added error checks to make MOPAC calculations more robust
+    - Added features to preserve atom order and template labels when generating reactions
+    - Added coverage dependent effects to surface kinetics
+    - Added support for halogen families in autogen tree script
+    - Enabled pyrms for RMG Simulations and Edge Analysis
+    - Added Liquid-Surface Reactor for RMG Electrocat
+    - Added support for forbidden structures, more general than forbidden molecules
+    - Removed hard-coded template matching code for Bimolec hydroperoxide decomposition
+    - Added support for 2-parameter Troe reactions, only had 3-parameter Troe before
+    - Included noncyclic long distance GAV correction for halogen regardless of its existence in the cycle
+    - Added support for pdep networks with halogens
+    - Added atom labels to molecule to_group method in order to keep the atom labels during conversion
+    - Moved rmgrc to template file so user's settings won't be overwritten every pull from RMG-Py
+    - Implemented two backup conformer embedding algorithms for robustness
+    - Added Nitrogen groups to transport
+    - Removed check for adsorbate getting adsorbed again which prevents Surface_Dissociation_to_Bidentate family
+    - Modified the liquid reactor to be able to simulate as CSTR, semi-batch, and/or vapor liquid mass transfer interface
+    - Added fragment code to rmgpy/molecule
+    - Added PDEP improvements: simulation least squares methods and the Georgievskii et al. 2013 CSE variant to Arkane
+    - Allow users to load thermo or kinetic libraries from a user-specified location
+    - Add radical flux tolerance
+    - Improved kH estimation code for solute
+    - Allow irreversible PDEP reactions by setting Keq=inf
+    - only calculate frequency and x in get_partition_function if semiclassical correction is needed
+    - Implemented deadend radical species selection algorithm
+    - Enable Metal, Facet, site and terrace specification in Molecule
+    - Increase species label max length for chemkin to avoid S(14567) style species
+    - Don't replace PDep kinetics of a library reaction
+    - Added solvation to surfaces
+    - Added some charge transfer reactions
+    - Added lithium
+
+
+- Auto Generated Trees
+    - Enabled estimator to ascend autogenerated rate tree if uncertainty is too high in a lower node
+    - Made some major improvements to automated tree extension generation and the cascade algorithm
+    - Added support for quadruple bonds in auto tree generation
+    - Added binding energies for N-S and C#S
+    - Removed hard-coded special treatment for Peroxyl Disproportionation family during template matching
+    - Increased ArrheniusBM fitting temperature upper limit to 2000K for RMG-database rate trees
+    - Skipped number of products check for ATG tree generation of Intra_R_Add_Endocyclic and Intra_R_Add_Exocyclic
+
+- RMS
+    - Add Transitory Edge Analysis
+    - Added surface reactions to RMS yaml format
+    - Updated developer installation instructions to use main RMS branch
+    - Add comment as input to to_rms() function
+    - Change RMS to use keyword variables to avoid twin PR with RMG whenever RMG changes struct
+
+- Arkane
+    - Added check for convergence and other common errors in QM parsers
+    - Updated the documentation that tabulates which levels of theory are supported by Arkane
+    - Read actual scan angles for rotor calculations
+    - Corrected Fourier fitting in torsion.pyx
+    - Added Psi4 ESS adapter to Arkane
+    - Added commit strings for RMG-Py and RMG-database to Arkane logs
+    - Added BAC confidence interval estimates to Arkane logs
+    - Added leave-one-out cross-validation for evaluating BAC fits
+    - Enabled parsing of scan log files with linear bend (something like L 1 2 3 B)
+    - Enabled assignment of PES (angles vs energies) directly in the Arkane input file
+    - Added a readme file for Arkane
+    - Updated QChem parser to only return the negative frequency from the last frequency block instead of the first
+    - Added more unit tests
+    - Save meaningful reaction label for PDEP reactions when creating RMG library
+    - Added more examples
+    - Added Arkane citation info: https://doi.org/10.1002/kin.21637, https://doi.org/10.1021/acs.jcim.2c00965
+    - Allow RMG to read Arkane YAML files through the RMGObject even if they have mol or aux keywords
+
+
+- Bugfixes
+    - Added check for multiplicity of reverse products if the family template reactants have multiplicity constraints
+    - Added check for vdW multiplicity constraints in forward direction
+    - Added check to see that empty surface site template group only matches empty surface site structure (and not vdW species with empty site)
+    - Fixed regex bug in checking multiplicity of adjacency list
+    - Fixed bug where RMG can output mechanisms in which two species have the same name
+    - Added QM fallback to ML or GAV in case of bad conformer ID error from rdkit
+    - Fixed many broken links in documentation
+    - Fixed species missing metal attribute error
+    - Fixed some automated tree generation parallelization bugs
+    - Changed tree generation get_training_set method to use deepcopy to clear atom labels and to parse out the metal from the entry
+    - Added a save_order attribute to some methods to preserve atom order in cases that need it
+    - Fixed load chemkin function to allow extended elements and species that start with digits
+    - Handle string data properly when averaging children solute
+    - Fixed bug in get_w0 where a_dict didn't match the molecule because it was made before the molecule was deepcopied
+    - Added check for pdep net reactions when removing species to prevent forbidden species from ending up in net reactions
+    - Fixed bug where add_atom_labels_for_reaction mislabels reactants if family is its own reverse
+    - Fixed bug where save_training_reactions occasionally mixes up atom labels
+    - Added Ctc atom type to prevent RMG from crashing when trying to make [C+]#[C-] molecule, which was then added to the forbidden structures
+    - Fixed bug where generate_resonance_structure does not preserve atom when keep_isomorphic=False and save_order=True
+    - Fixed bugs related to RMS object construction, particularly Multi/Pdep/Arrhenius and falloff
+    - Added check to always draw CO as 'CO' instead of 'OC'
+    - Converted ThermoData object to a NASA object for compatibility with RMS
+    - Corrected pyrms core/edge species/reaction handling for phase systems
+    - Fixed incorrect reading in load_chemkin_file for surface species with site density specified
+    - Added properties so group can be pickled without losing important information like ring membership
+    - Fixed bug where atom map changes even if save_order=True
+    - PDEP networks update before writing/filtering to avoid differences in barrier energy corrections between networks
+    - Check for debug mode so rms can be imported in debug mode
+    - Fixed group property has_wildcards to avoid AttributeError
+    - Fixed several calls missing the 'r' at the start of regex pattern string
+    - Fixed Fragment count_internal_rotors and is_atom_in_cycle attribute errors
+    - Added missing term in Troe kinetics formula
+    - Fixed some broken links in documentation
+    - Change cython variables from cpdef to cdef to avoid warnings
+    - Updated load_transport_file to skip any species in the transport file that's not in the species dictionary instead of crashing
+    - Fixed CI error "Unable to dlopen(cxxpath) in parent! cannot open shared object file: File name too long"
+
+
+- Testing
+    - Updated reference number of reactions for Arkane test_reactions unit test
+    - Changed molecule for rmgpy/data/thermoTest.py test_identifying_missing_group test because group is no longer missing
+    - Added continuous integration test for links in documentation
+    - Changed kinetics database tests to look for auto_generated tag instead of the hardcoded family list
+    - Updated rmg test data with new 2+2 cycloaddition species and reactions
+    - Remove cti file generation from regression tests to avoid Cantera IO error
+    - Added tests to check number of reactants and products defined in ATG rate rules
+    - CI is now done with mamba to drastically reduce runtime
+    - Move regression testing into main CI.yaml
+    - Simplify condition checking for scheduled vs pushed CI
+    - Remove redundant step creating stable_regression_results dir for running on a schedule or push to main because it already is the stable result
+    - Update CI.yml to allow CI tests on forks
+    - Added "phony" target so make test will always remake when run (instead of checking whether the test folder is up to date)
+    - Add a unit test to make a sample molecule for every atom type
+    - Update CI.yml and environment.yml to allow CI to run on MacOS
+    - Add regression testing for RMS's CSTR and constant V ideal gas reactors
+    - Bugfix on CI documentation testing so errors are reported as failures
+    - Relax tolerance on HinderedRotor.get_enthalpy() test to accomodate slightly different answer likely due to numerical issues
+    - Regression tests report failure if a model changes significantly
+    - Allow CI testing to be called from other repos
+    - Regression tests pass by default and the user must look at the report to see details of comparison
+    - Generate summary of regression test results to be displayed on annotation of PR results
+
+- Miscellaneous
+    - Added Docker install
+    - Added check to only publish documentation documentation from RMG official fork
+    - Fixed RMG-Py 3.1.0 release note bullet formatting
+    - Changed installation instructions for WSL users to install graphviz system wide to include all dependencies
+    - Changed get_all_solute_data function for RMG-website use in order to apply halogen or radical correction on top of library or GAV
+    - Added openSUSE installation instructions
+    - Changed default branch to main
+    - Changed rmg.py shebang to use python-jl instead of python3 for compatibility with RMS/pyrms
+    - Updated ketoenol template image to 1,3 sigmatropic rearrangement
+    - Updated 2+2_cycloaddition images in documentation
+    - Added licensing information to the README file
+    - Updated installation instructions with main instead of master branch, latest Anaconda link, and ssh instead of https clone from github
+    - Added support for Sticking Reactions in HTML reports
+    - Added reminder in documentation to activate rmg_env before making tests
+    - Check that family tree is not autogenerated before calling add_rules_from_training and fill_rules_by_averaging_up
+    - Added warning to not to call add_rules_from_training and fill_rules_by_averaging_up on ATG trees, and return statement before error
+    - Replaced BurkeH2O2 library with PrimaryH2O2 in relevant RMG examples
+    - Added instructions to Documentation for fixing libmkl_ts.so.2 ImportError
+    - Added new RMG-database paper to cite https://pubs.acs.org/doi/10.1021/acs.jcim.2c00965
+    - Added .bib file for easy citation
+    - Updated RMG-Py install instructions to remove old Julia instructions and to use mamba solver
+    - Use conda-forge ncurses for compatibility with docker
+    - Use conda-forge pyjulia instead of customized RMG channel version for better standardization
+    - Update Cantera version requirement to 2.6
+    - Upgrade to OpenMOPAC to fix license issues
+    - Updated list of developers
+    - Added Jupyter Notebook example for simulating and analyzing superminimal model
+    - Robot automatically marks issues and PR's as stale after 90 days of inactivity and closes them after 30 more days of inactivity
+
+
+RMG-Database Version 3.2.0
+==========================
+Date: August 2, 2023
+
+- Thermochemistry
+    - Identified and fitted thermo for missing groups using the following libraries:
+        'Klippenstein_Glarborg2016', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo',
+        'primaryThermoLibrary', 'primaryNS', 'NitrogenCurran', 'NOx2018', 'FFCM1(-)',
+        'SulfurLibrary', 'SulfurGlarborgH2S', 'SABIC_aromatics'
+    - Added more solutes and solvents to the solvent library
+    - Updated GAV method for solvation thermo to use more groups
+    - Added the following new halogen thermo libraries:
+        - CHOF_G4
+        - CHOCl_G4
+        - CHOBr_G4
+        - CHOFCl_G4
+        - CHOClBr_G4
+        - CHOFBr_G4
+        - CHOFClBr_G4
+        - Chlorination
+        - halogens
+        - 2-BTP
+        - 2-BTP_G4
+    - Added new halogens group entries for group.py, radical.py nonring.py, and longDistanceInteraction_noncyclic.py
+    - Added the following species to the primaryThermoLibrary: F, HF, F2, Br, HBr, Br2, NO, NO2, CO, OCCCO
+    - Updated halogen group entries with molecule symmetry number correction
+    - Added corrections for overestimation of triplet and multidentate adsorbates
+    - Added CO2, COOH, and HCOO to the Pt(111) thermo database
+    - Added halogens statmech library
+    - Added F/Cl/Br-benzene group additivity values
+    - Added "heavy halogen interaction" long distance thermo group
+    - Added thermo library with 1D rotor scans for species in ketoenol, retroene, and 1,3 sigmatropic rearrangement training reactions
+    - Added more Pt(111) thermo data
+    - Added correction to S6ddd thermo group
+
+- Kinetics
+    - Added coverage-dependent kinetics for surface reactions
+    - Added new halogens kinetics families and libraries
+    - Added the following new families:
+        - 1,3 sigmatropic rearrangement
+        - Intra halogen migration family 
+        - Surface_Abstraction_Beta
+        - Surface_Abstraction_Beta_double_vdW
+        - Surface_Adsorption_Dissociative_Double
+        - Surface_Dissociation_to_Bidentate
+        - XY_elimination_hydroxy
+    - Autogenerated the following family trees:
+        - 1,3_Insertion_CO2
+        - 1,3_NH3_elimination
+        - 1,3_sigmatropic_rearrangement
+        - 2+2_cycloaddition
+        - Bimolec_Hydroperoxide_Decomposition
+        - Birad_recombination
+        - CO Disproportionation
+        - Cyclopentadiene_scission
+        - Diels alder addition
+        - Disproportionation
+        - Ketoenol
+        - Peroxyl Disproportionation
+        - Retroene
+        - Substitution_O
+    - Added new rates and refit the following family trees:
+        - 1,3_Insertion CO2
+        - 1,3 sigmatropic rate tree
+        - Diels Alder Addition
+        - Intra_R_Add_Endo/Exocyclic
+        - retroene
+        - ketoenol
+        - aromatic_H_abstraction (new rates from Hou et al.)
+        - Surface_Adsorption_Bidentate
+        - Surface_Adsorption_Double
+        - Surface_Adsorption_Single
+        - Surface_Adsorption_vdW
+        - Surface_Bidentate_Dissociation
+        - Surface_Dissociation
+        - Surface_Dissociation_Beta
+        - Surface_vdW_to_Bidentate
+    - Added PrimaryH2O2 library with rates by Konnov
+    - Updated reactions for PrimaryNitrogenLibrary
+    - Added surface library reactions for ammonia
+    - Merged all 2+2_cycloaddition families in to one 2+2_cycloaddition family
+    - Generate Intra R Add Endo/Exocyclic rate trees from the ring opening direction to help distinguish between endo/exo 
+    - Added training reactions and groups related to PAH formation
+    - Save additional DFT settings information for metal binding energy calculations
+    - Added corrections to primaryH2O2 library
+    - Added corrections to Klippenstein_Glarborg2016 library related to singlet/triplet carbene reactions and other incorrectly imported reactions
+
+- Transport
+    - Added NIST transport library for fluorines
+    - Added new halogen transport groups
+    - Added Nitrogen groups to transport
+
+- QM Corrections
+    - Added frequency scaling factors AEC and BAC for wB97X-D3/def2-TZVP and B97-D3/def2-mSVP
+    - Added notebooks demonstrating how to update AEC and BAC
+    - Updated AECs for CCSD(T)-F12/cc-pVXZ-F12 st X = D, T
+    - Added frequency factors for b2plypd3/def2tzvp, b2plypd3/aug-cc-pvtz, b2plypd3/cc-pvtz
+    - Updated BAC using correct frequency scaling factor for:
+        - wB97X-D3/def2-TZVP
+        - B97-D3/def2-mSVP
+        - CCSD(T)-F12/cc-pVTZ-F12//wB97X-D3/def2-TZVP
+        - CCSD(T)-F12/cc-pVDZ-F12//wB97X-D3/def2-TZVP
+
+- Bugfixes
+    - Fixed the number of unpaired radicals in surface vdW families
+    - Fixed typos in training reactions field names
+    - Fixed enthalpy errors in adsorption corrections for O-containing species on Pt(111)
+    - Fixed some errors in surface training reaction rates
+    - Fixed some minor errors in the solvent library
+    - Fixed typos in coverage dependent kinetics parameters
+    - Used forbidden group to fix error where unsymmetric head node leads to Undeterminable Kinetics Error
+    - Removed duplicates in XY_addition_multiplebond
+    - Fixed typo in R_Recombination training reaction units
+    - Fixed incorrectly imported species H2CCC and C3H2 in the CurranPentane library
+    - Fixed master to main in trigger script
+    - Added the missing reactant and product number in the intra_R_Add families
+    - Fixed Intra_R_Add_Endocyclic/Exocyclic families by generating from the ring opening direction and enumerating backbones
+
+- Miscellaneous
+    - Updated Github Actions workflow for better handling of dual RMG-Py and RMG-database pull requests
+    - Added the Blowers-Masel tree generation notebook
+    - Added [C-]#[C+] to forbidden structures
+    - Added thermally forbidden 2pi + 2pi cycloaddition to forbidden structures
+    - Changed Github Actions to run on main branch instead of master
+    - Updated 2+2_cycloaddition reaction family images
+
+
 RMG-Py Version 3.1.0
 ====================
 Date: April 23, 2021