From bddbafd665a5029bd3d8e494b705a0878c920921 Mon Sep 17 00:00:00 2001 From: Sevy Harris Date: Sun, 3 Jul 2022 11:59:28 -0400 Subject: [PATCH] added release notes for RMG-Py and RMG-database --- .../source/users/rmg/releaseNotes.rst | 216 ++++++++++++++++++ 1 file changed, 216 insertions(+) diff --git a/documentation/source/users/rmg/releaseNotes.rst b/documentation/source/users/rmg/releaseNotes.rst index 49e9471d74f..94ffe51f99c 100644 --- a/documentation/source/users/rmg/releaseNotes.rst +++ b/documentation/source/users/rmg/releaseNotes.rst @@ -3,6 +3,222 @@ ************* Release Notes ************* + +RMG-Py Version 3.2.0 +==================== +Date: July 7, 2022 + +- 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 + - 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 + +- 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 + - Added surface reactions to RMS yaml format + +- 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 + +- 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 + +- 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 + +- Miscellaneous + - 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 + + +RMG-Database Version 3.2.0 +========================== +Date: July 7, 2022 + +- Thermochemistry + - 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 + + +- Kinetics + - Added coverage-dependent kinetics for surface reactions + - Added the following new families: + - Surface_Adsorption_Dissociative_Double + - Surface_Abstraction_Beta_double_vdW + - Surface_Abstraction_Beta + - XY_elimination_hydroxy + - Intra halogen migration family + - 1,3 sigmatropic rearrangement + - Autogenerated the following family trees: + - Diels alder addition + - Substitution_O + - Ketoenol + - Retroene + - Disproportionation + - Cyclopentadiene_scission + - 1,3_NH3_elimination + - CO Disproportionation + - Peroxyl Disproportionation + - Bimolec_Hydroperoxide_Decomposition + - 1,3_sigmatropic_rearrangement + - Added PrimaryH2O2 library with rates by Konnov + - Added surface library reactions for ammonia + - Added more nodes to Surface_Adsorption_Double, Surface_Adsorption_Single, Surface_Adsorption_vdW, Surface_Dissociation, and Surface_Dissociation_Beta families + - Added new halogens kinetics families and libraries + - Added new rates and refit retroene rate tree + - Added new rates and refit ketoenol rate tree + - Added new rates and refit Intra R Add Endo/Exocyclic rate trees + - Added training reactions for Diels Alder Addition family + + +- 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 ωB97X-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 factor for b2plypd3/def2tzvp + - Updated BAC using correct frequency scaling factor for: + - wB97X-D3/def2-TZVP + - B97-D3/def2-mSVP + - CCSD(T)-F12/cc-pVTZ-F12//ωB97X-D3/def2-TZVP + - CCSD(T)-F12/cc-pVDZ-F12//ωB97X-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