diff --git a/documentation/source/users/rmg/releaseNotes.rst b/documentation/source/users/rmg/releaseNotes.rst index 707a8c9710..6873b9da34 100644 --- a/documentation/source/users/rmg/releaseNotes.rst +++ b/documentation/source/users/rmg/releaseNotes.rst @@ -4,6 +4,317 @@ Release Notes ************* +RMG-Py Version 2.1.7 +==================== +Date: February 12, 2018 + +- 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 + + +RMG-database Version 2.1.7 +========================== +Date: February 12, 2018 + +- Charged atom types: + - Update adjlists with new atom types across the entire database + - Added sulfur groups to all relevant kinetics families + - New thermo group additivity values for sulfur/oxygen species + +- Additions: + - Benzene bonds can now react in in R_Addition_MultipleBond + - Many new training reactions and groups added in R_Addition_MultipleBond + - New Singlet_Val6_to_triplet kinetics family + - New Sulfur GlarborgBozzelli kinetics and thermo libraries + - New Sulfur GlarborgMarshall kinetics and thermo libraries + - New Sulfur GlarborgH2S kinetics and thermo libraries + - New Sulfur GlarborgNS kinetics and thermo libraries + - New NOx and NOx/LowT kinetics libraries + - New SOx kinetics library + - New BurcatNS thermo library + - New SOxNOx thermo library + - New 2+2_cycloaddition_CS kinetics family + - New Cyclic_Thioether_Formation kinetics family + - New Lai_Hexylbenzene kinetics and thermo libraries + +- Changes: + - 1,2-Birad_to_alkene family is now irreversible + - OxygenSingTrip kinetics library removed (replaced by Singlet_Val6_to_triplet family) + - Ozone is no longer forbidden + +- Fixes: + - Corrected adjlist for phenyl radical in JetSurf2.0 and USC-Mech-ii + - Some singlet thermo groups relocated from radical.py to group.py + + +RMG-Py Version 2.1.6 +==================== +Date: December 21, 2017 + +- 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 + +RMG-database Version 2.1.6 +========================== +Date: December 21, 2017 + +- Additions: + - New training reactions added for [NH2] related H_Abstractions + - 14 new kinetics libraries related to aromatics formation (see RMG-database #222 for details) + +- Other changes: + - Removed some global forbidden groups which are no longer needed + - Forbid CO and CS biradicals + - Updated lone_electron_pair_bond family and removed from recommended list + +- Fixes: + - Fixed unit errors in some H_Abstraction and R_Addition_MultipleBond depositories + + +RMG-Py Version 2.1.5 +==================== +Date: October 18, 2017 + +- 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 + +RMG-database Version 2.1.5 +========================== +Date: October 18, 2017 + +- Additions: + - New thermo groups added for species relevant in cyclopentadiene and natural gas pyrolysis + - Added C2H4+O_Klipp2017 kinetics library + +- Fixes: + - Prevent charged carbenes from reacting in Singlet_Carbene_Intra_Disproportionation + - Updated H_Abstraction rates in ethylamine library and corresponding training reactions + + +RMG-Py Version 2.1.4 +==================== +Date: September 08, 2017 + +- Accelerator tools: + - Dynamics criterion provides another method to expand the mechanism by adding reactions to the core + - Surface algorithm enables better control of species movement to the core when using the dynamics criterion + - Multiple sets of model parameters can now be specified in a input file to allow different stages of model generation + - A species number termination criterion can now be set to limit model size + - Multiple items can now be added per iteration to speed up model construction + - New ModelSettings and SimulatorSettings classes for storing input parameters + +- New features: + - Kinetics libraries can now be automatically generated during RMG runs to be used as seeds for subsequent runs + - Loading automatically generated seed mechanisms recreates the original template reaction objects to allow restarting runs from the seed mechanism + - Carbene constraints can now be set in the species constraint block using maxSingletCarbenes and maxCarbeneRadicals + - Chirality is now considered for determining symmetry numbers + - Thermodynamic pruning has been added to allow removal of edge species with unfavorable free energy (beta) + +- Other changes: + - RMG-Py exception classes have been consolidated in the rmgpy.exceptions module + - Species labels will now inherit the label from a matched thermo library entry + - Sensitivity analysis is now available for LiquidReactor + +- Fixes: + - Fixed sensitivity analysis following changes to the simulate method + - Add memory handling when generating collision matrix for pressure dependence + - Improved error checking for MOPAC + - Prevent infinite loops when retrieving thermo groups + +- Known issues: + - Seed mechanisms cannot be loaded if the database settings are different from the original ones used to generate the seed + +RMG-database Version 2.1.4 +========================== +Date: September 08, 2017 + +- New kinetics families for propargyl recombination route to benzene: + - Singlet_Carbene_Intra_Disproportionation + - Intra_5_membered_conjugated_C=C_C=C_addition + - Intra_Diels_alder_monocyclic + - Concerted_Intra_Diels_alder_monocyclic_1,2_shift + - Intra_2+2_cycloaddition_Cd + - Cyclopentadiene_scission + - 6_membered_central_C-C_shift + +- Renamed kinetics families: + - Intra_Diels_Alder --> Intra_Retro_Diels_alder_bicyclic + - H_shift_cyclopentadiene --> Intra_ene_reaction + +- Other additions: + - Klippenstein_Glarborg2016 kinetics and thermo libraries + - Group additivity values added for singlet carbenes, which are no longer forbidden + + +RMG-Py Version 2.1.3 +==================== +Date: July 27, 2017 + +- Thermo central database: + - Framework for tracking and submitting species to a central database have been added + - Following species submission, the central database will queue and submit quantum chemistry jobs for thermochemistry calculation + - This is an initial step towards self-improving thermochemistry prediction + +- Rotor handling in Cantherm: + - Free rotors can now be specified + - Limit number of terms used when fitting hinder rotor scans + - Fixed bug with ZPE calculation when using hindered rotors + +- New reaction degeneracy algorithm: + - Use atom ID's to distinguish degenerate reactions from duplicates due to other factors + - Degeneracy calculation now operates across all families rather than within each separately + - Multiple transition states are now identified based on template comparisons and kept as duplicate reactions + +- Nodal distances: + - Distances can now be assigned to trees in reaction families + - This enables better rate averages with multiple trees + - Fixed bug with finding the closest rate rule in the tree + +- New features: + - Added methods for automatically writing RMG-database files + - New symmetry algorithm improves symmetry number calculations for resonant and cyclic species + - Group additivity algorithm updated to apply new long distance corrections + - Specific colliders can now be specified for pressure-dependent rates + - Very short superminimal example added (hydrogen oxidation) for checking basic RMG operation + - Cantera now outputs a Chemkin file which can be directly imported into Chemkin + +- Fixes: + - Fixed bug with negative activation energies when using Evans-Polanyi rates + - Fixed walltime specification from command line when running RMG + - Fixes and unit tests added for diffusionLimited module + +- Known issues: + - The multiple transition state algorithm can result in undesired duplicate reactions for reactants with multiple resonance structures + +RMG-database Version 2.1.3 +========================== +Date: July 27, 2017 + +- Long-distance interaction thermo corrections: + - The gauche and int15 group files have been replaced by longDistanceInteraction_noncyclic + - New corrections for cyclic ortho/meta/para interactions are now available in longDistanceInteraction_cyclic + +- Changes: + - Oa_R_Recombination family renamed to Birad_R_Recombination + - More training reactions added for sulfur species in H_Abstraction + - RMG-database tests have been moved to RMG-Py + + +RMG-Py Version 2.1.2 +==================== +Date: May 18, 2017 + +- Improvements: + - New nitrogen atom types + - Kinetics libraries can now be specified as a list of strings in the input file + - New script to generate output HTML locally: generateChemkinHTML.py + - New kekulization module replaces RDKit for generating Kekule structures + - Benzene bonds can now be reacted in reaction families + - Removed cantherm.geometry module due to redundancy with statmech.conformer + +- Fixes: + - Reaction direction is now more deterministic after accounting for floating point error + - Multiple bugs with resonance structure generation for aromatics have been addressed + + +RMG-database Version 2.1.2 +========================== +Date: May 18, 2017 + +- Nitrogen improvements: + - Added ethylamine kinetics library + - Updated group additivity values for nitrogen species + - Added rate rules and training reactions for nitrogen species + +- Additions: + - New CO_Disproportionation family + - Added CurranPentane kinetics and thermo libraries + +- Fixes: + - Corrected some rates in FFCM1(-) to use MultiArrhenius kinetics + - Corrected a few adjlists in FFCM1(-) + + +RMG-Py Version 2.1.1 +==================== +Date: April 07, 2017 + +- Uncertainty analysis: + - Local and global uncertainty analysis now available for RMG-generated models + - Global uncertainty analysis uses MIT Uncertainty Quantification library, currently only supported on Linux systems + - Examples for each module are available in localUncertainty.ipynb and globalUncertainty.ipynb + +- Fixes: + - Clar structure generation no longer intercepts signals + - Fixes to SMILES generation + - Fix default spin state of [CH] + +RMG-database Version 2.1.1 +========================== +Date: April 07, 2017 + +- Additions: + - More species added to FFCM1(-) thermo library + +- Changes: + - Improved handling of excited species in FFCM1(-) kinetics library + - Replaced Klippenstein H2O2 kinetics and thermo libraries with BurkeH2O2inN2 and BurkeH2O2inArHe + +- Fixes: + - Corrected adjlists for some species in JetSurf2.0 kinetics and thermo libraries (also renamed from JetSurf0.2) + - Correct multiplicities for [C] and [CH] in multiple libraries ([C] from 5 to 3, [CH] from 4 to 2) + + RMG-Py Version 2.1.0 ==================== Date: March 07, 2017 diff --git a/meta.yaml b/meta.yaml index c4738ae9a4..0e65b76a37 100644 --- a/meta.yaml +++ b/meta.yaml @@ -77,7 +77,7 @@ requirements: - pyzmq - quantities - rdkit >=2015.09.2 - - rmgdatabase >=2.1.0 + - rmgdatabase >=2.1.7 - scipy - scoop - symmetry diff --git a/rmgpy/version.py b/rmgpy/version.py index 0ff6d68952..bf6459b8cd 100644 --- a/rmgpy/version.py +++ b/rmgpy/version.py @@ -34,4 +34,4 @@ This value can be accessed via `rmgpy.__version__`. """ -__version__ = '2.1.0' \ No newline at end of file +__version__ = '2.1.7' \ No newline at end of file