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Merge branch 'v2.1.6' into v2.1.7
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‎documentation/source/users/rmg/releaseNotes.rst‎

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Release Notes
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RMG-Py Version 2.1.6
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====================
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Date: December 21, 2017
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- Model resurrection:
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- Automatically attempts to save simulation after encountering a DASPK error
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- Adds species and reactions in order to modify model dynamics and fix the error
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- New features:
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- Add functionality to read RCCSD(T)-F12 energies from MolPro log files
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- Add liquidReactor support to flux diagram generation
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- Other changes:
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- Removed rmgpy.rmg.model.Species class and merged functionality into main rmgpy.species.Species class
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- Refactored parsing of RMG-generated kinetics comments from Chemkin files and fixed related issues
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- Refactored framework for generating reactions to reduce code duplication
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- Resonance methods renamed from generateResonanceIsomers to generate_resonance_structures across all modules
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- Raise CpInf to Cphigh for entropy calculations to prevent invalid results
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- Fixes:
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- Update sensitivity analysis to use ModelSettings and SimulatorSettings classes introduced in v2.1.5
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- Fixed generate_reactions methods in KineticsDatabase to be directly usable again
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- Fixed issues with aromaticity perception and generation of aromatic resonance structures
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RMG-database Version 2.1.6
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==========================
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Date: December 21, 2017
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- Additions:
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- New training reactions added for [NH2] related H_Abstractions
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- 14 new kinetics libraries related to aromatics formation (see RMG-database #222 for details)
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- Other changes:
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- Removed some global forbidden groups which are no longer needed
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- Forbid CO and CS biradicals
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- Updated lone_electron_pair_bond family and removed from recommended list
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- Fixes:
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- Fixed unit errors in some H_Abstraction and R_Addition_MultipleBond depositories
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RMG-Py Version 2.1.5
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====================
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Date: October 18, 2017
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- New bicyclic formula:
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- Estimates polycyclic corrections for unsaturated bicyclics by adjusting the correction for the saturated version
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- Can provide a decent estimate in many cases where there is not an exact match
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- Other changes:
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- Refactored simulation algorithm to properly add multiple objects per iteration
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- Print equilibrium constant and reverse rate coefficient values when using Cantherm to calculate kinetics
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- Speed up degeneracy calculation by reducing unnecessary operations
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- Fixes:
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- Loosen tolerance for bond order identification to account for floating point error
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- Fixed uncertainty analysis to allow floats as bond orders
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- Fixed some comment parsing issues in uncertainty analysis
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- Added product structure atom relabeling for families added in RMG-database v2.1.5
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- Fixed issue with automatic debugging of kinetics errors due to forbidden structures
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RMG-database Version 2.1.5
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==========================
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Date: October 18, 2017
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- Additions:
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- New thermo groups added for species relevant in cyclopentadiene and natural gas pyrolysis
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- Added C2H4+O_Klipp2017 kinetics library
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- Fixes:
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- Prevent charged carbenes from reacting in Singlet_Carbene_Intra_Disproportionation
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- Updated H_Abstraction rates in ethylamine library and corresponding training reactions
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RMG-Py Version 2.1.4
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====================
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Date: September 08, 2017
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- Accelerator tools:
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- Dynamics criterion provides another method to expand the mechanism by adding reactions to the core
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- Surface algorithm enables better control of species movement to the core when using the dynamics criterion
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- Multiple sets of model parameters can now be specified in a input file to allow different stages of model generation
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- A species number termination criterion can now be set to limit model size
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- Multiple items can now be added per iteration to speed up model construction
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- New ModelSettings and SimulatorSettings classes for storing input parameters
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- New features:
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- Kinetics libraries can now be automatically generated during RMG runs to be used as seeds for subsequent runs
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- Loading automatically generated seed mechanisms recreates the original template reaction objects to allow restarting runs from the seed mechanism
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- Carbene constraints can now be set in the species constraint block using maxSingletCarbenes and maxCarbeneRadicals
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- Chirality is now considered for determining symmetry numbers
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- Thermodynamic pruning has been added to allow removal of edge species with unfavorable free energy (beta)
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- Other changes:
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- RMG-Py exception classes have been consolidated in the rmgpy.exceptions module
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- Species labels will now inherit the label from a matched thermo library entry
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- Sensitivity analysis is now available for LiquidReactor
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- Fixes:
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- Fixed sensitivity analysis following changes to the simulate method
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- Add memory handling when generating collision matrix for pressure dependence
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- Improved error checking for MOPAC
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- Prevent infinite loops when retrieving thermo groups
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- Known issues:
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- Seed mechanisms cannot be loaded if the database settings are different from the original ones used to generate the seed
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RMG-database Version 2.1.4
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==========================
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Date: September 08, 2017
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- New kinetics families for propargyl recombination route to benzene:
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- Singlet_Carbene_Intra_Disproportionation
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- Intra_5_membered_conjugated_C=C_C=C_addition
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- Intra_Diels_alder_monocyclic
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- Concerted_Intra_Diels_alder_monocyclic_1,2_shift
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- Intra_2+2_cycloaddition_Cd
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- Cyclopentadiene_scission
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- 6_membered_central_C-C_shift
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- Renamed kinetics families:
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- Intra_Diels_Alder --> Intra_Retro_Diels_alder_bicyclic
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- H_shift_cyclopentadiene --> Intra_ene_reaction
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- Other additions:
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- Klippenstein_Glarborg2016 kinetics and thermo libraries
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- Group additivity values added for singlet carbenes, which are no longer forbidden
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RMG-Py Version 2.1.3
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====================
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Date: July 27, 2017
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- Thermo central database:
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- Framework for tracking and submitting species to a central database have been added
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- Following species submission, the central database will queue and submit quantum chemistry jobs for thermochemistry calculation
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- This is an initial step towards self-improving thermochemistry prediction
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- Rotor handling in Cantherm:
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- Free rotors can now be specified
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- Limit number of terms used when fitting hinder rotor scans
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- Fixed bug with ZPE calculation when using hindered rotors
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- New reaction degeneracy algorithm:
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- Use atom ID's to distinguish degenerate reactions from duplicates due to other factors
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- Degeneracy calculation now operates across all families rather than within each separately
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- Multiple transition states are now identified based on template comparisons and kept as duplicate reactions
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- Nodal distances:
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- Distances can now be assigned to trees in reaction families
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- This enables better rate averages with multiple trees
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- Fixed bug with finding the closest rate rule in the tree
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- New features:
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- Added methods for automatically writing RMG-database files
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- New symmetry algorithm improves symmetry number calculations for resonant and cyclic species
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- Group additivity algorithm updated to apply new long distance corrections
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- Specific colliders can now be specified for pressure-dependent rates
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- Very short superminimal example added (hydrogen oxidation) for checking basic RMG operation
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- Cantera now outputs a Chemkin file which can be directly imported into Chemkin
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- Fixes:
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- Fixed bug with negative activation energies when using Evans-Polanyi rates
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- Fixed walltime specification from command line when running RMG
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- Fixes and unit tests added for diffusionLimited module
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- Known issues:
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- The multiple transition state algorithm can result in undesired duplicate reactions for reactants with multiple resonance structures
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RMG-database Version 2.1.3
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==========================
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Date: July 27, 2017
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- Long-distance interaction thermo corrections:
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- The gauche and int15 group files have been replaced by longDistanceInteraction_noncyclic
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- New corrections for cyclic ortho/meta/para interactions are now available in longDistanceInteraction_cyclic
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- Changes:
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- Oa_R_Recombination family renamed to Birad_R_Recombination
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- More training reactions added for sulfur species in H_Abstraction
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- RMG-database tests have been moved to RMG-Py
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RMG-Py Version 2.1.2
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====================
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Date: May 18, 2017
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- Improvements:
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- New nitrogen atom types
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- Kinetics libraries can now be specified as a list of strings in the input file
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- New script to generate output HTML locally: generateChemkinHTML.py
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- New kekulization module replaces RDKit for generating Kekule structures
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- Benzene bonds can now be reacted in reaction families
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- Removed cantherm.geometry module due to redundancy with statmech.conformer
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- Fixes:
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- Reaction direction is now more deterministic after accounting for floating point error
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- Multiple bugs with resonance structure generation for aromatics have been addressed
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RMG-database Version 2.1.2
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==========================
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Date: May 18, 2017
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- Nitrogen improvements:
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- Added ethylamine kinetics library
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- Updated group additivity values for nitrogen species
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- Added rate rules and training reactions for nitrogen species
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- Additions:
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- New CO_Disproportionation family
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- Added CurranPentane kinetics and thermo libraries
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- Fixes:
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- Corrected some rates in FFCM1(-) to use MultiArrhenius kinetics
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- Corrected a few adjlists in FFCM1(-)
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RMG-Py Version 2.1.1
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====================
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Date: April 07, 2017
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- Uncertainty analysis:
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- Local and global uncertainty analysis now available for RMG-generated models
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- Global uncertainty analysis uses MIT Uncertainty Quantification library, currently only supported on Linux systems
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- Examples for each module are available in localUncertainty.ipynb and globalUncertainty.ipynb
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- Fixes:
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- Clar structure generation no longer intercepts signals
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- Fixes to SMILES generation
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- Fix default spin state of [CH]
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RMG-database Version 2.1.1
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==========================
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Date: April 07, 2017
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- Additions:
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- More species added to FFCM1(-) thermo library
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- Changes:
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- Improved handling of excited species in FFCM1(-) kinetics library
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- Replaced Klippenstein H2O2 kinetics and thermo libraries with BurkeH2O2inN2 and BurkeH2O2inArHe
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- Fixes:
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- Corrected adjlists for some species in JetSurf2.0 kinetics and thermo libraries (also renamed from JetSurf0.2)
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- Correct multiplicities for [C] and [CH] in multiple libraries ([C] from 5 to 3, [CH] from 4 to 2)
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RMG-Py Version 2.1.0
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====================
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Date: March 07, 2017

‎meta.yaml‎

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- pyzmq
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- quantities
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- rdkit >=2015.09.2
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- rmgdatabase >=2.1.0
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- rmgdatabase >=2.1.6
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- scipy
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- scoop
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- symmetry

‎rmgpy/version.py‎

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This value can be accessed via `rmgpy.__version__`.
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"""
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__version__ = '2.1.0'
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__version__ = '2.1.6'

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