Merge branch 'v2.1.7' into v2.1.8

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

meta.yaml

@@ -77,7 +77,7 @@ requirements:
     - pyzmq
     - quantities
     - rdkit >=2015.09.2
-    - rmgdatabase >=2.1.0
+    - rmgdatabase >=2.1.7
     - scipy
     - scoop
     - symmetry

rmgpy/version.py

@@ -34,4 +34,4 @@
 This value can be accessed via `rmgpy.__version__`.
 """
 
-__version__ = '2.1.0'
+__version__ = '2.1.7'