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Added solvation thermo groups for CtOt and OtCt. This makes the solvent effects for carbon monoxide, `+C#O-`, into that for `[CH2]=O`. Which it might not be like, but there are no Platts' groups for CO. Hopefully we can find some Abraham parameters to put in the library. But at least this should stop it crashing.
Closes ReactionMechanismGenerator/RMG-Py#382 Also must reorder the tree since the rules are listed in terms of templates that go XSRJ;C;YJ The tree must also obey this order in order for kinetics to be determined correctly. We should probably have a database test for this.
…base_fixes Database fixes corresponding to new unit tests
…somerization If it applies to the intra_substitutionCS_isomerization family, it should probably apply to all of these
It was causing errors in identifying the kinetics template.
Transferred from RMG-Java
Transferred from RMG-Java
Transferred from RMG-Java
Removed duplicated thermo entries, changed repeated indicies in kinetics libraries, changed atom types on a few thermo group entries to be more accurate.
Updates to sulfur chemistry
I combined the chembiodraw RMG families created by Nathan (in the same folder) into a PDF for people without access to chembiodraw.
…smGenerator/updateReference Update reference for H_abstraction rule 'C/H3/Cs;O_rad/NonDeO'
This is temporary because new changes to RMG-Py master are needed. When these changes are added to the new binary, we may once again use the binary for travis builds
This allows the aromatic bonds to have a ring correction of zero that doesn't match the generic ring group and has a match depth similar to that of other rings. Is also better for debugging and less alarming when looking at the thermo comments from group additivity.
Assign a rank of 10 to the topmost generic node, because it usually indicates a very poor estimate. Assign rank of 1 to the aromatic nodes in 'ring' groups, that way RMG selects the aromatic estimate rather than the others.
…smGenerator/ipsoDatabase Cyclic database improvements
This script takes thermo libraries and fits new polycyclic groups from them. It saves the all of the polycyclic groups to the file `new_polycyclic.py`. This file can be used to overwrite the original polycyclics thermo groups file in `input/thermo/groups/polycyclic.py`. **IMPORTANT:** It averages any data that is found within the libraries, but will overwrite any old thermo data. If old data is trustworthy, this script must be modified Uncertainties for the groups are calculated as 2s, where s is the sample standard deviation
Specify the kinetics library name below and run the script. It automatically overwrites the training reactions files it needs to. Then you should commit those files. This script only trains safely. In other words, if a single match from an RMG family is found, a training reaction is created. Sometimes, there are no matches from RMG reaction families, or multiple matches. This indicates an error that requires manual fixing, and a printout is given in the script.
…smGenerator/addTraining Training reactions and polycyclic thermo scripts
…ions. As for gas phase reactions, created a solvationReaction training database as well as a dictionary. The solvation reactions contain the reactants, solvent, and barrier correction.
…raction. Similar to training reactions for gas-phase. This is just for solvent=water.
In the future, these folders will correspond to a particular 'category'.. right now, we just have water.
These tree and groups are different than for gas-phase kinetics and reflect the calculations I've already done, as well as observations made.
…ane. Also contains a script for grabbing SMD output files and putting them in the training reactions. Modified the training for water too, but not cleaned up (some groups may be missing and the dictionary not starred).
This is to match the solvent name given in kinetics.
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This is needed for the solvation branch in ReactionMechanismGenerator/RMG-Py#126