Degeneracy & Multiple TS #1055
Degeneracy & Multiple TS #1055
Commits on Jun 23, 2017
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reset database at end of test methods
to allow independent testing of various unittests, the database must be removed after each testing set, to avoid multiple modular level variables from existing. Solvation parameters were also cleared theend of modules using solvation refactored rmgTest and modelTest to reduce database generation
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added method to reduce atomID renaming
this commit checks to see that the IDs are already properly named before renaming the atom ids. It also modified the numbering of assignAtomID to assign random numbers
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Add isIdentical method to Species
Analogous to Species.isIsomorphic() Calls Molecule.isIdentical()
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modularized adding kinetics to reactions in
cerm.enlargeseparated out the adding of kinetics step from the enlarge method, to enable easier testing of the method. Also moved the adding of kinetics attribute till after degeneracy is modified to avoid multiple counting of degeneracy.
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refactored Reaction.degeneracy property
modified the protocol for setting degeneracy to get RMG to update the kinetics rate constant to keep track of the degeneracy and reaction rates. Also moved setting degeneracy in copy methods to before setting kinetics as this would double-count degeneracy.
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remove degeneracy calculations from __generateReactions
degeneracy calculation was removed from __generateReactions since it is moving to a standalone method.
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refactor reaction.isIsomorphic and allow identical checking
separated method to compare isomorphism of multiple species to reduce code repitition. Added option to use isIdentical instead of isIsomorphic.
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undo work-in-progress test for rmgTest
This commit makes the test for multiple deterministic kinetics function. and activates it for the testing suite.
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make default resonance structures isomorphic
changed default resonance structure generation to keep isomorphic structures since they are needed to proper degeneracy and symmetry values
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separate degeneracy calculation for rxn.reverse objects
separated setting reverse reactions for ownReverse family, so it can be called after degeneracy has been found (reducing work load), and for easier testing (+ wrote a test method for this reaction). this required adding H_Abstraction to kineticsTest and removing forbidden structures from kinetics test so all reactions can be found. added tests that test that findDegeneracies returns multiple transition states and that it is able to deal with aromatic structures
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Allow checkForExistingReactions to track multiple TS
Modified the method to remove reactions with the same template and family, including reverse direction for ownReverse families. It should keep reactions with multiple transition states (unless an identical template was found). Also wrote three test methods to test for keeping separate transition states or removing the redundant reaction
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Allow input of species' objects to __generateReactions(products)
Allow input of species objects to the products variable of __generateReactions since this would reduce resonanceIsomer generation
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This commit recreates the degeneracy algorithm in react.py. It now can: 1. take into account atom IDs when determining degeneracy 1. keep multiple transition states for the same reaction 1. use isomorphic resonance structures when comparing reactions Max Liu created the base for this method.
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method to ensure species list has all different IDs
Method written in react.py to ensure that given two reactants, the IDs on all of their atoms are different. This is necessary to trace atom IDs in products (after the structures are merged).
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ensure that reverse reactions have correct degeneracies
When reactions are found with the reverse template, they often have the degeneracy of the reverse template. This method ensures the reaction has the degeneracy of the forward template by using the family.calculateDegeneracy method.
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reduced degeneracy for identical reactants
reactants which are identical should have half the reaction rate when using the degeneracy method, since the translational component of their rates is already taken into account in their concentration, so them swapping places doesn't have a real effect on reaction rate. The algorithm to reduce degeneracy was placed in a separate method in the react module to be applied separately from finding degeneracies.
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get react module to work on Species, not molecules
refactored the react module to lump together reactions based on species as opposed to molecule. This is necessary for obtaining accurate degeneracy values for reactions with multiple resonance isomers. deflating now also takes species objects
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updated the calculateDegeneracy method
modified calculatDegeneracy to account for changes in degeneracy: * uses species objects if possible * looks at templates when multiple transition states present * calls the updated degeneracy algorithm * contains option to not reduce same reactant degeneracy (since this should only occur once).
