Qchem Module for Cantherm - #255
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qchem.py: this new module works reads in information from qchem output files (e.g., opt+freq jobs, PES scan jobs). In it's present form, it works, but there is still one more thing that must be added - a read force constant matrix function. I've been advised to make this commit earlier rather than later, however. statmech.py is necessarily changed so that RMG/cantherm recognizes qchem files. In addition, I know I still have to make unittests, and update the documentation, which I'll get to shortly. Feel free to test it out and let me know what's wrong.
Mostly bug fixes.
Rather large example but should still be helpful.
didn't realize the qchem mod was not properly reading in atomic numbers. Caused cantherm to crash when trying to write cartesian coordinates of species to the output file
my isopentoxy example is too big (it has 30+ MB of qchem output files), so I am adding a smaller one. I will add other small ones in the future that include pdep. Also, I reverted a change in the C2H4+H example back to what is on the master RMG-Py brach.
it's too big and complicated ...
this one is for a unimolecular decomposition reaction using the Qchem mod
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Reformulated as #256 |
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to_smiles() shortcuts small species through two lookup tables that were keyed on the chemical formula. A formula says nothing about charge, so any charged species whose formula matched an entry was handed the neutral species' SMILES, silently: the O(-.) anion came out as '[O]' and read back at net charge zero, and H(-) came out as 'H+' - the proton's entry, which is not even parseable SMILES. Anything keyed on the SMILES (Chemkin and YAML export, species dictionaries, library matching) therefore saw a different species than the mechanism contained, and two species differing by an electron could collide onto one identifier. The defect was never limited to single atoms, and not to ions either. The O2 anion collided with the neutral biradical's '[O][O]'; cyclic ozone collided with ozone's '[O-][O+]=O'; the carbene form of CO collided with '[C-]#[O+]'. Those last two are net-neutral species in the standard libraries, so the collision reached ordinary neutral chemistry as well as the plasma set. Both tables are now keyed on the charge signature - the formula together with the charges the atoms carry. Net charge alone would not do it, because an ion pair such as H(+).OH(-) is net neutral and would still collide with water. Every previous entry keeps its exact string; the proton's entry is corrected from the unparseable 'H+' to '[H+]', matching what SMILES_LOOKUPS already reads. The electron keeps its entry because no backend can write it: RDKit raises on element 'e' and OpenBabel emits an unparseable '[ReactionMechanismGenerator#255-]'. Separately, a written SMILES is now checked against the molecule's net charge before a backend's output is accepted, so a backend that cannot represent the charge causes the next backend to be tried and, failing that, an exception - rather than a wrong-but-parseable string that propagates silently. The check runs only for charged molecules, so neutral chemistry pays nothing for it. The adjacency-list path is unchanged; it was correct throughout and is the reference the SMILES side is now made to agree with.
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Added a module for cantherm that allows users to perform rate theory calculations with Qchem output files. Similar to the Gaussian module. Added a couple simple examples as well