Extraction of CML-CompChem from Gaussian, GAMESS-US and QChem #1
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The designation '<property dictRef="cc:zeropoint">' was not correct, as the list contains more than just the ZeroPointEnergy. Also resolved ambigous dictRefs of individual terms. See testcase in l716.thermochemistry.energies.xml for new output.
and fixed bug that energies are extracted from "terse" Gaussian output.
* Added support for: G3, G3MP2, G3B3, G3MP2B3, G4 and G4MP2 * Needed to find new markers for the beginning and end of jobs to have the final "Mixed" archive end up in it's own job. * Added a workaround to l9999.molecule.array.xml to enable extracting the coordinates from SP and Mixed operations in the composite methods, as in those the coordinate line includes a freeze-code (0) between the Symbol and the X-coordinate.
1. Terminlology: In the Archive the "forces" are actually gradients (inverted sign). Therefore the dictRef has been corrected from cc:forces to cc:gradients. 2. Bugfix: The arrays with cc:forceConstants and cc:gradients have been pulled-up too far in the xml tree, so that they appeared in the root cml:module.
The Object returned by evaluateValue(fromElement, value) can be a String, int, double or null, where the middle two can't be just casted into a Sting. Just replacing the cast ti Sting by .toString() raises an NPE, when null is returned.
fixed: adding the attributes `spinMultiplicity` and `formalCharge` to `cml:molecule`s
This patch tries to remove extra spaces before parsing the date with JodaTime. see https://bitbucket.org/oliver_stueker/jumbo-converters/issue/3
GAMESS VERSION = 12 JAN 2009 (R1)
…p, cc:press in terse file
…semi-empirical methods
…odules in ROHF and UHF calculations
…in job 2 of rohf calculation
…ital eigenvalues, orbital eigens and density matrices
…f cc:thirdDerivativesMethod for third derivatives method
…module and modules l716 and l601.polariz to finalization child module otherComponents
…ontain table of arrays
…them as attribs to all molecules
…_total in finalization propertyList
…nt to finalization property list, added module cc:multipole to finalization module
…t archive sections from Linux and Windows
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Work to improve support of extracting from Gaussian files as well as parsers for GAMESS-US and QChem.