Introducing LogFile.parse(), and parse() of child classes renamed to extract(). Addition of fupdate and cupdate to GAMESS.extract().
Moved generic conversion of attributes to arrays from .extract() to .parse() - conversion takes place only if attribute is not already an array. Also: fixed dimensions of geovalues in Jaguar parser so that it can be converted to an array (there is no first energy change, so it is set to zero); moenergies is not converted to an array, kept as a list of rank-1 arrays, as per wiki. No changes when running tests.
Moved conversion of moenergies and scfvalues to lists of arrays to LogFile.parse() from specific parsers. No changes in tests.
Added IOError arounf call to openlogfile in ccopen, which returns None.
Set LogFile.parsed to False at end of LogFile.clean().
Rewrote condition for self.extract() call in LogFile.parse() to an AttributeError exception.
Moved to LogFile.parse(): creation of default coreelectrons; setting default value of nmo to nbasis; setting self.parsed to True after parsing.
Volume.py: Calculates electron density now. I realised that there was no shortcut (at least that I could think of). You just need to iterate over all of the occupied orbitals and add up the squares of the wavefunctions.
Move to LogFile.parse from extract method of specific parsers: opening/closing file object, initializing and final update of self.progress.
Volume: Minor type correction (float-->integer) required for the Numeric version I'm using on Windows.
Created LogFile.updateprogress() for updating LogFile.progress; replaced code with a call to the method in all parsers.
Modifying LogFile.__setattr__ to update LogFile.logger for elements of LogFile.attrlist.
Oops, moving back to revision 492. Previous commit belongs in the parser-refactoring branch.
Wrote gbasis for Jaguar. Looks fine, but after adding some more tests, there are several failures for different parsers, so need to look into these.
Corrected a basis fn test. Passes for Gaussian. All of the GAMESS ones have only half the correct number due to symmetry issues. Am unsure about the Jaguar ones, as I thought I had it all figured out.
GAMESS parser now handles gbasis correctly for symmetrical molecules.
Fixed names and docstrings of MP tests for messages in testall.py
GAMESSUK gbasis now works fine for symmetrical molecules. Corrected small error in GAMESS gbasis.
Removed all reference to gbasis for Jaguar. Be gone!
Jaguar parser, atomcoords: Got two more tests to pass by avoiding including the input geometry twice