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[cclib-svn] SF.net SVN: cclib: [148] trunk/src/cclib/method
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From: <ate...@us...> - 2006-05-22 22:21:12
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Revision: 148 Author: atenderholt Date: 2006-05-22 15:20:58 -0700 (Mon, 22 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=148&view=rev Log Message: ----------- Added overlap population analysis. Still need to do extensive testing. Modified Paths: -------------- trunk/src/cclib/method/__init__.py Added Paths: ----------- trunk/src/cclib/method/opa.py Modified: trunk/src/cclib/method/__init__.py =================================================================== --- trunk/src/cclib/method/__init__.py 2006-05-22 15:32:53 UTC (rev 147) +++ trunk/src/cclib/method/__init__.py 2006-05-22 22:20:58 UTC (rev 148) @@ -1,3 +1,4 @@ from density import Density from cspa import CSPA from mpa import MPA +from opa import OPA Added: trunk/src/cclib/method/opa.py =================================================================== --- trunk/src/cclib/method/opa.py (rev 0) +++ trunk/src/cclib/method/opa.py 2006-05-22 22:20:58 UTC (rev 148) @@ -0,0 +1,140 @@ +""" +cclib is a parser for computational chemistry log files. + +See http://cclib.sf.net for more information. + +Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt + + This program is free software; you can redistribute and/or modify it + under the terms of the GNU General Public License as published by the + Free Software Foundation; either version 2, or (at your option) any later + version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY, without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + +Contributions (monetary as well as code :-) are encouraged. +""" +import re,time +import Numeric +import random # For sometimes running the progress updater +from calculationmethod import Method + +class OPA(Method): + """The overlap population analysis""" + def __init__(self,*args): + + # Call the __init__ method of the superclass + super(OPA, self).__init__(logname="OPA",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "OPA of" % (self.parser) + + def __repr__(self): + """Return a representation of the object.""" + return 'OPA("%s")' % (self.parser) + + def calculate(self,indices=None,fupdate=0.05): + """Perform an overlap population analysis given the results of a parser""" + + if not self.parser.parsed: + self.parser.parse() + + #do we have the needed info in the parser? + if not hasattr(self.parser,"mocoeffs") \ + and not ( hasattr(self.parser,"aooverlaps") \ + or hasattr(self.parser, "fooverlaps") ) \ + and not hasattr(self.parser,"nbasis"): + self.logger.error("Missing mocoeffs, aooverlaps/fooverlaps or nbasis") + return False #let the caller of function know we didn't finish + + unrestricted=(len(self.parser.mocoeffs)==2) + nmocoeffs=len(self.parser.mocoeffs[0]) + nbasis=self.parser.nbasis + + if not indices: +#build list of groups of orbitals in each atom for atomresults + if hasattr(self.parser,"aonames"): + names=self.parser.aonames + elif hasattr(self.parser,"foonames"): + names=self.parser.fonames + + atoms=[] + indices=[] + + name=names[0].split('_')[0] + atoms.append(name) + indices.append([0]) + + for i in range(1,len(names)): + name=names[i].split('_')[0] + try: + index=atoms.index(name) + except ValueError: #not found in atom list + atoms.append(name) + indices.append([i]) + else: + indices[index].append(i) + + #determine number of steps, and whether process involves beta orbitals + nstep=nmocoeffs + nfrag=len(indices) #nfrag + self.logger.info("Creating attribute aoresults: array[3]") + if unrestricted: + self.results=Numeric.ones([2,nmocoeffs,nfrag,nfrag],"f") + nstep+=nmocoeffs + else: + self.results=Numeric.ones([1,nmocoeffs,nfrag,nfrag],"f") + + #intialize progress if available + if self.progress: + self.progress.initialize(nstep) + + step=0 + for spin in range(len(self.parser.mocoeffs)): + + for i in range(nmocoeffs): + + if self.progress and random.random()<fupdate: + self.progress.update(step,"Mulliken Population Analysis") + + # OP_{AB,i} = \sum_{a in A} \sum_{b in B} 2 c_{ai} c_{bi} S_{ab} + # = \sum_{a in A} c_{ai} \sum_{b in B} c_{bi} S_{ab} + # = \sum_{a in A} c_{ai} \sub_{b in B} C_{Bi} + # where C_{Bi} = C(i) times S(a) + + ci = self.parser.mocoeffs[spin][i] + + if hasattr(self.parser,"aooverlaps"): + temp = Numeric.multiply(ci,self.parser.aooverlaps) + elif hasattr(self.parser,"fooverlaps"): + temp = Numeric.multiply(ci,self.parser.fooverlaps) + + for A in range(len(indices)-1): + + for B in range(A+1,len(indices)): + + tempb=0 + for b in indices[B]: + tempb+=temp[:,b] + + tempresult=0 + for a in indices[A]: + tempresult+=ci[a]*tempb[a] + + self.results[spin][i][A][B]=2*tempresult + self.results[spin][i][B][A]=2*tempresult + + step+=1 + + if self.progress: + self.progress.update(nstep,"Done") + + return True + +if __name__=="__main__": + import doctest,opa + doctest.testmod(opa,verbose=False) Property changes on: trunk/src/cclib/method/opa.py ___________________________________________________________________ Name: svn:executable + * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
