Logo Search packages:      
Sourcecode: cclib version File versions  Download package

cda.py

00001 """
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""

__revision__ = "$Revision: 453 $"

import random # For sometimes running the progress updater

import numpy

from fragments import FragmentAnalysis


00015 class CDA(FragmentAnalysis):
    """Charge Decomposition Analysis (CDA)"""
    
    def __init__(self, *args):
    
        # Call the __init__ method of the superclass.
        super(FragmentAnalysis, self).__init__(logname="CDA", *args)
        
00023     def __str__(self):
        """Return a string representation of the object."""
        return "CDA of" % (self.data)

00027     def __repr__(self):
        """Return a representation of the object."""
        return 'CDA("%s")' % (self.data)
    
00031     def calculate(self, fragments, cupdate=0.05):
        """Perform the charge decomposition analysis.
        
        Inputs:
            fragments - list of ccData data objects
        """
    

        retval = super(CDA, self).calculate(fragments, cupdate)
        if not retval:
            return False

        # At this point, there should be a mocoeffs and fooverlaps
        #   in analogy to a ccData object.

        donations = []
        bdonations = []
        repulsions = []
        residuals = []

        if len(self.mocoeffs) == 2:
            occs = 1
        else:
            occs = 2

        # Intialize progress if available.
        nstep = self.data.homos[0]
        if len(self.data.homos) == 2:
            nstep += self.data.homos[1]
        if self.progress:
            self.progress.initialize(nstep)

        # Begin the actual method.
        step = 0
        for spin in range(len(self.mocoeffs)):

            size = len(self.mocoeffs[spin])
            homo = self.data.homos[spin]

            if len(fragments[0].homos) == 2:
                homoa = fragments[0].homos[spin]
            else:
                homoa = fragments[0].homos[0]

            if len(fragments[1].homos) == 2:
                homob = fragments[1].homos[spin]
            else:
                homob = fragments[1].homos[0]

            offset = fragments[0].nbasis

            self.logger.info("Creating donations, bdonations, and repulsions: array[]")
            donations.append(numpy.zeros(size, "d"))
            bdonations.append(numpy.zeros(size, "d"))
            repulsions.append(numpy.zeros(size, "d"))
            residuals.append(numpy.zeros(size, "d"))

            for i in range(self.data.homos[spin] + 1):

                # Calculate donation for each MO.
                for k in range(0, homoa + 1):
                    for n in range(offset + homob + 1, self.data.nbasis):
                        donations[spin][i] += 2 * occs * self.mocoeffs[spin][i,k] \
                                                * self.mocoeffs[spin][i,n] * self.fooverlaps[k][n]

                for l in range(offset, offset + homob + 1):
                    for m in range(homoa + 1, offset):
                        bdonations[spin][i] += 2 * occs * self.mocoeffs[spin][i,l] \
                                                * self.mocoeffs[spin][i,m] * self.fooverlaps[l][m]

                for k in range(0, homoa + 1):
                    for m in range(offset, offset+homob + 1):
                        repulsions[spin][i] += 2 * occs * self.mocoeffs[spin][i,k] \
                                                * self.mocoeffs[spin][i, m] * self.fooverlaps[k][m]

                for m in range(homoa + 1, offset):
                    for n in range(offset + homob + 1, self.data.nbasis):
                        residuals[spin][i] += 2 * occs * self.mocoeffs[spin][i,m] \
                                                * self.mocoeffs[spin][i, n] * self.fooverlaps[m][n]

                step += 1
                if self.progress and random.random() < cupdate:
                    self.progress.update(step, "Charge Decomposition Analysis...")

        if self.progress:
            self.progress.update(nstep, "Done.")

        self.donations = donations
        self.bdonations = bdonations
        self.repulsions = repulsions
        self.residuals = residuals

        return True

Generated by  Doxygen 1.6.0   Back to index