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data.py

00001 """
cclib (http://cclib.sf.net) is (c) 2007, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""


import cPickle as pickle
import os
import sys

import numpy


00014 class ccData(object):
    """Class for objects containing data from cclib parsers and methods.

    Description of cclib attributes:
        aonames -- atomic orbital names (list)
        aooverlaps -- atomic orbital overlap matrix (array[2])
        atombasis -- indices of atomic orbitals on each atom (list of lists)
        atomcoords -- atom coordinates (array[3], angstroms)
        atommasses -- atom masses (array[1], daltons)
        atomnos -- atomic numbers (array[1])
        charge -- net charge of the system (integer)
        ccenergies -- molecular energies with Coupled-Cluster corrections (array[2], eV)
        coreelectrons -- number of core electrons in atom pseudopotentials (array[1])
        etenergies -- energies of electronic transitions (array[1], 1/cm)
        etoscs -- oscillator strengths of electronic transitions (array[1])
        etrotats -- rotatory strengths of electronic transitions (array[1], ??)
        etsecs -- singly-excited configurations for electronic transitions (list of lists)
        etsyms -- symmetries of electronic transitions (list)
        fonames -- fragment orbital names (list)
        fooverlaps -- fragment orbital overlap matrix (array[2])
        fragnames -- names of fragments (list)
        frags -- indices of atoms in a fragment (list of lists)
        gbasis -- coefficients and exponents of Gaussian basis functions (PyQuante format)
        geotargets -- targets for convergence of geometry optimization (array[1])
        geovalues -- current values for convergence of geometry optmization (array[1])
        hessian -- elements of the force constant matrix (array[1])
        homos -- molecular orbital indices of HOMO(s) (array[1])
        mocoeffs -- molecular orbital coefficients (list of arrays[2])
        moenergies -- molecular orbital energies (list of arrays[1], eV)
        mosyms -- orbital symmetries (list of lists)
        mpenergies -- molecular electronic energies with Moller-Plesset corrections (array[2], eV)
        mult -- multiplicity of the system (integer)
        natom -- number of atoms (integer)
        nbasis -- number of basis functions (integer)
        nmo -- number of molecular orbitals (integer)
        nocoeffs -- natural orbital coefficients (array[2])
        scfenergies -- molecular electronic energies after SCF (Hartree-Fock, DFT) (array[1], eV)
        scftargets -- targets for convergence of the SCF (array[2])
        scfvalues -- current values for convergence of the SCF (list of arrays[2])
        vibdisps -- cartesian displacement vectors (array[3], delta angstrom)
        vibfreqs -- vibrational frequencies (array[1], 1/cm)
        vibirs -- IR intensities (array[1], km/mol)
        vibramans -- Raman intensities (array[1], A^4/Da)
        vibsyms -- symmetries of vibrations (list)
    (1) The term 'array' refers to a numpy array
    (2) The number of dimensions of an array is given in square brackets
    (3) Python indexes arrays/lists starting at zero, so if homos==[10], then
            the 11th molecular orbital is the HOMO
    """

00064     def __init__(self, attributes=None):
        """Initialize the cclibData object.
        
        Normally called in the parse() method of a Logfile subclass.
        
        Inputs:
            attributes - dictionary of attributes to load
        """

        # Names of all supported attributes.
        self._attrlist = ['aonames', 'aooverlaps', 'atombasis',
                          'atomcoords', 'atommasses', 'atomnos',
                          'ccenergies', 'charge', 'coreelectrons',
                          'etenergies', 'etoscs', 'etrotats', 'etsecs', 'etsyms',
                          'fonames', 'fooverlaps', 'fragnames', 'frags',
                          'gbasis', 'geotargets', 'geovalues', 'grads',
                          'hessian', 'homos',
                          'mocoeffs', 'moenergies', 'mosyms', 'mpenergies', 'mult',
                          'natom', 'nbasis', 'nmo', 'nocoeffs',
                          'scfenergies', 'scftargets', 'scfvalues',
                          'vibdisps', 'vibfreqs', 'vibirs', 'vibramans', 'vibsyms']

        # The expected types for all supported attributes.
        self._attrtypes = { "aonames":        list,
                            "aooverlaps":     numpy.ndarray,
                            "atombasis":      list,
                            "atomcoords":     numpy.ndarray,
                            "atommasses":     numpy.ndarray,
                            "atomnos":        numpy.ndarray,
                            "charge":         int,
                            "coreelectrons":  numpy.ndarray,
                            "etenergies":     numpy.ndarray,
                            "etoscs":         numpy.ndarray,
                            "etrotats":       numpy.ndarray,
                            "etsecs":         list,
                            "etsyms":         list,
                            'gbasis':         list,
                            "geotargets":     numpy.ndarray,
                            "geovalues":      numpy.ndarray,
                            "grads":          numpy.ndarray,
                            "hessian":        numpy.ndarray,
                            "homos":          numpy.ndarray,
                            "mocoeffs":       list,
                            "moenergies":     list,
                            "mosyms":         list,
                            "mpenergies":     numpy.ndarray,
                            "mult":           int,
                            "natom":          int,
                            "nbasis":         int,
                            "nmo":            int,
                            "nocoeffs":       numpy.ndarray,
                            "scfenergies":    numpy.ndarray,
                            "scftargets":     numpy.ndarray,
                            "scfvalues":      list,
                            "vibdisps":       numpy.ndarray,
                            "vibfreqs":       numpy.ndarray,
                            "vibirs":         numpy.ndarray,
                            "vibramans":      numpy.ndarray,
                            "vibsyms":        list,
                          }

        # Arrays are double precision by default, but these will be integer arrays.
        self._intarrays = ['atomnos', 'coreelectrons', 'homos']

        # Attributes that should be lists of arrays (double precision).
        self._listsofarrays = ['mocoeffs', 'moenergies', 'scfvalues']
        
        if attributes:
            self.setattributes(attributes)
        
00134     def listify(self):
        """Converts all attributes that are arrays or lists of arrays to lists."""
        
        for k, v in self._attrtypes.iteritems():
            if hasattr(self, k):
                if v == numpy.ndarray:
                    setattr(self, k, getattr(self, k).tolist())
                elif v == list and k in self._listsofarrays:
                    setattr(self, k, [x.tolist() for x in getattr(self, k)])
    
00144     def arrayify(self):
        """Converts appropriate attributes to arrays or lists of arrays."""
        
        for k, v in self._attrtypes.iteritems():
            if hasattr(self, k):
                precision = 'd'
                if k in self._intarrays:
                    precision = 'i'
                if v == numpy.ndarray:
                    setattr(self, k, numpy.array(getattr(self, k), precision))
                elif v == list and k in self._listsofarrays:
                    setattr(self, k, [numpy.array(x, precision)
                                      for x in getattr(self, k)])

00158     def getattributes(self, tolists=False):
        """Returns a dictionary of existing data attributes.
        
        Inputs:
            tolists - flag to convert attributes to lists where applicable
        """
    
        if tolists:
            self.listify()
        attributes = {}
        for attr in self._attrlist:
            if hasattr(self, attr):
                attributes[attr] = getattr(self,attr)
        if tolists:
            self.arrayofy()
        return attributes

00175     def setattributes(self, attributes):
        """Sets data attributes given in a dictionary.
        
        Inputs:
            attributes - dictionary of attributes to set
        Outputs:
            invalid - list of attributes names that were not set, which
                      means they are not specified in self._attrlist
        """
    
        if type(attributes) is not dict:
            raise TypeError, "attributes must be in a dictionary"
    
        valid = [a for a in attributes if a in self._attrlist]
        invalid = [a for a in attributes if a not in self._attrlist]
    
        for attr in valid:
            setattr(self, attr, attributes[attr])
        self.arrayify()
        return invalid

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