Example of how to calculate the nuclear repulsion energy from parsed cclib data

nuclear_repulsion_energy.py

import cclib
import numpy
import urllib

def nuclear_repulsion_energy(data):
    nre = 0.0
    for i in range(data.natom):
        ri = data.atomcoords[0][i]
        zi = data.atomnos[i]
        for j in range(i+1, data.natom):
            rj = data.atomcoords[0][j]
            zj = data.atomnos[j]
            d = numpy.linalg.norm(ri-rj)
            nre += zi*zj/d
    return nre

if __name__ == "__main__":
    logurl = "https://raw.githubusercontent.com/cclib/cclib/master/data/QChem/basicQChem4.2/water_mp4sdq.out"
    logfile = cclib.parser.ccopen(urllib.urlopen(logurl))
    data = logfile.parse()
    a2b = cclib.parser.utils.convertor(1.0, "Angstrom", "bohr")
    print "In hartrees:", nuclear_repulsion_energy(data) / a2b