sumCube.py

#!/usr/bin/env python3
#
# Script to sum cube files
# by Patrick Melix
# 2018/06/07
#
# You can import the module and then call .main() or use it as a script
from ase.io.cube import read_cube, write_cube
import os, glob
import numpy as np

def main(inList,outFile, subtract=False):
    #if output exists mv to .bak
    if os.path.isfile(outFile):
        print('ATTENTION: {:} exists, moving to *.bak'.format(outFile))
        os.rename(outFile, outFile+'.bak')

    cubeData = []

    for iFile,inFile in enumerate(inList):
        if not os.path.isfile(inFile):
            raise ValueError('File {:} does not exist'.format(inFile))

        print(inFile)
        with open(inFile) as f:
            if iFile == 0: #read first cube
                baseCube = read_cube(f)
                atoms = baseCube['atoms']
                origin = baseCube['origin']
                continue
            else: #reduce memory footprint by just keeping one
                dct = read_cube(f)

        assert baseCube['data'].shape == dct['data'].shape

        if subtract:
            baseCube['data'] -= dct['data']
        else:
            baseCube['data'] += dct['data']

    with open(outFile,'w') as f:
        write_cube(f, atoms, data=baseCube['data'], origin=origin)

    return



if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser(description='Sum up cube files')
    parser.add_argument('--subtract', help='Subtract not Sum', action='store_true')
    parser.add_argument('-file', type=str, nargs='+', default=[], help='input files')
    parser.add_argument('-output', type=str, help='output file')
    args = parser.parse_args()
    main(args.file,args.output, args.subtract)