[CP2K-user] [CP2K:12539] merging cube filed for the aimd simulation

Patrick Gono patri... at gmail.com
Tue Dec 3 09:40:53 UTC 2019

Dear Raitis,

You may take a look at Cube-Toolz (

However, as cube files are human readable and quite easy to parse, you can
always do the operations you need yourself. For example, the following
Python3 script implements a class that can parse a density cube file:

import scipy as sp
class Cube:
    def __init__(self, filename):
        self.filename = filename

        with open(self.filename, 'r') as f:
            raw_data = f.readlines()

        self.natoms = int(raw_data[2].split()[0])
        self.nx, self.ny, self.nz = [int(line.split()[0]) for line in

        print('Cube file {:s} parsed'.format(filename))

    def parse_density(self, raw_data):
        """ builds an nx times ny times nz array representing the spin
density """

        data = []
        for line in raw_data[self.natoms + 6:]:
            data.extend(float(x) for x in line.split())

        self.density = sp.zeros((self.nx, self.ny, self.nz))
        for i in range(self.nx):
            for j in range(self.ny):
                for k in range(self.nz):
                    self.density[i, j, k] = data[i * self.ny * self.nz + j
* self.nz + k]

You can then calculate the average density by simply summing up the density
array of each cube file.

Yours sincerely,
Patrick Gono

On Mon, Nov 25, 2019 at 9:58 AM Raitis <raitis... at gmail.com> wrote:

> Dear all,
> I am trying to compute Raman spectra for my system by following this
> tutorial: https://brehm-research.de/files/spec_tutorial_2018.pdf
> At the electron density data calculation step I messed up and got cube
> files for each frame separately (I believe it is because I forgot to put
> "=" in front of results.cube).
> Is there a way to merge all the cube files of md simulation in one?
> Raitis
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