error in conversion of cube to xsf file

ASE
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1

Dear all,

I need to convert cube files to xsf files for some simulations (details not important).

While searching for various options to perform this conversion I found ASE as one option (Version 3.27.0). However, problems arise with the following script:

import ase
from ase.io.cube import read_cube_data
from ase.io import write

data, atoms = read_cube_data(“electron_density.cube“)

origin = atoms.info.get(“cube_origin“, (0, 0, 0))

write(“electron_density-ASE.xsf“, atoms, data=data, origin = origin)

While it yields an xsf-file, the cell dimensions are changed the grid data appears shifted with respect to the atomic coordinates.

An attempted fix did not work:

cell = atoms.set_cell([3, 3, 6]) # example for lattice vector

atoms.set_pbc([True, True, True])

atoms.wrap()

I tried the same conversion with the c2x program and it yields the desired xsf file.
The described shifts become immediately apparent when opening the files with VESTA (version 3.90.3a).

I would appreciate it if someone could point out my mistake or if this is a bug.

Kind regards,
Max

p.s. Please excuse me for not attaching example files. This was unfortunately blocked.

2

Hi,

Normally it is possible to attach files. Maybe the file was too large and it needs to run on a smaller file, or you could generate the cubedata programmatically so the script reproduces the problem without any external files. I would need a functioning minimal example in order to look at this.

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