Hello,
I've been trying to export Cube files using Turbomole's
proper program, but it seems that the exported volumetric data is always spatially shifted for some reason.
Minimal reproducible example:For a simple H2 molecule with the symmetry axis along z (cf. .xyz file at the bottom), this picture shows what the total density exported by Turbomole 7.3.1 as a Cube file looks like (visualized using VMD, but I've tried VESTA as well with similar results):
Clearly, there is some shift of the density that shouldn't be there. Note that this uses the atom positions contained in the Cube file itself; using those from the original .xyz file is even worse:
All of this works perfectly fine with .plt files, however, as shown here:
Unfortunately, I have to use Cube files, because some tools that I want to use only work with those, and I haven't found any utility that can convert .plt to .cub.
Am I doing anything wrong or is this just broken?
Thank you very much in advance for any suggestions!
Kind regards
.xyz file:
2
h2
h 0.0 0.0 -0.37
h 0.0 0.0 0.37
UPDATE: For the time being, I figured out a workaround: Export as .plt, convert this to .dx using
https://www.mdanalysis.org/GridDataFormats/, then convert this to .cub using
babel. This seems to produce correct Cube files. But it would still be nice if this could work correctly out-of-the-box in Turbomole.