[DFTB-Plus-User] Waveplot - CUBEMANIP .different size fragments.

[Jacek Jakowski]

I did not use cubemanip.py  but I used awk.  You can ignore different
number of atoms, but you need to make sure  that the origin  (of the 3D
mesh) generated by waveplot in all cube  files is the same.  You need to
rerun waveplot and make sure that all three files  generate the same mesh.

Jacek


On Tue, Oct 16, 2012 at 1:23 AM, R.Perez Garcia <
r.perez.garcia at student.rug.nl> wrote:

> Dear DFTB list,
> I am wondering if any of you did use the cubemanip.py written by prof.
> Aradi? In my system I have two parts and I would like to see what is the
> difference of charge between the whole system and the sum of the two
> independent parts.
> By doing something similar to this:
> cubemanip '(($1)-(($2)+($3)))' total/WP/wp-abs2.cube
> parts/COPOLYM/WP/wp-abs2.cube parts/PCBM/WP/wp-abs2.cube >>
> finalDiff_b4.cube
> I believe I can not get the right output as I get several warnings:
> Warning: Nr. of atoms in 'total/WP/wp-abs2.cube' and
> 'parts/COPOLYM/WP/wp-abs2.cube' differ
> Warning: Origins in 'total/WP/wp-abs2.cube' and
> 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> Warning: Grid vectors in 'total/WP/wp-abs2.cube' and
> 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> Warning: Grid vectors in 'total/WP/wp-abs2.cube' and
> 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> Warning: Nr. of atoms in 'total/WP/wp-abs2.cube' and
> 'parts/PCBM/WP/wp-abs2.cube' differ
> Warning: Origins in 'total/WP/wp-abs2.cube' and
> 'parts/PCBM/WP/wp-abs2.cube' differ!
> Warning: Grid vectors in 'total/WP/wp-abs2.cube' and
> 'parts/PCBM/WP/wp-abs2.cube' differ!
> Warning: Grid vectors in 'total/WP/wp-abs2.cube' and
> 'parts/PCBM/WP/wp-abs2.cube' differ!
> Do you have any idea how to tackle this issue? i.e. solve it within VMD, I
> mean performing the operations with the visualization tool..
> Thank you very much for your attention.
> Best regards: Rodrigo
>
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