[CP2K-user] [CP2K:11281] cubecruncher used for electron density differences-problem

[Fatemeh Khalili]

dear Nicholas  Dimakis,

another way to subtracting cubes is the following code (shared by Tassem
El-Sayed) :
"https://github.com/funkymunkycool/Cube-Toolz"

with this command:
e.g: "python2.7 cube_tools.py -s 1.cube 2.cube "

On Sun, Feb 17, 2019 at 4:10 AM Nicholas Dimakis <ndim... at gmail.com> wrote:

> Hello
>
> I am new to this group and I am trying to obtain electron density
> differences using cube files (attached). I am using cubecruncher (on
> macOS), where I do
>
> $ ./cubecruncher.x -i MoS2-1water1.cube -substract MoS2-1water1-slab.cube
> -o 1.cube
>
>  Reading from cube          MoS2-1water1.cube
>
>  Writing to   cube          1.cube
>
> Reading cube ...  Done
>
>    23.410000000000000        5.0000000000000001E-004   0.0000000000000000
>
>
>   -11.704699999999999        20.268400000000000        0.0000000000000000
>
>
>    0.0000000000000000        0.0000000000000000        11.005332000000001
>
>
>    5221.9100357117386
>
> Writing cube ...  Done
>
> and
>
> $ ./cubecruncher.x -i 1.cube -substract MoS2-1water1-water.cube -o 2.cube
>
>  Reading from cube          1.cube
>
>  Writing to   cube          2.cube
>
> Reading cube ...  Done
>
>    23.410000000000000        5.0000000000000001E-004   0.0000000000000000
>
>
>   -11.704699999999999        20.268400000000000        0.0000000000000000
>
>
>    0.0000000000000000        0.0000000000000000        11.005332000000001
>
>
>    5221.9100357117386
>
> Writing cube ...  Done
>
> However, the final file 2.cube does not seem to be correct. Moreover I
> found that if I do
>
>  ./cubecruncher.x -i MoS2-1water1-water.cube -substract
> MoS2-1water1-water.cube -o test.cube
>
>  Reading from cube          MoS2-1water1-water.cube
>
>  Writing to   cube          test.cube
>
> Reading cube ...  Done
>
>    23.410000000000000        5.0000000000000001E-004   0.0000000000000000
>
>
>   -11.704699999999999        20.268400000000000        0.0000000000000000
>
>
>    0.0000000000000000        0.0000000000000000        1.3843440000000000
>
>
>    656.85613359754439
>
> Writing cube ...  Done
>
> the output cube (i.e., test.cube) is not a zero density file as expected
> by it seems similar to the original.
>
> Thank you,
>
>
> Nick
>
> cube files can be found here
>
>
> https://drive.google.com/file/d/1pikUv9RQKYc3w0E0W4iA4H5RLaaODYVn/view?usp=sharing
>
> https://drive.google.com/file/d/11XzpX7ISZdZWtvCi1d1i8I1D0LtrW81l/view?usp=sharing
>
> https://drive.google.com/file/d/1LjfoZreh6-stIi6Mk0YSUSKbKLa3v4ri/view?usp=sharing
>
> https://drive.google.com/file/d/1euo52DFENdtQhuMco2jlLUAphSPJB5Jz/view?usp=sharing
>
> https://drive.google.com/file/d/1UtaUJnyZZBmuAq_2FydezchX7h_FNtEt/view?usp=sharing
>
>
>
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-- 
Best Regards,
Fatemeh Khalili
PhD candidate
Department of Physics
Shahid Beheshti University
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