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

[Marcella Iannuzzi]

Dear Nick

you have a typo in your command line
it is -subtract and not -substract
regards
Marcella


On Sunday, February 17, 2019 at 1:39:59 AM UTC+1, Nicholas Dimakis 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
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20190217/667ca621/attachment.htm>