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

[Nicholas Dimakis]

Hi

Thank you all for your replies. I found that the problem was with the 
actual cube files that were not same size. This issue is now resolved.

Nick

On Sunday, February 17, 2019 at 1:43:10 PM UTC-6, Varesh wrote:
>
> 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 <ndi... at gmail.com 
> <javascript:>> 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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