[CP2K-user] [CP2K:11062] Re: cube files

[Fatemeh Khalili]

dear all,
the code has been updated on github,
https://github.com/funkymunkycool/Cube-Toolz
You can integrate your cube file in 3 different ways with cube_tools ( Dr.
Al-Moatasem El-Sayed):
The first is to integrate over the whole file. This is a nice test to start
with, as you should get the number of electrons if you integrate over an
electron density file. This is done via the following command:
python cube_tools.py -i 1 file.cube

The number you choose in this command doesn't matter. But this should work
and should give you the integral of the whole cube file.

You can integrate a sphere of a particular radius around a certain atom. To
do this, the command is:
python cube_tools.py -ia 13 4 file.cube

Here, the numbers do matter. The first number is the atom number. You can
find this by using VMD for example or by finding it in the cube file.
Remember that the numbering starts from zero, i.e. the first atom has id 0.
The second number is the radius of a sphere. So this command would
integrate a sphere of radius 4 Angstrom around atom number 13.

Finally, you can integrate a sphere of a particular radius around any
arbitrary point. This is accomplished by:
python cube_tools.py -ir 4.3 3.2 2.6 4 file.cube

On Wed, Dec 19, 2018 at 10:05 AM cy16resch11004 via cp2k <
cp... at googlegroups.com> wrote:

> Dear varesh,
>
> i also tried with this code, but i am not able do intergrate of cube on
> particular atoms. do you have any suggestions?
>
> On Wednesday, December 19, 2018 at 1:09:09 AM UTC+5:30, Varesh wrote:
>>
>> Dear all,
>> would you plz advice me about density cube file integration?
>> I find some related code but it dosen't work for me!
>> https://github.com/funkymunkycool/Cube-Toolz
>>
>> --
>> Best Regards,
>> Fatemeh Khalili
>> PhD candidate
>> Department of Physics
>> Shahid Beheshti University
>>
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-- 
Best Regards,
Fatemeh Khalili
PhD candidate
Department of Physics
Shahid Beheshti University
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