[CP2K-user] [CP2K:15264] Re: Printing electrostatic potential on each atom

[Lucas Bandeira]

OK. Thank you very much for your help, Nicholas. I will try it here, and if
I have any problem I will email you.

Yours sincerely,

Lucas Bandeira

On Wed, Apr 28, 2021 at 5:53 PM Nicholas Winner <nwi... at berkeley.edu>
wrote:

> Coincidentally, it was just merged into pymatgen, so you can get it from
> the main branch. You can pull it from github (
> https://github.com/materialsproject/pymatgen ) and follow installation
> instructions there are some basic tutorials for other functionality. Once
> you have pymatgen, you can get the average electrostatic potential around
> each atom by using the following code snippet. Simply provide (a) the path
> to the cube file you want to analyze, and (b) the radius of the sphere to
> use for averaging around the different species. The atom_averages will be
> returned in atomic units (Ha), but the radii are provided in Angstroms, as
> internally pymatgen uses eV and Angstroms.
>
> from pymatgen.io.cube import Cube
> cube = Cube('path_to_your_hartree_file')
> radii = {'O': 0.871514401, ...}
> atom_averages = cube.get_atomic_site_averages(atomic_site_radii=radii)
>
> Here are the atomic site radii I personally use. Disclaimer: They are the
> values that are used internally by VASP for atomic site averaging. My own
> tests show that they transfer fine to CP2K. Let me know if you have issues.
>
> -Nick
>
> *atomic site radii*
> Ac: 0.949509702
> Ag: 1.089687061
> Al: 1.29725804
> Am: 1.0355554
> Ar: 1.007092989
> As: 1.028808863
> At: 1.197141072
> Au: 1.171867133
> B: 0.956370674
> Ba: 1.181016738
> Be: 1.239553998
> Bi: 1.358435791
> Br: 0.985961987
> C: 0.871514401
> Ca: 1.078814977
> Cd: 1.036283951
> Ce: 0.918807009
> Cl: 1.172653177
> Cm: 1.109928571
> Co: 1.012465916
> Cr: 1.10367272
> Cs: 1.095764548
> Cu: 0.91348204
> Dy: 0.965340843
> Er: 0.857571445
> Eu: 0.944011403
> F: 0.893437208
> Fe: 0.978689415
> Fr: 1.006272353
> Ga: 1.236680757
> Gd: 0.954830498
> Ge: 1.126694961
> H: 1.106577076
> H1: 1.106577076
> He: 0.644015437
> Hf: 1.208965988
> Hg: 1.179009031
> Ho: 0.970128474
> I: 1.150347999
> In: 1.437219142
> Ir: 1.239202246
> K: 1.069952195
> Kr: 1.209265531
> La: 0.916143122
> Li: 1.215288872
> Lu: 0.928082257
> Mg: 1.037846085
> Mn: 0.989049662
> Mo: 1.19104237
> N: 0.883769703
> Na: 1.397780021
> Nb: 1.036792122
> Nd: 0.927736454
> Ne: 0.911583912
> Ni: 0.948389642
> Np: 1.026944224
> O: 0.899483759
> Os: 1.158290899
> P: 1.19512333
> Pa: 0.955065185
> Pb: 1.444092849
> Pd: 1.084788257
> Pm: 0.933436512
> Po: 1.195151212
> Pr: 0.920534844
> Pt: 1.168113403
> Pu: 1.036977614
> Ra: 0.948110246
> Rb: 1.480382262
> Re: 1.150128956
> Rh: 1.143610716
> Rn: 1.216761009
> Ru: 1.211902419
> S: 1.209009282
> Sb: 1.134558557
> Sc: 1.273982785
> Se: 1.046971046
> Si: 1.233210468
> Sm: 0.940676508
> Sn: 1.363174078
> Sr: 1.155565676
> Ta: 1.214488968
> Tb: 0.958209181
> Tc: 1.128600762
> Te: 1.152446887
> Th: 0.956444797
> Ti: 1.220368396
> Tl: 1.437513192
> Tm: 0.917283411
> U: 0.964605202
> V: 1.168608341
> W: 1.145255565
> Xe: 1.49732734
> Y: 1.019887789
> Yb: 0.924662502
> Zn: 0.922234027
> Zr: 1.030481454
>
> On Wednesday, April 28, 2021 at 1:11:37 PM UTC-7 ban... at gmail.com
> wrote:
>
>> Thank you, Nicholas. I am so sorry, but I have never used pymatgen. I
>> would love it if you could share your pymatgen extension with me and give
>> me some guidance/explanation for using it.
>>
>> Yours sincerely,
>>
>> Lucas Bandeira
>>
>> On Tue, Apr 27, 2021 at 3:50 PM Nicholas Winner <n... at berkeley.edu>
>> wrote:
>>
>>> I don't believe CP2K can do this natively. What I have done is (1) load
>>> the V_HARTREE cube file into memory, (2) to define an atomic site radius
>>> based on each species, (3) create a spherical mask around the atomic site
>>> based on those radii in the 3D matrix of the cube's data, (4) then you can
>>> either integrate to get the total potential around the site, or more
>>> commonly you can get the average of the electrostatic potential.
>>>
>>> My development branch of pymatgen can do this, which I can share if you
>>> are can work with that. Alternatively, it should be in the main pymatgen
>>> branch in another week or two.
>>>
>>> -Nick
>>> On Tuesday, April 27, 2021 at 11:42:43 AM UTC-7 ban... at gmail.com
>>> wrote:
>>>
>>>> Dear cp2k community,
>>>>
>>>> I am performing some calculations analyzing adsorption on transition
>>>> metals, and I need to print the electrostatic potential on each atom in the
>>>> system. How can I do this?
>>>>
>>>> Yours faithfully,
>>>>
>>>> Lucas Bandeira
>>>>
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