[CP2K-user] [CP2K:20356] Re: D3_EXCLUDE_KIND notation

[Marcella Iannuzzi]

Hi Sam 

The order of &KIND sections does not matter. 
The indexing starts from 1
The list is the one either in &COOR or in an external coordinates file 
(e.g. xyz)
The Na atom in your list is kind 3

Best
Marcella


On Thursday, June 20, 2024 at 12:49:48 AM UTC+2 varn... at gmail.com wrote:

> Hi Marcella,
>
> Thank you for the reply!
>
> When you say coordinates' list, do you mean the &COORD section withing the 
> &SUBSYS section? Does the order of the &KIND sections matter at all? Also, 
> do you know if it is indexed starting at 0 or at 1?
>
> Just to make sure I am understanding, here is an example set of COORDS:
> H ... ... ...
> O ... ... ...
> H ... ... ...
> Na ... ... ...
>
> So, in this case, is it correct to say that if I want to exclude Na from 
> the D3 corrections, the I should use D3_EXCLUDE_KIND 2 ? (since H appears 
> first, O second, and Na third).
>
> Thanks again for the help!
>
> Best,
> Sam
>
> On Monday, June 17, 2024 at 11:55:15 PM UTC-7 Marcella Iannuzzi wrote:
>
>> Hello Sam,
>>
>> The required index is the order of appearance in the coordinates' list.
>> Regards
>> Marcella
>>
>> On Tuesday, June 18, 2024 at 12:08:10 AM UTC+2 varn... at gmail.com wrote:
>>
>>> Hello,
>>>
>>> I have a very simple question about the D3_EXCLUDE_KIND method.
>>>
>>> In the system definition, the KINDS are specified using elements 
>>> symbols, e.g. H, O, Au and so forth. However, D3_EXCLUDE_KIND is asking for 
>>> integers. Are the integers simply determined based on the order you specify 
>>> in KIND? Are they indexed from 0 or from 1? Or is it the element number? 
>>> (e.g. H corresponds to 1 and O corresponds to 8).
>>>
>>> Thank you for the help!
>>>
>>> Best,
>>> Sam
>>>
>>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/c2036807-c677-4644-9541-3b50e758af1bn%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20240620/c3048156/attachment-0001.htm>