[CP2K-user] [CP2K:20372] Re: D3_EXCLUDE_KIND notation

[Sam Varner]

Thank you so much! I was assuming it was 0 indexed and was getting strange 
behavior, so fixing this should solve my issue.

Perhaps this information should be added to the documentation, since I 
don't think there is anyway to obtain it from there currently. Not to 
mention, this info is required for properly using the D3_EXCLUDE_KIND 
method.

Best,
Sam

On Thursday, June 20, 2024 at 12:36:46 AM UTC-7 Marcella Iannuzzi wrote:

> 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
>>>>
>>>

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