D3_EXCLUDE_KIND notation

[Sam Varner]

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

[Marcella Iannuzzi]

Hello Sam,

The required index is the order of appearance in the coordinates' list.

Regards

Marcella

[Sam Varner]

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

[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

[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