[CP2K:5819] Removing DFTB interaction between particular atoms?

[Ralph Koitz]

Dear Rafael,

Thanks for trying my suggestion. I played around with it some more and got
something more reasonable after making the following changes:

   - Instead of using atom symbol X, you have to use a 'real' element for
   your non-interacting carbons. I called it B.
   - Drop the KIND X // ELEMENT C ... part in &SUBSYSTEMS.
   - In the xc.spl and cx.spl files, remove lines 2 and 3. (The format is
   different for homo- and heteronuclear interactions, compare e.g. oo.spl and
   oh.spl in a water setup).
   - In the xx.spl, in the spline section, leave the first two columns as
   is, set the others to zero. The first line after Spline should be "0 0 -1"
   to turn off also the very short-range repulsion.

I attached the xx.spl file and param_table files.

Using these settings the following things work seemingly fine:

   - A graphene sheet with only one "B" atom behaves like an unmodified
   graphene sheet
   - A graphene sheet with two adjacent "B" still looks physical, but the
   B-B bond compresses, presumably because all repulsion has been turned off.
   C-C and C-"B" bonds remain mostly unperturbed.

Let me know how this works out for you.


Ralph

On Thu, Nov 6, 2014 at 12:42 AM, Rafael Soler-Crespo <
rasole... at gmail.com> wrote:

> Hi Ralph,
>
> Thanks for your insightful (and quite creative!) reply. It looks like a
> great starting point for what I intend to do so I can replicate the paper.
> I followed your suggestion, and I generated xc.spl, cx.spl and xx.spl
> files. I also made the xx.spl file all zeros essentially. I also added them
> to the scc_parameter file (which I renamed parameter_table some time ago).
> I'm attaching the files here. Then, I adjusted my geometry to have two X
> atoms in the XYZ input (which is attached too) to represent my initial
> break or crack.
>
> When I tried to run my job, it wouldn't start as the KIND X was not
> defined in the input. I defined the KIND X using:
>
>   &KIND X
>    ELEMENT C
>   &END KIND
>
> But when CP2K runs it says:
>
>  *** 00:18:09 WARNING in atomic_kind_types:read_atomic_kind :: Information
> ***
>  *** provided in the input file regarding POTENTIAL for KIND <X> will be
> ***
>  *** ignored!atomic_kind_types.F line 2341
>
> And the results look extremely unphysical (3 carbon atoms collapsing
> essentially one into the other). I thought that removing xx.spl, xc.spl and
> cx.spl would perhaps make it work, but it didn't work either. When I make
> change X atoms to C atoms in the input structure, everything is back to
> normal. This makes me think the problem is related to how KIND is working
> when selecting parameters to use (treating them as if they weren't there?).
> When I print their charges and mass, it all looks right. Do you have any
> idea if I am defining my KIND incorrectly, or what could be my issue?
>
> I've also attached my input, to keep the mailing list clean.
>
> Thanks,
> Rafael
>
> On Wednesday, November 5, 2014 11:25:14 AM UTC-6, Ralph wrote:
>>
>> Hi,
>>
>> I think it should be feasible to do this without changes to the code. In
>> your DFTB calculation, find the Slater-Koster parameter file for Carbon,
>> should be something like 'cc.spl', make three copies of that file 'cx.spl',
>> 'xc.spl', 'xx.spl'. Then edit the file that assigns parameters to atoms
>> ('scc_parameter' ?), it contains a list of what spl file to use for
>> which interaction. Add the following lines:
>>   C   X  cx.spl
>>   X   C  xc.spl
>>   X   X  xx.spl
>> (the C C interaction should already be there).
>>
>> You can then replace your two desired carbons in graphene by atoms of
>> type X, and tune their interaction by modifying the xx.spl file. In the
>> simplest case, set all columns to zero to turn off all interactions. You
>> can also scale the interaction, or turn off orbital-specific components.
>> X atoms will still behave like C atoms to other C atoms.
>>
>> See my slides from the cp2k tutorial for details on setting up a dftb
>> calculation and on the format of the .spl files.
>>     http://ralph.koitz.info/doc/dftb_cp2k.pdf
>>
>> Hope that helps,
>> Ralph
>>
>> On Wed, Nov 5, 2014 at 4:35 PM, Rafael Soler-Crespo <raso... at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm trying to perform a calculation to replicate a MD paper on CP2K
>>> using DFTB to see if the findings still hold (out of curiosity). In this
>>> paper, a crack is imposed on graphene by removing explicitly atoms from the
>>> material. I want to do this a little differently by turning off
>>> interactions between two neighboring carbon atoms. My system has around
>>> 7000 carbon atoms, and I want to forcefully zero any interactions between
>>> two adjacent C atoms. I searched around the documentation, but I couldn't
>>> find a great way to do this. Is it possible for someone to let me know if
>>> this is possible in CP2K, and if it is not, if it could be coded in
>>> principle?
>>>
>>> Thanks,
>>> Rafael
>>>
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