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Re: [lammps-users] can new atom's property be calculated using an existing pair_style?
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Re: [lammps-users] can new atom's property be calculated using an existing pair_style?


From: Quang Ha <quang.t.ha.20@...24...>
Date: Wed, 25 Oct 2017 14:21:34 -0400

Is there any implemented fixes that calculate the atom properties and do timestep update (i.e. update the change of the property at each time step) that I could use as a reference? I feel lost skimming through the documentation page with such abundant available options...

QT

On 25 October 2017 at 10:31, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Wed, Oct 25, 2017 at 9:51 AM, Quang Ha <quang.t.ha.20@...24...> wrote:
> Thanks, Axel.
>
> A quick follow-up question - if I just want my new property (i.e.
> concentration) to diffuse from one atom to nearby, would it be sufficient to
> write only my fix subroutine or does it have to be coupled with a pair_style
> as well?

you can read from and write to your custom property from anywhere you like.

the only issue, that you have to be careful with is whether you access
that property from "ghost" atoms, i.e. atoms that are copies from
neighboring subdomains.
these are usually not updated unless explicitly requested, and you may
have to do an explicit reverse and/or forward communication to update
those after you made changes to "local" atoms (index in atom->x[] <
atom->nlocal).

axel.

>
> Quang
>
> On 24 October 2017 at 18:13, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Tue, Oct 24, 2017 at 1:56 PM, Quang Ha <quang.t.ha.20@...24...> wrote:
>> > Hi,
>> >
>> > I am skeptical this is not possible, but just want to ask before
>> > shooting.
>> > For the new property, says foo, defined using fix property/atom command,
>> > can
>> > I allocate an existing pair_style so that the value of foo property can
>> > be
>> > calculated at each time step? Example: I want to have LJ potential to be
>> > applied to foo. Can I called the existing LJ potential pair_style or do
>> > I
>> > have to write new cpp/h files to define the pair_style for foo?
>>
>> you are not making sense here.
>> the LJ potential is a pairwise interaction. what fix property/atom
>> provides is a per-atom property. how will you generate the latter from
>> the former?
>> pair style hybrid is an example for how you can maintain multiple
>> instances of a pair style, however, if you want to capture any results
>> from that, you will have to do your own data management, since each
>> pair style will tally its results into global arrays and variables.
>>
>> axel.
>>
>>
>> >
>> > Thanks,
>> > Quang
>> >
>> >
>> > ------------------------------------------------------------------------------
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>> > lammps-users@...396...sourceforge.net
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>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.