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Re: [lammps-users] adding energy to a single atom
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Re: [lammps-users] adding energy to a single atom


From: Fernanda S Teixeira <nandast@...6816...>
Date: Mon, 17 Jul 2017 09:35:43 -0300

Thank you Steve.

Em Sáb, 2017-07-15 às 11:11 -0600, Steve Plimpton escreveu:
Fix heat will not work b/c it expects there to be some atoms
in the group, not zero before deposition takes place.


You could just thermostat (e.g. with fix langevin) the atom(s)
that you deposit.


Steve

On Sat, Jul 15, 2017 at 6:39 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Sat, Jul 15, 2017 at 8:19 AM,  <nandast@...6816...> wrote:
> Hi Axel
>
>    For my experimental configuration, ions are deposited. So, besides kinect
> energy, there is ionization potential energy. This energy is released as
> heat when the ion becomes a neutral. So I am trying to mimic this. I was
> thinking in add this energy as more velocity for the incoming ions, but I
> will spend that energy in stopping. It is a slightly different scenario. Do
> you think it is the only way?

it is really up to you how you build your model, but the kind of
operation you want to perform is not built into LAMMPS.

so you would have to, for example, write a custom fix style for your
purpose. that fix could track atoms by having a custom property added,
and then when its kinetic energy drops below a pre-defined value, i.e.
it has hit the surface, you add a certain amount of kinetic energy
(i.e. random velocities) to the atoms within a given distance. at that
you change the custom property to indicate, that this ion has been
neutralized. not a trivial thing to program, but not too difficult
either.

axel.

>
> Thank you
>
> Fernanda
>
> Citando Axel Kohlmeyer <akohlmey@...24...>:
>
>
>> On Fri, Jul 14, 2017 at 4:31 PM, Fernanda S Teixeira <nandast@...6816...>
>> wrote:
>>
>>> Dear LAMMPS users and developers,
>>>
>>>    I would like to add no translational energy to a single atom (heat).
>>> This single atom is an addatom inserted by "fix deposit" that I want to
>>> release thermal energy after being stopped by the substrate.
>>>   I have tried to use "fix heat" but I got a message: "Fix heat group has
>>> no atoms" even after deposition.
>>>
>>
>> fix deposit allows you to add a kinetic energy, i.e. velocity to deposited
>> atoms. that energy is automatically released (or rather transferred) to
>> the
>> substrate, when the atoms collide with it.
>>
>>
>>>
>>>   Additionaly, I want to add energy only to atoms just deposited, not to
>>> the atoms deposited many steps before.
>>>
>>
>> you sound like you are talking about some other kind of "internal" energy,
>> however with classical MD point particles there is only kinetic energy.
>>
>> axel.
>>
>>
>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>>
>>> Fernanda S Teixeira
>>> --
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> 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@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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--
Dra. Fernanda de Sá Teixeira
Especialista em Laboratório
Laboratório de Filmes Finos
(http://fap.if.usp.br/~lff)
Instituto de Física da USP
Fone/Fax: 11 3091 6625 / 11 3091 7140