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Re: [lammps-users] Assigning BornMayer potential+ ZBL potential
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Re: [lammps-users] Assigning BornMayer potential+ ZBL potential


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 17 Jul 2017 08:03:20 -0400

please understand, that this is a mailing list about LAMMPS and not a classroom.
the questions you are rising are questions you should as a person tutoring you.
the fact that you are new to the field and that you need help does not
automatically entitle you to get this help from this list and ask
questions that are for the most part considered off-topic.

i will give you the following advice, but if that is insufficient,
please find yourself a local tutor, that you can discuss with in
person. i will not go into further details.

1.) when learning how to do proper tabulation, start with an example
for which an analytical potential does exist, e.g. using pair style
lj/cut or morse or similar.
2.) for example start with the melt example to replace lj/cut with
table. then look for an example with 2 or three atom types, e.g.
micelle and replace the lj/cut part with table
3.) study the documentation of pair style table *very* carefully. most
of your questions are explained in there and the rest is moderately
easy to figure out.
4.) if you are struggling with any of these steps, you are most likely
either lacking understanding of the fundamental concepts or the
practical skills to translate a manual into an input deck and to
systematically debug it, as well and test and confirm the correctness
of your steps. teaching these is not just off-topic, but *far* beyond
the scope of this list and something that you have to refer to your
adviser/supervisor to. it is their responsibility to see to it that
you are properly trained for the tasks assigned to you, not the job of
this list.

thanks for your understanding,
      axel.

On Mon, Jul 17, 2017 at 6:07 AM, Meral Sharkas <eng_meral.sh10@...16...> wrote:
> Thank you Axel for your help,
>
> So after looking further in the literature I found that the function
> governing the system can be described as :
>
> V(r)=F(r) VBm(r) + (1- F(r)) VZbl(r)
>
> VBm : Bornmayer Potential
> VZbl: Ziegler Biersack potential
>
>
> So I just want to confirm that I understood correctly how to create the
> tabulated potential please. Should i generate a code to evaluate the
> potential energy for each pair of atoms (ex: Zr-O, Zr-Zr)...etc for
> different "r" by substituting in the mentioned above relation and then use
> pair_style table to assign the potential to lammps and then use pair write
> to check on the evaluated potential?
>
> Also will each pair of atoms have a separated potential file or the whole
> potential of the system will be in the same file?
>
> I apologize if it is a vague question, I am just trying to get through this
> field from scratch
>
> Thanks in advance
>
>
> On Saturday, June 24, 2017 7:05 PM, Axel Kohlmeyer <akohlmey@...24...>
> wrote:
>
>
>
>
> On Fri, Jun 23, 2017 at 2:54 PM, Meral Sharkas via lammps-users
> <lammps-users@lists.sourceforge.net> wrote:
>
> Dear Lammps users,
>
> I am new in the molecular dynamics field, I am trying to simulate radiation
> damage in Zircon (ZrSiO4). I am facing issues in assigning the potential in
> LAMMPS. According to the literature, the potential is a Born Mayer
> potential, coulombic part and the Born mayer potential is joined smoothly to
> a repulsive ziegler Biersack Littmark (ZBL) for very short range
> interactions.
>
> My questions please are:
>
> 1-Is this type of potential expressed by "Hybrid overlay style" in LAMMPS?
> if Not; how can I join the ZBL to Born Mayer potential?
>
>
> pair style hybrid/overlay will just add potentials.
> so you either have to program a custom pair style or generate (and test)
> tables for pair style table and overlay then with a suitable coulomb style.
>
>
>
> 2- As per the literature, potential parameters are for Si-O , Zr-O and O-O,
> and when I add the coefficients for these pairs, I have an error "All pair
> coeff are not set", so is there a missing information i should I add to
> lammps?
>
>
> yes. you have no Si-Zr parameters. if they are not supposed to interact (or
> come near each other), you can just choose parameters resulting in zero
> potential energy.
>
>
> axel.
>
>
>
>
> I hope you can guide me..
>
> Thank you in advance..
>
> Regards
>
>
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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.