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Re: [lammps-users] Reading Energy in Custom Pair Function
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Re: [lammps-users] Reading Energy in Custom Pair Function


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 17 Jun 2017 21:14:40 -0400



On Fri, Jun 16, 2017 at 8:36 PM, S M <smatrix_2012@...8...> wrote:
Hi,

I am writing a custom pair potential, where I first need to read the energy of every particle before the custom pair potential is applied, and then apply the custom pair potential to certain particles based on their energy readings.

I am guessing that I need to use the "pair->vdW" command.

Can anybody suggest a definite strategy in terms of writing necessary codes?

​not based on such insufficient and vague information provided. in fact, your e-mail can serve as an example for how *not* to ask questions.

- you say you are writing a custom pair potential, but you are not saying what its purpose is, what its underlying physics is, whether it is top be used in combination with another (pairwise?) potential and so on.

- you ask about very unspecific things, e.g., "energy". there is a gazillion kinds of energies. in MD​ specifically we differentiate between kinetic and potential energy and the potential energy by the parts of the model. do you need the "energy" at previous or the same time step?

- you "guess" what you should be doing (and are guessing something without a reference to any part of the source code). not to mention, that it cannot be a "command"

​- you talk about "certain particles ​based on their energy readings", which is a vague as it gets.


yet at the end, you ask about receiving specific help and a definite strategy. how can anybody can provide "definite" help without having *any* kind of useful information? the only "definite" strategy that can be provided has to be as vague as your inquiry:

- make sure you have sufficient C++ programming (and reading other people's sources) skills
- read the part of the LAMMPS manual concerning modifying and extending LAMMPS
- read the LAMMPS developer's guide
- with the information of the developer's guide in mind, study relevant parts of the LAMMPS source code
- keep in mind, that per-atom energies either need to be computed (kinetic energy) or explicitly requested to be tallied during force computation (potential energy).
- keep in mind, that forces/energies are computed in "stages" and you cannot easily go back to a previous stage unless you are playing tricks, e.g. hook a pairwise computation into fix to be run at a later stage. but also keep in mind, that adding to forces *after* the second part of the velocity verlet integration is ignored.

axel.

 


S


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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.