Dear Sir
I am really in trouble. I need your advice.
For my research, I have been given a project for radiation damage on iron
core iron oxide. Here I have to use Si2+ (5Mev) for radiation. and target
would be Fe_FeO_Fe3O4.
I have no one who can advise me on MD simulation.
then you should refuse to do this project. it is flat out a bad idea to
let somebody do a project without proper training and qualified
supervision. you are bound to make many mistakes and chances high, that
even if you are successful , your work will be of low quality. doing
simulation studies is as much a craft as it is science, thus without a
proper training and gaining practical experience on simulation basics, you
have little chance to become more than a so-called "expert beginner", i.e.
somebody that is an expert at doing things like a beginner (including
mistakes and inefficiencies and not being able to tell good quality results
from bad).
I am reading several papers and doing tutorials and examples for LAMMPS.
you need to study a text book on simulations and some statistical
mechanics. most of what you need to learn is independent of LAMMPS. you are
entering at too high a level, thus you will not be able to tell a mistake
in methodology from a mistake in using the software: that is very bad.
also, don't expect to get tutoring and supervision from the mailing list. a
mailing list is neither a classroom, nor can it replace a tutor.
I want to go step by step.
For this reason, I want to generate iron core iron oxide (Fe_FeO_Fe3O4)
structure.
there is the first big mistake here: this is a complex system. you have to
learn simpler ones first. besides the structure, this is also going to be
challenging in terms of the force field. which potential/force field are
you planning to use. as i already explained to you, you need to settle that
question *first* as that determined how you have to enter your geometry
and what per-atom properties and topology data you need to provide.
Can you tell me, How can I generate that structure? Do you think, I should
use ASE (Atomic Simulation Environment). I never did programming before,
so before learning, I have to confirm that this is the only way to do that.
there are *many* ways to enter geometries into LAMMPS, most of them are
showcased in the bundled examples, shown in postings to the mailing list
and here: http://lammps.sandia.gov/prepost.html
the fact, that you keep reposting the same query without showing any
indication that you have learned from previous responses to your inquiries,
give a bad indication of your ability to pick up skills on your own and
take advice. this in turn makes it not attractive to even invest time in
trying to explain something to you.
If there is an easy way, please let me know. any kind of advice would be
helpful for me.
please remember the saying: no pain, no gain.
also, what is easy for one person, is difficult to the next.
some people find it easy to use LAMMPS' internal builder functionality,
others prefer external tools to generate geometries and convert them to
data files.
however, this is all pointless without knowing whether there is a suitable
force field that can actually correctly represent what you are after, which
requires a proper and thorough study of the published literature.
axel.