Hello,
I am a student internship at Sanofi R & D in Vitry sur Seine, in France.
During this course, I realize the DM simulations with LAMMPS software.
I have some questions for developers or users of LAMMPS, if it is
possible please:
1) For example, when we use units LJ in LAMMPS input script file: I do not
understand how units of distance and energy works (Sigma, Epsilon), ?
please learn how to utilize (fundamental) text books or at least
a search engine on the web. there are a gazillion examples on
how MD for lennard jones particles is implemented in reduced
units and how that works.
in short your unit of distance is 1 sigma and your
unit of energy is 1 epsilon. that is it. the correlation
to "real" units is simple, since in reduced units,
the unit of time is derived from sigma and epsilon
(and mass). so for as long as you keep the same
relation between sigma, epsilon and mass, it will
always be "the same simulation" just on a different
timescale. if you increase all the masses by the
same factor, all atoms move slower, if you increase
sigma, atoms will move faster.
2) Could you tell me, please, is that it is possible to modify the forms of
potential and how? I mean, for examples, forms of potential of the
Lennard-Jones (9-6) , and ( 6-4).
U(rij) ) (15/4) [(ó/rij)9- (ó/rij)6] and
U(rij) ) (15/4) [(ó/rij)6- (ó/rij)4]
please read the documentation about modifying LAMMPS to
add your own pair styles or use tabulated potentials.
all is documented *very* well and has been discussed
on this mailing list many times. just check out the
mailing list archives.
3) I used benchmarck script example of polymer melt, with file "in. fene", I
have this error message, when I modified or adapted to the properties of my
system:
FENE bond too long: %ld %d %d %g
A FENE bond has stretched dangerously far. It's interaction strength will be
truncated to attempt to prevent the bond from blowing up. FENE bond too
long: %ld %g I do not understand the meaning of these %ld %d %d %g, could
you explain to mee, what it can do reference, please? I think that : %ld
: ID
%d : atom 1
%d : atom 2
%g : Distance between atom 1 and atom 1
that mean you have messed up your input and
are doing an unphysical simulation.
4) I see that for "atom_style command", only the default values for
"atom_style", could you please, tell me what these defaults?
the documentation says.
atom_style atomic
that *is* the default and that is correct. there is nothing
else that needs to be written.
axel.