LJ units & potential

Dear users in manual for the calculation of thermal conductivity of Ar(LJ potential) real units have been used whereas LJ potential itself is in LJ units
Please clarify me

Thanks & Regards

Dear Amal

Generally, LJ potential is not in LJ units, If you don't using at
reduced units for epsilon and sigma.

Farrokh

Thank you Dr. Farrokh for reply.
Suppose the actual mass is 39.94 gm/mole. Then if I do not use reduced unit what should be the input form and that time what should be written in place of command "units"?
If I do not use reduced unit, would the units of outputs be according to the units of inputs?
On the other hand if I use reduced unit what should be the input form?
what would be the values of sigma, epsilon etc? should those values(sigma, epsilon) are to be supplied manually in the script or already build up and whenever the command “units LJ” is used automatically those values are used in calculation?

Thanks & Regards

I'm not sure if I understand your question. I will make an attempt.

Dear users in manual for the calculation of thermal conductivity of Ar(LJ
potential) real units have been used whereas LJ potential itself is in LJ
units

     I think you are misunderstanding what "LJ" units are.
     It's quite normal to use Lennard-Jones pair styles when using
"real" units. Recall the Lennard-Jones potential:
U(r) = 4 * epsilon ((sigma/r)^12 - (sigma/r)^6)
    In this formula the "epsilon" parameter has units of energy, but
this could be anything. In LAMMPS users can choose to specify their
energies in: kCal/mole, eV, Joules, ergs, Hartrees. When people
select one of these unit systems, LAMMPS (as a convenience) will
automatically convert temperatures so that the system is maintained at
the desired temperature (300K, for example).
    If a user selects "LJ" units, then they are essentially leaving
these energy units unspecified. In that case, they must manually
convert the temperature they want to run the simulation at into these
unspecified energy units (when using a fix like npt or nvt, for
example). This is optional. Users are not required to use "LJ" units
just because they are using a Lennard-Jones pair style. Many people
use Lennard-Jones pair styles with "real" units.
   Does this address your concern?

Andrew

P.S. I don't know if this is relevant, but for some unit systems,
like "LJ", the energies printed to the terminal are per-atom energies
(energy/num_atoms), not the total energy (extensive). (See
http://lammps.sandia.gov/doc/units.html)
Cheers!

Thank you Dr. Farrokh for reply.
Suppose the actual mass is 39.94 gm/mole. Then if I do not use reduced unit
what should be the input form

Then you would tell LAMMPS that the mass of that particle is 39.94

and that time what should be written in place
of command "units"?

You would use
"units real"

If I do not use reduced unit, would the units of outputs be according to
the units of inputs?

It certainly seems that way to me. However, again, be careful that
when using "units lj", the energies which are printed to the terminal
are divided by the number of atoms. (So they are smaller by a factor
of n).

On the other hand if I use reduced unit what should be the input form?
what would be the values of sigma, epsilon etc? should those values(sigma,
epsilon) are to be supplied manually in the script or already build up and
whenever the command "units LJ" is used automatically those values are used
in calculation?

If you use "units lj", your epsilon, sigma values and masses can be
anything you want. (They don't have to be "1.0". In fact, sometimes
you want to mix multiple particles together with different sizes and
epsilon parameters.) If you use "units lj", then you just have to be
careful to convert your desired temperatures, pressures, masses,
timesteps, and charges in terms of whatever units you are using to
express epsilon, sigma, and mass). For a list of these expressions,
see http://lammps.sandia.gov/doc/units.html, and scroll down.

Cheers
Andrew

Thank you Dr. Farrokh for reply.
Suppose the actual mass is 39.94 gm/mole. Then if I do not use reduced unit
what should be the input form and that time what should be written in place
of command "units"?

have a look at the documentation of the units command.

If I do not use reduced unit, would the units of outputs be according to
the units of inputs?

have a look at the documentation of the units command!

On the other hand if I use reduced unit what should be the input form?
what would be the values of sigma, epsilon etc? should those values(sigma,

if you have only one atom type the most convenient choice for reduced
mass would be 1.0 as would be epsilon and sigma.

epsilon) are to be supplied manually in the script or already build up and
whenever the command "units LJ" is used automatically those values are used
in calculation?

you are missing the most important point about reduced units:
changing the unit of mass is equivalent to changing the
unit of time (which is a derived). similarly for the unit of
length or energy. so if you double the mass or divide the
time by sqrt(2), the trajectories should be the same.

think about the common trick in japanese godzilla movies.
godzilla is usually just a guy in a godzilla suit walking around
little models made to scale. but they overcrank the movie camera,
so that when the movie is played back at normal speed it
looks as if this is a huge monster. MD is not much different.

axel.