How can I change the pair_coeff so that when two spheres just touch each other, they are at the bottom of LJ potential curve?

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1

Dear LAMMPS users,

I intend to exert a kind of force which will be attractive in the short range, and will be no interaction in the long range. Axel answered me in this mailing list several weeks ago, and he suggested me to use pair_style Python to customize the potential. This is a good idea but I will try it next step. The first step is, I finally understood that to some extent, I can directly use LJ potential.

image.png

Based on Wikipedia, the x-axis reflects the distance between the centroid of two particles. I intend to let rm=d. d is the diameter of the particle in my system. In this sense, I think: 1. the particle will not overlap; 2. from just touch to the cutoff point, the interaction between two spheres will be the attraction; 3. after cutoff point, there will be not interaction. Are these assumptions correct? And I will let the particles be in Brownian motion.

So in LAMMPS, I choose lj unit, and about setting up diameter and par_coeff, what I wrote is

set type 1 diameter 1
set type 1 density 1

pair_style lj/cut 2.5
pair_coeff 1 1 10 0.89089871814

which means that I set epsilon=10.0, sigma=0.5^(1/6) because rm=2^(1/6)*sigma. But after running, I found that the interaction between particles is repulsive - once they are close enough (but not touch), they will kick away each other. I pasted my script at the end of this mail, and attached the .xyz file I dumped.

My question is that what the unit of length is in LJ unit system. More precisely, in the documentation, it said that distance=sigma, which looks like sigma is the unit of length. For example, when we set diameter to be 1, it is 1 sigma. But since we still need to set sigma in the pair_coeff command, it sounds like that sigma is not the unit of the length. Otherwise, when we set sigma = 0.89, it means that sigma = 0.89 sigma, which is confused.

#########################lj_test.txt##########################

variable x index 1
variable y index 1
variable z index 1
variable t index 100000
variable N index 80

units lj
timestep 0.00000001
atom_style sphere

boundary p p p
region A block 0 5 0 5 0 5
create_box 1 A
change_box all boundary p p p units box

create_atoms 1 random $N 22322 NULL

set type 1 diameter 1
set type 1 density 1

pair_style lj/cut 2.5
pair_coeff 1 1 10 0.89089871814

neighbor 1 bin
neigh_modify every 1 delay 1 check no

group one type 1

fix first_fix one langevin 1.0 1.0 100 12345
fix second_fix all nve

dump myDump1 one xyz 1000 lj_mpl_$N.xyz

run $t

lj_mpl_80.xyz (211 KB)

2

Dear LAMMPS users,

I intend to exert a kind of force which will be attractive in the short
range, and will be no interaction in the long range. Axel answered me in
this mailing list several weeks ago, and he suggested me to use pair_style
Python to customize the potential. This is a good idea but I will try it
next step. The first step is, I finally understood that to some extent, I
can directly use LJ potential.

!image.png|512x381
Based on Wikipedia, the x-axis reflects the distance between the centroid
of two particles. I intend to let rm=d. d is the diameter of the particle
in my system. In this sense, I think: 1. the particle will not overlap; 2.
from just touch to the cutoff point, the interaction between two spheres
will be the attraction; 3. after cutoff point, there will be not
interaction. Are these assumptions correct? And I will let the particles be
in Brownian motion.

So in LAMMPS, I choose lj unit, and about setting up diameter and
par_coeff, what I wrote is

set type 1 diameter 1
set type 1 density 1

​diameter and density have no meaning and are ignored with pair style
lj/cut. pair style lj/cut *only* computes interactions between point
particles.​

pair_style lj/cut 2.5
pair_coeff 1 1 10 0.89089871814

which means that I set epsilon=10.0, sigma=0.5^(1/6) because
rm=2^(1/6)*sigma. But after running, I found that the interaction between
particles is repulsive - once they are close enough (but not touch), they
will kick away each other. I pasted my script at the end of this mail, and
attached the .xyz file I dumped.

​when doing experiments with only one atom type in reduced units, there is
no benefit in using values of epsilon and sigma different from 1.0.

My question is that what the unit of length is in LJ unit system. More
precisely, in the documentation, it said that distance=sigma, which looks
like

​the unit of length is *one* sigma that you choose to be your reference
sigma. it need not be the sigma, that you use in any particular set of
pair_coeff commands, but it is hugely convenient to represent all lengths
and energies relative to a given interaction, especially when there is only
one pair.​

sigma is the unit of length. For example, when we set diameter to be 1, it
is 1 sigma. But since we still need to set sigma in the pair_coeff command,
it sounds like that sigma is not the unit of the length. Otherwise, when we
set sigma = 0.89, it means that sigma = 0.89 sigma, which is confused.

​this is primarily confusing because you don't seem to have yet fully
grasped​ the concept of reduced units.

​also, i suspect, the concepts of (soft) potentials and their interactions
is not yet fully in your mind as well.

all of those problems are quite off-topic for this mailing list. perhaps a
look into a text book or somebody in your local condensed matter physics
research group might help.

axel.​