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1

Hi all! I was running a sample simulation with two particles in a box of size 8.

I used the following as pair styles:

  1. pair_style lj/cut 1.1224
    2)pair_style lj/cut 1.1224 and then

pair_modify shift yes

3)pair_style lj/smooth/linear 1.1224

and I dumped the positions of all the atoms in the 3 cases. But in all the cases the coordinates of the atoms are same . Why is this happening?

2

Hi all! I was running a sample simulation with two particles in a box of
size 8.
I used the following as pair styles:
1) pair_style lj/cut 1.1224
2)pair_style lj/cut 1.1224 and then
   pair_modify shift yes
3)pair_style lj/smooth/linear 1.1224
and I dumped the positions of all the atoms in the 3 cases. But in all the
cases the coordinates of the atoms are same . Why is this happening?

because of your input, of course. there is not enough information to
say anything more specific.

3

#initialisation
units lj
atom_style bond

#potentials

pair_style lj/smooth/linear 1.1224

read_data data.xyz

pair_coeff 1 1 1.0 1.0 1.1224

write_data checkbond.data

#velocity

velocity all create 1.0 1
fix 1 all nvt temp 1.0 1.0 0.1

thermo_style custom step temp etotal press pe

dump 1 all atom 100 dump.run.txt
dump_modify 1 scale no sort id

timestep 0.005

thermo 100
run_style verlet
run 1000000

write_data pretunnel.data

this is the input script

4

[...]

this is the input script

which is practically worthless without the data file.

5

LAMMPS description
2 atoms

1 atom types

-4.000000 4.000000 xlo xhi
-4.0000000 4.000000 ylo yhi
-4.000000 4.000000 zlo zhi

Masses

1 1.0

Atoms

1 1 1 -1.000000 -1.00000 -1.000000
2 2 1 1.000000 1.000000 1.000000

this is the data file

6

LAMMPS description
    2 atoms

    1 atom types

-4.000000 4.000000 xlo xhi
-4.0000000 4.000000 ylo yhi
-4.000000 4.000000 zlo zhi

Masses

1 1.0

Atoms

1 1 1 -1.000000 -1.00000 -1.000000
2 2 1 1.000000 1.000000 1.000000

this is the data file

ok. i don't even have to run this. of course, you *have* to get the
same thing happening (i.e. nothing), since those two atoms are farther
apart than the cutoff.

axel.

7

But at some point of the simulation they should be within the cutoff distance?

8

But at some point of the simulation they should be within the cutoff
distance?

maybe yes, maybe no. for as long as they are far enough apart they'll
just drift along across their initial directions.