# Input file for simulation of 3 atoms.

Dear users,

I am trying to make an input file for a system of 3 atoms. I want to run the simulation such that all the initial atoms are at the origin and they finally arrange themselves in an equilateral triangle arrangement. I thought I would have to write 3 different fix commands for the 3 atoms to make them reach to their respective positions and according to my understanding their different positions at different timesteps between the initial and the final positions should be reflected through the dump command in different dump files. But, I am not able to figure out the proper dump command and its arguments(and maybe the fix command also) to implement this. I have gone through the documentation of dump, fix and compute commands but I'm finding it difficult to do this.

I have attached my input file and log file. Someone help me out please.

Thanks and regards,

in.mod1 (2.59 KB)

log.lammps (6.42 KB)

Dear users,

I am trying to make an input file for a system of 3 atoms. I want to run
the simulation such that all the initial atoms are at the origin and they
finally arrange themselves in an equilateral triangle arrangement. I
thought I would have to write 3 different fix commands for the 3 atoms to
make them reach to their respective positions and according to my
understanding their different positions at different timesteps between the
initial and the final positions should be reflected through the dump
command in different dump files. But, I am not able to figure out the
proper dump command and its arguments(and maybe the fix command also) to
implement this. I have gone through the documentation of dump, fix and
compute commands but I'm finding it difficult to do this.

your main problem is that you are neglecting the physics of your model.
there are two massive problems:

1) the LJ potential diverges at distance r=0, hence you getting NaN (which
stands for "not a number").
2) even if you had a potential that is finite at r=0, there would be no
force when you place atoms *exactly* on top of each other for symmetry
reasons. also, it would be impossible to determine the direction of the
force.

​there are more conceptual problems:
- why atom style "tri"? "atomic" would be more adequate​
- what is the point of fix move on *all* atoms?
- what is the point of starting from a high potential energy position when
you can already analytically determine the result (for 3 equidistant
atoms)? why not start from a simple approximation/guess?
- why run an MD, when a minimization would be the obvious choice to perform
the process you are describing?

in short, you need some serious help. much more than what anybody can
provide over e-mail.

axel.