Cluster Size Distribution and Coord/atom not behaving as expected

LAMMPS LAMMPS General Discussion
1

Dear LAMMPS users,

I am trying to obtain a cluster size distribution for nanoparticle - polymer system, where the nanoparticle is modelled as an icosahedra. I am trying to define a cluster based on the “Central” atom of the icosahedra. I am attaching a small portion of my script for reference. I am showing the pair potentials relevant to the “Central” atom group only.

group CEN type 1 (This is atom group of my interest to calculate the cluster size dist)
group PAR type 2
group POL type 3

pair_coeff 1 2 mie/cut 0.0 1.0 100.0 50.0 (#No non-bonded interaction between particles on vertex and central atom)
pair_modify shift yes

pair_coeff 1 1 mie/cut 0.0 1.0 100.0 50.0 (#No non-bonded interaction between central atoms of different icosahedra)
pair_modify shift yes

pair_coeff 1 3 mie/cut 0.0 1.0 100.0 50.0 (#No non-bonded interaction between central atoms and monomer beads)

comm_modify cutoff 10.0 (#I do not provide any neighbor commands. (Default settings apply)).

#CLUSTER SIZE DISTRIBUTION

compute cluster CEN cluster/atom 3.134
compute cc2 CEN chunk/atom c_cluster compress yes
compute size CEN property/chunk cc2 count
fix 6 all ave/histo 1 1 1 0 32 32 c_size mode vector ave running beyond ignore file tmp.histo

I use max value as 32 in ave/histo since I have 32 central atoms in my system (32 nanoparticles)
The output file looks something like this:

For timestep 0:

Histogrammed data for fix 6

TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value

Bin Coord Count Count/Total

0 32 32 0 0 1
1 0.5 0 0
2 1.5 32 1
3 2.5 0 0
4 3.5 0 0
5 4.5 0 0
6 5.5 0 0
7 6.5 0 0

For timestep 1:

1 32 64 0 0 1
1 0.5 0 0
2 1.5 64 1
3 2.5 0 0
4 3.5 0 0
5 4.5 0 0
6 5.5 0 0
7 6.5 0 0

and so on…
Also, this is a system with small clusters and not in any way a single cluster system. I am unable to find where the issue lies.

Secondly, I use

COORD/ATOM

compute ccord CEN coord/atom cutoff 3.134 group CEN
dump 3 CEN custom ${thermo_steps} coord.dat id c_ccord
dump_modify 3 sort id

The output looks something like this:

ITEM: ATOMS id c_ccord
13 0
26 0
39 0
52 0
65 0
78 0
91 0
104 0
117 0

Again, this output doesn’t correspond to a system with clusters.

Any suggestions would be helpful.

Regards
Sameer

2

Are you sure you are interpreting the printed data correctly?
What I see is that you have 32 different clusters, i.e. none of the central atoms come closer than the applied cutoff of 3.134 length units to each other. That seems quite reasonable from the description of the system you are providing.

It is perfectly consistent with the first set of results and their interpretation, though.
Please also compare carefully with the documentation of the respective commands.

If there is a discrepancy to your actual system, you have to provide more details.
Please also note that you should be providing the exact LAMMPS version and platform you are running on.

1 Like