regarding compute cluster/atom

Hi all,

I am trying to cluster the first nearest neighbours in a BCC structure using the compute cluster/atom command. However, when I do

compute 1 all cluster/atom 2.55 (my lattice parameter is 2.88)

its returning the same cluster ID for all atoms (returning 1). I am outputting the cluster IDs using dump custom. According to the webpage, the cluster ID should be the smallest atom ID of that cluster.

dump 2 all custom 1 ini_test.dump id type x y z c_1

I checked my implementation by specifying a distance less than first nearest neighbor distance in which case the cluster ID should be same as the atom ID. I get this right.

Can anybody please suggest on what I might be doing incorrectly?

Hi all,

I am trying to cluster the first nearest neighbours in a BCC structure using
the compute cluster/atom command. However, when I do

compute 1 all cluster/atom 2.55 (my lattice parameter is 2.88)

its returning the same cluster ID for all atoms (returning 1). I am
outputting the cluster IDs using dump custom. According to the webpage, the
cluster ID should be the smallest atom ID of that cluster.

are you sure you want cluster/atom compute and not coord/atom ?

axel.

Hi,

Yes I want to use cluster/atom to know which atoms are exactly neighbors to which. I think coord/atom just gives me the coordination number of each atom. Thanking you.

regards,
Karthik

Hi,

Yes I want to use cluster/atom to know which atoms are exactly neighbors

yes, but that is not what cluster/atom computes. have a look at the
documentation:

"...each of which is within the cutoff distance from one or more other
atoms in the cluster."

so, if you have a bulk crystal, the entire(!) crystal is the cluster.

axel.

Hi,

Thanks for your clarification. I understand what cluster/atom does now.

regards,
Karthik