the cluster anlysis with lammps

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1

Dear LAMMPS user ,

I have a problem for cluster analysis with LAMMPS,

I want to study the cluster evolution of growing from small to large and analyze every clusters’ mean velocity and coordinate

for I know that I can use the command of “compute cluster/atom” in LAMMPS to get the number of clustesr and give every atom an ID, if the atom is in the same cluster the ID is the same,

My question is how to define these atoms in the same cluster as a group and analyze this group differently (the structure, mean velocity and coordinate) with time(trajectory).

LU

Lu XIE

GREMI -Université d’Orléans

14, rue d’Issoudun

BP6744 F-45067 ORLEANS Cedex2

1 Like
2

Dear LAMMPS user ,

I have a problem for cluster analysis with LAMMPS,

I want to study the cluster evolution of growing from small to large and
analyze every clusters’ mean velocity and coordinate

for I know that I can use the command of “compute cluster/atom” in LAMMPS
to get the number of clustesr and give every atom an ID, if the atom is in
the same cluster the ID is the same,

My question is how to define these atoms in the same cluster as a group and
analyze this group differently (the structure, mean velocity and coordinate)
with time(trajectory).

this is probably best done in post-processing. just add the output of
the compute to the dump file with the coordinates and then script a
program/script that follows the clusters around and does the analysis
you want.

axel.

3

Thanks so much! Axes
With your suggestion, I write a script for the post prcessing , for it works
all right expect the mean coordinate.
For in LAMMPS, I use periodic boundary condition and output x y z style,
when I calculated, it create some error
Do you have some method for this?
Thanks a lot again for your help!
Lu

4

Thanks so much! Axes
With your suggestion, I write a script for the post prcessing , for it works
all right expect the mean coordinate.
For in LAMMPS, I use periodic boundary condition and output x y z style,
when I calculated, it create some error
Do you have some method for this?

sorry, but my crystal ball doesn't work anymore. if your scripts
prints an error, than it is likely a problem with your script. how
should i be able to fix it? magic? mind control?

axel.