I have three nanoparticles in the simulation domain surrounded by water molecules. I want to study the aggregation effect on the nanofluid thermal properties. For that I want to calculate the rdf of each nanoparticle within the system. My nanoparticle is Al2O3 of equal diameters. But lammps only deals with the atoms and I have 1000 atoms in each nanoparticle. From the manual I am able to get Al-Al, Al-O and O-O rdf.
Question: How can I calculate the rdf of 1 nanoparticle - 2 nanoparticle? If this can be done then I can extend it for 1np-3np rdf and 2np-3np rdf. Please help
Define each nanoparticle as a chunk. See the compute chunk/atom
command. Then use compute com/chunk and fix ave/chunk to
write out the nanoparticle COMs every N timesteps. Post-process
that file to get the RDF of your nanoparticles.
There is no compute rdf/chunk command in LAMMPS to do it
You said to use "compute com/chunk and fix ave/chunk to
write out the nanoparticle COMs every N timesteps". How is this different from using the fix ave/time command? Thanks
This works well when I have one type of atom in the nanoparticle. What if I have two or more type of atoms in the same nanoparticle.
For example, if I use the below command:
group copper region mysphere
compute 1 copper chunk/atom type region mysphere
compute 12 alo com/chunk 1
fix 1 copper ave/time 100 1 100 c_12[*] file 1.out mode vector
Then it gives me COM of copper only (i.e only one type). But instead of this if I have alumina (Al2O3) then I will get two COMs i.e one for Al and one for O.
My query is: How to get one COM coordinates of the nanoparticle which has two types of atoms or so? Please help!
I was wrong. You do want to use fix ave/time to output (to a file)
the results of compute com/chunk, i.e. one value per chunk.
You don’t want to time average, just output the values once
every N steps.
Fix ave/chunk does something different based on the atoms
in each chunk.
The problem I am facing now is that I am unable to get the COM coordinates of one nanoparticle in the output file because when I put three nanoparticles within the simulation domain then due to PBC, nanoparticles moves and half of the nanoparticle comes from the other side of the domain (please see the attached picture). As far as the simulation is concerned, this is equivalent to having the entire nanoparticle intact in either the top or bottom half of the box. For example, LAMMPS output only two COM coordinates in the following case and the 3rd one was (nan, nan, nan).
Please suggest me how to overcome this problem.