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Re: [lammps-users] Testing radial distribution function (rdf) calculation results
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Re: [lammps-users] Testing radial distribution function (rdf) calculation results


From: Ali Morshedi <morshedi1370@...24...>
Date: Wed, 22 Nov 2017 13:57:28 -0800

Sorry, I sent the mail accidentally half done before. The complete version:

Dear all,

My own rdf calculations show different results from lammps. Here is a simple test case:

I have 4 atoms at positions x=[1,2,3,4] and y=0 z=0 for all.
box dimensions so that we have no pbc contribution:
-5   10     xlo  xhi
-5    5      ylo  yhi
-5    5      zlo  zhi
we have vol=1500 and number density is: rho=4/1500
If rmax=1.5 and nbin=2  --> rbin=0.75.

The relative number density for each bin and each atom:
0   30.3152
0   60.6305
0   60.6305
0   30.3152
where the columns correspond to bins and rows to atoms. The mean for the second bin: 45.4728

using:
compute 1 all rdf 2
fix 2 all ave/time 1 1 1 c_1[*] file tmp.rdf mode vector

Lammps gives:

# Time-averaged data for fix 2
# TimeStep Number-of-rows
# Row c_1[1] c_1[2] c_1[3]
0 2
1 0.375 0 0
2 1.125 60.6305 1.5

(60.635=~45.4728) As you can see, it's as if lammps is not considering the first and last atoms and is computing the average for two atoms. The coordination number is correct however.

I'm attaching the runfile and data file that reproduce this. I'm using 11Aug2017 version of lammps.

Thank you and best regards,
Ali

On Wed, Nov 22, 2017 at 1:35 PM, Ali Morshedi <morshedi1370@...24...> wrote:
Dear all,

My own rdf calculations show different results from lammps. Here is a simple test case:

I have 4 atoms at positions x=[1,2,3,4] and y=0 z=0 for all.
box dimensions:

Assume a large simulation box (no pbc contribution).

If rmax=1.5 and nbin=2,

Attachment: data.dat
Description: Binary data

Attachment: runfile
Description: Binary data