sukhos / g3-distribution Goto Github PK

For more details see the original paper: https://doi.org/10.1063/5.0007964

- Files distributed

g3.h
g3.cpp

g3input.dat - file with input parameters (see below)
config.dat - a simple example of configuration file (here, and orthorhombic
             cut of a single configuration of alpha-quartz is provided).

README - this file

- Compiling the code

g++ -std=gnu++11 -O3 g3.cpp -o g3

- Running the code

./g3

- Input file

the name is hard-coded to be "g3input.dat", one can change it in g3.cpp

- Content of the input file

nAtom - number of atoms
nType - number of atomic types 
nConf - number of configs to read in and analyse 
nrGrid - number of grid points along radial axis
naGrid - number of grid points along cos axis
Rmin - minimal distance in collecting the final g3 (see more below)
Rmax - maximal distance in collecting the final g3 (see more below)
LRcut - cutoff to be used along radial axis
TypeC - atomic type of the central atom in the triangle
TypeE - atomic type of the end atom in the triangle
input - name of the input file with configurations
output - name of the output file with calculated g3

If not specified, the default values are used (see g3.h for specific values).

Central atom is atom B and end atoms are A and C (see fig.1 in the main article):

"A mixed radial, angular, three-body distribution function as a tool for 
local structure characterization: Application to single-component structures"
Sergey V. Sukhomlinov and Martin H. Müser

- Structure of the input configuration file

coded for a standard LAMMS dump config file. Please note that currently only orthorhombic
box is implemented. The coordinates should be in the same units as the box unit vectors.

- Some info on g3 implementation

there is a classical way of implementing calculation of any distribution function.
Break the distance into bins, then calculate how many pairs/triplets etc. fall into this
bin, then proceed to normalize, such that the ideal gas gives one.

Here we proceeded in a slightly different way. Initially we do not make bins, but rather place
nrGrid (or naGrid) points onto an axis from 0 to LRcut. Whenever we have a pair of atoms,
the distance is calculated and the two nearst grid points are identified (the same would
hold for the cosine axis when triplets are considered). This distance gives a weight to
each of these two grid points, which is proportional to negative distance to them. For example,
if the distance falls exactly in the middle between two nearest grid points, it contributes
1/2 to each of the points. For triplets one would have not just a 1D segment, but rather a
cuboid.

The total g3 is calculated. At the end, integration over one of the distances from Rmin
to Rmax is performed.

- Output and plotting

the output format is compatible with gnuplot.

set pm3d map
splot "g3distr.dat"

These two commands will do the job, and a figure similar to those in the article will be
produced.