In-plane RDF¶

Figshare: In-plane 2D RDF LAMMPS Trajectory. fMSI at 320 K. The pair histogram is normalized to an ideal gas.

seams rdf is the three-dimensional site-site g_IJ(r), not this in-plane calculation. The in-plane writer is Frame.rdf_2d.

CLI (3D site-site)¶

seams rdf dump-320.lammpstrj --types 2,2 --cutoff 12 --bins 240

Stdout is # r g count, then a header with types, rmax, bins, and volume, then one r g count row per bin.

Python¶

from pydseams import Frame

frame = Frame.from_file("dump-320.lammpstrj")
r, g = frame.rdf_2d(output_dir="output/", cutoff=12.0, binwidth=0.05)

rdf_2d returns bin centres and g(r). The engine also writes topoMonolayer/rdf.dat under output_dir.

The 3D counterpart on the same frame is frame.rdf(2, 2, cutoff=12.0, binwidth=0.05).

Lua¶

dseams.rdf returns a partial three-dimensional RDF and is not the in-plane calculation shown here:

local dseams = require("dseams")
local cloud = dseams.read("dump-320.lammpstrj", {type = 2})
local result = dseams.rdf(cloud, {type_i = 2, type_j = 2,
                                  cutoff = 12.0, bins = 240})
print(result.r[1], result.g[1])

The in-plane output writer is the low-level registration dseams.core.calcRDF. Its 1.x script depends on a CLI-injected accumulator, so Frame.rdf_2d is the supported library workflow for this page.

References¶

1. The in-plane RDF page in the 2020 d-SEAMS paper, doi:10.1021/acs.jcim.0c00031.