Entropy of Mixing Calculation based on MD Trajectory

This module evaluates trajectory data from md simulations and calculates the configurational entropy distribution.

Currently only binary mixtures are supported.

Installation

Clone the repository and install the julia module:

git clone [repo]
julia

then install the module from the directory

using Pkg
Pkg.add("./EntMix")

Usage

The easiest way to use the module is to use the provided script calc_entropy.jl. In order to use that one has to additionally install the Package ArgParse:

Pkg.add("ArgParse")

Using the provided script allows to calculate entropy from lammpstrj or xyz files directly:

julia EntMix/src/calc_entropy.jl -m 100 traj.lammpstrj 300

This will calculate the mixing entropy of the first 100 timesteps within traj.lammpstrj. The two molecules must be sorted identically within each timestep and the first 300 atoms are all part of the first molecule type.

A complete usage is provided via

julia calc_entropy.jl --help
  > usage: calc_entropy.jl [-f RADIAL_FACTOR] [-m MAXSTEP] [-s STARTSTEP]
  >                        [-d DENSFUNC] [-n] [-o OUTFILE] [-v] [-h]
  >                        trajfile amatoms
  > 
  > positional arguments:
  >   trajfile              xyz or lammpstrj file to use. Using a xyz file
  >                         will result in a non periodic box calculation.
  >                         Lammpstrj files will be treated as periodic if
  >                         not defined otherwise with --nonperiodic.
  >   amatoms               Number of atoms in the first molecule (type:
  >                         Int64)
  > 
  > optional arguments:
  >   -f, --radial_factor RADIAL_FACTOR
  >                         Factor to multiply the VdW radii of the atoms
  >                         (type: Float64, default: 0.6)
  >   -m, --maxstep MAXSTEP
  >                         Maximum step to use (default all steps) (type:
  >                         Int64)
  >   -s, --startstep STARTSTEP
  >                         Initial step to use default to first step in
  >                         file (type: Int64)
  >   -d, --densfunc DENSFUNC
  >                         Function to use for smearing. Available
  >                         options are: slater, gaus, rect (default:
  >                         "slater")
  >   -n, --nonperiodic     If set, the box will be treated as non
  >                         periodic. Only applicable for lammpstrj files
  >                         since xyz files are always non periodic.
  >   -o, --outfile OUTFILE
  >                         Output file to save the entropy values, if not
  >                         set, the values will be printed to the
  >                         console. Only applicable for lammpstrj files.
  >                         If set threads can be used with julia -t
  >                         <nthreads>.
  >   -v, --debug           Print debug information
  >   -h, --help            show this help message and exit