input_file.inp

#!/usr/bin/env mc_LJ

# Input file for the mc_LJ software
# All lines starting with # are ignored
# This file is case insensitive. You can separate the couples "keyword value"
# by using blank spaces or tabulations.

# we can use hard coded Lennard-Jones or Aziz potential
POTENTIAL   LJ
# Aziz potential is currently available only for Argon and Neon (mixtures are allowed)
# POTENTIAL  AZIZ
# ... or a user defined potential written in LUA
# it has to be : POTENTIAL PLUGIN {type} {path to plugin file} {potential function name} {gradient function name}
# for the moment {type} is PAIR or FFI :
# - PAIR means that the lua function just works on a pair of atoms
# - FFI  means that the lua function uses LUAJIT/FFI allowing to work on the whole atomic system
# Examples : 
# POTENTIAL PLUGIN PAIR plugins/lj_n_m.lua       lj_v_n_m_pair    lj_dv_n_m_pair
# POTENTIAL PLUGIN FFI  plugins/lj_n_m_ffi.lua   lj_v_n_m_ffi     lj_dv_n_m_ffi
# see the provided files in the plugins subdirectory

# unit of energy can be REDUCED (k_boltz*T/epsilon) or CHARMM (kcal/mol)
UNITS   REDUCED
#UNITS  CHARMM

#set the numb. of atoms
NATOMS  19
# reduced temperature
TEMP    0.25
# or temperature in Kelvin if CHARMM units are used
#TEMP   110

# number of steps : coded as an unsigned 64-bits integer so values of several billions
# are perfectly valid !
NSTEPS  10000000

#MAXIMAL distance move in Angstroems for MC moves
#DMAX   0.15
# or automatically optimised dmax : each UPDATE steps dmax is adjust for reaching
# TARGET (in %) of acceptance
DMAX    0.25    UPDATE  100 TARGET  30.0

# For each type of atom, set the Lennard Jones parameters
# Here example for reduced units
LJPARAMS    A  EPSILON 1.0 SIGMA   1.00
LJPARAMS    B  EPSILON 1.0 SIGMA   1.05

# Currently all parameters for the Aziz potential are hard coded, nothing to specify here

# Build the atomic system

#one type of atom, initial coordinates randomly generated
#ATOM    1   TO  END B   COOR    RANDOM
#or coordinates read from a xyz file
#ATOM    1   TO  END B   COOR    FILE   'file.xyz'   

# example of binary system built by hand
ATOM    1   TO  2     A   COOR    RANDOM
ATOM    3   TO  END   B   COOR    RANDOM

# regularly save energy to a file
SAVE    ENER    'ener.dat'  EACH    1000

# save initial and final coordinates to xyz files
SAVE    COOR    FIRST   XYZ 'init.xyz'
SAVE    COOR    LAST    XYZ 'last.xyz'

# regularly save the trajectory to a file (only dcd available for the moment)
SAVE    COOR    TRAJ    DCD 'traj.dcd'  EACH    1000

# monte carlo method to use :
# metropolis, no extra argument required
METHOD  METROP

# spatial averaging 
# METHOD  SPAV    WEPS    0.15    MEPS    10  NEPS    10