1# 2# define units 3# 4units lj 5 6# 7# specify periodic boundary conditions 8# 9boundary p p p 10 11# 12# define atom_style 13# full covers everything 14# 15atom_style full 16 17# 18# Setup the simulatioon box 19# 20variable blen equal 12.5 21region boxid block 0.0 ${blen} 0.0 ${blen} 0.0 ${blen} 22create_box 2 boxid 23 24# 25# Split the simulation into two regions 26# 27variable half_x equal ${blen}/2.0 28region boxa block 0.0 ${half_x} 0.0 ${blen} 0.0 ${blen} 29region boxb block ${half_x} ${blen} 0.0 ${blen} 0.0 ${blen} 30 31# 32# specify initial positions of atoms 33# sc = simple cubic 34# 0.5 = density in lj units 35# 36lattice sc 0.50 37# place atoms of type 1 in boxa 38# place atoms of type 2 in boxb 39create_atoms 1 region boxa 40create_atoms 2 region boxb 41 42# 43# define mass 44# 45# mass of atom type 1 46mass 1 1.0 47mass 2 1.0 48 49# 50# specify initial velocity of atoms 51# group = all 52# reduced temperature is T = 1.0 = lj-eps/kb 53# seed for random number generator 54# distribution is gaussian (e.g. Maxwell-Boltzmann) 55# 56velocity all create 1.0 87287 dist gaussian 57 58# 59# specify interaction potential 60# pairwise interaction via the Lennard-Jones potential with a cut-off at 2.5 lj-sigma 61# 62pair_style lj/cut 2.5 63# specify parameters between atoms of type 1 with an atom of type 1 64# epsilon = 1.0, sigma = 1.0, cutoff = 2.5 65pair_coeff 1 1 1.0 1.0 2.5 66pair_coeff 2 2 1.2 0.9 2.5 67 68# 69# specify parameters for neighbor list 70# rnbr = rcut + 0.3 71# 72neighbor 0.3 bin 73 74# 75# Specify timestep 76# 77timestep 0.001 78 79# 80# Write thermodynamic parameters to log 81# 82thermo_style custom step pe ke etotal temp press density 83thermo 1000 84thermo_modify norm no 85 86# 87# Setup plumed and that we are going to run npt equilibration 88# 89fix 1 all plumed plumedfile plumed.dat outfile p.log 90fix 2 all npt temp 1.0 1.0 0.1 iso 0.0 0.0 0.4 91 92# 93# save trajectory and restart file 94# dumpid = 1 95# filename = output.xyz 96# 97dump 1 all xyz 1000 output.xyz 98dump_modify 1 element Ar Ne 99restart 100000 lj.equilibration.restart 100 101# 102# Run 5000000 of equilibration 103# 104run 100000 105