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