1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
# Rodrigo Freitas - rodrigof@berkeley.edu
#
# Description: nonequilibrium thermodynamic integration. Further details in:
# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
# https://doi.org/10.1016/j.commatsci.2015.10.050
#--------------------------- System setup -------------------------------------#
units metal
lattice fcc 3.621
region sim_box block 0 4 0 4 0 4
create_box 1 sim_box
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
#------------------------------------------------------------------------------#
#---------------------- Simulation setup --------------------------------------#
# The order of the fix commands is important: thermostat AFTER thermodynamic integration force interpolation.
fix f1 all nve
fix f2 all ti/spring 3.728 2000 1000 function 2
fix f3 all langevin 100.0 100.0 0.1 666 zero yes
# Compute temperature using center-of-mass coordinates.
compute c1 all temp/com
fix_modify f3 temp c1
# Output variables.
variable step equal step
variable dU equal pe-f_f2 # Used on the integration.
variable lambda equal f_f2[1] # For reference or integration.
variable dlambda equal f_f2[2] # For reference or integration.
# Thermo output.
thermo_style custom step pe
thermo 100
#------------------------------------------------------------------------------#
#------------------------- Running the simulation -----------------------------#
# Setup initial velocities to accelerate equilibration.
velocity all create 200.0 9999 mom yes rot yes dist gaussian
# Forward nonequilibrium thermodynamic integration.
run 1000 # Equilibrate system at lambda = 0.
fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
screen no file forward.dat title '# step dU lambda dlambda'
run 2000 # Lambda switching: 0 -> 1.
unfix f4
# Backward nonequilibrium thermodynamic integration.
run 1000 # Equilibrate system at lambda = 1.
fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
screen no file backward.dat title '# step dU lambda dlambda'
run 2000 # Lambda switching: 1 -> 0.
unfix f4
#------------------------------------------------------------------------------#
|
