shc-python-tools/example/quench.lmp at master · ksaaskil/shc-python-tools · GitHub

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
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
# Expects these variables to be defined:
# variable filename string '090415a'
# variable data_file string ${filename}_Si.dat # Where to read the structure
# variable restartfile string ${filename}.quenched.restart
# variable steps_heating equal 500000
# variable steps_quench equal 1000000
# variable steps_cooled equal 500000

dimension 3
log ${filename}.log
boundary p p p
units metal
atom_style atomic

# This is needed to run scatter_atoms later
atom_modify map yes

pair_style sw
read_data ${datafile}
pair_coeff * * Si_vbwm.sw Si

min_style cg
min_modify line quadratic
thermo 100

minimize 0 1.0e-1 1000 1000
write_restart ${restartfile}
# quit
#undump minim_coords

variable seed1 equal 3423435
variable seed2 equal 23422327
variable seed3 equal 8760859

variable Tquench equal 2400
variable Tfinal equal 300
variable Tdamp equal 0.5
variable Pquench equal 1
variable Pdamp equal 0.5

fix NVE all nve
timestep 0.0025
thermo 1000

velocity all create ${Tquench} 4928459 dist gaussian

thermo_style custom step temp etotal cpu cpuremain

fix NVT0 all langevin ${Tquench} ${Tquench} ${Tdamp} ${seed1} # zero yes
# fix NPT0 all npt temp 0.1 ${Tquench} ${Tdamp} iso 0.1 ${Pquench} ${Pdamp}
# fix NPH0 all nph aniso 1 1 ${Pdamp}
# fix LANGEVIN all langevin
dump quench_coords all xyz 1000 ${filename}_traj_quench.xyz
dump_modify quench_coords element Si

run ${steps_heating}
#unfix NPH0
unfix NVT0
write_restart ${filename}.heated.restart
#fix NPT1 all npt temp ${Tquench} ${Tquench} ${Tdamp} iso ${Pquench} ${Pquench} ${Pdamp}
fix NVT1 all langevin ${Tquench} ${Tfinal} ${Tdamp} ${seed2}
run ${steps_quench}
#undump quench_coords
unfix NVT1
write_restart ${filename}.cooled.restart

unfix NVE
fix NPH2 all nph iso 0 0 ${Pdamp}
fix NVT2 all langevin ${Tfinal} ${Tfinal} ${Tdamp} ${seed3}

#dump vels all custom 50 ${filename}.vels.SiO2.dat id type vx vy vz
#dump_modify vels format "%d %d %.8g %.8g %.8g"
#dump_modify vels sort id
#compute myRDF all rdf 50
#fix 1 all ave/time 100 1 100 c_myRDF file ${filename}.tmp.rdf mode vector
#dump quench_coords all xyz 25 ${filename}_traj2_quench.xyz
restart 1000000 ${filename}.*.quench.restart
run ${steps_cooled}
#unfix NPT2
# undump quench_coords
minimize 0 1.0e-3 1000 1000

dump coords all xyz 1 ${filename}_quenched_coords.xyz
dump_modify coords sort id # Important for SED calculation
run 0
undump coords
write_restart ${restartfile}
# quit

variable v1 equal xlo
variable v2 equal xhi
variable v3 equal ylo
variable v4 equal yhi
variable v5 equal zlo
variable v6 equal zhi
print "The system boundaries are "
print "${v1} ${v2}"
print "${v3} ${v4}"
print "${v5} ${v6}"

quit