forked from lijiext/lammps
provide more simulator model variant input examples
This commit is contained in:
Axel Kohlmeyer
parent
264f6e1630
commit
4619018ead
|
|
@ -0,0 +1,118 @@
|
|||
# VOH example
|
||||
|
||||
100 atoms
|
||||
4 atom types
|
||||
|
||||
0 25.000 xlo xhi
|
||||
0 25.000 ylo yhi
|
||||
0 25.000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0080
|
||||
2 12.0107
|
||||
3 15.9994
|
||||
4 50.9415
|
||||
|
||||
Atoms
|
||||
|
||||
1 2 0.0 12.35333 12.56112 11.08925
|
||||
2 4 0.0 12.32916 12.62071 13.13099
|
||||
3 3 0.0 14.09425 12.56218 13.76130
|
||||
4 3 0.0 11.42814 11.10330 13.76732
|
||||
5 3 0.0 11.63260 13.89286 13.64097
|
||||
6 1 0.0 10.61647 11.29221 14.30535
|
||||
7 1 0.0 14.38026 13.34626 14.29055
|
||||
8 1 0.0 11.32479 12.58820 10.70253
|
||||
9 1 0.0 12.90918 13.42567 10.69612
|
||||
10 1 0.0 12.84043 11.63643 10.74688
|
||||
11 2 0.0 0.93670 23.74637 24.45218
|
||||
12 4 0.0 2.18151 24.36876 0.94725
|
||||
13 3 0.0 3.93452 24.44779 0.28384
|
||||
14 3 0.0 2.13668 23.10529 2.33362
|
||||
15 3 0.0 1.76108 0.74666 1.48323
|
||||
16 1 0.0 1.82070 23.45305 3.20745
|
||||
17 1 0.0 4.35555 0.34186 0.31083
|
||||
18 1 0.0 24.90472 23.68735 24.82586
|
||||
19 1 0.0 0.97611 24.45631 23.61244
|
||||
20 1 0.0 1.24583 22.75250 24.09589
|
||||
21 2 0.0 2.25730 12.18969 18.74792
|
||||
22 4 0.0 0.67140 13.31162 19.37385
|
||||
23 3 0.0 0.71106 13.43250 21.24545
|
||||
24 3 0.0 24.08603 12.44025 18.87949
|
||||
25 3 0.0 0.70486 14.71920 18.75808
|
||||
26 1 0.0 23.49516 12.95430 18.26686
|
||||
27 1 0.0 0.79723 14.34808 21.60818
|
||||
28 1 0.0 2.24383 12.10285 17.65239
|
||||
29 1 0.0 3.19860 12.66607 19.06030
|
||||
30 1 0.0 2.20214 11.18299 19.18774
|
||||
31 2 0.0 9.32237 8.16220 23.74501
|
||||
32 4 0.0 9.41775 7.26178 21.91463
|
||||
33 3 0.0 8.54752 8.34565 20.65588
|
||||
34 3 0.0 8.50942 5.62151 22.00137
|
||||
35 3 0.0 10.87539 7.02683 21.48455
|
||||
36 1 0.0 9.06507 4.82324 21.80615
|
||||
37 1 0.0 9.11458 8.67119 19.91477
|
||||
38 1 0.0 9.82196 7.53487 24.49616
|
||||
39 1 0.0 9.81855 9.14254 23.70532
|
||||
40 1 0.0 8.27176 8.30387 24.03831
|
||||
41 2 0.0 9.10113 13.98748 23.44281
|
||||
42 4 0.0 8.84954 12.89163 21.73780
|
||||
43 3 0.0 10.01387 13.54293 20.42005
|
||||
44 3 0.0 7.08992 13.11522 21.12954
|
||||
45 3 0.0 9.12937 11.39982 21.99065
|
||||
46 1 0.0 6.55309 12.28287 21.08224
|
||||
47 1 0.0 10.67858 12.89258 20.08249
|
||||
48 1 0.0 8.42108 13.62252 24.22498
|
||||
49 1 0.0 10.13926 13.89766 23.79639
|
||||
50 1 0.0 8.88118 15.04646 23.24289
|
||||
51 2 0.0 17.73225 3.40708 8.28945
|
||||
52 4 0.0 18.49877 5.29835 8.37599
|
||||
53 3 0.0 19.48472 5.62627 6.81505
|
||||
54 3 0.0 19.66498 5.40961 9.84118
|
||||
55 3 0.0 17.38120 6.34466 8.51889
|
||||
56 1 0.0 19.41208 6.07779 10.52927
|
||||
57 1 0.0 19.15960 6.37609 6.25924
|
||||
58 1 0.0 17.15579 3.19557 9.20103
|
||||
59 1 0.0 17.07197 3.31049 7.41454
|
||||
60 1 0.0 18.54903 2.67524 8.20436
|
||||
61 2 0.0 5.18346 20.97409 24.28840
|
||||
62 4 0.0 7.06396 20.17968 24.34847
|
||||
63 3 0.0 7.63220 19.82889 22.59578
|
||||
64 3 0.0 7.00272 18.55243 0.28036
|
||||
65 3 0.0 8.05085 21.13715 0.03620
|
||||
66 1 0.0 7.56109 18.51690 1.09952
|
||||
67 1 0.0 8.44257 20.31624 22.30833
|
||||
68 1 0.0 4.83239 21.17976 0.30904
|
||||
69 1 0.0 5.19182 21.91237 23.71419
|
||||
70 1 0.0 4.49282 20.26573 23.80772
|
||||
71 2 0.0 21.82701 12.79861 20.63056
|
||||
72 4 0.0 21.27646 11.09990 19.63611
|
||||
73 3 0.0 19.52930 10.64327 20.13923
|
||||
74 3 0.0 22.41924 9.70346 20.14638
|
||||
75 3 0.0 21.34556 11.30206 18.11274
|
||||
76 1 0.0 22.94464 9.30084 19.40876
|
||||
77 1 0.0 18.86743 10.62817 19.40629
|
||||
78 1 0.0 22.85378 13.07853 20.35349
|
||||
79 1 0.0 21.14666 13.62206 20.37063
|
||||
80 1 0.0 21.78702 12.62668 21.71522
|
||||
81 2 0.0 4.84801 10.63893 5.85720
|
||||
82 4 0.0 2.99668 11.06158 5.10490
|
||||
83 3 0.0 3.09505 11.09458 3.23258
|
||||
84 3 0.0 2.48053 12.76555 5.69567
|
||||
85 3 0.0 1.96195 10.01780 5.55634
|
||||
86 1 0.0 1.65323 12.78746 6.24245
|
||||
87 1 0.0 2.52753 10.43264 2.76734
|
||||
88 1 0.0 4.80984 10.62196 6.95551
|
||||
89 1 0.0 5.18492 9.65688 5.49273
|
||||
90 1 0.0 5.56737 11.40648 5.53568
|
||||
91 2 0.0 13.58126 9.47098 19.40329
|
||||
92 4 0.0 14.17691 10.17243 21.22692
|
||||
93 3 0.0 14.44428 12.02521 21.10583
|
||||
94 3 0.0 15.81206 9.37183 21.67632
|
||||
95 3 0.0 13.12907 9.86545 22.30960
|
||||
96 1 0.0 15.80034 8.83149 22.50703
|
||||
97 1 0.0 13.87232 12.57457 21.69672
|
||||
98 1 0.0 13.42563 8.38456 19.45392
|
||||
99 1 0.0 12.63978 9.95672 19.10431
|
||||
100 1 0.0 14.35123 9.68789 18.64825
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000
|
||||
|
||||
read_data data.VOH
|
||||
|
||||
kim_style define NULL H C O V
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 300
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
|
||||
units metal
|
||||
kim_style init ex_sim_model_Si_mod_tersoff
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
|
||||
# temperatures
|
||||
variable tlo equal 1800.0
|
||||
variable thi equal 2400.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
|
||||
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del
|
||||
kim_style define ex_sim_model_Si_mod_tersoff Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all langevin ${thi} ${thi} 0.1 48278
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
run 100
|
||||
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
|
||||
units metal
|
||||
kim_style init ex_sim_model_Si_mod_tersoff
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
|
||||
# temperatures
|
||||
variable tlo equal 1800.0
|
||||
variable thi equal 2400.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0 &
|
||||
basis 0.0 0.5 0.5 &
|
||||
basis 0.5 0.0 0.5 &
|
||||
basis 0.5 0.5 0.0 &
|
||||
basis 0.25 0.25 0.25 &
|
||||
basis 0.25 0.75 0.75 &
|
||||
basis 0.75 0.25 0.75 &
|
||||
basis 0.75 0.75 0.25
|
||||
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
|
||||
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del
|
||||
kim_style define NULL Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all langevin ${thi} ${thi} 0.1 48278
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
run 100
|
||||
|
||||
|
|
@ -16,18 +16,19 @@ variable zz equal 20*$z
|
|||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton on
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 2 box
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
kim_style define ex_sim_model_Si_mod_tersoff Si Si
|
||||
kim_style define LennardJones_Ar Ar
|
||||
|
||||
mass * 39.95
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
Loading…
Reference in New Issue