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update kim examples to temp. current state of code

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This commit is contained in:
Ryan S. Elliott
2019-06-23 10:34:43 -05:00
parent 33be7f259b
commit c11caf4509
4 changed files with 2 additions and 218 deletions
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118
examples/kim/data.VOH
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@ -1,118 +0,0 @@
# 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

23
examples/kim/in.kim.VOH.simulator_model
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# 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 H C O V
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.voh
run 300

69
examples/kim/in.kim.ex_si.simulator_model
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@ -1,69 +0,0 @@
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 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

10
examples/kim/in.kim.lj.simulator_model
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@ -14,9 +14,7 @@ variable xx equal 20*$x
variable yy equal 20*$y variable yy equal 20*$y
variable zz equal 20*$z variable zz equal 20*$z
echo both kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode
#kim_style model LennardJones_Ar metal
kim_style model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode
newton on newton on
lattice fcc 4.4300 lattice fcc 4.4300
@ -24,10 +22,7 @@ region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box create_box 1 box
create_atoms 1 box create_atoms 1 box
#pair_style lj/cut 8.1500 kim_interactions Au
#pair_coeff 1 1 0.0104 3.4000
kim_style setup Au
mass 1 39.95 mass 1 39.95
velocity all create 200.0 232345 loop geom velocity all create 200.0 232345 loop geom
@ -36,6 +31,5 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
fix 1 all nve fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100 run 100