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update missing data files and adjust input files for potentials comparison

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This commit is contained in:
Axel Kohlmeyer
2018-03-21 16:03:21 -04:00
parent 96061b854b
commit 57dbad59c0
14 changed files with 418692 additions and 3 deletions
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78
bench/POTENTIALS/data.airebo Normal file
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LAMMPS data file from restart file: timestep = 1, procs = 1
60 atoms
2 atom types
-2.1 2.1 xlo xhi
-2.1 2.1 ylo yhi
0 25.5790000000 zlo zhi
Masses
1 12.01
2 1.00794
Atoms
1 1 0.0000000000 0.0000000000 0.0000000000
2 2 0.9010066786 -0.6310205743 0.0000000000
3 2 -0.9010066786 -0.6310205743 0.0000000000
4 1 0.0000000000 0.8470061967 1.2789591482
5 2 0.9010066786 1.4780267710 1.2789591482
6 2 -0.9010066786 1.4780267710 1.2789591482
7 1 0.0000000000 0.0000000000 2.5579182965
8 2 0.9010066786 -0.6310205743 2.5579182965
9 2 -0.9010066786 -0.6310205743 2.5579182965
10 1 0.0000000000 0.8470061967 3.8368774447
11 2 0.9010066786 1.4780267710 3.8368774447
12 2 -0.9010066786 1.4780267710 3.8368774447
13 1 0.0000000000 0.0000000000 5.1158365929
14 2 0.9010066786 -0.6310205743 5.1158365929
15 2 -0.9010066786 -0.6310205743 5.1158365929
16 1 0.0000000000 0.8470061967 6.3947957411
17 2 0.9010066786 1.4780267710 6.3947957411
18 2 -0.9010066786 1.4780267710 6.3947957411
19 1 0.0000000000 0.0000000000 7.6737548894
20 2 0.9010066786 -0.6310205743 7.6737548894
21 2 -0.9010066786 -0.6310205743 7.6737548894
22 1 0.0000000000 0.8470061967 8.9527140376
23 2 0.9010066786 1.4780267710 8.9527140376
24 2 -0.9010066786 1.4780267710 8.9527140376
25 1 0.0000000000 0.0000000000 10.2316731858
26 2 0.9010066786 -0.6310205743 10.2316731858
27 2 -0.9010066786 -0.6310205743 10.2316731858
28 1 0.0000000000 0.8470061967 11.5106323340
29 2 0.9010066786 1.4780267710 11.5106323340
30 2 -0.9010066786 1.4780267710 11.5106323340
31 1 0.0000000000 0.0000000000 12.7895914823
32 2 0.9010066786 -0.6310205743 12.7895914823
33 2 -0.9010066786 -0.6310205743 12.7895914823
34 1 0.0000000000 0.8470061967 14.0685506305
35 2 0.9010066786 1.4780267710 14.0685506305
36 2 -0.9010066786 1.4780267710 14.0685506305
37 1 0.0000000000 0.0000000000 15.3475097787
38 2 0.9010066786 -0.6310205743 15.3475097787
39 2 -0.9010066786 -0.6310205743 15.3475097787
40 1 0.0000000000 0.8470061967 16.6264689269
41 2 0.9010066786 1.4780267710 16.6264689269
42 2 -0.9010066786 1.4780267710 16.6264689269
43 1 0.0000000000 0.0000000000 17.9054280752
44 2 0.9010066786 -0.6310205743 17.9054280752
45 2 -0.9010066786 -0.6310205743 17.9054280752
46 1 0.0000000000 0.8470061967 19.1843872234
47 2 0.9010066786 1.4780267710 19.1843872234
48 2 -0.9010066786 1.4780267710 19.1843872234
49 1 0.0000000000 0.0000000000 20.4633463716
50 2 0.9010066786 -0.6310205743 20.4633463716
51 2 -0.9010066786 -0.6310205743 20.4633463716
52 1 0.0000000000 0.8470061967 21.7423055198
53 2 0.9010066786 1.4780267710 21.7423055198
54 2 -0.9010066786 1.4780267710 21.7423055198
55 1 0.0000000000 0.0000000000 23.0212646681
56 2 0.9010066786 -0.6310205743 23.0212646681
57 2 -0.9010066786 -0.6310205743 23.0212646681
58 1 0.0000000000 0.8470061967 24.3002238163
59 2 0.9010066786 1.4780267710 24.3002238163
60 2 -0.9010066786 1.4780267710 24.3002238163

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bench/POTENTIALS/data.protein Symbolic link
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../data.rhodo

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# PETN-I unit cell (space group P4¯21c)
58 atoms
4 atom types
0.0 9.491065 xlo xhi
0.0 9.491065 ylo yhi
0.0 6.99123 zlo zhi
Masses
1 12.0000
2 1.0080
3 15.9990
4 14.0000
Atoms
1 4 0.863455358E-13 1.732320000 4.630010000 0.892350000
2 3 0.863455358E-13 2.969950000 4.192650000 1.864890000
3 3 0.863455358E-13 1.373230000 3.777920000 0.096380000
4 3 0.863455358E-13 1.320990000 5.707670000 1.097690000
5 2 0.863455358E-13 2.884650000 5.896680000 3.317770000
6 2 0.863455358E-13 3.827980000 6.263410000 2.178970000
7 1 0.863455358E-13 5.909570000 4.291490000 2.540550000
8 4 0.863455358E-13 7.726490000 4.862430000 0.940970000
9 3 0.863455358E-13 6.554310000 5.406520000 1.911000000
10 3 0.863455358E-13 8.126280000 5.645810000 0.107790000
11 3 0.863455358E-13 8.070620000 3.697510000 1.039000000
12 2 0.863455358E-13 6.526620000 3.514030000 3.084250000
13 2 0.863455358E-13 5.500710000 3.475690000 1.894580000
14 1 0.863455358E-13 4.305160000 3.663690000 4.373270000
15 4 0.863455358E-13 4.891690000 1.789930000 5.975440000
16 3 0.863455358E-13 5.388500000 3.060710000 5.142620000
17 3 0.863455358E-13 5.709330000 1.320000000 6.723350000
18 3 0.863455358E-13 3.766570000 1.413750000 5.785210000
19 2 0.863455358E-13 3.859620000 2.802480000 3.723820000
20 2 0.863455358E-13 3.303550000 3.975170000 4.811250000
21 1 0.863455358E-13 5.224790000 5.919230000 4.377750000
22 4 0.863455358E-13 4.644030000 7.696520000 6.100900000
23 3 0.863455358E-13 4.146850000 6.645990000 4.999010000
24 3 0.863455358E-13 3.883440000 7.981690000 7.010630000
25 3 0.863455358E-13 5.786660000 8.025100000 5.996670000
26 2 0.863455358E-13 5.906020000 6.611630000 3.756700000
27 2 0.863455358E-13 6.077870000 5.531160000 4.915880000
28 1 0.863455358E-13 3.552720000 5.288480000 2.602930000
29 1 0.863455358E-13 4.757460000 4.786420000 3.446050000
30 1 0.863455358E-13 10.623310000 10.011360000 7.901960000
31 4 0.863455358E-13 12.340670000 9.278570000 9.658210000
32 3 0.863455358E-13 11.173160000 8.908900000 8.591070000
33 3 0.863455358E-13 12.634410000 8.404450000 10.434380000
34 3 0.863455358E-13 12.808850000 10.398130000 9.459970000
35 2 0.863455358E-13 11.336750000 10.607430000 7.235710000
36 2 0.863455358E-13 10.314820000 10.962610000 8.407430000
37 1 0.863455358E-13 8.366600000 8.930150000 7.823850000
38 4 0.863455358E-13 6.680390000 9.584210000 9.655230000
39 3 0.863455358E-13 7.796220000 10.005630000 8.544820000
40 3 0.863455358E-13 6.439700000 10.424020000 10.460020000
41 3 0.863455358E-13 6.239040000 8.465520000 9.442190000
42 2 0.863455358E-13 7.687150000 8.335850000 7.127770000
43 2 0.863455358E-13 8.728770000 7.913540000 8.234250000
44 1 0.863455358E-13 10.045160000 8.333570000 6.100600000
45 4 0.863455358E-13 9.373710000 6.690820000 4.302840000
46 3 0.863455358E-13 8.940460000 7.828420000 5.375480000
47 3 0.863455358E-13 8.526330000 6.420240000 3.522270000
48 3 0.863455358E-13 10.474540000 6.234360000 4.499290000
49 2 0.863455358E-13 10.719930000 7.694230000 6.776840000
50 2 0.863455358E-13 10.913160000 8.873910000 5.574960000
51 1 0.863455358E-13 8.940970000 10.671300000 6.139780000
52 4 0.863455358E-13 9.619090000 12.332990000 4.329510000
53 3 0.863455358E-13 10.055950000 11.263880000 5.506630000
54 3 0.863455358E-13 10.434090000 12.566040000 3.507610000
55 3 0.863455358E-13 8.506740000 12.768990000 4.512780000
56 2 0.863455358E-13 8.359930000 11.424490000 6.758000000
57 2 0.863455358E-13 8.018410000 10.320200000 5.568000000
58 1 0.863455358E-13 9.486900000 9.503450000 6.990810000

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bench/POTENTIALS/data.rebo Symbolic link
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data.airebo

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bench/POTENTIALS/in.bop
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@ -17,7 +17,7 @@ pair_coeff * * CdTe.bop Cd Te
mass 1 112.4
mass 2 127.6
communicate single cutoff 14.7
comm_modify cutoff 14.7
velocity all create 1000.0 376847 loop geom

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bench/POTENTIALS/in.eff
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@ -10,7 +10,7 @@ pair_coeff * *
neigh_modify one 6000 page 60000
communicate single vel yes
comm_modify vel yes
compute effTemp all temp/eff

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bench/POTENTIALS/in.granular
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@ -4,7 +4,7 @@ units lj
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
comm_modify vel yes
read_data data.granular

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bench/POTENTIALS/in.meamc Normal file
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# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100