Example geometries

Example geometries#

Graphite geometry#

We will use the energy minimization example

# LAMMPS data file written by OVITO Basic 3.5.4
8 atoms
1 atom types
0.0 3.57371 xlo xhi
0.0 3.57371 ylo yhi
0.0 3.57371 zlo zhi
6.0e-16 2.0e-16 2.0e-16 xy xz yz

Masses

1 12.0107  # C

Atoms  # charge

1 1 0.0 0.8934275 2.6802825 0.8934275
2 1 0.0 1.0e-16 1.0e-16 1.786855
3 1 0.0 0.8934275 0.8934275 2.6802825
4 1 0.0 3.0e-16 1.786855 0.0
5 1 0.0 2.6802825 2.6802825 2.6802825
6 1 0.0 1.786855 0.0 1.2325951644e-32
7 1 0.0 2.6802825 0.8934275 0.8934275
8 1 0.0 1.786855 1.786855 1.7868551~

Diamond geometry#

# LAMMPS data file written by OVITO Basic 3.5.4
12 atoms
1 atom types
0.0 2.4693712944 xlo xhi
0.0 2.1385382723 ylo yhi
0.0 35.5630722147 zlo zhi
-1.2346856472 0.0 0.0 xy xz yz

Masses

1 12.0107  # C

Atoms  # charge

1 1 0.0 1.2346856472 0.7128460908 10.0493181116
2 1 0.0 0.0 0.0 10.0478126082
3 1 0.0 1.2346856472 0.7128460908 1.8065447967
4 1 0.0 0.0 0.0 1.8050392933
5 1 0.0 -1.1102230246e-16 1.4256921816 21.9036755165
6 1 0.0 1.2346856472 0.7128460908 21.9021700131
7 1 0.0 -1.1102230246e-16 1.4256921816 13.6609022016
8 1 0.0 1.2346856472 0.7128460908 13.6593966982
9 1 0.0 0.0 0.0 33.7580329214
10 1 0.0 -1.1102230246e-16 1.4256921816 33.756527418
11 1 0.0 0.0 0.0 25.5152596065
12 1 0.0 -1.1102230246e-16 1.4256921816 25.51375410311

Fe pristine geometry#

# LAMMPS data file written by OVITO Basic 3.5.4
64 atoms
1 atom types
0.0 9.928115229 xlo xhi
0.0 9.3603168038 ylo yhi
0.0 8.1062721395 zlo zhi
-3.309371743 -3.309371743 4.6801584019 xy xz yz

Masses

1 55.8450

Atoms  # charge

1 1 0.0 0.0 0.0 0.0
2 1 0.0 -0.8273429357 -1.1700396005 2.0265680349
3 1 0.0 -1.6546858715 -2.3400792009 4.0531360698
4 1 0.0 -2.4820288072 -3.5101188014 6.0797041046
5 1 0.0 -0.8273429357 2.3400792009 4.4110497768e-16
6 1 0.0 -1.6546858715 1.1700396005 2.0265680349
7 1 0.0 -2.4820288072 2.7179875977e-16 4.0531360698
8 1 0.0 -3.309371743 -1.1700396005 6.0797041046
9 1 0.0 -1.6546858715 4.6801584019 8.8220995536e-16
10 1 0.0 -2.4820288072 3.5101188014 2.0265680349
11 1 0.0 -3.309371743 2.3400792009 4.0531360698
12 1 0.0 -4.1367146787 1.1700396005 6.0797041046
13 1 0.0 -2.4820288072 7.0202376028 9.4426108224e-16
14 1 0.0 -3.309371743 5.8501980023 2.0265680349
15 1 0.0 -4.1367146787 4.6801584019 4.0531360698
16 1 0.0 -4.9640576145 3.5101188014 6.0797041046
17 1 0.0 2.4820288072 -4.9754154846e-17 -9.0892236054e-17
18 1 0.0 1.6546858715 -1.1700396005 2.0265680349
19 1 0.0 0.8273429357 -2.3400792009 4.0531360698
20 1 0.0 -1.4030788196e-16 -3.5101188014 6.0797041046
21 1 0.0 1.6546858715 2.3400792009 3.5021274162e-16
22 1 0.0 0.8273429357 1.1700396005 2.0265680349
23 1 0.0 -8.1736722967e-17 4.9754154846e-17 4.0531360698
24 1 0.0 -0.8273429357 -1.1700396005 6.0797041046
25 1 0.0 0.8273429357 4.6801584019 7.913177193e-16
26 1 0.0 1.7465830188e-16 3.5101188014 2.0265680349
27 1 0.0 -0.8273429357 2.3400792009 4.0531360698
28 1 0.0 -1.6546858715 1.1700396005 6.0797041046
29 1 0.0 -1.6347344593e-16 7.0202376028 1.232422697e-15
30 1 0.0 -0.8273429357 5.8501980023 2.0265680349
31 1 0.0 -1.6546858715 4.6801584019 4.0531360698
32 1 0.0 -2.4820288072 3.5101188014 6.0797041046
33 1 0.0 4.9640576145 -9.9508309692e-17 -1.8178447211e-16
34 1 0.0 4.1367146787 -1.1700396005 2.0265680349
35 1 0.0 3.309371743 -2.3400792009 4.0531360698
36 1 0.0 2.4820288072 -3.5101188014 6.0797041046
37 1 0.0 4.1367146787 2.3400792009 2.5932050557e-16
38 1 0.0 3.309371743 1.1700396005 2.0265680349
39 1 0.0 2.4820288072 1.3154450589e-16 4.0531360698
40 1 0.0 1.6546858715 -1.1700396005 6.0797041046
41 1 0.0 3.309371743 4.6801584019 7.0042548325e-16
42 1 0.0 2.4820288072 3.5101188014 2.0265680349
43 1 0.0 1.6546858715 2.3400792009 4.0531360698
44 1 0.0 0.8273429357 1.1700396005 6.0797041046
45 1 0.0 2.4820288072 7.0202376028 1.1415304609e-15
46 1 0.0 1.6546858715 5.8501980023 2.0265680349
47 1 0.0 0.8273429357 4.6801584019 4.0531360698
48 1 0.0 -3.3813174782e-16 3.5101188014 6.0797041046
49 1 0.0 7.4460864217 -1.9000840873e-16 1.0637714263e-16
50 1 0.0 6.618743486 -1.1700396005 2.0265680349
51 1 0.0 5.7914005502 -2.3400792009 4.0531360698
52 1 0.0 4.9640576145 -3.5101188014 6.0797041046
53 1 0.0 6.618743486 2.3400792009 4.8244676125e-16
54 1 0.0 5.7914005502 1.1700396005 2.0265680349
55 1 0.0 4.9640576145 -5.4359751954e-16 4.0531360698
56 1 0.0 4.1367146787 -1.1700396005 6.0797041046
57 1 0.0 5.7914005502 4.6801584019 7.6654249306e-16
58 1 0.0 4.9640576145 3.5101188014 2.0265680349
59 1 0.0 4.1367146787 2.3400792009 4.0531360698
60 1 0.0 3.309371743 1.1700396005 6.0797041046
61 1 0.0 4.9640576145 7.0202376028 1.0506382249e-15
62 1 0.0 4.1367146787 5.8501980023 2.0265680349
63 1 0.0 3.309371743 4.6801584019 4.0531360698
64 1 0.0 2.4820288072 3.5101188014 6.0797041046

Fe defective geometry#

# LAMMPS data file written by OVITO Basic 3.5.4
63 atoms
1 atom types
0.0 9.928115229 xlo xhi
0.0 9.3603168038 ylo yhi
0.0 8.1062721395 zlo zhi
-3.309371743 -3.309371743 4.6801584019 xy xz yz

Masses

1 55.8450

Atoms  # charge

1 1 0.0 0.0 0.0 0.0
2 1 0.0 -0.8273429357 -1.1700396005 2.0265680349
3 1 0.0 -1.6546858715 -2.3400792009 4.0531360698
4 1 0.0 -2.4820288072 -3.5101188014 6.0797041046
5 1 0.0 -0.8273429357 2.3400792009 4.4110497768e-16
6 1 0.0 -1.6546858715 1.1700396005 2.0265680349
7 1 0.0 -2.4820288072 2.7179875977e-16 4.0531360698
8 1 0.0 -3.309371743 -1.1700396005 6.0797041046
9 1 0.0 -1.6546858715 4.6801584019 8.8220995536e-16
10 1 0.0 -2.4820288072 3.5101188014 2.0265680349
11 1 0.0 -3.309371743 2.3400792009 4.0531360698
12 1 0.0 -4.1367146787 1.1700396005 6.0797041046
13 1 0.0 -2.4820288072 7.0202376028 9.4426108224e-16
14 1 0.0 -3.309371743 5.8501980023 2.0265680349
15 1 0.0 -4.1367146787 4.6801584019 4.0531360698
16 1 0.0 -4.9640576145 3.5101188014 6.0797041046
17 1 0.0 2.4820288072 -4.9754154846e-17 -9.0892236054e-17
18 1 0.0 1.6546858715 -1.1700396005 2.0265680349
19 1 0.0 0.8273429357 -2.3400792009 4.0531360698
20 1 0.0 -1.4030788196e-16 -3.5101188014 6.0797041046
21 1 0.0 1.6546858715 2.3400792009 3.5021274162e-16
22 1 0.0 0.8273429357 1.1700396005 2.0265680349
23 1 0.0 -8.1736722967e-17 4.9754154846e-17 4.0531360698
24 1 0.0 -0.8273429357 -1.1700396005 6.0797041046
25 1 0.0 0.8273429357 4.6801584019 7.913177193e-16
26 1 0.0 1.7465830188e-16 3.5101188014 2.0265680349
27 1 0.0 -0.8273429357 2.3400792009 4.0531360698
28 1 0.0 -1.6546858715 1.1700396005 6.0797041046
29 1 0.0 -1.6347344593e-16 7.0202376028 1.232422697e-15
30 1 0.0 -0.8273429357 5.8501980023 2.0265680349
31 1 0.0 -1.6546858715 4.6801584019 4.0531360698
32 1 0.0 -2.4820288072 3.5101188014 6.0797041046
33 1 0.0 4.9640576145 -9.9508309692e-17 -1.8178447211e-16
34 1 0.0 4.1367146787 -1.1700396005 2.0265680349
35 1 0.0 3.309371743 -2.3400792009 4.0531360698
36 1 0.0 2.4820288072 -3.5101188014 6.0797041046
37 1 0.0 4.1367146787 2.3400792009 2.5932050557e-16
38 1 0.0 3.309371743 1.1700396005 2.0265680349
39 1 0.0 2.4820288072 1.3154450589e-16 4.0531360698
40 1 0.0 1.6546858715 -1.1700396005 6.0797041046
41 1 0.0 3.309371743 4.6801584019 7.0042548325e-16
42 1 0.0 2.4820288072 3.5101188014 2.0265680349
43 1 0.0 1.6546858715 2.3400792009 4.0531360698
44 1 0.0 0.8273429357 1.1700396005 6.0797041046
45 1 0.0 2.4820288072 7.0202376028 1.1415304609e-15
46 1 0.0 1.6546858715 5.8501980023 2.0265680349
47 1 0.0 0.8273429357 4.6801584019 4.0531360698
48 1 0.0 -3.3813174782e-16 3.5101188014 6.0797041046
49 1 0.0 7.4460864217 -1.9000840873e-16 1.0637714263e-16
50 1 0.0 6.618743486 -1.1700396005 2.0265680349
51 1 0.0 5.7914005502 -2.3400792009 4.0531360698
52 1 0.0 4.9640576145 -3.5101188014 6.0797041046
53 1 0.0 6.618743486 2.3400792009 4.8244676125e-16
54 1 0.0 5.7914005502 1.1700396005 2.0265680349
55 1 0.0 4.9640576145 -5.4359751954e-16 4.0531360698
56 1 0.0 4.1367146787 -1.1700396005 6.0797041046
57 1 0.0 5.7914005502 4.6801584019 7.6654249306e-16
58 1 0.0 4.9640576145 3.5101188014 2.0265680349
59 1 0.0 4.1367146787 2.3400792009 4.0531360698
60 1 0.0 3.309371743 1.1700396005 6.0797041046
61 1 0.0 4.9640576145 7.0202376028 1.0506382249e-15
62 1 0.0 4.1367146787 5.8501980023 2.0265680349
63 1 0.0 3.309371743 4.6801584019 4.0531360698
Contents