Why did lammps randomly move atom 90’s x coordinate in timesetp 0? Everything else is working just fine, but this specifically has gone wonky.
My lammps code:
LAMMPS Input Script
units real
atom_style full
create a box first
include vacuum in the x and y, z should be fixed.
boundary p p p
Define force field parameters
pair_style lj/cut/coul/long 10.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style cvff
kspace_style pppm 1.0e-4
read_data CH.data
Set up simulation
neighbor 2.0 bin
neigh_modify delay 5 every 1
Define MD run
fix 1 all nvt temp 300.0 300.0 100.0
Define output
thermo 100
thermo_style custom step temp etotal pe ke press vol
dump 1 all xyz 500 output.xyz
Run simulation
timestep 1.0
run 100000
CH.data’s atom section:
Atoms
1 1 1 -0.23900000 1.000 1.00000 0.00000 2 1 2 -0.17980000 -0.519 1.00000 0.00000 3 1 3 -0.17890000 -1.066 1.00000 1.42437 4 1 4 -0.17960000 -2.591 0.99820 1.42601 5 1 5 -0.17990000 -3.126 1.00002 2.85351 6 1 6 -0.17980000 -4.649 0.99643 2.85840 7 1 7 -0.18000000 -5.178 0.99646 4.28610 8 1 8 -0.18030000 -6.700 0.99107 4.28936 9 1 9 -0.18040000 -7.226 0.98931 5.71652 10 1 10 -0.18050000 -8.746 0.98212 5.71654 11 1 11 -0.18060000 -9.271 0.97856 7.14283 12 1 12 -0.18070000 -10.790 0.96957 7.13961 13 1 13 -0.18060000 -11.315 0.96782 8.56576 14 1 14 -0.18060000 -12.834 0.96064 8.56254 15 1 15 -0.18080000 -13.357 0.96070 9.98859 16 1 16 -0.18070000 -14.876 0.95171 9.98699 17 1 17 -0.18060000 -15.397 0.95359 11.41335 18 1 18 -0.18090000 -16.918 0.94640 11.41174 19 1 19 -0.18050000 -17.440 0.94646 12.83730 20 1 20 -0.18060000 -18.960 0.93748 12.83570 21 1 21 -0.18050000 -19.485 0.93933 14.26211 22 1 22 -0.18040000 -21.005 0.92855 14.26213 23 1 23 -0.18030000 -21.532 0.93219 15.68917 24 1 24 -0.18010000 -23.053 0.92322 15.69244 25 1 25 -0.17980000 -23.582 0.92866 17.12020 26 1 26 -0.17960000 -25.105 0.91787 17.12347 27 1 27 -0.17990000 -25.642 0.92144 18.54954 28 1 28 -0.17900000 -27.167 0.91243 18.55118 29 1 29 -0.17930000 -27.715 0.91773 19.97525 30 1 30 -0.23890000 -29.235 0.91052 19.97199 31 1 31 0.08070000 1.379 0.99870 -1.02622 32 1 32 0.08070000 1.389 0.11283 0.50998 33 1 33 0.08070000 1.389 1.88842 0.50772 34 1 34 0.08850000 -0.881 0.11632 -0.53835 35 1 35 0.08850000 -0.881 1.88367 -0.53835 36 1 36 0.08960000 -0.698 1.88352 1.96054 37 1 37 0.08960000 -0.697 0.11742 1.96084 38 1 38 0.08960000 -2.962 0.11426 0.89447 39 1 39 0.08960000 -2.964 1.88115 0.89181 40 1 40 0.08970000 -2.758 1.88490 3.38697 41 1 41 0.08970000 -2.754 0.11823 3.38948 42 1 42 0.08990000 -5.020 0.11088 2.32738 43 1 43 0.08990000 -5.025 1.87812 2.32508 44 1 44 0.09000000 -4.810 1.88163 4.81930 45 1 45 0.09000000 -4.804 0.11437 4.82036 46 1 46 0.09010000 -7.070 0.10615 3.75760 47 1 47 0.09010000 -7.076 1.87307 3.75618 48 1 48 0.09010000 -6.859 1.87436 6.24999 49 1 49 0.09010000 -6.851 0.10752 6.25063 50 1 50 0.09020000 -9.115 0.09695 5.18310 51 1 51 0.09020000 -9.123 1.86448 5.18448 52 1 52 0.09030000 -8.905 1.86431 7.67633 53 1 53 0.09030000 -8.894 0.09683 7.67579 54 1 54 0.09030000 -11.156 0.08313 6.60691 55 1 55 0.09030000 -11.167 1.85026 6.60405 56 1 56 0.09040000 -10.948 1.85476 9.09735 57 1 57 0.09040000 -10.938 0.08628 9.10006 58 1 58 0.09040000 -13.201 0.07362 8.03164 59 1 59 0.09040000 -13.211 1.84149 8.02755 60 1 60 0.09030000 -12.990 1.84779 10.51945 61 1 61 0.09030000 -12.980 0.08029 10.52340 62 1 62 0.09040000 -15.242 0.06398 9.45695 63 1 63 0.09040000 -15.253 1.83147 9.45074 64 1 64 0.09040000 -15.030 1.84120 11.94267 65 1 65 0.09040000 -15.022 0.07350 11.94873 66 1 66 0.09030000 -17.285 0.06071 10.87922 67 1 67 0.09030000 -17.292 1.82731 10.87571 68 1 68 0.09040000 -17.074 1.83520 13.36726 69 1 69 0.09040000 -17.062 0.06749 13.37198 70 1 70 0.09030000 -19.324 0.04907 12.30526 71 1 71 0.09030000 -19.337 1.81645 12.29852 72 1 72 0.09020000 -19.118 1.82748 14.79126 73 1 73 0.09020000 -19.106 0.06058 14.79821 74 1 74 0.09020000 -21.369 0.03949 13.73260 75 1 75 0.09020000 -21.382 1.80710 13.72328 76 1 76 0.09010000 -21.164 1.82074 16.21591 77 1 77 0.09010000 -21.153 0.05343 16.22598 78 1 78 0.09000000 -23.418 0.03434 15.16312 79 1 79 0.09000000 -23.429 1.80126 15.15254 80 1 80 0.09000000 -23.215 1.81821 17.64635 81 1 81 0.09000000 -23.202 0.05142 17.65763 82 1 82 0.08980000 -25.468 0.02883 16.59332 83 1 83 0.08980000 -25.480 1.79552 16.58313 84 1 84 0.08950000 -25.275 1.80940 19.07979 85 1 85 0.08950000 -25.265 0.04309 19.08805 86 1 86 0.08960000 -27.528 0.02370 18.01871 87 1 87 0.08960000 -27.539 1.79034 18.00815 88 1 88 0.08860000 -27.357 1.80599 20.50822 89 1 89 0.08860000 -27.349 0.03888 20.51800 90 1 90 0.08070000 -29.628 1.79315 19.45754 91 1 91 0.08070000 -29.616 0.91570 20.99792 92 1 92 0.08070000 -29.619 0.01855 19.46739
First timestep of output:
92
Atoms. Timestep: 0
1 1 1 0
2 -0.519 1 0
3 -1.066 1 1.42437
4 -2.591 0.9982 1.42601
5 -3.126 1.00002 2.85351
6 -4.649 0.99643 2.8584
7 -5.178 0.99646 4.2861
8 -6.7 0.99107 4.28936
9 -7.226 0.98931 5.71652
10 -8.746 0.98212 5.71654
11 -9.271 0.97856 7.14283
12 -10.79 0.96957 7.13961
13 -11.315 0.96782 8.56576
14 -12.834 0.96064 8.56254
15 -13.357 0.9607 9.98859
16 -14.876 0.95171 9.98699
17 -15.397 0.95359 11.4133
18 -16.918 0.9464 11.4117
19 -17.44 0.94646 12.8373
20 -18.96 0.93748 12.8357
21 -19.485 0.93933 14.2621
22 -21.005 0.92855 14.2621
23 -21.532 0.93219 15.6892
24 -23.053 0.92322 15.6924
25 -23.582 0.92866 17.1202
26 -25.105 0.91787 17.1235
27 -25.642 0.92144 18.5495
28 -27.167 0.91243 18.5512
29 -27.715 0.91773 19.9752
30 -29.235 0.91052 19.972
31 1.379 0.9987 -1.02622
32 1.389 0.11283 0.50998
33 1.389 1.88842 0.50772
34 -0.881 0.11632 -0.53835
35 -0.881 1.88367 -0.53835
36 -0.698 1.88352 1.96054
37 -0.697 0.11742 1.96084
38 -2.962 0.11426 0.89447
39 -2.964 1.88115 0.89181
40 -2.758 1.8849 3.38697
41 -2.754 0.11823 3.38948
42 -5.02 0.11088 2.32738
43 -5.025 1.87812 2.32508
44 -4.81 1.88163 4.8193
45 -4.804 0.11437 4.82036
46 -7.07 0.10615 3.7576
47 -7.076 1.87307 3.75618
48 -6.859 1.87436 6.24999
49 -6.851 0.10752 6.25063
50 -9.115 0.09695 5.1831
51 -9.123 1.86448 5.18448
52 -8.905 1.86431 7.67633
53 -8.894 0.09683 7.67579
54 -11.156 0.08313 6.60691
55 -11.167 1.85026 6.60405
56 -10.948 1.85476 9.09735
57 -10.938 0.08628 9.10006
58 -13.201 0.07362 8.03164
59 -13.211 1.84149 8.02755
60 -12.99 1.84779 10.5195
61 -12.98 0.08029 10.5234
62 -15.242 0.06398 9.45695
63 -15.253 1.83147 9.45074
64 -15.03 1.8412 11.9427
65 -15.022 0.0735 11.9487
66 -17.285 0.06071 10.8792
67 -17.292 1.82731 10.8757
68 -17.074 1.8352 13.3673
69 -17.062 0.06749 13.372
70 -19.324 0.04907 12.3053
71 -19.337 1.81645 12.2985
72 -19.118 1.82748 14.7913
73 -19.106 0.06058 14.7982
74 -21.369 0.03949 13.7326
75 -21.382 1.8071 13.7233
76 -21.164 1.82074 16.2159
77 -21.153 0.05343 16.226
78 -23.418 0.03434 15.1631
79 -23.429 1.80126 15.1525
80 -23.215 1.81821 17.6464
81 -23.202 0.05142 17.6576
82 -25.468 0.02883 16.5933
83 -25.48 1.79552 16.5831
84 -25.275 1.8094 19.0798
85 -25.265 0.04309 19.088
86 -27.528 0.0237 18.0187
87 -27.539 1.79034 18.0082
88 -27.357 1.80599 20.5082
89 -27.349 0.03888 20.518
90 20.372 1.79315 19.4575
91 -29.616 0.9157 20.9979
92 -29.619 0.01855 19.4674