Dear Lammps users,
I am doubting the very basic concept of energy conservation in MD simulations. In nature, if the system is isolated total energy is conserved. In simulation, I am not sure that the developers of many empirical potentials consider the energy conservation during their development process. For me it looks they only want to fit them to experimental properties. The energy conservation is closely related with the functional forms of potentials?
Does anybody give me some references for this concerns?
Below shows input script and output for two LJ particles in the box, and shows total energy does not conserve but fluctuate under NVE. Is it correct?
Thank you.
Joe
##Input Script##
boundary f f f
atom_style atomic
units metal
lattice diamond 3.567
region box block -50 +50 -50 +50 -50 +50 units box
atom_modify map array
neighbor 2.0 nsq
create_box 2 box
create_atoms 1 single 0 0 0 units box
create_atoms 2 single 2.7 0 0 units box
mass 1 12.011
mass 2 12.011
timestep 0.001
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
group myatom id 2
velocity myatom set -50.0 0 0 units box
variable dimerdistance equal x[2]-x[1]
Setup output
thermo 1
thermo_style custom step temp pe ke etotal v_dimerdistance
thermo_modify norm no
compute sys_pe all pe
shell mkdir Dump
dump mindump all custom 1 ./Dump/*.dump id type xs ys zs
fix 11 all nve
run 60
###Output ###
Lattice spacing in x,y,z = 3.567 3.567 3.567
Created orthogonal box = (-50 -50 -50) to (50 50 50)
2 by 2 by 2 processor grid
Created 1 atoms
Created 1 atoms
1 atoms in group myatom
Setting up run …
Memory usage per processor = 1.25893 Mbytes
Step Temp PotEng KinEng TotEng dimerdis
0 12038.246 0 1.5560654 1.5560654 2.7
1 12038.246 0 1.5560654 1.5560654 2.65
2 12038.246 0 1.5560654 1.5560654 2.6
3 12038.246 0 1.5560654 1.5560654 2.55
4 12038.246 0 1.5560654 1.5560654 2.5
5 12046.929 -0.01840987 1.5571877 1.5387779 2.45
6 12065.653 -0.020825329 1.559608 1.5387827 2.3999279
7 12087.334 -0.023622031 1.5624106 1.5387886 2.3497726
8 12112.527 -0.026871283 1.565667 1.5387957 2.299521
9 12141.906 -0.030660062 1.5694645 1.5388044 2.2491574
10 12176.299 -0.035095044 1.5739102 1.5388152 2.1986636
11 12216.73 -0.040307835 1.5791363 1.5388285 2.1480172
12 12264.468 -0.046461839 1.5853069 1.5388451 2.0971917
13 12321.101 -0.053761336 1.5926273 1.538866 2.0461553
14 12388.629 -0.062463612 1.6013559 1.5388923 1.9948691
15 12469.592 -0.072895337 1.6118213 1.538926 1.9432859
16 12567.247 -0.085474911 1.6244442 1.5389693 1.8913479
17 12685.804 -0.10074329 1.6397689 1.5390256 1.8389841
18 12830.764 -0.11940696 1.6585064 1.5390995 1.7861061
19 13009.391 -0.14239846 1.6815958 1.5391973 1.7326043
20 13231.383 -0.17096217 1.7102905 1.5393283 1.6783405
21 13509.815 -0.20677578 1.7462806 1.5395049 1.6231408
22 13862.458 -0.25212005 1.7918634 1.5397433 1.5667841
23 14313.506 -0.31010402 1.8501659 1.5400619 1.5089887
24 14895.441 -0.38491877 1.9253869 1.5404681 1.4493957
25 15649.52 -0.48194935 2.0228592 1.5409098 1.3875521
26 16618.564 -0.60702985 2.148118 1.5410881 1.3229059
27 17807.955 -0.76209454 2.3018588 1.5397642 1.2548509
28 19026.014 -0.92700278 2.4593053 1.5323025 1.1829572
29 19323.896 -0.99330982 2.4978096 1.5044998 1.1078499
30 15855.195 -0.59831636 2.0494448 1.4511284 1.0342825
31 7689.8417 0.581329 0.99399005 1.5753191 0.98001656
32 8004.2491 0.52714785 1.0346304 1.5617783 0.98159773
33 16145.168 -0.63502786 2.0869268 1.451899 1.0374451
34 19355.553 -0.99618216 2.5019016 1.5057194 1.1113017
35 18972.123 -0.92023901 2.4523393 1.5321003 1.1862965
36 17744.497 -0.75458279 2.2936562 1.5390735 1.2579978
37 16563.807 -0.60076919 2.1410401 1.5402709 1.325868
38 15605.333 -0.47708149 2.0171477 1.5400662 1.3903558
39 14860.094 -0.38119479 1.9208179 1.5396231 1.4520673
40 14284.932 -0.30725169 1.8464724 1.5392207 1.5115504
41 13838.957 -0.24991936 1.7888257 1.5389063 1.5692534
42 13490.108 -0.20506217 1.7437333 1.5386711 1.6255314
43 13214.531 -0.16961521 1.7081122 1.538497 1.6806629
44 12994.709 -0.14133011 1.6796979 1.5383678 1.7348668
45 12817.746 -0.11855246 1.6568237 1.5382712 1.7883153
46 12674.076 -0.10005458 1.6382529 1.5381983 1.841145
47 12556.528 -0.084915913 1.6230586 1.5381427 1.8934645
48 12459.669 -0.072438705 1.6105386 1.5380999 1.9453614
49 12379.338 -0.062088405 1.600155 1.5380666 1.996906
50 12312.317 -0.053451371 1.5914919 1.5380405 2.0481557
51 12256.093 -0.046204498 1.5842244 1.5380199 2.0991573
52 12208.687 -0.040093201 1.5780966 1.5380034 2.1499493
53 12168.527 -0.034915265 1.5729055 1.5379902 2.2005633
54 12134.355 -0.030508881 1.5684885 1.5379796 2.2510257
55 12105.159 -0.026743679 1.5647146 1.5379709 2.3013585
56 12080.118 -0.023513954 1.5614778 1.5379639 2.35158
57 12058.563 -0.020733492 1.5586915 1.5379581 2.4017057
58 12039.944 -0.018331594 1.5562849 1.5379533 2.4517486
59 12031.309 0 1.5551687 1.5551687 2.5017198
60 12031.309 0 1.5551687 1.5551687 2.551691
Loop time of 2.36701 on 8 procs for 60 steps with 2 atoms
Pair time (%) = 2.61366e-05 (0.00110421)
Neigh time (%) = 1.34408e-05 (0.000567841)
Comm time (%) = 0.0168602 (0.712302)
Outpt time (%) = 2.34915 (99.2456)
Other time (%) = 0.000955939 (0.040386)
Nlocal: 0.25 ave 1 max 0 min
Histogram: 6 0 0 0 0 0 0 0 0 2
Nghost: 1.75 ave 2 max 1 min
Histogram: 2 0 0 0 0 0 0 0 0 6
Neighs: 0.125 ave 1 max 0 min
Histogram: 7 0 0 0 0 0 0 0 0 1
Total # of neighbors = 1
Ave neighs/atom = 0.5
Neighbor list builds = 2
Dangerous builds = 0