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Moved fix_bd_sphere to src/USER-MISC folder, examples to examples/USER/misc folder, and added one-liner on README file.

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This commit is contained in:
Sam Cameron
2020-12-11 12:11:02 +00:00
parent ee99a2e960
commit f81a17abbd
9 changed files with 5 additions and 0 deletions
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26
examples/USER/misc/bd_sphere/README.txt Normal file
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The input file in2ddipole.bd demonstrates how to run a 2d simulation
of particles undergoing overdamped brownian motion in both
translational and rotational degrees of freedom. Dipole
updating is turned on, so the package DIPOLE must be built
for this example to work.
The input file in3d_virial_on.bd demonstrates how to run a
similar simulation but in 3d. In this case, the virial
contribution of the brownian dynamics (the sum
sum_i <r_i dot sqrt{2D_t}W>/(3*volume) where W is
a random variable with mean 0 and variance dt) is
calculated via the fix_modify command. For long
enough times, this will be equal to rho*D_t*gamma_t
(the ideal gas term in equilibrium systems). Note that
no dipole updating is performed.
To confirm rotational diffusion is working correctly,
run the above simulations with dump files on and
measure \sum_i<e_i(0) dot e_i(t)> where e_i is the
dipole vector of particle i, and one should
find that this decays as an exponential with
timescale 1/((d-1)*D_r).
Note that both of the simulations above are not long
enough to get good statistics on e.g. ideal gas
pressure, rotational diffusion, or translational diffusion.

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examples/USER/misc/bd_sphere/in2ddipole.bd Normal file
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# 2d overdamped brownian dynamics
variable rng string gaussian
variable gamma_t equal 4.0
variable gamma_r equal 1.0
variable D_t equal 7.0
variable D_r equal 13.0
variable seed equal 1974019
variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r}
log log_${params}_2d.lammps.log
units lj
atom_style hybrid dipole sphere
dimension 2
newton off
lattice sq 0.4
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
#compute d all property/atom mux muy muz
fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 2 all enforce2d
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50001
run 50000
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
# uncomment next three lines for dump output
#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type &
# x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 1000
# main run
run 120000

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examples/USER/misc/bd_sphere/in3d_virial_on.bd Normal file
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# 3d overdamped brownian dynamics
variable rng string uniform
variable gamma_t equal 10.0
variable gamma_r equal 1.0
variable D_t equal 5.0
variable D_r equal 15.0
variable seed equal 553910
variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r}
log log_${params}_3d.lammps.log
units lj
atom_style sphere
dimension 3
newton off
lattice sc 0.4
region box block -8 8 -8 8 -8 8
create_box 1 box
create_atoms 1 box
#mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng}
fix_modify 1 virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50001
run 50000
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
# uncomment the next three lines for dump file
#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type &
# x y xu yu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 1000
# main run
run 120000

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units lj
atom_style hybrid dipole sphere
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
1024 settings made for dipole/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
#compute d all property/atom mux muy muz
fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} dipole
fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} dipole
fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian dipole
fix 2 all enforce2d
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50001
run 50000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes
Step Temp E_pair c_press
0 1 0 0
50000 7.3671759e+10 0 0
Loop time of 11.2219 on 1 procs for 50000 steps with 1024 atoms
Performance: 0.038 tau/day, 4455.573 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.028513 | 0.028513 | 0.028513 | 0.0 | 0.25
Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00
Modify | 11.048 | 11.048 | 11.048 | 0.0 | 98.45
Other | | 0.1458 | | | 1.30
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 65.0000 ave 65 max 65 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
# uncomment next three lines for dump output
#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 1000
# main run
run 120000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 7.3671759e+10 0 0 0 0 0 0
1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 0
2000 705025.5 0 0.27078701 0.27355073 0 0.54433774 0
3000 750845.29 0 0.41036556 0.39710766 0 0.80747321 0
4000 752542.47 0 0.53097803 0.53654063 0 1.0675187 0
5000 731812.26 0 0.66927129 0.65872533 0 1.3279966 0
6000 716119.24 0 0.79097615 0.76825364 0 1.5592298 0
7000 726294.28 0 0.93322099 0.91220222 0 1.8454232 0
8000 673771.54 0 1.0789689 1.031843 0 2.1108119 0
9000 757173.95 0 1.2328252 1.2024778 0 2.435303 0
10000 693711.95 0 1.3972184 1.3045575 0 2.7017759 0
11000 774897.65 0 1.584036 1.4168797 0 3.0009157 0
12000 764910.09 0 1.7344079 1.5751172 0 3.3095251 0
13000 752859.5 0 1.8538323 1.7336107 0 3.5874429 0
14000 746333.26 0 2.0392353 1.9027299 0 3.9419652 0
15000 735704.24 0 2.1714465 2.000952 0 4.1723985 0
16000 722768.01 0 2.258542 2.1084289 0 4.3669709 0
17000 741408.63 0 2.4194247 2.2469958 0 4.6664206 0
18000 713609.29 0 2.5366244 2.3325203 0 4.8691447 0
19000 770066.65 0 2.6662758 2.4726928 0 5.1389686 0
20000 739828.53 0 2.792873 2.6188232 0 5.4116962 0
21000 719478.96 0 2.9109491 2.7872008 0 5.6981499 0
22000 737448.77 0 3.0162218 2.9213733 0 5.9375951 0
23000 714695.3 0 3.1309486 3.0325142 0 6.1634628 0
24000 712386.78 0 3.31348 3.1323675 0 6.4458475 0
25000 747298.11 0 3.5148965 3.2978465 0 6.812743 0
26000 737240.19 0 3.7117818 3.4245004 0 7.1362822 0
27000 720878.36 0 3.8342853 3.5681829 0 7.4024682 0
28000 776824.55 0 3.9904931 3.6853691 0 7.6758622 0
29000 714696.4 0 4.0733919 3.8807741 0 7.954166 0
30000 725827.3 0 4.2213715 4.0552488 0 8.2766204 0
31000 737978.89 0 4.2918759 4.1795647 0 8.4714407 0
32000 766620.93 0 4.4620184 4.2765194 0 8.7385378 0
33000 714739.71 0 4.5942749 4.426881 0 9.0211559 0
34000 694821.06 0 4.686348 4.5057433 0 9.1920912 0
35000 721948.38 0 4.7526371 4.5689873 0 9.3216245 0
36000 713621.16 0 4.8645036 4.6355302 0 9.5000339 0
37000 704079.85 0 4.9652601 4.8235856 0 9.7888457 0
38000 706914.29 0 5.1045998 4.9585169 0 10.063117 0
39000 736940.33 0 5.2172626 5.1168713 0 10.334134 0
40000 738302.73 0 5.3720228 5.3207578 0 10.692781 0
41000 746518.85 0 5.5376524 5.5192708 0 11.056923 0
42000 719970.82 0 5.7610696 5.6335312 0 11.394601 0
43000 736875.87 0 5.8769052 5.7504356 0 11.627341 0
44000 765218.38 0 6.0308866 5.9650683 0 11.995955 0
45000 739382.69 0 6.1577029 6.0736304 0 12.231333 0
46000 730967.87 0 6.3846223 6.2090389 0 12.593661 0
47000 758881.95 0 6.5604053 6.3883315 0 12.948737 0
48000 751135.53 0 6.6160248 6.5199017 0 13.135926 0
49000 721058.97 0 6.6124519 6.6938253 0 13.306277 0
50000 686287.15 0 6.8527601 6.8518895 0 13.70465 0
51000 735175.7 0 6.9928329 6.8663476 0 13.85918 0
52000 760085.67 0 7.1009497 7.0345784 0 14.135528 0
53000 741211.89 0 7.2287282 7.2318431 0 14.460571 0
54000 723668.97 0 7.3732634 7.3847301 0 14.757994 0
55000 751846.88 0 7.5566634 7.4927365 0 15.0494 0
56000 762648.27 0 7.7651818 7.5379796 0 15.303161 0
57000 710175.2 0 7.9051989 7.6644542 0 15.569653 0
58000 740068.94 0 8.0296854 7.8307471 0 15.860433 0
59000 728119.43 0 8.1562433 8.039333 0 16.195576 0
60000 728768.48 0 8.316192 8.1643843 0 16.480576 0
61000 707538.83 0 8.3727565 8.3895027 0 16.762259 0
62000 713931.41 0 8.4657927 8.5517529 0 17.017546 0
63000 742604.95 0 8.6550684 8.7189851 0 17.374053 0
64000 738981.54 0 8.7331005 8.9208616 0 17.653962 0
65000 701685.87 0 8.898571 8.977933 0 17.876504 0
66000 716151.39 0 9.0229699 9.1292403 0 18.15221 0
67000 732641.29 0 9.151611 9.3249179 0 18.476529 0
68000 740870.85 0 9.233452 9.4667607 0 18.700213 0
69000 733159.17 0 9.1743719 9.5648134 0 18.739185 0
70000 693562.75 0 9.3414089 9.7425241 0 19.083933 0
71000 748694.53 0 9.5036102 9.8686571 0 19.372267 0
72000 721046.02 0 9.7116931 10.0195 0 19.731193 0
73000 736631.66 0 9.7095662 10.205306 0 19.914872 0
74000 751264.08 0 9.9413234 10.327844 0 20.269167 0
75000 729223.27 0 10.211903 10.412516 0 20.624419 0
76000 747811 0 10.332266 10.544251 0 20.876517 0
77000 717505.01 0 10.521195 10.737774 0 21.258969 0
78000 712288.89 0 10.712514 10.874932 0 21.587446 0
79000 728912.34 0 10.755227 10.968257 0 21.723484 0
80000 743505.67 0 11.026063 11.070234 0 22.096298 0
81000 732218.14 0 11.321417 11.31773 0 22.639147 0
82000 777186.61 0 11.480074 11.401465 0 22.881539 0
83000 734805.95 0 11.7524 11.62552 0 23.37792 0
84000 753703.38 0 11.863318 11.833925 0 23.697243 0
85000 755730.75 0 12.068564 11.937143 0 24.005707 0
86000 725021.19 0 12.258195 12.034586 0 24.292781 0
87000 731844.67 0 12.341844 12.331792 0 24.673636 0
88000 707368.15 0 12.431452 12.547314 0 24.978766 0
89000 784756.28 0 12.405699 12.686021 0 25.09172 0
90000 760278.97 0 12.542669 12.851925 0 25.394593 0
91000 753765.97 0 12.703534 13.08092 0 25.784454 0
92000 705869.22 0 12.971838 13.210092 0 26.18193 0
93000 741699.59 0 13.110745 13.383115 0 26.49386 0
94000 717372.41 0 13.252109 13.466388 0 26.718497 0
95000 721820.49 0 13.373146 13.660605 0 27.033751 0
96000 777409.97 0 13.596822 13.886961 0 27.483782 0
97000 741480.91 0 13.752545 14.204624 0 27.957169 0
98000 725755.72 0 13.918302 14.219292 0 28.137594 0
99000 729710.24 0 14.065417 14.213142 0 28.278559 0
100000 700366.74 0 14.278054 14.324135 0 28.602189 0
101000 722737.18 0 14.398464 14.46904 0 28.867505 0
102000 758930.85 0 14.408098 14.637964 0 29.046061 0
103000 725233.66 0 14.526482 14.719688 0 29.24617 0
104000 752416.52 0 14.641393 14.952087 0 29.59348 0
105000 769047.5 0 14.780788 15.182945 0 29.963733 0
106000 734849.98 0 14.840982 15.316112 0 30.157094 0
107000 720210.74 0 15.010029 15.372792 0 30.382821 0
108000 741216.55 0 15.113143 15.488575 0 30.601718 0
109000 714158.43 0 15.057499 15.592865 0 30.650364 0
110000 743262.25 0 15.381281 15.798368 0 31.179649 0
111000 728836.92 0 15.488226 16.034645 0 31.522871 0
112000 753490.67 0 15.679979 16.350819 0 32.030799 0
113000 730699.5 0 15.82813 16.680136 0 32.508266 0
114000 705526.22 0 16.099699 16.920095 0 33.019794 0
115000 752408.36 0 16.393466 17.053935 0 33.447401 0
116000 713697.16 0 16.634939 17.35349 0 33.98843 0
117000 690041.5 0 16.727379 17.457936 0 34.185315 0
118000 745594.37 0 16.838659 17.585392 0 34.424052 0
119000 714487.42 0 17.064214 17.743478 0 34.807692 0
120000 716557.14 0 17.105558 17.845925 0 34.951483 0
Loop time of 27.2068 on 1 procs for 120000 steps with 1024 atoms
Performance: 3810.806 tau/day, 4410.656 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.0015633 | 0.0015633 | 0.0015633 | 0.0 | 0.01
Comm | 0.021682 | 0.021682 | 0.021682 | 0.0 | 0.08
Output | 0.0032539 | 0.0032539 | 0.0032539 | 0.0 | 0.01
Modify | 26.802 | 26.802 | 26.802 | 0.0 | 98.51
Other | | 0.3781 | | | 1.39
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 1049
Dangerous builds = 0
Total wall time: 0:00:38

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examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log Normal file
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units lj
atom_style sphere
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.001 seconds
#mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng}
fix 1 all bd/sphere 10 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng}
fix 1 all bd/sphere 10 1 ${D_t} ${D_r} ${seed} rng ${rng}
fix 1 all bd/sphere 10 1 5 ${D_r} ${seed} rng ${rng}
fix 1 all bd/sphere 10 1 5 15 ${seed} rng ${rng}
fix 1 all bd/sphere 10 1 5 15 553910 rng ${rng}
fix 1 all bd/sphere 10 1 5 15 553910 rng uniform
fix_modify 1 virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50001
run 50000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 3.581 | 3.581 | 3.581 Mbytes
Step Temp E_pair c_press
0 1 0 -32553.271
50000 5.2351457e+10 0 -15026.42
Loop time of 16.0183 on 1 procs for 50000 steps with 4096 atoms
Performance: 0.027 tau/day, 3121.426 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.074984 | 0.074984 | 0.074984 | 0.0 | 0.47
Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.00
Modify | 15.366 | 15.366 | 15.366 | 0.0 | 95.93
Other | | 0.5772 | | | 3.60
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 817.000 ave 817 max 817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
# uncomment the next three lines for dump file
#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type # x y xu yu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 1000
# main run
run 120000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 3.956 | 3.956 | 3.956 Mbytes
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 5.2351457e+10 0 0 0 0 0 -233.83012
1000 522590.88 0 0.10259269 0.10487519 0.10391005 0.31137793 -13.730626
2000 521776.08 0 0.20662097 0.2118237 0.20371673 0.62216139 -141.90848
3000 529408.9 0 0.30711557 0.3105565 0.30293728 0.92060935 28.335187
4000 518069.42 0 0.39918073 0.40643835 0.40168024 1.2072993 -12.262269
5000 520487.75 0 0.50222348 0.50854461 0.50304351 1.5138116 303.56775
6000 527970.5 0 0.60443861 0.60363711 0.59884932 1.806925 218.55799
7000 519424.68 0 0.69529071 0.70025532 0.70347351 2.0990195 -363.51723
8000 521925.72 0 0.80545039 0.81520807 0.79930708 2.4199655 510.47732
9000 518397.28 0 0.91236827 0.9050426 0.89431985 2.7117307 537.74151
10000 525696.47 0 0.99494325 0.99433832 0.98574884 2.9750304 411.56896
11000 524505.88 0 1.0863677 1.1232636 1.0810609 3.2906921 32.652569
12000 525350.08 0 1.1816136 1.2412674 1.189996 3.612877 45.304061
13000 524598.12 0 1.2841566 1.3381915 1.2906249 3.912973 -376.50739
14000 525438.09 0 1.3964076 1.4420032 1.3915611 4.2299719 -31.273339
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20000 525623.21 0 1.9718697 2.0048196 2.0068177 5.983507 73.884028
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23000 519629.76 0 2.2297952 2.2661611 2.2805197 6.776476 57.65702
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30000 526092.8 0 2.961898 2.9361476 2.9319586 8.8300042 206.28635
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32000 521173.83 0 3.159344 3.1397814 3.1455147 9.4446401 328.73193
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34000 522930.45 0 3.3489514 3.3433962 3.3391822 10.03153 178.73773
35000 530664.64 0 3.4445399 3.4843743 3.4205275 10.349442 146.02898
36000 521443.26 0 3.520475 3.6171115 3.5179112 10.655498 244.07172
37000 529669.54 0 3.6076942 3.7233869 3.6169718 10.948053 79.46077
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39000 523237.65 0 3.8088585 3.9559041 3.8748751 11.639638 -70.265271
40000 522798.75 0 3.89319 4.0420406 3.9196106 11.854841 91.631855
41000 524228.77 0 3.9863379 4.1602581 4.0393136 12.18591 113.26515
42000 524546.08 0 4.0969366 4.2738786 4.1218115 12.492627 313.83957
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56000 524987.68 0 5.5282178 5.5825979 5.5127172 16.623533 84.654044
57000 525610.66 0 5.6202713 5.6925409 5.5964466 16.909259 407.16526
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60000 522185.96 0 5.9067925 5.9909357 5.903525 17.801253 330.09637
61000 527694.33 0 6.0576096 6.0907943 6.0202838 18.168688 310.22884
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63000 526642.55 0 6.2261061 6.2832608 6.2023277 18.711695 -130.32823
64000 514826.49 0 6.3032614 6.3628539 6.3184362 18.984552 195.43036
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66000 527425.07 0 6.5122194 6.5052947 6.5518104 19.569324 8.0143425
67000 525258.85 0 6.6292334 6.6417881 6.6438938 19.914915 152.1905
68000 527067.89 0 6.7569918 6.6951219 6.7357134 20.187827 -337.54654
69000 522395.33 0 6.8401085 6.7836633 6.8243746 20.448146 34.755329
70000 522200.34 0 6.9549662 6.8773008 6.9537894 20.786056 352.30283
71000 527550.11 0 7.0441399 6.9837133 7.0860791 21.113932 171.42143
72000 529564.22 0 7.1744229 7.0581688 7.1507041 21.383296 269.04569
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76000 518470.58 0 7.5747768 7.5354904 7.5612252 22.671492 274.53956
77000 518459.51 0 7.6660567 7.6557812 7.7020797 23.023918 430.07722
78000 516646.23 0 7.7596088 7.7130901 7.7896654 23.262364 536.21298
79000 517511.57 0 7.9021784 7.82098 7.8840028 23.607161 193.80468
80000 520654.84 0 7.991107 7.8932454 8.0049184 23.889271 -6.0066355
81000 522331.74 0 8.0616391 7.9990606 8.0954141 24.156114 47.271954
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91000 527450.69 0 8.8250902 8.8445728 9.0456076 26.715271 325.68024
92000 519060.77 0 8.9054775 8.9412744 9.1259074 26.972659 130.73028
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100000 520863.58 0 9.7452168 9.7659565 9.9878877 29.499061 -108.52324
101000 526760.86 0 9.8073751 9.8508213 10.127532 29.785728 120.22249
102000 519249.89 0 9.9315855 9.9767409 10.221605 30.129931 -176.50647
103000 525003.9 0 10.023982 10.062451 10.315002 30.401435 422.1401
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107000 527105.8 0 10.364015 10.485036 10.795177 31.644228 183.82165
108000 522024.28 0 10.450786 10.544065 10.902961 31.897812 -39.692553
109000 519497.83 0 10.556206 10.61633 11.046222 32.218758 173.75988
110000 521070.8 0 10.64856 10.745382 11.071387 32.465329 -128.45389
111000 525657.64 0 10.830485 10.852954 11.188295 32.871734 -214.60249
112000 519426.33 0 10.987769 10.97575 11.26012 33.223639 292.35901
113000 526472.45 0 11.029941 11.086376 11.418772 33.535089 189.69245
114000 520070.28 0 11.107229 11.183295 11.454757 33.745281 -40.433571
115000 525812.59 0 11.153992 11.305378 11.537521 33.99689 -106.38733
116000 524464.26 0 11.256779 11.413082 11.633295 34.303156 -159.59643
117000 519838.94 0 11.344413 11.480104 11.706366 34.530883 -2.0346135
118000 524075.83 0 11.441416 11.597533 11.783056 34.822005 -350.05313
119000 533816.71 0 11.52766 11.681986 11.917713 35.127359 -521.58975
120000 524509.31 0 11.63865 11.792667 12.080379 35.511696 273.09647
Loop time of 39.6359 on 1 procs for 120000 steps with 4096 atoms
Performance: 2615.809 tau/day, 3027.557 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.0059817 | 0.0059817 | 0.0059817 | 0.0 | 0.02
Comm | 0.039473 | 0.039473 | 0.039473 | 0.0 | 0.10
Output | 0.0063653 | 0.0063653 | 0.0063653 | 0.0 | 0.02
Modify | 38.085 | 38.085 | 38.085 | 0.0 | 96.09
Other | | 1.499 | | | 3.78
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 992
Dangerous builds = 0
Total wall time: 0:00:55