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lammps/examples/KAPPA/log.mp.1Feb14
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
lattice fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region box block 0 $x 0 $y 0 $z
region box block 0 10 0 $y 0 $z
region box block 0 10 0 10 0 $z
region box block 0 10 0 10 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
2 by 1 by 4 MPI processor grid
create_atoms 1 box
Created 8000 atoms
mass 1 1.0
velocity all create $t 87287
velocity all create 1.35 87287
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
fix 1 all nvt temp 1.35 $t 0.5
fix 1 all nvt temp 1.35 1.35 0.5
thermo 100
run 1000
Memory usage per processor = 2.14238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
800 1.3419994 -3.7155648 0 -1.7028172 0.82925677
900 1.3562214 -3.6965608 0 -1.662483 0.88908144
1000 1.3732016 -3.7100024 0 -1.6504575 0.83982823
Loop time of 0.862547 on 8 procs for 1000 steps with 8000 atoms
Pair time (%) = 0.478427 (55.4668)
Neigh time (%) = 0.220096 (25.517)
Comm time (%) = 0.10999 (12.7517)
Outpt time (%) = 0.00030601 (0.0354775)
Other time (%) = 0.0537277 (6.22896)
Nlocal: 1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost: 2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs: 27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1
Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# 2nd equilibration run
compute ke all ke/atom
variable temp atom c_ke/1.5
fix 1 all nve
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp file profile.mp units reduced
fix 3 all thermal/conductivity 10 z 20
variable tdiff equal f_2[11][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff
thermo 1000
run 20000
Memory usage per processor = 2.1433 Mbytes
Step Temp E_pair TotEng 3 tdiff
1000 1.35 -3.7100024 -1.6852556 0 0
2000 1.3488972 -3.708116 -1.6850231 877.52861 0.25969396
3000 1.3658991 -3.735305 -1.6867124 1757.5984 0.40713773
4000 1.3660888 -3.7368211 -1.6879441 2599.882 0.63176318
5000 1.3702365 -3.7439731 -1.6888753 3417.2012 0.68861496
6000 1.3802047 -3.7607288 -1.6906806 4247.6303 0.8258624
7000 1.3981219 -3.7883507 -1.69143 5036.1985 0.90753031
8000 1.3968279 -3.7880683 -1.6930884 5807.0759 0.99392296
9000 1.3960267 -3.7866214 -1.6928431 6584.6398 1.0833481
10000 1.4067029 -3.8038141 -1.6940234 7372.3357 1.0359437
11000 1.4037578 -3.7984096 -1.6930361 8133.4913 1.0506296
12000 1.4112365 -3.8109671 -1.6943769 8908.2356 1.1033313
13000 1.4066326 -3.8036805 -1.6939953 9674.5783 1.1492152
14000 1.4136249 -3.8155288 -1.6953566 10429.951 1.1101441
15000 1.402741 -3.7983064 -1.6944579 11194.927 1.1163151
16000 1.412565 -3.8138997 -1.695317 11931.815 1.2199073
17000 1.4023686 -3.7975376 -1.6942476 12695.415 1.1800489
18000 1.4200941 -3.8257695 -1.6958947 13456.945 1.1583648
19000 1.4016117 -3.7972936 -1.6951388 14216.201 1.1846518
20000 1.4105524 -3.8113272 -1.6957631 14977.184 1.2831156
21000 1.4068217 -3.8054214 -1.6954526 15739.554 1.147926
Loop time of 20.7938 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.73079 (46.7967)
Neigh time (%) = 4.8843 (23.4893)
Comm time (%) = 5.15718 (24.8016)
Outpt time (%) = 0.000606179 (0.0029152)
Other time (%) = 1.02088 (4.90955)
Nlocal: 1000 ave 1176 max 820 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Nghost: 2318.88 ave 2663 max 1967 min
Histogram: 3 1 0 0 0 0 0 0 2 2
Neighs: 27860.2 ave 36167 max 18992 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Total # of neighbors = 222882
Ave neighs/atom = 27.8603
Neighbor list builds = 3543
Dangerous builds = 0
# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation
fix 3 all thermal/conductivity 10 z 20
fix ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
run 20000
Memory usage per processor = 2.33403 Mbytes
Step Temp E_pair TotEng 3 tdiff ave
21000 1.4068217 -3.8054214 -1.6954526 0 1.147926 1.147926
22000 1.3967994 -3.7893902 -1.694453 767.0398 1.1920832 1.1700046
23000 1.4170976 -3.822137 -1.6967564 1517.2987 1.1545977 1.164869
24000 1.4202355 -3.8249732 -1.6948862 2277.7333 1.1750006 1.1674019
25000 1.4205956 -3.8264595 -1.6958326 3028.6456 1.168964 1.1677143
26000 1.4105028 -3.8099425 -1.6944527 3771.4445 1.1535799 1.1653586
27000 1.4121218 -3.8137079 -1.6957899 4524.007 1.1582776 1.164347
28000 1.4073732 -3.8055739 -1.6947781 5297.7257 1.1390419 1.1611839
29000 1.3935065 -3.7848004 -1.6948019 6040.6442 1.106954 1.1551583
30000 1.4126276 -3.8136783 -1.6950018 6777.7617 1.122798 1.1519223
31000 1.4220569 -3.8292934 -1.6964746 7529.6983 1.1517202 1.1519039
32000 1.4157206 -3.8184427 -1.6951273 8293.9624 1.1600224 1.1525805
33000 1.4300672 -3.8403564 -1.6955237 9056.1085 1.1581575 1.1530095
34000 1.4114669 -3.8123726 -1.6954368 9827.2549 1.169357 1.1541771
35000 1.4087756 -3.8085583 -1.695659 10582.235 1.254384 1.1608576
36000 1.4071234 -3.8063392 -1.695918 11335.664 1.1886748 1.1625962
37000 1.4150044 -3.8175559 -1.6953146 12067.647 1.1452763 1.1615774
38000 1.4208299 -3.8269499 -1.6959714 12785.237 1.1689649 1.1619878
39000 1.4132869 -3.8147648 -1.6950995 13548.517 1.1134294 1.1594321
40000 1.4071151 -3.8068479 -1.6964391 14307.339 1.1772366 1.1603223
41000 1.4126121 -3.8153948 -1.6967416 15087.11 1.1408062 1.159393
Loop time of 21.9152 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 9.77976 (44.6255)
Neigh time (%) = 5.01423 (22.8802)
Comm time (%) = 6.03064 (27.5181)
Outpt time (%) = 0.000575513 (0.00262609)
Other time (%) = 1.08999 (4.97365)
Nlocal: 1000 ave 1167 max 820 min
Histogram: 3 1 0 0 0 0 0 0 0 4
Nghost: 2292.38 ave 2619 max 1989 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Neighs: 27929.9 ave 37820 max 19105 min
Histogram: 4 0 0 0 0 0 0 0 3 1
Total # of neighbors = 223439
Ave neighs/atom = 27.9299
Neighbor list builds = 3624
Dangerous builds = 0
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