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lammps/examples/KAPPA/log.13Oct16.ehex.g++.8
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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix ehex to add/subtract energy from 2 regions
# 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
# heat layers
region hot block INF INF INF INF 0 1
region cold block INF INF INF INF 10 11
compute Thot all temp/region hot
compute Tcold all temp/region cold
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 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 1.3419995 -3.7155648 0 -1.7028172 0.82925676
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
Performance: 485876.777 tau/day, 1124.715 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48042 | 0.50311 | 0.52772 | 1.9 | 56.59
Neigh | 0.22997 | 0.23203 | 0.23466 | 0.3 | 26.10
Comm | 0.081187 | 0.10484 | 0.1285 | 4.2 | 11.79
Output | 0.00027299 | 0.00028226 | 0.000314 | 0.1 | 0.03
Modify | 0.028298 | 0.032276 | 0.037612 | 2.0 | 3.63
Other | | 0.01658 | | | 1.86
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
fix 1 all nve
fix hot all ehex 1 100.0 region hot
fix cold all ehex 1 -100.0 region cold
thermo_style custom step temp c_Thot c_Tcold
thermo 1000
run 10000
Memory usage per processor = 2.80761 Mbytes
Step Temp c_Thot c_Tcold
1000 1.35 1.431295 1.2955644
2000 1.3537291 1.6418772 1.1875127
3000 1.3615152 1.6451299 1.1769094
4000 1.3612129 1.5281727 1.2022419
5000 1.3552182 1.6672955 1.2212864
6000 1.3643442 1.6072213 1.2390567
7000 1.3665773 1.6909819 1.1466611
8000 1.375741 1.6144274 1.1691231
9000 1.3701136 1.8238424 1.136342
10000 1.3563004 1.8059065 1.1547129
11000 1.3794051 1.692299 1.0515688
Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
Performance: 409265.976 tau/day, 947.375 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1863 | 5.0134 | 5.8326 | 28.0 | 47.50
Neigh | 2.1559 | 2.4232 | 2.6516 | 14.2 | 22.96
Comm | 0.80561 | 1.8126 | 2.8852 | 58.4 | 17.17
Output | 0.00044537 | 0.00064856 | 0.00077057 | 0.5 | 0.01
Modify | 0.81915 | 0.94285 | 1.0571 | 9.5 | 8.93
Other | | 0.3628 | | | 3.44
Nlocal: 1000 ave 1105 max 883 min
Histogram: 1 1 2 0 0 0 0 0 2 2
Nghost: 2319.38 ave 2502 max 2114 min
Histogram: 1 3 0 0 0 0 0 0 0 4
Neighs: 27387.9 ave 32453 max 21803 min
Histogram: 2 2 0 0 0 0 0 0 0 4
Total # of neighbors = 219103
Ave neighs/atom = 27.3879
Neighbor list builds = 1696
Dangerous builds = 0
# thermal conductivity calculation
compute ke all ke/atom
variable temp atom c_ke/1.5
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
variable tdiff equal f_2[11][3]-f_2[1][3]
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
run 20000
Memory usage per processor = 3.0578 Mbytes
Step Temp c_Thot c_Tcold v_tdiff f_ave
11000 1.3794051 1.6903393 1.0515688 0 0
12000 1.3799777 1.8004888 1.1032219 -0.63860014 0
13000 1.3733605 1.7823094 1.0553582 -0.65827891 -0.65827891
14000 1.3749743 1.7852256 1.1674016 -0.68463005 -0.67145448
15000 1.3863795 1.8538127 1.0056247 -0.73524813 -0.69271903
16000 1.3731955 1.7518546 1.0741458 -0.74810775 -0.70656621
17000 1.3771856 1.9016869 1.0090502 -0.73999567 -0.7132521
18000 1.3766032 1.7616195 1.1142155 -0.73769104 -0.71732526
19000 1.3815934 1.7791247 1.1406987 -0.73617832 -0.72001855
20000 1.3725543 1.8637436 1.0799364 -0.73435569 -0.7218107
21000 1.3817369 1.8808771 1.0642524 -0.76702329 -0.72683432
22000 1.3968704 1.840287 1.072304 -0.82496419 -0.7366473
23000 1.3895558 1.9427293 1.0766665 -0.75363908 -0.73819201
24000 1.3900493 1.9883976 1.1081017 -0.86394774 -0.74867166
25000 1.3838912 1.8853041 1.0795751 -0.83043902 -0.75496145
26000 1.3912105 1.9330259 1.1070335 -0.79880182 -0.75809291
27000 1.3891151 1.8548451 1.0676153 -0.81856523 -0.7621244
28000 1.3942624 1.9796706 1.1251407 -0.81762456 -0.76559316
29000 1.3819302 1.8619138 1.0495292 -0.78627491 -0.76680973
30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172
31000 1.3822489 1.8220413 1.0322271 -0.7550338 -0.76999077
Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
Performance: 379649.018 tau/day, 878.817 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.4811 | 10.102 | 12.63 | 68.7 | 44.39
Neigh | 4.0495 | 4.9884 | 5.8366 | 37.8 | 21.92
Comm | 1.6695 | 4.9483 | 8.493 | 130.7 | 21.74
Output | 0.0010517 | 0.0017769 | 0.0019059 | 0.7 | 0.01
Modify | 1.6903 | 1.9371 | 2.2355 | 14.8 | 8.51
Other | | 0.7799 | | | 3.43
Nlocal: 1000 ave 1121 max 857 min
Histogram: 2 0 1 1 0 0 0 0 1 3
Nghost: 2299.75 ave 2541 max 2067 min
Histogram: 3 1 0 0 0 0 0 0 2 2
Neighs: 27487.2 ave 33361 max 20651 min
Histogram: 2 1 1 0 0 0 0 0 0 4
Total # of neighbors = 219898
Ave neighs/atom = 27.4872
Neighbor list builds = 3474
Dangerous builds = 0
Total wall time: 0:00:34
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