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lammps/examples/KAPPA/log.heat.7Jun16
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log.heat.7Jun16
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LAMMPS (7 Jun 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix heat 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 0.889036 on 8 procs for 1000 steps with 8000 atoms
Performance: 485919.613 tau/day, 1124.814 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 | 0.47867 | 0.4928 | 0.5006 | 1.0 | 55.43
Neigh | 0.23302 | 0.23557 | 0.23833 | 0.3 | 26.50
Comm | 0.1001 | 0.11264 | 0.12817 | 2.6 | 12.67
Output | 0.00032806 | 0.00034043 | 0.00040531 | 0.1 | 0.04
Modify | 0.028788 | 0.031511 | 0.033365 | 0.9 | 3.54
Other | | 0.01618 | | | 1.82
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 heat 1 100.0 region hot
fix cold all heat 1 -100.0 region cold
thermo_style custom step temp c_Thot c_Tcold
thermo 1000
run 10000
Memory usage per processor = 2.55761 Mbytes
Step Temp Thot Tcold
1000 1.35 1.431295 1.2955644
2000 1.3518468 1.5562602 1.154905
3000 1.3477229 1.5890075 1.2395414
4000 1.3487175 1.5491615 1.2019696
5000 1.3594394 1.5780597 1.1824492
6000 1.3583923 1.541735 1.1675586
7000 1.3700321 1.6735877 1.1279114
8000 1.3631993 1.6367675 1.0697225
9000 1.3739201 1.6846211 1.1138829
10000 1.3751455 1.8039471 1.1500399
11000 1.3716416 1.833336 1.1267278
Loop time of 10.488 on 8 procs for 10000 steps with 8000 atoms
Performance: 411900.216 tau/day, 953.473 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.138 | 4.9118 | 5.6168 | 26.2 | 46.83
Neigh | 2.1715 | 2.4541 | 2.7147 | 14.7 | 23.40
Comm | 0.94395 | 1.8449 | 2.9212 | 55.3 | 17.59
Output | 0.00043416 | 0.00046757 | 0.00054884 | 0.2 | 0.00
Modify | 1.0234 | 1.0946 | 1.2539 | 8.7 | 10.44
Other | | 0.1821 | | | 1.74
Nlocal: 1000 ave 1131 max 878 min
Histogram: 3 1 0 0 0 0 0 1 1 2
Nghost: 2312.88 ave 2525 max 2114 min
Histogram: 2 2 0 0 0 0 0 1 1 2
Neighs: 27457 ave 33797 max 21031 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Total # of neighbors = 219656
Ave neighs/atom = 27.457
Neighbor list builds = 1691
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.heat
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 = 2.8078 Mbytes
Step Temp Thot Tcold tdiff ave
11000 1.3716416 1.833336 1.1267278 0 0
12000 1.3703433 1.7829467 1.1194444 -0.66044316 0
13000 1.3686734 1.8334366 1.1193477 -0.71431978 -0.71431978
14000 1.3856987 1.8048077 1.1052708 -0.73112558 -0.72272268
15000 1.3820117 1.7460559 1.110725 -0.72927647 -0.72490728
16000 1.3911309 1.923603 1.1161499 -0.77407515 -0.73719925
17000 1.3841301 1.7276486 1.0283807 -0.77278638 -0.74431667
18000 1.3888918 1.7944951 1.0532944 -0.75665895 -0.74637372
19000 1.3876032 1.838174 1.059715 -0.71342263 -0.74166642
20000 1.3724644 1.8297128 1.1439176 -0.77352223 -0.7456484
21000 1.3798921 1.7968403 1.0288381 -0.70077132 -0.74066206
22000 1.3763952 1.8202225 1.0658157 -0.75629111 -0.74222496
23000 1.3911378 1.8691478 1.018589 -0.76094865 -0.74392711
24000 1.3867754 1.7826523 1.09347 -0.80367344 -0.74890597
25000 1.385877 1.9029313 1.0815131 -0.73559505 -0.74788206
26000 1.3791773 1.8904022 1.0151678 -0.7729123 -0.74966993
27000 1.3800063 1.729283 1.127594 -0.71473941 -0.74734123
28000 1.3757197 1.7823772 1.084523 -0.73849831 -0.74678855
29000 1.3777555 1.8287284 1.0715132 -0.70375514 -0.74425717
30000 1.3821118 1.7382856 1.1078333 -0.79892499 -0.74729427
31000 1.3870476 1.8410063 1.1235958 -0.76218423 -0.74807795
Loop time of 22.3813 on 8 procs for 20000 steps with 8000 atoms
Performance: 386036.860 tau/day, 893.604 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 | 7.4578 | 9.8912 | 11.96 | 64.5 | 44.19
Neigh | 4.0721 | 5.0195 | 5.8898 | 36.9 | 22.43
Comm | 1.9554 | 4.7393 | 7.8917 | 125.4 | 21.18
Output | 0.00099301 | 0.0017841 | 0.0019252 | 0.7 | 0.01
Modify | 2.2325 | 2.321 | 2.4866 | 6.5 | 10.37
Other | | 0.4085 | | | 1.83
Nlocal: 1000 ave 1134 max 850 min
Histogram: 2 1 0 1 0 0 0 1 0 3
Nghost: 2307.75 ave 2561 max 2083 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Neighs: 27561.1 ave 34071 max 19891 min
Histogram: 2 1 1 0 0 0 0 0 1 3
Total # of neighbors = 220489
Ave neighs/atom = 27.5611
Neighbor list builds = 3442
Dangerous builds = 0
Total wall time: 0:00:33
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