forked from lijiext/lammps
226 lines
8.4 KiB
Groff
226 lines
8.4 KiB
Groff
|
LAMMPS (13 Oct 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 0.872163 on 8 procs for 1000 steps with 8000 atoms
|
||
|
|
|
||
|
|
Performance: 495320.223 tau/day, 1146.575 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 | 0.48598 | 0.49768 | 0.50892 | 1.1 | 57.06
|
||
|
|
Neigh | 0.22855 | 0.23236 | 0.23463 | 0.5 | 26.64
|
||
|
|
Comm | 0.082584 | 0.093727 | 0.10748 | 2.9 | 10.75
|
||
|
|
Output | 0.0002718 | 0.00028038 | 0.00031757 | 0.1 | 0.03
|
||
|
|
Modify | 0.028934 | 0.031425 | 0.03322 | 0.8 | 3.60
|
||
|
|
Other | | 0.01668 | | | 1.91
|
||
|
|
|
||
|
|
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 c_Thot c_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 10.3395 on 8 procs for 10000 steps with 8000 atoms
|
||
|
|
|
||
|
|
Performance: 417815.278 tau/day, 967.165 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 | 4.2189 | 4.9657 | 5.6225 | 25.3 | 48.03
|
||
|
|
Neigh | 2.1359 | 2.4223 | 2.6741 | 14.8 | 23.43
|
||
|
|
Comm | 0.83801 | 1.6773 | 2.6984 | 57.1 | 16.22
|
||
|
|
Output | 0.00042701 | 0.00046191 | 0.00052905 | 0.1 | 0.00
|
||
|
|
Modify | 1.0143 | 1.0895 | 1.1846 | 5.7 | 10.54
|
||
|
|
Other | | 0.1844 | | | 1.78
|
||
|
|
|
||
|
|
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 c_Thot c_Tcold v_tdiff f_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 22.4057 on 8 procs for 20000 steps with 8000 atoms
|
||
|
|
|
||
|
|
Performance: 385616.132 tau/day, 892.630 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 | 7.6116 | 10.003 | 12.262 | 64.3 | 44.65
|
||
|
|
Neigh | 4.038 | 4.9528 | 5.8822 | 37.6 | 22.10
|
||
|
|
Comm | 1.6649 | 4.7143 | 7.6339 | 124.9 | 21.04
|
||
|
|
Output | 0.00098443 | 0.0017504 | 0.0018921 | 0.7 | 0.01
|
||
|
|
Modify | 2.1819 | 2.3289 | 2.6598 | 12.6 | 10.39
|
||
|
|
Other | | 0.4047 | | | 1.81
|
||
|
|
|
||
|
|
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
|