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lammps/examples/KAPPA/log.13Oct16.mp.g++.8
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LAMMPS (13 Oct 2016)
# 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
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 0.875524 on 8 procs for 1000 steps with 8000 atoms
Performance: 493418.774 tau/day, 1142.173 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 | 0.48279 | 0.49681 | 0.51174 | 1.2 | 56.74
Neigh | 0.22868 | 0.23169 | 0.23454 | 0.4 | 26.46
Comm | 0.084792 | 0.098391 | 0.11603 | 3.4 | 11.24
Output | 0.00027204 | 0.00027871 | 0.00031137 | 0.1 | 0.03
Modify | 0.027863 | 0.032316 | 0.039397 | 2.3 | 3.69
Other | | 0.01605 | | | 1.83
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
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.mp
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 = 2.8078 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff
1000 1.35 -3.7100044 -1.6852575 0 0
2000 1.3572899 -3.7210084 -1.6853282 873.12373 0.26058005
3000 1.359979 -3.7268343 -1.6871208 1750.6998 0.40845169
4000 1.3677509 -3.7394553 -1.6880853 2565.8064 0.63828485
5000 1.3742987 -3.750287 -1.6890966 3373.2897 0.70173279
6000 1.3950535 -3.7827674 -1.6904487 4162.6672 0.83210131
7000 1.3843852 -3.7679238 -1.6916056 4947.5882 0.92719731
8000 1.396125 -3.7861373 -1.6922116 5703.4508 0.92426948
9000 1.4135104 -3.812624 -1.6926234 6465.5676 1.0412501
10000 1.4092351 -3.8065359 -1.6929474 7242.2986 1.0772505
11000 1.3966916 -3.7874302 -1.6926547 8007.3229 1.056805
12000 1.4111272 -3.8089829 -1.6925567 8750.8648 1.097621
13000 1.4091888 -3.8074873 -1.6939684 9514.7196 1.0734167
14000 1.4132159 -3.8134636 -1.6939046 10284.269 1.1643391
15000 1.3991348 -3.7928819 -1.694442 11051.851 1.0716016
16000 1.4055537 -3.8013252 -1.6932583 11836.812 1.1506479
17000 1.4127928 -3.8141054 -1.6951811 12626.124 1.1301728
18000 1.4118868 -3.8119733 -1.6944077 13391.631 1.1521394
19000 1.4209268 -3.826811 -1.6956872 14180.009 1.0929393
20000 1.4093812 -3.8083875 -1.6945801 14969.574 1.2113183
21000 1.4202317 -3.8255696 -1.6954884 15735.893 1.161082
Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms
Performance: 409982.223 tau/day, 949.033 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 | 7.4932 | 10.005 | 12.426 | 70.1 | 47.48
Neigh | 4.0592 | 5.0894 | 6.0544 | 41.7 | 24.15
Comm | 1.7793 | 5.0312 | 8.5027 | 134.6 | 23.87
Output | 0.00058484 | 0.00060964 | 0.0007031 | 0.1 | 0.00
Modify | 0.39735 | 0.4211 | 0.43467 | 2.3 | 2.00
Other | | 0.5269 | | | 2.50
Nlocal: 1000 ave 1188 max 806 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost: 2300.5 ave 2645 max 1963 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27897 ave 37064 max 18367 min
Histogram: 2 2 0 0 0 0 0 0 0 4
Total # of neighbors = 223176
Ave neighs/atom = 27.897
Neighbor list builds = 3537
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 = 3.05853 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff f_ave
21000 1.4202317 -3.8255696 -1.6954884 0 1.161082 1.161082
22000 1.4090517 -3.808543 -1.6952296 745.83128 1.1780376 1.1695598
23000 1.4261394 -3.8350237 -1.696082 1516.9526 1.1393504 1.15949
24000 1.4103907 -3.8098769 -1.6945553 2290.0213 1.1962529 1.1686807
25000 1.4205929 -3.8266444 -1.6960213 3028.2748 1.1355183 1.1620482
26000 1.4148587 -3.8168728 -1.69485 3788.0858 1.1902606 1.1667503
27000 1.4226648 -3.8297832 -1.6960528 4580.4932 1.2378446 1.1769066
28000 1.4167854 -3.8205958 -1.6956834 5328.2357 1.2038835 1.1802787
29000 1.4208636 -3.8267081 -1.6956791 6077.036 1.1970863 1.1821462
30000 1.420575 -3.8256917 -1.6950955 6840.5407 1.1884497 1.1827766
31000 1.4233235 -3.8318045 -1.6970861 7576.9859 1.2088723 1.1851489
32000 1.418912 -3.8229407 -1.6948388 8319.9854 1.1604002 1.1830865
33000 1.4161289 -3.8211375 -1.6972096 9097.8598 1.1381183 1.1796274
34000 1.3982574 -3.7915345 -1.6944106 9819.5817 1.1809721 1.1797235
35000 1.4211314 -3.8267235 -1.6952929 10604.381 1.157812 1.1782627
36000 1.4181668 -3.8217718 -1.6947876 11332.942 1.1843186 1.1786412
37000 1.4092823 -3.8094817 -1.6958226 12068.55 1.1043391 1.1742705
38000 1.4220481 -3.8278441 -1.6950386 12815.406 1.1996255 1.1756791
39000 1.4146432 -3.8175526 -1.6958531 13565.714 1.149226 1.1742868
40000 1.4088356 -3.8079173 -1.694928 14309.801 1.1710565 1.1741253
41000 1.4058693 -3.8043119 -1.6957716 15067.894 1.1839862 1.1745949
Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms
Performance: 391962.361 tau/day, 907.320 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 | 6.8314 | 10.063 | 12.978 | 88.0 | 45.65
Neigh | 3.8802 | 5.2398 | 6.5269 | 52.7 | 23.77
Comm | 1.828 | 5.8112 | 10.14 | 160.2 | 26.36
Output | 0.00050211 | 0.00052819 | 0.00060391 | 0.1 | 0.00
Modify | 0.39313 | 0.41984 | 0.4453 | 3.3 | 1.90
Other | | 0.5084 | | | 2.31
Nlocal: 1000 ave 1188 max 810 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Nghost: 2304.5 ave 2648 max 1970 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27885.2 ave 36431 max 18556 min
Histogram: 2 2 0 0 0 0 0 0 1 3
Total # of neighbors = 223082
Ave neighs/atom = 27.8852
Neighbor list builds = 3626
Dangerous builds = 0
Total wall time: 0:00:44
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