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lammps/examples/KAPPA/log.13Oct16.langevin.g++.8
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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# thermostatting 2 regions via fix langevin
# 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 tlo equal 1.0
variable thi equal 1.70
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
#variable tlo equal 0.3
#variable thi equal 1.0
# 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 0.876399 on 8 procs for 1000 steps with 8000 atoms
Performance: 492926.111 tau/day, 1141.033 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 | 0.47963 | 0.4975 | 0.51846 | 1.6 | 56.77
Neigh | 0.22878 | 0.23186 | 0.23458 | 0.4 | 26.46
Comm | 0.081789 | 0.096763 | 0.11865 | 3.6 | 11.04
Output | 0.000247 | 0.00025409 | 0.00028944 | 0.1 | 0.03
Modify | 0.02689 | 0.033982 | 0.042612 | 2.9 | 3.88
Other | | 0.01604 | | | 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
fix 1 all nve
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
variable tdiff equal c_Thot-c_Tcold
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
thermo 1000
run 10000
Memory usage per processor = 3.30761 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff
1000 1.35 1.431295 1.2955644 -0 -0 0.13573065
2000 1.3593243 1.6602094 1.0898701 -0.13903162 0.14234352 0.57033928
3000 1.3412163 1.6308839 1.0677742 -0.2214765 0.25871329 0.56310968
4000 1.3275359 1.5248034 1.0792345 -0.26908328 0.34211202 0.44556887
5000 1.3230922 1.6266046 1.0523802 -0.33175886 0.43533756 0.5742244
6000 1.3037036 1.6021737 1.0408166 -0.3639815 0.49869333 0.56135712
7000 1.2903225 1.5701119 1.0603548 -0.40000421 0.55547714 0.50975712
8000 1.3050677 1.6420218 1.0221774 -0.46368839 0.60293974 0.61984444
9000 1.2950977 1.7153984 1.0583242 -0.51871512 0.66389344 0.65707419
10000 1.3100216 1.6680668 1.0871293 -0.57485359 0.7161839 0.58093752
11000 1.297052 1.6486494 1.088903 -0.60276081 0.75900024 0.55974633
Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms
Performance: 372451.299 tau/day, 862.156 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 | 4.0544 | 4.9719 | 5.8426 | 34.5 | 42.87
Neigh | 2.0735 | 2.3933 | 2.7208 | 18.8 | 20.63
Comm | 0.91559 | 1.9788 | 3.1216 | 70.5 | 17.06
Output | 0.0005753 | 0.00068495 | 0.00080419 | 0.3 | 0.01
Modify | 1.9354 | 1.9837 | 2.0321 | 2.6 | 17.10
Other | | 0.2705 | | | 2.33
Nlocal: 1000 ave 1112 max 841 min
Histogram: 1 1 0 2 0 0 0 0 1 3
Nghost: 2294.38 ave 2506 max 2077 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Neighs: 27441.9 ave 32651 max 19438 min
Histogram: 1 1 0 2 0 0 0 0 0 4
Total # of neighbors = 219535
Ave neighs/atom = 27.4419
Neighbor list builds = 1674
Dangerous builds = 0
# thermal conductivity calculation
# reset langevin thermostats to zero energy accumulation
compute ke all ke/atom
variable temp atom c_ke/1.5
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
fix cold all langevin 1 1 1.0 287859 tally yes
fix_modify hot temp Thot
fix_modify cold temp Tcold
fix ave all ave/time 10 100 1000 v_tdiff ave running
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
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.langevin
run 20000
Memory usage per processor = 3.5578 Mbytes
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
11000 1.297052 1.6473904 1.088903 -0 -0 0.55848738 0
12000 1.2792808 1.6043738 1.0658375 -0.012256975 0.04611547 0.53853632 0.54492428
13000 1.2787101 1.7035572 1.1159037 -0.073806664 0.099529002 0.58765348 0.5581748
14000 1.289918 1.4642237 1.1073937 -0.11428779 0.13931657 0.35683005 0.56816328
15000 1.2932964 1.5032665 1.0523148 -0.17247717 0.19001309 0.45095174 0.57436291
16000 1.3025037 1.5424316 1.1185175 -0.22598282 0.22640921 0.42391405 0.56973168
17000 1.3009667 1.5582105 1.0745661 -0.27544101 0.26143452 0.48364439 0.5700118
18000 1.2970255 1.5019842 1.0228322 -0.31195285 0.31203237 0.479152 0.56544644
19000 1.2880631 1.5290587 1.0976483 -0.34645573 0.34243366 0.43141047 0.56338309
20000 1.3119675 1.6284144 1.1102294 -0.40922326 0.39217092 0.51818503 0.56614474
21000 1.2838063 1.6670934 0.97721382 -0.43809329 0.46021572 0.68987962 0.5686161
22000 1.2925041 1.7050682 1.0984963 -0.4871305 0.50520177 0.6065719 0.57226368
23000 1.2746463 1.6388503 1.0286701 -0.51212873 0.56478515 0.6101802 0.57290996
24000 1.2745381 1.7085713 1.1362975 -0.54529463 0.58540408 0.57227375 0.57296767
25000 1.2776401 1.5259253 1.0415158 -0.58389862 0.62623289 0.48440948 0.57386374
26000 1.2661888 1.4760829 0.99145001 -0.62638032 0.68155754 0.48463289 0.57021631
27000 1.2923677 1.6070495 1.0300276 -0.70014343 0.70236265 0.5770219 0.57001637
28000 1.2961449 1.7052335 1.0805793 -0.74856241 0.75775659 0.62465427 0.56927907
29000 1.2969474 1.5520176 1.1249649 -0.78900962 0.79539202 0.42705264 0.56986986
30000 1.2900596 1.6556864 1.0302676 -0.84180996 0.87187683 0.6254189 0.57245841
31000 1.2923209 1.6752068 1.0156911 -0.89036148 0.88285227 0.65951571 0.57358134
Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms
Performance: 358418.039 tau/day, 829.671 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 | 7.5967 | 9.9644 | 12.189 | 62.9 | 41.34
Neigh | 3.9305 | 4.7817 | 5.594 | 34.5 | 19.84
Comm | 1.7656 | 4.5624 | 7.6382 | 122.3 | 18.93
Output | 0.0011697 | 0.0018933 | 0.0020008 | 0.6 | 0.01
Modify | 4.1386 | 4.2107 | 4.3622 | 3.8 | 17.47
Other | | 0.5848 | | | 2.43
Nlocal: 1000 ave 1118 max 875 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost: 2298.62 ave 2535 max 2063 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs: 27462.4 ave 32904 max 21333 min
Histogram: 2 2 0 0 0 0 0 0 0 4
Total # of neighbors = 219699
Ave neighs/atom = 27.4624
Neighbor list builds = 3340
Dangerous builds = 0
Total wall time: 0:00:36
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