Homec4science
Diffusion lammps (lammm-master) Browse

lammps/examples/KAPPA/log.langevin.12Sep13
00d9f400ba98lammm-master

Last Change
Raw File

log.langevin.12Sep13
View Options

LAMMPS (10 Sep 2013)
# Sample LAMMPS input script for thermal conductivity of Ar
# use thermostatting method 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 0.5999999999999999778
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 1.3500000000000000888 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 1.3500000000000000888 $t 0.5
fix 1 all nvt temp 1.3500000000000000888 1.3500000000000000888 0.5
thermo 100
run 1000
Memory usage per processor = 2.15017 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 1.3419994 -3.7155648 0 -1.7028172 0.82925677
900 1.3562214 -3.6965608 0 -1.662483 0.88908144
1000 1.3732016 -3.7100024 0 -1.6504575 0.83982823
Loop time of 0.97534 on 8 procs for 1000 steps with 8000 atoms
Pair time (%) = 0.546534 (56.0352)
Neigh time (%) = 0.238185 (24.4207)
Comm time (%) = 0.131359 (13.468)
Outpt time (%) = 0.000289977 (0.0297308)
Other time (%) = 0.0589725 (6.04636)
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 1.3500000000000000888
unfix 1
# 2nd equilibration run
fix 1 all nve
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
fix hot all langevin 1.6999999999999999556 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.6999999999999999556 1.6999999999999999556 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 = 2.60798 Mbytes
Step Temp Thot Tcold hot cold tdiff
1000 1.35 1.4312938 1.2955632 -0 -0 0.13573057
2000 1.3600182 1.4938327 1.1089359 -0.12327243 0.13841286 0.38489675
3000 1.3392692 1.6479324 1.0942283 -0.22042205 0.25598524 0.55370413
4000 1.3471697 1.651889 1.1414137 -0.28373342 0.33177173 0.51047523
5000 1.334676 1.6458917 1.0783534 -0.34031535 0.40560755 0.56753829
6000 1.3190799 1.7086162 1.0615588 -0.37644049 0.48354454 0.64705733
7000 1.3249795 1.629343 1.0564243 -0.42503728 0.52993342 0.57291862
8000 1.3229688 1.6502146 1.1114894 -0.47659986 0.59009825 0.53872521
9000 1.3126211 1.5294993 1.0554547 -0.51927956 0.63860042 0.47404463
10000 1.3129013 1.6801776 1.1008841 -0.58086618 0.69160264 0.57929342
11000 1.3142376 1.5852877 1.0923244 -0.62980209 0.7406649 0.49296336
Loop time of 12.5268 on 8 procs for 10000 steps with 8000 atoms
Pair time (%) = 5.45526 (43.5488)
Neigh time (%) = 2.46362 (19.6668)
Comm time (%) = 2.16206 (17.2595)
Outpt time (%) = 0.000730932 (0.00583496)
Other time (%) = 2.4451 (19.519)
Nlocal: 1000 ave 1115 max 861 min
Histogram: 1 2 1 0 0 0 0 0 1 3
Nghost: 2287.75 ave 2520 max 2084 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Neighs: 27417.8 ave 34089 max 20302 min
Histogram: 1 2 1 0 0 0 0 1 1 2
Total # of neighbors = 219342
Ave neighs/atom = 27.4178
Neighbor list builds = 1680
Dangerous builds = 0
# thermal conductivity calculation
# rest 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 1.6999999999999999556 ${thi} 1.0 59804 tally yes
fix hot all langevin 1.6999999999999999556 1.6999999999999999556 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
#fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp # file tmp.langevin.profile units reduced
run 20000
Memory usage per processor = 2.60798 Mbytes
Step Temp Thot Tcold hot cold tdiff ave
11000 1.3142376 1.5805779 1.0923244 -0 -0 0.48825352 0
12000 1.3225589 1.6154238 1.0342455 -0.051194062 0.046031906 0.58117829 0.54242131
13000 1.3119407 1.6548145 1.0714553 -0.081528355 0.10507007 0.58335923 0.54757509
14000 1.3061547 1.7079311 0.9801908 -0.11986269 0.14930552 0.72774029 0.54255768
15000 1.2957396 1.5670317 1.0093755 -0.15855886 0.19356024 0.55765623 0.55143106
16000 1.3180385 1.6721325 1.0297962 -0.23192621 0.24323028 0.64233637 0.56253776
17000 1.3140155 1.693781 1.062984 -0.27316253 0.29027073 0.63079703 0.56712207
18000 1.3145256 1.7182561 1.0112929 -0.31606959 0.3514788 0.70696323 0.57126619
19000 1.3029832 1.671437 1.0286076 -0.36077476 0.3703359 0.64282944 0.57227786
20000 1.3169429 1.6862866 1.0526037 -0.41113477 0.42252001 0.63368298 0.57730048
21000 1.304035 1.5546028 1.0678413 -0.44818715 0.47665155 0.48676144 0.57750064
22000 1.3038162 1.6037462 1.1158159 -0.48677585 0.52085209 0.48793029 0.5775028
23000 1.308484 1.8036478 1.0301731 -0.53897224 0.55633511 0.77347468 0.57780744
24000 1.2999222 1.6781069 1.0415262 -0.56108402 0.60571058 0.6365807 0.57778018
25000 1.2985672 1.6777481 1.1020937 -0.62070929 0.65867799 0.57565434 0.57862472
26000 1.2792285 1.6449327 1.0902922 -0.65913559 0.73111032 0.55464042 0.57741553
27000 1.2767155 1.4922686 1.121709 -0.70930887 0.78358989 0.37055954 0.576284
28000 1.2801575 1.6613064 1.0472095 -0.74451574 0.82536406 0.61409695 0.57539385
29000 1.2951069 1.6182462 1.0399072 -0.81139634 0.87944086 0.578339 0.57766082
30000 1.2858636 1.7333034 1.0312729 -0.84679466 0.9135831 0.70203052 0.5783587
31000 1.2921828 1.5891728 1.058652 -0.90491088 0.9466585 0.53052079 0.57794447
Loop time of 26.0148 on 8 procs for 20000 steps with 8000 atoms
Pair time (%) = 10.9369 (42.0409)
Neigh time (%) = 4.91944 (18.9101)
Comm time (%) = 5.07596 (19.5118)
Outpt time (%) = 0.00115007 (0.00442083)
Other time (%) = 5.08143 (19.5328)
Nlocal: 1000 ave 1125 max 883 min
Histogram: 3 1 0 0 0 0 0 1 0 3
Nghost: 2298.62 ave 2501 max 2080 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Neighs: 27465.4 ave 34253 max 21476 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Total # of neighbors = 219723
Ave neighs/atom = 27.4654
Neighbor list builds = 3351
Dangerous builds = 0
c4science · Help