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lammps/examples/KAPPA/log.heatflux.1Feb14
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LAMMPS (1 Feb 2014)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Green-Kubo method via compute heat/flux and fix ave/correlate
# settings
variable x equal 10
variable y equal 10
variable z equal 10
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
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
variable d equal 200*$s
variable d equal 200*10
# 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 10
create_box 1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
2 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 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
Memory usage per processor = 2.10761 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
800 1.3489121 -3.7082852 0 -1.6854229 0.86438062
900 1.3708803 -3.6966168 0 -1.6408104 0.92141491
1000 1.3640742 -3.7075323 0 -1.6619325 0.86651245
Loop time of 0.464189 on 8 procs for 1000 steps with 4000 atoms
Pair time (%) = 0.235336 (50.6983)
Neigh time (%) = 0.104871 (22.5922)
Comm time (%) = 0.0896717 (19.3179)
Outpt time (%) = 0.000278324 (0.0599591)
Other time (%) = 0.0340324 (7.33158)
Nlocal: 500 ave 510 max 479 min
Histogram: 1 0 0 0 0 2 1 1 0 3
Nghost: 1519 ave 1539 max 1509 min
Histogram: 2 0 4 0 0 0 0 1 0 1
Neighs: 13553.8 ave 14051 max 12567 min
Histogram: 1 0 0 0 1 0 2 1 1 2
Total # of neighbors = 108430
Ave neighs/atom = 27.1075
Neighbor list builds = 155
Dangerous builds = 0
velocity all scale $t
velocity all scale 1.35
unfix 1
# thermal conductivity calculation
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix 1 all nve
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
variable scale equal $s*dt/$t/$t/vol
variable scale equal 10*dt/$t/$t/vol
variable scale equal 10*dt/1.35/$t/vol
variable scale equal 10*dt/1.35/1.35/vol
variable k11 equal trap(f_JJ[3])*${scale}
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
variable k22 equal trap(f_JJ[4])*${scale}
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
variable k33 equal trap(f_JJ[5])*${scale}
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
thermo $d
thermo 2000
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
Memory usage per processor = 3.25202 Mbytes
Step Temp Jx Jy Jz k11 k22 k33
0 1.35 0.012562011 -0.087289131 -0.037038204 0.014431103 0.69678942 0.125453
2000 1.3488448 -0.082686441 -0.05888314 0.15641005 9.6556473 4.8724539 39.132688
4000 1.3506828 0.055310422 -0.038254827 -0.081110393 3.4422239 2.3744865 7.4870977
6000 1.3324005 -0.10634454 -0.011811473 0.024430149 3.6509701 11.111829 2.7413472
8000 1.3465517 -0.13857537 -0.058386681 -0.013220164 6.5578792 6.6188014 3.6355334
10000 1.3454126 -0.044292047 -0.0055045339 -0.051726965 5.6920768 6.5502293 7.8616795
12000 1.3601798 0.18989029 -0.094977713 -0.059726722 5.2989118 8.8331032 7.972481
14000 1.3414287 0.0064865781 0.056749763 0.12775935 4.453589 6.4962925 7.9502167
16000 1.3249032 0.0023833148 0.0074389705 -0.12452498 5.2719354 6.164126 7.9937329
18000 1.3486905 0.24719037 -0.13649854 -0.051766952 3.7849335 5.4803263 6.9701788
20000 1.3572854 0.065005524 0.050772448 0.12768096 3.378611 5.6519702 7.1233623
22000 1.352508 -0.042516792 -0.070285937 -0.03879074 5.4717313 5.4908509 6.7550818
24000 1.3559841 -0.015758535 -0.098318418 0.027238601 6.0025309 5.2571093 6.0763852
26000 1.3442105 -0.047372234 0.036647228 -0.0052159685 6.8263856 4.6880057 6.1674781
28000 1.3522633 0.025172759 -0.016031105 0.12001218 6.3114313 4.1003669 5.7234478
30000 1.3593364 -0.044078855 0.0089521622 0.13278909 5.4296394 3.8944372 5.2946242
32000 1.3412479 -0.013107683 -0.089437735 -0.089978727 5.0171818 4.2838538 6.7869585
34000 1.3490784 -0.069828566 -0.018570411 0.018866428 5.1053455 3.7588109 5.7177159
36000 1.3630314 -0.017768864 0.067999673 0.016212961 5.3345297 3.6547014 5.5137046
38000 1.3564307 0.080792723 0.12705697 0.0023785227 5.1062587 3.6140422 5.5464591
40000 1.3546707 -0.030425013 0.17303248 -0.043210574 4.5874798 3.6033647 5.2304191
42000 1.3549663 0.10109213 -0.056635329 0.047756306 4.1930341 3.4788566 5.3322825
44000 1.3557286 0.0083871709 -0.08039758 0.0060697507 4.8453948 3.7579315 4.9727852
46000 1.3434325 0.048348267 -0.12296683 -0.012320195 4.6106895 3.6890294 4.6654515
48000 1.3520456 0.052909962 0.034221069 0.011730009 4.8097414 3.897061 4.5042484
50000 1.3480467 0.084823081 -0.093901701 0.091139125 4.6836534 3.7687187 4.4227539
52000 1.3473278 -0.12531922 -0.065273509 0.11638381 4.9413341 3.8765808 4.5227649
54000 1.3672128 0.11139848 0.034992201 -0.022009105 4.695476 3.5100821 5.0401349
56000 1.341716 0.12258667 -0.089117615 0.041707151 4.5195052 3.3873269 4.972056
58000 1.359732 0.063106883 -0.026013959 -0.026567969 4.3259743 3.6185582 4.721062
60000 1.3587911 0.05591296 -0.12996822 0.095669495 4.1958916 3.5682633 4.8210022
62000 1.3483527 0.048201166 -0.030400186 -0.018919104 4.0886746 3.7373315 4.8825261
64000 1.3531159 -0.10850158 -0.093503261 0.095145743 3.9415737 3.6946305 4.6787173
66000 1.3534358 0.0070478917 -0.13855333 -0.0028185444 3.989283 3.7940811 4.5848181
68000 1.3509679 -0.17972456 -0.15918151 -0.0092253402 4.1168514 3.689533 4.9348847
70000 1.3496439 0.025102803 -0.12080911 0.0099284856 4.0474517 3.6265752 4.8809921
72000 1.3382578 0.2235088 0.10981254 0.049251118 3.9059236 3.5169408 4.9528845
74000 1.3529223 0.012949328 0.11733173 0.12107899 4.0011677 3.4205986 4.7288624
76000 1.3442459 0.090185942 0.038587691 -0.023131667 3.9854752 3.4013375 4.7967661
78000 1.3423941 0.072006425 -0.009752458 0.058791886 3.87483 3.3898574 5.0306248
80000 1.3501112 -0.041057888 -0.11150244 -0.052369732 3.7648956 3.2969166 4.9549774
82000 1.358605 0.14838249 0.055223984 0.019108344 3.8986959 3.2556248 4.8872754
84000 1.357958 -0.087190849 0.029998974 0.089839797 4.4229469 3.2567955 4.7704664
86000 1.3340187 0.10824995 -0.013149214 0.042146878 3.9867785 3.2596969 4.6510248
88000 1.3428375 -0.033908572 -0.11261352 0.099056349 3.8033502 3.1706434 4.5328732
90000 1.3299574 0.055893064 -0.22127211 -0.042737098 3.7086395 3.118066 4.5709281
92000 1.3488719 0.040126575 0.074080804 0.019410656 3.8714376 3.0342566 4.4798044
94000 1.3621842 -0.087519994 0.028392459 0.047179422 3.7841822 3.1603745 4.3925598
96000 1.3578003 0.081511213 -0.0083540805 0.015204759 3.7117805 3.0610774 4.2886014
98000 1.3477904 -0.13903407 0.1146023 0.059812672 3.7445818 3.284994 4.3000618
100000 1.3583776 0.16015243 0.19139469 0.097636877 3.8265662 3.280556 4.2276263
Loop time of 49.3099 on 8 procs for 100000 steps with 4000 atoms
Pair time (%) = 26.5664 (53.8764)
Neigh time (%) = 10.8228 (21.9485)
Comm time (%) = 8.59585 (17.4323)
Outpt time (%) = 0.0256916 (0.0521023)
Other time (%) = 3.29916 (6.69066)
Nlocal: 500 ave 519 max 493 min
Histogram: 4 1 0 1 0 0 1 0 0 1
Nghost: 1547 ave 1558 max 1523 min
Histogram: 1 0 0 0 0 2 1 0 2 2
Neighs: 13544.8 ave 14633 max 13111 min
Histogram: 2 1 3 1 0 0 0 0 0 1
Total # of neighbors = 108358
Ave neighs/atom = 27.0895
Neighbor list builds = 16041
Dangerous builds = 0
variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"
running average conductivity: 3.77824951481468
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