LAMMPS (20 Nov 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # 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) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.00238204 secs 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 ... 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 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.637 | 3.637 | 3.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.35 -4.1241917 0 -2.0996979 -3.1962625 100 1.2012012 -3.7818636 0 -1.9805123 0.545419 200 1.2756106 -3.7405462 0 -1.8276087 0.69596781 300 1.3359812 -3.7005395 0 -1.6970686 0.82843639 400 1.3666035 -3.6744778 0 -1.625085 0.90012457 500 1.3714892 -3.6899498 0 -1.6332303 0.91591558 600 1.3344614 -3.7013669 0 -1.7001752 0.80561151 700 1.3250911 -3.7159546 0 -1.7288148 0.81630277 800 1.3431795 -3.7142241 0 -1.6999586 0.80394574 900 1.3632046 -3.6916836 0 -1.647388 0.89695206 1000 1.3767454 -3.699803 0 -1.6352011 0.86173631 Loop time of 3.44896 on 1 procs for 1000 steps with 4000 atoms Performance: 125255.147 tau/day, 289.942 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1719 | 2.1719 | 2.1719 | 0.0 | 62.97 Neigh | 1.0628 | 1.0628 | 1.0628 | 0.0 | 30.82 Comm | 0.08199 | 0.08199 | 0.08199 | 0.0 | 2.38 Output | 0.0019281 | 0.0019281 | 0.0019281 | 0.0 | 0.06 Modify | 0.10078 | 0.10078 | 0.10078 | 0.0 | 2.92 Other | | 0.02958 | | | 0.86 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4648 ave 4648 max 4648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108548 ave 108548 max 108548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108548 Ave neighs/atom = 27.137 Neighbor list builds = 154 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 NULL 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 Per MPI rank memory allocation (min/avg/max) = 5.523 | 5.523 | 5.523 Mbytes Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 0 1.35 -0.11591984 -0.10773062 -0.26245238 1.2288441 1.0613523 6.2991543 2000 1.3444258 0.19904933 -0.11749488 -0.19859053 6.5200149 -4.8797208 15.02756 4000 1.3542437 -0.048905125 -0.039253789 0.0035847096 -1.5099856 1.1738342 1.2239191 6000 1.3590556 -0.082789357 0.037439553 -0.17931485 -0.034121174 0.75107454 5.6581584 8000 1.3469532 0.12952846 -0.063533011 0.043040368 1.9319176 1.5509865 6.8035363 10000 1.3503318 -0.00076910181 -0.012584776 0.08982824 1.0517947 1.1217884 5.9425074 12000 1.3605117 0.0060074346 -0.15943769 0.075515487 0.29860675 1.5354737 4.9090278 14000 1.3563917 -0.11440519 -0.0689911 -0.11582436 1.548405 0.52547193 6.8144057 16000 1.3603906 0.011712891 -0.051377269 0.028652441 2.3835396 0.26512986 6.6526331 18000 1.3617578 0.034316604 -0.026198278 -0.022232429 2.1376294 0.28710214 6.3776587 20000 1.3389051 -0.16307103 -0.15725338 0.19896859 2.3019762 0.43695234 5.3452571 22000 1.3513947 0.10952945 0.0054761632 -0.045775824 2.1849731 0.7600205 5.0410689 24000 1.3566869 -0.070165098 0.065459191 0.020948238 2.2832081 0.533334 4.4175861 26000 1.3556496 -0.14712281 -0.08806022 0.058080813 2.4128055 0.72522908 4.7418189 28000 1.3536046 0.035772475 0.049625175 0.025769986 2.6799099 0.49080547 4.4849385 30000 1.3536487 -0.047922052 -0.015789388 0.084197932 3.3222415 0.37725763 4.9323619 32000 1.366978 0.20394045 -0.10303696 0.03013217 3.8821109 0.60283754 4.4541689 34000 1.3662345 0.0062075834 0.086219419 0.053669215 3.5657197 0.73975397 4.152686 36000 1.360335 0.03831334 0.083517826 -0.2047312 3.3189601 1.7135838 4.2145836 38000 1.368097 0.066727351 0.11069738 -0.04690248 3.3894319 1.6393038 4.2022298 40000 1.3622476 0.027663925 0.10051682 -0.086819642 3.5105701 1.7782425 3.9273638 42000 1.3591465 -0.024817489 -0.07413276 0.016143568 3.3299868 2.4300755 3.6713323 44000 1.3553126 0.0010480296 0.050253247 0.095692597 3.4499462 2.7245525 4.0772309 46000 1.3484325 0.096700293 -0.024430078 -0.053743485 3.9004501 2.4711934 3.5783693 48000 1.3467565 -0.097411041 -0.022025065 0.04616221 3.9381988 2.2529061 3.6422642 50000 1.355378 -0.24057689 0.094538809 0.027896969 3.8487766 2.2188061 3.5076472 52000 1.34975 0.045559268 -0.072755229 -0.068340329 3.9057848 2.3135021 3.3691848 54000 1.3546967 -0.077518306 0.059813674 0.023097731 4.0226684 2.240138 3.4850899 56000 1.3713567 0.08015731 0.080002945 0.12116897 3.7852023 2.1564139 3.4383084 58000 1.3547662 -0.04817222 -0.058956621 0.0033366132 3.6828883 2.1339323 3.3023815 60000 1.3533302 0.10752128 -0.00032354912 0.031418181 3.9866932 2.1405615 3.4262858 62000 1.3463151 -0.0029695185 -0.15129395 0.08607402 4.045341 2.0437014 3.2603754 64000 1.3582338 0.038980169 -0.023715472 0.025482601 4.0126007 2.0052233 3.1311449 66000 1.35787 0.15156975 0.092707473 -0.11289979 3.866998 2.0478591 2.9667639 68000 1.3539487 0.0052112222 -0.043990756 0.11130282 3.8150784 2.1436615 2.9891044 70000 1.3716243 0.082585219 0.087046634 0.02551765 3.830993 1.9823538 2.9481202 72000 1.3506077 0.11594739 -0.086272072 -0.0055328619 3.8910112 2.0420053 3.126251 74000 1.3691257 -0.01634324 -0.097609243 0.040548112 3.6799781 1.9368463 3.1231432 76000 1.3692285 0.065198555 0.13504931 -0.027255226 3.849896 1.8819547 3.0538984 78000 1.34922 -0.070220946 -0.039070926 -0.056837084 3.8951937 3.0904346 3.0043877 80000 1.343431 -0.047182686 0.11265671 -0.038240543 3.9413528 4.0127755 3.0467287 82000 1.3514865 -0.018732063 -0.13348693 0.049421212 3.8699027 3.897709 3.0740472 84000 1.3488147 0.040307423 0.10886512 0.074828252 4.2164449 4.0182912 3.226727 86000 1.3673468 0.060788026 0.11800246 -0.024130782 4.1269307 4.0269346 3.3269402 88000 1.3614759 0.093392082 -0.023139875 0.022374347 4.1009862 3.9259671 3.2271651 90000 1.3451536 0.020780236 0.0052171931 0.0094648306 4.145138 3.8571869 3.1096175 92000 1.3483158 0.041052113 -0.1543279 -0.015470228 4.1086056 3.8754049 3.1240836 94000 1.3584244 0.057588488 -0.014873839 -0.014819466 4.1328202 3.7839865 3.1058926 96000 1.3574471 -0.019839524 0.085583418 0.038318532 4.1155578 4.1684463 3.0346716 98000 1.3645479 0.0066118868 -0.032550014 -0.018003609 4.0429015 4.1584079 3.1712457 100000 1.3507875 -0.027832799 -0.10177279 -0.13412665 3.9551879 4.0353115 3.0640829 Loop time of 378.248 on 1 procs for 100000 steps with 4000 atoms Performance: 114210.793 tau/day, 264.377 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 247.22 | 247.22 | 247.22 | 0.0 | 65.36 Neigh | 111.07 | 111.07 | 111.07 | 0.0 | 29.36 Comm | 8.3885 | 8.3885 | 8.3885 | 0.0 | 2.22 Output | 0.020037 | 0.020037 | 0.020037 | 0.0 | 0.01 Modify | 8.4781 | 8.4781 | 8.4781 | 0.0 | 2.24 Other | | 3.073 | | | 0.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4731 ave 4731 max 4731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108298 ave 108298 max 108298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108298 Ave neighs/atom = 27.0745 Neighbor list builds = 16052 Dangerous builds = 0 variable kappa equal (v_k11+v_k22+v_k33)/3.0 print "running average conductivity: ${kappa}" running average conductivity: 3.68486074860761 Total wall time: 0:06:21