LAMMPS (4 May 2022) using 1 OpenMP thread(s) per MPI task # sample LAMMPS input script for thermal conductivity of liquid LJ # use fix heat to add/subtract energy from 2 regions # 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 = 1.8820721 1.8820721 1.8820721 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 (18.820721 18.820721 37.641441) 2 by 1 by 4 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441) create_atoms CPU = 0.001 seconds 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 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule 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 27 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 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 0.944921 on 8 procs for 1000 steps with 8000 atoms Performance: 457180.899 tau/day, 1058.289 timesteps/s 98.4% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53036 | 0.5381 | 0.55265 | 1.0 | 56.95 Neigh | 0.24246 | 0.24602 | 0.25063 | 0.5 | 26.04 Comm | 0.092773 | 0.10258 | 0.11364 | 2.3 | 10.86 Output | 0.0003103 | 0.0004958 | 0.0017848 | 0.0 | 0.05 Modify | 0.033332 | 0.043019 | 0.054672 | 3.7 | 4.55 Other | | 0.0147 | | | 1.56 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 heat 1 100.0 region hot fix cold all heat 1 -100.0 region cold thermo_style custom step temp c_Thot c_Tcold thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold thermo 1000 run 10000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.156 | 3.156 | 3.156 Mbytes Step Temp Temp_hot Temp_cold 1000 1.35 1.431295 1.2955644 2000 1.3518468 1.5562602 1.154905 3000 1.3477229 1.5890075 1.2395414 4000 1.3487175 1.5491615 1.2019696 5000 1.3594394 1.5780597 1.1824492 6000 1.3583923 1.541735 1.1675586 7000 1.3700321 1.6735877 1.1279114 8000 1.3631993 1.6367675 1.0697225 9000 1.3739201 1.6846211 1.1138829 10000 1.3751455 1.8039471 1.1500399 11000 1.3716416 1.833336 1.1267278 Loop time of 11.4492 on 8 procs for 10000 steps with 8000 atoms Performance: 377320.435 tau/day, 873.427 timesteps/s 98.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6062 | 5.3944 | 6.169 | 26.0 | 47.12 Neigh | 2.3148 | 2.6122 | 2.8769 | 14.9 | 22.82 Comm | 0.82337 | 1.7921 | 2.9417 | 59.6 | 15.65 Output | 0.00052195 | 0.00073566 | 0.0020974 | 0.0 | 0.01 Modify | 1.4086 | 1.4856 | 1.6791 | 9.2 | 12.98 Other | | 0.1641 | | | 1.43 Nlocal: 1000 ave 1131 max 878 min Histogram: 3 1 0 0 0 0 0 1 1 2 Nghost: 2312.88 ave 2525 max 2114 min Histogram: 2 2 0 0 0 0 0 1 1 2 Neighs: 27457 ave 33797 max 21031 min Histogram: 3 1 0 0 0 0 0 0 1 3 Total # of neighbors = 219656 Ave neighs/atom = 27.457 Neighbor list builds = 1691 Dangerous builds = 0 # thermal conductivity calculation compute ke all ke/atom variable temp atom c_ke/1.5 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.heat variable tdiff equal f_2[1][3]-f_2[11][3] fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000 variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903) thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname v_tdiff dTemp_step colname f_ave dTemp run 20000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.406 | 3.407 | 3.408 Mbytes Step Temp Temp_hot Temp_cold dTemp_step dTemp 11000 1.3716416 1.833336 1.1267278 0 0 12000 1.3703433 1.7829467 1.1194444 0.66044316 0 13000 1.3686734 1.8334366 1.1193477 0.71431978 0.71431978 14000 1.3856987 1.8048077 1.1052708 0.73112558 0.72272268 15000 1.3820117 1.7460559 1.110725 0.72927647 0.72490728 16000 1.3911309 1.923603 1.1161499 0.77407515 0.73719925 17000 1.3841301 1.7276486 1.0283807 0.77278638 0.74431667 18000 1.3888918 1.7944951 1.0532944 0.75665895 0.74637372 19000 1.3876032 1.838174 1.059715 0.71342263 0.74166642 20000 1.3724644 1.8297128 1.1439176 0.77352223 0.7456484 21000 1.3798921 1.7968403 1.0288381 0.70077132 0.74066206 22000 1.3763952 1.8202225 1.0658157 0.75629111 0.74222496 23000 1.3911378 1.8691478 1.018589 0.76094865 0.74392711 24000 1.3867754 1.7826523 1.09347 0.80367344 0.74890597 25000 1.385877 1.9029313 1.0815131 0.73559505 0.74788206 26000 1.3791773 1.8904022 1.0151678 0.7729123 0.74966993 27000 1.3800063 1.729283 1.127594 0.71473941 0.74734123 28000 1.3757197 1.7823772 1.084523 0.73849831 0.74678855 29000 1.3777555 1.8287284 1.0715132 0.70375514 0.74425717 30000 1.3821118 1.7382856 1.1078333 0.79892499 0.74729427 31000 1.3870476 1.8410063 1.1235958 0.76218423 0.74807795 Loop time of 26.9314 on 8 procs for 20000 steps with 8000 atoms Performance: 320814.865 tau/day, 742.627 timesteps/s 97.4% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5017 | 11.183 | 13.664 | 67.1 | 41.52 Neigh | 4.5072 | 5.5343 | 6.4781 | 37.9 | 20.55 Comm | 2.6028 | 5.7342 | 9.01 | 118.2 | 21.29 Output | 0.0041722 | 0.0082705 | 0.0088616 | 1.7 | 0.03 Modify | 3.7207 | 4.0439 | 4.4497 | 13.7 | 15.02 Other | | 0.4277 | | | 1.59 Nlocal: 1000 ave 1134 max 850 min Histogram: 2 1 0 1 0 0 0 1 0 3 Nghost: 2307.75 ave 2561 max 2083 min Histogram: 4 0 0 0 0 0 0 0 2 2 Neighs: 27561.1 ave 34071 max 19891 min Histogram: 2 1 1 0 0 0 0 0 1 3 Total # of neighbors = 220489 Ave neighs/atom = 27.561125 Neighbor list builds = 3442 Dangerous builds = 0 print "Running average thermal conductivity: $(v_kappa:%.2f)" Running average thermal conductivity: 3.55 Total wall time: 0:00:39