LAMMPS (4 May 2022) using 1 OpenMP thread(s) per MPI task # sample LAMMPS input script for thermal conductivity of liquid LJ # use fix ehex 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 = 0.000 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 0.925673 on 8 procs for 1000 steps with 8000 atoms Performance: 466687.339 tau/day, 1080.295 timesteps/s 98.5% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5071 | 0.52493 | 0.5485 | 1.7 | 56.71 Neigh | 0.23405 | 0.23912 | 0.24396 | 0.7 | 25.83 Comm | 0.084007 | 0.10338 | 0.12987 | 4.9 | 11.17 Output | 0.00030358 | 0.00048259 | 0.0017229 | 0.0 | 0.05 Modify | 0.035045 | 0.043306 | 0.051758 | 3.2 | 4.68 Other | | 0.01446 | | | 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 ehex 1 100.0 region hot fix cold all ehex 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) = 3.406 | 3.406 | 3.406 Mbytes Step Temp Temp_hot Temp_cold 1000 1.35 1.431295 1.2955644 2000 1.3537291 1.6418772 1.1875127 3000 1.3615152 1.6451299 1.1769094 4000 1.3612129 1.5281727 1.2022419 5000 1.3552182 1.6672955 1.2212864 6000 1.3643442 1.6072213 1.2390567 7000 1.3665773 1.6909819 1.1466611 8000 1.375741 1.6144274 1.1691231 9000 1.3701136 1.8238424 1.136342 10000 1.3563004 1.8059065 1.1547129 11000 1.3794051 1.692299 1.0515688 Loop time of 10.4087 on 8 procs for 10000 steps with 8000 atoms Performance: 415036.696 tau/day, 960.733 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2937 | 5.0957 | 5.741 | 23.2 | 48.96 Neigh | 2.1995 | 2.4735 | 2.7099 | 13.0 | 23.76 Comm | 0.81056 | 1.5944 | 2.6024 | 51.8 | 15.32 Output | 0.00049738 | 0.00074599 | 0.0021147 | 0.0 | 0.01 Modify | 0.92166 | 1.0638 | 1.1348 | 7.9 | 10.22 Other | | 0.1804 | | | 1.73 Nlocal: 1000 ave 1105 max 883 min Histogram: 1 1 2 0 0 0 0 0 2 2 Nghost: 2319.38 ave 2502 max 2114 min Histogram: 1 3 0 0 0 0 0 0 0 4 Neighs: 27387.9 ave 32453 max 21803 min Histogram: 2 2 0 0 0 0 0 0 0 4 Total # of neighbors = 219103 Ave neighs/atom = 27.387875 Neighbor list builds = 1696 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.ehex 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) = 3.656 | 3.657 | 3.658 Mbytes Step Temp Temp_hot Temp_cold dTemp_step dTemp 11000 1.3794051 1.6903393 1.0515688 0 0 12000 1.3799777 1.8004888 1.1032219 0.63860014 0 13000 1.3733605 1.7823094 1.0553582 0.65827891 0.65827891 14000 1.3749743 1.7852256 1.1674016 0.68463005 0.67145448 15000 1.3863795 1.8538127 1.0056247 0.73524813 0.69271903 16000 1.3731955 1.7518546 1.0741458 0.74810775 0.70656621 17000 1.3771856 1.9016869 1.0090502 0.73999567 0.7132521 18000 1.3766032 1.7616195 1.1142155 0.73769104 0.71732526 19000 1.3815934 1.7791247 1.1406987 0.73617832 0.72001855 20000 1.3725543 1.8637436 1.0799364 0.73435569 0.7218107 21000 1.3817369 1.8808771 1.0642524 0.76702329 0.72683432 22000 1.3968704 1.840287 1.072304 0.82496419 0.7366473 23000 1.3895558 1.9427293 1.0766665 0.75363908 0.73819201 24000 1.3900493 1.9883976 1.1081017 0.86394774 0.74867166 25000 1.3838912 1.8853041 1.0795751 0.83043902 0.75496145 26000 1.3912105 1.9330259 1.1070335 0.79880182 0.75809291 27000 1.3891151 1.8548451 1.0676153 0.81856523 0.7621244 28000 1.3942624 1.9796706 1.1251407 0.81762456 0.76559316 29000 1.3819302 1.8619138 1.0495292 0.78627491 0.76680973 30000 1.3968366 1.883107 1.1004588 0.83902548 0.77082172 31000 1.3822489 1.8220413 1.0322271 0.7550338 0.76999077 Loop time of 23.253 on 8 procs for 20000 steps with 8000 atoms Performance: 371564.581 tau/day, 860.103 timesteps/s 98.9% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0778 | 10.624 | 13.006 | 62.2 | 45.69 Neigh | 4.358 | 5.32 | 6.1917 | 35.5 | 22.88 Comm | 1.5574 | 4.6136 | 8.0947 | 127.6 | 19.84 Output | 0.0025729 | 0.0027796 | 0.0041615 | 1.0 | 0.01 Modify | 2.0737 | 2.2922 | 2.4432 | 9.2 | 9.86 Other | | 0.4005 | | | 1.72 Nlocal: 1000 ave 1121 max 857 min Histogram: 2 0 1 1 0 0 0 0 1 3 Nghost: 2299.75 ave 2541 max 2067 min Histogram: 3 1 0 0 0 0 0 0 2 2 Neighs: 27487.2 ave 33361 max 20651 min Histogram: 2 1 1 0 0 0 0 0 0 4 Total # of neighbors = 219898 Ave neighs/atom = 27.48725 Neighbor list builds = 3474 Dangerous builds = 0 print "Running average thermal conductivity: $(v_kappa:%.2f)" Running average thermal conductivity: 3.45 Total wall time: 0:00:34