variable t equal 15000 thermo $t thermo 15000 fix 1 all nvt temp 300.0 300.0 1.0 compute ke all ke/atom variable temperature atom c_ke/(1.5*8.617e-5) fix 2 all ave/spatial 1 100 100 x lower 2.46 v_temperature file temp.graphenedoped50 units box fix 3 all thermal/conductivity 300 x 46 variable tdiff equal f_2[45][3]-f_2[1][3] thermo_style custom step temp pe ke etotal press lx ly lz f_3 v_tdiff run 100000 Memory usage per processor = 1.81922 Mbytes Step Temp PotEng KinEng TotEng Press Lx Ly Lz 3 tdiff 1602000 283.83525 -5295.5901 855.36562 -4440.2245 -37.277735 115.26193 56.651266 20.253497 0 0 1605000 314.4173 -4962.9036 947.52764 -4015.3759 -5.2685289 115.26193 56.651266 20.253497 21.194554 1423.0765 1620000 296.91418 -4666.5456 894.78026 -3771.7653 77.418572 115.26193 56.651266 20.253497 128.15151 -746.59396 1635000 298.56372 -4666.719 899.75132 -3766.9676 38.055854 115.26193 56.651266 20.253497 231.79954 -196.05289 1650000 296.95722 -4707.1261 894.90996 -3812.2161 -47.031877 115.26193 56.651266 20.253497 300.47609 101.91365 1665000 301.72637 -4825.6281 909.28227 -3916.3458 81.553745 115.26193 56.651266 20.253497 366.017 366.76302 1680000 299.23029 -4921.9834 901.7601 -4020.2233 -5.3980485 115.26193 56.651266 20.253497 414.72023 363.78372 1695000 314.6097 -4953.8046 948.10746 -4005.6971 79.589265 115.26193 56.651266 20.253497 458.90049 245.61735 1702000 309.10747 -4978.5173 931.52596 -4046.9913 54.053615 115.26193 56.651266 20.253497 476.85742 230.53984 Loop time of 412.845 on 1 procs (1 MPI x 1 OpenMP) for 100000 steps with 1012 atoms Performance: 20.928 ns/day 1.147 hours/ns 242.221 timesteps/s MPI task walltime distribution Section | min time | avg time | max time |%total | %CPU --------------------------------------------------------------- Pair | 394.91 | 394.91 | 394.91 | 95.66 | 100.0 Neigh | 8.3743 | 8.3743 | 8.3743 | 2.03 | 99.8 Comm | 0.93749 | 0.93749 | 0.93749 | 0.23 | 100.0 Output | 0 | 0 | 0 | 0.00 | 100.0 Modify | 7.7025 | 7.7025 | 7.7025 | 1.87 | 96.0 Other | | 0.9218 | | 0.22 | Nlocal: 1012 ave 1012 max 1012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1262 ave 1262 max 1262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17368 ave 17368 max 17368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17368 Ave neighs/atom = 17.1621 Neighbor list builds = 4561 Dangerous builds = 0 write_restart equil.restart4 fix 2 all ave/spatial 1 100 100 x lower 2.46 v_temperature file temp.graphenedoped50 units box run 100000 Memory usage per processor = 1.94057 Mbytes Step Temp PotEng KinEng TotEng Press Lx Ly Lz 3 tdiff 1702000 309.10747 -4978.5173 931.52596 -4046.9913 54.053615 115.26193 56.651266 20.253497 476.85742 0 1710000 303.56335 -4979.787 914.8182 -4064.9688 -22.579754 115.26193 56.651266 20.253497 505.30638 88.244018 1725000 314.61377 -5000.9256 948.11974 -4052.8059 99.360706 115.26193 56.651266 20.253497 560.46905 -329.48037 1740000 299.49214 -5095.1398 902.54921 -4192.5906 61.383656 115.26193 56.651266 20.253497 618.87973 -271.2505 1755000 301.15875 -5142.8123 907.57171 -4235.2406 -18.963918 115.26193 56.651266 20.253497 667.53289 1056.0878 1770000 297.64606 -5095.3671 896.98586 -4198.3812 15.05251 115.26193 56.651266 20.253497 703.9969 -472.5086 1785000 293.56405 -5093.0909 884.68432 -4208.4065 -40.110952 115.26193 56.651266 20.253497 744.50616 275.82519 1800000 298.08036 -5061.3542 898.29466 -4163.0595 41.205619 115.26193 56.651266 20.253497 783.99476 -80.462861 1802000 309.70153 -5076.6757 933.31621 -4143.3595 -60.352685 115.26193 56.651266 20.253497 787.33368 363.95526 Loop time of 479.141 on 1 procs (1 MPI x 1 OpenMP) for 100000 steps with 1012 atoms Performance: 18.032 ns/day 1.331 hours/ns 208.707 timesteps/s MPI task walltime distribution Section | min time | avg time | max time |%total | %CPU --------------------------------------------------------------- Pair | 457.26 | 457.26 | 457.26 | 95.43 | 100.0 Neigh | 10.812 | 10.812 | 10.812 | 2.26 | 99.9 Comm | 1.6249 | 1.6249 | 1.6249 | 0.34 | 97.1 Output | 0.019413 | 0.019413 | 0.019413 | 0.00 | 100.0 Modify | 8.2964 | 8.2964 | 8.2964 | 1.73 | 97.7 Other | | 1.125 | | 0.23 | Nlocal: 1012 ave 1012 max 1012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1441 ave 1441 max 1441 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19302 ave 19302 max 19302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19302 Ave neighs/atom = 19.0731 Neighbor list builds = 4220 Dangerous builds = 0 write_restart equil.restart5 fix 3 all thermal/conductivity 300 x 46 fix ave all ave/time 1 1 1000 v_tdiff ave running thermo_style custom step temp epair etotal f_3 v_tdiff f_ave run 100000 Memory usage per processor = 2.0666 Mbytes Step Temp E_pair TotEng 3 tdiff ave 1802000 309.70153 -5076.6757 -4143.3595 0 363.95526 363.95526 1815000 309.92678 -5095.5938 -4161.5988 26.995548 16.67335 236.48136 1830000 306.26635 -5117.148 -4194.1841 69.410247 625.0748 124.4087 1845000 300.26008 -5116.4725 -4211.609 104.86772 -381.31761 104.5272 1860000 309.14523 -5105.0302 -4173.3904 176.64831 -99.682698 102.89818 1875000 296.22582 -5108.9063 -4216.2004 222.66671 -175.50518 112.61612 1890000 297.49215 -5173.9248 -4277.4028 252.47187 -185.88547 99.593718 1902000 301.77292 -5129.5114 -4220.0888 300.74914 263.54368 83.767038 Loop time of 488.262 on 1 procs (1 MPI x 1 OpenMP) for 100000 steps with 1012 atoms Performance: 17.695 ns/day 1.356 hours/ns 204.808 timesteps/s MPI task walltime distribution Section | min time | avg time | max time |%total | %CPU --------------------------------------------------------------- Pair | 465.01 | 465.01 | 465.01 | 95.24 | 100.0 Neigh | 12.671 | 12.671 | 12.671 | 2.60 | 100.0 Comm | 1.7186 | 1.7186 | 1.7186 | 0.35 | 90.0 Output | 0 | 0 | 0 | 0.00 | 100.0 Modify | 7.8432 | 7.8432 | 7.8432 | 1.61 | 98.4 Other | | 1.016 | | 0.21 | Nlocal: 1012 ave 1012 max 1012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1369 ave 1369 max 1369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20916 ave 20916 max 20916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20916 Ave neighs/atom = 20.668 Neighbor list builds = 4515 Dangerous builds = 0 ------------------------------------------------------------------------ This simulation made use of algorithms and methodologies described in the following references: The LAMMPS Molecular Dynamics Simulator, Version 2 Jul 2013 http://lammps.sandia.gov S.J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J. Comp. Phys., 117, 1-19 (1995) A.P. Thompson, S.J. Plimpton, W. Mattson, General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions, J. Chem. Phys., 131, 154107 (2009) S.J. Plimpton and A.P. Thompson, Computational Aspects of Many-body Potentials, MRS Bulletin, 37, 513-521 (2012)