#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 500000 500000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 500 1 500 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996396 0.671164 8304 2 97.063 29.2392 2768 Per MPI rank memory allocation (min/avg/max) = 11.62 | 11.73 | 12.2 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 14728.258 92859.489 1.3074058 428.55654 61.920788 322.8213 0 0 24859.725 -169619.75 -448.40969 0 -144375.28 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.61493e-06 8304 2 103.7 0.000109335 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.49455e-06 8304 2 103.7 0.000100765 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.44107e-06 8304 2 103.7 9.68636e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.32822e-06 8304 2 103.7 9.63497e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.6754e-06 8304 2 103.7 9.57391e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.5943e-06 8304 2 103.7 9.9367e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.86342e-06 8304 2 103.7 0.000111884 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.50911e-06 8304 2 103.7 0.000110212 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.29813e-06 8304 2 103.7 0.00010073 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.80845e-06 8304 2 103.7 0.000100881 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.17191e-06 8304 2 103.7 0.000119649 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.33762e-06 8304 2 103.7 0.00010867 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46391e-06 8304 2 103.7 9.71348e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.59829e-06 8304 2 103.7 0.000110666 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.29339e-06 8304 2 103.7 0.00010948 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.38619e-06 8304 2 103.7 0.000101809 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.58318e-06 8304 2 103.7 0.000120688 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.43702e-06 8304 2 103.7 9.97722e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.52949e-06 8304 2 103.7 0.000105729 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.91511e-06 8304 2 103.7 0.000115351 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.28222e-06 8304 2 103.7 0.000106217 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.63581e-06 8304 2 103.7 0.00012052 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.37555e-06 8304 2 103.7 0.000102191 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.55743e-06 8304 2 103.7 0.000110127 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.46957e-06 8304 2 103.7 0.000142403 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.46319e-06 8304 2 103.7 0.000102682 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.30865e-06 8304 2 103.7 9.81592e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 2.31425e-06 8304 2 103.7 0.000134193 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.34699e-06 8304 2 103.7 0.000107942 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.42519e-06 8304 2 103.7 0.000122219 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.78511e-06 8304 2 103.7 0.000107743 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.59405e-06 8304 2 103.7 0.000100883 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.24976e-06 8304 2 103.7 0.00010567 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.51744e-06 8304 2 103.7 0.00010533 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.39123e-06 8304 2 103.7 0.000107096 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.18512e-06 8304 2 103.7 9.73207e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.51215e-06 8304 2 103.7 0.00012017 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.51111e-06 8304 2 103.7 9.78372e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.87862e-06 8304 2 103.7 0.000132528 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.245e-06 8304 2 103.7 0.000102795 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.75805e-06 8304 2 103.7 0.000114855 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.78107e-06 8304 2 103.7 0.00011218 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.63103e-06 8304 2 103.7 0.000107812 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.73728e-06 8304 2 103.7 0.000103311 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.57975e-06 8304 2 103.7 0.000105091 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.26006e-06 8304 2 103.7 0.000113123 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.41258e-06 8304 2 103.7 0.000118778 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.34211e-06 8304 2 103.7 9.85431e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.59243e-06 8304 2 103.7 0.00012351 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.39352e-06 8304 2 103.7 0.000101979 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.36185e-06 8304 2 103.7 0.000114684 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.31843e-06 8304 2 103.7 0.000113118 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.67978e-06 8304 2 103.7 9.95373e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.39109e-06 8304 2 103.7 0.00010967 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.47222e-06 8304 2 103.7 9.99085e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.36883e-06 8304 2 103.7 9.64311e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.54522e-06 8304 2 103.7 0.000106945 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.44005e-06 8304 2 103.7 0.000101731 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.42683e-06 8304 2 103.7 0.000104693 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.45654e-06 8304 2 103.7 9.76873e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.20886e-06 8304 2 103.7 9.5642e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.58433e-06 8304 2 103.7 0.000105315 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.31211e-06 8304 2 103.7 0.000100314 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.23332e-06 8304 2 103.7 0.000118279 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.24666e-06 8304 2 103.7 0.000103089 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.85204e-06 8304 2 103.7 0.000104259 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.79387e-06 8304 2 103.7 0.000109214 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.40963e-06 8304 2 103.7 0.000108612 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.3274e-06 8304 2 103.7 0.000109187 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.15474e-06 8304 2 103.7 0.000110593 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.48714e-06 8304 2 103.7 0.000105192 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.6045e-06 8304 2 103.7 0.000108555 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 2.04497e-06 8304 2 103.7 0.000139982 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.95553e-06 8304 2 103.7 0.000161703 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.58571e-06 8304 2 103.7 0.000111647 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.24513e-06 8304 2 103.7 0.000103617 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.24735e-06 8304 2 103.7 0.00010081 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.40653e-06 8304 2 103.7 0.0001004 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.47428e-06 8304 2 103.7 0.000115165 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.32664e-06 8304 2 103.7 0.000114471 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.50866e-06 8304 2 103.7 0.000103921 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 2.33618e-06 8304 2 103.7 0.000144295 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.30555e-06 8304 2 103.7 0.000117036 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.41812e-06 8304 2 103.7 0.000105466 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.418e-06 8304 2 103.7 0.000114349 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.41704e-06 8304 2 103.7 9.56846e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.66817e-06 8304 2 103.7 9.64225e-05 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.71361e-06 8304 2 103.7 0.000110978 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.68126e-06 8304 2 103.7 0.000103744 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.23551e-06 8304 2 103.7 9.78789e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.2759e-06 8304 2 103.7 0.000117013 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.39677e-06 8304 2 103.7 0.000117019 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.56767e-06 8304 2 103.7 0.000104128 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.4247e-06 8304 2 103.7 0.000108296 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.46515e-06 8304 2 103.7 0.000118014 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 2.11426e-06 8304 2 103.7 0.000151028 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.65778e-06 8304 2 103.7 0.000115634 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.85212e-06 8304 2 103.7 0.000102971 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.38003e-06 8304 2 103.7 0.00011034 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.64101e-06 8304 2 103.7 0.000106536 2768 5000000 5000000 -1920.4113 92859.489 1.3074058 299.47351 43.492839 120.27629 0 0 21169.383 -184046.45 -448.40969 0 -162713.29 5652.4095 Loop time of 16345 on 32 procs for 5000000 steps with 9101 atoms Performance: 26.430 ns/day, 0.908 hours/ns, 305.904 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9896.1 | 11200 | 12616 | 637.0 | 68.52 Bond | 4.1279 | 9.9285 | 25.99 | 145.1 | 0.06 Neigh | 791.25 | 794.29 | 797.42 | 9.0 | 4.86 Comm | 1369.4 | 2759 | 4033.2 |1237.0 | 16.88 Output | 0.010557 | 0.012797 | 0.014908 | 1.2 | 0.00 Modify | 1458.3 | 1520.6 | 1590.9 | 112.3 | 9.30 Other | | 61.4 | | | 0.38 Nlocal: 284.406 ave 306 max 264 min Histogram: 2 1 6 2 4 9 3 2 2 1 Nghost: 4986.81 ave 5071 max 4951 min Histogram: 7 9 3 4 2 4 1 0 0 2 Neighs: 88297.3 ave 100616 max 77033 min Histogram: 1 2 3 9 4 5 2 2 2 2 Total # of neighbors = 2825513 Ave neighs/atom = 310.46182 Ave special neighs/atom = 1.8929788 Neighbor list builds = 238778 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.64101e-06 8304 2 103.7 0.000106536 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.86 | 12.21 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 5000000 5000000 -1919.4883 92859.489 1.3074058 299.47351 43.492839 120.27629 0 0 21169.383 -184046.45 -448.40969 0 -162713.29 5652.4095 Loop time of 6.84378e-06 on 32 procs for 0 steps with 9101 atoms 110.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.844e-06 | | |100.00 Nlocal: 284.406 ave 306 max 264 min Histogram: 2 1 6 2 4 9 3 2 2 1 Nghost: 4986.81 ave 5071 max 4951 min Histogram: 7 9 3 4 2 4 1 0 0 2 Neighs: 88297.3 ave 100616 max 77033 min Histogram: 1 2 3 9 4 5 2 2 2 2 Total # of neighbors = 2825513 Ave neighs/atom = 310.46182 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out