#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 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 200000 200000 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 v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 v_surfacetension file 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.68274e-13 8304 2 103.7 1.057e-10 2768 Per MPI rank memory allocation (min/avg/max) = 12.61 | 12.71 | 12.81 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 -416.82664 92859.489 1.3074058 296.00634 31.74667 122.2988 0 0 21483.784 -182905.41 -291.74384 0 -161267.58 5586.9684 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27647e-06 8304 2 103.7 0.000112427 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.33196e-06 8304 2 103.7 9.61314e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.08693e-06 8304 2 103.7 9.81216e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.55464e-06 8304 2 103.7 9.27145e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16133e-06 8304 2 103.7 9.23931e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.58736e-06 8304 2 103.7 0.000101834 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.45847e-06 8304 2 103.7 0.000117601 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.32543e-06 8304 2 103.7 9.5992e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.52102e-06 8304 2 103.7 0.000101512 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21171e-06 8304 2 103.7 9.28895e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.48579e-06 8304 2 103.7 0.000113848 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.35394e-06 8304 2 103.7 0.000100991 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.89209e-06 8304 2 103.7 0.000128619 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.60827e-06 8304 2 103.7 0.000107722 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.32007e-06 8304 2 103.7 0.000112968 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.74205e-06 8304 2 103.7 0.000130741 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.28656e-06 8304 2 103.7 0.000109914 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.27469e-06 8304 2 103.7 0.000101552 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1526e-06 8304 2 103.7 0.000103288 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.49728e-06 8304 2 103.7 0.00010459 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.50841e-06 8304 2 103.7 0.000137439 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.24373e-06 8304 2 103.7 0.000114706 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.69826e-06 8304 2 103.7 9.33911e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.15019e-06 8304 2 103.7 0.000105435 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.63625e-06 8304 2 103.7 0.000112573 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.61681e-06 8304 2 103.7 0.000114854 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.37802e-06 8304 2 103.7 0.000108541 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.34969e-06 8304 2 103.7 0.000107239 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.48752e-06 8304 2 103.7 0.000112975 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.73963e-06 8304 2 103.7 9.77868e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.40667e-06 8304 2 103.7 0.000104293 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.23024e-06 8304 2 103.7 9.63214e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.53449e-06 8304 2 103.7 0.000119167 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.33382e-06 8304 2 103.7 9.75278e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.49853e-06 8304 2 103.7 0.00010764 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.18179e-06 8304 2 103.7 0.000105693 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.33251e-06 8304 2 103.7 0.000112377 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19735e-06 8304 2 103.7 0.000105516 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.44146e-06 8304 2 103.7 0.000119865 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.32199e-06 8304 2 103.7 9.32367e-05 2768 2000000 2000000 -670.46759 92859.489 1.3074058 301.94543 46.095302 103.49493 0 0 21434.212 -182734.9 -291.74384 0 -161151.1 5699.0659 Loop time of 15409.6 on 16 procs for 2000000 steps with 9101 atoms Performance: 11.214 ns/day, 2.140 hours/ns, 129.790 timesteps/s 99.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11867 | 12676 | 13776 | 432.8 | 82.26 Bond | 2.3316 | 7.0088 | 10.73 | 84.5 | 0.05 Neigh | 725.91 | 727.13 | 727.98 | 2.2 | 4.72 Comm | 268.1 | 1103.6 | 2065.1 |1434.0 | 7.16 Output | 0.01309 | 0.014888 | 0.01651 | 0.9 | 0.00 Modify | 585.19 | 855.51 | 1316.7 | 984.7 | 5.55 Other | | 40.28 | | | 0.26 Nlocal: 568.812 ave 591 max 540 min Histogram: 1 2 1 0 2 3 1 2 0 4 Nghost: 7793.25 ave 7881 max 7686 min Histogram: 2 2 0 1 1 1 3 3 2 1 Neighs: 255731 ave 274290 max 239787 min Histogram: 3 0 3 1 0 3 2 2 1 1 Total # of neighbors = 4091696 Ave neighs/atom = 449.58752 Ave special neighs/atom = 1.8929788 Neighbor list builds = 96046 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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 2000000 2 0.97 1.32199e-06 8304 2 103.7 9.32367e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.61 | 12.71 | 12.81 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 2000000 2000000 -669.36929 92859.489 1.3074058 301.94543 46.095302 103.49493 0 0 21434.212 -182734.9 -291.74384 0 -161151.1 5699.0659 Loop time of 8.05838e-06 on 16 procs for 0 steps with 9101 atoms 109.4% CPU use with 16 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 | | 8.058e-06 | | |100.00 Nlocal: 568.812 ave 591 max 540 min Histogram: 1 2 1 0 2 3 1 2 0 4 Nghost: 7793.25 ave 7881 max 7686 min Histogram: 2 2 0 1 1 1 3 3 2 1 Neighs: 255731 ave 274290 max 239787 min Histogram: 3 0 3 1 0 3 2 2 1 1 Total # of neighbors = 4091696 Ave neighs/atom = 449.58752 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:29:31