#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 4 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 400000 400000 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 2.5_averages.txt off 1 fix 3 movable ave/time 400 1 400 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 4000000 2.5.restart dump sci all custom 400000 2.5.xyz id mol type q xs ys zs timestep 1 run 4000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.85341e-13 11184 2 103.7 8.0334e-11 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 335929.19 143799.62 1.371895 297.37957 276.1468 362.97776 0 0 271595.53 -52433.342 -383.45046 -378985.51 -159184.19 8165.8117 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.33419e-06 11184 2 103.7 9.59926e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.23862e-06 11184 2 103.7 9.07758e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27856e-06 11184 2 103.7 0.000103604 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.45339e-06 11184 2 103.7 0.000106557 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.15835e-06 11184 2 103.7 9.09732e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.29304e-06 11184 2 103.7 9.09013e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2671e-06 11184 2 103.7 9.77907e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.78007e-06 11184 2 103.7 0.000114019 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.28558e-06 11184 2 103.7 9.06464e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.2439e-06 11184 2 103.7 9.41551e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.19062e-06 11184 2 103.7 8.94261e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2307e-06 11184 2 103.7 9.92265e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.59308e-06 11184 2 103.7 9.54923e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.3877e-06 11184 2 103.7 9.50957e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.75965e-06 11184 2 103.7 0.00010714 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.13028e-06 11184 2 103.7 9.31246e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.41742e-06 11184 2 103.7 0.000107258 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.62613e-06 11184 2 103.7 0.000110202 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.51357e-06 11184 2 103.7 0.000107031 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.36271e-06 11184 2 103.7 9.55281e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.33238e-06 11184 2 103.7 9.12286e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.52611e-06 11184 2 103.7 0.000121804 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.37379e-06 11184 2 103.7 0.00010451 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.64211e-06 11184 2 103.7 0.000112631 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.39624e-06 11184 2 103.7 9.55039e-05 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.67364e-06 11184 2 103.7 0.000105457 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.23093e-06 11184 2 103.7 9.05454e-05 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.35748e-06 11184 2 103.7 9.68061e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.4899e-06 11184 2 103.7 9.44574e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.49336e-06 11184 2 103.7 9.5904e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.09572e-06 11184 2 103.7 9.31758e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.25882e-06 11184 2 103.7 9.70951e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.46479e-06 11184 2 103.7 0.000101265 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.29527e-06 11184 2 103.7 9.77513e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.05697e-06 11184 2 103.7 0.000100752 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.40357e-06 11184 2 103.7 9.09801e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.50592e-06 11184 2 103.7 9.78738e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.39918e-06 11184 2 103.7 0.000103527 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37868e-06 11184 2 103.7 9.02347e-05 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.14876e-06 11184 2 103.7 9.7484e-05 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.47109e-06 11184 2 103.7 0.000101314 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.26409e-06 11184 2 103.7 0.000105611 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.53022e-06 11184 2 103.7 0.000103568 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.17954e-06 11184 2 103.7 0.00010442 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.5174e-06 11184 2 103.7 0.000114671 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.14659e-06 11184 2 103.7 9.17162e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.36299e-06 11184 2 103.7 0.000118708 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.22356e-06 11184 2 103.7 9.41725e-05 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.21065e-06 11184 2 103.7 0.000106098 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.18359e-06 11184 2 103.7 9.60096e-05 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.28911e-06 11184 2 103.7 0.000102484 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.58981e-06 11184 2 103.7 0.000106273 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.19135e-06 11184 2 103.7 9.26167e-05 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.16548e-06 11184 2 103.7 8.90027e-05 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.24844e-06 11184 2 103.7 9.15284e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.54302e-06 11184 2 103.7 9.03815e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.32003e-06 11184 2 103.7 0.000106277 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.16335e-06 11184 2 103.7 0.000104812 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.32652e-06 11184 2 103.7 0.000100151 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.23924e-06 11184 2 103.7 9.63951e-05 3728 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.22828e-06 11184 2 103.7 0.000101285 3728 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.32692e-06 11184 2 103.7 9.48002e-05 3728 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.36464e-06 11184 2 103.7 9.6836e-05 3728 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.32853e-06 11184 2 103.7 9.97749e-05 3728 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.19242e-06 11184 2 103.7 9.25306e-05 3728 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.51132e-06 11184 2 103.7 9.95457e-05 3728 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.28368e-06 11184 2 103.7 8.96012e-05 3728 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.23609e-06 11184 2 103.7 9.90019e-05 3728 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.28846e-06 11184 2 103.7 9.34856e-05 3728 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.45223e-06 11184 2 103.7 9.05269e-05 3728 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.4213e-06 11184 2 103.7 0.0001033 3728 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.66415e-06 11184 2 103.7 0.000107928 3728 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.84566e-06 11184 2 103.7 0.0001211 3728 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.48846e-06 11184 2 103.7 0.000108524 3728 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.20435e-06 11184 2 103.7 0.000105764 3728 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.49061e-06 11184 2 103.7 9.8283e-05 3728 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.15395e-06 11184 2 103.7 9.45909e-05 3728 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.27191e-06 11184 2 103.7 8.6561e-05 3728 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.18532e-06 11184 2 103.7 9.71733e-05 3728 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.63216e-06 11184 2 103.7 0.00010874 3728 4000000 4000000 335010.37 143799.62 1.371895 299.81766 278.30351 349.89678 0 0 270996.99 -51936.177 -383.45046 -378993.5 -159304.48 8232.7597 Loop time of 51217.8 on 32 procs for 4000000 steps with 13901 atoms Performance: 6.748 ns/day, 3.557 hours/ns, 78.098 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21659 | 26276 | 36360 |3337.2 | 51.30 Bond | 8.1428 | 29.206 | 72.147 | 415.5 | 0.06 Kspace | 7928.5 | 18075 | 22763 |4053.2 | 35.29 Neigh | 1899.2 | 1903.3 | 1908.1 | 6.1 | 3.72 Comm | 2080.1 | 2224.4 | 2394 | 215.2 | 4.34 Output | 0.016414 | 0.0194 | 0.022208 | 1.3 | 0.00 Modify | 2463 | 2590.6 | 2679.6 | 145.7 | 5.06 Other | | 118.6 | | | 0.23 Nlocal: 434.406 ave 523 max 386 min Histogram: 8 9 7 0 0 0 0 0 0 8 Nghost: 8254.16 ave 8712 max 7540 min Histogram: 8 0 0 0 0 0 7 9 0 8 Neighs: 243733 ave 344872 max 194162 min Histogram: 10 10 3 1 0 0 0 0 4 4 Total # of neighbors = 7799467 Ave neighs/atom = 561.07237 Ave special neighs/atom = 1.8838932 Neighbor list builds = 200197 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 2.5.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.63216e-06 11184 2 103.7 0.00010874 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 4000000 4000000 335011.29 143799.62 1.371895 299.81766 278.30351 349.89678 0 0 270996.99 -51936.177 -383.45046 -378993.5 -159304.48 8232.7597 Loop time of 7.40475e-06 on 32 procs for 0 steps with 13901 atoms 113.9% 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 Kspace | 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 | | 7.405e-06 | | |100.00 Nlocal: 434.406 ave 523 max 386 min Histogram: 8 9 7 0 0 0 0 0 0 8 Nghost: 8254.16 ave 8712 max 7540 min Histogram: 8 0 0 0 0 0 7 9 0 8 Neighs: 243733 ave 344872 max 194162 min Histogram: 10 10 3 1 0 0 0 0 4 4 Total # of neighbors = 7799467 Ave neighs/atom = 561.07237 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out