#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 2699 = # 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.63389e-13 8097 2 103.7 1.00442e-10 2699 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.16 | 14.78 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 -370.75965 138878.49 1.4411859 295.14439 36.187694 64.059394 0 0 35953.424 -63507.872 -317.08001 -295419.68 -322873.88 6628.1823 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.1353e-06 8097 2 103.7 9.26529e-05 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26749e-06 8097 2 103.7 9.19331e-05 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34681e-06 8097 2 103.7 0.000101694 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.45785e-06 8097 2 103.7 8.99179e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.51069e-06 8097 2 103.7 0.000108771 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.29829e-06 8097 2 103.7 9.42683e-05 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.08639e-06 8097 2 103.7 0.00010409 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.22479e-06 8097 2 103.7 9.93475e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.23675e-06 8097 2 103.7 9.97567e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.4451e-06 8097 2 103.7 0.000102241 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2563e-06 8097 2 103.7 0.000100976 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32743e-06 8097 2 103.7 9.54571e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.37835e-06 8097 2 103.7 9.40603e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.47884e-06 8097 2 103.7 0.000118331 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.3837e-06 8097 2 103.7 0.000109916 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12691e-06 8097 2 103.7 0.000104981 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.26471e-06 8097 2 103.7 9.44344e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.30755e-06 8097 2 103.7 9.33155e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.09136e-06 8097 2 103.7 0.000102103 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20402e-06 8097 2 103.7 0.000105997 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.11623e-06 8097 2 103.7 8.94995e-05 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.19986e-06 8097 2 103.7 9.38338e-05 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.14812e-06 8097 2 103.7 9.09387e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.3025e-06 8097 2 103.7 0.000110804 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17676e-06 8097 2 103.7 0.0001012 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.2816e-06 8097 2 103.7 9.12844e-05 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.40736e-06 8097 2 103.7 0.000103052 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.16191e-06 8097 2 103.7 9.0527e-05 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.16274e-06 8097 2 103.7 0.00011103 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.42081e-06 8097 2 103.7 0.000109437 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.26956e-06 8097 2 103.7 0.00010423 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.21075e-06 8097 2 103.7 0.000101337 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.11192e-06 8097 2 103.7 9.07518e-05 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.46561e-06 8097 2 103.7 9.94107e-05 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14185e-06 8097 2 103.7 9.63201e-05 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19739e-06 8097 2 103.7 9.9977e-05 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.70802e-06 8097 2 103.7 0.000105149 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19151e-06 8097 2 103.7 0.00010014 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.15143e-06 8097 2 103.7 8.99357e-05 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11601e-06 8097 2 103.7 9.05294e-05 2699 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.30866e-06 8097 2 103.7 0.000109976 2699 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.53279e-06 8097 2 103.7 9.02989e-05 2699 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.77563e-06 8097 2 103.7 0.000113685 2699 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.3617e-06 8097 2 103.7 0.000108828 2699 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.10855e-06 8097 2 103.7 9.63621e-05 2699 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.09029e-06 8097 2 103.7 9.04815e-05 2699 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.1571e-06 8097 2 103.7 9.42768e-05 2699 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.58862e-06 8097 2 103.7 9.01952e-05 2699 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.2743e-06 8097 2 103.7 0.00011912 2699 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.12984e-06 8097 2 103.7 9.92063e-05 2699 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.32098e-06 8097 2 103.7 9.55442e-05 2699 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.59463e-06 8097 2 103.7 0.000130429 2699 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.11754e-06 8097 2 103.7 0.000108043 2699 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.37926e-06 8097 2 103.7 9.48982e-05 2699 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.37802e-06 8097 2 103.7 0.000109085 2699 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.16136e-06 8097 2 103.7 9.5282e-05 2699 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.29412e-06 8097 2 103.7 0.000107115 2699 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.24126e-06 8097 2 103.7 0.0001014 2699 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.12046e-06 8097 2 103.7 0.000104593 2699 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.36021e-06 8097 2 103.7 9.97278e-05 2699 3000000 3000000 108.20773 138878.49 1.4411859 298.3607 40.34364 40.89792 0 0 36221.87 -63588.6 -317.08001 -295421.59 -322707.07 6700.4125 Loop time of 42168.9 on 16 procs for 3000000 steps with 10558 atoms Performance: 6.147 ns/day, 3.905 hours/ns, 71.142 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6654.9 | 23649 | 31709 |6285.6 | 56.08 Bond | 3.4268 | 10.568 | 16.915 | 154.8 | 0.03 Kspace | 6459.7 | 14538 | 31567 |8033.5 | 34.48 Neigh | 1648 | 1652 | 1656.8 | 6.4 | 3.92 Comm | 803.37 | 967.42 | 1050.9 | 305.8 | 2.29 Output | 0.016201 | 0.01811 | 0.019835 | 0.8 | 0.00 Modify | 1219.9 | 1284.7 | 1420.5 | 219.1 | 3.05 Other | | 67.47 | | | 0.16 Nlocal: 659.875 ave 809 max 350 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 8167.88 ave 9734 max 6925 min Histogram: 4 0 0 7 1 0 0 0 0 4 Neighs: 307270 ave 406684 max 87912 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 4916315 Ave neighs/atom = 465.64832 Ave special neighs/atom = 1.5849593 Neighbor list builds = 148309 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.36021e-06 8097 2 103.7 9.97278e-05 2699 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.16 | 14.78 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 3000000 3000000 108.75064 138878.49 1.4411859 298.3607 40.34364 40.89792 0 0 36221.87 -63588.6 -317.08001 -295421.59 -322707.07 6700.4125 Loop time of 4.01681e-06 on 16 procs for 0 steps with 10558 atoms 124.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.017e-06 | | |100.00 Nlocal: 659.875 ave 809 max 350 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 8167.88 ave 9734 max 6925 min Histogram: 4 0 0 7 1 0 0 0 0 4 Neighs: 307270 ave 406684 max 87912 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 4916315 Ave neighs/atom = 465.64832 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out