#------------------------------------------------------------------------------- # 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 1928 = # 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 v_surfacetension 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 v_surfacetension file 2.5_instantaneous.txt 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) = 0.31959374 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033035281 estimated relative force accuracy = 9.9484767e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.24754e-13 5784 2 103.7 9.23279e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.5 | 12.73 | 13.23 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 -166.60781 138878.58 0.6255125 295.5991 34.184209 41.390978 0 0 16336.753 52515.414 -151.29725 -193856.02 -124928.28 3928.0542 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.32265e-06 5784 2 103.7 9.62389e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11458e-06 5784 2 103.7 0.000100302 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34099e-06 5784 2 103.7 0.000100935 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18407e-06 5784 2 103.7 0.00010765 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.47147e-06 5784 2 103.7 0.000119209 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.5928e-06 5784 2 103.7 9.10858e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.09763e-06 5784 2 103.7 9.49554e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21935e-06 5784 2 103.7 9.77699e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.4597e-06 5784 2 103.7 0.000117734 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 9.92921e-07 5784 2 103.7 9.24632e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.06185e-06 5784 2 103.7 9.53654e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.42547e-06 5784 2 103.7 0.00010471 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.1959e-06 5784 2 103.7 9.68563e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.3807e-06 5784 2 103.7 9.10986e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.51358e-06 5784 2 103.7 0.000106698 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.20044e-06 5784 2 103.7 9.55313e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.27086e-06 5784 2 103.7 9.64458e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.61101e-06 5784 2 103.7 0.00012983 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.46147e-06 5784 2 103.7 9.17247e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.21719e-06 5784 2 103.7 9.10479e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.1572e-06 5784 2 103.7 0.000105359 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.37361e-06 5784 2 103.7 0.000109618 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.11202e-06 5784 2 103.7 9.58196e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.22597e-06 5784 2 103.7 0.000101255 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.36745e-06 5784 2 103.7 9.76027e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.10003e-06 5784 2 103.7 8.91301e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.1372e-06 5784 2 103.7 9.11789e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28054e-06 5784 2 103.7 0.000104566 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.31396e-06 5784 2 103.7 9.26317e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.69834e-06 5784 2 103.7 0.000127102 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.1457e-06 5784 2 103.7 0.000105449 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.11055e-06 5784 2 103.7 0.000101969 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.07513e-06 5784 2 103.7 8.61298e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.24691e-06 5784 2 103.7 9.14069e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.31362e-06 5784 2 103.7 9.00061e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.02271e-06 5784 2 103.7 9.92625e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.48512e-06 5784 2 103.7 0.000113071 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.11428e-06 5784 2 103.7 9.94937e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.1786e-06 5784 2 103.7 9.22282e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.04497e-06 5784 2 103.7 9.07345e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.25977e-06 5784 2 103.7 9.74129e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.64098e-06 5784 2 103.7 0.000114884 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.35856e-06 5784 2 103.7 0.000122226 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.46918e-06 5784 2 103.7 0.000110494 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.42912e-06 5784 2 103.7 0.000104064 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.42659e-06 5784 2 103.7 0.000103817 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.12526e-06 5784 2 103.7 9.59793e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.07172e-06 5784 2 103.7 9.1191e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.90752e-06 5784 2 103.7 0.000138778 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.22403e-06 5784 2 103.7 0.000101172 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.14523e-06 5784 2 103.7 0.000100906 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.16865e-06 5784 2 103.7 0.000104098 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.22114e-06 5784 2 103.7 0.000104578 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.13506e-06 5784 2 103.7 0.0001065 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.25761e-06 5784 2 103.7 0.000117036 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.55105e-06 5784 2 103.7 9.89168e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.33092e-06 5784 2 103.7 0.000104608 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.15247e-06 5784 2 103.7 8.88624e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.15268e-06 5784 2 103.7 9.71778e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.05833e-06 5784 2 103.7 9.01548e-05 1928 3000000 3000000 -120.22597 138878.58 0.6255125 295.57899 22.876122 35.656952 0 0 16383.151 52576.351 -151.29725 -193872.3 -124854.27 3927.787 Loop time of 17260.2 on 32 procs for 3000000 steps with 6387 atoms Performance: 15.017 ns/day, 1.598 hours/ns, 173.810 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 108.31 | 4117 | 8798.4 |6159.3 | 23.85 Bond | 2.6152 | 5.8863 | 16.973 | 153.6 | 0.03 Kspace | 6452.3 | 11174 | 15227 |3760.3 | 64.74 Neigh | 469.3 | 473.83 | 481.84 | 21.6 | 2.75 Comm | 320.79 | 512.17 | 647.95 | 564.5 | 2.97 Output | 0.0099556 | 0.011547 | 0.013033 | 0.9 | 0.00 Modify | 828.98 | 927.65 | 1061.8 | 310.7 | 5.37 Other | | 49.36 | | | 0.29 Nlocal: 199.594 ave 410 max 0 min Histogram: 13 3 0 0 0 0 0 0 4 12 Nghost: 2706.38 ave 4087 max 1324 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51431 ave 115696 max 0 min Histogram: 16 0 0 0 0 0 0 1 10 5 Total # of neighbors = 1645793 Ave neighs/atom = 257.67857 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145207 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) = 0.31959374 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033035281 estimated relative force accuracy = 9.9484767e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.05833e-06 5784 2 103.7 9.01548e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.5 | 12.7 | 13.23 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 -119.75858 138878.58 0.6255125 295.57899 22.876122 35.656952 0 0 16383.151 52576.351 -151.29725 -193872.3 -124854.27 3927.787 Loop time of 7.35222e-06 on 32 procs for 0 steps with 6387 atoms 110.1% 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 | | 7.352e-06 | | |100.00 Nlocal: 199.594 ave 410 max 0 min Histogram: 13 3 0 0 0 0 0 0 4 12 Nghost: 2706.38 ave 4087 max 1324 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51431 ave 115696 max 0 min Histogram: 16 0 0 0 0 0 0 1 10 5 Total # of neighbors = 1645793 Ave neighs/atom = 257.67857 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 12:51:43