#------------------------------------------------------------------------------- # 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 3659 = # 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.51652e-13 10977 2 103.7 7.51328e-11 3659 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.1 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 338263.69 142807.9 1.3823791 300.48363 270.8173 390.18985 0 0 273407.92 -65423.452 -383.2647 -382454.94 -173809.46 8166.8523 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.357e-06 10977 2 103.7 0.0001152 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.18965e-06 10977 2 103.7 9.45346e-05 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.18287e-06 10977 2 103.7 9.95771e-05 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15264e-06 10977 2 103.7 9.21084e-05 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.50643e-06 10977 2 103.7 9.88826e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.51984e-06 10977 2 103.7 0.000116853 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.43972e-06 10977 2 103.7 9.54029e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.52474e-06 10977 2 103.7 0.000108997 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.19939e-06 10977 2 103.7 9.45696e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.17925e-06 10977 2 103.7 9.09049e-05 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.53697e-06 10977 2 103.7 0.000101859 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.45658e-06 10977 2 103.7 9.72016e-05 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.16854e-06 10977 2 103.7 0.000102728 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.80046e-06 10977 2 103.7 0.000105235 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.19135e-06 10977 2 103.7 9.51788e-05 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.27502e-06 10977 2 103.7 9.44782e-05 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.57837e-06 10977 2 103.7 0.000105649 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.41337e-06 10977 2 103.7 0.000123031 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.24506e-06 10977 2 103.7 9.9692e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.20841e-06 10977 2 103.7 8.86468e-05 3659 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.14936e-06 10977 2 103.7 9.24854e-05 3659 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.44931e-06 10977 2 103.7 9.09673e-05 3659 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.1615e-06 10977 2 103.7 9.24645e-05 3659 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.27876e-06 10977 2 103.7 9.77852e-05 3659 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.21499e-06 10977 2 103.7 0.000111541 3659 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.16681e-06 10977 2 103.7 0.000121794 3659 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.81482e-06 10977 2 103.7 0.000112659 3659 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.28326e-06 10977 2 103.7 9.49428e-05 3659 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.20732e-06 10977 2 103.7 9.68784e-05 3659 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.47982e-06 10977 2 103.7 0.000108488 3659 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.14112e-06 10977 2 103.7 0.000109246 3659 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.17019e-06 10977 2 103.7 9.72059e-05 3659 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.4337e-06 10977 2 103.7 9.65819e-05 3659 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.11611e-06 10977 2 103.7 9.77426e-05 3659 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.2597e-06 10977 2 103.7 9.63213e-05 3659 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.15727e-06 10977 2 103.7 8.76737e-05 3659 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.26386e-06 10977 2 103.7 0.000100728 3659 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.37285e-06 10977 2 103.7 0.000104761 3659 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.8815e-06 10977 2 103.7 0.0001149 3659 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.17588e-06 10977 2 103.7 9.91307e-05 3659 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.34098e-06 10977 2 103.7 9.37905e-05 3659 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.41612e-06 10977 2 103.7 8.97976e-05 3659 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.11371e-06 10977 2 103.7 9.11296e-05 3659 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.31218e-06 10977 2 103.7 0.000110033 3659 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.4305e-06 10977 2 103.7 9.82337e-05 3659 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.02207e-06 10977 2 103.7 0.000112688 3659 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.30706e-06 10977 2 103.7 0.00010302 3659 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.37513e-06 10977 2 103.7 0.0001009 3659 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.42345e-06 10977 2 103.7 0.000102119 3659 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.30494e-06 10977 2 103.7 9.17976e-05 3659 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.2257e-06 10977 2 103.7 9.82138e-05 3659 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.19784e-06 10977 2 103.7 9.35952e-05 3659 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.2865e-06 10977 2 103.7 9.56013e-05 3659 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.2553e-06 10977 2 103.7 8.99612e-05 3659 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.25267e-06 10977 2 103.7 9.35719e-05 3659 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.16182e-06 10977 2 103.7 0.000105217 3659 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.61291e-06 10977 2 103.7 0.000118412 3659 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.59914e-06 10977 2 103.7 0.000111675 3659 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.30794e-06 10977 2 103.7 8.9048e-05 3659 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.35074e-06 10977 2 103.7 9.51867e-05 3659 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.60509e-06 10977 2 103.7 0.000118695 3659 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.18843e-06 10977 2 103.7 9.22436e-05 3659 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.16215e-06 10977 2 103.7 9.13361e-05 3659 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.09914e-06 10977 2 103.7 9.19445e-05 3659 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.12179e-06 10977 2 103.7 0.0001001 3659 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.24704e-06 10977 2 103.7 0.000111757 3659 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.19869e-06 10977 2 103.7 0.0001042 3659 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.5042e-06 10977 2 103.7 9.46031e-05 3659 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.28848e-06 10977 2 103.7 9.83756e-05 3659 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.16295e-06 10977 2 103.7 9.69672e-05 3659 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.3134e-06 10977 2 103.7 9.23275e-05 3659 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.19369e-06 10977 2 103.7 9.15244e-05 3659 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.21943e-06 10977 2 103.7 9.18071e-05 3659 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.06442e-06 10977 2 103.7 9.86265e-05 3659 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.39416e-06 10977 2 103.7 0.000105769 3659 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.04649e-06 10977 2 103.7 9.12481e-05 3659 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.09323e-06 10977 2 103.7 9.35898e-05 3659 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.2824e-06 10977 2 103.7 9.80927e-05 3659 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.73328e-06 10977 2 103.7 0.000120748 3659 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.47574e-06 10977 2 103.7 0.000105395 3659 4000000 4000000 337842.91 142807.9 1.3823791 299.7949 303.31937 389.21601 0 0 272795.64 -64733.953 -383.2647 -382419.57 -173665.35 8148.1334 Loop time of 50875.3 on 32 procs for 4000000 steps with 13738 atoms Performance: 6.793 ns/day, 3.533 hours/ns, 78.624 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 | 20290 | 25886 | 36115 |3468.8 | 50.88 Bond | 5.7077 | 28.621 | 72.543 | 428.7 | 0.06 Kspace | 7868.6 | 18176 | 23855 |4173.0 | 35.73 Neigh | 1883 | 1887.7 | 1893.2 | 7.2 | 3.71 Comm | 2035.2 | 2198.5 | 2383.5 | 241.3 | 4.32 Output | 0.014992 | 0.017892 | 0.020633 | 1.3 | 0.00 Modify | 2437.8 | 2578.5 | 2679.6 | 159.2 | 5.07 Other | | 119.9 | | | 0.24 Nlocal: 429.312 ave 522 max 376 min Histogram: 6 9 7 2 0 0 0 0 1 7 Nghost: 8165 ave 8704 max 7388 min Histogram: 8 0 0 0 0 0 10 6 0 8 Neighs: 240025 ave 343736 max 185198 min Histogram: 7 10 7 0 0 0 0 0 1 7 Total # of neighbors = 7680794 Ave neighs/atom = 559.09113 Ave special neighs/atom = 1.8702868 Neighbor list builds = 199644 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.47574e-06 10977 2 103.7 0.000105395 3659 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.1 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 337843.83 142807.9 1.3823791 299.7949 303.31937 389.21601 0 0 272795.64 -64733.953 -383.2647 -382419.57 -173665.35 8148.1334 Loop time of 1.38113e-05 on 32 procs for 0 steps with 13738 atoms 107.0% 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 | | 1.381e-05 | | |100.00 Nlocal: 429.312 ave 522 max 376 min Histogram: 6 9 7 2 0 0 0 0 1 7 Nghost: 8165 ave 8704 max 7388 min Histogram: 8 0 0 0 0 0 10 6 0 8 Neighs: 240025 ave 343736 max 185198 min Histogram: 7 10 7 0 0 0 0 0 1 7 Total # of neighbors = 7680794 Ave neighs/atom = 559.09113 Ave special neighs/atom = 1.8702868 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out