#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 500000 500000 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 2.4_averages.txt off 1 fix 3 movable ave/time 500 1 500 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 2.4_instantaneous.txt restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.31977901 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032810461 estimated relative force accuracy = 9.8807729e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10935 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.998809 0.722275 5784 2 97.929 19.1909 1928 Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.44 | 13.35 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 -2938.8081 137802.93 0.63039506 427.16581 16.237787 19.689904 0 0 17551.233 44028.756 -152.47823 -193963.95 -132348.04 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.17202e-06 5784 2 103.7 0.000100036 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.44694e-06 5784 2 103.7 9.79618e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.25249e-06 5784 2 103.7 0.000110611 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.51451e-06 5784 2 103.7 0.000111515 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.10433e-06 5784 2 103.7 8.89561e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.63753e-06 5784 2 103.7 0.000100538 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.10057e-06 5784 2 103.7 0.000100073 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.27216e-06 5784 2 103.7 8.70473e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.45596e-06 5784 2 103.7 0.000103767 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.07731e-06 5784 2 103.7 9.32367e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.10746e-06 5784 2 103.7 9.61597e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32788e-06 5784 2 103.7 9.75565e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.47818e-06 5784 2 103.7 0.00010558 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.14018e-06 5784 2 103.7 9.45234e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.19339e-06 5784 2 103.7 9.33748e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16505e-06 5784 2 103.7 8.68459e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12108e-06 5784 2 103.7 9.38659e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.35029e-06 5784 2 103.7 9.85137e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30897e-06 5784 2 103.7 0.000112053 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.47562e-06 5784 2 103.7 9.7834e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.10168e-06 5784 2 103.7 9.98308e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.30383e-06 5784 2 103.7 9.44165e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.7169e-06 5784 2 103.7 0.000124033 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.43681e-06 5784 2 103.7 0.000109326 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.43967e-06 5784 2 103.7 9.23738e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.1008e-06 5784 2 103.7 9.05196e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.51779e-06 5784 2 103.7 0.000107519 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.25771e-06 5784 2 103.7 9.74128e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.08628e-06 5784 2 103.7 8.84403e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.09741e-06 5784 2 103.7 9.42291e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.02317e-06 5784 2 103.7 9.3015e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.10281e-06 5784 2 103.7 8.64603e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.13529e-06 5784 2 103.7 8.74916e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2268e-06 5784 2 103.7 9.23981e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.03137e-06 5784 2 103.7 9.34077e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.42646e-06 5784 2 103.7 0.000102204 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.51848e-06 5784 2 103.7 0.000113596 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.20015e-06 5784 2 103.7 9.14738e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.13265e-06 5784 2 103.7 9.28961e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.12024e-06 5784 2 103.7 9.53233e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.34167e-06 5784 2 103.7 9.97504e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.27939e-06 5784 2 103.7 0.000107354 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.54212e-06 5784 2 103.7 0.000119697 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.43506e-06 5784 2 103.7 0.000105103 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.32749e-06 5784 2 103.7 9.65805e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.17467e-06 5784 2 103.7 9.41754e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.24275e-06 5784 2 103.7 9.02238e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.1523e-06 5784 2 103.7 9.47911e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.20446e-06 5784 2 103.7 8.94852e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.18469e-06 5784 2 103.7 9.13291e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.08877e-06 5784 2 103.7 9.18332e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.60063e-06 5784 2 103.7 0.000110837 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.59564e-06 5784 2 103.7 9.34093e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.26073e-06 5784 2 103.7 9.24307e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.15961e-06 5784 2 103.7 0.000106394 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.1481e-06 5784 2 103.7 9.40938e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.20428e-06 5784 2 103.7 0.000101022 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.38223e-06 5784 2 103.7 0.000116401 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.46777e-06 5784 2 103.7 0.000102073 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.27896e-06 5784 2 103.7 9.24546e-05 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.39806e-06 5784 2 103.7 0.000104478 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.3295e-06 5784 2 103.7 9.25548e-05 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.38388e-06 5784 2 103.7 0.000106589 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.2902e-06 5784 2 103.7 0.000103851 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.41096e-06 5784 2 103.7 9.85518e-05 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.37871e-06 5784 2 103.7 9.18251e-05 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.20809e-06 5784 2 103.7 8.76841e-05 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.03756e-06 5784 2 103.7 9.25816e-05 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.48747e-06 5784 2 103.7 0.000126314 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.19722e-06 5784 2 103.7 0.000106594 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.79482e-06 5784 2 103.7 0.000148536 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.40743e-06 5784 2 103.7 0.00013879 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.19382e-06 5784 2 103.7 9.41126e-05 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.54055e-06 5784 2 103.7 0.000127155 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.66665e-06 5784 2 103.7 0.000106148 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.35108e-06 5784 2 103.7 0.000135723 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.14157e-06 5784 2 103.7 0.000107712 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.08306e-06 5784 2 103.7 0.000102585 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.29462e-06 5784 2 103.7 0.000108848 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.13314e-06 5784 2 103.7 0.000103392 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.19938e-06 5784 2 103.7 9.1728e-05 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.36793e-06 5784 2 103.7 0.000102636 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.20025e-06 5784 2 103.7 9.62127e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.13314e-06 5784 2 103.7 9.04121e-05 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.58636e-06 5784 2 103.7 0.000128036 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.16315e-06 5784 2 103.7 9.07287e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.15571e-06 5784 2 103.7 0.000101715 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.11691e-06 5784 2 103.7 9.60029e-05 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.24365e-06 5784 2 103.7 0.000104283 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.38902e-06 5784 2 103.7 0.00010094 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.86404e-06 5784 2 103.7 0.000120853 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.50612e-06 5784 2 103.7 0.000129313 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.3217e-06 5784 2 103.7 9.92807e-05 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.49099e-06 5784 2 103.7 9.7465e-05 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.29007e-06 5784 2 103.7 0.000105081 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.38281e-06 5784 2 103.7 9.5717e-05 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.06065e-06 5784 2 103.7 8.7302e-05 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.0774e-06 5784 2 103.7 9.30116e-05 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.28839e-06 5784 2 103.7 0.000101941 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.67337e-06 5784 2 103.7 0.000121099 1928 5000000 5000000 -232.37787 137802.93 0.63039506 301.07843 28.224425 35.576016 0 0 16271.883 52720.312 -152.47823 -193996.65 -124940.66 4000.8661 Loop time of 29286 on 32 procs for 5000000 steps with 6387 atoms Performance: 14.751 ns/day, 1.627 hours/ns, 170.730 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.062 | 6862.2 | 15340 |8022.7 | 23.43 Bond | 4.5104 | 11.065 | 26.182 | 156.1 | 0.04 Kspace | 10211 | 18767 | 25738 |4886.3 | 64.08 Neigh | 1041 | 1046.8 | 1056.8 | 14.6 | 3.57 Comm | 408.85 | 830.63 | 1090.4 | 883.6 | 2.84 Output | 0.013139 | 0.014881 | 0.016321 | 0.8 | 0.00 Modify | 1489.2 | 1690.1 | 1979 | 473.6 | 5.77 Other | | 77.86 | | | 0.27 Nlocal: 199.594 ave 408 max 0 min Histogram: 14 1 1 0 0 0 0 0 3 13 Nghost: 2724.72 ave 5247 max 154 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 51337.3 ave 115607 max 0 min Histogram: 16 0 0 0 0 0 2 2 4 8 Total # of neighbors = 1642793 Ave neighs/atom = 257.20886 Ave special neighs/atom = 1.8738062 Neighbor list builds = 242161 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.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) = 0.31977901 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032810461 estimated relative force accuracy = 9.8807729e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10935 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.67337e-06 5784 2 103.7 0.000121099 1928 Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.65 | 13.35 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 5000000 5000000 -232.01931 137802.93 0.63039506 301.07843 28.224425 35.576016 0 0 16271.883 52720.312 -152.47823 -193996.65 -124940.66 4000.8661 Loop time of 7.23256e-06 on 32 procs for 0 steps with 6387 atoms 116.2% 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 | | 7.233e-06 | | |100.00 Nlocal: 199.594 ave 408 max 0 min Histogram: 14 1 1 0 0 0 0 0 3 13 Nghost: 2724.72 ave 5247 max 154 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 51337.3 ave 115607 max 0 min Histogram: 16 0 0 0 0 0 2 2 4 8 Total # of neighbors = 1642793 Ave neighs/atom = 257.20886 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out