#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 2768 = # 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25979226 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0025175327 estimated relative force accuracy = 7.5814749e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997766 0.739266 8304 2 96.6648 30.985 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13 | 13.39 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 13541.423 92859.489 1.3074058 428.55654 319.12104 287.21984 0 0 25632.184 47201.834 -225.64505 -216564.12 -143123.76 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.41508e-06 8304 2 103.7 0.000112699 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.35681e-06 8304 2 103.7 8.97959e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.02925e-06 8304 2 103.7 9.47028e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.75551e-06 8304 2 103.7 0.000106223 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.24016e-06 8304 2 103.7 9.96635e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.31965e-06 8304 2 103.7 9.77075e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.35949e-06 8304 2 103.7 0.00011739 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.25417e-06 8304 2 103.7 9.14961e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.72114e-06 8304 2 103.7 0.000119202 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2511e-06 8304 2 103.7 8.89355e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.19528e-06 8304 2 103.7 9.88922e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.34124e-06 8304 2 103.7 9.19379e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11323e-06 8304 2 103.7 0.00010021 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.60111e-06 8304 2 103.7 0.00010394 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12892e-06 8304 2 103.7 0.000101357 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.30181e-06 8304 2 103.7 9.36572e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.31076e-06 8304 2 103.7 0.000106903 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.07892e-06 8304 2 103.7 9.64277e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.15094e-06 8304 2 103.7 0.000113734 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20903e-06 8304 2 103.7 8.849e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2202e-06 8304 2 103.7 0.000101991 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.30002e-06 8304 2 103.7 0.000102416 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.51873e-06 8304 2 103.7 0.000101035 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.33926e-06 8304 2 103.7 0.000108939 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.11496e-06 8304 2 103.7 9.04731e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.16623e-06 8304 2 103.7 0.000106445 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.08589e-06 8304 2 103.7 9.28485e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.1415e-06 8304 2 103.7 9.34616e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.31321e-06 8304 2 103.7 0.000103215 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.68962e-06 8304 2 103.7 0.000110052 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.18631e-06 8304 2 103.7 9.25125e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.17378e-06 8304 2 103.7 9.01164e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.30255e-06 8304 2 103.7 9.25905e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.23318e-06 8304 2 103.7 9.81203e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27015e-06 8304 2 103.7 9.24464e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10263e-06 8304 2 103.7 0.000109132 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0371e-06 8304 2 103.7 9.32472e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19105e-06 8304 2 103.7 9.68534e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.12813e-06 8304 2 103.7 0.000105696 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2111e-06 8304 2 103.7 9.58477e-05 2768 2000000 2000000 2732.3179 92859.489 1.3074058 301.39993 50.557891 63.35363 0 0 22333.357 33658.475 -225.64505 -218001.62 -161895.88 5688.7697 Loop time of 15680.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 11.020 ns/day, 2.178 hours/ns, 127.546 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8059.6 | 9003.4 | 10163 | 544.1 | 57.42 Bond | 2.1951 | 5.4353 | 9.6973 | 102.0 | 0.03 Kspace | 2888.9 | 4047.9 | 4992.1 | 811.1 | 25.81 Neigh | 501.83 | 502.44 | 503.04 | 1.3 | 3.20 Comm | 1051.8 | 1059.6 | 1066.5 | 10.7 | 6.76 Output | 0.010718 | 0.01297 | 0.015128 | 1.2 | 0.00 Modify | 1008.7 | 1014.1 | 1020.5 | 9.1 | 6.47 Other | | 47.7 | | | 0.30 Nlocal: 284.406 ave 299 max 264 min Histogram: 1 1 2 2 2 8 6 5 2 3 Nghost: 7375.5 ave 7430 max 7317 min Histogram: 1 1 5 4 4 3 4 7 1 2 Neighs: 160088 ave 177537 max 143722 min Histogram: 4 3 3 2 2 5 7 2 2 2 Total # of neighbors = 5122831 Ave neighs/atom = 562.88661 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98278 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25979226 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0025175327 estimated relative force accuracy = 7.5814749e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2111e-06 8304 2 103.7 9.58477e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13.09 | 13.58 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 2000000 2000000 2733.2928 92859.489 1.3074058 301.39993 50.557891 63.35363 0 0 22333.357 33658.475 -225.64505 -218001.62 -161895.88 5688.7697 Loop time of 8.394e-06 on 32 procs for 0 steps with 9101 atoms 121.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.394e-06 | | |100.00 Nlocal: 284.406 ave 299 max 264 min Histogram: 1 1 2 2 2 8 6 5 2 3 Nghost: 7375.5 ave 7430 max 7317 min Histogram: 1 1 5 4 4 3 4 7 1 2 Neighs: 160088 ave 177537 max 143722 min Histogram: 4 3 3 2 2 5 7 2 2 2 Total # of neighbors = 5122831 Ave neighs/atom = 562.88661 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out