#------------------------------------------------------------------------------- # Stage 2.5: 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25563703 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0025705484 estimated relative force accuracy = 7.7411303e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 4.21121e-11 6600 1 103.7 4.02542e-09 2200 Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.41 | 12.42 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 21.65541 66053.388 0.99636723 294.93528 0 0 0 0 5823.1649 86094.881 -114.26037 -115746.19 -23828.147 3867.3634 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.09503e-06 6600 1 103.7 8.56732e-05 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.14979e-06 6600 1 103.7 0.000107727 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.17234e-06 6600 1 103.7 0.000106652 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.74362e-06 6600 1 103.7 9.94967e-05 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.18399e-06 6600 1 103.7 0.000107866 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.38845e-06 6600 1 103.7 0.000109916 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.98805e-06 6600 1 103.7 0.000153735 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.58634e-06 6600 1 103.7 0.000130543 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.16545e-06 6600 1 103.7 0.000113319 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.19619e-06 6600 1 103.7 9.49433e-05 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.17285e-06 6600 1 103.7 9.61492e-05 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.52109e-06 6600 1 103.7 0.000123031 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.20201e-06 6600 1 103.7 9.64156e-05 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.47739e-06 6600 1 103.7 0.00010705 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.59718e-06 6600 1 103.7 0.00010327 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.17677e-06 6600 1 103.7 9.29587e-05 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.50943e-06 6600 1 103.7 0.000120499 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.2099e-06 6600 1 103.7 0.000100985 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.26922e-06 6600 1 103.7 0.000121692 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.83948e-06 6600 1 103.7 0.00013014 2200 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.46785e-06 6600 1 103.7 9.44562e-05 2200 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.4729e-06 6600 1 103.7 0.000101338 2200 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.26416e-06 6600 1 103.7 9.18898e-05 2200 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.18052e-06 6600 1 103.7 9.90322e-05 2200 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.43022e-06 6600 1 103.7 0.000111185 2200 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.30013e-06 6600 1 103.7 0.000123477 2200 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.19084e-06 6600 1 103.7 9.39175e-05 2200 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.36899e-06 6600 1 103.7 9.26054e-05 2200 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.25223e-06 6600 1 103.7 9.30311e-05 2200 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.54964e-06 6600 1 103.7 0.000111099 2200 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.50065e-06 6600 1 103.7 0.000102613 2200 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.41778e-06 6600 1 103.7 0.000100873 2200 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.23018e-06 6600 1 103.7 9.99557e-05 2200 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 2.02255e-06 6600 1 103.7 0.000164052 2200 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.32058e-06 6600 1 103.7 9.89829e-05 2200 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.14531e-06 6600 1 103.7 9.7447e-05 2200 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.17742e-06 6600 1 103.7 9.06633e-05 2200 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.19649e-06 6600 1 103.7 9.24458e-05 2200 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37228e-06 6600 1 103.7 9.82819e-05 2200 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.63131e-06 6600 1 103.7 0.000109268 2200 2000000 2000000 68.856451 66053.388 0.99636723 296.8141 0 0 0 0 5625.2498 86496.684 -114.26037 -115733.53 -23611.598 3891.9997 Loop time of 33765.5 on 8 procs for 2000000 steps with 6600 atoms Performance: 5.118 ns/day, 4.690 hours/ns, 59.232 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23430 | 24763 | 26576 | 603.0 | 73.34 Bond | 2.3454 | 2.564 | 2.7557 | 8.6 | 0.01 Kspace | 4500 | 6316.5 | 7655.4 |1196.0 | 18.71 Neigh | 1501 | 1502.1 | 1503.4 | 2.6 | 4.45 Comm | 440.43 | 446.89 | 452.78 | 23.3 | 1.32 Output | 0.015983 | 0.017043 | 0.01795 | 0.5 | 0.00 Modify | 685.13 | 685.87 | 687.04 | 2.1 | 2.03 Other | | 48.25 | | | 0.14 Nlocal: 825 ave 841 max 810 min Histogram: 1 0 2 0 2 0 1 0 1 1 Nghost: 10403.2 ave 10446 max 10347 min Histogram: 1 0 0 0 3 0 2 0 0 2 Neighs: 473354 ave 507978 max 441669 min Histogram: 2 0 1 1 1 0 0 1 0 2 Total # of neighbors = 3786829 Ave neighs/atom = 573.76197 Ave special neighs/atom = 2 Neighbor list builds = 99323 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25563703 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0025705484 estimated relative force accuracy = 7.7411303e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.63131e-06 6600 1 103.7 0.000109268 2200 Per MPI rank memory allocation (min/avg/max) = 12.38 | 12.41 | 12.42 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 69.305176 66053.388 0.99636723 296.8141 0 0 0 0 5625.2498 86496.684 -114.26037 -115733.53 -23611.598 3891.9997 Loop time of 3.715e-06 on 8 procs for 0 steps with 6600 atoms 121.1% CPU use with 8 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 | | 3.715e-06 | | |100.00 Nlocal: 825 ave 841 max 810 min Histogram: 1 0 2 0 2 0 1 0 1 1 Nghost: 10403.2 ave 10446 max 10347 min Histogram: 1 0 0 0 3 0 2 0 0 2 Neighs: 473354 ave 507978 max 441669 min Histogram: 2 0 1 1 1 0 0 1 0 2 Total # of neighbors = 3786829 Ave neighs/atom = 573.76197 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 18:15:06