#------------------------------------------------------------------------------- # 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 1937 = # 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) = 0.25433811 grid = 25 25 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0037697153 estimated relative force accuracy = 1.1352386e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4199 1250 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.998682 0.744971 5811 2 97.2809 57.7356 1937 Per MPI rank memory allocation (min/avg/max) = 12.7 | 12.76 | 12.94 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 29890.267 65046.256 1.3074059 428.49853 71.082664 538.56799 0 0 20093.498 38209.919 -158.00458 -146866.6 -87953.53 5662.15 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.39867e-06 5811 2 103.7 9.5839e-05 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.07915e-06 5811 2 103.7 0.000105221 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32088e-06 5811 2 103.7 0.000105531 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.31766e-06 5811 2 103.7 0.000127286 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.22192e-06 5811 2 103.7 9.57694e-05 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.25495e-06 5811 2 103.7 9.43507e-05 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.50121e-06 5811 2 103.7 0.000112668 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.15482e-06 5811 2 103.7 0.000109702 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.38004e-06 5811 2 103.7 0.000100179 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39651e-06 5811 2 103.7 9.35556e-05 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.31104e-06 5811 2 103.7 8.73859e-05 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.31051e-06 5811 2 103.7 9.89593e-05 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.32318e-06 5811 2 103.7 0.000103684 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.56177e-06 5811 2 103.7 0.000110438 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26928e-06 5811 2 103.7 0.000111795 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.64224e-06 5811 2 103.7 0.000124507 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12798e-06 5811 2 103.7 9.83251e-05 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.31807e-06 5811 2 103.7 0.000102313 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.13517e-06 5811 2 103.7 9.42428e-05 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.16662e-06 5811 2 103.7 0.000105245 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.49133e-06 5811 2 103.7 0.000115581 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.21071e-06 5811 2 103.7 8.75313e-05 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.55677e-06 5811 2 103.7 0.000115947 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.08368e-06 5811 2 103.7 9.16033e-05 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.4714e-06 5811 2 103.7 0.000107554 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.8822e-06 5811 2 103.7 0.00012756 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.15974e-06 5811 2 103.7 9.51833e-05 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29046e-06 5811 2 103.7 9.06945e-05 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.07195e-06 5811 2 103.7 8.93868e-05 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.36026e-06 5811 2 103.7 0.000113304 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.31646e-06 5811 2 103.7 0.000116583 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.68818e-06 5811 2 103.7 0.000100649 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.09712e-06 5811 2 103.7 9.00426e-05 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.1548e-06 5811 2 103.7 9.55322e-05 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.12868e-06 5811 2 103.7 0.000102641 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.27945e-06 5811 2 103.7 0.000100272 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.36009e-06 5811 2 103.7 9.13705e-05 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.2879e-06 5811 2 103.7 9.31138e-05 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.65763e-06 5811 2 103.7 0.000119959 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3311e-06 5811 2 103.7 0.000113563 1937 2000000 2000000 2492.7036 65046.256 1.3074059 298.79439 36.254942 57.044099 0 0 15533.257 20463.18 -158.00458 -149496.03 -113406.29 3948.2484 Loop time of 10666.5 on 32 procs for 2000000 steps with 6371 atoms Performance: 16.200 ns/day, 1.481 hours/ns, 187.502 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 | 5902.1 | 6227.1 | 6422.5 | 163.8 | 58.38 Bond | 2.19 | 4.4675 | 8.5409 | 83.0 | 0.04 Kspace | 2202.6 | 2389.3 | 2726.2 | 264.9 | 22.40 Neigh | 345.71 | 347.48 | 349.23 | 7.2 | 3.26 Comm | 860.86 | 877.39 | 894.67 | 33.9 | 8.23 Output | 0.010706 | 0.012601 | 0.014376 | 1.0 | 0.00 Modify | 781.68 | 786.51 | 790.28 | 7.1 | 7.37 Other | | 34.34 | | | 0.32 Nlocal: 199.094 ave 214 max 184 min Histogram: 1 2 3 4 3 9 3 4 0 3 Nghost: 6604.75 ave 6676 max 6545 min Histogram: 2 3 6 5 1 4 4 4 2 1 Neighs: 111980 ave 121258 max 102128 min Histogram: 2 1 3 2 5 9 5 1 2 2 Total # of neighbors = 3583373 Ave neighs/atom = 562.45064 Ave special neighs/atom = 1.8932664 Neighbor list builds = 95432 Dangerous builds = 1 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) = 0.25433811 grid = 25 25 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0037697153 estimated relative force accuracy = 1.1352386e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4199 1250 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3311e-06 5811 2 103.7 0.000113563 1937 Per MPI rank memory allocation (min/avg/max) = 12.7 | 12.85 | 12.95 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 2493.8316 65046.256 1.3074059 298.79439 36.254942 57.044099 0 0 15533.257 20463.18 -158.00458 -149496.03 -113406.29 3948.2484 Loop time of 7.33159e-06 on 32 procs for 0 steps with 6371 atoms 114.7% 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 | | 7.332e-06 | | |100.00 Nlocal: 199.094 ave 214 max 184 min Histogram: 1 2 3 4 3 9 3 4 0 3 Nghost: 6604.75 ave 6676 max 6545 min Histogram: 2 3 6 5 1 4 4 4 2 1 Neighs: 111980 ave 121258 max 102128 min Histogram: 2 1 3 2 5 9 5 1 2 2 Total # of neighbors = 3583373 Ave neighs/atom = 562.45064 Ave special neighs/atom = 1.8932664 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out