#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 2812 = # 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_1 subset_solution1 group/group subset_NaCl pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_solution1_NaCl_1.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25903784 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027883831 estimated relative force accuracy = 8.397133e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 16 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.4573e-10 8436 2 103.7 1.61451e-08 2812 Per MPI rank memory allocation (min/avg/max) = 12.71 | 13.51 | 14.41 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 1763.03 187465.26 1.5728449 290.6352 54.225535 76.526449 0 0 49681.016 -133218.91 -450.24149 -384167.65 -467574.79 8641.625 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33692e-06 8436 2 103.7 9.77694e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.27997e-06 8436 2 103.7 0.000100976 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.25614e-06 8436 2 103.7 9.43976e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.454e-06 8436 2 103.7 0.000111609 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.53518e-06 8436 2 103.7 0.000102647 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.42854e-06 8436 2 103.7 9.73996e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.51956e-06 8436 2 103.7 0.000108309 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16646e-06 8436 2 103.7 9.45444e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.1388e-06 8436 2 103.7 9.91505e-05 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34378e-06 8436 2 103.7 0.00010166 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.26222e-06 8436 2 103.7 8.90165e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21738e-06 8436 2 103.7 9.42884e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.10623e-06 8436 2 103.7 0.00010671 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.22007e-06 8436 2 103.7 0.000109576 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.46971e-06 8436 2 103.7 0.000110885 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.56374e-06 8436 2 103.7 0.000101396 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.09295e-06 8436 2 103.7 0.000103632 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.04076e-06 8436 2 103.7 0.000103137 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.48768e-06 8436 2 103.7 9.3737e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.27031e-06 8436 2 103.7 9.6077e-05 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.37716e-06 8436 2 103.7 0.000105933 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.12061e-06 8436 2 103.7 9.47587e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.15235e-06 8436 2 103.7 0.000114116 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.37743e-06 8436 2 103.7 0.000103082 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.34656e-06 8436 2 103.7 9.21285e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.2824e-06 8436 2 103.7 9.66813e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.18904e-06 8436 2 103.7 9.48924e-05 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.18941e-06 8436 2 103.7 9.23248e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.20163e-06 8436 2 103.7 9.50194e-05 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.61347e-06 8436 2 103.7 0.000110277 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.40496e-06 8436 2 103.7 0.000111624 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.19396e-06 8436 2 103.7 0.000111821 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.3681e-06 8436 2 103.7 9.43289e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.18686e-06 8436 2 103.7 9.4601e-05 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.55609e-06 8436 2 103.7 0.000109705 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19568e-06 8436 2 103.7 0.000116026 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.19199e-06 8436 2 103.7 9.59404e-05 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.07813e-06 8436 2 103.7 8.99463e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.13438e-06 8436 2 103.7 9.47857e-05 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11941e-06 8436 2 103.7 9.31222e-05 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.08713e-06 8436 2 103.7 9.47894e-05 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.37375e-06 8436 2 103.7 0.000105978 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.52061e-06 8436 2 103.7 0.000111808 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.28957e-06 8436 2 103.7 9.91114e-05 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.3483e-06 8436 2 103.7 9.60197e-05 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.19756e-06 8436 2 103.7 9.79131e-05 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.19888e-06 8436 2 103.7 9.46411e-05 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.2222e-06 8436 2 103.7 9.08937e-05 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.32502e-06 8436 2 103.7 0.000103664 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.27731e-06 8436 2 103.7 9.73544e-05 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.15883e-06 8436 2 103.7 9.16297e-05 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34255e-06 8436 2 103.7 9.58853e-05 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.17967e-06 8436 2 103.7 9.42832e-05 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.1021e-06 8436 2 103.7 8.90639e-05 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.32202e-06 8436 2 103.7 0.000102792 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.22359e-06 8436 2 103.7 9.49559e-05 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.66188e-06 8436 2 103.7 0.000125984 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.19524e-06 8436 2 103.7 9.6105e-05 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.17709e-06 8436 2 103.7 9.68909e-05 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10811e-06 8436 2 103.7 9.6112e-05 2812 3000000 3000000 1532.2012 187465.26 1.5728449 294.14517 42.686136 72.130201 0 0 49414.324 -133242.92 -450.24149 -384166.67 -467880.44 8745.9891 Loop time of 54259 on 32 procs for 3000000 steps with 12788 atoms Performance: 4.777 ns/day, 5.024 hours/ns, 55.290 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 | 4459.5 | 15576 | 26620 |7313.5 | 28.71 Bond | 3.4287 | 9.0613 | 20.901 | 171.2 | 0.02 Kspace | 8042.3 | 19131 | 30238 |6630.2 | 35.26 Neigh | 2117.7 | 2122.8 | 2131.3 | 9.5 | 3.91 Comm | 956.73 | 1283.3 | 1471.2 | 508.6 | 2.37 Output | 0.01406 | 0.016725 | 0.019425 | 1.2 | 0.00 Modify | 15908 | 16046 | 16262 | 105.5 | 29.57 Other | | 91.17 | | | 0.17 Nlocal: 399.625 ave 564 max 200 min Histogram: 4 8 0 4 0 0 0 0 1 15 Nghost: 6316.59 ave 8708 max 3646 min Histogram: 4 4 0 4 4 3 1 4 0 8 Neighs: 175636 ave 303962 max 46024 min Histogram: 12 0 0 1 3 1 3 0 0 12 Total # of neighbors = 5620352 Ave neighs/atom = 439.50203 Ave special neighs/atom = 1.3678449 Neighbor list builds = 148991 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25903784 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027883831 estimated relative force accuracy = 8.397133e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10811e-06 8436 2 103.7 9.6112e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.09 | 14.59 | 15.95 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 3000000 3000000 1532.6095 187465.26 1.5728449 294.14517 42.686136 72.130201 0 0 49414.324 -133242.92 -450.24149 -384166.67 -467880.44 8745.9891 Loop time of 7.26513e-06 on 32 procs for 0 steps with 12788 atoms 130.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.265e-06 | | |100.00 Nlocal: 399.625 ave 564 max 200 min Histogram: 4 8 0 4 0 0 0 0 1 15 Nghost: 6316.59 ave 8708 max 3646 min Histogram: 4 4 0 4 4 3 1 4 0 8 Neighs: 175636 ave 303962 max 46024 min Histogram: 12 0 0 1 3 1 3 0 0 12 Total # of neighbors = 5620352 Ave neighs/atom = 439.50203 Ave special neighs/atom = 1.3678449 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 26:42:06