#------------------------------------------------------------------------------- # Stage 2.4: 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 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 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 2.4_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 2.4_instantaneous.txt restart 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24986972 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035923427 estimated relative force accuracy = 1.0818233e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00147 0.117624 8304 2 97.6153 10.1648 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.61 | 14.13 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-06 693.23917 195628.7 0.62058908 428.55654 8.6669946 24.734343 0 0 26079.215 8899.5292 -107.10742 -209790.47 -174778.32 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20281e-06 8304 2 103.7 9.65271e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.22243e-06 8304 2 103.7 0.000100917 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.37371e-06 8304 2 103.7 0.000114223 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39124e-06 8304 2 103.7 0.000105903 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.1678e-06 8304 2 103.7 0.0001005 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.18508e-06 8304 2 103.7 0.000100933 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.31505e-06 8304 2 103.7 9.823e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.34183e-06 8304 2 103.7 0.000109762 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.41872e-06 8304 2 103.7 0.000118025 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21168e-06 8304 2 103.7 0.000102977 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25529e-06 8304 2 103.7 0.000106899 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.91537e-06 8304 2 103.7 0.000136787 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.07107e-06 8304 2 103.7 0.000101127 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20651e-06 8304 2 103.7 0.000100635 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.67911e-06 8304 2 103.7 0.00011209 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.34195e-06 8304 2 103.7 9.89581e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.32128e-06 8304 2 103.7 0.000102399 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17062e-06 8304 2 103.7 9.91135e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.21303e-06 8304 2 103.7 0.000111085 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.10377e-06 8304 2 103.7 9.45548e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.28714e-06 8304 2 103.7 9.7827e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.2563e-06 8304 2 103.7 9.09732e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.10049e-06 8304 2 103.7 0.000105453 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.42773e-06 8304 2 103.7 9.53916e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.31888e-06 8304 2 103.7 9.10629e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.04161e-06 8304 2 103.7 9.05927e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.20139e-06 8304 2 103.7 0.000101286 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.48305e-06 8304 2 103.7 9.61891e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.29633e-06 8304 2 103.7 8.66993e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.11155e-06 8304 2 103.7 9.37315e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.19183e-06 8304 2 103.7 0.000104268 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.01043e-06 8304 2 103.7 0.000108942 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.5595e-06 8304 2 103.7 0.000118268 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29327e-06 8304 2 103.7 0.000125167 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.51245e-06 8304 2 103.7 0.000103618 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.12376e-06 8304 2 103.7 9.69098e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.21917e-06 8304 2 103.7 9.18133e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.63748e-06 8304 2 103.7 0.000121696 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.23231e-06 8304 2 103.7 8.82304e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.16711e-06 8304 2 103.7 9.00247e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.286e-06 8304 2 103.7 0.000103324 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.53091e-06 8304 2 103.7 0.000117505 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.19091e-06 8304 2 103.7 9.87965e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.43335e-06 8304 2 103.7 0.000106642 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.2817e-06 8304 2 103.7 0.000124202 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.55661e-06 8304 2 103.7 0.000110598 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.10976e-06 8304 2 103.7 9.38597e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.07285e-06 8304 2 103.7 9.35013e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.78003e-06 8304 2 103.7 0.000120343 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.43013e-06 8304 2 103.7 9.51672e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.63649e-06 8304 2 103.7 0.000139663 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.27334e-06 8304 2 103.7 8.9866e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.22018e-06 8304 2 103.7 9.17798e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.50797e-06 8304 2 103.7 0.000134399 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.15572e-06 8304 2 103.7 9.07234e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.56262e-06 8304 2 103.7 0.000102105 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.34391e-06 8304 2 103.7 0.000105582 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.19261e-06 8304 2 103.7 9.5663e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.67205e-06 8304 2 103.7 0.000154277 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.16338e-06 8304 2 103.7 0.00011856 2768 3000000 3000000 -145.39281 195628.7 0.62058908 297.92389 51.52059 74.933334 0 0 21097.666 27886.39 -107.10742 -209745.24 -160634.73 5623.1613 Loop time of 34882.8 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.431 ns/day, 3.230 hours/ns, 86.002 timesteps/s 98.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7463 | 10962 | 25305 |9904.8 | 31.43 Bond | 2.7971 | 7.2269 | 18.027 | 165.4 | 0.02 Kspace | 5620.7 | 20037 | 31158 |7366.6 | 57.44 Neigh | 1813.1 | 1820.2 | 1834 | 15.2 | 5.22 Comm | 254 | 660.88 | 905.42 | 907.5 | 1.89 Output | 0.014004 | 0.016265 | 0.018365 | 1.0 | 0.00 Modify | 1143.6 | 1328.6 | 1577.9 | 474.5 | 3.81 Other | | 67.24 | | | 0.19 Nlocal: 284.406 ave 579 max 0 min Histogram: 12 0 0 3 1 1 3 0 0 12 Nghost: 4489.41 ave 8872 max 6 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133227 ave 310710 max 0 min Histogram: 12 4 0 0 0 1 3 3 1 8 Total # of neighbors = 4263260 Ave neighs/atom = 468.43863 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149888 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24986972 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035923427 estimated relative force accuracy = 1.0818233e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.16338e-06 8304 2 103.7 0.00011856 2768 Per MPI rank memory allocation (min/avg/max) = 11.18 | 12.73 | 14.12 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 -144.91655 195628.7 0.62058908 297.92389 51.52059 74.933334 0 0 21097.666 27886.39 -107.10742 -209745.24 -160634.73 5623.1613 Loop time of 1.14955e-05 on 32 procs for 0 steps with 9101 atoms 119.3% 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 | | 1.15e-05 | | |100.00 Nlocal: 284.406 ave 579 max 0 min Histogram: 12 0 0 3 1 1 3 0 0 12 Nghost: 4489.41 ave 8872 max 6 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133227 ave 310710 max 0 min Histogram: 12 4 0 0 0 1 3 3 1 8 Total # of neighbors = 4263260 Ave neighs/atom = 468.43863 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_NVT.out