#------------------------------------------------------------------------------- # 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 = 0.002 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) = 0.2499137 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035866273 estimated relative force accuracy = 1.0801022e-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 1.00167 0.0827992 8304 2 97.5511 12.981 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.66 | 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-06 703.19832 195013.51 0.62254678 428.55654 7.8836461 23.48229 0 0 26172.676 8616.5817 -107.44529 -209788.93 -174968.31 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.55763e-06 8304 2 103.7 0.000113221 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.74401e-06 8304 2 103.7 0.000117113 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27491e-06 8304 2 103.7 9.65981e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.2834e-06 8304 2 103.7 0.000105092 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.14271e-06 8304 2 103.7 0.000105361 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.03935e-06 8304 2 103.7 9.397e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.35716e-06 8304 2 103.7 0.000117868 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.5286e-06 8304 2 103.7 0.000109035 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.37223e-06 8304 2 103.7 9.8823e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.05529e-06 8304 2 103.7 0.00010233 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.31467e-06 8304 2 103.7 0.000104033 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.97654e-06 8304 2 103.7 0.000152296 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.29069e-06 8304 2 103.7 0.000107934 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.26404e-06 8304 2 103.7 9.68595e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.28853e-06 8304 2 103.7 0.000100848 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.22035e-06 8304 2 103.7 9.20982e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.06829e-06 8304 2 103.7 8.889e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.22694e-06 8304 2 103.7 9.47279e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25043e-06 8304 2 103.7 0.000102486 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.34955e-06 8304 2 103.7 0.000104759 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.16818e-06 8304 2 103.7 8.84805e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.20459e-06 8304 2 103.7 0.000102855 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.04361e-06 8304 2 103.7 9.48196e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.25254e-06 8304 2 103.7 0.000102226 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.53485e-06 8304 2 103.7 0.000142866 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.25e-06 8304 2 103.7 8.99876e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.30919e-06 8304 2 103.7 0.00010041 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.16951e-06 8304 2 103.7 9.44363e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.30617e-06 8304 2 103.7 0.000107295 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.10379e-06 8304 2 103.7 9.68501e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.16659e-06 8304 2 103.7 9.17722e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.34704e-06 8304 2 103.7 0.000116436 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.41386e-06 8304 2 103.7 0.000132626 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.17588e-06 8304 2 103.7 0.000117438 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.36387e-06 8304 2 103.7 9.48738e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10834e-06 8304 2 103.7 9.73516e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.30314e-06 8304 2 103.7 0.000102033 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.26251e-06 8304 2 103.7 9.22236e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.4669e-06 8304 2 103.7 0.000112565 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.22492e-06 8304 2 103.7 0.000102733 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.2592e-06 8304 2 103.7 0.000111518 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.63432e-06 8304 2 103.7 0.000103096 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.04872e-06 8304 2 103.7 9.75655e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.42467e-06 8304 2 103.7 0.000105603 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.30943e-06 8304 2 103.7 0.00011093 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.3347e-06 8304 2 103.7 0.000115128 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.37508e-06 8304 2 103.7 0.000106402 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.14132e-06 8304 2 103.7 0.000111051 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.22939e-06 8304 2 103.7 8.84377e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.33093e-06 8304 2 103.7 0.000100208 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.16066e-06 8304 2 103.7 0.000109561 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.39939e-06 8304 2 103.7 0.000104308 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.24934e-06 8304 2 103.7 0.0001074 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.35453e-06 8304 2 103.7 0.00010597 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.23495e-06 8304 2 103.7 9.71161e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.1177e-06 8304 2 103.7 9.36846e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.21527e-06 8304 2 103.7 9.7674e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.14522e-06 8304 2 103.7 9.08925e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.08355e-06 8304 2 103.7 0.000109619 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.7714e-06 8304 2 103.7 0.000145694 2768 3000000 3000000 -13.189304 195013.51 0.62254678 302.01175 40.660402 63.640881 0 0 21292.916 27723.567 -107.44529 -209763.21 -160642.43 5700.3176 Loop time of 34966.4 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.413 ns/day, 3.238 hours/ns, 85.797 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 | 1.8247 | 10957 | 25627 |9819.6 | 31.34 Bond | 2.6153 | 6.9642 | 17.843 | 172.5 | 0.02 Kspace | 5345.5 | 20089 | 31197 |7293.3 | 57.45 Neigh | 1850.4 | 1856.2 | 1864.7 | 12.1 | 5.31 Comm | 265.68 | 654.43 | 896.18 | 893.1 | 1.87 Output | 0.015352 | 0.017629 | 0.019717 | 0.9 | 0.00 Modify | 1153 | 1336.7 | 1582.7 | 463.3 | 3.82 Other | | 66.25 | | | 0.19 Nlocal: 284.406 ave 583 max 0 min Histogram: 12 0 0 2 2 2 2 0 0 12 Nghost: 4488.75 ave 8888 max 9 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133486 ave 319314 max 0 min Histogram: 12 0 3 3 2 0 0 0 7 5 Total # of neighbors = 4271548 Ave neighs/atom = 469.3493 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149628 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) = 0.2499137 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035866273 estimated relative force accuracy = 1.0801022e-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 1.7714e-06 8304 2 103.7 0.000145694 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.81 | 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 -12.866081 195013.51 0.62254678 302.01175 40.660402 63.640881 0 0 21292.916 27723.567 -107.44529 -209763.21 -160642.43 5700.3176 Loop time of 8.07194e-06 on 32 procs for 0 steps with 9101 atoms 97.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.072e-06 | | |100.00 Nlocal: 284.406 ave 583 max 0 min Histogram: 12 0 0 2 2 2 2 0 0 12 Nghost: 4488.75 ave 8888 max 9 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133486 ave 319314 max 0 min Histogram: 12 0 3 3 2 0 0 0 7 5 Total # of neighbors = 4271548 Ave neighs/atom = 469.3493 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