#------------------------------------------------------------------------------- # 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 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 v_surfacetension 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 v_surfacetension 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 timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.1029e-12 8304 2 103.7 1.30839e-10 2768 Per MPI rank memory allocation (min/avg/max) = 11.91 | 13.13 | 13.54 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 -532.59891 192519.71 0.63061093 295.05328 49.918988 61.077957 0 0 20776.984 86759.947 -216.28484 -268025.54 -160377.61 5568.9799 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.58833e-06 8304 2 103.7 0.000117575 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.3403e-06 8304 2 103.7 9.78439e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.37042e-06 8304 2 103.7 0.000105286 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.30694e-06 8304 2 103.7 0.00010348 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.60441e-06 8304 2 103.7 8.98051e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.30779e-06 8304 2 103.7 9.63895e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.73617e-06 8304 2 103.7 0.000118378 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.48702e-06 8304 2 103.7 0.000101759 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 2.14231e-06 8304 2 103.7 0.000126431 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.06936e-06 8304 2 103.7 8.59804e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.14333e-06 8304 2 103.7 0.000107899 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.42833e-06 8304 2 103.7 9.27495e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.20542e-06 8304 2 103.7 0.00010777 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.13634e-06 8304 2 103.7 0.000108183 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.58937e-06 8304 2 103.7 0.000118402 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.32808e-06 8304 2 103.7 0.000100681 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.22214e-06 8304 2 103.7 9.99672e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.90257e-06 8304 2 103.7 0.000110166 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.26493e-06 8304 2 103.7 9.11396e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13168e-06 8304 2 103.7 9.36152e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.70586e-06 8304 2 103.7 0.000125397 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.47461e-06 8304 2 103.7 9.7359e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.25865e-06 8304 2 103.7 0.000105121 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.51755e-06 8304 2 103.7 0.00010244 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.2579e-06 8304 2 103.7 9.71832e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.20431e-06 8304 2 103.7 9.60241e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.24762e-06 8304 2 103.7 0.000111997 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.56897e-06 8304 2 103.7 9.41502e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.56036e-06 8304 2 103.7 0.000105025 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.69788e-06 8304 2 103.7 0.00012537 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.26489e-06 8304 2 103.7 9.35351e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.50552e-06 8304 2 103.7 0.000108503 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.15117e-06 8304 2 103.7 9.38141e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.19717e-06 8304 2 103.7 9.29135e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.36223e-06 8304 2 103.7 9.62785e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.14679e-06 8304 2 103.7 9.03646e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.47439e-06 8304 2 103.7 0.000106653 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.39254e-06 8304 2 103.7 0.000107942 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.15169e-06 8304 2 103.7 9.69174e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 2.20875e-06 8304 2 103.7 0.000169671 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.47254e-06 8304 2 103.7 0.000107658 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.16852e-06 8304 2 103.7 9.42007e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.17425e-06 8304 2 103.7 0.000115675 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.6968e-06 8304 2 103.7 0.000145929 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.19095e-06 8304 2 103.7 0.000116642 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.41048e-06 8304 2 103.7 0.00011455 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.09186e-06 8304 2 103.7 9.33354e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.26887e-06 8304 2 103.7 9.6436e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27929e-06 8304 2 103.7 9.70898e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.12761e-06 8304 2 103.7 9.28413e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.29054e-06 8304 2 103.7 0.000113849 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.08088e-06 8304 2 103.7 0.000106354 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.54814e-06 8304 2 103.7 0.000103395 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.47919e-06 8304 2 103.7 0.000108125 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.25827e-06 8304 2 103.7 9.83347e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.39142e-06 8304 2 103.7 0.000103584 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.38229e-06 8304 2 103.7 9.34214e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.72497e-06 8304 2 103.7 0.000100598 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.34248e-06 8304 2 103.7 0.00010362 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.02928e-06 8304 2 103.7 8.754e-05 2768 3000000 3000000 -418.24326 192519.71 0.63061093 299.67087 48.917423 52.834566 0 0 20967.695 86599.924 -216.28484 -268018.9 -160349.53 5656.1346 Loop time of 24804.4 on 32 procs for 3000000 steps with 9101 atoms Performance: 10.450 ns/day, 2.297 hours/ns, 120.946 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 266.01 | 6004.7 | 12371 |7129.1 | 24.21 Bond | 2.8711 | 7.6985 | 20.96 | 182.0 | 0.03 Kspace | 9640.9 | 16023 | 21813 |4389.3 | 64.60 Neigh | 776.74 | 782.8 | 792.31 | 20.0 | 3.16 Comm | 428.01 | 688.29 | 874.55 | 648.9 | 2.77 Output | 0.014193 | 0.016196 | 0.018074 | 0.9 | 0.00 Modify | 1103.7 | 1236 | 1424.3 | 368.3 | 4.98 Other | | 61.55 | | | 0.25 Nlocal: 284.406 ave 565 max 0 min Histogram: 13 3 0 0 0 0 0 0 0 16 Nghost: 3147.53 ave 4763 max 1570 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74576.8 ave 161513 max 0 min Histogram: 16 0 0 0 0 0 0 0 8 8 Total # of neighbors = 2386457 Ave neighs/atom = 262.21921 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149978 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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.02928e-06 8304 2 103.7 8.754e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.91 | 13.13 | 13.54 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 -417.82366 192519.71 0.63061093 299.67087 48.917423 52.834566 0 0 20967.695 86599.924 -216.28484 -268018.9 -160349.53 5656.1346 Loop time of 1.21119e-05 on 32 procs for 0 steps with 9101 atoms 107.1% 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 | | 1.211e-05 | | |100.00 Nlocal: 284.406 ave 565 max 0 min Histogram: 13 3 0 0 0 0 0 0 0 16 Nghost: 3147.53 ave 4763 max 1570 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74576.8 ave 161513 max 0 min Histogram: 16 0 0 0 0 0 0 0 8 8 Total # of neighbors = 2386457 Ave neighs/atom = 262.21921 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 18:18:59