#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3659 = # 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 fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.37885e-13 10977 2 103.7 8.80789e-11 3659 Per MPI rank memory allocation (min/avg/max) = 17.45 | 20.67 | 29.39 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 337770.13 142807.9 1.3823791 300.25952 284.80766 384.58859 0 0 273024.45 -65012.345 -383.2647 -382416.63 -173735.14 8160.7613 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.16125e-06 10977 2 103.7 9.25812e-05 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.17825e-06 10977 2 103.7 9.61927e-05 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.67572e-06 10977 2 103.7 0.000131175 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.14341e-06 10977 2 103.7 9.19314e-05 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.51211e-06 10977 2 103.7 8.99862e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.14485e-06 10977 2 103.7 9.85079e-05 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.20448e-06 10977 2 103.7 9.55557e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.14785e-06 10977 2 103.7 9.58825e-05 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.2506e-06 10977 2 103.7 9.77903e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.4419e-06 10977 2 103.7 0.000103201 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.1675e-06 10977 2 103.7 9.51658e-05 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.07096e-06 10977 2 103.7 0.000103087 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.38573e-06 10977 2 103.7 9.21168e-05 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.53328e-06 10977 2 103.7 0.000117912 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.22e-06 10977 2 103.7 0.000103032 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.19469e-06 10977 2 103.7 0.000101701 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.36748e-06 10977 2 103.7 9.12925e-05 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.39904e-06 10977 2 103.7 9.24631e-05 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.74924e-06 10977 2 103.7 0.000118225 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.53572e-06 10977 2 103.7 0.00012123 3659 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.24253e-06 10977 2 103.7 0.000108007 3659 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.0912e-06 10977 2 103.7 9.2382e-05 3659 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.30495e-06 10977 2 103.7 0.000110403 3659 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.11208e-06 10977 2 103.7 0.000101119 3659 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.19144e-06 10977 2 103.7 0.000102467 3659 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.21303e-06 10977 2 103.7 9.99566e-05 3659 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.60686e-06 10977 2 103.7 0.000107115 3659 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.27944e-06 10977 2 103.7 8.9691e-05 3659 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.23258e-06 10977 2 103.7 0.000106775 3659 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.72216e-06 10977 2 103.7 0.000101662 3659 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.36234e-06 10977 2 103.7 9.60658e-05 3659 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.3224e-06 10977 2 103.7 0.000103692 3659 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.24677e-06 10977 2 103.7 9.35915e-05 3659 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.36727e-06 10977 2 103.7 0.000103524 3659 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.33286e-06 10977 2 103.7 0.000102031 3659 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.5537e-06 10977 2 103.7 9.14634e-05 3659 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.23803e-06 10977 2 103.7 9.534e-05 3659 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.17981e-06 10977 2 103.7 9.90742e-05 3659 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.58335e-06 10977 2 103.7 0.000107617 3659 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.3306e-06 10977 2 103.7 0.000104343 3659 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.3173e-06 10977 2 103.7 0.000101189 3659 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.28696e-06 10977 2 103.7 9.70258e-05 3659 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.46907e-06 10977 2 103.7 9.00742e-05 3659 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.24777e-06 10977 2 103.7 9.0049e-05 3659 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.13391e-06 10977 2 103.7 9.98229e-05 3659 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.28705e-06 10977 2 103.7 0.000106958 3659 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.27754e-06 10977 2 103.7 9.03331e-05 3659 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.2147e-06 10977 2 103.7 9.35752e-05 3659 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.34881e-06 10977 2 103.7 9.38637e-05 3659 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.15599e-06 10977 2 103.7 9.4951e-05 3659 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.4677e-06 10977 2 103.7 0.000101379 3659 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 9.83482e-07 10977 2 103.7 0.000106074 3659 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.05106e-06 10977 2 103.7 9.19993e-05 3659 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.13094e-06 10977 2 103.7 9.21829e-05 3659 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.19041e-06 10977 2 103.7 9.40734e-05 3659 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.76963e-06 10977 2 103.7 0.000117656 3659 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.44956e-06 10977 2 103.7 0.000106189 3659 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.43891e-06 10977 2 103.7 9.65701e-05 3659 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.45465e-06 10977 2 103.7 0.000114591 3659 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.29463e-06 10977 2 103.7 9.36309e-05 3659 3000000 3000000 337507.24 142807.9 1.3823791 298.90439 258.55894 363.60291 0 0 272761.51 -64800.251 -383.2647 -382430.62 -173847.2 8123.9302 Loop time of 103858 on 8 procs for 3000000 steps with 13738 atoms Performance: 2.496 ns/day, 9.616 hours/ns, 28.886 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50689 | 61586 | 84729 |5412.6 | 59.30 Bond | 17.508 | 56.403 | 147.18 | 696.6 | 0.05 Kspace | 11852 | 35099 | 46048 |7201.1 | 33.80 Neigh | 4580.1 | 4583.1 | 4586.4 | 3.3 | 4.41 Comm | 842.73 | 886.41 | 930.9 | 104.1 | 0.85 Output | 0.029976 | 0.033435 | 0.036499 | 1.2 | 0.00 Modify | 1508.8 | 1524.8 | 1545.1 | 32.5 | 1.47 Other | | 122 | | | 0.12 Nlocal: 1717.25 ave 2069 max 1558 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13681 ave 14424 max 12400 min Histogram: 2 0 0 0 0 0 1 2 1 2 Neighs: 960476 ave 1.34578e+06 max 774584 min Histogram: 2 4 0 0 0 0 0 0 0 2 Total # of neighbors = 7683806 Ave neighs/atom = 559.31038 Ave special neighs/atom = 1.8702868 Neighbor list builds = 149754 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.29463e-06 10977 2 103.7 9.36309e-05 3659 Per MPI rank memory allocation (min/avg/max) = 17.45 | 20.72 | 29.39 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 337508.2 142807.9 1.3823791 298.90439 258.55894 363.60291 0 0 272761.51 -64800.251 -383.2647 -382430.62 -173847.2 8123.9302 Loop time of 3.03062e-06 on 8 procs for 0 steps with 13738 atoms 140.2% CPU use with 8 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 | | 3.031e-06 | | |100.00 Nlocal: 1717.25 ave 2069 max 1558 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13681 ave 14424 max 12400 min Histogram: 2 0 0 0 0 0 1 2 1 2 Neighs: 960476 ave 1.34578e+06 max 774584 min Histogram: 2 4 0 0 0 0 0 0 0 2 Total # of neighbors = 7683806 Ave neighs/atom = 559.31038 Ave special neighs/atom = 1.8702868 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out