#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 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 = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00484 0.0888843 10977 2 97.6686 10.155 3659 Per MPI rank memory allocation (min/avg/max) = 13.08 | 13.63 | 14.1 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 338573.63 142807.9 1.3823791 416.85345 44.268893 264.30648 0 0 277765.28 -89848.537 -383.2647 -382578.18 -194352.86 11329.671 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.13284e-06 10977 2 103.7 9.70459e-05 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.73623e-06 10977 2 103.7 0.000123716 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27181e-06 10977 2 103.7 9.54646e-05 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15465e-06 10977 2 103.7 9.69657e-05 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.4474e-06 10977 2 103.7 0.00010323 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.2941e-06 10977 2 103.7 9.50734e-05 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.1589e-06 10977 2 103.7 9.5486e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.46958e-06 10977 2 103.7 0.000112109 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.38658e-06 10977 2 103.7 9.17681e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.39079e-06 10977 2 103.7 9.45897e-05 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.42886e-06 10977 2 103.7 9.5993e-05 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.25605e-06 10977 2 103.7 0.000100516 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.3442e-06 10977 2 103.7 8.63207e-05 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.32958e-06 10977 2 103.7 0.000100276 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.35634e-06 10977 2 103.7 9.43876e-05 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.32206e-06 10977 2 103.7 9.12363e-05 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.13092e-06 10977 2 103.7 0.000114864 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.22505e-06 10977 2 103.7 9.95478e-05 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.11088e-06 10977 2 103.7 9.97738e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.28803e-06 10977 2 103.7 8.87949e-05 3659 1000000 1000000 338262.69 142807.9 1.3823791 300.48363 270.8173 390.18985 0 0 273407.92 -65423.48 -383.2647 -382454.94 -173809.49 8166.8523 Loop time of 12729.3 on 32 procs for 1000000 steps with 13738 atoms Performance: 6.787 ns/day, 3.536 hours/ns, 78.559 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5163.1 | 6479.6 | 9029.4 |1731.5 | 50.90 Bond | 1.3761 | 7.1392 | 18.189 | 214.6 | 0.06 Kspace | 1983.5 | 4549.3 | 5883.2 |2081.5 | 35.74 Neigh | 468.25 | 469.49 | 470.88 | 3.6 | 3.69 Comm | 507.27 | 552.26 | 603.69 | 127.0 | 4.34 Output | 0.016248 | 0.019231 | 0.022039 | 1.3 | 0.00 Modify | 603.67 | 641.83 | 671.81 | 89.9 | 5.04 Other | | 29.74 | | | 0.23 Nlocal: 429.312 ave 524 max 384 min Histogram: 10 10 3 1 0 0 0 0 1 7 Nghost: 8159.5 ave 8671 max 7393 min Histogram: 8 0 0 0 0 0 9 7 0 8 Neighs: 240067 ave 343048 max 187294 min Histogram: 7 14 3 0 0 0 0 0 1 7 Total # of neighbors = 7682144 Ave neighs/atom = 559.1894 Ave special neighs/atom = 1.8702868 Neighbor list builds = 49897 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25972621 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 = 8228 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.28803e-06 10977 2 103.7 8.87949e-05 3659 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.1 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 1000000 1000000 338263.68 142807.9 1.3823791 300.48363 270.8173 390.18985 0 0 273407.92 -65423.48 -383.2647 -382454.94 -173809.49 8166.8523 Loop time of 7.85884e-06 on 32 procs for 0 steps with 13738 atoms 113.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.859e-06 | | |100.00 Nlocal: 429.312 ave 524 max 384 min Histogram: 10 10 3 1 0 0 0 0 1 7 Nghost: 8159.5 ave 8671 max 7393 min Histogram: 8 0 0 0 0 0 9 7 0 8 Neighs: 240067 ave 343048 max 187294 min Histogram: 7 14 3 0 0 0 0 0 1 7 Total # of neighbors = 7682144 Ave neighs/atom = 559.1894 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 2.5_NVT.out