#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 ps 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 2812 = # 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 1000 1000 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 1 1 1 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 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.991932 0.808629 8436 2 97.0726 46.0985 2812 Per MPI rank memory allocation (min/avg/max) = 13.91 | 14.04 | 14.18 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 13941.586 93962.523 1.2789064 429.73544 29.024937 169.45257 0 0 22332.819 52597.326 -220.49494 -205873.42 -130744.8 8166.1181 10000 10000 2227.8636 93962.523 1.2789064 295.33481 44.303622 99.288148 0 0 19656.797 46379.805 -220.49494 -206909.64 -140729.45 5612.1482 Loop time of 131.025 on 16 procs for 10000 steps with 9188 atoms Performance: 6.594 ns/day, 3.640 hours/ns, 76.321 timesteps/s 99.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 83.176 | 87.932 | 94.848 | 29.9 | 67.11 Bond | 0.018087 | 0.051627 | 0.075784 | 7.1 | 0.04 Kspace | 20.481 | 27.427 | 32.244 | 54.0 | 20.93 Neigh | 5.3152 | 5.3243 | 5.3274 | 0.2 | 4.06 Comm | 4.0676 | 4.1016 | 4.1586 | 1.4 | 3.13 Output | 0.015164 | 0.016908 | 0.018403 | 0.8 | 0.01 Modify | 5.5984 | 5.6334 | 5.9397 | 3.3 | 4.30 Other | | 0.538 | | | 0.41 Nlocal: 574.25 ave 600 max 545 min Histogram: 1 0 2 1 1 3 6 1 0 1 Nghost: 9005 ave 9088 max 8947 min Histogram: 3 1 2 1 4 1 1 1 1 1 Neighs: 322450 ave 336985 max 307073 min Histogram: 3 0 1 1 2 2 2 3 0 2 Total # of neighbors = 5159198 Ave neighs/atom = 561.5148 Ave special neighs/atom = 1.9037875 Neighbor list builds = 510 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.42346e-06 8436 2 103.7 0.000100145 2812 Per MPI rank memory allocation (min/avg/max) = 13.91 | 14.07 | 14.18 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 10000 10000 2228.6633 93962.523 1.2789064 295.33481 44.303622 99.288148 0 0 19656.797 46379.805 -220.49494 -206909.64 -140729.45 5612.1482 Loop time of 1.20278e-05 on 16 procs for 0 steps with 9188 atoms 113.8% CPU use with 16 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 | | 1.203e-05 | | |100.00 Nlocal: 574.25 ave 600 max 545 min Histogram: 1 0 2 1 1 3 6 1 0 1 Nghost: 9005 ave 9088 max 8947 min Histogram: 3 1 2 1 4 1 1 1 1 1 Neighs: 322450 ave 336985 max 307073 min Histogram: 3 0 1 1 2 2 2 3 0 2 Total # of neighbors = 5159198 Ave neighs/atom = 561.5148 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out