#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 200 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 20000 20000 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 20 1 20 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 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 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 0.992743 0.752798 8436 2 96.6024 39.773 2812 Per MPI rank memory allocation (min/avg/max) = 13.92 | 14.03 | 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 24554.333 93962.523 1.2789064 429.73544 369.51207 354.0537 0 0 24972.134 64435.033 -220.49494 -203923.09 -113792.35 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.11361e-06 8436 2 103.7 9.36979e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.18448e-06 8436 2 103.7 0.000100736 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.1296e-06 8436 2 103.7 0.000101381 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19899e-06 8436 2 103.7 9.17686e-05 2812 200000 200000 1890.2108 93962.523 1.2789064 302.0573 41.655454 74.396805 0 0 19536.945 46190.314 -220.49494 -206927.8 -141084.49 5739.8934 Loop time of 2462.8 on 16 procs for 200000 steps with 9188 atoms Performance: 7.016 ns/day, 3.421 hours/ns, 81.208 timesteps/s 99.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1672.7 | 1724.4 | 1775.1 | 69.5 | 70.02 Bond | 0.30424 | 0.95795 | 1.4329 | 27.3 | 0.04 Kspace | 402.14 | 452.22 | 503.39 | 135.9 | 18.36 Neigh | 98.331 | 98.371 | 98.401 | 0.2 | 3.99 Comm | 80.008 | 81.542 | 83.134 | 10.6 | 3.31 Output | 0.016787 | 0.018543 | 0.020166 | 0.8 | 0.00 Modify | 98.465 | 99.067 | 100.1 | 5.2 | 4.02 Other | | 6.263 | | | 0.25 Nlocal: 574.25 ave 591 max 555 min Histogram: 1 0 0 5 2 3 1 0 2 2 Nghost: 9044.88 ave 9120 max 8884 min Histogram: 1 0 0 2 1 1 2 3 1 5 Neighs: 322536 ave 334535 max 306577 min Histogram: 1 0 2 0 2 5 2 0 1 3 Total # of neighbors = 5160571 Ave neighs/atom = 561.66424 Ave special neighs/atom = 1.9037875 Neighbor list builds = 9966 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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 200000 2 0.97 1.19899e-06 8436 2 103.7 9.17686e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.92 | 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 200000 200000 1891.0935 93962.523 1.2789064 302.0573 41.655454 74.396805 0 0 19536.945 46190.314 -220.49494 -206927.8 -141084.49 5739.8934 Loop time of 4.36244e-06 on 16 procs for 0 steps with 9188 atoms 126.1% 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 | | 4.362e-06 | | |100.00 Nlocal: 574.25 ave 591 max 555 min Histogram: 1 0 0 5 2 3 1 0 2 2 Nghost: 9044.88 ave 9120 max 8884 min Histogram: 1 0 0 2 1 1 2 3 1 5 Neighs: 322536 ave 334535 max 306577 min Histogram: 1 0 2 0 2 5 2 0 1 3 Total # of neighbors = 5160571 Ave neighs/atom = 561.66424 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