#------------------------------------------------------------------------------- # 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 2768 = # of frozen angles find clusters CPU = 0.002 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 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.999086 0.120343 8304 2 97.9807 15.9244 2768 Per MPI rank memory allocation (min/avg/max) = 11.5 | 11.63 | 12.12 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 5692.5718 87313.677 1.3904469 428.55654 13.355982 111.32773 0 0 23706.075 -171360.23 0 0 -147529.47 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.31915e-06 8304 2 103.7 0.000100411 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.65202e-06 8304 2 103.7 0.000123571 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.58334e-06 8304 2 103.7 0.000112151 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.46848e-06 8304 2 103.7 9.9973e-05 2768 200000 200000 989.89447 103346.52 1.1747375 294.67338 46.322387 153.36654 0 0 21108.701 -169659.25 0 0 -148350.86 5561.8096 Loop time of 626.281 on 32 procs for 200000 steps with 9101 atoms Performance: 27.591 ns/day, 0.870 hours/ns, 319.345 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 326.18 | 407.2 | 502.91 | 261.9 | 65.02 Bond | 0.14516 | 0.3809 | 0.91698 | 28.6 | 0.06 Neigh | 29.314 | 29.388 | 29.455 | 0.8 | 4.69 Comm | 36.464 | 130.89 | 213.04 | 471.5 | 20.90 Output | 0.0099688 | 0.012171 | 0.014268 | 1.2 | 0.00 Modify | 53.719 | 55.599 | 58.555 | 21.1 | 8.88 Other | | 2.814 | | | 0.45 Nlocal: 284.406 ave 314 max 251 min Histogram: 1 3 2 2 5 5 7 5 1 1 Nghost: 3668.09 ave 3749 max 3581 min Histogram: 2 4 3 4 2 4 2 2 6 3 Neighs: 80033.1 ave 101497 max 60986 min Histogram: 5 1 7 3 0 1 5 4 4 2 Total # of neighbors = 2561058 Ave neighs/atom = 281.40402 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9673 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.46848e-06 8304 2 103.7 9.9973e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.5 | 11.68 | 12.12 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 990.73868 103346.52 1.1747375 294.67338 46.322387 153.36654 0 0 21108.701 -169659.25 0 0 -148350.86 5561.8096 Loop time of 6.92894e-06 on 32 procs for 0 steps with 9101 atoms 111.4% 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 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 | | 6.929e-06 | | |100.00 Nlocal: 284.406 ave 314 max 251 min Histogram: 1 3 2 2 5 5 7 5 1 1 Nghost: 3668.09 ave 3749 max 3581 min Histogram: 2 4 3 4 2 4 2 2 6 3 Neighs: 80033.1 ave 101497 max 60986 min Histogram: 5 1 7 3 0 1 5 4 4 2 Total # of neighbors = 2561058 Ave neighs/atom = 281.40402 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out