#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # 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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00254 0.762326 11904 2 97.5667 38.403 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.18 | 15.84 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 4467.2663 139006.3 1.4192018 417.33588 117.37395 708.83542 0 0 42503.293 14962.287 -396.67289 -379342.84 -321051.05 12355.398 10000 10000 583.17474 139006.3 1.4192018 294.9225 342.91782 661.85005 0 0 37842.735 23526.762 -396.67289 -380001.28 -317627.02 8731.3002 Loop time of 224.143 on 16 procs for 10000 steps with 13901 atoms Performance: 3.855 ns/day, 6.226 hours/ns, 44.614 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 110.53 | 134.6 | 173.59 | 191.4 | 60.05 Bond | 0.034845 | 0.16422 | 0.37916 | 30.3 | 0.07 Kspace | 28.261 | 67.473 | 91.688 | 271.9 | 30.10 Neigh | 10.117 | 10.128 | 10.139 | 0.2 | 4.52 Comm | 4.322 | 4.4867 | 4.6529 | 5.1 | 2.00 Output | 0.021508 | 0.023898 | 0.026119 | 1.0 | 0.01 Modify | 6.4179 | 6.5541 | 6.8175 | 3.8 | 2.92 Other | | 0.7111 | | | 0.32 Nlocal: 868.812 ave 1002 max 778 min Histogram: 2 2 5 1 2 0 0 0 0 4 Nghost: 10627 ave 11130 max 9930 min Histogram: 4 0 0 0 0 2 2 4 0 4 Neighs: 502388 ave 652502 max 410114 min Histogram: 3 2 5 2 0 0 0 0 0 4 Total # of neighbors = 8038212 Ave neighs/atom = 578.24703 Ave special neighs/atom = 2.0450327 Neighbor list builds = 559 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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.10344e-06 11904 2 103.7 9.74624e-05 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.28 | 15.85 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 584.36049 139006.3 1.4192018 294.9225 342.91782 661.85005 0 0 37842.735 23526.762 -396.67289 -380001.28 -317627.02 8731.3002 Loop time of 1.25143e-05 on 16 procs for 0 steps with 13901 atoms 107.4% 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 | | 1.251e-05 | | |100.00 Nlocal: 868.812 ave 1002 max 778 min Histogram: 2 2 5 1 2 0 0 0 0 4 Nghost: 10627 ave 11130 max 9930 min Histogram: 4 0 0 0 0 2 2 4 0 4 Neighs: 502388 ave 652502 max 410114 min Histogram: 3 2 5 2 0 0 0 0 0 4 Total # of neighbors = 8038212 Ave neighs/atom = 578.24703 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out