#------------------------------------------------------------------------------- # 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 3728 = # 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00481 0.0879286 11184 2 97.7024 10.3752 3728 Per MPI rank memory allocation (min/avg/max) = 17.47 | 18.14 | 19.62 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 334521.46 143799.62 1.371895 417.38826 43.018436 239.04662 0 0 276214.51 -77425.729 -383.45046 -379121.69 -180050.84 11461.157 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.28106e-06 11184 2 103.7 9.50577e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.26079e-06 11184 2 103.7 9.19471e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.58706e-06 11184 2 103.7 0.000118056 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.2711e-06 11184 2 103.7 0.000110535 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.28543e-06 11184 2 103.7 9.26901e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.17245e-06 11184 2 103.7 8.98145e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2262e-06 11184 2 103.7 8.65472e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.38015e-06 11184 2 103.7 8.73781e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.59608e-06 11184 2 103.7 0.000102602 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.28512e-06 11184 2 103.7 0.000108135 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.26308e-06 11184 2 103.7 0.000103549 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.26517e-06 11184 2 103.7 0.000101163 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.67186e-06 11184 2 103.7 0.000104387 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.17696e-06 11184 2 103.7 9.37168e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.38896e-06 11184 2 103.7 9.817e-05 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.42037e-06 11184 2 103.7 9.12909e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.21072e-06 11184 2 103.7 8.91308e-05 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.59678e-06 11184 2 103.7 0.000108377 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.19283e-06 11184 2 103.7 9.46183e-05 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.31624e-06 11184 2 103.7 0.000108397 3728 1000000 1000000 336053.76 143799.62 1.371895 300.02436 285.30279 377.29377 0 0 271586.02 -52622.201 -383.45046 -378998.54 -159372.13 8238.4355 Loop time of 33908.3 on 8 procs for 1000000 steps with 13901 atoms Performance: 2.548 ns/day, 9.419 hours/ns, 29.491 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16711 | 20092 | 27997 |3010.4 | 59.25 Bond | 6.4859 | 18.317 | 47.49 | 380.2 | 0.05 Kspace | 3569.9 | 11507 | 14905 |3995.4 | 33.93 Neigh | 1496.3 | 1497.2 | 1498.4 | 1.9 | 4.42 Comm | 261.81 | 277.26 | 293.77 | 65.5 | 0.82 Output | 0.030381 | 0.03403 | 0.037328 | 1.3 | 0.00 Modify | 473.72 | 480.08 | 488.52 | 23.8 | 1.42 Other | | 36.82 | | | 0.11 Nlocal: 1737.62 ave 2079 max 1603 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13812.4 ave 14443 max 12636 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 975591 ave 1.34588e+06 max 819510 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 7804730 Ave neighs/atom = 561.45097 Ave special neighs/atom = 1.8838932 Neighbor list builds = 50044 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.31624e-06 11184 2 103.7 0.000108397 3728 Per MPI rank memory allocation (min/avg/max) = 17.84 | 20.77 | 29.38 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 336054.85 143799.62 1.371895 300.02436 285.30279 377.29377 0 0 271586.02 -52622.201 -383.45046 -378998.54 -159372.13 8238.4355 Loop time of 2.953e-06 on 8 procs for 0 steps with 13901 atoms 131.2% CPU use with 8 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 | | 2.953e-06 | | |100.00 Nlocal: 1737.62 ave 2079 max 1603 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13812.4 ave 14443 max 12636 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 975591 ave 1.34588e+06 max 819510 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 7804730 Ave neighs/atom = 561.45097 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out