#------------------------------------------------------------------------------- # 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 = 0.001 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) = 0.20470278 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0030085707 estimated relative force accuracy = 9.0602213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.995766 1.05459 8304 2 96.8375 48.3786 2768 Per MPI rank memory allocation (min/avg/max) = 13.25 | 13.49 | 13.83 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 20113.853 92859.489 1.3074058 428.55654 69.441646 301.59987 0 0 25092.086 4922.753 -116.30764 -171119.93 -140734.05 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.4105e-06 8304 2 103.7 0.000103084 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.23923e-06 8304 2 103.7 9.35599e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.3714e-06 8304 2 103.7 9.39336e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.49792e-06 8304 2 103.7 0.000122701 2768 200000 200000 2633.2925 92859.489 1.3074058 297.99556 35.211211 126.39196 0 0 22430.294 -12350.201 -116.30764 -171998.58 -161756.89 5624.514 Loop time of 2393.23 on 32 procs for 200000 steps with 9101 atoms Performance: 7.220 ns/day, 3.324 hours/ns, 83.569 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1492.5 | 1686 | 1868.7 | 222.4 | 70.45 Bond | 0.26928 | 0.65072 | 1.1411 | 31.4 | 0.03 Kspace | 206.59 | 389.11 | 581.99 | 462.5 | 16.26 Neigh | 80.299 | 80.378 | 80.445 | 0.4 | 3.36 Comm | 110.86 | 111.61 | 112.32 | 3.4 | 4.66 Output | 0.011077 | 0.013375 | 0.015513 | 1.2 | 0.00 Modify | 116.38 | 116.84 | 117.57 | 2.8 | 4.88 Other | | 8.598 | | | 0.36 Nlocal: 284.406 ave 304 max 258 min Histogram: 1 1 1 4 4 6 6 2 6 1 Nghost: 11120.5 ave 11178 max 11075 min Histogram: 7 5 4 0 0 2 5 4 3 2 Neighs: 286703 ave 319382 max 250667 min Histogram: 2 2 1 6 4 4 4 3 4 2 Total # of neighbors = 9174489 Ave neighs/atom = 1008.0748 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9854 Dangerous builds = 1 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) = 0.20470278 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0030085707 estimated relative force accuracy = 9.0602213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.49792e-06 8304 2 103.7 0.000122701 2768 Per MPI rank memory allocation (min/avg/max) = 13.27 | 13.7 | 13.85 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 200000 200000 2634.0764 92859.489 1.3074058 297.99556 35.211211 126.39196 0 0 22430.294 -12350.201 -116.30764 -171998.58 -161756.89 5624.514 Loop time of 1.229e-05 on 32 procs for 0 steps with 9101 atoms 113.9% 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 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 | | 1.229e-05 | | |100.00 Nlocal: 284.406 ave 304 max 258 min Histogram: 1 1 1 4 4 6 6 2 6 1 Nghost: 11120.5 ave 11178 max 11075 min Histogram: 7 5 4 0 0 2 5 4 3 2 Neighs: 286703 ave 319382 max 250667 min Histogram: 2 2 1 6 4 4 4 3 4 2 Total # of neighbors = 9174489 Ave neighs/atom = 1008.0748 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