#------------------------------------------------------------------------------- # Stage 2.5: 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 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 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 1000000 2.5.restart dump sci all custom 100000 2.5.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) = 0.32117505 grid = 40 40 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0030103868 estimated relative force accuracy = 9.0656904e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13122 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.39409e-13 8304 2 103.7 7.61133e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 13.03 | 14.06 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 -392.40811 185662.09 0.65390321 297.53765 40.166443 81.680258 0 0 20915.112 87115.564 -224.27355 -268661.93 -160509.41 5615.8711 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.1754e-06 8304 2 103.7 9.2031e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.25734e-06 8304 2 103.7 9.55636e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.23225e-06 8304 2 103.7 9.70105e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18767e-06 8304 2 103.7 9.69535e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.06865e-06 8304 2 103.7 9.33308e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.35037e-06 8304 2 103.7 0.00010715 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.31077e-06 8304 2 103.7 0.00010965 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.47386e-06 8304 2 103.7 0.000104527 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.14313e-06 8304 2 103.7 8.67246e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.5124e-06 8304 2 103.7 0.000115443 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.27182e-06 8304 2 103.7 0.000100006 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.1275e-06 8304 2 103.7 9.01155e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.10991e-06 8304 2 103.7 9.50145e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.26429e-06 8304 2 103.7 0.000101265 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.4357e-06 8304 2 103.7 0.000100848 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.29386e-06 8304 2 103.7 9.25356e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.09097e-06 8304 2 103.7 8.46947e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.34725e-06 8304 2 103.7 0.000112312 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.38152e-06 8304 2 103.7 9.39892e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36005e-06 8304 2 103.7 9.95301e-05 2768 1000000 1000000 -591.56068 185662.09 0.65390321 297.87218 41.076969 77.586825 0 0 20802.084 87357.661 -224.27355 -268670.57 -160392.16 5622.1853 Loop time of 8133.22 on 32 procs for 1000000 steps with 9101 atoms Performance: 10.623 ns/day, 2.259 hours/ns, 122.953 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 | 1.2476 | 2008.3 | 4153.1 |4052.5 | 24.69 Bond | 1.0004 | 2.6897 | 5.7681 | 89.3 | 0.03 Kspace | 3059.7 | 5240 | 7319.7 |2553.8 | 64.43 Neigh | 257.28 | 260.32 | 266.89 | 19.4 | 3.20 Comm | 38.572 | 193.03 | 278.58 | 675.1 | 2.37 Output | 0.013398 | 0.015459 | 0.017261 | 1.0 | 0.00 Modify | 359.39 | 407.98 | 484.12 | 255.9 | 5.02 Other | | 20.88 | | | 0.26 Nlocal: 284.406 ave 569 max 0 min Histogram: 9 7 0 0 0 0 0 0 3 13 Nghost: 3071.88 ave 5894 max 20 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 76611.4 ave 165259 max 0 min Histogram: 12 4 0 0 0 0 0 4 4 8 Total # of neighbors = 2451566 Ave neighs/atom = 269.37326 Ave special neighs/atom = 1.8929788 Neighbor list builds = 49840 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.5.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) = 0.32117505 grid = 40 40 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0030103868 estimated relative force accuracy = 9.0656904e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13122 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36005e-06 8304 2 103.7 9.95301e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 13.03 | 14.06 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 -591.14011 185662.09 0.65390321 297.87218 41.076969 77.586825 0 0 20802.084 87357.661 -224.27355 -268670.57 -160392.16 5622.1853 Loop time of 8.48634e-06 on 32 procs for 0 steps with 9101 atoms 114.9% 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 | | 8.486e-06 | | |100.00 Nlocal: 284.406 ave 569 max 0 min Histogram: 9 7 0 0 0 0 0 0 3 13 Nghost: 3071.88 ave 5894 max 20 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 76611.4 ave 165259 max 0 min Histogram: 12 4 0 0 0 0 0 4 4 8 Total # of neighbors = 2451566 Ave neighs/atom = 269.37326 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:31:09