#------------------------------------------------------------------------------- # 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 = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00478 0.0879422 11184 2 97.7057 10.082 3728 Per MPI rank memory allocation (min/avg/max) = 13.46 | 13.65 | 14.1 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 334589.74 143799.62 1.371895 417.38826 42.791813 238.58018 0 0 276202.59 -77390.217 -383.45046 -379121.18 -180027.44 11461.157 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.54394e-06 11184 2 103.7 0.00011248 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.34403e-06 11184 2 103.7 0.000101176 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.29292e-06 11184 2 103.7 9.59385e-05 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.53705e-06 11184 2 103.7 0.000119055 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.50422e-06 11184 2 103.7 9.15321e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.43045e-06 11184 2 103.7 9.19709e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2768e-06 11184 2 103.7 8.83221e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.17925e-06 11184 2 103.7 0.000105277 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.18935e-06 11184 2 103.7 8.80959e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.51779e-06 11184 2 103.7 9.66262e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.25479e-06 11184 2 103.7 9.29804e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.26734e-06 11184 2 103.7 0.00011046 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.3378e-06 11184 2 103.7 9.82122e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.17061e-06 11184 2 103.7 0.000114081 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.17264e-06 11184 2 103.7 9.4004e-05 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.2478e-06 11184 2 103.7 0.00010318 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.42403e-06 11184 2 103.7 9.95531e-05 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17461e-06 11184 2 103.7 9.27477e-05 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.8732e-06 11184 2 103.7 9.59253e-05 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.53999e-06 11184 2 103.7 0.000112225 3728 1000000 1000000 335928.31 143799.62 1.371895 297.37957 276.1468 362.97776 0 0 271595.53 -52433.362 -383.45046 -378985.51 -159184.21 8165.8117 Loop time of 13208.4 on 32 procs for 1000000 steps with 13901 atoms Performance: 6.541 ns/day, 3.669 hours/ns, 75.709 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5551.5 | 6612.7 | 9134.2 |1659.1 | 50.06 Bond | 1.4789 | 7.4084 | 17.973 | 205.1 | 0.06 Kspace | 2291.8 | 4828.1 | 5910.1 |1956.9 | 36.55 Neigh | 481.97 | 483.66 | 485.71 | 4.4 | 3.66 Comm | 534.87 | 574.13 | 620.49 | 111.0 | 4.35 Output | 0.017692 | 0.020718 | 0.023552 | 1.2 | 0.00 Modify | 634.89 | 669.28 | 690.26 | 71.5 | 5.07 Other | | 33.12 | | | 0.25 Nlocal: 434.406 ave 524 max 385 min Histogram: 7 10 6 1 0 0 0 0 1 7 Nghost: 8231.34 ave 8735 max 7528 min Histogram: 8 0 0 0 0 1 12 3 0 8 Neighs: 243821 ave 346305 max 195262 min Histogram: 8 13 3 0 0 0 0 0 4 4 Total # of neighbors = 7802265 Ave neighs/atom = 561.27365 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 = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.53999e-06 11184 2 103.7 0.000112225 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 335929.19 143799.62 1.371895 297.37957 276.1468 362.97776 0 0 271595.53 -52433.362 -383.45046 -378985.51 -159184.21 8165.8117 Loop time of 7.74247e-06 on 32 procs for 0 steps with 13901 atoms 113.8% 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 | | 7.742e-06 | | |100.00 Nlocal: 434.406 ave 524 max 385 min Histogram: 7 10 6 1 0 0 0 0 1 7 Nghost: 8231.34 ave 8735 max 7528 min Histogram: 8 0 0 0 0 1 12 3 0 8 Neighs: 243821 ave 346305 max 195262 min Histogram: 8 13 3 0 0 0 0 0 4 4 Total # of neighbors = 7802265 Ave neighs/atom = 561.27365 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