#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 2 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 200000 200000 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 2.6_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32415005 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030008343 estimated relative force accuracy = 9.0369235e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11664 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 7.14429e-13 8304 2 103.7 8.00782e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 13.46 | 14.38 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 0 1e-06 -222.97957 132115.2 0.91893312 295.95417 51.185693 87.279044 0 0 21051.633 89405.874 -315.17262 -271104.17 -160508.2 5585.9838 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.41045e-06 8304 2 103.7 0.000104249 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.3147e-06 8304 2 103.7 9.3049e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.13423e-06 8304 2 103.7 9.39205e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.92342e-06 8304 2 103.7 0.000128009 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.10166e-06 8304 2 103.7 8.85314e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.28664e-06 8304 2 103.7 9.39915e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.03647e-06 8304 2 103.7 8.88685e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.45709e-06 8304 2 103.7 9.92248e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33158e-06 8304 2 103.7 9.07684e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.09639e-06 8304 2 103.7 9.87963e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2078e-06 8304 2 103.7 8.98506e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21636e-06 8304 2 103.7 9.63547e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.24741e-06 8304 2 103.7 9.29857e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.7784e-06 8304 2 103.7 0.000123761 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.10935e-06 8304 2 103.7 9.67428e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.15506e-06 8304 2 103.7 8.86545e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.43147e-06 8304 2 103.7 0.000107978 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.39474e-06 8304 2 103.7 0.000114347 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.97706e-06 8304 2 103.7 0.000134765 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.21899e-06 8304 2 103.7 0.000101166 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13153e-06 8304 2 103.7 9.26878e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.54053e-06 8304 2 103.7 0.000107478 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.56978e-06 8304 2 103.7 0.000101542 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.19083e-06 8304 2 103.7 9.2257e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.36944e-06 8304 2 103.7 0.00010591 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.41349e-06 8304 2 103.7 0.000113608 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.80378e-06 8304 2 103.7 0.000105231 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.32258e-06 8304 2 103.7 8.73349e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.38301e-06 8304 2 103.7 9.83096e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.14808e-06 8304 2 103.7 9.28976e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.36926e-06 8304 2 103.7 0.000100374 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.20049e-06 8304 2 103.7 9.28541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.20621e-06 8304 2 103.7 9.86024e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.46465e-06 8304 2 103.7 0.000106294 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19139e-06 8304 2 103.7 8.77425e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.15261e-06 8304 2 103.7 8.53175e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.15038e-06 8304 2 103.7 0.000105151 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.60569e-06 8304 2 103.7 0.00010259 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.18171e-06 8304 2 103.7 9.74035e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.65735e-06 8304 2 103.7 0.000127213 2768 2000000 2000000 -128.48903 132115.2 0.91893312 292.66978 42.400638 76.311481 0 0 21334.588 88808.618 -315.17262 -271095.05 -160833.13 5523.9927 Loop time of 13199.8 on 32 procs for 2000000 steps with 9101 atoms Performance: 13.091 ns/day, 1.833 hours/ns, 151.517 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.452 | 4113.8 | 6268.2 |3399.4 | 31.17 Bond | 1.8965 | 5.3484 | 12.211 | 112.5 | 0.04 Kspace | 4900.8 | 7072.2 | 11179 |2611.3 | 53.58 Neigh | 519.56 | 521.24 | 524.24 | 6.0 | 3.95 Comm | 420.36 | 588.37 | 662.23 | 375.9 | 4.46 Output | 0.01049 | 0.012737 | 0.014779 | 1.2 | 0.00 Modify | 802.16 | 859.61 | 996.92 | 252.0 | 6.51 Other | | 39.29 | | | 0.30 Nlocal: 284.406 ave 392 max 0 min Histogram: 4 1 2 1 0 0 0 4 0 20 Nghost: 3954.47 ave 5295 max 2143 min Histogram: 8 0 4 0 0 4 0 2 2 12 Neighs: 77127.8 ave 122897 max 0 min Histogram: 4 1 3 4 0 0 0 1 13 6 Total # of neighbors = 2468089 Ave neighs/atom = 271.18877 Ave special neighs/atom = 1.8929788 Neighbor list builds = 99670 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.6.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) = 0.32415005 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030008343 estimated relative force accuracy = 9.0369235e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11664 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.65735e-06 8304 2 103.7 0.000127213 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 13.47 | 14.38 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 2000000 2000000 -127.98716 132115.2 0.91893312 292.66978 42.400638 76.311481 0 0 21334.588 88808.618 -315.17262 -271095.05 -160833.13 5523.9927 Loop time of 8.623e-06 on 32 procs for 0 steps with 9101 atoms 107.6% 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 | | 8.623e-06 | | |100.00 Nlocal: 284.406 ave 392 max 0 min Histogram: 4 1 2 1 0 0 0 4 0 20 Nghost: 3954.47 ave 5295 max 2143 min Histogram: 8 0 4 0 0 4 0 2 2 12 Neighs: 77127.8 ave 122897 max 0 min Histogram: 4 1 3 4 0 0 0 1 13 6 Total # of neighbors = 2468089 Ave neighs/atom = 271.18877 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: 12:45:49