#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24986972 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035923427 estimated relative force accuracy = 1.0818233e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.12159e-13 8304 2 103.7 1.16088e-10 2768 Per MPI rank memory allocation (min/avg/max) = 11.18 | 12.73 | 14.12 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 -144.91191 195628.7 0.62058908 297.92389 51.52059 74.933334 0 0 21097.665 27886.415 -107.10742 -209745.24 -160634.7 5623.1613 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20328e-06 8304 2 103.7 0.000101232 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.13163e-06 8304 2 103.7 0.000100322 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.44827e-06 8304 2 103.7 0.000101881 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.55357e-06 8304 2 103.7 0.000112571 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.28964e-06 8304 2 103.7 9.47932e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.35816e-06 8304 2 103.7 9.93814e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22298e-06 8304 2 103.7 0.000103166 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.26675e-06 8304 2 103.7 9.13574e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.57044e-06 8304 2 103.7 0.000120414 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.17466e-06 8304 2 103.7 0.000103128 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25354e-06 8304 2 103.7 0.000114688 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21231e-06 8304 2 103.7 9.72831e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.29957e-06 8304 2 103.7 8.98507e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.29511e-06 8304 2 103.7 0.00010317 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23801e-06 8304 2 103.7 9.61513e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.53887e-06 8304 2 103.7 0.000115958 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.48159e-06 8304 2 103.7 0.000121932 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16445e-06 8304 2 103.7 0.000104347 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.48665e-06 8304 2 103.7 0.000115882 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.23539e-06 8304 2 103.7 9.19056e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.03675e-06 8304 2 103.7 9.26438e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.34842e-06 8304 2 103.7 0.000110296 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.20096e-06 8304 2 103.7 9.27925e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.26838e-06 8304 2 103.7 9.64807e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.05827e-06 8304 2 103.7 8.75316e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.14628e-06 8304 2 103.7 8.89753e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.15089e-06 8304 2 103.7 9.37137e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.25537e-06 8304 2 103.7 9.64228e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.09457e-06 8304 2 103.7 9.69614e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.19142e-06 8304 2 103.7 0.000117737 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.17603e-06 8304 2 103.7 0.000107678 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.22913e-06 8304 2 103.7 9.36697e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.34778e-06 8304 2 103.7 0.000109205 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.50122e-06 8304 2 103.7 0.000117966 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14435e-06 8304 2 103.7 9.34377e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.36003e-06 8304 2 103.7 0.000106942 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.25116e-06 8304 2 103.7 0.00010147 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.50333e-06 8304 2 103.7 0.000108534 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.30776e-06 8304 2 103.7 9.85152e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.16861e-06 8304 2 103.7 0.000101682 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.11296e-06 8304 2 103.7 9.44851e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.2857e-06 8304 2 103.7 0.000118995 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.19089e-06 8304 2 103.7 8.95588e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.10978e-06 8304 2 103.7 8.97491e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.49776e-06 8304 2 103.7 0.000113029 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.3687e-06 8304 2 103.7 0.000115667 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.57464e-06 8304 2 103.7 9.95831e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.57598e-06 8304 2 103.7 0.000113976 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.41554e-06 8304 2 103.7 9.58598e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.23722e-06 8304 2 103.7 9.47597e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.37737e-06 8304 2 103.7 0.000109919 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.17467e-06 8304 2 103.7 0.000114551 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.38858e-06 8304 2 103.7 0.000102287 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.15773e-06 8304 2 103.7 9.70737e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.43567e-06 8304 2 103.7 9.02478e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.15524e-06 8304 2 103.7 8.84873e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.14548e-06 8304 2 103.7 9.09799e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.51367e-06 8304 2 103.7 0.000106546 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.09082e-06 8304 2 103.7 9.86843e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.12065e-06 8304 2 103.7 9.18529e-05 2768 3000000 3000000 -164.2149 195628.7 0.62058908 296.8674 45.365491 65.700955 0 0 20979.929 28351.479 -107.10742 -209727.42 -160284.95 5603.2206 Loop time of 34637.3 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.483 ns/day, 3.207 hours/ns, 86.612 timesteps/s 98.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8783 | 10913 | 25049 |9833.6 | 31.51 Bond | 2.7961 | 7.2582 | 17.749 | 172.0 | 0.02 Kspace | 5580.7 | 19793 | 30869 |7342.6 | 57.14 Neigh | 1799.7 | 1806.6 | 1820.4 | 15.3 | 5.22 Comm | 254.84 | 665.22 | 908.21 | 908.2 | 1.92 Output | 0.013021 | 0.01523 | 0.017299 | 1.0 | 0.00 Modify | 1191.2 | 1377.2 | 1622.7 | 460.6 | 3.98 Other | | 74.47 | | | 0.21 Nlocal: 284.406 ave 584 max 0 min Histogram: 12 0 0 2 2 1 3 0 0 12 Nghost: 4483.28 ave 8886 max 6 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133041 ave 309850 max 0 min Histogram: 12 4 0 0 0 1 3 2 4 6 Total # of neighbors = 4257300 Ave neighs/atom = 467.78376 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149894 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24986972 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035923427 estimated relative force accuracy = 1.0818233e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.12065e-06 8304 2 103.7 9.18529e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.18 | 12.74 | 14.12 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 3000000 3000000 -163.77185 195628.7 0.62058908 296.8674 45.365491 65.700955 0 0 20979.929 28351.479 -107.10742 -209727.42 -160284.95 5603.2206 Loop time of 1.18155e-05 on 32 procs for 0 steps with 9101 atoms 121.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.182e-05 | | |100.00 Nlocal: 284.406 ave 584 max 0 min Histogram: 12 0 0 2 2 1 3 0 0 12 Nghost: 4483.28 ave 8886 max 6 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133041 ave 309850 max 0 min Histogram: 12 4 0 0 0 1 3 2 4 6 Total # of neighbors = 4257300 Ave neighs/atom = 467.78376 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: 19:19:01