#------------------------------------------------------------------------------- # 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) = 0.31993305 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031567238 estimated relative force accuracy = 9.50638e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.83102e-13 8304 2 103.7 1.05175e-10 2768 Per MPI rank memory allocation (min/avg/max) = 11.89 | 13.13 | 13.54 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 -251.87525 195066.49 0.62237772 299.81888 51.466867 56.653562 0 0 21077.984 86171.026 -213.46104 -267687.39 -160330.26 5658.9282 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.28865e-06 8304 2 103.7 9.76393e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.68471e-06 8304 2 103.7 0.000116594 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.57556e-06 8304 2 103.7 0.000117646 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.35719e-06 8304 2 103.7 9.49441e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.72056e-06 8304 2 103.7 0.000122117 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.52438e-06 8304 2 103.7 9.7099e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.30706e-06 8304 2 103.7 0.000108807 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.18487e-06 8304 2 103.7 9.45948e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.35995e-06 8304 2 103.7 9.4595e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.13233e-06 8304 2 103.7 9.36037e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.27218e-06 8304 2 103.7 0.000100219 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.49283e-06 8304 2 103.7 9.64092e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 9.92706e-07 8304 2 103.7 9.04056e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.18582e-06 8304 2 103.7 9.95186e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.16055e-06 8304 2 103.7 9.67451e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.27309e-06 8304 2 103.7 0.000100355 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.26995e-06 8304 2 103.7 9.38731e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15003e-06 8304 2 103.7 0.000101191 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.6308e-06 8304 2 103.7 0.000109876 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.18631e-06 8304 2 103.7 9.77915e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.55012e-06 8304 2 103.7 9.63166e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.19859e-06 8304 2 103.7 0.000100157 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.36351e-06 8304 2 103.7 0.000112505 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.24846e-06 8304 2 103.7 9.38215e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.25119e-06 8304 2 103.7 8.90669e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.06119e-06 8304 2 103.7 9.1317e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.45253e-06 8304 2 103.7 0.000103102 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.18964e-06 8304 2 103.7 0.000104416 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.24752e-06 8304 2 103.7 9.75468e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.44202e-06 8304 2 103.7 9.50131e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.05475e-06 8304 2 103.7 8.88665e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.05077e-06 8304 2 103.7 8.69859e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.26544e-06 8304 2 103.7 0.000112714 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.14222e-06 8304 2 103.7 9.36617e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.28669e-06 8304 2 103.7 0.000101593 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.30323e-06 8304 2 103.7 0.000106615 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.44925e-06 8304 2 103.7 0.000114898 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.23571e-06 8304 2 103.7 0.000108585 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.17745e-06 8304 2 103.7 0.000116611 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.33606e-06 8304 2 103.7 0.000114436 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.34274e-06 8304 2 103.7 9.54148e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.3468e-06 8304 2 103.7 9.56377e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.21423e-06 8304 2 103.7 9.56205e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.15627e-06 8304 2 103.7 9.56841e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.18144e-06 8304 2 103.7 9.46031e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.26481e-06 8304 2 103.7 0.000101678 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.19039e-06 8304 2 103.7 9.45861e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.09928e-06 8304 2 103.7 9.51682e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.55648e-06 8304 2 103.7 0.000133217 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.16984e-06 8304 2 103.7 0.000100367 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.12365e-06 8304 2 103.7 9.65006e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.39841e-06 8304 2 103.7 0.000110325 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.22991e-06 8304 2 103.7 0.000127193 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.1691e-06 8304 2 103.7 0.000107844 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.12413e-06 8304 2 103.7 9.23046e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.27659e-06 8304 2 103.7 9.71205e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.62509e-06 8304 2 103.7 0.000116805 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.22988e-06 8304 2 103.7 9.55662e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.38994e-06 8304 2 103.7 0.000122961 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.20511e-06 8304 2 103.7 8.75602e-05 2768 3000000 3000000 -43.178707 195066.49 0.62237772 299.2491 47.249591 56.955723 0 0 21325.934 85862.504 -213.46104 -267668.51 -160375.86 5648.174 Loop time of 24303.1 on 32 procs for 3000000 steps with 9101 atoms Performance: 10.665 ns/day, 2.250 hours/ns, 123.441 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 | 219.94 | 5800.7 | 11872 |7209.2 | 23.87 Bond | 3.2336 | 7.878 | 15.832 | 155.6 | 0.03 Kspace | 9781.8 | 15863 | 21503 |4384.1 | 65.27 Neigh | 658.87 | 665.26 | 674.46 | 21.0 | 2.74 Comm | 412.43 | 658.92 | 845.2 | 640.7 | 2.71 Output | 0.013984 | 0.016009 | 0.017949 | 1.0 | 0.00 Modify | 1122.2 | 1245.5 | 1422 | 347.2 | 5.12 Other | | 62.09 | | | 0.26 Nlocal: 284.406 ave 568 max 0 min Histogram: 14 2 0 0 0 0 0 0 0 16 Nghost: 3124.66 ave 4723 max 1557 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74664.7 ave 160620 max 0 min Histogram: 16 0 0 0 0 0 0 0 6 10 Total # of neighbors = 2389271 Ave neighs/atom = 262.5284 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149990 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) = 0.31993305 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031567238 estimated relative force accuracy = 9.50638e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.20511e-06 8304 2 103.7 8.75602e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.89 | 13.13 | 13.54 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 -42.752616 195066.49 0.62237772 299.2491 47.249591 56.955723 0 0 21325.934 85862.504 -213.46104 -267668.51 -160375.86 5648.174 Loop time of 8.57987e-06 on 32 procs for 0 steps with 9101 atoms 115.8% 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 | | 8.58e-06 | | |100.00 Nlocal: 284.406 ave 568 max 0 min Histogram: 14 2 0 0 0 0 0 0 0 16 Nghost: 3124.66 ave 4723 max 1557 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74664.7 ave 160620 max 0 min Histogram: 16 0 0 0 0 0 0 0 6 10 Total # of neighbors = 2389271 Ave neighs/atom = 262.5284 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: 18:01:50