#------------------------------------------------------------------------------- # 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) = 0.2499137 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035866273 estimated relative force accuracy = 1.0801022e-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 6.08402e-13 8304 2 103.7 8.00355e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.81 | 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 -12.864129 195013.51 0.62254678 302.01175 40.660402 63.640881 0 0 21292.916 27723.578 -107.44529 -209763.21 -160642.42 5700.3176 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20091e-06 8304 2 103.7 9.5995e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.10025e-06 8304 2 103.7 9.10276e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.1656e-06 8304 2 103.7 9.92162e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.83781e-06 8304 2 103.7 0.000105165 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.28511e-06 8304 2 103.7 0.000103816 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.33908e-06 8304 2 103.7 0.000107805 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.45368e-06 8304 2 103.7 0.000107282 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.11385e-06 8304 2 103.7 9.22167e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.17332e-06 8304 2 103.7 9.20947e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.23363e-06 8304 2 103.7 0.000160214 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.38291e-06 8304 2 103.7 0.000100002 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.10979e-06 8304 2 103.7 9.44928e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.10396e-06 8304 2 103.7 9.75104e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.21823e-06 8304 2 103.7 9.74037e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.37059e-06 8304 2 103.7 0.000103343 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.44035e-06 8304 2 103.7 9.44594e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12443e-06 8304 2 103.7 9.82343e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14373e-06 8304 2 103.7 9.5928e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.35592e-06 8304 2 103.7 9.69651e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.14616e-06 8304 2 103.7 0.000101095 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.18277e-06 8304 2 103.7 0.000101199 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.33123e-06 8304 2 103.7 9.30647e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.20959e-06 8304 2 103.7 9.15303e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.13148e-06 8304 2 103.7 0.000115674 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.10066e-06 8304 2 103.7 0.000120045 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.5703e-06 8304 2 103.7 9.78685e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.62828e-06 8304 2 103.7 0.000109525 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.12885e-06 8304 2 103.7 9.26143e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.32693e-06 8304 2 103.7 0.000101136 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26489e-06 8304 2 103.7 0.000100495 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.31065e-06 8304 2 103.7 9.90227e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.05574e-06 8304 2 103.7 9.73656e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.36535e-06 8304 2 103.7 0.000103804 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.25413e-06 8304 2 103.7 9.48934e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.2693e-06 8304 2 103.7 0.000102312 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.1763e-06 8304 2 103.7 0.000101178 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.09005e-06 8304 2 103.7 8.57831e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.33528e-06 8304 2 103.7 9.96547e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.10192e-06 8304 2 103.7 9.03544e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.32354e-06 8304 2 103.7 0.000105725 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.25059e-06 8304 2 103.7 9.27757e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.23099e-06 8304 2 103.7 9.78691e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.08724e-06 8304 2 103.7 9.489e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.57614e-06 8304 2 103.7 0.000112587 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.13089e-06 8304 2 103.7 9.22171e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.6519e-06 8304 2 103.7 0.000104426 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.70652e-06 8304 2 103.7 0.000106794 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.19129e-06 8304 2 103.7 9.71089e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.36105e-06 8304 2 103.7 0.000105497 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.36126e-06 8304 2 103.7 0.000100816 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.04701e-06 8304 2 103.7 9.58235e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34122e-06 8304 2 103.7 0.000104034 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.2934e-06 8304 2 103.7 0.00010792 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.47267e-06 8304 2 103.7 0.000113898 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.22849e-06 8304 2 103.7 9.66063e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.16233e-06 8304 2 103.7 9.34956e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18698e-06 8304 2 103.7 0.000103028 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.17581e-06 8304 2 103.7 9.97849e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.24742e-06 8304 2 103.7 0.000103941 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.38442e-06 8304 2 103.7 9.63625e-05 2768 3000000 3000000 123.76009 195013.51 0.62254678 300.96283 35.649367 78.992346 0 0 21461.777 27702.878 -107.44529 -209762.99 -160483.69 5680.5196 Loop time of 34802.1 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.448 ns/day, 3.222 hours/ns, 86.202 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 | 1.8015 | 10898 | 25140 |9727.2 | 31.31 Bond | 2.6905 | 6.9494 | 19.527 | 188.7 | 0.02 Kspace | 5608.2 | 19934 | 30978 |7233.1 | 57.28 Neigh | 1843.4 | 1849.5 | 1858.3 | 12.3 | 5.31 Comm | 271.63 | 658.94 | 900.85 | 889.6 | 1.89 Output | 0.013636 | 0.015821 | 0.017881 | 1.0 | 0.00 Modify | 1199.1 | 1381.9 | 1625.8 | 452.1 | 3.97 Other | | 73.32 | | | 0.21 Nlocal: 284.406 ave 583 max 0 min Histogram: 12 0 0 1 3 2 2 0 0 12 Nghost: 4486.69 ave 8887 max 8 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133528 ave 314005 max 0 min Histogram: 12 0 4 2 2 0 0 0 7 5 Total # of neighbors = 4272881 Ave neighs/atom = 469.49577 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149749 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) = 0.2499137 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035866273 estimated relative force accuracy = 1.0801022e-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 1.38442e-06 8304 2 103.7 9.63625e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.18 | 12.81 | 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 124.21654 195013.51 0.62254678 300.96283 35.649367 78.992346 0 0 21461.777 27702.878 -107.44529 -209762.99 -160483.69 5680.5196 Loop time of 7.41816e-06 on 32 procs for 0 steps with 9101 atoms 112.9% 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 | | 7.418e-06 | | |100.00 Nlocal: 284.406 ave 583 max 0 min Histogram: 12 0 0 1 3 2 2 0 0 12 Nghost: 4486.69 ave 8887 max 8 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 133528 ave 314005 max 0 min Histogram: 12 0 4 2 2 0 0 0 7 5 Total # of neighbors = 4272881 Ave neighs/atom = 469.49577 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: 19:23:08