#------------------------------------------------------------------------------- # 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) = 0.32403899 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030162601 estimated relative force accuracy = 9.0833777e-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 7.02771e-13 8304 2 103.7 7.63407e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 13.19 | 13.57 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 -356.8686 132487.99 0.91634748 297.35236 45.629097 84.835284 0 0 21014.573 89283.452 -314.28581 -271053.21 -160624.72 5612.3739 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.56079e-06 8304 2 103.7 0.000101554 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.2869e-06 8304 2 103.7 0.000101831 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14527e-06 8304 2 103.7 9.56135e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.82164e-06 8304 2 103.7 0.000115684 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.26263e-06 8304 2 103.7 0.000106197 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.35998e-06 8304 2 103.7 0.000104868 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.12252e-06 8304 2 103.7 9.935e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21948e-06 8304 2 103.7 0.000104601 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.16128e-06 8304 2 103.7 9.74081e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24273e-06 8304 2 103.7 9.93282e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.31763e-06 8304 2 103.7 0.000107214 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.19007e-06 8304 2 103.7 9.59893e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.31961e-06 8304 2 103.7 9.23164e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.1884e-06 8304 2 103.7 9.10275e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.36637e-06 8304 2 103.7 0.000139948 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.30381e-06 8304 2 103.7 0.000100905 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.55969e-06 8304 2 103.7 9.82927e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16475e-06 8304 2 103.7 9.31459e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.16019e-06 8304 2 103.7 0.000105585 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.4014e-06 8304 2 103.7 8.76493e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.25225e-06 8304 2 103.7 0.00013603 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.22777e-06 8304 2 103.7 8.96814e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.17149e-06 8304 2 103.7 9.41951e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.3847e-06 8304 2 103.7 9.2328e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17205e-06 8304 2 103.7 9.44855e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.22858e-06 8304 2 103.7 9.22976e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.07972e-06 8304 2 103.7 9.50095e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.17753e-06 8304 2 103.7 8.6094e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12365e-06 8304 2 103.7 0.000111292 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.21606e-06 8304 2 103.7 9.47898e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.14379e-06 8304 2 103.7 9.27958e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.12065e-06 8304 2 103.7 0.000100328 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.2503e-06 8304 2 103.7 9.46312e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.3629e-06 8304 2 103.7 9.47539e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15544e-06 8304 2 103.7 8.78931e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.4419e-06 8304 2 103.7 9.0918e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.2631e-06 8304 2 103.7 9.6855e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.16153e-06 8304 2 103.7 9.13849e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.37639e-06 8304 2 103.7 0.000113883 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.2327e-06 8304 2 103.7 0.000103857 2768 2000000 2000000 -849.10784 132487.99 0.91634748 295.32606 45.921344 76.973348 0 0 20637.658 89695.43 -314.28581 -271036.05 -160580.06 5574.1285 Loop time of 13155.3 on 32 procs for 2000000 steps with 9101 atoms Performance: 13.135 ns/day, 1.827 hours/ns, 152.030 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 | 33.13 | 4113.9 | 6077.3 |3444.9 | 31.27 Bond | 1.8286 | 5.3355 | 10.343 | 105.2 | 0.04 Kspace | 5022.9 | 7003.8 | 11118 |2660.8 | 53.24 Neigh | 534.83 | 536.1 | 538.71 | 5.7 | 4.08 Comm | 418.24 | 591.63 | 663.9 | 379.3 | 4.50 Output | 0.010324 | 0.012572 | 0.014601 | 1.2 | 0.00 Modify | 809.68 | 864.8 | 999.48 | 250.7 | 6.57 Other | | 39.69 | | | 0.30 Nlocal: 284.406 ave 402 max 0 min Histogram: 4 1 3 0 0 1 1 1 3 18 Nghost: 3949.09 ave 5346 max 2102 min Histogram: 8 0 4 0 3 1 0 4 0 12 Neighs: 76720.4 ave 121035 max 0 min Histogram: 4 1 4 2 1 0 0 1 9 10 Total # of neighbors = 2455052 Ave neighs/atom = 269.75629 Ave special neighs/atom = 1.8929788 Neighbor list builds = 99734 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) = 0.32403899 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030162601 estimated relative force accuracy = 9.0833777e-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 1.2327e-06 8304 2 103.7 0.000103857 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 13.16 | 13.57 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 -848.55528 132487.99 0.91634748 295.32606 45.921344 76.973348 0 0 20637.658 89695.43 -314.28581 -271036.05 -160580.06 5574.1285 Loop time of 1.30652e-05 on 32 procs for 0 steps with 9101 atoms 117.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.307e-05 | | |100.00 Nlocal: 284.406 ave 402 max 0 min Histogram: 4 1 3 0 0 1 1 1 3 18 Nghost: 3949.09 ave 5346 max 2102 min Histogram: 8 0 4 0 3 1 0 4 0 12 Neighs: 76720.4 ave 121035 max 0 min Histogram: 4 1 4 2 1 0 0 1 9 10 Total # of neighbors = 2455052 Ave neighs/atom = 269.75629 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: 12:48:07