#------------------------------------------------------------------------------- # Stage 2.4: 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 file 2.4_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 file 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.995245 0.579299 8304 2 96.4496 41.4393 2768 Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.77 | 13.22 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 23766.907 92859.489 1.3074058 428.55654 259.66061 267.41129 0 0 26382.021 104307.12 -448.40969 -270663.75 -139447.54 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20285e-06 8304 2 103.7 9.80435e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34683e-06 8304 2 103.7 0.000121269 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.16538e-06 8304 2 103.7 9.15479e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.23806e-06 8304 2 103.7 9.28095e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.17122e-06 8304 2 103.7 0.00010565 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.22627e-06 8304 2 103.7 9.75508e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.24352e-06 8304 2 103.7 0.000105999 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10439e-06 8304 2 103.7 9.59718e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.32389e-06 8304 2 103.7 8.98338e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.31549e-06 8304 2 103.7 9.74204e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.78236e-06 8304 2 103.7 0.000117119 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.4568e-06 8304 2 103.7 9.59658e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.34871e-06 8304 2 103.7 9.75268e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.13755e-06 8304 2 103.7 9.78124e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.24537e-06 8304 2 103.7 0.000105661 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13184e-06 8304 2 103.7 8.79606e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21939e-06 8304 2 103.7 9.84021e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.09242e-06 8304 2 103.7 9.15697e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1335e-06 8304 2 103.7 0.000104401 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.45262e-06 8304 2 103.7 9.99387e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.43767e-06 8304 2 103.7 9.54047e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.23652e-06 8304 2 103.7 8.96316e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.56793e-06 8304 2 103.7 0.000124364 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.18065e-06 8304 2 103.7 9.98044e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.71212e-06 8304 2 103.7 0.000101561 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.33443e-06 8304 2 103.7 9.10287e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.22403e-06 8304 2 103.7 9.28755e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.61427e-06 8304 2 103.7 0.000108789 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.38105e-06 8304 2 103.7 0.000100247 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.18322e-06 8304 2 103.7 9.54611e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.26193e-06 8304 2 103.7 0.000113469 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.27288e-06 8304 2 103.7 8.86146e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.52307e-06 8304 2 103.7 0.000107536 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.6526e-06 8304 2 103.7 0.000110241 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.41023e-06 8304 2 103.7 9.71788e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.06662e-06 8304 2 103.7 9.73881e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.43643e-06 8304 2 103.7 9.06015e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.288e-06 8304 2 103.7 9.33023e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.50708e-06 8304 2 103.7 0.00011305 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.50662e-06 8304 2 103.7 0.000108794 2768 2000000 2000000 2543.4359 92859.489 1.3074058 304.48972 41.735473 73.097743 0 0 22365.187 89719.581 -448.40969 -273850.55 -161650.95 5747.088 Loop time of 11447.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.095 ns/day, 1.590 hours/ns, 174.708 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4420.8 | 4816.4 | 5253.6 | 237.6 | 42.07 Bond | 2.1877 | 5.2252 | 9.9631 | 103.5 | 0.05 Kspace | 4268.4 | 4712.6 | 5110 | 241.2 | 41.17 Neigh | 322.49 | 323.34 | 324.03 | 2.0 | 2.82 Comm | 713.63 | 724.46 | 734.54 | 18.4 | 6.33 Output | 0.011283 | 0.013529 | 0.015662 | 1.2 | 0.00 Modify | 819.26 | 826 | 832.59 | 11.3 | 7.22 Other | | 39.66 | | | 0.35 Nlocal: 284.406 ave 311 max 263 min Histogram: 3 4 2 5 4 6 4 1 1 2 Nghost: 4984.5 ave 5045 max 4923 min Histogram: 2 2 2 8 2 3 7 3 0 3 Neighs: 88697 ave 102317 max 79015 min Histogram: 2 3 7 4 3 8 0 4 0 1 Total # of neighbors = 2838304 Ave neighs/atom = 311.86727 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98339 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.50662e-06 8304 2 103.7 0.000108794 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 13.15 | 13.34 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 2544.5648 92859.489 1.3074058 304.48972 41.735473 73.097743 0 0 22365.187 89719.581 -448.40969 -273850.55 -161650.95 5747.088 Loop time of 1.16474e-05 on 32 procs for 0 steps with 9101 atoms 109.2% 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 | | 1.165e-05 | | |100.00 Nlocal: 284.406 ave 311 max 263 min Histogram: 3 4 2 5 4 6 4 1 1 2 Nghost: 4984.5 ave 5045 max 4923 min Histogram: 2 2 2 8 2 3 7 3 0 3 Neighs: 88697 ave 102317 max 79015 min Histogram: 2 3 7 4 3 8 0 4 0 1 Total # of neighbors = 2838304 Ave neighs/atom = 311.86727 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out