#------------------------------------------------------------------------------- # Stage 2.5: 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 2.10398e-10 3000 1 103.7 1.22977e-08 1000 Per MPI rank memory allocation (min/avg/max) = 8.79 | 8.795 | 8.801 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 -3727.6426 26763.922 1.1177434 297.90029 0 0 0 0 2567.0096 -16552.361 -116.16932 0 -13985.351 1775.0804 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.33976e-06 3000 1 103.7 0.000109865 1000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.58224e-06 3000 1 103.7 0.000111456 1000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.18808e-06 3000 1 103.7 9.29505e-05 1000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.13089e-06 3000 1 103.7 0.000100915 1000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.3653e-06 3000 1 103.7 0.00015753 1000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.74248e-06 3000 1 103.7 0.000113139 1000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.336e-06 3000 1 103.7 0.000120271 1000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.0765e-06 3000 1 103.7 9.69623e-05 1000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.22561e-06 3000 1 103.7 8.87765e-05 1000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.87196e-06 3000 1 103.7 0.00018829 1000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.9046e-06 3000 1 103.7 0.00013532 1000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 2.01355e-06 3000 1 103.7 0.000147222 1000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.20712e-06 3000 1 103.7 0.000109142 1000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.6872e-06 3000 1 103.7 0.000124612 1000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21637e-06 3000 1 103.7 8.99016e-05 1000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.22755e-06 3000 1 103.7 0.000109335 1000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.76037e-06 3000 1 103.7 0.0001126 1000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.31264e-06 3000 1 103.7 0.000113133 1000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.26568e-06 3000 1 103.7 0.00010345 1000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.17285e-06 3000 1 103.7 9.4665e-05 1000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.37583e-06 3000 1 103.7 0.000122114 1000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.3577e-06 3000 1 103.7 0.000126336 1000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.34461e-06 3000 1 103.7 0.000146663 1000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.59032e-06 3000 1 103.7 0.000128458 1000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.95638e-06 3000 1 103.7 0.000153848 1000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.01264e-06 3000 1 103.7 0.000107888 1000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.57361e-06 3000 1 103.7 0.000117202 1000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.12605e-06 3000 1 103.7 9.12038e-05 1000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.37627e-06 3000 1 103.7 0.000137695 1000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.45407e-06 3000 1 103.7 9.8738e-05 1000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.21104e-06 3000 1 103.7 0.000102444 1000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.59569e-06 3000 1 103.7 0.000128561 1000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.43513e-06 3000 1 103.7 0.000126453 1000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.63991e-06 3000 1 103.7 0.000122222 1000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 2.16811e-06 3000 1 103.7 0.00012987 1000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.47299e-06 3000 1 103.7 0.000108467 1000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 2.14574e-06 3000 1 103.7 0.000143598 1000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.263e-06 3000 1 103.7 9.80381e-05 1000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.23414e-06 3000 1 103.7 0.000101154 1000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.75612e-06 3000 1 103.7 0.000149725 1000 2000000 2000000 -445.09542 26763.922 1.1177434 293.40142 0 0 0 0 2712.8962 -13041.416 -116.16932 0 -10328.52 1748.2732 Loop time of 2999.26 on 32 procs for 2000000 steps with 3000 atoms Performance: 57.614 ns/day, 0.417 hours/ns, 666.832 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 | 1626.4 | 1833.5 | 2021 | 232.1 | 61.13 Bond | 1.1703 | 1.3481 | 1.9964 | 12.9 | 0.04 Neigh | 101.94 | 102.16 | 102.3 | 1.0 | 3.41 Comm | 461.51 | 628.86 | 845.24 | 371.7 | 20.97 Output | 0.0038934 | 0.0051068 | 0.0063518 | 1.0 | 0.00 Modify | 392.58 | 413.67 | 444.9 | 92.1 | 13.79 Other | | 19.73 | | | 0.66 Nlocal: 93.75 ave 103 max 83 min Histogram: 1 2 3 4 5 4 1 3 4 5 Nghost: 3852.38 ave 3885 max 3823 min Histogram: 3 3 7 2 1 1 7 7 0 1 Neighs: 33271.1 ave 38972 max 29409 min Histogram: 5 4 4 3 4 5 2 1 2 2 Total # of neighbors = 1064675 Ave neighs/atom = 354.89167 Ave special neighs/atom = 2 Neighbor list builds = 87197 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.75612e-06 3000 1 103.7 0.000149725 1000 Per MPI rank memory allocation (min/avg/max) = 8.79 | 8.796 | 8.804 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 -443.5811 26763.922 1.1177434 293.40142 0 0 0 0 2712.8962 -13041.416 -116.16932 0 -10328.52 1748.2732 Loop time of 6.88906e-06 on 32 procs for 0 steps with 3000 atoms 109.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 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 | | 6.889e-06 | | |100.00 Nlocal: 93.75 ave 103 max 83 min Histogram: 1 2 3 4 5 4 1 3 4 5 Nghost: 3852.38 ave 3885 max 3823 min Histogram: 3 3 7 2 1 1 7 7 0 1 Neighs: 33271.1 ave 38972 max 29409 min Histogram: 5 4 4 3 4 5 2 1 2 2 Total # of neighbors = 1064675 Ave neighs/atom = 354.89167 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out