#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 ps 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 20000 20000 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 20 1 20 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 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs timestep 1 run 200000 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.29972e-13 8304 2 103.7 7.70228e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.5 | 11.68 | 12.12 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-06 990.74259 103346.52 1.1747375 294.67338 46.322387 153.36654 0 0 21108.7 -169659.23 0 0 -148350.84 5561.8096 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.37362e-06 8304 2 103.7 0.000101715 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.58907e-06 8304 2 103.7 0.000113641 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.99622e-06 8304 2 103.7 0.000118718 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.38297e-06 8304 2 103.7 9.88678e-05 2768 200000 200000 1219.5006 102705.23 1.1820726 298.16608 44.336403 125.2932 0 0 21130.95 -169470.91 0 0 -148170.33 5627.7324 Loop time of 627.295 on 32 procs for 200000 steps with 9101 atoms Performance: 27.547 ns/day, 0.871 hours/ns, 318.829 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 328.94 | 405.2 | 501.7 | 251.7 | 64.59 Bond | 0.14791 | 0.37866 | 0.90822 | 28.5 | 0.06 Neigh | 29.192 | 29.249 | 29.314 | 0.7 | 4.66 Comm | 36.017 | 131.1 | 208.23 | 452.5 | 20.90 Output | 0.0085437 | 0.01066 | 0.012706 | 1.2 | 0.00 Modify | 55.969 | 58.13 | 61.276 | 23.2 | 9.27 Other | | 3.23 | | | 0.51 Nlocal: 284.406 ave 314 max 257 min Histogram: 1 3 6 2 4 9 2 1 2 2 Nghost: 3679.06 ave 3735 max 3626 min Histogram: 2 3 1 4 4 8 5 3 1 1 Neighs: 79932.5 ave 101382 max 64392 min Histogram: 6 4 5 2 0 2 5 5 2 1 Total # of neighbors = 2557841 Ave neighs/atom = 281.05054 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9688 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.38297e-06 8304 2 103.7 9.88678e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.5 | 11.68 | 12.12 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 200000 200000 1220.4654 102705.23 1.1820726 298.16608 44.336403 125.2932 0 0 21130.95 -169470.91 0 0 -148170.33 5627.7324 Loop time of 6.89766e-06 on 32 procs for 0 steps with 9101 atoms 104.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 6.898e-06 | | |100.00 Nlocal: 284.406 ave 314 max 257 min Histogram: 1 3 6 2 4 9 2 1 2 2 Nghost: 3679.06 ave 3735 max 3626 min Histogram: 2 3 1 4 4 8 5 3 1 1 Neighs: 79932.5 ave 101382 max 64392 min Histogram: 6 4 5 2 0 2 5 5 2 1 Total # of neighbors = 2557841 Ave neighs/atom = 281.05054 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: 0:20:56