#------------------------------------------------------------------------------- # 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 sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.14904e-13 8304 2 103.7 7.91402e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.74 | 12.17 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 2212.9883 92859.489 1.3074058 292.89689 50.493259 115.81215 0 0 21202.859 -168752.42 -448.40969 0 -147383.26 5528.2792 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25333e-06 8304 2 103.7 0.000111049 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.68173e-06 8304 2 103.7 0.000109201 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.74657e-06 8304 2 103.7 0.000114098 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.52827e-06 8304 2 103.7 0.000120897 2768 200000 200000 712.48759 92859.489 1.3074058 300.82565 46.101685 116.00873 0 0 21199.982 -173894.49 -448.40969 0 -152532.4 5677.9304 Loop time of 598.774 on 32 procs for 200000 steps with 9101 atoms Performance: 28.859 ns/day, 0.832 hours/ns, 334.016 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 396.75 | 439.35 | 498.32 | 103.5 | 73.37 Bond | 0.14031 | 0.38679 | 0.7404 | 26.8 | 0.06 Neigh | 29.845 | 29.939 | 30.007 | 0.7 | 5.00 Comm | 23.766 | 65.876 | 122.34 | 285.0 | 11.00 Output | 0.0090214 | 0.011226 | 0.013295 | 1.2 | 0.00 Modify | 43.749 | 60.396 | 84.426 | 177.2 | 10.09 Other | | 2.818 | | | 0.47 Nlocal: 284.406 ave 309 max 266 min Histogram: 4 3 4 2 6 6 2 3 1 1 Nghost: 4939.69 ave 5047 max 4802 min Histogram: 1 2 1 4 7 3 4 2 4 4 Neighs: 88319.2 ave 101293 max 79142 min Histogram: 3 2 7 4 6 4 4 1 0 1 Total # of neighbors = 2826214 Ave neighs/atom = 310.53884 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9562 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 sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.52827e-06 8304 2 103.7 0.000120897 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.74 | 12.17 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 713.49539 92859.489 1.3074058 300.82565 46.101685 116.00873 0 0 21199.982 -173894.49 -448.40969 0 -152532.4 5677.9304 Loop time of 9.97453e-06 on 32 procs for 0 steps with 9101 atoms 160.4% 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 | | 9.975e-06 | | |100.00 Nlocal: 284.406 ave 309 max 266 min Histogram: 4 3 4 2 6 6 2 3 1 1 Nghost: 4939.69 ave 5047 max 4802 min Histogram: 1 2 1 4 7 3 4 2 4 4 Neighs: 88319.2 ave 101293 max 79142 min Histogram: 3 2 7 4 6 4 4 1 0 1 Total # of neighbors = 2826214 Ave neighs/atom = 310.53884 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: 0:19:55