#------------------------------------------------------------------------------- # Stage 2.3: NVT integration for 100 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # of frozen angles find clusters CPU = 0.000 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 10000 10000 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 2.3_averages.txt off 1 fix 3 movable ave/time 10 1 10 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 2.3_instantaneous.txt restart 100000 2.3.restart dump sci all custom 10000 2.3.xyz id mol type q xs ys zs timestep 1 run 100000 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.995999 0.0520504 6600 1 98.42 11.2877 2200 Per MPI rank memory allocation (min/avg/max) = 10.89 | 11.08 | 11.27 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 -2203.4049 59592.665 1.1043881 296.89675 0 0 0 0 6597.049 -26685.807 0 0 -20088.758 3893.0834 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.77942e-06 6600 1 103.7 0.000108869 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 2.16861e-06 6600 1 103.7 0.000117678 2200 100000 100000 -2511.1501 71431.48 0.92135052 299.06344 0 0 0 0 6118.362 -36890.144 0 0 -30771.782 3921.4943 Loop time of 1370.52 on 8 procs for 100000 steps with 6600 atoms Performance: 6.304 ns/day, 3.807 hours/ns, 72.965 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 866.83 | 1051.2 | 1244.8 | 473.8 | 76.70 Bond | 0.10232 | 0.1154 | 0.12314 | 1.8 | 0.01 Neigh | 67.432 | 67.526 | 67.6 | 0.8 | 4.93 Comm | 23.332 | 217.07 | 401.27 |1043.8 | 15.84 Output | 0.015141 | 0.016199 | 0.017056 | 0.5 | 0.00 Modify | 31.552 | 32.08 | 32.639 | 5.9 | 2.34 Other | | 2.543 | | | 0.19 Nlocal: 825 ave 857 max 790 min Histogram: 1 1 1 0 0 0 2 1 1 1 Nghost: 7480.38 ave 7625 max 7342 min Histogram: 2 1 1 0 0 0 0 1 1 2 Neighs: 442995 ave 542150 max 352736 min Histogram: 4 0 0 0 0 0 0 0 2 2 Total # of neighbors = 3543960 Ave neighs/atom = 536.96364 Ave special neighs/atom = 2 Neighbor list builds = 4877 Dangerous builds = 0 undump sci restart 0 dump sci all custom 100000 2.3.xyz id mol type q xs ys zs run 0 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 2.16861e-06 6600 1 103.7 0.000117678 2200 Per MPI rank memory allocation (min/avg/max) = 10.89 | 11.08 | 11.28 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 100000 100000 -2510.4175 71431.48 0.92135052 299.06344 0 0 0 0 6118.362 -36890.144 0 0 -30771.782 3921.4943 Loop time of 3.70087e-06 on 8 procs for 0 steps with 6600 atoms 121.6% CPU use with 8 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 | | 3.701e-06 | | |100.00 Nlocal: 825 ave 857 max 790 min Histogram: 1 1 1 0 0 0 2 1 1 1 Nghost: 7480.38 ave 7625 max 7342 min Histogram: 2 1 1 0 0 0 0 1 1 2 Neighs: 442995 ave 542150 max 352736 min Histogram: 4 0 0 0 0 0 0 0 2 2 Total # of neighbors = 3543960 Ave neighs/atom = 536.96364 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:40:29