#------------------------------------------------------------------------------- # 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 = 0.001 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 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 0.99586 0.053661 6600 1 98.5707 10.2874 2200 Per MPI rank memory allocation (min/avg/max) = 10.57 | 11.1 | 11.34 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 0 1e-06 -748.35688 72622.896 0.90623529 300.54572 0 0 0 0 6539.424 -20061.123 0 0 -13521.699 3940.9308 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.317e-06 6600 1 103.7 9.74407e-05 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.37685e-06 6600 1 103.7 9.83283e-05 2200 100000 100000 704.05906 70653.335 0.93149787 298.67308 0 0 0 0 6056.8229 -26124.332 0 0 -20067.509 3916.3757 Loop time of 1409.92 on 8 procs for 100000 steps with 6600 atoms Performance: 6.128 ns/day, 3.916 hours/ns, 70.926 timesteps/s 98.9% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 811.22 | 1030.1 | 1284.2 | 593.0 | 73.06 Bond | 0.10549 | 0.11335 | 0.1239 | 1.5 | 0.01 Neigh | 68.993 | 69.079 | 69.153 | 0.7 | 4.90 Comm | 21.802 | 275.94 | 494.61 |1146.2 | 19.57 Output | 0.015141 | 0.016164 | 0.017036 | 0.5 | 0.00 Modify | 31.87 | 32.186 | 32.658 | 4.1 | 2.28 Other | | 2.504 | | | 0.18 Nlocal: 825 ave 857 max 788 min Histogram: 1 2 0 0 0 1 1 1 0 2 Nghost: 7392.5 ave 7503 max 7328 min Histogram: 1 4 0 0 0 1 1 0 0 1 Neighs: 436396 ave 544095 max 337839 min Histogram: 2 2 0 0 0 0 0 2 1 1 Total # of neighbors = 3491170 Ave neighs/atom = 528.96515 Ave special neighs/atom = 2 Neighbor list builds = 4861 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 1.37685e-06 6600 1 103.7 9.83283e-05 2200 Per MPI rank memory allocation (min/avg/max) = 10.57 | 11.1 | 11.34 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 100000 100000 704.67441 70653.335 0.93149787 298.67308 0 0 0 0 6056.8229 -26124.332 0 0 -20067.509 3916.3757 Loop time of 3.19562e-06 on 8 procs for 0 steps with 6600 atoms 125.2% 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 | | 3.196e-06 | | |100.00 Nlocal: 825 ave 857 max 788 min Histogram: 1 2 0 0 0 1 1 1 0 2 Nghost: 7392.5 ave 7503 max 7328 min Histogram: 1 4 0 0 0 1 1 0 0 1 Neighs: 436396 ave 544095 max 337839 min Histogram: 2 2 0 0 0 0 0 2 1 1 Total # of neighbors = 3491170 Ave neighs/atom = 528.96515 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: 0:41:31