#------------------------------------------------------------------------------- # 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 WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.12621e-12 8304 2 103.7 8.94289e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.88 | 12.21 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 2693.3346 98053.008 1.2381572 297.77078 52.225258 116.07046 0 0 23157.694 -185145.75 0 0 -161819.76 5620.2713 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.38219e-06 8304 2 103.7 9.74239e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.60287e-06 8304 2 103.7 0.000107122 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.49006e-06 8304 2 103.7 0.000130783 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39797e-06 8304 2 103.7 0.000102652 2768 200000 200000 2669.965 99763.48 1.2169286 298.87262 49.915095 117.77627 0 0 23168.027 -184051.24 0 0 -160715.52 5641.068 Loop time of 740.137 on 32 procs for 200000 steps with 9101 atoms Performance: 23.347 ns/day, 1.028 hours/ns, 270.220 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 240.36 | 434.95 | 606.3 | 583.3 | 58.77 Bond | 0.1485 | 0.38051 | 0.61376 | 26.3 | 0.05 Neigh | 36.009 | 36.106 | 36.239 | 1.3 | 4.88 Comm | 44.228 | 199.7 | 357.14 | 729.0 | 26.98 Output | 0.0093918 | 0.011676 | 0.013829 | 1.2 | 0.00 Modify | 49.789 | 65.806 | 103.2 | 267.5 | 8.89 Other | | 3.182 | | | 0.43 Nlocal: 284.406 ave 346 max 200 min Histogram: 3 3 3 4 3 0 0 0 8 8 Nghost: 4241.53 ave 5380 max 3054 min Histogram: 15 1 0 0 0 0 0 0 0 16 Neighs: 85921.2 ave 123662 max 39479 min Histogram: 4 4 0 2 6 0 1 4 6 5 Total # of neighbors = 2749478 Ave neighs/atom = 302.10724 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9574 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 WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39797e-06 8304 2 103.7 0.000102652 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.88 | 12.21 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 2670.9407 99763.48 1.2169286 298.87262 49.915095 117.77627 0 0 23168.027 -184051.24 0 0 -160715.52 5641.068 Loop time of 7.17697e-06 on 32 procs for 0 steps with 9101 atoms 105.4% 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 | | 7.177e-06 | | |100.00 Nlocal: 284.406 ave 346 max 200 min Histogram: 3 3 3 4 3 0 0 0 8 8 Nghost: 4241.53 ave 5380 max 3054 min Histogram: 15 1 0 0 0 0 0 0 0 16 Neighs: 85921.2 ave 123662 max 39479 min Histogram: 4 4 0 2 6 0 1 4 6 5 Total # of neighbors = 2749478 Ave neighs/atom = 302.10724 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: 0:24:44