#------------------------------------------------------------------------------- # Stage 2.4: 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 = 0.002 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 file 2.4_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 file 2.4_instantaneous.txt restart 200000 2.4.restart dump sci all custom 20000 2.4.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 1.00023 0.0893345 8304 2 97.8685 12.7661 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.79 | 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 7594.9212 83836.018 1.448125 428.55654 9.2631108 70.925409 0 0 25449.721 -180619.19 0 0 -155089.28 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.53407e-06 8304 2 103.7 0.000118142 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.37405e-06 8304 2 103.7 0.000120972 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.64049e-06 8304 2 103.7 0.000109242 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.72213e-06 8304 2 103.7 0.000110394 2768 200000 200000 2692.425 98053.008 1.2381572 297.77078 52.225258 116.07046 0 0 23157.694 -185145.77 0 0 -161819.78 5620.2713 Loop time of 741.101 on 32 procs for 200000 steps with 9101 atoms Performance: 23.317 ns/day, 1.029 hours/ns, 269.869 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 | 239.7 | 437.4 | 610.02 | 580.4 | 59.02 Bond | 0.14578 | 0.38275 | 0.66398 | 25.7 | 0.05 Neigh | 35.981 | 36.085 | 36.23 | 1.3 | 4.87 Comm | 43.899 | 201.02 | 361.78 | 723.7 | 27.12 Output | 0.011219 | 0.013495 | 0.015605 | 1.1 | 0.00 Modify | 47.771 | 63.374 | 100.25 | 268.9 | 8.55 Other | | 2.827 | | | 0.38 Nlocal: 284.406 ave 343 max 204 min Histogram: 4 2 2 2 4 2 0 4 4 8 Nghost: 4239.03 ave 5389 max 3036 min Histogram: 8 8 0 0 0 0 0 0 0 16 Neighs: 86338.6 ave 125280 max 39937 min Histogram: 7 1 0 0 6 2 2 4 8 2 Total # of neighbors = 2762835 Ave neighs/atom = 303.57488 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9547 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.4.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 1.72213e-06 8304 2 103.7 0.000110394 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 2693.3311 98053.008 1.2381572 297.77078 52.225258 116.07046 0 0 23157.694 -185145.77 0 0 -161819.78 5620.2713 Loop time of 7.0355e-06 on 32 procs for 0 steps with 9101 atoms 110.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.036e-06 | | |100.00 Nlocal: 284.406 ave 343 max 204 min Histogram: 4 2 2 2 4 2 0 4 4 8 Nghost: 4239.03 ave 5389 max 3036 min Histogram: 8 8 0 0 0 0 0 0 0 16 Neighs: 86338.6 ave 125280 max 39937 min Histogram: 7 1 0 0 6 2 2 4 8 2 Total # of neighbors = 2762835 Ave neighs/atom = 303.57488 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out