#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 ns 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 200000 200000 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 200 1 200 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 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 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 8.00804e-13 8304 2 103.7 8.28777e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.9 | 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 2205.4457 99608.125 1.2188266 300.41655 52.95482 124.71768 0 0 22391.991 -178568.55 0 0 -155998.89 5670.2089 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.3918e-06 8304 2 103.7 0.000103462 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.44416e-06 8304 2 103.7 9.59512e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.23681e-06 8304 2 103.7 9.91485e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.54942e-06 8304 2 103.7 0.000109896 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.57276e-06 8304 2 103.7 0.000102087 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 2.01827e-06 8304 2 103.7 0.000131166 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.44319e-06 8304 2 103.7 9.65586e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.67525e-06 8304 2 103.7 0.000125173 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.54943e-06 8304 2 103.7 0.000104265 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.42309e-06 8304 2 103.7 0.000101271 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.47211e-06 8304 2 103.7 0.000122381 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.4522e-06 8304 2 103.7 0.000102481 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.41209e-06 8304 2 103.7 9.47689e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.44627e-06 8304 2 103.7 9.33125e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.5627e-06 8304 2 103.7 0.000100815 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.43218e-06 8304 2 103.7 9.84685e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.37591e-06 8304 2 103.7 0.000104227 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.42455e-06 8304 2 103.7 0.000142246 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20395e-06 8304 2 103.7 0.000118305 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.64278e-06 8304 2 103.7 0.000118949 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.36834e-06 8304 2 103.7 0.000107966 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.65775e-06 8304 2 103.7 0.00012261 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21342e-06 8304 2 103.7 0.000113571 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.42253e-06 8304 2 103.7 0.000106634 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.29337e-06 8304 2 103.7 0.000113618 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.40505e-06 8304 2 103.7 0.000124971 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.45687e-06 8304 2 103.7 0.000139518 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.23505e-06 8304 2 103.7 0.000102378 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.71377e-06 8304 2 103.7 0.000115909 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.35795e-06 8304 2 103.7 0.000118721 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.50879e-06 8304 2 103.7 0.000104647 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.0651e-06 8304 2 103.7 0.000102381 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.77897e-06 8304 2 103.7 0.000111848 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 2.43272e-06 8304 2 103.7 0.000161914 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.57691e-06 8304 2 103.7 0.000104143 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.44063e-06 8304 2 103.7 0.000106214 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.38627e-06 8304 2 103.7 0.000104847 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.23421e-06 8304 2 103.7 9.49543e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.48789e-06 8304 2 103.7 0.000103507 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.20865e-06 8304 2 103.7 0.000103268 2768 2000000 2000000 874.47204 99499.006 1.2201633 295.55787 41.500372 114.21704 0 0 22697.853 -186548.99 0 0 -163695.42 5578.5039 Loop time of 7104.91 on 32 procs for 2000000 steps with 9101 atoms Performance: 24.321 ns/day, 0.987 hours/ns, 281.495 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2540.5 | 4289.7 | 5741.6 |1730.1 | 60.38 Bond | 1.4205 | 3.7874 | 7.1684 | 80.9 | 0.05 Neigh | 352.38 | 353.82 | 355.43 | 4.3 | 4.98 Comm | 482.08 | 1823 | 3319.1 |2357.1 | 25.66 Output | 0.0096173 | 0.011851 | 0.01393 | 1.2 | 0.00 Modify | 493.65 | 605.42 | 856.31 | 594.3 | 8.52 Other | | 29.26 | | | 0.41 Nlocal: 284.406 ave 341 max 225 min Histogram: 4 6 5 1 0 0 2 2 4 8 Nghost: 4210.78 ave 5311 max 3100 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 84632.7 ave 117096 max 49945 min Histogram: 7 1 4 4 0 0 0 4 7 5 Total # of neighbors = 2708245 Ave neighs/atom = 297.57664 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95923 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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 2000000 2 0.97 1.20865e-06 8304 2 103.7 0.000103268 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.9 | 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 2000000 2000000 875.52051 99499.006 1.2201633 295.55787 41.500372 114.21704 0 0 22697.853 -186548.99 0 0 -163695.42 5578.5039 Loop time of 6.68831e-06 on 32 procs for 0 steps with 9101 atoms 112.1% 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 | | 6.688e-06 | | |100.00 Nlocal: 284.406 ave 341 max 225 min Histogram: 4 6 5 1 0 0 2 2 4 8 Nghost: 4210.78 ave 5311 max 3100 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 84632.7 ave 117096 max 49945 min Histogram: 7 1 4 4 0 0 0 4 7 5 Total # of neighbors = 2708245 Ave neighs/atom = 297.57664 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: 6:54:07