#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 200 ps with a timestep of 1 fs # Temperature 298.15 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 8303 = # 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 298.15 298.15 100 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 0.994854 0.916743 24909 2 96.3327 121.378 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.74 | 13.17 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 35212.622 290456.39 1.2538436 428.46899 116.39622 1103.9078 0 0 91641.976 -459494.42 0 0 -366632.14 24261.4 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.80716e-06 24909 2 103.7 0.000107449 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.71284e-06 24909 2 103.7 0.000101533 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.58909e-06 24909 2 103.7 0.000105609 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.75348e-06 24909 2 103.7 0.00012153 8303 200000 200000 -372.99436 322479.38 1.1293339 302.1865 141.35434 391.92751 0 0 63348.081 -526074.18 0 0 -462192.82 17110.848 Loop time of 1557.4 on 32 procs for 200000 steps with 27300 atoms Performance: 11.095 ns/day, 2.163 hours/ns, 128.419 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 997.53 | 1135.2 | 1327.1 | 222.7 | 72.89 Bond | 0.42036 | 0.86916 | 1.5699 | 32.5 | 0.06 Neigh | 85.298 | 85.455 | 85.71 | 1.0 | 5.49 Comm | 46.545 | 215.29 | 380.43 | 516.8 | 13.82 Output | 0.022735 | 0.027565 | 0.03226 | 1.7 | 0.00 Modify | 88.006 | 115.82 | 195.99 | 291.3 | 7.44 Other | | 4.707 | | | 0.30 Nlocal: 853.125 ave 932 max 785 min Histogram: 1 1 5 4 7 9 2 2 0 1 Nghost: 5283.59 ave 5409 max 5140 min Histogram: 3 2 2 2 6 3 4 4 2 4 Neighs: 238369 ave 295619 max 197222 min Histogram: 3 7 5 1 0 5 6 2 2 1 Total # of neighbors = 7627821 Ave neighs/atom = 279.40736 Ave special neighs/atom = 1.892967 Neighbor list builds = 10606 Dangerous builds = 1 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 1.75348e-06 24909 2 103.7 0.00012153 8303 Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.77 | 13.18 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 -372.07979 322479.38 1.1293339 302.1865 141.35434 391.92751 0 0 63348.081 -526074.18 0 0 -462192.82 17110.848 Loop time of 7.86103e-06 on 32 procs for 0 steps with 27300 atoms 108.1% 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 | | 7.861e-06 | | |100.00 Nlocal: 853.125 ave 932 max 785 min Histogram: 1 1 5 4 7 9 2 2 0 1 Nghost: 5283.59 ave 5409 max 5140 min Histogram: 3 2 2 2 6 3 4 4 2 4 Neighs: 238369 ave 295619 max 197222 min Histogram: 3 7 5 1 0 5 6 2 2 1 Total # of neighbors = 7627821 Ave neighs/atom = 279.40736 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out