#------------------------------------------------------------------------------- # 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 8303 = # 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 1.16873e-12 24909 2 103.7 8.62173e-11 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.8 | 13.19 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-06 757.6254 329121.76 1.1065415 298.2021 159.9552 360.44872 0 0 64367.694 -521377.22 0 0 -456489.13 16885.237 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.52795e-06 24909 2 103.7 0.000101769 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.91089e-06 24909 2 103.7 0.000124051 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.58223e-06 24909 2 103.7 0.000115562 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.62716e-06 24909 2 103.7 0.000103378 8303 200000 200000 195.78482 329863.05 1.1040548 299.91347 141.66949 373.21032 0 0 64267.979 -527515.34 0 0 -462732.48 16982.141 Loop time of 1544.32 on 32 procs for 200000 steps with 27300 atoms Performance: 11.189 ns/day, 2.145 hours/ns, 129.507 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 | 957.74 | 1141.9 | 1307.5 | 330.7 | 73.94 Bond | 0.22604 | 0.84523 | 1.3728 | 33.3 | 0.05 Neigh | 84.513 | 84.731 | 84.959 | 1.2 | 5.49 Comm | 50.321 | 208.45 | 402.96 | 788.1 | 13.50 Output | 0.022523 | 0.027296 | 0.031911 | 1.7 | 0.00 Modify | 92.516 | 103.21 | 122.45 | 91.6 | 6.68 Other | | 5.201 | | | 0.34 Nlocal: 853.125 ave 936 max 778 min Histogram: 4 5 1 4 3 4 1 3 4 3 Nghost: 5286.72 ave 5548 max 5076 min Histogram: 9 3 4 0 0 0 4 6 4 2 Neighs: 239608 ave 290455 max 190189 min Histogram: 4 7 4 1 0 0 3 2 6 5 Total # of neighbors = 7667469 Ave neighs/atom = 280.85967 Ave special neighs/atom = 1.892967 Neighbor list builds = 10566 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 1.62716e-06 24909 2 103.7 0.000103378 8303 Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.8 | 13.19 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 196.60797 329863.05 1.1040548 299.91347 141.66949 373.21032 0 0 64267.979 -527515.34 0 0 -462732.48 16982.141 Loop time of 8.10825e-06 on 32 procs for 0 steps with 27300 atoms 108.7% 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 | | 8.108e-06 | | |100.00 Nlocal: 853.125 ave 936 max 778 min Histogram: 4 5 1 4 3 4 1 3 4 3 Nghost: 5286.72 ave 5548 max 5076 min Histogram: 9 3 4 0 0 0 4 6 4 2 Neighs: 239608 ave 290455 max 190189 min Histogram: 4 7 4 1 0 0 3 2 6 5 Total # of neighbors = 7667469 Ave neighs/atom = 280.85967 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:51:37