#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 100 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 10000 10000 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 10 1 10 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 100000 2.4.restart dump sci all custom 10000 2.4.xyz id mol type q xs ys zs timestep 1 run 100000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.995791 0.664079 8304 2 97.3161 23.1125 2768 Per MPI rank memory allocation (min/avg/max) = 12.7 | 13.1 | 13.3 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 9017.8043 92859.489 1.3074058 428.55654 225.18486 138.43431 0 0 23865.772 -175142.55 -225.64506 0 -150913.16 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.22912e-06 8304 2 103.7 0.000103514 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.2527e-06 8304 2 103.7 0.000100623 2768 100000 100000 -637.12521 92859.489 1.3074058 298.95808 38.230578 97.982653 0 0 21091.785 -180203.1 -225.64506 0 -158975.1 5642.6811 Loop time of 959.655 on 16 procs for 100000 steps with 9101 atoms Performance: 9.003 ns/day, 2.666 hours/ns, 104.204 timesteps/s 99.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 711.88 | 808.74 | 857.31 | 124.5 | 84.27 Bond | 0.11309 | 0.3865 | 0.53281 | 15.2 | 0.04 Neigh | 44.599 | 44.65 | 44.699 | 0.4 | 4.65 Comm | 16.097 | 64.329 | 166.67 | 475.3 | 6.70 Output | 0.013657 | 0.015461 | 0.017079 | 0.9 | 0.00 Modify | 31.335 | 39.05 | 64.464 | 135.2 | 4.07 Other | | 2.488 | | | 0.26 Nlocal: 568.812 ave 597 max 526 min Histogram: 1 0 0 0 3 3 4 2 2 1 Nghost: 9013.12 ave 9090 max 8890 min Histogram: 1 0 0 1 3 2 5 0 1 3 Neighs: 319428 ave 347145 max 275173 min Histogram: 1 0 0 0 2 5 3 2 2 1 Total # of neighbors = 5110852 Ave neighs/atom = 561.57038 Ave special neighs/atom = 1.8929788 Neighbor list builds = 4860 Dangerous builds = 0 undump sci restart 0 dump sci all custom 100000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.2527e-06 8304 2 103.7 0.000100623 2768 Per MPI rank memory allocation (min/avg/max) = 13.09 | 13.16 | 13.3 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 100000 100000 -636.03912 92859.489 1.3074058 298.95808 38.230578 97.982653 0 0 21091.785 -180203.1 -225.64506 0 -158975.1 5642.6811 Loop time of 4.07081e-06 on 16 procs for 0 steps with 9101 atoms 118.2% CPU use with 16 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 | | 4.071e-06 | | |100.00 Nlocal: 568.812 ave 597 max 526 min Histogram: 1 0 0 0 3 3 4 2 2 1 Nghost: 9013.12 ave 9090 max 8890 min Histogram: 1 0 0 1 3 2 5 0 1 3 Neighs: 319428 ave 347145 max 275173 min Histogram: 1 0 0 0 2 5 3 2 2 1 Total # of neighbors = 5110852 Ave neighs/atom = 561.57038 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