#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # of frozen angles find clusters CPU = 0.000 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 100000 100000 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 100 1 100 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 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.995771 0.0517624 6600 1 98.5726 10.6999 2200 Per MPI rank memory allocation (min/avg/max) = 10.87 | 11.12 | 11.64 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 -1568.0449 72400.411 0.90902013 447.33389 0 0 0 0 6394.4926 -25280.52 0 0 -18886.027 5865.703 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.27422e-06 6600 1 103.7 9.47412e-05 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.40828e-06 6600 1 103.7 9.15558e-05 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.16879e-06 6600 1 103.7 0.00010337 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.25378e-06 6600 1 103.7 9.56907e-05 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.50947e-06 6600 1 103.7 9.40662e-05 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.35174e-06 6600 1 103.7 9.09242e-05 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.19883e-06 6600 1 103.7 0.000116324 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.28118e-06 6600 1 103.7 8.86762e-05 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.09017e-06 6600 1 103.7 9.28671e-05 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.11185e-06 6600 1 103.7 9.28896e-05 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.2883e-06 6600 1 103.7 9.71512e-05 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.58186e-06 6600 1 103.7 0.000118135 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.16199e-06 6600 1 103.7 9.67063e-05 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.39993e-06 6600 1 103.7 9.40059e-05 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.3151e-06 6600 1 103.7 8.94514e-05 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.18112e-06 6600 1 103.7 0.000112816 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.19683e-06 6600 1 103.7 0.000103946 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.57824e-06 6600 1 103.7 0.000121019 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 2.10959e-06 6600 1 103.7 0.000135535 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.38817e-06 6600 1 103.7 9.96629e-05 2200 1000000 1000000 -1003.3733 70192.433 0.93761433 299.04826 0 0 0 0 5840.8433 -29735.624 0 0 -23894.781 3921.2952 Loop time of 14143.3 on 8 procs for 1000000 steps with 6600 atoms Performance: 6.109 ns/day, 3.929 hours/ns, 70.705 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8510.6 | 10604 | 12829 |1648.3 | 74.98 Bond | 1.0289 | 1.1651 | 1.3164 | 7.5 | 0.01 Neigh | 704.19 | 705.16 | 706.11 | 2.6 | 4.99 Comm | 276.21 | 2502.1 | 4596.2 |3396.6 | 17.69 Output | 0.016105 | 0.017177 | 0.018088 | 0.5 | 0.00 Modify | 305.51 | 308.04 | 309.59 | 8.6 | 2.18 Other | | 22.34 | | | 0.16 Nlocal: 825 ave 875 max 788 min Histogram: 1 1 0 2 2 1 0 0 0 1 Nghost: 7372.38 ave 7493 max 7304 min Histogram: 1 3 1 0 1 0 0 1 0 1 Neighs: 434189 ave 529268 max 356800 min Histogram: 4 0 0 0 0 0 0 0 3 1 Total # of neighbors = 3473510 Ave neighs/atom = 526.28939 Ave special neighs/atom = 2 Neighbor list builds = 48693 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.38817e-06 6600 1 103.7 9.96629e-05 2200 Per MPI rank memory allocation (min/avg/max) = 10.87 | 11.17 | 11.65 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 1000000 1000000 -1002.6126 70192.433 0.93761433 299.04826 0 0 0 0 5840.8433 -29735.624 0 0 -23894.781 3921.2952 Loop time of 3.4145e-06 on 8 procs for 0 steps with 6600 atoms 117.1% CPU use with 8 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 | | 3.415e-06 | | |100.00 Nlocal: 825 ave 875 max 788 min Histogram: 1 1 0 2 2 1 0 0 0 1 Nghost: 7372.38 ave 7493 max 7304 min Histogram: 1 3 1 0 1 0 0 1 0 1 Neighs: 434189 ave 529268 max 356800 min Histogram: 4 0 0 0 0 0 0 0 3 1 Total # of neighbors = 3473510 Ave neighs/atom = 526.28939 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out