#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2699 = # 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 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00049 0.0670747 8097 2 97.6711 9.56808 2699 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.13 | 17.06 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 -3661.2758 138878.49 1.4411859 405.32842 5.1582302 20.450483 0 0 37796.43 -79507.692 -317.08001 -295523.21 -337208.86 9102.6318 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.24715e-06 8097 2 103.7 9.18011e-05 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.12451e-06 8097 2 103.7 9.33052e-05 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.07009e-06 8097 2 103.7 9.77444e-05 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.29615e-06 8097 2 103.7 9.74372e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.52741e-06 8097 2 103.7 0.000116627 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.49537e-06 8097 2 103.7 0.000124415 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.15177e-06 8097 2 103.7 0.000108269 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.74418e-06 8097 2 103.7 0.000128998 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.2616e-06 8097 2 103.7 9.37588e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.53325e-06 8097 2 103.7 0.000133254 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.22558e-06 8097 2 103.7 9.78901e-05 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.25787e-06 8097 2 103.7 0.000117499 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.18507e-06 8097 2 103.7 9.7241e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.28894e-06 8097 2 103.7 9.50549e-05 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.32631e-06 8097 2 103.7 0.000103205 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.29491e-06 8097 2 103.7 0.000102707 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.04086e-06 8097 2 103.7 9.77616e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.20864e-06 8097 2 103.7 9.84754e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.09073e-06 8097 2 103.7 0.000105249 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.66453e-06 8097 2 103.7 0.000108335 2699 1000000 1000000 63.600471 138878.49 1.4411859 296.66873 38.049249 51.2144 0 0 36216.236 -63623.774 -317.08001 -295427.35 -322745.63 6662.4151 Loop time of 26079.6 on 8 procs for 1000000 steps with 10558 atoms Performance: 3.313 ns/day, 7.244 hours/ns, 38.344 timesteps/s 98.7% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4458.6 | 15471 | 20789 |5127.7 | 59.32 Bond | 1.3165 | 5.7671 | 9.5769 | 125.4 | 0.02 Kspace | 3339.8 | 8664.7 | 19691 |6859.9 | 33.22 Neigh | 1078.5 | 1080.1 | 1082 | 3.3 | 4.14 Comm | 287.6 | 318.54 | 341.41 | 105.6 | 1.22 Output | 0.028673 | 0.031955 | 0.035143 | 1.2 | 0.00 Modify | 487.62 | 504.9 | 524.11 | 58.0 | 1.94 Other | | 34.33 | | | 0.13 Nlocal: 1319.75 ave 1589 max 718 min Histogram: 2 0 0 0 0 0 0 0 3 3 Nghost: 11021 ave 13027 max 9492 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 614131 ave 817686 max 179489 min Histogram: 2 0 0 0 0 0 0 1 1 4 Total # of neighbors = 4913048 Ave neighs/atom = 465.33889 Ave special neighs/atom = 1.5849593 Neighbor list builds = 49428 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.66453e-06 8097 2 103.7 0.000108335 2699 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.25 | 17.24 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 64.136158 138878.49 1.4411859 296.66873 38.049249 51.2144 0 0 36216.236 -63623.774 -317.08001 -295427.35 -322745.63 6662.4151 Loop time of 3.39375e-06 on 8 procs for 0 steps with 10558 atoms 128.9% 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 Kspace | 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 | | 3.394e-06 | | |100.00 Nlocal: 1319.75 ave 1589 max 718 min Histogram: 2 0 0 0 0 0 0 0 3 3 Nghost: 11021 ave 13027 max 9492 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 614131 ave 817686 max 179489 min Histogram: 2 0 0 0 0 0 0 1 1 4 Total # of neighbors = 4913048 Ave neighs/atom = 465.33889 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out