#------------------------------------------------------------------------------- # 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 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 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00069 0.10904 8304 2 97.6898 10.1954 2768 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.15 | 13.65 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 0 1e-06 -3531.696 140505.98 1.42352 406.71708 6.4561645 22.970202 0 0 36299.564 -67104.674 -315.99625 -291760.57 -322536.25 9247.778 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.29056e-06 8304 2 103.7 0.00010163 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.08635e-06 8304 2 103.7 9.38244e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.25305e-06 8304 2 103.7 9.3212e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.38174e-06 8304 2 103.7 0.000107393 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.17382e-06 8304 2 103.7 0.000106756 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.64736e-06 8304 2 103.7 0.000124985 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.14844e-06 8304 2 103.7 9.01734e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.57805e-06 8304 2 103.7 0.000112012 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.12685e-06 8304 2 103.7 8.78241e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.25832e-06 8304 2 103.7 9.06816e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.19042e-06 8304 2 103.7 9.68389e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.31517e-06 8304 2 103.7 9.56799e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.41923e-06 8304 2 103.7 0.000103248 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.39963e-06 8304 2 103.7 9.54531e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.21967e-06 8304 2 103.7 9.79031e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16569e-06 8304 2 103.7 9.96522e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.51112e-06 8304 2 103.7 9.84552e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.84488e-06 8304 2 103.7 0.000132325 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.24458e-06 8304 2 103.7 0.000100713 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.47885e-06 8304 2 103.7 0.000104793 2768 1000000 1000000 -433.11648 140505.98 1.42352 295.63473 42.814832 76.967432 0 0 34342.416 -50742.012 -315.99625 -291935.36 -308215.17 6722.0299 Loop time of 9472.9 on 32 procs for 1000000 steps with 10721 atoms Performance: 9.121 ns/day, 2.631 hours/ns, 105.564 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1296.8 | 4420.4 | 6171.1 |2790.2 | 46.66 Bond | 0.97122 | 2.637 | 4.924 | 82.6 | 0.03 Kspace | 1837.9 | 3592.8 | 6735.1 |3105.7 | 37.93 Neigh | 444.94 | 445.67 | 447.14 | 2.7 | 4.70 Comm | 359.9 | 464.74 | 508.28 | 222.5 | 4.91 Output | 0.01301 | 0.015537 | 0.017916 | 1.2 | 0.00 Modify | 489.18 | 524.85 | 611.8 | 179.1 | 5.54 Other | | 21.73 | | | 0.23 Nlocal: 335.031 ave 411 max 160 min Histogram: 4 4 0 0 0 0 0 2 8 14 Nghost: 6415.44 ave 7582 max 4738 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 156538 ave 229403 max 43584 min Histogram: 8 0 0 0 0 4 0 4 10 6 Total # of neighbors = 5009208 Ave neighs/atom = 467.23328 Ave special neighs/atom = 1.6069397 Neighbor list builds = 49613 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.47885e-06 8304 2 103.7 0.000104793 2768 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.24 | 13.65 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 -432.4967 140505.98 1.42352 295.63473 42.814832 76.967432 0 0 34342.416 -50742.012 -315.99625 -291935.36 -308215.17 6722.0299 Loop time of 8.07469e-06 on 32 procs for 0 steps with 10721 atoms 120.0% 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 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 | | 8.075e-06 | | |100.00 Nlocal: 335.031 ave 411 max 160 min Histogram: 4 4 0 0 0 0 0 2 8 14 Nghost: 6415.44 ave 7582 max 4738 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 156538 ave 229403 max 43584 min Histogram: 8 0 0 0 0 4 0 4 10 6 Total # of neighbors = 5009208 Ave neighs/atom = 467.23328 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out