#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32678321 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029937681 estimated relative force accuracy = 9.0156437e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 5.64582e-12 8304 2 103.7 4.62137e-10 2768 Per MPI rank memory allocation (min/avg/max) = 12.61 | 13.09 | 13.28 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 -283.35951 97415.051 1.2462657 296.81502 46.361176 58.899149 0 0 21197.636 90416.975 -427.44005 -273261.76 -161541.89 5602.232 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.37949e-06 8304 2 103.7 9.97593e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.60785e-06 8304 2 103.7 0.000110354 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.24716e-06 8304 2 103.7 9.85797e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.56578e-06 8304 2 103.7 9.52609e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.19968e-06 8304 2 103.7 8.86149e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.24617e-06 8304 2 103.7 8.84761e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.2863e-06 8304 2 103.7 9.61658e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.2718e-06 8304 2 103.7 9.05075e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.2444e-06 8304 2 103.7 9.24917e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24036e-06 8304 2 103.7 9.2932e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.36223e-06 8304 2 103.7 0.000100352 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.46682e-06 8304 2 103.7 0.000102831 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.48732e-06 8304 2 103.7 0.000124634 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.7256e-06 8304 2 103.7 0.000131304 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.59512e-06 8304 2 103.7 0.000115152 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.48643e-06 8304 2 103.7 0.000111693 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.39547e-06 8304 2 103.7 9.864e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.38673e-06 8304 2 103.7 0.000105292 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.16113e-06 8304 2 103.7 9.60258e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.56606e-06 8304 2 103.7 0.00010725 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.24915e-06 8304 2 103.7 9.47838e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15134e-06 8304 2 103.7 0.000104509 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.65658e-06 8304 2 103.7 0.000116481 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.18959e-06 8304 2 103.7 9.27438e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.26083e-06 8304 2 103.7 9.64656e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.52662e-06 8304 2 103.7 0.00010027 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.26902e-06 8304 2 103.7 9.95837e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.21597e-06 8304 2 103.7 0.000105164 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.3347e-06 8304 2 103.7 9.79078e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.28962e-06 8304 2 103.7 8.99514e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.36241e-06 8304 2 103.7 8.77431e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15971e-06 8304 2 103.7 0.000105009 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.67461e-06 8304 2 103.7 0.000108732 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2454e-06 8304 2 103.7 9.86129e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.39247e-06 8304 2 103.7 0.00011597 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.20669e-06 8304 2 103.7 0.000103411 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.63177e-06 8304 2 103.7 9.99408e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.2515e-06 8304 2 103.7 0.000118918 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.46346e-06 8304 2 103.7 9.52388e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.47042e-06 8304 2 103.7 0.000103956 2768 2000000 2000000 219.19959 97415.051 1.2462657 300.72356 47.417171 52.849898 0 0 21529.937 90038.492 -427.44005 -273251.75 -161583.06 5676.0035 Loop time of 10871.7 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.895 ns/day, 1.510 hours/ns, 183.965 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 | 4093.4 | 4471.6 | 4934.6 | 251.9 | 41.13 Bond | 2.1777 | 5.3077 | 10.901 | 111.1 | 0.05 Kspace | 4184.3 | 4655.1 | 5039.5 | 248.8 | 42.82 Neigh | 275.56 | 276.17 | 276.91 | 2.5 | 2.54 Comm | 687.52 | 702.08 | 713.62 | 23.9 | 6.46 Output | 0.0095231 | 0.011802 | 0.013925 | 1.2 | 0.00 Modify | 718.28 | 726.83 | 738.98 | 20.4 | 6.69 Other | | 34.55 | | | 0.32 Nlocal: 284.406 ave 302 max 262 min Histogram: 2 2 1 3 2 6 8 2 2 4 Nghost: 4806.41 ave 4843 max 4744 min Histogram: 2 1 2 1 2 5 2 9 5 3 Neighs: 84517.1 ave 93766 max 73812 min Histogram: 1 2 2 5 3 3 9 5 0 2 Total # of neighbors = 2704548 Ave neighs/atom = 297.17042 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98645 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32678321 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029937681 estimated relative force accuracy = 9.0156437e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.47042e-06 8304 2 103.7 0.000103956 2768 Per MPI rank memory allocation (min/avg/max) = 12.62 | 13.13 | 13.28 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 2000000 2000000 220.22897 97415.051 1.2462657 300.72356 47.417171 52.849898 0 0 21529.937 90038.492 -427.44005 -273251.75 -161583.06 5676.0035 Loop time of 9.88956e-06 on 32 procs for 0 steps with 9101 atoms 107.4% 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 | | 9.89e-06 | | |100.00 Nlocal: 284.406 ave 302 max 262 min Histogram: 2 2 1 3 2 6 8 2 2 4 Nghost: 4806.41 ave 4843 max 4744 min Histogram: 2 1 2 1 2 5 2 9 5 3 Neighs: 84517.1 ave 93766 max 73812 min Histogram: 1 2 2 5 3 3 9 5 0 2 Total # of neighbors = 2704548 Ave neighs/atom = 297.17042 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