#------------------------------------------------------------------------------- # 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 3275 = # 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) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00179 0.0739539 9825 1 97.5292 10.883 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.27 | 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 -7974.594 143778.81 1.3074423 420.87983 5.8446879 16.239556 0 0 41437.001 -94309.581 -318.5841 -317478.44 -370328.94 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.18783e-06 9825 1 103.7 9.5917e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.40125e-06 9825 1 103.7 0.000135109 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.19447e-06 9825 1 103.7 9.35405e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.56737e-06 9825 1 103.7 0.000103392 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.05439e-06 9825 1 103.7 9.17362e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.34981e-06 9825 1 103.7 0.000111673 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.86416e-06 9825 1 103.7 0.000137889 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.3404e-06 9825 1 103.7 0.000101253 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.1697e-06 9825 1 103.7 9.58485e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.59755e-06 9825 1 103.7 9.67334e-05 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.24406e-06 9825 1 103.7 9.16155e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.11222e-06 9825 1 103.7 9.21155e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.32593e-06 9825 1 103.7 9.49367e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.27436e-06 9825 1 103.7 9.31775e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.29212e-06 9825 1 103.7 0.000106148 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.52866e-06 9825 1 103.7 0.000107798 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.19894e-06 9825 1 103.7 9.6496e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.36327e-06 9825 1 103.7 0.000111637 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.32745e-06 9825 1 103.7 0.000108809 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.32686e-06 9825 1 103.7 9.22601e-05 3275 1000000 1000000 -7298.976 143778.81 1.3074423 301.7083 47.728228 60.779262 0 0 36858.052 -72958.762 -318.5841 -317338.32 -353330.52 7120.9356 Loop time of 9213.71 on 32 procs for 1000000 steps with 12250 atoms Performance: 9.377 ns/day, 2.559 hours/ns, 108.534 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 | 4342 | 5172.1 | 5882.2 | 610.5 | 56.13 Bond | 1.1947 | 2.6275 | 4.9994 | 74.0 | 0.03 Kspace | 1874.6 | 2588.7 | 3423 | 866.4 | 28.10 Neigh | 312.23 | 312.64 | 313.08 | 1.2 | 3.39 Comm | 511.95 | 538.47 | 555.33 | 62.5 | 5.84 Output | 0.01429 | 0.017122 | 0.019709 | 1.3 | 0.00 Modify | 560.68 | 573.03 | 596.18 | 53.6 | 6.22 Other | | 26.12 | | | 0.28 Nlocal: 382.812 ave 406 max 352 min Histogram: 2 2 5 1 0 4 5 4 5 4 Nghost: 7248.69 ave 7509 max 6922 min Histogram: 7 1 1 3 0 3 5 0 5 7 Neighs: 187534 ave 209373 max 155241 min Histogram: 4 2 2 0 0 5 5 6 3 5 Total # of neighbors = 6001076 Ave neighs/atom = 489.88376 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49821 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) = 0.25493894 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037055622 estimated relative force accuracy = 1.115919e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.32686e-06 9825 1 103.7 9.22601e-05 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.41 | 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 -7298.1765 143778.81 1.3074423 301.7083 47.728228 60.779262 0 0 36858.052 -72958.762 -318.5841 -317338.32 -353330.52 7120.9356 Loop time of 9.62941e-06 on 32 procs for 0 steps with 12250 atoms 111.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 9.629e-06 | | |100.00 Nlocal: 382.812 ave 406 max 352 min Histogram: 2 2 5 1 0 4 5 4 5 4 Nghost: 7248.69 ave 7509 max 6922 min Histogram: 7 1 1 3 0 3 5 0 5 7 Neighs: 187534 ave 209373 max 155241 min Histogram: 4 2 2 0 0 5 5 6 3 5 Total # of neighbors = 6001076 Ave neighs/atom = 489.88376 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out