#------------------------------------------------------------------------------- # Stage 2.5: 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 2.5_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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.85341e-13 11184 2 103.7 8.0334e-11 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 335929.19 143799.62 1.371895 297.37957 276.1468 362.97776 0 0 271595.53 -52433.342 -383.45046 -378985.51 -159184.19 8165.8117 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.33419e-06 11184 2 103.7 9.59926e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.23862e-06 11184 2 103.7 9.07758e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27856e-06 11184 2 103.7 0.000103604 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.45339e-06 11184 2 103.7 0.000106557 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.15835e-06 11184 2 103.7 9.09732e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.29304e-06 11184 2 103.7 9.09013e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2671e-06 11184 2 103.7 9.77907e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.78007e-06 11184 2 103.7 0.000114019 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.28558e-06 11184 2 103.7 9.06464e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.2439e-06 11184 2 103.7 9.41551e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.19062e-06 11184 2 103.7 8.94261e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2307e-06 11184 2 103.7 9.92265e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.59308e-06 11184 2 103.7 9.54923e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.3877e-06 11184 2 103.7 9.50957e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.75965e-06 11184 2 103.7 0.00010714 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.13028e-06 11184 2 103.7 9.31246e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.41742e-06 11184 2 103.7 0.000107258 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.62613e-06 11184 2 103.7 0.000110202 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.51357e-06 11184 2 103.7 0.000107031 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.36271e-06 11184 2 103.7 9.55281e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.33238e-06 11184 2 103.7 9.12286e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.52611e-06 11184 2 103.7 0.000121804 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.37379e-06 11184 2 103.7 0.00010451 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.64211e-06 11184 2 103.7 0.000112631 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.39624e-06 11184 2 103.7 9.55039e-05 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.67364e-06 11184 2 103.7 0.000105457 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.23093e-06 11184 2 103.7 9.05454e-05 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.35748e-06 11184 2 103.7 9.68061e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.4899e-06 11184 2 103.7 9.44574e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.49336e-06 11184 2 103.7 9.5904e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.09572e-06 11184 2 103.7 9.31758e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.25882e-06 11184 2 103.7 9.70951e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.46479e-06 11184 2 103.7 0.000101265 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.29527e-06 11184 2 103.7 9.77513e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.05697e-06 11184 2 103.7 0.000100752 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.40357e-06 11184 2 103.7 9.09801e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.50592e-06 11184 2 103.7 9.78738e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.39918e-06 11184 2 103.7 0.000103527 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37868e-06 11184 2 103.7 9.02347e-05 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.14876e-06 11184 2 103.7 9.7484e-05 3728 2000000 2000000 335469.73 143799.62 1.371895 299.03571 277.88905 343.43183 0 0 271300.99 -52066.698 -383.45046 -379011.73 -159156.12 8211.288 Loop time of 26130.4 on 32 procs for 2000000 steps with 13901 atoms Performance: 6.613 ns/day, 3.629 hours/ns, 76.539 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10903 | 13193 | 18186 |2336.5 | 50.49 Bond | 4.5816 | 14.857 | 36.15 | 291.0 | 0.06 Kspace | 4387.3 | 9422.5 | 11745 |2786.1 | 36.06 Neigh | 956.94 | 960.58 | 964.19 | 6.1 | 3.68 Comm | 1073.8 | 1147.6 | 1232.4 | 147.1 | 4.39 Output | 0.015036 | 0.018008 | 0.020783 | 1.3 | 0.00 Modify | 1265.3 | 1325.8 | 1366.7 | 93.4 | 5.07 Other | | 65.68 | | | 0.25 Nlocal: 434.406 ave 535 max 388 min Histogram: 11 7 6 0 0 0 0 1 4 3 Nghost: 8231.84 ave 8730 max 7494 min Histogram: 7 1 0 0 0 2 5 9 1 7 Neighs: 243819 ave 352083 max 199890 min Histogram: 14 8 2 0 0 0 0 1 3 4 Total # of neighbors = 7802216 Ave neighs/atom = 561.27012 Ave special neighs/atom = 1.8838932 Neighbor list builds = 100101 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.14876e-06 11184 2 103.7 9.7484e-05 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 335470.82 143799.62 1.371895 299.03571 277.88905 343.43183 0 0 271300.99 -52066.698 -383.45046 -379011.73 -159156.12 8211.288 Loop time of 8.57209e-06 on 32 procs for 0 steps with 13901 atoms 111.6% 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 | | 8.572e-06 | | |100.00 Nlocal: 434.406 ave 535 max 388 min Histogram: 11 7 6 0 0 0 0 1 4 3 Nghost: 8231.84 ave 8730 max 7494 min Histogram: 7 1 0 0 0 2 5 9 1 7 Neighs: 243819 ave 352083 max 199890 min Histogram: 14 8 2 0 0 0 0 1 3 4 Total # of neighbors = 7802216 Ave neighs/atom = 561.27012 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out