#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.96554e-13 9825 1 103.7 8.1215e-11 3275 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.59 | 14.82 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 -7063.4304 143340.91 1.3114365 291.52522 41.627309 73.309895 0 0 37105.268 -73116.689 -319.55737 -317468.04 -353364.53 6880.5939 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.38879e-06 9825 1 103.7 9.38202e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.27026e-06 9825 1 103.7 0.000102437 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.46986e-06 9825 1 103.7 0.000111627 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.24316e-06 9825 1 103.7 9.72836e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.2479e-06 9825 1 103.7 0.000102392 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.59614e-06 9825 1 103.7 0.000101388 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.4376e-06 9825 1 103.7 0.000120992 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.6406e-06 9825 1 103.7 0.000107888 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.68366e-06 9825 1 103.7 0.000106791 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.2763e-06 9825 1 103.7 0.000116803 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.59022e-06 9825 1 103.7 9.15425e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.21675e-06 9825 1 103.7 9.77636e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.12881e-06 9825 1 103.7 9.08674e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.15955e-06 9825 1 103.7 9.16069e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.10931e-06 9825 1 103.7 9.41484e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.38974e-06 9825 1 103.7 8.7617e-05 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.11312e-06 9825 1 103.7 9.27944e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.15817e-06 9825 1 103.7 0.00011412 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.04365e-06 9825 1 103.7 9.46864e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.14433e-06 9825 1 103.7 9.9657e-05 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.22561e-06 9825 1 103.7 0.000101501 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.33522e-06 9825 1 103.7 0.000102285 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.08427e-06 9825 1 103.7 9.2574e-05 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.21751e-06 9825 1 103.7 9.35352e-05 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.13777e-06 9825 1 103.7 8.86138e-05 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.24057e-06 9825 1 103.7 9.64191e-05 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.17927e-06 9825 1 103.7 8.83299e-05 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.23953e-06 9825 1 103.7 9.48948e-05 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.11583e-06 9825 1 103.7 9.6365e-05 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.29599e-06 9825 1 103.7 9.09474e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.1771e-06 9825 1 103.7 0.000108966 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.222e-06 9825 1 103.7 9.4437e-05 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.18995e-06 9825 1 103.7 9.23126e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.14017e-06 9825 1 103.7 0.000100223 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.33822e-06 9825 1 103.7 9.52294e-05 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.12893e-06 9825 1 103.7 0.00010057 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.54218e-06 9825 1 103.7 0.000115273 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.26557e-06 9825 1 103.7 9.38909e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.39441e-06 9825 1 103.7 0.000103154 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.06812e-06 9825 1 103.7 0.000109711 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.25135e-06 9825 1 103.7 0.000113373 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.5693e-06 9825 1 103.7 0.000113822 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.76222e-06 9825 1 103.7 9.38335e-05 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.12495e-06 9825 1 103.7 8.59661e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.15595e-06 9825 1 103.7 9.02771e-05 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.35216e-06 9825 1 103.7 9.33993e-05 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.46789e-06 9825 1 103.7 0.000124534 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.19426e-06 9825 1 103.7 8.90741e-05 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.45975e-06 9825 1 103.7 9.80712e-05 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.48238e-06 9825 1 103.7 9.65987e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.13093e-06 9825 1 103.7 0.000102573 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.26012e-06 9825 1 103.7 9.64163e-05 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.14366e-06 9825 1 103.7 9.37028e-05 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.25845e-06 9825 1 103.7 9.69602e-05 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.14494e-06 9825 1 103.7 9.08841e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.37947e-06 9825 1 103.7 0.000111093 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.44306e-06 9825 1 103.7 0.000122361 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.2487e-06 9825 1 103.7 8.86017e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.29134e-06 9825 1 103.7 9.12026e-05 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.30375e-06 9825 1 103.7 9.95163e-05 3275 3000000 3000000 -7113.7989 143340.91 1.3114365 295.51929 35.992567 59.837145 0 0 37140.324 -73175.001 -319.55737 -317447.89 -353386.74 6974.8623 Loop time of 41479.3 on 16 procs for 3000000 steps with 12250 atoms Performance: 6.249 ns/day, 3.841 hours/ns, 72.325 timesteps/s 99.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23655 | 28277 | 30595 |1395.6 | 68.17 Bond | 3.8824 | 10.904 | 16.79 | 129.6 | 0.03 Kspace | 6793 | 9114.9 | 13742 |2462.9 | 21.97 Neigh | 1618.7 | 1620.4 | 1622.2 | 2.9 | 3.91 Comm | 977.37 | 1032.6 | 1063.4 | 97.7 | 2.49 Output | 0.017255 | 0.019373 | 0.021322 | 0.9 | 0.00 Modify | 1313.5 | 1344.9 | 1398.1 | 86.3 | 3.24 Other | | 78.28 | | | 0.19 Nlocal: 765.625 ave 822 max 702 min Histogram: 1 3 0 1 1 3 2 1 3 1 Nghost: 9213.44 ave 9524 max 9012 min Histogram: 4 2 1 4 1 0 0 1 1 2 Neighs: 376279 ave 417976 max 314645 min Histogram: 3 1 0 0 0 2 3 1 3 3 Total # of neighbors = 6020463 Ave neighs/atom = 491.46637 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149580 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.30375e-06 9825 1 103.7 9.95163e-05 3275 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.62 | 14.83 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 3000000 3000000 -7112.9159 143340.91 1.3114365 295.51929 35.992567 59.837145 0 0 37140.324 -73175.001 -319.55737 -317447.89 -353386.74 6974.8623 Loop time of 3.97763e-06 on 16 procs for 0 steps with 12250 atoms 132.0% CPU use with 16 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 | | 3.978e-06 | | |100.00 Nlocal: 765.625 ave 822 max 702 min Histogram: 1 3 0 1 1 3 2 1 3 1 Nghost: 9213.44 ave 9524 max 9012 min Histogram: 4 2 1 4 1 0 0 1 1 2 Neighs: 376279 ave 417976 max 314645 min Histogram: 3 1 0 0 0 2 3 1 3 3 Total # of neighbors = 6020463 Ave neighs/atom = 491.46637 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 2.6_Custom.out