#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (39.00424 48.916 48.670243) with tilt (0 0 0) kspace_style pppm 0.00001 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (39.00424 48.916 48.670243) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 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 ... WARNING: System is not charge neutral, net charge = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25609786 grid = 30 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0033114692 estimated relative force accuracy = 9.972391e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5632 2160 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.30718e-12 8304 2 103.7 9.7188e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.89 | 13.07 | 13.2 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 2425.3968 92859.485 1.3074059 291.10797 46.948292 89.333506 0 0 22144.537 30931.574 -225.64506 -214942.52 -161730.12 5494.5143 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970101 0.000304881 8304 2 103.7 0.0349536 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970006 1.97362e-05 8304 2 103.7 0.00221558 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970001 4.0957e-06 8304 2 103.7 0.000473045 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970018 5.44874e-05 8304 2 103.7 0.00626476 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970005 1.59469e-05 8304 2 103.7 0.00178988 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969966 0.000103683 8304 2 103.7 0.0117828 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969984 4.95979e-05 8304 2 103.7 0.00566629 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969988 3.60594e-05 8304 2 103.7 0.00406862 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969981 5.74527e-05 8304 2 103.7 0.00653969 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969974 7.80761e-05 8304 2 103.7 0.00888161 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969929 0.00021423 8304 2 103.7 0.0245158 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969993 2.20681e-05 8304 2 103.7 0.00249364 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.96997 9.14378e-05 8304 2 103.7 0.0104214 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97002 6.18654e-05 8304 2 103.7 0.00706057 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97005 0.000150179 8304 2 103.7 0.0171889 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970017 5.13921e-05 8304 2 103.7 0.00592072 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970029 8.58416e-05 8304 2 103.7 0.0098012 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970029 8.80311e-05 8304 2 103.7 0.0100912 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970011 3.36393e-05 8304 2 103.7 0.00386397 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970082 0.000247789 8304 2 103.7 0.0284303 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.34458e-06 8304 2 103.7 0.000100395 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969994 1.94028e-05 8304 2 103.7 0.00217332 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969988 3.81918e-05 8304 2 103.7 0.00430244 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970029 8.70428e-05 8304 2 103.7 0.00994782 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969969 9.27629e-05 8304 2 103.7 0.0105713 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969991 2.92142e-05 8304 2 103.7 0.00326341 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97002 5.98441e-05 8304 2 103.7 0.00681379 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969967 9.863e-05 8304 2 103.7 0.011228 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969974 8.03266e-05 8304 2 103.7 0.00908841 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969998 8.83443e-06 8304 2 103.7 0.000964838 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969989 3.29655e-05 8304 2 103.7 0.0037585 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970035 0.000104215 8304 2 103.7 0.0119173 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970029 8.55885e-05 8304 2 103.7 0.00979023 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970047 0.000142424 8304 2 103.7 0.0162719 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970012 3.76036e-05 8304 2 103.7 0.00427507 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970031 9.32493e-05 8304 2 103.7 0.0106844 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970014 4.2664e-05 8304 2 103.7 0.00488409 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970027 7.90826e-05 8304 2 103.7 0.00907254 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970012 3.75407e-05 8304 2 103.7 0.00420198 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 2.88545e-06 8304 2 103.7 0.000257626 2768 2000000 2000000 21.585046 97587.585 1.2440623 298.46261 44.264407 67.214036 0 0 21262.595 32136.497 -214.7126 -214932.13 -161421.56 5633.3293 Loop time of 15784.1 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.948 ns/day, 2.192 hours/ns, 126.710 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 | 8518.8 | 8922.3 | 9268.8 | 197.6 | 56.53 Bond | 2.657 | 5.5387 | 10.401 | 94.5 | 0.04 Kspace | 2818.4 | 3165.8 | 3578.1 | 332.9 | 20.06 Neigh | 723.6 | 724.34 | 724.91 | 1.2 | 4.59 Comm | 1010.4 | 1021.7 | 1033.2 | 18.8 | 6.47 Output | 0.0095509 | 0.011751 | 0.013832 | 1.2 | 0.00 Modify | 1471.7 | 1565.9 | 1891.3 | 307.1 | 9.92 Other | | 378.5 | | | 2.40 Nlocal: 284.406 ave 304 max 267 min Histogram: 3 2 5 3 5 2 4 4 2 2 Nghost: 6979.09 ave 7047 max 6927 min Histogram: 4 6 3 1 5 3 3 3 2 2 Neighs: 152323 ave 165859 max 142392 min Histogram: 5 3 4 3 5 4 1 4 1 2 Total # of neighbors = 4874322 Ave neighs/atom = 535.58093 Ave special neighs/atom = 1.8929788 Neighbor list builds = 103719 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) = 0.25678742 grid = 30 36 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030686649 estimated relative force accuracy = 9.2411932e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5984 2160 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 2.88545e-06 8304 2 103.7 0.000257626 2768 Per MPI rank memory allocation (min/avg/max) = 12.92 | 13.11 | 13.21 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 19.31424 97587.585 1.2440623 298.46261 44.264407 67.214036 0 0 21262.595 32710.478 -214.7126 -215506.08 -161421.53 5633.3293 Loop time of 1.46079e-05 on 32 procs for 0 steps with 9101 atoms 107.2% 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 | | 1.461e-05 | | |100.00 Nlocal: 284.406 ave 304 max 267 min Histogram: 3 2 5 3 5 2 4 4 2 2 Nghost: 6979.09 ave 7047 max 6927 min Histogram: 4 6 3 1 5 3 3 3 2 2 Neighs: 152323 ave 165859 max 142392 min Histogram: 5 3 4 3 5 4 1 4 1 2 Total # of neighbors = 4874322 Ave neighs/atom = 535.58093 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:40:45