#------------------------------------------------------------------------------- # Stage 2.4: 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # 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 npt temp 298.2 298.2 100 aniso 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 2.4_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_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 2.4_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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00254 0.762326 11904 2 97.5667 38.403 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.18 | 15.84 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 4467.2663 139006.3 1.4192018 417.33588 117.37395 708.83542 0 0 42503.293 14962.287 -396.67289 -379342.84 -321051.05 12355.398 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969996 3.91844e-05 11904 2 103.7 0.00443659 3968 SHAKE stats (type/ave/delta/count) on step 100000 1 0.96998 0.000156367 11904 2 103.701 0.0177897 3968 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970065 0.000113139 11904 2 103.7 0.0127187 3968 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970091 0.000304337 11904 2 103.701 0.0346659 3968 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970006 4.89283e-05 11904 2 103.7 0.0055802 3968 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970004 4.30325e-05 11904 2 103.7 0.00484176 3968 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970023 0.000157359 11904 2 103.701 0.0179448 3968 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970045 0.000236274 11904 2 103.699 0.026903 3968 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970052 0.000192267 11904 2 103.701 0.0220499 3968 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970037 7.06761e-05 11904 2 103.7 0.0079649 3968 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969979 0.000139182 11904 2 103.701 0.0158867 3968 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970098 0.00019182 11904 2 103.701 0.0219403 3968 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970018 7.24966e-05 11904 2 103.7 0.00826839 3968 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969916 0.000114547 11904 2 103.7 0.0129861 3968 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969944 0.00015589 11904 2 103.7 0.0178355 3968 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970015 0.000154829 11904 2 103.7 0.0175793 3968 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970083 0.000103814 11904 2 103.699 0.0118696 3968 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970008 8.61322e-05 11904 2 103.7 0.0097238 3968 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970012 0.000178643 11904 2 103.7 0.0203205 3968 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970037 0.000173994 11904 2 103.7 0.0198243 3968 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969968 0.000154288 11904 2 103.701 0.0176948 3968 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969993 5.00512e-05 11904 2 103.7 0.00564154 3968 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970001 0.000131183 11904 2 103.7 0.014887 3968 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970066 6.54322e-05 11904 2 103.7 0.00736736 3968 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969963 0.000181876 11904 2 103.7 0.0206914 3968 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970035 0.000194867 11904 2 103.7 0.0221044 3968 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.969974 0.000226521 11904 2 103.7 0.0257282 3968 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.969933 9.01891e-05 11904 2 103.7 0.0101677 3968 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970004 0.000222977 11904 2 103.699 0.025515 3968 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969979 0.000123579 11904 2 103.699 0.0140206 3968 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969999 0.000207375 11904 2 103.7 0.0236285 3968 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969914 0.000163952 11904 2 103.7 0.0184499 3968 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970055 6.05499e-05 11904 2 103.7 0.00685997 3968 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970003 0.000137614 11904 2 103.699 0.0155112 3968 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970047 0.00032307 11904 2 103.7 0.0368246 3968 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969985 0.000111115 11904 2 103.7 0.012518 3968 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970031 0.000187372 11904 2 103.7 0.0214308 3968 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969978 0.00026492 11904 2 103.701 0.030149 3968 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969981 0.000151375 11904 2 103.699 0.0173423 3968 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970045 9.28915e-05 11904 2 103.7 0.0105699 3968 2000000 2000000 -554.82075 139066.28 1.4185897 302.69446 355.36928 657.6534 0 0 37377.341 23291.324 -396.50181 -380062.06 -318380.37 8961.3922 Loop time of 47304.3 on 16 procs for 2000000 steps with 13901 atoms Performance: 3.653 ns/day, 6.570 hours/ns, 42.279 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22732 | 26912 | 34347 |2536.3 | 56.89 Bond | 9.3164 | 31.829 | 73.694 | 434.5 | 0.07 Kspace | 6887.6 | 14373 | 18576 |3494.3 | 30.38 Neigh | 2061.5 | 2064.4 | 2067.7 | 3.9 | 4.36 Comm | 861.35 | 894.61 | 929.47 | 70.7 | 1.89 Output | 0.021467 | 0.02394 | 0.026261 | 1.0 | 0.00 Modify | 2336.3 | 2659.9 | 2792.8 | 311.7 | 5.62 Other | | 368.1 | | | 0.78 Nlocal: 868.812 ave 999 max 792 min Histogram: 3 5 3 1 0 0 0 0 0 4 Nghost: 10687 ave 11144 max 9955 min Histogram: 4 0 0 0 0 0 4 1 3 4 Neighs: 502144 ave 645916 max 418384 min Histogram: 4 2 6 0 0 0 0 0 0 4 Total # of neighbors = 8034301 Ave neighs/atom = 577.96569 Ave special neighs/atom = 2.0450327 Neighbor list builds = 108797 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) = 0.26023345 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027965615 estimated relative force accuracy = 8.4217619e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970045 9.28915e-05 11904 2 103.7 0.0105699 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.45 | 16.24 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 -287.36035 139066.28 1.4185897 302.69446 355.36928 657.6534 0 0 37377.341 23204.958 -396.50181 -379975.7 -318380.38 8961.3922 Loop time of 4.09656e-06 on 16 procs for 0 steps with 13901 atoms 131.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.097e-06 | | |100.00 Nlocal: 868.812 ave 999 max 792 min Histogram: 3 5 3 1 0 0 0 0 0 4 Nghost: 10687 ave 11144 max 9955 min Histogram: 4 0 0 0 0 0 4 1 3 4 Neighs: 502144 ave 645916 max 418384 min Histogram: 4 2 6 0 0 0 0 0 0 4 Total # of neighbors = 8034301 Ave neighs/atom = 577.96569 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out