#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 10 ps 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 iso 1 1 100 drag 0 mtk yes nreset 200 fix 2 movable ave/time 1 999 1000 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 1 1 1 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 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 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 10000 10000 -255.15856 140461.2 1.4045016 299.14655 323.1502 688.61798 0 0 37361.319 24045.239 -392.56413 -380003.7 -317585.38 8856.355 Loop time of 238.97 on 16 procs for 10000 steps with 13901 atoms Performance: 3.616 ns/day, 6.638 hours/ns, 41.846 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 | 109.21 | 133.8 | 177.51 | 209.1 | 55.99 Bond | 0.025894 | 0.16526 | 0.38625 | 31.3 | 0.07 Kspace | 30.409 | 74.347 | 99.053 | 282.1 | 31.11 Neigh | 10.101 | 10.111 | 10.122 | 0.2 | 4.23 Comm | 4.5147 | 4.7073 | 4.9181 | 6.4 | 1.97 Output | 0.021645 | 0.024002 | 0.026181 | 0.9 | 0.01 Modify | 12.872 | 14.395 | 15.067 | 19.8 | 6.02 Other | | 1.417 | | | 0.59 Nlocal: 868.812 ave 1006 max 792 min Histogram: 5 3 2 2 0 0 0 0 0 4 Nghost: 10563.4 ave 11021 max 9820 min Histogram: 4 0 0 0 0 0 4 2 2 4 Neighs: 497446 ave 655144 max 409190 min Histogram: 3 3 6 0 0 0 0 0 0 4 Total # of neighbors = 7959132 Ave neighs/atom = 572.55823 Ave special neighs/atom = 2.0450327 Neighbor list builds = 577 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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) = 0.2600883 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028132645 estimated relative force accuracy = 8.4720624e-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 10000 1 0.970008 1.293e-06 11904 2 103.7 0.000104071 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.23 | 15.85 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 10000 10000 -208.60644 140461.2 1.4045016 299.14655 323.1502 688.61798 0 0 37361.319 23748.696 -392.56413 -379707.17 -317585.38 8856.355 Loop time of 4.93194e-06 on 16 procs for 0 steps with 13901 atoms 119.1% 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 | | 4.932e-06 | | |100.00 Nlocal: 868.812 ave 1006 max 792 min Histogram: 5 3 2 2 0 0 0 0 0 4 Nghost: 10563.4 ave 11021 max 9820 min Histogram: 4 0 0 0 0 0 4 2 2 4 Neighs: 497446 ave 655144 max 409190 min Histogram: 3 3 6 0 0 0 0 0 0 4 Total # of neighbors = 7959132 Ave neighs/atom = 572.55823 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