#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 10 ps with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 87) 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 (33.78995 48.916 87) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 0.9869233 0.9869233 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 ... WARNING: System is not charge neutral, net charge = 0.0406 (../kspace.cpp:325) 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 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 = 5 7 13 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 1 1.00553 0.0906705 11904 2 97.7498 10.024 3968 Per MPI rank memory allocation (min/avg/max) = 13.21 | 13.69 | 14.16 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 -2846.0521 143799.62 1.371895 417.33588 56.026944 266.65552 0 0 42078.782 -3901.959 -383.45046 -379109.91 -340610.4 12355.398 10000 10000 -577.36585 139375.65 1.4154408 299.51143 336.93484 485.02008 0 0 37671.646 22103.781 -395.62169 -378988.75 -318391.37 8867.1574 Loop time of 142.365 on 32 procs for 10000 steps with 13901 atoms Performance: 6.069 ns/day, 3.955 hours/ns, 70.242 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.006 | 70.527 | 93.522 | 139.7 | 49.54 Bond | 0.020601 | 0.09026 | 0.21985 | 23.4 | 0.06 Kspace | 21.102 | 44.337 | 53.829 | 177.8 | 31.14 Neigh | 6.9528 | 6.9646 | 6.9772 | 0.2 | 4.89 Comm | 5.7886 | 6.0809 | 6.5284 | 8.8 | 4.27 Output | 0.014401 | 0.017285 | 0.019996 | 1.3 | 0.01 Modify | 10.857 | 12.987 | 13.461 | 21.4 | 9.12 Other | | 1.361 | | | 0.96 Nlocal: 434.406 ave 506 max 383 min Histogram: 1 7 9 6 1 0 0 0 1 7 Nghost: 8342.97 ave 8659 max 7797 min Histogram: 8 0 0 0 0 0 0 14 2 8 Neighs: 250235 ave 324296 max 208814 min Histogram: 4 13 6 0 1 0 0 0 0 8 Total # of neighbors = 8007511 Ave neighs/atom = 576.03849 Ave special neighs/atom = 2.0450327 Neighbor list builds = 523 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) = 0.26024034 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027919444 estimated relative force accuracy = 8.4078576e-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 10000 1 0.970014 4.13006e-05 11904 2 103.7 0.0046608 3968 Per MPI rank memory allocation (min/avg/max) = 13.52 | 13.71 | 14.16 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 -493.04983 139375.65 1.4154408 299.51143 336.93484 485.02008 0 0 37671.646 23082.869 -395.62169 -379967.81 -318391.34 8867.1574 Loop time of 9.42238e-06 on 32 procs for 0 steps with 13901 atoms 103.8% 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 | | 9.422e-06 | | |100.00 Nlocal: 434.406 ave 506 max 383 min Histogram: 1 7 9 6 1 0 0 0 1 7 Nghost: 8342.97 ave 8659 max 7797 min Histogram: 8 0 0 0 0 0 0 14 2 8 Neighs: 250235 ave 324296 max 208814 min Histogram: 4 13 6 0 1 0 0 0 0 8 Total # of neighbors = 8007511 Ave neighs/atom = 576.03849 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