#------------------------------------------------------------------------------- # 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 = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 84.1) 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 84.1) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 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 ... 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) = 0.26029305 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 = 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 1.00266 0.969541 11904 2 97.607 23.8685 3968 Per MPI rank memory allocation (min/avg/max) = 13.22 | 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 0 1e-06 5276.969 139006.3 1.4192018 417.33588 128.09957 494.98117 0 0 42701.815 15197.087 -396.67289 -379296.13 -320774.14 12355.398 10000 10000 -943.20515 141607.97 1.3931277 295.54502 309.40186 498.91745 0 0 36939.266 24738.193 -389.38508 -380005.3 -317519.52 8749.73 Loop time of 141.122 on 32 procs for 10000 steps with 13901 atoms Performance: 6.122 ns/day, 3.920 hours/ns, 70.861 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 | 55.654 | 69.909 | 92.06 | 146.4 | 49.54 Bond | 0.016428 | 0.08951 | 0.20687 | 22.4 | 0.06 Kspace | 20.435 | 42.79 | 57.216 | 188.9 | 30.32 Neigh | 7.7776 | 7.7896 | 7.8059 | 0.3 | 5.52 Comm | 5.8093 | 6.167 | 6.556 | 8.8 | 4.37 Output | 0.015356 | 0.018187 | 0.020905 | 1.3 | 0.01 Modify | 10.773 | 13.008 | 13.618 | 21.8 | 9.22 Other | | 1.351 | | | 0.96 Nlocal: 434.406 ave 515 max 369 min Histogram: 1 6 5 6 5 1 0 0 4 4 Nghost: 8276.28 ave 8785 max 7601 min Histogram: 8 0 0 0 0 6 6 4 0 8 Neighs: 247098 ave 332118 max 186834 min Histogram: 3 5 9 6 1 0 0 0 1 7 Total # of neighbors = 7907133 Ave neighs/atom = 568.81757 Ave special neighs/atom = 2.0450327 Neighbor list builds = 603 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) = 0.25990968 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028399001 estimated relative force accuracy = 8.5522747e-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 0.969995 1.6561e-05 11904 2 103.7 0.00186326 3968 Per MPI rank memory allocation (min/avg/max) = 13.56 | 13.72 | 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 -973.33397 141607.97 1.3931277 295.54502 309.40186 498.91745 0 0 36939.266 24182.971 -389.38508 -379450.09 -317519.53 8749.73 Loop time of 8.17956e-06 on 32 procs for 0 steps with 13901 atoms 112.7% 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 | | 8.18e-06 | | |100.00 Nlocal: 434.406 ave 515 max 369 min Histogram: 1 6 5 6 5 1 0 0 4 4 Nghost: 8276.28 ave 8785 max 7601 min Histogram: 8 0 0 0 0 6 6 4 0 8 Neighs: 247098 ave 332118 max 186834 min Histogram: 3 5 9 6 1 0 0 0 1 7 Total # of neighbors = 7907133 Ave neighs/atom = 568.81757 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