#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 1 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- change_box all triclinic Changing box ... triclinic box = (0 0 0) to (5.64056 5.64056 5.64056) 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 (5.64056 5.64056 5.64056) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 x 1 1 100 y 1 1 100 z 1 1 100 drag 0 mtk yes nreset 20000 fix 2 movable ave/time 1 99999 100000 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 100 1 100 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 1000000 2.5.restart dump sci all custom 100000 2.5.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.29166098 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00027054584 estimated relative force accuracy = 8.1474075e-07 using double precision KISS FFT 3d grid and FFT values/proc = 1815 128 generated 0 of 1 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 = 1 1 1 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 WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:965) Per MPI rank memory allocation (min/avg/max) = 6.704 | 7.541 | 7.71 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 33968.233 179.45959 2.1630931 221.16328 0 0 0 0 93.790309 -382.75569 -0.59158899 -436.93401 -725.8994 4.6147201 1000000 1000000 -1384.0653 204.12438 1.9017219 345.90265 0 0 0 0 64.379155 -354.17502 -0.52010601 -436.97713 -726.77299 7.2174906 Loop time of 279.146 on 6 procs for 1000000 steps with 8 atoms Performance: 309.516 ns/day, 0.078 hours/ns, 3582.357 timesteps/s 98.9% CPU use with 6 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.942 | 12.764 | 17.404 | 84.6 | 4.57 Bond | 0.46727 | 0.51492 | 0.56455 | 5.4 | 0.18 Kspace | 93.879 | 98.954 | 102.02 | 33.7 | 35.45 Neigh | 0.03463 | 0.034871 | 0.035116 | 0.1 | 0.01 Comm | 54.646 | 56.187 | 57.846 | 16.9 | 20.13 Output | 0.00099324 | 0.0010357 | 0.0010902 | 0.1 | 0.00 Modify | 95.719 | 100.51 | 107.46 | 48.8 | 36.01 Other | | 10.18 | | | 3.65 Nlocal: 1.33333 ave 3 max 1 min Histogram: 5 0 0 0 0 0 0 0 0 1 Nghost: 1197.33 ave 1269 max 1086 min Histogram: 1 0 0 1 0 0 2 0 0 2 Neighs: 301.667 ave 701 max 203 min Histogram: 5 0 0 0 0 0 0 0 0 1 Total # of neighbors = 1810 Ave neighs/atom = 226.25 Ave special neighs/atom = 0 Neighbor list builds = 583 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.27661212 grid = 6 6 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00088101585 estimated relative force accuracy = 2.6531531e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1430 72 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule Per MPI rank memory allocation (min/avg/max) = 7.694 | 7.696 | 7.699 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 1000000 1000000 -1376.8693 204.12438 1.9017219 345.90265 0 0 0 0 64.379155 -376.64926 -0.52010601 -414.50031 -726.77041 7.2174906 Loop time of 3.86667e-06 on 6 procs for 0 steps with 8 atoms 125.0% CPU use with 6 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 | | 3.867e-06 | | |100.00 Nlocal: 1.33333 ave 3 max 1 min Histogram: 5 0 0 0 0 0 0 0 0 1 Nghost: 1197.33 ave 1269 max 1086 min Histogram: 1 0 0 1 0 0 2 0 0 2 Neighs: 301.667 ave 701 max 203 min Histogram: 5 0 0 0 0 0 0 0 0 1 Total # of neighbors = 1810 Ave neighs/atom = 226.25 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 Total wall time: 0:07:46