#------------------------------------------------------------------------------- # Stage 2.5: 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2699 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (45.402 32.1502 62.648044) 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 (45.402 32.1502 62.648044) 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 2.5_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 2.5_instantaneous.txt restart 10000 2.5.restart dump sci all custom 1000 2.5.xyz id mol type q xs ys zs timestep 1 run 10000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.024 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 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 = 7 5 9 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 2 0.97 1.21081e-12 8097 2 103.7 8.2963e-11 2699 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.17 | 14.34 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 3970.5127 91446.309 1.3291045 300.12154 39.049396 103.72601 0 0 24323.594 20085.281 -226.3957 -220255.76 -175704.11 5580.5478 10000 10000 -252.50214 96208.667 1.2633135 298.6697 39.065735 87.029914 0 0 22846.673 21568.321 -215.18905 -220262.32 -175721.23 5553.5519 Loop time of 131.98 on 16 procs for 10000 steps with 8938 atoms Performance: 6.546 ns/day, 3.666 hours/ns, 75.769 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 80.997 | 84.627 | 89.933 | 26.4 | 64.12 Bond | 0.038343 | 0.052267 | 0.072627 | 4.5 | 0.04 Kspace | 20.3 | 25.656 | 29.262 | 48.2 | 19.44 Neigh | 6.5334 | 6.54 | 6.5458 | 0.2 | 4.96 Comm | 2.8548 | 2.9115 | 2.9759 | 2.2 | 2.21 Output | 0.013468 | 0.015186 | 0.01675 | 0.9 | 0.01 Modify | 9.6411 | 10.885 | 11.377 | 16.8 | 8.25 Other | | 1.293 | | | 0.98 Nlocal: 558.625 ave 588 max 530 min Histogram: 1 1 2 0 4 3 2 2 0 1 Nghost: 8662.69 ave 8734 max 8597 min Histogram: 1 1 3 4 0 1 2 1 2 1 Neighs: 298029 ave 316849 max 282601 min Histogram: 2 1 2 1 4 1 2 1 1 1 Total # of neighbors = 4768457 Ave neighs/atom = 533.5038 Ave special neighs/atom = 1.8722309 Neighbor list builds = 523 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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) = 0.25750646 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.003000023 estimated relative force accuracy = 9.0344802e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.970024 7.16546e-05 8097 2 103.7 0.00813538 2699 Per MPI rank memory allocation (min/avg/max) = 14.08 | 14.19 | 14.34 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 -114.43777 96208.667 1.2633135 298.6697 39.065735 87.029914 0 0 22846.673 20567.707 -215.18905 -219261.72 -175721.24 5553.5519 Loop time of 4.92675e-06 on 16 procs for 0 steps with 8938 atoms 118.0% 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 | | 4.927e-06 | | |100.00 Nlocal: 558.625 ave 588 max 530 min Histogram: 1 1 2 0 4 3 2 2 0 1 Nghost: 8662.69 ave 8734 max 8597 min Histogram: 1 1 3 4 0 1 2 1 2 1 Neighs: 298029 ave 316849 max 282601 min Histogram: 2 1 2 1 4 1 2 1 1 1 Total # of neighbors = 4768457 Ave neighs/atom = 533.5038 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:04:17