#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 ps with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 1000 1000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal 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_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00148 0.0774694 9825 1 97.5257 11.6128 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.26 | 13.65 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 -8884.2294 143340.91 1.3114365 420.87983 5.8820453 38.386046 0 0 40023.03 -92447.214 -319.55737 -317381.09 -369761.01 9933.6285 10000 10000 -7265.0588 143340.91 1.3114365 297.04057 44.393748 69.392569 0 0 36933.283 -72546.686 -319.55737 -317415.75 -352915.37 7010.7677 Loop time of 96.4294 on 32 procs for 10000 steps with 12250 atoms Performance: 8.960 ns/day, 2.679 hours/ns, 103.703 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 41.624 | 52.357 | 63.318 | 78.2 | 54.30 Bond | 0.011635 | 0.029282 | 0.052879 | 7.1 | 0.03 Kspace | 17.586 | 28.561 | 39.336 | 106.5 | 29.62 Neigh | 3.1197 | 3.1263 | 3.1342 | 0.2 | 3.24 Comm | 5.1748 | 5.4644 | 5.6988 | 8.3 | 5.67 Output | 0.01221 | 0.014875 | 0.017427 | 1.3 | 0.02 Modify | 6.1897 | 6.3984 | 6.8611 | 7.2 | 6.64 Other | | 0.4778 | | | 0.50 Nlocal: 382.812 ave 425 max 334 min Histogram: 1 3 2 3 4 4 7 3 3 2 Nghost: 7261.97 ave 7664 max 6815 min Histogram: 4 2 6 0 5 3 0 0 4 8 Neighs: 188369 ave 225611 max 146940 min Histogram: 3 1 4 2 3 1 9 7 1 1 Total # of neighbors = 6027799 Ave neighs/atom = 492.06522 Ave special neighs/atom = 1.6481633 Neighbor list builds = 487 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.15611e-06 9825 1 103.7 9.59419e-05 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.33 | 13.65 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 -7264.2716 143340.91 1.3114365 297.04057 44.393748 69.392569 0 0 36933.283 -72546.686 -319.55737 -317415.75 -352915.37 7010.7677 Loop time of 8.01006e-06 on 32 procs for 0 steps with 12250 atoms 125.6% 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 | | 8.01e-06 | | |100.00 Nlocal: 382.812 ave 425 max 334 min Histogram: 1 3 2 3 4 4 7 3 3 2 Nghost: 7261.97 ave 7664 max 6815 min Histogram: 4 2 6 0 5 3 0 0 4 8 Neighs: 188369 ave 225611 max 146940 min Histogram: 3 1 4 2 3 1 9 7 1 1 Total # of neighbors = 6027799 Ave neighs/atom = 492.06522 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out