#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 50 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2812 = # 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 5000 5000 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 5 1 5 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 50000 2.4.restart dump sci all custom 5000 2.4.xyz id mol type q xs ys zs timestep 1 run 50000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25553612 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034265209 estimated relative force accuracy = 1.0318866e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00194 0.0840082 8436 2 97.27 12.64 2812 Per MPI rank memory allocation (min/avg/max) = 12.7 | 14.11 | 14.71 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-06 673.72959 127841.08 1.4258274 415.64004 11.3772 101.87696 0 0 34171.529 -36689.031 -300.656 -268005.48 -270409.73 8849.777 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.32028e-06 8436 2 103.7 9.94903e-05 2812 50000 50000 978.1093 127841.08 1.4258274 293.38804 54.665233 109.89479 0 0 29684.934 -18968.936 -300.656 -268002.52 -257121.96 6246.7964 Loop time of 786.952 on 16 procs for 50000 steps with 10468 atoms Performance: 5.490 ns/day, 4.372 hours/ns, 63.536 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 150.09 | 449.48 | 590.48 | 825.2 | 57.12 Bond | 0.07583 | 0.24205 | 0.37966 | 22.9 | 0.03 Kspace | 113.82 | 255.39 | 555.42 |1096.9 | 32.45 Neigh | 31.292 | 31.337 | 31.393 | 0.7 | 3.98 Comm | 17.96 | 21.446 | 23.035 | 43.3 | 2.73 Output | 0.016108 | 0.018132 | 0.02008 | 0.9 | 0.00 Modify | 26.221 | 27.405 | 30.626 | 32.8 | 3.48 Other | | 1.634 | | | 0.21 Nlocal: 654.25 ave 780 max 354 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8676.88 ave 10146 max 7349 min Histogram: 4 0 0 1 6 1 0 0 0 4 Neighs: 326988 ave 434050 max 105583 min Histogram: 4 0 0 0 0 0 0 3 2 7 Total # of neighbors = 5231802 Ave neighs/atom = 499.79003 Ave special neighs/atom = 1.6709973 Neighbor list builds = 2470 Dangerous builds = 0 undump sci restart 0 dump sci all custom 50000 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) = 0.25553612 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034265209 estimated relative force accuracy = 1.0318866e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.32028e-06 8436 2 103.7 9.94903e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.12 | 14.14 | 14.71 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 50000 50000 978.68504 127841.08 1.4258274 293.38804 54.665233 109.89479 0 0 29684.934 -18968.936 -300.656 -268002.52 -257121.96 6246.7964 Loop time of 8.91631e-06 on 16 procs for 0 steps with 10468 atoms 110.1% 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 | | 8.916e-06 | | |100.00 Nlocal: 654.25 ave 780 max 354 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8676.88 ave 10146 max 7349 min Histogram: 4 0 0 1 6 1 0 0 0 4 Neighs: 326988 ave 434050 max 105583 min Histogram: 4 0 0 0 0 0 0 3 2 7 Total # of neighbors = 5231802 Ave neighs/atom = 499.79003 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out