#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 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 2768 = # 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 20000 20000 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 v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 20 1 20 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 v_surfacetension file 2.5_instantaneous.txt restart 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.20470278 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0030085707 estimated relative force accuracy = 9.0602213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.20948e-13 8304 2 103.7 7.47207e-11 2768 Per MPI rank memory allocation (min/avg/max) = 13.27 | 13.7 | 13.85 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 2634.0806 92859.489 1.3074058 297.99556 35.211211 126.39196 0 0 22430.294 -12350.189 -116.30764 -171998.58 -161756.87 5624.514 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.39531e-06 8304 2 103.7 9.52551e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.71162e-06 8304 2 103.7 0.000104465 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14072e-06 8304 2 103.7 8.91223e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19403e-06 8304 2 103.7 9.9538e-05 2768 200000 200000 3011.9634 92859.489 1.3074058 302.612 49.10789 116.82733 0 0 22311.773 -12092.598 -116.30764 -172004.42 -161619.31 5711.647 Loop time of 2390.18 on 32 procs for 200000 steps with 9101 atoms Performance: 7.230 ns/day, 3.320 hours/ns, 83.676 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1518.4 | 1680.9 | 1846.4 | 241.9 | 70.33 Bond | 0.24683 | 0.64547 | 1.1477 | 30.4 | 0.03 Kspace | 222.89 | 388.47 | 551.5 | 502.8 | 16.25 Neigh | 79.583 | 79.637 | 79.705 | 0.4 | 3.33 Comm | 110.68 | 112.2 | 113.46 | 7.1 | 4.69 Output | 0.0089041 | 0.011215 | 0.01335 | 1.3 | 0.00 Modify | 118.92 | 119.59 | 120.66 | 3.8 | 5.00 Other | | 8.705 | | | 0.36 Nlocal: 284.406 ave 308 max 259 min Histogram: 1 1 2 5 7 5 6 1 3 1 Nghost: 11128.5 ave 11190 max 11067 min Histogram: 2 4 8 1 1 0 4 5 5 2 Neighs: 286722 ave 333407 max 261232 min Histogram: 4 9 2 8 2 1 1 1 3 1 Total # of neighbors = 9175094 Ave neighs/atom = 1008.1413 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9807 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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) = 0.20470278 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0030085707 estimated relative force accuracy = 9.0602213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19403e-06 8304 2 103.7 9.9538e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.71 | 13.85 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 200000 200000 3012.8985 92859.489 1.3074058 302.612 49.10789 116.82733 0 0 22311.773 -12092.598 -116.30764 -172004.42 -161619.31 5711.647 Loop time of 8.77062e-06 on 32 procs for 0 steps with 9101 atoms 114.4% 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 | | 8.771e-06 | | |100.00 Nlocal: 284.406 ave 308 max 259 min Histogram: 1 1 2 5 7 5 6 1 3 1 Nghost: 11128.5 ave 11190 max 11067 min Histogram: 2 4 8 1 1 0 4 5 5 2 Neighs: 286722 ave 333407 max 261232 min Histogram: 4 9 2 8 2 1 1 1 3 1 Total # of neighbors = 9175094 Ave neighs/atom = 1008.1413 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 1:19:45