#------------------------------------------------------------------------------- # 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) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.68909e-13 8304 2 103.7 8.00071e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.54 | 12.83 | 13.13 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 2561.7959 92859.489 1.3074058 298.43579 46.722967 95.367327 0 0 22335.891 86804.268 -448.40969 -270982.75 -161700.5 5632.823 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.20059e-06 8304 2 103.7 0.000124969 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19357e-06 8304 2 103.7 0.00010176 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.07323e-06 8304 2 103.7 9.5067e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25485e-06 8304 2 103.7 9.07783e-05 2768 200000 200000 3260.7544 92859.489 1.3074058 302.68885 42.505699 110.73748 0 0 22583.605 86503.361 -448.40969 -270976.64 -161736.43 5713.0974 Loop time of 961.122 on 32 procs for 200000 steps with 9101 atoms Performance: 17.979 ns/day, 1.335 hours/ns, 208.090 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 439.67 | 466.04 | 503.22 | 67.0 | 48.49 Bond | 0.18922 | 0.5439 | 0.79712 | 22.8 | 0.06 Kspace | 334.6 | 372.25 | 398.31 | 74.7 | 38.73 Neigh | 30.462 | 30.525 | 30.589 | 0.5 | 3.18 Comm | 28.763 | 31.761 | 33.186 | 23.0 | 3.30 Output | 0.008462 | 0.010757 | 0.012897 | 1.3 | 0.00 Modify | 55.22 | 56.455 | 58.358 | 12.1 | 5.87 Other | | 3.537 | | | 0.37 Nlocal: 284.406 ave 303 max 264 min Histogram: 3 0 3 2 7 4 6 4 2 1 Nghost: 4927.72 ave 5024 max 4819 min Histogram: 2 2 3 1 3 6 8 2 3 2 Neighs: 88656.2 ave 98099 max 79240 min Histogram: 1 2 4 4 5 4 6 3 2 1 Total # of neighbors = 2836998 Ave neighs/atom = 311.72377 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9809 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) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25485e-06 8304 2 103.7 9.07783e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.54 | 12.84 | 13.13 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 3261.712 92859.489 1.3074058 302.68885 42.505699 110.73748 0 0 22583.605 86503.361 -448.40969 -270976.64 -161736.43 5713.0974 Loop time of 7.31284e-06 on 32 procs for 0 steps with 9101 atoms 115.4% 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 | | 7.313e-06 | | |100.00 Nlocal: 284.406 ave 303 max 264 min Histogram: 3 0 3 2 7 4 6 4 2 1 Nghost: 4927.72 ave 5024 max 4819 min Histogram: 2 2 3 1 3 6 8 2 3 2 Neighs: 88656.2 ave 98099 max 79240 min Histogram: 1 2 4 4 5 4 6 3 2 1 Total # of neighbors = 2836998 Ave neighs/atom = 311.72377 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: 0:32:06