#------------------------------------------------------------------------------- # 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 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 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00069 0.10904 8304 2 97.6898 10.1954 2768 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.15 | 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 -3531.696 140505.98 1.42352 406.71708 6.4561645 22.970202 0 0 36299.564 -67104.674 -315.99625 -291760.57 -322536.25 9247.778 10000 10000 -467.53125 140505.98 1.42352 303.8401 39.016667 64.876186 0 0 34214.998 -50323.853 -315.99625 -291890.34 -307895.31 6908.6005 Loop time of 98.6351 on 32 procs for 10000 steps with 10721 atoms Performance: 8.760 ns/day, 2.740 hours/ns, 101.384 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.533 | 44.692 | 66.574 | 288.9 | 45.31 Bond | 0.010044 | 0.027489 | 0.05282 | 8.9 | 0.03 Kspace | 16.365 | 38.318 | 70.685 | 313.3 | 38.85 Neigh | 4.3757 | 4.3873 | 4.4051 | 0.4 | 4.45 Comm | 3.6155 | 4.7209 | 5.2694 | 25.4 | 4.79 Output | 0.01238 | 0.014733 | 0.016999 | 1.1 | 0.01 Modify | 5.6002 | 6.0595 | 6.9598 | 19.6 | 6.14 Other | | 0.4151 | | | 0.42 Nlocal: 335.031 ave 421 max 160 min Histogram: 5 3 0 0 0 0 0 8 4 12 Nghost: 6448.25 ave 7750 max 4683 min Histogram: 8 0 0 0 8 0 0 0 6 10 Neighs: 157124 ave 229511 max 41852 min Histogram: 8 0 0 0 0 4 1 3 8 8 Total # of neighbors = 5027983 Ave neighs/atom = 468.98452 Ave special neighs/atom = 1.6069397 Neighbor list builds = 488 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.37015e-06 8304 2 103.7 9.9509e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.16 | 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 -466.98812 140505.98 1.42352 303.8401 39.016667 64.876186 0 0 34214.998 -50323.853 -315.99625 -291890.34 -307895.31 6908.6005 Loop time of 1.41426e-05 on 32 procs for 0 steps with 10721 atoms 110.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.414e-05 | | |100.00 Nlocal: 335.031 ave 421 max 160 min Histogram: 5 3 0 0 0 0 0 8 4 12 Nghost: 6448.25 ave 7750 max 4683 min Histogram: 8 0 0 0 8 0 0 0 6 10 Neighs: 157124 ave 229511 max 41852 min Histogram: 8 0 0 0 0 4 1 3 8 8 Total # of neighbors = 5027983 Ave neighs/atom = 468.98452 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out