#------------------------------------------------------------------------------- # 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 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 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 0.991854 0.602613 8436 2 96.9689 39.7099 2812 Per MPI rank memory allocation (min/avg/max) = 12.75 | 13.98 | 14.61 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 6316.6931 130091.43 1.4011632 415.64004 111.0517 404.90865 0 0 31846.584 -14834.533 -295.4552 -266249.55 -248721.54 8849.777 10000 10000 -289.45045 130091.43 1.4011632 302.33881 40.607755 273.9998 0 0 28985.639 -18356.971 -295.4552 -267593.38 -256650.1 6437.3756 Loop time of 158.311 on 16 procs for 10000 steps with 10468 atoms Performance: 5.458 ns/day, 4.398 hours/ns, 63.167 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 | 30.205 | 89.059 | 116.19 | 363.2 | 56.26 Bond | 0.014853 | 0.050211 | 0.091917 | 9.1 | 0.03 Kspace | 24.485 | 51.722 | 110.71 | 477.6 | 32.67 Neigh | 6.6347 | 6.6473 | 6.6614 | 0.3 | 4.20 Comm | 3.5822 | 4.3034 | 4.61 | 19.4 | 2.72 Output | 0.016708 | 0.018769 | 0.02066 | 0.9 | 0.01 Modify | 5.8045 | 6.0362 | 6.9233 | 15.3 | 3.81 Other | | 0.4745 | | | 0.30 Nlocal: 654.25 ave 775 max 365 min Histogram: 4 0 0 0 0 0 0 0 2 10 Nghost: 8627.5 ave 10101 max 7261 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 320666 ave 418545 max 109066 min Histogram: 4 0 0 0 0 0 0 1 4 7 Total # of neighbors = 5130655 Ave neighs/atom = 490.12753 Ave special neighs/atom = 1.6709973 Neighbor list builds = 521 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 10000 2 0.97 1.18568e-06 8436 2 103.7 9.2964e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.12 | 14.69 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 -288.85591 130091.43 1.4011632 302.33881 40.607755 273.9998 0 0 28985.639 -18356.971 -295.4552 -267593.38 -256650.1 6437.3756 Loop time of 4.144e-06 on 16 procs for 0 steps with 10468 atoms 122.2% 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 | | 4.144e-06 | | |100.00 Nlocal: 654.25 ave 775 max 365 min Histogram: 4 0 0 0 0 0 0 0 2 10 Nghost: 8627.5 ave 10101 max 7261 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 320666 ave 418545 max 109066 min Histogram: 4 0 0 0 0 0 0 1 4 7 Total # of neighbors = 5130655 Ave neighs/atom = 490.12753 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