#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 ns 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 100000 100000 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 100 1 100 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 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25754655 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028834269 estimated relative force accuracy = 8.6833543e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00195 0.324273 8304 2 97.6648 32.6213 2768 Per MPI rank memory allocation (min/avg/max) = 12.44 | 13.18 | 13.7 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 -2249.4178 142877.44 1.4042668 410.14353 12.689934 52.38414 0 0 32981.535 -36282.703 -323.19871 -277942.46 -281178.56 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.65817e-06 8304 2 103.7 0.000131218 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26008e-06 8304 2 103.7 9.29495e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.29031e-06 8304 2 103.7 9.94343e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16981e-06 8304 2 103.7 9.87762e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.36473e-06 8304 2 103.7 9.70962e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.12747e-06 8304 2 103.7 9.2641e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20811e-06 8304 2 103.7 0.000108864 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.35549e-06 8304 2 103.7 9.3485e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.51492e-06 8304 2 103.7 0.000105602 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.07715e-06 8304 2 103.7 0.000105158 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.15067e-06 8304 2 103.7 9.81895e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.78732e-06 8304 2 103.7 0.000115612 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.42976e-06 8304 2 103.7 9.8363e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.13009e-06 8304 2 103.7 0.00010379 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.41945e-06 8304 2 103.7 0.000116701 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18157e-06 8304 2 103.7 9.97237e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.25689e-06 8304 2 103.7 0.000111681 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.05077e-06 8304 2 103.7 9.23408e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.75259e-06 8304 2 103.7 0.000110381 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20238e-06 8304 2 103.7 0.000108219 2768 1000000 1000000 -438.65628 142877.44 1.4042668 297.82969 40.294294 82.77182 0 0 29513.87 -20143.669 -323.19871 -277834.82 -268341.55 6530.4635 Loop time of 9485.62 on 32 procs for 1000000 steps with 10381 atoms Performance: 9.109 ns/day, 2.635 hours/ns, 105.423 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 | 909.22 | 4238.8 | 6110.2 |3082.0 | 44.69 Bond | 0.88787 | 2.6268 | 5.5299 | 82.2 | 0.03 Kspace | 1984.8 | 3866.3 | 7201.4 |3238.8 | 40.76 Neigh | 404.61 | 405.38 | 406.55 | 3.0 | 4.27 Comm | 301.96 | 430.93 | 480.54 | 284.4 | 4.54 Output | 0.012023 | 0.014461 | 0.016827 | 1.2 | 0.00 Modify | 476.59 | 519.94 | 628.15 | 225.8 | 5.48 Other | | 21.61 | | | 0.23 Nlocal: 324.406 ave 422 max 128 min Histogram: 8 0 0 0 0 0 0 6 5 13 Nghost: 6066.34 ave 7607 max 3905 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 149687 ave 219338 max 26623 min Histogram: 8 0 0 0 0 3 1 4 1 15 Total # of neighbors = 4789983 Ave neighs/atom = 461.41826 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49734 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25754655 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028834269 estimated relative force accuracy = 8.6833543e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20238e-06 8304 2 103.7 0.000108219 2768 Per MPI rank memory allocation (min/avg/max) = 12.44 | 13.25 | 13.75 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 1000000 1000000 -438.09158 142877.44 1.4042668 297.82969 40.294294 82.77182 0 0 29513.87 -20143.669 -323.19871 -277834.82 -268341.55 6530.4635 Loop time of 7.47606e-06 on 32 procs for 0 steps with 10381 atoms 112.0% 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 | | 7.476e-06 | | |100.00 Nlocal: 324.406 ave 422 max 128 min Histogram: 8 0 0 0 0 0 0 6 5 13 Nghost: 6066.34 ave 7607 max 3905 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 149687 ave 219338 max 26623 min Histogram: 8 0 0 0 0 3 1 4 1 15 Total # of neighbors = 4789983 Ave neighs/atom = 461.41826 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out