#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 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 200000 200000 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 2.5_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25882176 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026318283 estimated relative force accuracy = 7.9256727e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15950 6480 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 4.4139e-10 8304 2 103.7 4.88328e-08 2768 Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.16 | 16.25 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 2.2418448 97735.508 1.2421794 300.27411 50.524406 71.814348 0 0 21205.312 34565.627 -214.38764 -217190.91 -161297.64 5667.5205 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.17652e-06 8304 2 103.7 9.23726e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.38379e-06 8304 2 103.7 9.38438e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36941e-06 8304 2 103.7 0.000118536 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.34751e-06 8304 2 103.7 0.000107738 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.27594e-06 8304 2 103.7 9.28448e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.38284e-06 8304 2 103.7 9.88818e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.2436e-06 8304 2 103.7 0.000113497 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.56678e-06 8304 2 103.7 0.000122612 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33351e-06 8304 2 103.7 0.00010249 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.1909e-06 8304 2 103.7 0.000100372 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.26044e-06 8304 2 103.7 9.93553e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.72123e-06 8304 2 103.7 0.000114879 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.08508e-06 8304 2 103.7 9.7229e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.16282e-06 8304 2 103.7 9.61297e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.37831e-06 8304 2 103.7 9.84181e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18442e-06 8304 2 103.7 0.000103868 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.35702e-06 8304 2 103.7 9.61344e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.41812e-06 8304 2 103.7 9.91698e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31576e-06 8304 2 103.7 0.000107367 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.26892e-06 8304 2 103.7 0.000108722 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.51351e-06 8304 2 103.7 0.000106835 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.25953e-06 8304 2 103.7 0.000104411 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.29133e-06 8304 2 103.7 9.78253e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.66645e-06 8304 2 103.7 0.000129342 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.57834e-06 8304 2 103.7 0.000105575 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.22872e-06 8304 2 103.7 9.58936e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.47341e-06 8304 2 103.7 0.000111477 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.14503e-06 8304 2 103.7 9.93755e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12569e-06 8304 2 103.7 9.87221e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.4456e-06 8304 2 103.7 9.98782e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.50792e-06 8304 2 103.7 0.000108745 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.12513e-06 8304 2 103.7 9.57354e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.52016e-06 8304 2 103.7 0.000108327 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.21631e-06 8304 2 103.7 0.000110586 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19923e-06 8304 2 103.7 0.000100214 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.34731e-06 8304 2 103.7 9.34982e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.2277e-06 8304 2 103.7 9.60353e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.10544e-06 8304 2 103.7 0.000101005 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.49059e-06 8304 2 103.7 9.08544e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35599e-06 8304 2 103.7 0.000108654 2768 2000000 2000000 42.45532 97735.508 1.2421794 302.29096 47.824306 60.232485 0 0 21170.268 34601.797 -214.38764 -217189.74 -161309.61 5705.5874 Loop time of 42197.2 on 8 procs for 2000000 steps with 9101 atoms Performance: 4.095 ns/day, 5.861 hours/ns, 47.397 timesteps/s 99.2% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27676 | 30246 | 32557 |1005.3 | 71.68 Bond | 7.7646 | 10.963 | 13.582 | 56.7 | 0.03 Kspace | 5502.9 | 7817.7 | 10392 |1980.0 | 18.53 Neigh | 2796.6 | 2797.4 | 2798.3 | 1.5 | 6.63 Comm | 508.05 | 513.47 | 517.75 | 13.5 | 1.22 Output | 0.018896 | 0.020257 | 0.021435 | 0.6 | 0.00 Modify | 756.33 | 758.72 | 760.79 | 4.7 | 1.80 Other | | 52.87 | | | 0.13 Nlocal: 1137.62 ave 1158 max 1115 min Histogram: 1 1 0 1 1 0 1 1 1 1 Nghost: 11501.4 ave 11549 max 11457 min Histogram: 2 1 0 0 1 0 0 3 0 1 Neighs: 608380 ave 622124 max 592075 min Histogram: 1 1 1 0 1 0 0 2 0 2 Total # of neighbors = 4867041 Ave neighs/atom = 534.7809 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98882 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25882176 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026318283 estimated relative force accuracy = 7.9256727e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15950 6480 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35599e-06 8304 2 103.7 0.000108654 2768 Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.16 | 16.25 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 2000000 2000000 43.458517 97735.508 1.2421794 302.29096 47.824306 60.232485 0 0 21170.268 34601.797 -214.38764 -217189.74 -161309.61 5705.5874 Loop time of 3.05113e-06 on 8 procs for 0 steps with 9101 atoms 131.1% CPU use with 8 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 | | 3.051e-06 | | |100.00 Nlocal: 1137.62 ave 1158 max 1115 min Histogram: 1 1 0 1 1 0 1 1 1 1 Nghost: 11501.4 ave 11549 max 11457 min Histogram: 2 1 0 0 1 0 0 3 0 1 Neighs: 608380 ave 622124 max 592075 min Histogram: 1 1 1 0 1 0 0 2 0 2 Total # of neighbors = 4867041 Ave neighs/atom = 534.7809 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_Custom.out