#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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 300000 300000 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 300 1 300 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 restart 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24720763 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033477167 estimated relative force accuracy = 1.0081549e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00008 0.0545489 6000 1 97.8974 9.3061 2000 Per MPI rank memory allocation (min/avg/max) = 8.28 | 9.514 | 10.6 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 1355.5564 119945.8 0.49881188 447.33728 0 0 0 0 9616.3424 60989.286 -52.002031 -101750.05 -31144.419 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.38179e-06 6000 1 103.7 0.000111233 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.16652e-06 6000 1 103.7 0.00010625 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.38128e-06 6000 1 103.7 0.000114566 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.09584e-06 6000 1 103.7 8.84752e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 2.06861e-06 6000 1 103.7 0.000136805 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.18453e-06 6000 1 103.7 0.0001005 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.29292e-06 6000 1 103.7 9.9977e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.183e-06 6000 1 103.7 9.65682e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.99323e-06 6000 1 103.7 0.000121363 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.65675e-06 6000 1 103.7 0.0001232 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.23378e-06 6000 1 103.7 9.1418e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.53194e-06 6000 1 103.7 9.45296e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.14802e-06 6000 1 103.7 9.22626e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.84092e-06 6000 1 103.7 0.000136256 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.52452e-06 6000 1 103.7 0.000121387 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.32923e-06 6000 1 103.7 0.000138503 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.21555e-06 6000 1 103.7 9.58173e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.1133e-06 6000 1 103.7 0.000112765 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.6694e-06 6000 1 103.7 0.000141592 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.92761e-06 6000 1 103.7 0.000127837 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.3667e-06 6000 1 103.7 9.52753e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.32682e-06 6000 1 103.7 0.000105388 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.15663e-06 6000 1 103.7 9.64783e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.09487e-06 6000 1 103.7 8.96036e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.30371e-06 6000 1 103.7 0.000103806 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.18038e-06 6000 1 103.7 9.09905e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.13621e-06 6000 1 103.7 9.1034e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.19403e-06 6000 1 103.7 9.91609e-05 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.18294e-06 6000 1 103.7 0.00010086 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.15314e-06 6000 1 103.7 9.63736e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.10218e-06 6000 1 103.7 9.67277e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.25794e-06 6000 1 103.7 9.40518e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.18347e-06 6000 1 103.7 9.39417e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.24479e-06 6000 1 103.7 9.6366e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.23219e-06 6000 1 103.7 0.000108098 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.62601e-06 6000 1 103.7 0.000102537 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.04818e-06 6000 1 103.7 9.02085e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.1336e-06 6000 1 103.7 9.28961e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.71753e-06 6000 1 103.7 0.000125138 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.38222e-06 6000 1 103.7 0.000102751 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.62234e-06 6000 1 103.7 0.000115844 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.26251e-06 6000 1 103.7 0.000101016 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.17814e-06 6000 1 103.7 9.02148e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.38429e-06 6000 1 103.7 0.000109898 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.24172e-06 6000 1 103.7 0.000103835 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.20498e-06 6000 1 103.7 9.76535e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.21497e-06 6000 1 103.7 9.29845e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.0617e-06 6000 1 103.7 9.40923e-05 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.24543e-06 6000 1 103.7 9.66374e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.26235e-06 6000 1 103.7 9.95849e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.41414e-06 6000 1 103.7 0.000104058 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.38685e-06 6000 1 103.7 0.000105855 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.64347e-06 6000 1 103.7 0.000112144 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.25469e-06 6000 1 103.7 9.18599e-05 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.23752e-06 6000 1 103.7 0.000105839 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.50988e-06 6000 1 103.7 0.000101992 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.34985e-06 6000 1 103.7 0.000117408 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.18325e-06 6000 1 103.7 9.56465e-05 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.1841e-06 6000 1 103.7 9.84002e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.42648e-06 6000 1 103.7 0.000116473 2000 3000000 3000000 -138.40166 119945.8 0.49881188 298.59171 0 0 0 0 5090.2611 75650.546 -52.002031 -101738.46 -20997.652 3559.2906 Loop time of 24844.9 on 32 procs for 3000000 steps with 6000 atoms Performance: 10.433 ns/day, 2.300 hours/ns, 120.749 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.768 | 7746.9 | 18284 |8691.2 | 31.18 Bond | 2.5716 | 3.5127 | 7.2528 | 47.4 | 0.01 Kspace | 3529.1 | 14128 | 21967 |6469.9 | 56.87 Neigh | 1174.2 | 1181.3 | 1192.2 | 17.1 | 4.75 Comm | 318.31 | 672.97 | 896.77 | 809.9 | 2.71 Output | 0.0097249 | 0.011491 | 0.013055 | 0.9 | 0.00 Modify | 902.28 | 1066.9 | 1306.4 | 481.6 | 4.29 Other | | 44.79 | | | 0.18 Nlocal: 187.5 ave 388 max 0 min Histogram: 13 2 1 0 0 0 0 1 4 11 Nghost: 4076.34 ave 7475 max 673 min Histogram: 8 0 0 7 1 0 8 0 0 8 Neighs: 92142.5 ave 229191 max 0 min Histogram: 16 0 0 0 1 3 1 2 3 6 Total # of neighbors = 2948560 Ave neighs/atom = 491.42667 Ave special neighs/atom = 2 Neighbor list builds = 148958 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24720763 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033477167 estimated relative force accuracy = 1.0081549e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.42648e-06 6000 1 103.7 0.000116473 2000 Per MPI rank memory allocation (min/avg/max) = 8.315 | 9.727 | 10.6 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 3000000 3000000 -138.17353 119945.8 0.49881188 298.59171 0 0 0 0 5090.2611 75650.546 -52.002031 -101738.46 -20997.652 3559.2906 Loop time of 7.11244e-06 on 32 procs for 0 steps with 6000 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 | | 7.112e-06 | | |100.00 Nlocal: 187.5 ave 388 max 0 min Histogram: 13 2 1 0 0 0 0 1 4 11 Nghost: 4076.34 ave 7475 max 673 min Histogram: 8 0 0 7 1 0 8 0 0 8 Neighs: 92142.5 ave 229191 max 0 min Histogram: 16 0 0 0 1 3 1 2 3 6 Total # of neighbors = 2948560 Ave neighs/atom = 491.42667 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out