#------------------------------------------------------------------------------- # Stage 2.5: 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 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 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 3000000 2.5.restart dump sci all custom 300000 2.5.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) = 0.24992822 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035847612 estimated relative force accuracy = 1.0795402e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.23897e-13 8304 2 103.7 7.98508e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.75 | 14.13 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 -288.00631 194808.45 0.62320209 300.27613 35.95419 56.857996 0 0 20936.765 28299.569 -107.55839 -209789.54 -160460.39 5667.5585 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.18897e-06 8304 2 103.7 0.000104914 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34457e-06 8304 2 103.7 9.48777e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21034e-06 8304 2 103.7 9.31763e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.26055e-06 8304 2 103.7 9.94651e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.42552e-06 8304 2 103.7 8.7006e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.36484e-06 8304 2 103.7 0.000105033 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19623e-06 8304 2 103.7 9.37422e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.57479e-06 8304 2 103.7 0.00011696 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.19571e-06 8304 2 103.7 0.000102868 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15533e-06 8304 2 103.7 9.43905e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.16702e-06 8304 2 103.7 9.65456e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.1217e-06 8304 2 103.7 9.42912e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.18726e-06 8304 2 103.7 9.69595e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.30835e-06 8304 2 103.7 9.21272e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33827e-06 8304 2 103.7 9.89983e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.3708e-06 8304 2 103.7 0.000104889 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.56598e-06 8304 2 103.7 0.000111679 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.36169e-06 8304 2 103.7 9.48407e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.08104e-06 8304 2 103.7 9.68422e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 2.1347e-06 8304 2 103.7 0.000130601 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.09608e-06 8304 2 103.7 9.3179e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.36911e-06 8304 2 103.7 0.000141786 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.31401e-06 8304 2 103.7 9.29191e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.71872e-06 8304 2 103.7 0.000141715 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.31613e-06 8304 2 103.7 9.22869e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.71652e-06 8304 2 103.7 0.000119267 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.30444e-06 8304 2 103.7 9.89195e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.20573e-06 8304 2 103.7 9.83938e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.21861e-06 8304 2 103.7 9.07337e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.35966e-06 8304 2 103.7 0.000131569 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.05803e-06 8304 2 103.7 9.5242e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.07834e-06 8304 2 103.7 9.26695e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.33944e-06 8304 2 103.7 9.81929e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.64208e-06 8304 2 103.7 0.000108515 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.3935e-06 8304 2 103.7 0.000114321 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.2631e-06 8304 2 103.7 9.17177e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.26452e-06 8304 2 103.7 0.000106096 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.12858e-06 8304 2 103.7 9.16853e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.33084e-06 8304 2 103.7 0.000102002 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.32199e-06 8304 2 103.7 9.44528e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.06619e-06 8304 2 103.7 9.84912e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.42355e-06 8304 2 103.7 9.94076e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.17509e-06 8304 2 103.7 9.95748e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.68768e-06 8304 2 103.7 0.000127074 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.40018e-06 8304 2 103.7 0.000112393 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.10568e-06 8304 2 103.7 9.13376e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.61755e-06 8304 2 103.7 0.000118853 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.5452e-06 8304 2 103.7 0.000102793 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.06914e-06 8304 2 103.7 9.39155e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.44963e-06 8304 2 103.7 9.3772e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.00286e-06 8304 2 103.7 0.000104993 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.19579e-06 8304 2 103.7 8.74778e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.44857e-06 8304 2 103.7 0.000112589 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.03538e-06 8304 2 103.7 9.31459e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.14373e-06 8304 2 103.7 9.90094e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.48055e-06 8304 2 103.7 0.000122506 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18586e-06 8304 2 103.7 9.09159e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.2238e-06 8304 2 103.7 9.81737e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19602e-06 8304 2 103.7 0.000103651 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.31715e-06 8304 2 103.7 9.60521e-05 2768 3000000 3000000 -174.22611 194808.45 0.62320209 293.67438 37.297832 56.74076 0 0 21063.23 28221.784 -107.55839 -209780.53 -160401.47 5542.954 Loop time of 34634.8 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.484 ns/day, 3.207 hours/ns, 86.618 timesteps/s 98.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7738 | 10908 | 24596 |9747.5 | 31.49 Bond | 2.8072 | 7.3595 | 19.839 | 173.5 | 0.02 Kspace | 5920 | 19701 | 30810 |7300.1 | 56.88 Neigh | 1855.4 | 1863.7 | 1878.2 | 15.8 | 5.38 Comm | 219.27 | 681.22 | 952.63 | 975.2 | 1.97 Output | 0.01505 | 0.017246 | 0.019297 | 0.9 | 0.00 Modify | 1211.2 | 1398.5 | 1656.3 | 476.7 | 4.04 Other | | 74.68 | | | 0.22 Nlocal: 284.406 ave 585 max 0 min Histogram: 12 0 0 1 1 6 0 0 0 12 Nghost: 4475.94 ave 8849 max 1 min Histogram: 4 0 8 0 3 5 0 4 4 4 Neighs: 133466 ave 314807 max 0 min Histogram: 12 4 0 0 1 3 0 1 4 7 Total # of neighbors = 4270898 Ave neighs/atom = 469.27788 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149801 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24992822 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035847612 estimated relative force accuracy = 1.0795402e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.31715e-06 8304 2 103.7 9.60521e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.18 | 12.78 | 14.13 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 -173.82385 194808.45 0.62320209 293.67438 37.297832 56.74076 0 0 21063.23 28221.784 -107.55839 -209780.53 -160401.47 5542.954 Loop time of 8.16003e-06 on 32 procs for 0 steps with 9101 atoms 108.8% 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 | | 8.16e-06 | | |100.00 Nlocal: 284.406 ave 585 max 0 min Histogram: 12 0 0 1 1 6 0 0 0 12 Nghost: 4475.94 ave 8849 max 1 min Histogram: 4 0 8 0 3 5 0 4 4 4 Neighs: 133466 ave 314807 max 0 min Histogram: 12 4 0 0 1 3 0 1 4 7 Total # of neighbors = 4270898 Ave neighs/atom = 469.27788 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 19:17:47