#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 5 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 500000 500000 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 500 1 500 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 5000000 2.5.restart dump sci all custom 500000 2.5.xyz id mol type q xs ys zs timestep 1 run 5000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 5.82867e-14 8304 2 103.7 4.448e-12 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.71 | 11.98 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-06 298.90276 94659.812 1.2825404 297.98425 41.66013 98.733098 0 0 20885.304 -173140.39 -439.88145 0 -152114.69 5624.3006 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33599e-06 8304 2 103.7 0.000111028 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.4506e-06 8304 2 103.7 0.000125753 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36636e-06 8304 2 103.7 0.000101915 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.33979e-06 8304 2 103.7 9.44189e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.28329e-06 8304 2 103.7 9.78513e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.51597e-06 8304 2 103.7 0.000113076 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.67898e-06 8304 2 103.7 9.75824e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.29211e-06 8304 2 103.7 0.00011883 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.88801e-06 8304 2 103.7 0.000120798 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.33849e-06 8304 2 103.7 0.000104523 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.32708e-06 8304 2 103.7 9.72816e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.71056e-06 8304 2 103.7 9.51641e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.43755e-06 8304 2 103.7 0.000103111 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.42068e-06 8304 2 103.7 0.000103375 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.54628e-06 8304 2 103.7 0.000105618 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.58148e-06 8304 2 103.7 0.000101789 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.44856e-06 8304 2 103.7 0.000108189 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.19739e-06 8304 2 103.7 0.000105953 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.74454e-06 8304 2 103.7 9.85861e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.97779e-06 8304 2 103.7 0.000109316 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.50835e-06 8304 2 103.7 0.000122615 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.49511e-06 8304 2 103.7 0.00010566 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22928e-06 8304 2 103.7 9.26089e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 2.15957e-06 8304 2 103.7 0.00015294 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.15825e-06 8304 2 103.7 9.63197e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.52062e-06 8304 2 103.7 0.000107443 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.56174e-06 8304 2 103.7 0.00010794 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.42492e-06 8304 2 103.7 0.000103121 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.32439e-06 8304 2 103.7 9.75823e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.7409e-06 8304 2 103.7 0.000109369 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.48602e-06 8304 2 103.7 0.000118819 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.54863e-06 8304 2 103.7 9.87742e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.73107e-06 8304 2 103.7 0.000107169 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.3861e-06 8304 2 103.7 0.000104368 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.29755e-06 8304 2 103.7 9.87273e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.37087e-06 8304 2 103.7 0.00012469 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.26051e-06 8304 2 103.7 9.76937e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.68588e-06 8304 2 103.7 0.000102269 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.97553e-06 8304 2 103.7 0.000134418 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.49325e-06 8304 2 103.7 0.000108775 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.3502e-06 8304 2 103.7 0.000125822 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.39063e-06 8304 2 103.7 9.66361e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.39077e-06 8304 2 103.7 0.000104914 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.64872e-06 8304 2 103.7 0.000119863 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.63177e-06 8304 2 103.7 0.000112586 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.29558e-06 8304 2 103.7 0.000104084 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.72166e-06 8304 2 103.7 0.000113809 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.48792e-06 8304 2 103.7 0.00010785 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.80049e-06 8304 2 103.7 0.000108463 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.83988e-06 8304 2 103.7 0.000116771 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.30147e-06 8304 2 103.7 0.000118106 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.68206e-06 8304 2 103.7 0.000102146 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.30825e-06 8304 2 103.7 9.77871e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.19584e-06 8304 2 103.7 0.000109876 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.07115e-06 8304 2 103.7 9.19381e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.51986e-06 8304 2 103.7 0.000109757 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.22522e-06 8304 2 103.7 9.64331e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.39283e-06 8304 2 103.7 9.68313e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.40287e-06 8304 2 103.7 0.000120501 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.30546e-06 8304 2 103.7 0.000107272 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.72702e-06 8304 2 103.7 9.75787e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.61611e-06 8304 2 103.7 0.000118819 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.40381e-06 8304 2 103.7 0.000109339 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.56487e-06 8304 2 103.7 0.00012481 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.39847e-06 8304 2 103.7 9.59505e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.47533e-06 8304 2 103.7 9.93567e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.43735e-06 8304 2 103.7 9.40372e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.6747e-06 8304 2 103.7 0.00011965 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.35996e-06 8304 2 103.7 0.000122751 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.48799e-06 8304 2 103.7 0.000132544 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.38152e-06 8304 2 103.7 9.90774e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.22172e-06 8304 2 103.7 9.90278e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.5647e-06 8304 2 103.7 0.000100387 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.98004e-06 8304 2 103.7 0.000131614 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.86323e-06 8304 2 103.7 0.000120463 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.15514e-06 8304 2 103.7 0.000108775 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.3222e-06 8304 2 103.7 0.000118311 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.31641e-06 8304 2 103.7 0.000102345 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.27695e-06 8304 2 103.7 9.85444e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.45746e-06 8304 2 103.7 0.000103712 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.29938e-06 8304 2 103.7 0.000115028 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.77708e-06 8304 2 103.7 0.000132449 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.28898e-06 8304 2 103.7 0.000112224 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.11143e-06 8304 2 103.7 9.38051e-05 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.52464e-06 8304 2 103.7 9.62209e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.43592e-06 8304 2 103.7 9.95598e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.90284e-06 8304 2 103.7 0.000119957 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.53299e-06 8304 2 103.7 0.000112605 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.33505e-06 8304 2 103.7 0.000102694 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.97885e-06 8304 2 103.7 0.000104646 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.46057e-06 8304 2 103.7 0.000109453 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.64557e-06 8304 2 103.7 0.000106277 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.84499e-06 8304 2 103.7 0.000106846 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.53673e-06 8304 2 103.7 9.87631e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.27202e-06 8304 2 103.7 9.8435e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.62612e-06 8304 2 103.7 0.000119457 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.43364e-06 8304 2 103.7 0.000112651 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.45901e-06 8304 2 103.7 0.000103574 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.47213e-06 8304 2 103.7 9.82548e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.29448e-06 8304 2 103.7 9.10781e-05 2768 5000000 5000000 -603.09953 94659.812 1.2825404 303.03983 39.778311 107.89196 0 0 20457.892 -170259.08 -439.88145 0 -149653.51 5719.722 Loop time of 14267.5 on 32 procs for 5000000 steps with 9101 atoms Performance: 30.279 ns/day, 0.793 hours/ns, 350.446 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9882.6 | 10796 | 11732 | 443.4 | 75.67 Bond | 3.7057 | 9.6845 | 15.766 | 114.8 | 0.07 Neigh | 726.77 | 729.13 | 730.6 | 3.6 | 5.11 Comm | 603.29 | 1439.5 | 2425.3 |1185.9 | 10.09 Output | 0.0089902 | 0.01122 | 0.013321 | 1.2 | 0.00 Modify | 1078.5 | 1233.2 | 1634.8 | 406.3 | 8.64 Other | | 60.4 | | | 0.42 Nlocal: 284.406 ave 302 max 268 min Histogram: 3 2 1 5 6 4 2 7 1 1 Nghost: 4876.22 ave 5001 max 4766 min Histogram: 2 3 4 2 6 6 3 4 1 1 Neighs: 86628.9 ave 93681 max 79859 min Histogram: 5 1 1 4 6 5 2 4 2 2 Total # of neighbors = 2772126 Ave neighs/atom = 304.59576 Ave special neighs/atom = 1.8929788 Neighbor list builds = 239094 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.29448e-06 8304 2 103.7 9.10781e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.71 | 11.98 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 5000000 5000000 -602.10844 94659.812 1.2825404 303.03983 39.778311 107.89196 0 0 20457.892 -170259.08 -439.88145 0 -149653.51 5719.722 Loop time of 7.51612e-06 on 32 procs for 0 steps with 9101 atoms 108.1% 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 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 | | 7.516e-06 | | |100.00 Nlocal: 284.406 ave 302 max 268 min Histogram: 3 2 1 5 6 4 2 7 1 1 Nghost: 4876.22 ave 5001 max 4766 min Histogram: 2 3 4 2 6 6 3 4 1 1 Neighs: 86628.9 ave 93681 max 79859 min Histogram: 5 1 1 4 6 5 2 4 2 2 Total # of neighbors = 2772126 Ave neighs/atom = 304.59576 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_NVT.out