#------------------------------------------------------------------------------- # Stage 2.4: 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 2.4_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 2.4_instantaneous.txt restart 5000000 2.4.restart dump sci all custom 500000 2.4.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 0.994332 0.730423 8304 2 96.9753 43.3857 2768 Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.67 | 12.16 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 23864.538 92859.489 1.3074058 428.55654 252.17843 572.08464 0 0 26147.68 -154740.42 -448.40969 0 -127768.47 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.76104e-06 8304 2 103.7 0.000111019 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26986e-06 8304 2 103.7 0.000102981 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.39514e-06 8304 2 103.7 0.000120886 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.31222e-06 8304 2 103.7 0.000101616 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.8049e-06 8304 2 103.7 0.000109907 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.3405e-06 8304 2 103.7 0.000107744 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.39045e-06 8304 2 103.7 0.000100846 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.15372e-06 8304 2 103.7 0.000125774 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.52789e-06 8304 2 103.7 9.26749e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.16098e-06 8304 2 103.7 9.5972e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 2.0088e-06 8304 2 103.7 0.000144914 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.24105e-06 8304 2 103.7 0.00010242 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.33998e-06 8304 2 103.7 9.83549e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 2.00914e-06 8304 2 103.7 0.000110443 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 2.14825e-06 8304 2 103.7 0.000138666 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.30028e-06 8304 2 103.7 0.000104484 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 2.27274e-06 8304 2 103.7 0.000124643 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.77957e-06 8304 2 103.7 0.000143573 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.45961e-06 8304 2 103.7 9.2522e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.77544e-06 8304 2 103.7 0.000114442 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 2.0681e-06 8304 2 103.7 0.000123614 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.68237e-06 8304 2 103.7 0.000107487 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.24107e-06 8304 2 103.7 0.000115844 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.60435e-06 8304 2 103.7 0.000109056 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.63178e-06 8304 2 103.7 0.000107491 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.36559e-06 8304 2 103.7 0.000110418 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.28071e-06 8304 2 103.7 9.71963e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.36044e-06 8304 2 103.7 9.74642e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.21318e-06 8304 2 103.7 9.70337e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.46792e-06 8304 2 103.7 0.000120244 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 2.14364e-06 8304 2 103.7 0.000101426 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.55458e-06 8304 2 103.7 0.000112155 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.58691e-06 8304 2 103.7 0.000104379 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.35796e-06 8304 2 103.7 9.30308e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.65393e-06 8304 2 103.7 0.000111803 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.86201e-06 8304 2 103.7 0.000121174 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.32651e-06 8304 2 103.7 0.000101312 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.66238e-06 8304 2 103.7 9.99711e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.54168e-06 8304 2 103.7 0.000104928 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.60238e-06 8304 2 103.7 0.000108362 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.85249e-06 8304 2 103.7 0.000121652 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.24549e-06 8304 2 103.7 9.13122e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.4386e-06 8304 2 103.7 0.00011144 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.70638e-06 8304 2 103.7 0.000117565 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.54507e-06 8304 2 103.7 0.000125738 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.89548e-06 8304 2 103.7 0.000103953 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.26255e-06 8304 2 103.7 0.000128982 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.36457e-06 8304 2 103.7 0.000114901 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.81108e-06 8304 2 103.7 0.000103148 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.48633e-06 8304 2 103.7 9.55419e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.80615e-06 8304 2 103.7 0.000125525 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.17966e-06 8304 2 103.7 0.000103862 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.22356e-06 8304 2 103.7 0.00011238 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.19012e-06 8304 2 103.7 0.000121587 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.83914e-06 8304 2 103.7 0.000112633 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.32765e-06 8304 2 103.7 0.000101304 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.74326e-06 8304 2 103.7 0.000112064 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.41508e-06 8304 2 103.7 0.00012214 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.23731e-06 8304 2 103.7 0.000102208 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.28658e-06 8304 2 103.7 9.53916e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.86058e-06 8304 2 103.7 0.000110919 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.62186e-06 8304 2 103.7 9.95927e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.86714e-06 8304 2 103.7 0.000102134 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.44303e-06 8304 2 103.7 0.000100482 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.44053e-06 8304 2 103.7 0.000107052 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.67171e-06 8304 2 103.7 0.000122807 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.89834e-06 8304 2 103.7 9.72714e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.43674e-06 8304 2 103.7 0.000100986 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.5077e-06 8304 2 103.7 0.00011321 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.96306e-06 8304 2 103.7 0.000113739 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.2106e-06 8304 2 103.7 0.000108702 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.4299e-06 8304 2 103.7 0.000103353 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.5557e-06 8304 2 103.7 0.000109702 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.70831e-06 8304 2 103.7 9.64078e-05 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.33069e-06 8304 2 103.7 0.000101008 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.27486e-06 8304 2 103.7 0.000115302 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.72795e-06 8304 2 103.7 0.000121088 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.57407e-06 8304 2 103.7 0.000127308 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.60241e-06 8304 2 103.7 0.000111638 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.32967e-06 8304 2 103.7 8.96402e-05 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.83958e-06 8304 2 103.7 0.000126023 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.27379e-06 8304 2 103.7 0.000110017 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.37131e-06 8304 2 103.7 0.000111036 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.33278e-06 8304 2 103.7 0.000106563 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.28882e-06 8304 2 103.7 0.000125316 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.36751e-06 8304 2 103.7 0.000119135 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.32103e-06 8304 2 103.7 0.000139435 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.32274e-06 8304 2 103.7 0.000105767 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.66137e-06 8304 2 103.7 0.00012262 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.4002e-06 8304 2 103.7 0.000105508 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.30973e-06 8304 2 103.7 9.95087e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.5348e-06 8304 2 103.7 0.000104641 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.30629e-06 8304 2 103.7 0.000114223 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.76232e-06 8304 2 103.7 0.000134332 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.27265e-06 8304 2 103.7 9.13093e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.49464e-06 8304 2 103.7 9.69784e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.27616e-06 8304 2 103.7 9.55941e-05 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.52947e-06 8304 2 103.7 9.46948e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.38648e-06 8304 2 103.7 0.00010203 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.51858e-06 8304 2 103.7 0.000102974 2768 5000000 5000000 426.82287 92859.489 1.3074058 299.39882 42.395683 126.36111 0 0 20673.22 -171097 -448.40969 0 -150255.02 5650.9998 Loop time of 14611.6 on 32 procs for 5000000 steps with 9101 atoms Performance: 29.566 ns/day, 0.812 hours/ns, 342.194 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 | 9943.9 | 10993 | 12126 | 484.3 | 75.24 Bond | 3.4795 | 9.6384 | 18.067 | 128.8 | 0.07 Neigh | 736.13 | 738.19 | 739.92 | 3.4 | 5.05 Comm | 631.94 | 1536.4 | 2750.2 |1304.2 | 10.52 Output | 0.010851 | 0.013158 | 0.015313 | 1.2 | 0.00 Modify | 1053.7 | 1274 | 1845.8 | 588.9 | 8.72 Other | | 60.33 | | | 0.41 Nlocal: 284.406 ave 302 max 266 min Histogram: 3 1 2 4 5 3 6 2 4 2 Nghost: 4927.09 ave 5074 max 4820 min Histogram: 2 3 5 4 7 6 2 1 0 2 Neighs: 88287.2 ave 98118 max 79827 min Histogram: 3 2 5 2 7 3 4 3 1 2 Total # of neighbors = 2825192 Ave neighs/atom = 310.42655 Ave special neighs/atom = 1.8929788 Neighbor list builds = 238853 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.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 1.51858e-06 8304 2 103.7 0.000102974 2768 Per MPI rank memory allocation (min/avg/max) = 11.59 | 11.77 | 12.17 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 427.92077 92859.489 1.3074058 299.39882 42.395683 126.36111 0 0 20673.22 -171097 -448.40969 0 -150255.02 5650.9998 Loop time of 7.93556e-06 on 32 procs for 0 steps with 9101 atoms 109.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.936e-06 | | |100.00 Nlocal: 284.406 ave 302 max 266 min Histogram: 3 1 2 4 5 3 6 2 4 2 Nghost: 4927.09 ave 5074 max 4820 min Histogram: 2 3 5 4 7 6 2 1 0 2 Neighs: 88287.2 ave 98118 max 79827 min Histogram: 3 2 5 2 7 3 4 3 1 2 Total # of neighbors = 2825192 Ave neighs/atom = 310.42655 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out