#------------------------------------------------------------------------------- # 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 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 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 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.0002 0.0548301 6000 1 97.8764 8.76344 2000 Per MPI rank memory allocation (min/avg/max) = 8.312 | 9.355 | 10.27 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 -349.39361 119078.03 0.50244692 447.33728 0 0 0 0 9622.5048 81332.032 -89.819258 -122254.47 -31299.932 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21629e-06 6000 1 103.7 0.00011839 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.27773e-06 6000 1 103.7 9.98781e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.53573e-06 6000 1 103.7 0.000108802 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.13505e-06 6000 1 103.7 0.0001024 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.25805e-06 6000 1 103.7 0.000133249 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.41846e-06 6000 1 103.7 0.000106954 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.4663e-06 6000 1 103.7 9.8336e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.26025e-06 6000 1 103.7 0.000124746 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.47979e-06 6000 1 103.7 0.000119672 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.29891e-06 6000 1 103.7 9.33388e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.15179e-06 6000 1 103.7 0.000100927 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.16224e-06 6000 1 103.7 9.65215e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.23065e-06 6000 1 103.7 0.000120374 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.42566e-06 6000 1 103.7 9.63259e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.59261e-06 6000 1 103.7 0.000119783 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.24996e-06 6000 1 103.7 0.000104157 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.41987e-06 6000 1 103.7 0.000105468 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.05133e-06 6000 1 103.7 9.62161e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.07241e-06 6000 1 103.7 9.4288e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.136e-06 6000 1 103.7 8.62038e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.92126e-06 6000 1 103.7 0.000141645 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.16578e-06 6000 1 103.7 0.000104963 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.28213e-06 6000 1 103.7 9.92983e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.66479e-06 6000 1 103.7 0.000126244 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.1502e-06 6000 1 103.7 0.00011156 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.47219e-06 6000 1 103.7 0.000104233 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.27116e-06 6000 1 103.7 0.000125722 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.92449e-06 6000 1 103.7 0.000130114 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.23248e-06 6000 1 103.7 0.000108143 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.82478e-06 6000 1 103.7 0.000170736 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.28277e-06 6000 1 103.7 0.000111086 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.16365e-06 6000 1 103.7 9.62806e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.12307e-06 6000 1 103.7 9.54379e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.39295e-06 6000 1 103.7 0.000105064 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.31286e-06 6000 1 103.7 9.81141e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.24677e-06 6000 1 103.7 9.19317e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.09852e-06 6000 1 103.7 0.000100695 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.04145e-06 6000 1 103.7 9.04585e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.51519e-06 6000 1 103.7 0.000104075 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.34208e-06 6000 1 103.7 0.000100175 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.18919e-06 6000 1 103.7 0.000107912 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.23302e-06 6000 1 103.7 9.9773e-05 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.50371e-06 6000 1 103.7 9.4296e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.09296e-06 6000 1 103.7 0.000100562 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.25728e-06 6000 1 103.7 0.000100681 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.25323e-06 6000 1 103.7 0.000103405 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.07647e-06 6000 1 103.7 9.10712e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.19061e-06 6000 1 103.7 9.78002e-05 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.31647e-06 6000 1 103.7 0.000103071 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.12865e-06 6000 1 103.7 9.43568e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.13939e-06 6000 1 103.7 9.67189e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.17341e-06 6000 1 103.7 9.20084e-05 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.21307e-06 6000 1 103.7 0.000104667 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.57804e-06 6000 1 103.7 0.000112208 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.56362e-06 6000 1 103.7 0.00011212 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.14781e-06 6000 1 103.7 9.42717e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.24107e-06 6000 1 103.7 9.83544e-05 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.2038e-06 6000 1 103.7 9.41535e-05 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.08406e-06 6000 1 103.7 9.19782e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.25321e-06 6000 1 103.7 0.000105505 2000 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.13805e-06 6000 1 103.7 9.18885e-05 2000 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.54078e-06 6000 1 103.7 0.00010915 2000 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.5299e-06 6000 1 103.7 9.36518e-05 2000 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.83061e-06 6000 1 103.7 0.000139426 2000 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.20821e-06 6000 1 103.7 9.29003e-05 2000 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.16742e-06 6000 1 103.7 9.31156e-05 2000 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.14897e-06 6000 1 103.7 0.000107855 2000 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.35496e-06 6000 1 103.7 0.000103857 2000 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.19478e-06 6000 1 103.7 9.68932e-05 2000 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.15282e-06 6000 1 103.7 0.000101314 2000 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.68053e-06 6000 1 103.7 0.000132636 2000 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.29122e-06 6000 1 103.7 0.000108586 2000 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.21073e-06 6000 1 103.7 9.54511e-05 2000 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.43426e-06 6000 1 103.7 0.000104341 2000 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.1885e-06 6000 1 103.7 9.50668e-05 2000 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.154e-06 6000 1 103.7 0.000119554 2000 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.55782e-06 6000 1 103.7 0.000103968 2000 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.53373e-06 6000 1 103.7 9.30265e-05 2000 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.14933e-06 6000 1 103.7 0.000102343 2000 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.32389e-06 6000 1 103.7 9.53056e-05 2000 SHAKE stats (type/ave/delta/count) on step 4050000 1 0.97 1.09842e-06 6000 1 103.7 9.14059e-05 2000 SHAKE stats (type/ave/delta/count) on step 4100000 1 0.97 1.13604e-06 6000 1 103.7 9.38261e-05 2000 SHAKE stats (type/ave/delta/count) on step 4150000 1 0.97 9.89873e-07 6000 1 103.7 9.41556e-05 2000 SHAKE stats (type/ave/delta/count) on step 4200000 1 0.97 1.17696e-06 6000 1 103.7 9.47309e-05 2000 SHAKE stats (type/ave/delta/count) on step 4250000 1 0.97 1.34584e-06 6000 1 103.7 9.66182e-05 2000 SHAKE stats (type/ave/delta/count) on step 4300000 1 0.97 1.41612e-06 6000 1 103.7 0.000117773 2000 SHAKE stats (type/ave/delta/count) on step 4350000 1 0.97 1.17482e-06 6000 1 103.7 9.99182e-05 2000 SHAKE stats (type/ave/delta/count) on step 4400000 1 0.97 1.12755e-06 6000 1 103.7 9.14471e-05 2000 SHAKE stats (type/ave/delta/count) on step 4450000 1 0.97 1.31455e-06 6000 1 103.7 9.53231e-05 2000 SHAKE stats (type/ave/delta/count) on step 4500000 1 0.97 1.06593e-06 6000 1 103.7 9.72459e-05 2000 SHAKE stats (type/ave/delta/count) on step 4550000 1 0.97 1.35856e-06 6000 1 103.7 0.000101835 2000 SHAKE stats (type/ave/delta/count) on step 4600000 1 0.97 1.70389e-06 6000 1 103.7 0.000105676 2000 SHAKE stats (type/ave/delta/count) on step 4650000 1 0.97 1.33793e-06 6000 1 103.7 9.80887e-05 2000 SHAKE stats (type/ave/delta/count) on step 4700000 1 0.97 1.28594e-06 6000 1 103.7 0.000102813 2000 SHAKE stats (type/ave/delta/count) on step 4750000 1 0.97 1.30527e-06 6000 1 103.7 0.000103413 2000 SHAKE stats (type/ave/delta/count) on step 4800000 1 0.97 1.45434e-06 6000 1 103.7 9.73993e-05 2000 SHAKE stats (type/ave/delta/count) on step 4850000 1 0.97 1.13503e-06 6000 1 103.7 9.40366e-05 2000 SHAKE stats (type/ave/delta/count) on step 4900000 1 0.97 1.2357e-06 6000 1 103.7 9.51206e-05 2000 SHAKE stats (type/ave/delta/count) on step 4950000 1 0.97 1.34698e-06 6000 1 103.7 9.24402e-05 2000 SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.23436e-06 6000 1 103.7 0.000101249 2000 5000000 5000000 -46.625706 119078.03 0.50244692 301.41176 0 0 0 0 5165.8664 95901.196 -89.819258 -122205.24 -21138.178 3592.9064 Loop time of 28517 on 32 procs for 5000000 steps with 6000 atoms Performance: 15.149 ns/day, 1.584 hours/ns, 175.334 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2314 | 8236.8 | 17356 |8808.9 | 28.88 Bond | 4.0494 | 5.1055 | 7.6206 | 32.9 | 0.02 Kspace | 7795.8 | 17066 | 25644 |6221.0 | 59.84 Neigh | 926.47 | 943.39 | 998.46 | 74.2 | 3.31 Comm | 27.405 | 714.01 | 1081.4 |1486.2 | 2.50 Output | 0.010386 | 0.012024 | 0.013425 | 0.8 | 0.00 Modify | 1270.4 | 1479 | 1772.2 | 540.3 | 5.19 Other | | 72.74 | | | 0.26 Nlocal: 187.5 ave 385 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 2899.66 ave 5729 max 0 min Histogram: 8 0 3 5 0 0 4 4 0 8 Neighs: 61903.4 ave 135419 max 0 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 1980910 Ave neighs/atom = 330.15167 Ave special neighs/atom = 2 Neighbor list builds = 247699 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.23436e-06 6000 1 103.7 0.000101249 2000 Per MPI rank memory allocation (min/avg/max) = 8.438 | 9.649 | 10.26 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 -46.353802 119078.03 0.50244692 301.41176 0 0 0 0 5165.8664 95901.196 -89.819258 -122205.24 -21138.178 3592.9064 Loop time of 6.73519e-06 on 32 procs for 0 steps with 6000 atoms 117.9% 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 | | 6.735e-06 | | |100.00 Nlocal: 187.5 ave 385 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 2899.66 ave 5729 max 0 min Histogram: 8 0 3 5 0 0 4 4 0 8 Neighs: 61903.4 ave 135419 max 0 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 1980910 Ave neighs/atom = 330.15167 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