#------------------------------------------------------------------------------- # 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 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.993312 0.774232 8304 2 97.0555 40.3057 2768 Per MPI rank memory allocation (min/avg/max) = 12.54 | 12.62 | 12.94 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 25793.854 92859.489 1.3074058 428.55654 51.329494 247.89677 0 0 26160.069 106502.5 -448.40969 -266470.92 -133509.12 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16479e-06 8304 2 103.7 9.29888e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.99223e-06 8304 2 103.7 0.000120813 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21156e-06 8304 2 103.7 9.27265e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.26223e-06 8304 2 103.7 8.58861e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.57829e-06 8304 2 103.7 9.48829e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.60023e-06 8304 2 103.7 0.000111243 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.2773e-06 8304 2 103.7 9.5741e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.03667e-06 8304 2 103.7 8.97278e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.16298e-06 8304 2 103.7 9.00244e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.29367e-06 8304 2 103.7 9.8191e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2404e-06 8304 2 103.7 9.2927e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.25465e-06 8304 2 103.7 9.80858e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.4685e-06 8304 2 103.7 0.000100068 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.76592e-06 8304 2 103.7 0.000108757 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.27143e-06 8304 2 103.7 0.000105488 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.71788e-06 8304 2 103.7 9.83435e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.35004e-06 8304 2 103.7 9.50676e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.1826e-06 8304 2 103.7 9.66686e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25919e-06 8304 2 103.7 9.69912e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.19264e-06 8304 2 103.7 9.96948e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.69766e-06 8304 2 103.7 0.000104134 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.13114e-06 8304 2 103.7 9.11003e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.42584e-06 8304 2 103.7 0.000113254 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20061e-06 8304 2 103.7 9.91329e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.34819e-06 8304 2 103.7 9.31767e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.05192e-06 8304 2 103.7 9.21464e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.34492e-06 8304 2 103.7 9.98539e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.34917e-06 8304 2 103.7 0.000102182 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18659e-06 8304 2 103.7 9.05466e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.6353e-06 8304 2 103.7 0.000125582 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.60793e-06 8304 2 103.7 0.0001066 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.27711e-06 8304 2 103.7 9.3875e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.20076e-06 8304 2 103.7 0.000108512 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.04724e-06 8304 2 103.7 0.000105241 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.34719e-06 8304 2 103.7 0.000129371 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17605e-06 8304 2 103.7 0.000108251 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.19855e-06 8304 2 103.7 0.000103103 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.26392e-06 8304 2 103.7 9.83121e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34553e-06 8304 2 103.7 0.000104149 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3711e-06 8304 2 103.7 0.000104329 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.21366e-06 8304 2 103.7 0.000105675 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.22782e-06 8304 2 103.7 0.000112521 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.17994e-06 8304 2 103.7 9.21962e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.18041e-06 8304 2 103.7 9.3529e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.19792e-06 8304 2 103.7 9.40557e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.13511e-06 8304 2 103.7 9.11259e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.15384e-06 8304 2 103.7 9.31839e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.40033e-06 8304 2 103.7 0.000118063 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.12226e-06 8304 2 103.7 9.29804e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.33995e-06 8304 2 103.7 9.5861e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.22382e-06 8304 2 103.7 9.73092e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.17857e-06 8304 2 103.7 9.9671e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.07157e-06 8304 2 103.7 9.21437e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.50909e-06 8304 2 103.7 0.000105982 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.18173e-06 8304 2 103.7 0.000104609 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.28791e-06 8304 2 103.7 8.86796e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.30516e-06 8304 2 103.7 0.00010862 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.17448e-06 8304 2 103.7 9.16128e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.27552e-06 8304 2 103.7 0.000108635 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.57641e-06 8304 2 103.7 0.000119689 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.58433e-06 8304 2 103.7 0.000104823 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.22004e-06 8304 2 103.7 8.99543e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 9.85979e-07 8304 2 103.7 9.04208e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.15537e-06 8304 2 103.7 9.77959e-05 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.22102e-06 8304 2 103.7 0.00011362 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.82726e-06 8304 2 103.7 0.000106729 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.66273e-06 8304 2 103.7 0.000114049 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.70792e-06 8304 2 103.7 8.88561e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.14327e-06 8304 2 103.7 9.96967e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.33597e-06 8304 2 103.7 9.07065e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.25019e-06 8304 2 103.7 9.12748e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.37475e-06 8304 2 103.7 9.56816e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.20434e-06 8304 2 103.7 9.87738e-05 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.21497e-06 8304 2 103.7 0.000102902 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.20615e-06 8304 2 103.7 9.47404e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.34054e-06 8304 2 103.7 8.97563e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.70933e-06 8304 2 103.7 0.000112896 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.23097e-06 8304 2 103.7 0.000105271 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.20868e-06 8304 2 103.7 9.0477e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.70689e-06 8304 2 103.7 0.000130499 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.48959e-06 8304 2 103.7 0.000104589 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.22604e-06 8304 2 103.7 0.000100182 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.22653e-06 8304 2 103.7 9.63307e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.18117e-06 8304 2 103.7 9.81466e-05 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.10486e-06 8304 2 103.7 9.42961e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.1653e-06 8304 2 103.7 9.88855e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.34019e-06 8304 2 103.7 9.07544e-05 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.2306e-06 8304 2 103.7 0.000106003 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.40413e-06 8304 2 103.7 0.000105128 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.22199e-06 8304 2 103.7 8.92578e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.55469e-06 8304 2 103.7 9.59653e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.29738e-06 8304 2 103.7 9.25902e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.47028e-06 8304 2 103.7 9.37643e-05 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.23233e-06 8304 2 103.7 9.85696e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.23842e-06 8304 2 103.7 8.68338e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.21871e-06 8304 2 103.7 0.00010451 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.25878e-06 8304 2 103.7 0.000155846 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.5066e-06 8304 2 103.7 0.000107295 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.41966e-06 8304 2 103.7 0.000118614 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.31737e-06 8304 2 103.7 9.72344e-05 2768 5000000 5000000 2714.1126 92859.489 1.3074058 299.63314 37.159931 71.164264 0 0 22401.936 86648.045 -448.40969 -271003.07 -161844.76 5655.4224 Loop time of 24027.8 on 32 procs for 5000000 steps with 9101 atoms Performance: 17.979 ns/day, 1.335 hours/ns, 208.092 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 | 11058 | 11684 | 12372 | 265.8 | 48.63 Bond | 5.3593 | 13.061 | 21.129 | 106.4 | 0.05 Kspace | 8684.1 | 9392.1 | 10016 | 299.8 | 39.09 Neigh | 763.95 | 765.3 | 766.85 | 3.1 | 3.19 Comm | 696.23 | 786.72 | 828.8 | 124.5 | 3.27 Output | 0.01196 | 0.014287 | 0.016467 | 1.2 | 0.00 Modify | 1281.9 | 1306.3 | 1355.1 | 57.8 | 5.44 Other | | 80.2 | | | 0.33 Nlocal: 284.406 ave 300 max 258 min Histogram: 1 0 0 5 2 6 5 6 3 4 Nghost: 4911.78 ave 4992 max 4783 min Histogram: 1 0 2 5 2 2 6 5 8 1 Neighs: 88654.8 ave 95982 max 76588 min Histogram: 1 0 0 5 4 4 7 5 2 4 Total # of neighbors = 2836954 Ave neighs/atom = 311.71893 Ave special neighs/atom = 1.8929788 Neighbor list builds = 245699 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) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.31737e-06 8304 2 103.7 9.72344e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.74 | 13.05 | 13.13 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 5000000 5000000 2715.1355 92859.489 1.3074058 299.63314 37.159931 71.164264 0 0 22401.936 86648.045 -448.40969 -271003.07 -161844.76 5655.4224 Loop time of 7.47634e-06 on 32 procs for 0 steps with 9101 atoms 108.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.476e-06 | | |100.00 Nlocal: 284.406 ave 300 max 258 min Histogram: 1 0 0 5 2 6 5 6 3 4 Nghost: 4911.78 ave 4992 max 4783 min Histogram: 1 0 2 5 2 2 6 5 8 1 Neighs: 88654.8 ave 95982 max 76588 min Histogram: 1 0 0 5 4 4 7 5 2 4 Total # of neighbors = 2836954 Ave neighs/atom = 311.71893 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