#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3659 = # 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 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 file 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.17568e-13 10977 2 103.7 8.84484e-11 3659 Per MPI rank memory allocation (min/avg/max) = 14.83 | 15.11 | 15.84 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 337952.67 142807.9 1.3823791 298.24549 282.68739 377.368 0 0 272984.17 -64853.607 -383.2647 -382421.77 -173631.15 8106.022 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.3849e-06 10977 2 103.7 9.59901e-05 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.26535e-06 10977 2 103.7 0.000111629 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.11672e-06 10977 2 103.7 0.000113943 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.97973e-06 10977 2 103.7 0.000112459 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.32478e-06 10977 2 103.7 9.88821e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.43099e-06 10977 2 103.7 9.57884e-05 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.13032e-06 10977 2 103.7 9.56306e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.13675e-06 10977 2 103.7 9.87697e-05 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.26136e-06 10977 2 103.7 9.34386e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.26144e-06 10977 2 103.7 0.000111902 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.10849e-06 10977 2 103.7 9.37846e-05 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.25845e-06 10977 2 103.7 0.000107673 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.1336e-06 10977 2 103.7 8.63964e-05 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.20491e-06 10977 2 103.7 8.85338e-05 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.06166e-06 10977 2 103.7 9.10971e-05 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.21175e-06 10977 2 103.7 0.000100478 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.31646e-06 10977 2 103.7 0.000104949 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.18027e-06 10977 2 103.7 0.000105603 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.18189e-06 10977 2 103.7 9.42758e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.53116e-06 10977 2 103.7 0.000107613 3659 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.11589e-06 10977 2 103.7 0.000107969 3659 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.18095e-06 10977 2 103.7 9.61226e-05 3659 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.23505e-06 10977 2 103.7 9.35296e-05 3659 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.47203e-06 10977 2 103.7 0.000107309 3659 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.54636e-06 10977 2 103.7 0.000108853 3659 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.2147e-06 10977 2 103.7 8.9523e-05 3659 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.7783e-06 10977 2 103.7 0.000109711 3659 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.16389e-06 10977 2 103.7 0.000115297 3659 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.40113e-06 10977 2 103.7 0.000101868 3659 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.15971e-06 10977 2 103.7 0.000108368 3659 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.41335e-06 10977 2 103.7 0.000107647 3659 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.39497e-06 10977 2 103.7 9.78885e-05 3659 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.17511e-06 10977 2 103.7 9.52316e-05 3659 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.27492e-06 10977 2 103.7 0.000100929 3659 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.17624e-06 10977 2 103.7 9.69893e-05 3659 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.1306e-06 10977 2 103.7 9.7448e-05 3659 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.11805e-06 10977 2 103.7 9.21405e-05 3659 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.17996e-06 10977 2 103.7 9.03187e-05 3659 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.13407e-06 10977 2 103.7 9.35999e-05 3659 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.10905e-06 10977 2 103.7 9.69613e-05 3659 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.41989e-06 10977 2 103.7 9.67155e-05 3659 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.20475e-06 10977 2 103.7 9.5656e-05 3659 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.141e-06 10977 2 103.7 9.26549e-05 3659 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.25845e-06 10977 2 103.7 8.69324e-05 3659 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.22964e-06 10977 2 103.7 0.000100854 3659 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.21041e-06 10977 2 103.7 0.000100678 3659 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.29095e-06 10977 2 103.7 0.000114475 3659 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.37071e-06 10977 2 103.7 0.00010975 3659 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.19692e-06 10977 2 103.7 0.000101573 3659 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.33607e-06 10977 2 103.7 9.88299e-05 3659 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.11041e-06 10977 2 103.7 8.89976e-05 3659 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.26943e-06 10977 2 103.7 9.18284e-05 3659 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.54992e-06 10977 2 103.7 0.000119831 3659 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.55994e-06 10977 2 103.7 0.000108727 3659 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.11261e-06 10977 2 103.7 9.32541e-05 3659 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.31567e-06 10977 2 103.7 9.32436e-05 3659 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.43756e-06 10977 2 103.7 9.18395e-05 3659 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.09289e-06 10977 2 103.7 8.81565e-05 3659 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.54207e-06 10977 2 103.7 0.000104144 3659 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.40858e-06 10977 2 103.7 9.51246e-05 3659 3000000 3000000 337478.97 142807.9 1.3823791 293.01835 264.65659 414.73478 0 0 272847.18 -64784.634 -383.2647 -382439.19 -173697.26 7963.9533 Loop time of 61167.4 on 16 procs for 3000000 steps with 13738 atoms Performance: 4.238 ns/day, 5.664 hours/ns, 49.046 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27439 | 34607 | 48383 |4038.0 | 56.58 Bond | 8.5237 | 35.231 | 91.74 | 513.3 | 0.06 Kspace | 7511.6 | 21366 | 28576 |5165.0 | 34.93 Neigh | 2568.1 | 2571.3 | 2575.3 | 4.3 | 4.20 Comm | 967.56 | 1034.1 | 1098.4 | 132.3 | 1.69 Output | 0.020315 | 0.022564 | 0.024641 | 0.9 | 0.00 Modify | 1416.5 | 1459.5 | 1503.5 | 78.0 | 2.39 Other | | 94.49 | | | 0.15 Nlocal: 858.625 ave 1035 max 745 min Histogram: 1 3 7 1 0 0 0 0 0 4 Nghost: 10358.3 ave 10969 max 9397 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 480204 ave 669455 max 373944 min Histogram: 4 4 4 0 0 0 0 0 0 4 Total # of neighbors = 7683272 Ave neighs/atom = 559.27151 Ave special neighs/atom = 1.8702868 Neighbor list builds = 149746 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) = 0.25972621 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029091964 estimated relative force accuracy = 8.7609584e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.40858e-06 10977 2 103.7 9.51246e-05 3659 Per MPI rank memory allocation (min/avg/max) = 14.83 | 15.11 | 15.84 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 337479.95 142807.9 1.3823791 293.01835 264.65659 414.73478 0 0 272847.18 -64784.634 -383.2647 -382439.19 -173697.26 7963.9533 Loop time of 4.20243e-06 on 16 procs for 0 steps with 13738 atoms 124.9% CPU use with 16 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 | | 4.202e-06 | | |100.00 Nlocal: 858.625 ave 1035 max 745 min Histogram: 1 3 7 1 0 0 0 0 0 4 Nghost: 10358.3 ave 10969 max 9397 min Histogram: 4 0 0 0 0 0 4 4 0 4 Neighs: 480204 ave 669455 max 373944 min Histogram: 4 4 4 0 0 0 0 0 0 4 Total # of neighbors = 7683272 Ave neighs/atom = 559.27151 Ave special neighs/atom = 1.8702868 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out