#------------------------------------------------------------------------------- # 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1928 = # 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 v_surfacetension 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 v_surfacetension file 2.5_instantaneous.txt 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) = 0.31977901 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032810461 estimated relative force accuracy = 9.8807729e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10935 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.14904e-13 5784 2 103.7 7.52323e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.65 | 13.35 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 -232.01721 137802.93 0.63039506 301.07843 28.224425 35.576016 0 0 16271.883 52720.32 -152.47823 -193996.65 -124940.65 4000.8661 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23104e-06 5784 2 103.7 9.96779e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.56504e-06 5784 2 103.7 0.000113446 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14894e-06 5784 2 103.7 9.99596e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.4141e-06 5784 2 103.7 0.000107718 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.33359e-06 5784 2 103.7 0.000101634 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.90094e-06 5784 2 103.7 0.000108467 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.26045e-06 5784 2 103.7 9.99491e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.34008e-06 5784 2 103.7 8.97315e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.27617e-06 5784 2 103.7 0.000110533 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.26528e-06 5784 2 103.7 9.75504e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12935e-06 5784 2 103.7 9.98472e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.38329e-06 5784 2 103.7 0.000105991 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22375e-06 5784 2 103.7 8.97164e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.50524e-06 5784 2 103.7 9.74456e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.06153e-06 5784 2 103.7 9.67339e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.2894e-06 5784 2 103.7 0.000102748 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12883e-06 5784 2 103.7 0.000104224 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.13601e-06 5784 2 103.7 8.90889e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.02733e-06 5784 2 103.7 9.02447e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.19569e-06 5784 2 103.7 8.93232e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.45976e-06 5784 2 103.7 0.000110531 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.34492e-06 5784 2 103.7 9.31695e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.49597e-06 5784 2 103.7 0.000117104 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.11928e-06 5784 2 103.7 9.07425e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.19001e-06 5784 2 103.7 0.00010992 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.25751e-06 5784 2 103.7 9.11497e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.28845e-06 5784 2 103.7 9.56751e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.40702e-06 5784 2 103.7 0.000115509 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.15193e-06 5784 2 103.7 9.73445e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26944e-06 5784 2 103.7 8.8643e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.53638e-06 5784 2 103.7 0.000104931 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.09049e-06 5784 2 103.7 9.7125e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.16885e-06 5784 2 103.7 8.77902e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.46534e-06 5784 2 103.7 0.000107249 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.26978e-06 5784 2 103.7 0.00011598 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.23127e-06 5784 2 103.7 9.50565e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0816e-06 5784 2 103.7 9.82167e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.09267e-06 5784 2 103.7 9.58391e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24895e-06 5784 2 103.7 9.67265e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.44139e-06 5784 2 103.7 0.000107365 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.10677e-06 5784 2 103.7 8.77693e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.10973e-06 5784 2 103.7 0.000112798 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.45045e-06 5784 2 103.7 0.000106834 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.38092e-06 5784 2 103.7 0.000108321 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.13278e-06 5784 2 103.7 8.82149e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.20336e-06 5784 2 103.7 9.91672e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 9.88372e-07 5784 2 103.7 9.61489e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.18674e-06 5784 2 103.7 0.000101647 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.24891e-06 5784 2 103.7 0.000109602 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.22283e-06 5784 2 103.7 9.6733e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.23331e-06 5784 2 103.7 8.80396e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.11515e-06 5784 2 103.7 8.9375e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.16605e-06 5784 2 103.7 9.46505e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.14641e-06 5784 2 103.7 9.13201e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.12764e-06 5784 2 103.7 9.27045e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.28817e-06 5784 2 103.7 0.000104472 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.01925e-06 5784 2 103.7 0.000102131 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.30801e-06 5784 2 103.7 0.000110817 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.50578e-06 5784 2 103.7 0.000112318 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.07915e-06 5784 2 103.7 9.50552e-05 1928 3000000 3000000 -12.267812 137802.93 0.63039506 303.96475 34.665922 39.118633 0 0 16409.475 52568.648 -152.47823 -194004.08 -124952.18 4039.2208 Loop time of 17663.6 on 32 procs for 3000000 steps with 6387 atoms Performance: 14.674 ns/day, 1.636 hours/ns, 169.841 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3698 | 4114.1 | 9206.1 |6205.2 | 23.29 Bond | 2.7786 | 6.6893 | 14.384 | 127.2 | 0.04 Kspace | 6171.8 | 11308 | 15494 |3771.0 | 64.02 Neigh | 616.33 | 619.39 | 625.18 | 11.2 | 3.51 Comm | 245.67 | 502.1 | 657.57 | 686.5 | 2.84 Output | 0.011087 | 0.012757 | 0.01417 | 0.8 | 0.00 Modify | 940.23 | 1060 | 1230.5 | 352.6 | 6.00 Other | | 53.12 | | | 0.30 Nlocal: 199.594 ave 415 max 0 min Histogram: 13 3 0 0 0 0 0 0 4 12 Nghost: 2726.53 ave 5299 max 144 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 51580.4 ave 119637 max 0 min Histogram: 16 0 0 0 0 0 3 2 4 7 Total # of neighbors = 1650574 Ave neighs/atom = 258.42712 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145410 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) = 0.31977901 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032810461 estimated relative force accuracy = 9.8807729e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10935 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.07915e-06 5784 2 103.7 9.50552e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.41 | 12.65 | 13.35 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 -11.790009 137802.93 0.63039506 303.96475 34.665922 39.118633 0 0 16409.475 52568.648 -152.47823 -194004.08 -124952.18 4039.2208 Loop time of 6.68675e-06 on 32 procs for 0 steps with 6387 atoms 123.8% 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 | | 6.687e-06 | | |100.00 Nlocal: 199.594 ave 415 max 0 min Histogram: 13 3 0 0 0 0 0 0 4 12 Nghost: 2726.53 ave 5299 max 144 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 51580.4 ave 119637 max 0 min Histogram: 16 0 0 0 0 0 3 2 4 7 Total # of neighbors = 1650574 Ave neighs/atom = 258.42712 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 13:02:30