#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 3488 = # 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 npt temp 298.2 298.2 100 iso 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.3243692 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0038119779 estimated relative force accuracy = 1.1479658e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.0057 0.129186 10464 2 97.1445 13.5551 3488 Per MPI rank memory allocation (min/avg/max) = 12.96 | 13.21 | 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 1863.795 126532.14 1.3192601 420.68252 43.972393 256.10778 0 0 37552.419 81241.08 -621.23002 -392118.87 -273025.29 10648.753 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969895 1.24578e-06 10464 2 103.7 0.000108494 3488 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969967 1.11935e-06 10464 2 103.7 0.000100692 3488 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27164e-06 10464 2 103.7 0.000100304 3488 SHAKE stats (type/ave/delta/count) on step 200000 1 0.96996 1.21833e-06 10464 2 103.7 0.000101512 3488 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970046 1.33647e-06 10464 2 103.7 9.70499e-05 3488 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969906 1.37156e-06 10464 2 103.7 0.000113314 3488 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969999 1.55299e-06 10464 2 103.7 0.000103987 3488 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969959 1.32132e-06 10464 2 103.7 9.94232e-05 3488 SHAKE stats (type/ave/delta/count) on step 450000 1 0.96999 1.25549e-06 10464 2 103.7 9.80582e-05 3488 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970048 1.73481e-06 10464 2 103.7 0.000126275 3488 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970061 1.55685e-06 10464 2 103.7 0.00010019 3488 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969993 1.31608e-06 10464 2 103.7 9.49979e-05 3488 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969987 1.32076e-06 10464 2 103.7 9.31866e-05 3488 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970009 1.9765e-06 10464 2 103.7 0.000118388 3488 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969933 1.20248e-06 10464 2 103.7 9.54604e-05 3488 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97003 1.48745e-06 10464 2 103.7 0.000100721 3488 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970075 1.38642e-06 10464 2 103.7 0.000100366 3488 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969994 1.37541e-06 10464 2 103.7 0.000101798 3488 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969996 1.32267e-06 10464 2 103.7 0.000106557 3488 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970008 1.28244e-06 10464 2 103.7 0.000103723 3488 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970073 1.39246e-06 10464 2 103.7 0.000100639 3488 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969963 1.45169e-06 10464 2 103.7 0.00010436 3488 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97014 2.22233e-06 10464 2 103.7 0.000144734 3488 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970013 1.61757e-06 10464 2 103.7 0.000106838 3488 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969918 1.18079e-06 10464 2 103.7 0.000107323 3488 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970001 1.29307e-06 10464 2 103.7 0.000109552 3488 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970009 1.42482e-06 10464 2 103.7 9.26281e-05 3488 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970021 1.20956e-06 10464 2 103.7 9.77403e-05 3488 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970015 1.58011e-06 10464 2 103.7 0.000110981 3488 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969935 1.5138e-06 10464 2 103.7 0.000114443 3488 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970098 1.62221e-06 10464 2 103.7 0.000127965 3488 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969933 1.38985e-06 10464 2 103.7 0.000113198 3488 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970019 1.39195e-06 10464 2 103.7 0.000101215 3488 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970016 1.27169e-06 10464 2 103.7 0.000106089 3488 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970078 1.27306e-06 10464 2 103.7 9.64809e-05 3488 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969949 1.38193e-06 10464 2 103.7 9.30539e-05 3488 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970008 1.22786e-06 10464 2 103.7 9.68914e-05 3488 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970036 1.37701e-06 10464 2 103.7 0.00010934 3488 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969956 1.05379e-06 10464 2 103.7 0.000108034 3488 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969861 1.29739e-06 10464 2 103.7 0.000127465 3488 2000000 2000000 457.33979 122022.49 1.3680167 298.60429 225.99379 303.86262 0 0 31547.989 103928.47 -644.18917 -391788.63 -255782.32 7558.5821 Loop time of 16452.2 on 32 procs for 2000000 steps with 11981 atoms Performance: 10.503 ns/day, 2.285 hours/ns, 121.565 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5253.2 | 6051.3 | 7456.3 | 951.4 | 36.78 Bond | 2.6798 | 11.941 | 32.393 | 280.9 | 0.07 Kspace | 5053.7 | 6486 | 7283.4 | 933.4 | 39.42 Neigh | 436.41 | 437.61 | 438.84 | 3.3 | 2.66 Comm | 826.69 | 859.54 | 893.13 | 75.3 | 5.22 Output | 0.013543 | 0.016257 | 0.018836 | 1.3 | 0.00 Modify | 1721.6 | 2155.8 | 2503.8 | 669.7 | 13.10 Other | | 450 | | | 2.73 Nlocal: 374.406 ave 439 max 337 min Histogram: 4 9 8 3 0 0 0 1 4 3 Nghost: 5503.81 ave 5689 max 5187 min Histogram: 7 1 0 0 0 0 3 9 6 6 Neighs: 117338 ave 149859 max 99230 min Histogram: 5 9 9 1 0 0 0 1 3 4 Total # of neighbors = 3754816 Ave neighs/atom = 313.39755 Ave special neighs/atom = 1.9988315 Neighbor list builds = 102339 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32529392 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0036767963 estimated relative force accuracy = 1.1072563e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969861 1.29739e-06 10464 2 103.7 0.000127465 3488 Per MPI rank memory allocation (min/avg/max) = 13.23 | 13.3 | 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 2000000 2000000 -357.62667 122022.49 1.3680167 298.60429 225.99379 303.86262 0 0 31547.989 105022.49 -644.18917 -392882.64 -255782.3 7558.5821 Loop time of 8.21878e-06 on 32 procs for 0 steps with 11981 atoms 114.1% 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 | | 8.219e-06 | | |100.00 Nlocal: 374.406 ave 439 max 337 min Histogram: 4 9 8 3 0 0 0 1 4 3 Nghost: 5503.81 ave 5689 max 5187 min Histogram: 7 1 0 0 0 0 3 9 6 6 Neighs: 117338 ave 149859 max 99230 min Histogram: 5 9 9 1 0 0 0 1 3 4 Total # of neighbors = 3754816 Ave neighs/atom = 313.39755 Ave special neighs/atom = 1.9988315 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out