#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 = 0.002 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 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 = 21978 9600 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00485 0.0887782 10977 2 97.6624 10.1629 3659 Per MPI rank memory allocation (min/avg/max) = 17.45 | 18.09 | 19.63 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 338591.75 142807.9 1.3823791 416.85345 44.221582 263.10612 0 0 277784.12 -89868.98 -383.2647 -382579.49 -194357.03 11329.671 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.53995e-06 10977 2 103.7 9.65188e-05 3659 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.47505e-06 10977 2 103.7 9.97117e-05 3659 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.10738e-06 10977 2 103.7 9.41783e-05 3659 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.37389e-06 10977 2 103.7 0.000109892 3659 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.16321e-06 10977 2 103.7 9.38715e-05 3659 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.5569e-06 10977 2 103.7 9.37961e-05 3659 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.18375e-06 10977 2 103.7 9.32396e-05 3659 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.3264e-06 10977 2 103.7 0.000115312 3659 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.33433e-06 10977 2 103.7 9.15405e-05 3659 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.72101e-06 10977 2 103.7 9.5948e-05 3659 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.15251e-06 10977 2 103.7 9.38424e-05 3659 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.09254e-06 10977 2 103.7 0.000100445 3659 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.11107e-06 10977 2 103.7 0.000101227 3659 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.23668e-06 10977 2 103.7 9.26201e-05 3659 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.70406e-06 10977 2 103.7 0.000117301 3659 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.23219e-06 10977 2 103.7 0.000106053 3659 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.13384e-06 10977 2 103.7 8.75977e-05 3659 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.50717e-06 10977 2 103.7 9.81811e-05 3659 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.15156e-06 10977 2 103.7 9.6616e-05 3659 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2351e-06 10977 2 103.7 9.81308e-05 3659 1000000 1000000 337769.04 142807.9 1.3823791 300.25952 284.80766 384.58859 0 0 273024.45 -65012.38 -383.2647 -382416.63 -173735.17 8160.7613 Loop time of 40547 on 8 procs for 1000000 steps with 13738 atoms Performance: 2.131 ns/day, 11.263 hours/ns, 24.663 timesteps/s 98.5% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18958 | 23824 | 33541 |3375.6 | 58.76 Bond | 4.8707 | 22.113 | 58.71 | 433.0 | 0.05 Kspace | 4141.1 | 13897 | 18783 |4438.9 | 34.27 Neigh | 1799.5 | 1800.7 | 1801.9 | 1.9 | 4.44 Comm | 341.14 | 357.01 | 373.41 | 58.9 | 0.88 Output | 0.035446 | 0.039298 | 0.042717 | 1.2 | 0.00 Modify | 588.89 | 594.31 | 600.97 | 16.7 | 1.47 Other | | 51.78 | | | 0.13 Nlocal: 1717.25 ave 2059 max 1575 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13675.1 ave 14358 max 12446 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 960374 ave 1.33434e+06 max 795519 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 7682989 Ave neighs/atom = 559.25091 Ave special neighs/atom = 1.8702868 Neighbor list builds = 49913 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25972621 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 = 21978 9600 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2351e-06 10977 2 103.7 9.81308e-05 3659 Per MPI rank memory allocation (min/avg/max) = 17.45 | 20.67 | 29.39 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 1000000 1000000 337770.12 142807.9 1.3823791 300.25952 284.80766 384.58859 0 0 273024.45 -65012.38 -383.2647 -382416.63 -173735.17 8160.7613 Loop time of 3.64413e-06 on 8 procs for 0 steps with 13738 atoms 116.6% CPU use with 8 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 | | 3.644e-06 | | |100.00 Nlocal: 1717.25 ave 2059 max 1575 min Histogram: 4 2 0 0 0 0 0 0 0 2 Nghost: 13675.1 ave 14358 max 12446 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 960374 ave 1.33434e+06 max 795519 min Histogram: 4 2 0 0 0 0 0 0 0 2 Total # of neighbors = 7682989 Ave neighs/atom = 559.25091 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 2.5_NVT.out