#------------------------------------------------------------------------------- # 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 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 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00137 0.0694262 8304 2 97.6112 10.0161 2768 Per MPI rank memory allocation (min/avg/max) = 12.42 | 13.2 | 13.76 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 -1625.9995 143908.11 1.3942094 410.14353 6.8056364 31.804632 0 0 33494.819 -38828.618 -320.88394 -277812.69 -283107.88 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.32348e-06 8304 2 103.7 0.000110569 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.44452e-06 8304 2 103.7 0.000100783 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.11278e-06 8304 2 103.7 9.80095e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.42805e-06 8304 2 103.7 9.47537e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.64591e-06 8304 2 103.7 0.000102142 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.31878e-06 8304 2 103.7 9.66756e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.17024e-06 8304 2 103.7 9.2689e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1663e-06 8304 2 103.7 9.61468e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25324e-06 8304 2 103.7 9.39303e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.1446e-06 8304 2 103.7 9.6023e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.39361e-06 8304 2 103.7 0.000131642 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.40021e-06 8304 2 103.7 0.000108653 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.36056e-06 8304 2 103.7 8.91886e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.35939e-06 8304 2 103.7 0.00011129 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.62432e-06 8304 2 103.7 0.000101053 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.46614e-06 8304 2 103.7 0.000108799 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21291e-06 8304 2 103.7 9.28756e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15425e-06 8304 2 103.7 9.44253e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.65943e-06 8304 2 103.7 0.000125941 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.45773e-06 8304 2 103.7 0.000112924 2768 1000000 1000000 -953.84915 143908.11 1.3942094 299.08846 45.224798 89.216046 0 0 29108.606 -19641.981 -320.88394 -277678.4 -268077.33 6558.0645 Loop time of 9473.94 on 32 procs for 1000000 steps with 10381 atoms Performance: 9.120 ns/day, 2.632 hours/ns, 105.553 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 899.66 | 4202.6 | 6085 |3078.4 | 44.36 Bond | 0.88346 | 2.5986 | 5.1822 | 79.0 | 0.03 Kspace | 1988.7 | 3878.5 | 7191.4 |3217.7 | 40.94 Neigh | 424.38 | 425.07 | 426.11 | 2.6 | 4.49 Comm | 305.23 | 426.7 | 476.37 | 268.7 | 4.50 Output | 0.014271 | 0.01665 | 0.018946 | 1.1 | 0.00 Modify | 475.55 | 517.34 | 615.56 | 207.6 | 5.46 Other | | 21.19 | | | 0.22 Nlocal: 324.406 ave 445 max 128 min Histogram: 8 0 0 0 0 0 3 6 13 2 Nghost: 6036.12 ave 7613 max 3871 min Histogram: 8 0 0 4 4 0 0 0 5 11 Neighs: 148453 ave 236898 max 27186 min Histogram: 8 0 0 0 1 3 3 2 13 2 Total # of neighbors = 4750482 Ave neighs/atom = 457.61314 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49626 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.45773e-06 8304 2 103.7 0.000112924 2768 Per MPI rank memory allocation (min/avg/max) = 12.43 | 13.23 | 13.76 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 -953.35452 143908.11 1.3942094 299.08846 45.224798 89.216046 0 0 29108.606 -19641.981 -320.88394 -277678.4 -268077.33 6558.0645 Loop time of 8.27406e-06 on 32 procs for 0 steps with 10381 atoms 111.0% 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 | | 8.274e-06 | | |100.00 Nlocal: 324.406 ave 445 max 128 min Histogram: 8 0 0 0 0 0 3 6 13 2 Nghost: 6036.12 ave 7613 max 3871 min Histogram: 8 0 0 4 4 0 0 0 5 11 Neighs: 148453 ave 236898 max 27186 min Histogram: 8 0 0 0 1 3 3 2 13 2 Total # of neighbors = 4750482 Ave neighs/atom = 457.61314 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out