#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00141 0.0740289 9825 1 97.5314 11.4907 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.26 | 13.65 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 -8928.0903 143340.91 1.3114365 420.87983 5.8062945 39.094569 0 0 39897.131 -92254.668 -319.55737 -317373.9 -369686.53 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.16733e-06 9825 1 103.7 9.3596e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.30521e-06 9825 1 103.7 9.35537e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.30213e-06 9825 1 103.7 0.000108768 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.11664e-06 9825 1 103.7 0.0001025 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.16827e-06 9825 1 103.7 9.9245e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.37783e-06 9825 1 103.7 0.000100952 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.37614e-06 9825 1 103.7 0.000105562 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.36289e-06 9825 1 103.7 0.000108965 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.17175e-06 9825 1 103.7 9.34056e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.42456e-06 9825 1 103.7 0.000111137 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.58878e-06 9825 1 103.7 0.000135189 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.3172e-06 9825 1 103.7 9.92463e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.29282e-06 9825 1 103.7 9.14806e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.02755e-06 9825 1 103.7 9.20313e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.19996e-06 9825 1 103.7 0.000100045 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.24266e-06 9825 1 103.7 0.00010731 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.25319e-06 9825 1 103.7 0.000110715 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.48042e-06 9825 1 103.7 0.000111207 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.19828e-06 9825 1 103.7 8.87465e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.16381e-06 9825 1 103.7 8.333e-05 3275 1000000 1000000 -7122.9339 143340.91 1.3114365 294.45612 31.899035 56.934369 0 0 37133.107 -73035.246 -319.55737 -317439.46 -353252.77 6949.7692 Loop time of 9367.84 on 32 procs for 1000000 steps with 12250 atoms Performance: 9.223 ns/day, 2.602 hours/ns, 106.748 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 | 4284.6 | 5192 | 5961.4 | 647.9 | 55.42 Bond | 1.1563 | 2.6561 | 5.2072 | 75.0 | 0.03 Kspace | 1937 | 2709.3 | 3620.2 | 901.5 | 28.92 Neigh | 318.2 | 318.73 | 319.43 | 2.1 | 3.40 Comm | 513.29 | 542.61 | 564.38 | 74.4 | 5.79 Output | 0.01257 | 0.015346 | 0.017962 | 1.3 | 0.00 Modify | 558.89 | 576.5 | 603.49 | 64.8 | 6.15 Other | | 26.08 | | | 0.28 Nlocal: 382.812 ave 415 max 347 min Histogram: 1 3 4 2 5 2 5 5 4 1 Nghost: 7272.97 ave 7526 max 6938 min Histogram: 6 2 1 3 0 3 2 3 3 9 Neighs: 188132 ave 211694 max 152857 min Histogram: 3 2 3 0 0 4 6 3 7 4 Total # of neighbors = 6020225 Ave neighs/atom = 491.44694 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49838 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.16381e-06 9825 1 103.7 8.333e-05 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.42 | 13.65 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 -7122.1126 143340.91 1.3114365 294.45612 31.899035 56.934369 0 0 37133.107 -73035.246 -319.55737 -317439.46 -353252.77 6949.7692 Loop time of 7.16116e-06 on 32 procs for 0 steps with 12250 atoms 99.5% 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 | | 7.161e-06 | | |100.00 Nlocal: 382.812 ave 415 max 347 min Histogram: 1 3 4 2 5 2 5 5 4 1 Nghost: 7272.97 ave 7526 max 6938 min Histogram: 6 2 1 3 0 3 2 3 3 9 Neighs: 188132 ave 211694 max 152857 min Histogram: 3 2 3 0 0 4 6 3 7 4 Total # of neighbors = 6020225 Ave neighs/atom = 491.44694 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out