#------------------------------------------------------------------------------- # 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 = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00144 0.0776551 9825 1 97.5309 11.5633 3275 Per MPI rank memory allocation (min/avg/max) = 14.11 | 14.42 | 14.83 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 -8924.2766 143340.91 1.3114365 420.87983 5.8161068 38.517832 0 0 39946.969 -92332.895 -319.55737 -317375.99 -369717.58 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.2855e-06 9825 1 103.7 8.91574e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.09031e-06 9825 1 103.7 9.33429e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.11342e-06 9825 1 103.7 9.25307e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15344e-06 9825 1 103.7 9.74777e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.11961e-06 9825 1 103.7 0.000101098 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.11976e-06 9825 1 103.7 9.46529e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.43136e-06 9825 1 103.7 9.21431e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.11054e-06 9825 1 103.7 9.13769e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.22832e-06 9825 1 103.7 9.11882e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.53142e-06 9825 1 103.7 0.000103929 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.1029e-06 9825 1 103.7 9.35755e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.34242e-06 9825 1 103.7 9.37927e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.38138e-06 9825 1 103.7 9.5313e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.18087e-06 9825 1 103.7 0.000124018 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.49446e-06 9825 1 103.7 0.000102516 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.24065e-06 9825 1 103.7 9.08644e-05 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.33672e-06 9825 1 103.7 9.67783e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.0818e-06 9825 1 103.7 9.0589e-05 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.30763e-06 9825 1 103.7 0.000103262 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.11127e-06 9825 1 103.7 9.23956e-05 3275 1000000 1000000 -7064.2804 143340.91 1.3114365 291.52522 41.627309 73.309895 0 0 37105.269 -73116.714 -319.55737 -317468.04 -353364.55 6880.5939 Loop time of 13590.4 on 16 procs for 1000000 steps with 12250 atoms Performance: 6.357 ns/day, 3.775 hours/ns, 73.581 timesteps/s 99.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7904.1 | 9258.6 | 9965.4 | 794.9 | 68.13 Bond | 1.3274 | 3.5201 | 6.2189 | 89.9 | 0.03 Kspace | 2280.9 | 2989.8 | 4348.6 |1402.0 | 22.00 Neigh | 524.91 | 525.31 | 525.77 | 1.2 | 3.87 Comm | 321.54 | 339.68 | 350.37 | 53.0 | 2.50 Output | 0.016368 | 0.01844 | 0.020373 | 0.9 | 0.00 Modify | 438.34 | 447.21 | 464.55 | 46.5 | 3.29 Other | | 26.27 | | | 0.19 Nlocal: 765.625 ave 803 max 708 min Histogram: 2 2 0 0 1 1 1 4 3 2 Nghost: 9239.81 ave 9573 max 9024 min Histogram: 4 2 2 1 2 1 0 0 2 2 Neighs: 376265 ave 405682 max 318113 min Histogram: 4 0 0 0 0 0 1 1 4 6 Total # of neighbors = 6020246 Ave neighs/atom = 491.44865 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49847 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 = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.11127e-06 9825 1 103.7 9.23956e-05 3275 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.59 | 14.82 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 -7063.4354 143340.91 1.3114365 291.52522 41.627309 73.309895 0 0 37105.269 -73116.714 -319.55737 -317468.04 -353364.55 6880.5939 Loop time of 4.17544e-06 on 16 procs for 0 steps with 12250 atoms 112.3% CPU use with 16 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 | | 4.175e-06 | | |100.00 Nlocal: 765.625 ave 803 max 708 min Histogram: 2 2 0 0 1 1 1 4 3 2 Nghost: 9239.81 ave 9573 max 9024 min Histogram: 4 2 2 1 2 1 0 0 2 2 Neighs: 376265 ave 405682 max 318113 min Histogram: 4 0 0 0 0 0 1 1 4 6 Total # of neighbors = 6020246 Ave neighs/atom = 491.44865 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