#------------------------------------------------------------------------------- # 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 = 0.002 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 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) = 0.32117505 grid = 40 40 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0030103868 estimated relative force accuracy = 9.0656904e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13122 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00271 0.479513 8304 2 97.1728 13.2842 2768 Per MPI rank memory allocation (min/avg/max) = 11.47 | 12.73 | 14.06 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 3695.0054 185662.09 0.65390321 428.55654 9.2224379 84.01349 0 0 27421.457 67206.347 -224.27355 -268822.64 -174101.6 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.29628e-06 8304 2 103.7 9.65667e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.72521e-06 8304 2 103.7 0.000130561 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21273e-06 8304 2 103.7 9.85739e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.33629e-06 8304 2 103.7 9.61625e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.22651e-06 8304 2 103.7 0.000104502 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.43807e-06 8304 2 103.7 9.83143e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.52557e-06 8304 2 103.7 0.000101332 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.52067e-06 8304 2 103.7 0.000117711 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.43966e-06 8304 2 103.7 9.36135e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.64452e-06 8304 2 103.7 0.000107176 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.09506e-06 8304 2 103.7 8.73678e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.11978e-06 8304 2 103.7 9.02839e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.19812e-06 8304 2 103.7 9.9034e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.22692e-06 8304 2 103.7 9.68446e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.15641e-06 8304 2 103.7 8.93057e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.41116e-06 8304 2 103.7 9.81123e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.20588e-06 8304 2 103.7 9.42884e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.35376e-06 8304 2 103.7 9.14877e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.11703e-06 8304 2 103.7 9.25259e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46085e-06 8304 2 103.7 0.000106369 2768 1000000 1000000 -392.79841 185662.09 0.65390321 297.53765 40.166443 81.680258 0 0 20915.112 87115.548 -224.27355 -268661.93 -160509.43 5615.8711 Loop time of 8123.09 on 32 procs for 1000000 steps with 9101 atoms Performance: 10.636 ns/day, 2.256 hours/ns, 123.106 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1742 | 2018.4 | 4182.2 |4073.5 | 24.85 Bond | 0.95956 | 2.7154 | 5.8312 | 85.4 | 0.03 Kspace | 3034.8 | 5234.6 | 7323.9 |2574.0 | 64.44 Neigh | 259.61 | 262.58 | 269.26 | 19.6 | 3.23 Comm | 38.479 | 191.64 | 278.43 | 673.4 | 2.36 Output | 0.014966 | 0.017012 | 0.018809 | 0.9 | 0.00 Modify | 344.55 | 393.72 | 470.4 | 261.5 | 4.85 Other | | 19.32 | | | 0.24 Nlocal: 284.406 ave 575 max 0 min Histogram: 10 6 0 0 0 0 0 0 3 13 Nghost: 3064.38 ave 5859 max 19 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 76997.1 ave 168067 max 0 min Histogram: 13 3 0 0 0 0 1 3 4 8 Total # of neighbors = 2463907 Ave neighs/atom = 270.72926 Ave special neighs/atom = 1.8929788 Neighbor list builds = 49842 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) = 0.32117505 grid = 40 40 90 stencil order = 5 estimated absolute RMS force accuracy = 0.0030103868 estimated relative force accuracy = 9.0656904e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13122 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46085e-06 8304 2 103.7 0.000106369 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 13.03 | 14.06 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 -392.41099 185662.09 0.65390321 297.53765 40.166443 81.680258 0 0 20915.112 87115.548 -224.27355 -268661.93 -160509.43 5615.8711 Loop time of 1.0211e-05 on 32 procs for 0 steps with 9101 atoms 110.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.021e-05 | | |100.00 Nlocal: 284.406 ave 575 max 0 min Histogram: 10 6 0 0 0 0 0 0 3 13 Nghost: 3064.38 ave 5859 max 19 min Histogram: 8 0 0 8 0 0 0 8 0 8 Neighs: 76997.1 ave 168067 max 0 min Histogram: 13 3 0 0 0 0 1 3 4 8 Total # of neighbors = 2463907 Ave neighs/atom = 270.72926 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out