#------------------------------------------------------------------------------- # 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 2699 = # 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00051 0.0673668 8097 2 97.6676 9.63579 2699 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.06 | 14.78 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 -3666.8719 138878.49 1.4411859 405.32842 5.1711486 20.266264 0 0 37823.01 -79544.074 -317.08001 -295526.76 -337222.39 9102.6318 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.60037e-06 8097 2 103.7 0.000107012 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.56881e-06 8097 2 103.7 0.000117796 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.35032e-06 8097 2 103.7 0.000102713 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.52816e-06 8097 2 103.7 0.000114468 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.33167e-06 8097 2 103.7 0.000106402 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32174e-06 8097 2 103.7 0.000108519 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20148e-06 8097 2 103.7 9.49078e-05 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.37154e-06 8097 2 103.7 9.71409e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.34876e-06 8097 2 103.7 9.73011e-05 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.23411e-06 8097 2 103.7 9.87197e-05 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.55228e-06 8097 2 103.7 0.000103728 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.23171e-06 8097 2 103.7 0.000111671 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.62071e-06 8097 2 103.7 0.00012396 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19734e-06 8097 2 103.7 9.29473e-05 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.14423e-06 8097 2 103.7 0.000113559 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.22594e-06 8097 2 103.7 8.87374e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.24457e-06 8097 2 103.7 9.08759e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10644e-06 8097 2 103.7 9.94985e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.11049e-06 8097 2 103.7 9.674e-05 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17825e-06 8097 2 103.7 0.000115099 2699 1000000 1000000 -371.41574 138878.49 1.4411859 295.14439 36.187694 64.059394 0 0 35953.424 -63507.895 -317.08001 -295419.68 -322873.9 6628.1823 Loop time of 15853.9 on 16 procs for 1000000 steps with 10558 atoms Performance: 5.450 ns/day, 4.404 hours/ns, 63.076 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2422 | 8588.2 | 11633 |3809.0 | 54.17 Bond | 1.2557 | 4.0713 | 7.1974 | 92.8 | 0.03 Kspace | 2727.9 | 5777.8 | 11954 |4651.6 | 36.44 Neigh | 619.25 | 620.85 | 622.58 | 4.0 | 3.92 Comm | 301.63 | 354.24 | 382.47 | 162.2 | 2.23 Output | 0.017541 | 0.019608 | 0.021462 | 0.9 | 0.00 Modify | 460.14 | 481.85 | 525.93 | 117.2 | 3.04 Other | | 26.87 | | | 0.17 Nlocal: 659.875 ave 788 max 355 min Histogram: 4 0 0 0 0 0 0 0 4 8 Nghost: 8186.19 ave 9796 max 6884 min Histogram: 4 0 0 5 3 0 0 0 0 4 Neighs: 307443 ave 406125 max 88439 min Histogram: 4 0 0 0 0 0 0 2 3 7 Total # of neighbors = 4919089 Ave neighs/atom = 465.91106 Ave special neighs/atom = 1.5849593 Neighbor list builds = 49453 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17825e-06 8097 2 103.7 0.000115099 2699 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.16 | 14.78 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 -370.76498 138878.49 1.4411859 295.14439 36.187694 64.059394 0 0 35953.424 -63507.895 -317.08001 -295419.68 -322873.9 6628.1823 Loop time of 4.49769e-06 on 16 procs for 0 steps with 10558 atoms 120.9% 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 | | 4.498e-06 | | |100.00 Nlocal: 659.875 ave 788 max 355 min Histogram: 4 0 0 0 0 0 0 0 4 8 Nghost: 8186.19 ave 9796 max 6884 min Histogram: 4 0 0 5 3 0 0 0 0 4 Neighs: 307443 ave 406125 max 88439 min Histogram: 4 0 0 0 0 0 0 2 3 7 Total # of neighbors = 4919089 Ave neighs/atom = 465.91106 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out