#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 2000 = # 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.0002 0.0548301 6000 1 97.8764 8.76344 2000 Per MPI rank memory allocation (min/avg/max) = 8.312 | 9.355 | 10.27 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 -349.39361 119078.03 0.50244692 447.33728 0 0 0 0 9622.5048 81332.032 -89.819258 -122254.47 -31299.932 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21629e-06 6000 1 103.7 0.00011839 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.27773e-06 6000 1 103.7 9.98781e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.53573e-06 6000 1 103.7 0.000108802 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.13505e-06 6000 1 103.7 0.0001024 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.25805e-06 6000 1 103.7 0.000133249 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.41846e-06 6000 1 103.7 0.000106954 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.4663e-06 6000 1 103.7 9.8336e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.26025e-06 6000 1 103.7 0.000124746 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.47979e-06 6000 1 103.7 0.000119672 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.29891e-06 6000 1 103.7 9.33388e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.15179e-06 6000 1 103.7 0.000100927 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.16224e-06 6000 1 103.7 9.65215e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.23065e-06 6000 1 103.7 0.000120374 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.42566e-06 6000 1 103.7 9.63259e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.59261e-06 6000 1 103.7 0.000119783 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.24996e-06 6000 1 103.7 0.000104157 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.41987e-06 6000 1 103.7 0.000105468 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.05133e-06 6000 1 103.7 9.62161e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.07241e-06 6000 1 103.7 9.4288e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.136e-06 6000 1 103.7 8.62038e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.92126e-06 6000 1 103.7 0.000141645 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.16578e-06 6000 1 103.7 0.000104963 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.28213e-06 6000 1 103.7 9.92983e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.66479e-06 6000 1 103.7 0.000126244 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.1502e-06 6000 1 103.7 0.00011156 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.47219e-06 6000 1 103.7 0.000104233 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.27116e-06 6000 1 103.7 0.000125722 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.92449e-06 6000 1 103.7 0.000130114 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.23248e-06 6000 1 103.7 0.000108143 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.82478e-06 6000 1 103.7 0.000170736 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.28277e-06 6000 1 103.7 0.000111086 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.16365e-06 6000 1 103.7 9.62806e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.12307e-06 6000 1 103.7 9.54379e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.39295e-06 6000 1 103.7 0.000105064 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.31286e-06 6000 1 103.7 9.81141e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.24677e-06 6000 1 103.7 9.19317e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.09852e-06 6000 1 103.7 0.000100695 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.04145e-06 6000 1 103.7 9.04585e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.51519e-06 6000 1 103.7 0.000104075 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.34208e-06 6000 1 103.7 0.000100175 2000 2000000 2000000 -97.114337 119078.03 0.50244692 295.37591 0 0 0 0 5036.4 96267.846 -89.819258 -122205.7 -20901.454 3520.9575 Loop time of 11468.8 on 32 procs for 2000000 steps with 6000 atoms Performance: 15.067 ns/day, 1.593 hours/ns, 174.385 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92071 | 3296.5 | 7060 |5575.9 | 28.74 Bond | 1.4921 | 2.0712 | 3.1536 | 20.0 | 0.02 Kspace | 3069.1 | 6891.4 | 10325 |3920.8 | 60.09 Neigh | 371.07 | 377.91 | 399.76 | 46.5 | 3.30 Comm | 10.761 | 285.14 | 428.26 | 940.8 | 2.49 Output | 0.012013 | 0.013633 | 0.015042 | 0.8 | 0.00 Modify | 505.87 | 587.17 | 703.53 | 342.6 | 5.12 Other | | 28.61 | | | 0.25 Nlocal: 187.5 ave 376 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 2900.72 ave 5703 max 0 min Histogram: 8 0 2 6 0 0 4 4 0 8 Neighs: 61721.1 ave 136950 max 0 min Histogram: 16 0 0 0 0 0 0 0 9 7 Total # of neighbors = 1975074 Ave neighs/atom = 329.179 Ave special neighs/atom = 2 Neighbor list builds = 99107 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.29701154 grid = 27 27 80 stencil order = 5 estimated absolute RMS force accuracy = 0.0036028167 estimated relative force accuracy = 1.0849775e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6800 2187 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.34208e-06 6000 1 103.7 0.000100175 2000 Per MPI rank memory allocation (min/avg/max) = 8.324 | 9.602 | 10.26 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 2000000 2000000 -96.779639 119078.03 0.50244692 295.37591 0 0 0 0 5036.4 96267.846 -89.819258 -122205.7 -20901.454 3520.9575 Loop time of 7.99762e-06 on 32 procs for 0 steps with 6000 atoms 111.8% 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 | | 7.998e-06 | | |100.00 Nlocal: 187.5 ave 376 max 0 min Histogram: 12 4 0 0 0 0 0 0 2 14 Nghost: 2900.72 ave 5703 max 0 min Histogram: 8 0 2 6 0 0 4 4 0 8 Neighs: 61721.1 ave 136950 max 0 min Histogram: 16 0 0 0 0 0 0 0 9 7 Total # of neighbors = 1975074 Ave neighs/atom = 329.179 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out