#------------------------------------------------------------------------------- # 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) = 0.25348658 grid = 24 24 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030125684 estimated relative force accuracy = 9.0722602e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999306 0.0559269 6000 1 98.0103 9.79722 2000 Per MPI rank memory allocation (min/avg/max) = 9.966 | 9.994 | 10.04 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 2916.1654 59830.193 1.0000033 447.33728 0 0 0 0 8819.7304 64563.384 -104.25214 -104364.72 -30981.61 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.32715e-06 6000 1 103.7 0.000115934 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.10824e-06 6000 1 103.7 0.000104338 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27129e-06 6000 1 103.7 9.84001e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.25035e-06 6000 1 103.7 0.000100063 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.09254e-06 6000 1 103.7 0.000101342 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.39446e-06 6000 1 103.7 0.000104785 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.91516e-06 6000 1 103.7 0.000146531 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.30362e-06 6000 1 103.7 0.000126158 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.47479e-06 6000 1 103.7 0.000117467 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.18404e-06 6000 1 103.7 9.0325e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.15379e-06 6000 1 103.7 9.76693e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.31771e-06 6000 1 103.7 9.93166e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.55011e-06 6000 1 103.7 9.47353e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.13958e-06 6000 1 103.7 9.40142e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21565e-06 6000 1 103.7 0.000114923 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.26552e-06 6000 1 103.7 9.9433e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.22734e-06 6000 1 103.7 0.000106681 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.66147e-06 6000 1 103.7 0.000109518 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.18178e-06 6000 1 103.7 9.85663e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.26684e-06 6000 1 103.7 9.44637e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.15304e-06 6000 1 103.7 0.000106258 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.04326e-06 6000 1 103.7 8.73032e-05 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.36468e-06 6000 1 103.7 9.49842e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.19221e-06 6000 1 103.7 0.000102345 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.42858e-06 6000 1 103.7 0.000101695 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.29811e-06 6000 1 103.7 0.000119867 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.22273e-06 6000 1 103.7 9.693e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.12423e-06 6000 1 103.7 0.00010767 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.083e-06 6000 1 103.7 9.72339e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.57018e-06 6000 1 103.7 0.000114424 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.30466e-06 6000 1 103.7 0.000122675 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.49438e-06 6000 1 103.7 0.000105196 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.1972e-06 6000 1 103.7 9.66206e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.3466e-06 6000 1 103.7 0.000109005 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.25682e-06 6000 1 103.7 0.000108454 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.34551e-06 6000 1 103.7 9.70417e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.21454e-06 6000 1 103.7 0.000109264 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.23502e-06 6000 1 103.7 9.071e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37759e-06 6000 1 103.7 0.00011884 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.19864e-06 6000 1 103.7 0.000106397 2000 2000000 2000000 289.0541 59830.193 1.0000033 298.93643 0 0 0 0 5240.7096 77468.111 -104.25214 -104338.99 -21630.169 3563.3997 Loop time of 10342.5 on 32 procs for 2000000 steps with 6000 atoms Performance: 16.708 ns/day, 1.436 hours/ns, 193.377 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5801 | 6059.7 | 6335 | 165.5 | 58.59 Bond | 1.952 | 2.2533 | 3.5319 | 18.2 | 0.02 Kspace | 2069.2 | 2348.7 | 2605.6 | 263.7 | 22.71 Neigh | 327.71 | 328.35 | 328.78 | 1.3 | 3.17 Comm | 837.85 | 848.55 | 860.67 | 21.8 | 8.20 Output | 0.0099781 | 0.011824 | 0.013544 | 1.0 | 0.00 Modify | 714.14 | 722.07 | 732.3 | 19.9 | 6.98 Other | | 32.9 | | | 0.32 Nlocal: 187.5 ave 202 max 172 min Histogram: 2 2 3 3 5 2 5 4 3 3 Nghost: 6517 ave 6585 max 6387 min Histogram: 1 1 1 3 1 4 5 7 4 5 Neighs: 107988 ave 119612 max 95355 min Histogram: 2 2 1 3 6 9 0 4 4 1 Total # of neighbors = 3455607 Ave neighs/atom = 575.9345 Ave special neighs/atom = 2 Neighbor list builds = 98503 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) = 0.25348658 grid = 24 24 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030125684 estimated relative force accuracy = 9.0722602e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.19864e-06 6000 1 103.7 0.000106397 2000 Per MPI rank memory allocation (min/avg/max) = 9.973 | 9.996 | 10.04 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 289.78557 59830.193 1.0000033 298.93643 0 0 0 0 5240.7096 77468.111 -104.25214 -104338.99 -21630.169 3563.3997 Loop time of 8.76175e-06 on 32 procs for 0 steps with 6000 atoms 108.1% 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 | | 8.762e-06 | | |100.00 Nlocal: 187.5 ave 202 max 172 min Histogram: 2 2 3 3 5 2 5 4 3 3 Nghost: 6517 ave 6585 max 6387 min Histogram: 1 1 1 3 1 4 5 7 4 5 Neighs: 107988 ave 119612 max 95355 min Histogram: 2 2 1 3 6 9 0 4 4 1 Total # of neighbors = 3455607 Ave neighs/atom = 575.9345 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_NPT.out