#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1937 = # 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) = 0.25683534 grid = 24 24 54 stencil order = 5 estimated absolute RMS force accuracy = 0.003135149 estimated relative force accuracy = 9.4414082e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4693 1152 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997727 0.629971 5811 2 96.4534 55.2117 1937 Per MPI rank memory allocation (min/avg/max) = 12.32 | 12.71 | 12.92 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 14672.573 65046.255 1.3074059 428.49853 89.704564 250.51607 0 0 18201.914 29102.575 -158.00458 -149929.29 -102284.58 5662.15 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.41916e-06 5811 2 103.7 0.000113426 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.32633e-06 5811 2 103.7 9.76496e-05 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.12009e-06 5811 2 103.7 9.46522e-05 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.41249e-06 5811 2 103.7 0.000100397 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.14704e-06 5811 2 103.7 8.87492e-05 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.2484e-06 5811 2 103.7 9.73095e-05 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.17936e-06 5811 2 103.7 9.77114e-05 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.6409e-06 5811 2 103.7 0.000121183 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.18648e-06 5811 2 103.7 9.94379e-05 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15376e-06 5811 2 103.7 9.54015e-05 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.21639e-06 5811 2 103.7 9.36512e-05 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.22347e-06 5811 2 103.7 9.75403e-05 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.73481e-06 5811 2 103.7 0.00011966 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.11325e-06 5811 2 103.7 8.93285e-05 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.50255e-06 5811 2 103.7 0.000102976 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.80241e-06 5811 2 103.7 0.000118833 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.27924e-06 5811 2 103.7 9.71972e-05 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.33229e-06 5811 2 103.7 9.66609e-05 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.13845e-06 5811 2 103.7 8.90814e-05 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.28758e-06 5811 2 103.7 0.000101726 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.56823e-06 5811 2 103.7 0.000116347 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.92177e-06 5811 2 103.7 0.000135034 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 2.09194e-06 5811 2 103.7 0.00012997 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.19329e-06 5811 2 103.7 8.80355e-05 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.14503e-06 5811 2 103.7 9.31893e-05 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 2.29578e-06 5811 2 103.7 0.000131573 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.00361e-06 5811 2 103.7 9.1869e-05 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 9.96298e-07 5811 2 103.7 9.06079e-05 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.03219e-06 5811 2 103.7 8.60906e-05 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.29526e-06 5811 2 103.7 9.56702e-05 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.20179e-06 5811 2 103.7 0.000135183 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.4653e-06 5811 2 103.7 9.30784e-05 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.14722e-06 5811 2 103.7 8.60501e-05 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.18045e-06 5811 2 103.7 0.000106855 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.23227e-06 5811 2 103.7 0.000100084 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.13417e-06 5811 2 103.7 9.46006e-05 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.18793e-06 5811 2 103.7 9.24727e-05 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.39623e-06 5811 2 103.7 0.000107538 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.42751e-06 5811 2 103.7 0.000103626 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3172e-06 5811 2 103.7 0.000124313 1937 2000000 2000000 2469.8899 65046.255 1.3074059 294.07734 33.060151 44.000732 0 0 15533.851 22002.097 -158.00458 -150947.98 -113334.98 3885.9177 Loop time of 11425.5 on 32 procs for 2000000 steps with 6371 atoms Performance: 15.124 ns/day, 1.587 hours/ns, 175.048 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 | 5685 | 6395.3 | 7309.9 | 539.0 | 55.97 Bond | 2.1076 | 4.1917 | 8.9511 | 86.9 | 0.04 Kspace | 2096.8 | 3018.3 | 3729.1 | 785.4 | 26.42 Neigh | 358.85 | 359.59 | 360.06 | 1.6 | 3.15 Comm | 833.75 | 854.22 | 867.02 | 34.8 | 7.48 Output | 0.0082987 | 0.010198 | 0.011997 | 1.1 | 0.00 Modify | 748.72 | 758.48 | 771.4 | 28.6 | 6.64 Other | | 35.31 | | | 0.31 Nlocal: 199.094 ave 214 max 181 min Histogram: 1 0 4 4 3 6 6 4 2 2 Nghost: 6436.62 ave 6554 max 6329 min Histogram: 1 2 3 6 3 7 5 4 0 1 Neighs: 111986 ave 131259 max 96904 min Histogram: 5 1 5 3 3 6 4 1 3 1 Total # of neighbors = 3583560 Ave neighs/atom = 562.47999 Ave special neighs/atom = 1.8932664 Neighbor list builds = 95270 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) = 0.25683534 grid = 24 24 54 stencil order = 5 estimated absolute RMS force accuracy = 0.003135149 estimated relative force accuracy = 9.4414082e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4693 1152 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3172e-06 5811 2 103.7 0.000124313 1937 Per MPI rank memory allocation (min/avg/max) = 12.71 | 12.85 | 12.93 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 2471.0057 65046.255 1.3074059 294.07734 33.060151 44.000732 0 0 15533.851 22002.097 -158.00458 -150947.98 -113334.98 3885.9177 Loop time of 7.70438e-06 on 32 procs for 0 steps with 6371 atoms 107.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.704e-06 | | |100.00 Nlocal: 199.094 ave 214 max 181 min Histogram: 1 0 4 4 3 6 6 4 2 2 Nghost: 6436.62 ave 6554 max 6329 min Histogram: 1 2 3 6 3 7 5 4 0 1 Neighs: 111986 ave 131259 max 96904 min Histogram: 5 1 5 3 3 6 4 1 3 1 Total # of neighbors = 3583560 Ave neighs/atom = 562.47999 Ave special neighs/atom = 1.8932664 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out