#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 2009 = # 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 300000 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25031202 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033302856 estimated relative force accuracy = 1.0029056e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00075 0.0720653 6027 2 97.749 11.2888 2009 Per MPI rank memory allocation (min/avg/max) = 10.94 | 12.27 | 13.55 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-06 768.33939 140334.36 0.61135344 429.78001 6.3037642 28.261372 0 0 16859.755 17828.033 -75.27119 -144705.18 -109982.83 5832.8145 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.49036e-06 6027 2 103.7 9.89983e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.32019e-06 6027 2 103.7 9.3533e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.05799e-06 6027 2 103.7 0.000102223 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.17955e-06 6027 2 103.7 0.000109407 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.22532e-06 6027 2 103.7 9.55545e-05 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.39336e-06 6027 2 103.7 9.62305e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.35015e-06 6027 2 103.7 0.000115676 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.51116e-06 6027 2 103.7 0.000109925 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.0396e-06 6027 2 103.7 8.78209e-05 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.02864e-06 6027 2 103.7 9.00374e-05 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.55182e-06 6027 2 103.7 0.000108756 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.56458e-06 6027 2 103.7 0.000126514 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.44557e-06 6027 2 103.7 0.000101791 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.18075e-06 6027 2 103.7 8.77107e-05 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.58345e-06 6027 2 103.7 0.00010904 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 2.11918e-06 6027 2 103.7 0.000158542 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.32065e-06 6027 2 103.7 0.000100057 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.21338e-06 6027 2 103.7 9.99941e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.51188e-06 6027 2 103.7 0.000114396 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.20545e-06 6027 2 103.7 0.000102343 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.29043e-06 6027 2 103.7 0.000101506 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.51089e-06 6027 2 103.7 0.000104755 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.2925e-06 6027 2 103.7 0.000101961 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.217e-06 6027 2 103.7 8.68799e-05 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.84933e-06 6027 2 103.7 0.00014603 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.6211e-06 6027 2 103.7 0.000120897 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.4675e-06 6027 2 103.7 0.000119705 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.14637e-06 6027 2 103.7 9.30385e-05 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.11733e-06 6027 2 103.7 8.84826e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.04034e-06 6027 2 103.7 8.91181e-05 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.22028e-06 6027 2 103.7 0.000106199 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.10898e-06 6027 2 103.7 9.09393e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.14414e-06 6027 2 103.7 0.000104974 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.31286e-06 6027 2 103.7 0.000104431 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.1069e-06 6027 2 103.7 9.04407e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.12023e-06 6027 2 103.7 9.98556e-05 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.63605e-06 6027 2 103.7 0.000109553 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.54445e-06 6027 2 103.7 0.000112512 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.41661e-06 6027 2 103.7 0.000118266 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.32097e-06 6027 2 103.7 9.77481e-05 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.18322e-06 6027 2 103.7 8.78808e-05 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.18001e-06 6027 2 103.7 9.79802e-05 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.13076e-06 6027 2 103.7 9.2412e-05 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.22679e-06 6027 2 103.7 0.000108733 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.34574e-06 6027 2 103.7 0.000104973 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.02521e-06 6027 2 103.7 8.92509e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.21397e-06 6027 2 103.7 0.000100815 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.49635e-06 6027 2 103.7 0.00011191 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.81119e-06 6027 2 103.7 0.000104543 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.22424e-06 6027 2 103.7 9.42118e-05 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.33603e-06 6027 2 103.7 9.32581e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.37009e-06 6027 2 103.7 9.55244e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.09984e-06 6027 2 103.7 0.000102108 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.1879e-06 6027 2 103.7 0.000101911 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.68181e-06 6027 2 103.7 9.85205e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.50847e-06 6027 2 103.7 0.000110355 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.06577e-06 6027 2 103.7 9.12325e-05 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.5107e-06 6027 2 103.7 0.000105814 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.38862e-06 6027 2 103.7 9.90873e-05 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.43521e-06 6027 2 103.7 0.000131515 2009 3000000 3000000 -371.54851 140334.36 0.61135344 293.33833 28.518017 43.608414 0 0 13053.486 31787.427 -75.27119 -144664.24 -99751.203 3981.0787 Loop time of 26121.2 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.923 ns/day, 2.419 hours/ns, 114.849 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5476 | 8035.1 | 18761 |8782.9 | 30.76 Bond | 2.8747 | 5.8151 | 19.14 | 147.4 | 0.02 Kspace | 4294.8 | 15078 | 23265 |6453.3 | 57.72 Neigh | 1172.7 | 1179.5 | 1190.8 | 17.4 | 4.52 Comm | 254.24 | 664.92 | 911.57 | 902.7 | 2.55 Output | 0.011726 | 0.013612 | 0.015305 | 0.9 | 0.00 Modify | 931.42 | 1111.9 | 1359.7 | 507.5 | 4.26 Other | | 45.99 | | | 0.18 Nlocal: 205.094 ave 435 max 0 min Histogram: 12 0 4 0 0 0 2 1 3 10 Nghost: 4013 ave 7800 max 182 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 94917.4 ave 230781 max 0 min Histogram: 16 0 0 0 0 2 1 4 5 4 Total # of neighbors = 3037358 Ave neighs/atom = 462.80024 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146524 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25031202 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033302856 estimated relative force accuracy = 1.0029056e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.43521e-06 6027 2 103.7 0.000131515 2009 Per MPI rank memory allocation (min/avg/max) = 10.96 | 12.45 | 13.55 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 3000000 3000000 -371.24773 140334.36 0.61135344 293.33833 28.518017 43.608414 0 0 13053.486 31787.427 -75.27119 -144664.24 -99751.203 3981.0787 Loop time of 8.32825e-06 on 32 procs for 0 steps with 6563 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 | | 8.328e-06 | | |100.00 Nlocal: 205.094 ave 435 max 0 min Histogram: 12 0 4 0 0 0 2 1 3 10 Nghost: 4013 ave 7800 max 182 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 94917.4 ave 230781 max 0 min Histogram: 16 0 0 0 0 2 1 4 5 4 Total # of neighbors = 3037358 Ave neighs/atom = 462.80024 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out