#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00481 0.0879286 11184 2 97.7024 10.3752 3728 Per MPI rank memory allocation (min/avg/max) = 17.47 | 18.14 | 19.62 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 334521.46 143799.62 1.371895 417.38826 43.018436 239.04662 0 0 276214.51 -77425.729 -383.45046 -379121.69 -180050.84 11461.157 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.28106e-06 11184 2 103.7 9.50577e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.26079e-06 11184 2 103.7 9.19471e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.58706e-06 11184 2 103.7 0.000118056 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.2711e-06 11184 2 103.7 0.000110535 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.28543e-06 11184 2 103.7 9.26901e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.17245e-06 11184 2 103.7 8.98145e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2262e-06 11184 2 103.7 8.65472e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.38015e-06 11184 2 103.7 8.73781e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.59608e-06 11184 2 103.7 0.000102602 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.28512e-06 11184 2 103.7 0.000108135 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.26308e-06 11184 2 103.7 0.000103549 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.26517e-06 11184 2 103.7 0.000101163 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.67186e-06 11184 2 103.7 0.000104387 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.17696e-06 11184 2 103.7 9.37168e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.38896e-06 11184 2 103.7 9.817e-05 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.42037e-06 11184 2 103.7 9.12909e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.21072e-06 11184 2 103.7 8.91308e-05 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.59678e-06 11184 2 103.7 0.000108377 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.19283e-06 11184 2 103.7 9.46183e-05 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.31624e-06 11184 2 103.7 0.000108397 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.08069e-06 11184 2 103.7 8.80715e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.22642e-06 11184 2 103.7 8.86508e-05 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.18074e-06 11184 2 103.7 0.000106579 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.58153e-06 11184 2 103.7 0.000110793 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.29256e-06 11184 2 103.7 0.000115164 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.25471e-06 11184 2 103.7 9.66535e-05 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.3454e-06 11184 2 103.7 0.000104932 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.26528e-06 11184 2 103.7 0.000113654 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.72607e-06 11184 2 103.7 0.000120872 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.2967e-06 11184 2 103.7 0.000102486 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.27519e-06 11184 2 103.7 9.08978e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.3245e-06 11184 2 103.7 9.43487e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.19614e-06 11184 2 103.7 0.000117215 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.2627e-06 11184 2 103.7 9.84287e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.30793e-06 11184 2 103.7 0.000103799 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.45249e-06 11184 2 103.7 0.000107286 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.3281e-06 11184 2 103.7 8.94581e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.51065e-06 11184 2 103.7 9.06413e-05 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.3234e-06 11184 2 103.7 0.000109853 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.20532e-06 11184 2 103.7 0.000106737 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.14674e-06 11184 2 103.7 8.88755e-05 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.28255e-06 11184 2 103.7 0.000105702 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.27193e-06 11184 2 103.7 0.000104024 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.50237e-06 11184 2 103.7 9.76292e-05 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.31162e-06 11184 2 103.7 9.854e-05 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.22698e-06 11184 2 103.7 9.78598e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.44361e-06 11184 2 103.7 9.96574e-05 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.23724e-06 11184 2 103.7 0.000107912 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.33627e-06 11184 2 103.7 0.000106981 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.29792e-06 11184 2 103.7 0.000102925 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.32004e-06 11184 2 103.7 9.58748e-05 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.26961e-06 11184 2 103.7 0.000104905 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.47882e-06 11184 2 103.7 9.37824e-05 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.45922e-06 11184 2 103.7 0.00010614 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.27532e-06 11184 2 103.7 9.0747e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.17143e-06 11184 2 103.7 8.62686e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.28617e-06 11184 2 103.7 9.81023e-05 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.29357e-06 11184 2 103.7 9.45389e-05 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.42612e-06 11184 2 103.7 0.000106269 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.26672e-06 11184 2 103.7 9.99136e-05 3728 3000000 3000000 335538.59 143799.62 1.371895 296.36453 295.36611 381.01237 0 0 271475.2 -52414.858 -383.45046 -379002.46 -159265.74 8137.9394 Loop time of 109220 on 8 procs for 3000000 steps with 13901 atoms Performance: 2.373 ns/day, 10.113 hours/ns, 27.467 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 54967 | 65248 | 89725 |5320.9 | 59.74 Bond | 21.234 | 59.717 | 151.38 | 681.0 | 0.05 Kspace | 11869 | 36445 | 46775 |7149.3 | 33.37 Neigh | 4838.4 | 4841.7 | 4844.3 | 2.8 | 4.43 Comm | 880.18 | 921.91 | 965.74 | 99.5 | 0.84 Output | 0.031872 | 0.035617 | 0.039033 | 1.3 | 0.00 Modify | 1557.3 | 1576.9 | 1598.9 | 36.2 | 1.44 Other | | 126.9 | | | 0.12 Nlocal: 1737.62 ave 2072 max 1571 min Histogram: 4 1 1 0 0 0 0 0 0 2 Nghost: 13811.9 ave 14395 max 12704 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 975156 ave 1.34197e+06 max 802841 min Histogram: 3 3 0 0 0 0 0 0 0 2 Total # of neighbors = 7801248 Ave neighs/atom = 561.20049 Ave special neighs/atom = 1.8838932 Neighbor list builds = 150130 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.26672e-06 11184 2 103.7 9.99136e-05 3728 Per MPI rank memory allocation (min/avg/max) = 17.84 | 20.77 | 29.38 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 335539.54 143799.62 1.371895 296.36453 295.36611 381.01237 0 0 271475.2 -52414.858 -383.45046 -379002.46 -159265.74 8137.9394 Loop time of 3.07425e-06 on 8 procs for 0 steps with 13901 atoms 134.2% CPU use with 8 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 | | 3.074e-06 | | |100.00 Nlocal: 1737.62 ave 2072 max 1571 min Histogram: 4 1 1 0 0 0 0 0 0 2 Nghost: 13811.9 ave 14395 max 12704 min Histogram: 2 0 0 0 0 0 0 2 2 2 Neighs: 975156 ave 1.34197e+06 max 802841 min Histogram: 3 3 0 0 0 0 0 0 0 2 Total # of neighbors = 7801248 Ave neighs/atom = 561.20049 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_Custom.out