#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 2200 = # of frozen angles find clusters CPU = 0.000 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 npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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) = 0.25565096 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0025687938 estimated relative force accuracy = 7.7358463e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999275 0.0497117 6600 1 97.9893 10.0992 2200 Per MPI rank memory allocation (min/avg/max) = 12 | 12.17 | 12.42 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 2090.6705 66008.132 0.99705035 447.33389 0 0 0 0 9635.089 72006.488 -114.33871 -115775.27 -34133.689 5865.703 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969972 1.62538e-06 6600 1 103.7 0.000128989 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969978 1.18399e-06 6600 1 103.7 8.99246e-05 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970005 1.53916e-06 6600 1 103.7 9.42662e-05 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969909 1.3284e-06 6600 1 103.7 0.00015148 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969921 1.08076e-06 6600 1 103.7 0.000103118 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969931 1.21036e-06 6600 1 103.7 9.94946e-05 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969909 1.22137e-06 6600 1 103.7 8.96564e-05 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969921 1.40498e-06 6600 1 103.7 0.000152401 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969938 1.09235e-06 6600 1 103.7 9.96841e-05 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969925 1.2468e-06 6600 1 103.7 0.000106924 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969967 1.42738e-06 6600 1 103.7 8.91873e-05 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970008 1.27808e-06 6600 1 103.7 0.000105104 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970126 1.17556e-06 6600 1 103.7 8.81749e-05 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970058 1.40026e-06 6600 1 103.7 9.77292e-05 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970064 1.71053e-06 6600 1 103.7 0.000128912 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970041 1.38493e-06 6600 1 103.7 9.76392e-05 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969988 1.69357e-06 6600 1 103.7 0.00012049 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970006 1.20049e-06 6600 1 103.7 9.24963e-05 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970074 1.59619e-06 6600 1 103.7 0.000124727 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970005 1.16611e-06 6600 1 103.7 9.33485e-05 2200 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969997 1.76055e-06 6600 1 103.7 0.000165883 2200 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970046 1.1617e-06 6600 1 103.7 9.38839e-05 2200 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970019 1.39909e-06 6600 1 103.7 0.00010695 2200 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970032 1.44575e-06 6600 1 103.7 0.000111219 2200 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969946 1.30199e-06 6600 1 103.7 0.000122933 2200 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970085 1.10091e-06 6600 1 103.7 9.32739e-05 2200 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970095 1.38054e-06 6600 1 103.7 0.000111444 2200 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970075 1.68181e-06 6600 1 103.7 0.000130554 2200 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970044 1.26536e-06 6600 1 103.7 0.000110872 2200 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970054 1.28646e-06 6600 1 103.7 8.9215e-05 2200 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970075 1.15852e-06 6600 1 103.7 9.3056e-05 2200 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970102 1.89794e-06 6600 1 103.7 0.000135869 2200 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970115 2.0124e-06 6600 1 103.7 0.000158291 2200 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970053 1.13294e-06 6600 1 103.7 9.05941e-05 2200 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969996 1.14019e-06 6600 1 103.7 9.41431e-05 2200 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969978 1.26844e-06 6600 1 103.7 9.58576e-05 2200 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969942 1.09586e-06 6600 1 103.7 9.74516e-05 2200 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970056 1.4901e-06 6600 1 103.7 0.000126524 2200 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970057 1.3597e-06 6600 1 103.7 0.000105458 2200 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969964 1.1377e-06 6600 1 103.7 0.000109542 2200 2000000 2000000 273.40908 66053.388 0.99636723 294.93528 0 0 0 0 5823.159 86104.095 -114.26037 -115752.5 -23825.243 3867.3634 Loop time of 31892.5 on 8 procs for 2000000 steps with 6600 atoms Performance: 5.418 ns/day, 4.430 hours/ns, 62.711 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20620 | 22191 | 23898 | 664.7 | 69.58 Bond | 2.3821 | 2.5374 | 2.73 | 7.2 | 0.01 Kspace | 4306.9 | 6014.5 | 7588.6 |1277.7 | 18.86 Neigh | 1432.7 | 1433.5 | 1434.3 | 1.7 | 4.49 Comm | 440.44 | 444.66 | 448.55 | 14.4 | 1.39 Output | 0.016539 | 0.01755 | 0.0184 | 0.5 | 0.00 Modify | 1447.8 | 1645.9 | 1728.5 | 264.4 | 5.16 Other | | 160 | | | 0.50 Nlocal: 825 ave 850 max 802 min Histogram: 1 0 0 1 2 2 1 0 0 1 Nghost: 10401.8 ave 10442 max 10377 min Histogram: 1 1 2 1 1 0 1 0 0 1 Neighs: 473516 ave 501774 max 448504 min Histogram: 1 1 1 0 0 3 0 0 1 1 Total # of neighbors = 3788128 Ave neighs/atom = 573.95879 Ave special neighs/atom = 2 Neighbor list builds = 103854 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) = 0.25563703 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0025705484 estimated relative force accuracy = 7.7411303e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969964 1.1377e-06 6600 1 103.7 0.000109542 2200 Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.41 | 12.42 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 24.519055 66053.388 0.99636723 294.93528 0 0 0 0 5823.159 86097.796 -114.26037 -115746.2 -23825.243 3867.3634 Loop time of 4.05562e-06 on 8 procs for 0 steps with 6600 atoms 123.3% 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 | | 4.056e-06 | | |100.00 Nlocal: 825 ave 850 max 802 min Histogram: 1 0 0 1 2 2 1 0 0 1 Nghost: 10401.8 ave 10442 max 10377 min Histogram: 1 1 2 1 1 0 1 0 0 1 Neighs: 473516 ave 501774 max 448504 min Histogram: 1 1 1 0 0 3 0 0 1 1 Total # of neighbors = 3788128 Ave neighs/atom = 573.95879 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