#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 200 ps with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 8303 = # of frozen angles find clusters CPU = 0.002 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 1 1 100 drag 0 mtk yes nreset 4000 fix 2 movable ave/time 1 19999 20000 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 20 1 20 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 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.992518 1.12928 24909 2 96.605 63.2761 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.54 | 15.01 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 26935.622 278556.86 1.3074059 428.54084 571.12129 1095.4738 0 0 83132.65 318013.41 -1345.0391 -800663.24 -397850.59 24265.468 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970019 1.16694e-06 24909 2 103.7 9.48474e-05 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970013 1.24037e-06 24909 2 103.7 9.84815e-05 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969983 1.17133e-06 24909 2 103.7 9.80236e-05 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970027 1.79027e-06 24909 2 103.7 0.000104749 8303 200000 200000 -152.54273 292483.1 1.2451553 295.71562 133.85813 308.00082 0 0 63380.701 267853.96 -1280.9966 -814955.5 -483278.98 16744.444 Loop time of 3258.1 on 32 procs for 200000 steps with 27300 atoms Performance: 5.304 ns/day, 4.525 hours/ns, 61.385 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 | 1187.6 | 1274.6 | 1342.3 | 101.9 | 39.12 Bond | 0.39651 | 1.1771 | 1.9559 | 30.0 | 0.04 Kspace | 1182 | 1251.5 | 1335.8 | 102.8 | 38.41 Neigh | 83.928 | 84.066 | 84.265 | 1.1 | 2.58 Comm | 146.43 | 149.22 | 151.02 | 11.8 | 4.58 Output | 0.024115 | 0.028943 | 0.033693 | 1.7 | 0.00 Modify | 318.09 | 407.23 | 480.46 | 341.0 | 12.50 Other | | 90.35 | | | 2.77 Nlocal: 853.125 ave 890 max 826 min Histogram: 4 4 4 5 3 3 3 2 1 3 Nghost: 7081.06 ave 7172 max 6993 min Histogram: 3 2 2 5 3 7 2 5 2 1 Neighs: 253335 ave 269717 max 238881 min Histogram: 2 4 2 7 4 4 2 3 1 3 Total # of neighbors = 8106714 Ave neighs/atom = 296.94923 Ave special neighs/atom = 1.892967 Neighbor list builds = 11148 Dangerous builds = 1 undump sci restart 0 dump sci all custom 200000 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) = 0.32364737 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035984908 estimated relative force accuracy = 1.0836748e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.970027 1.79027e-06 24909 2 103.7 0.000104749 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.58 | 15.01 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 200000 200000 3.5181022 292483.1 1.2451553 295.71562 133.85813 308.00082 0 0 63380.701 264797.46 -1280.9966 -811898.99 -483278.97 16744.444 Loop time of 9.60741e-06 on 32 procs for 0 steps with 27300 atoms 111.2% 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 | | 9.607e-06 | | |100.00 Nlocal: 853.125 ave 890 max 826 min Histogram: 4 4 4 5 3 3 3 2 1 3 Nghost: 7081.06 ave 7172 max 6993 min Histogram: 3 2 2 5 3 7 2 5 2 1 Neighs: 253335 ave 269717 max 238881 min Histogram: 2 4 2 7 4 4 2 3 1 3 Total # of neighbors = 8106714 Ave neighs/atom = 296.94923 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out