#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 ps 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 1000 1000 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 1 1 1 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 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 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 = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00478 0.0879422 11184 2 97.7057 10.082 3728 Per MPI rank memory allocation (min/avg/max) = 13.46 | 13.65 | 14.1 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 334589.74 143799.62 1.371895 417.38826 42.791813 238.58018 0 0 276202.59 -77390.217 -383.45046 -379121.18 -180027.44 11461.157 10000 10000 334797.66 143799.62 1.371895 295.63016 307.6218 383.01447 0 0 270925.67 -51492.766 -383.45046 -378976.63 -158853.09 8117.7741 Loop time of 131.039 on 32 procs for 10000 steps with 13901 atoms Performance: 6.593 ns/day, 3.640 hours/ns, 76.313 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 54.978 | 66.453 | 90.826 | 163.2 | 50.71 Bond | 0.014353 | 0.077567 | 0.18652 | 20.8 | 0.06 Kspace | 21.259 | 45.811 | 57.314 | 198.1 | 34.96 Neigh | 4.5651 | 4.5786 | 4.5919 | 0.3 | 3.49 Comm | 5.4513 | 5.8071 | 6.4167 | 11.5 | 4.43 Output | 0.01448 | 0.017324 | 0.019998 | 1.3 | 0.01 Modify | 7.2561 | 7.7042 | 7.965 | 7.6 | 5.88 Other | | 0.5906 | | | 0.45 Nlocal: 434.406 ave 524 max 376 min Histogram: 1 10 9 4 0 0 0 0 0 8 Nghost: 8194.28 ave 8564 max 7566 min Histogram: 8 0 0 0 0 0 0 12 4 8 Neighs: 243448 ave 340592 max 199604 min Histogram: 11 11 2 0 0 0 0 0 2 6 Total # of neighbors = 7790324 Ave neighs/atom = 560.41465 Ave special neighs/atom = 1.8838932 Neighbor list builds = 486 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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 = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 1 0.97 1.21363e-06 11184 2 103.7 8.98449e-05 3728 Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.65 | 14.11 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 10000 10000 334798.68 143799.62 1.371895 295.63016 307.6218 383.01447 0 0 270925.67 -51492.766 -383.45046 -378976.63 -158853.09 8117.7741 Loop time of 7.95694e-06 on 32 procs for 0 steps with 13901 atoms 119.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.957e-06 | | |100.00 Nlocal: 434.406 ave 524 max 376 min Histogram: 1 10 9 4 0 0 0 0 0 8 Nghost: 8194.28 ave 8564 max 7566 min Histogram: 8 0 0 0 0 0 0 12 4 8 Neighs: 243448 ave 340592 max 199604 min Histogram: 11 11 2 0 0 0 0 0 2 6 Total # of neighbors = 7790324 Ave neighs/atom = 560.41465 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_NVT.out