#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 3441 = # 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 100000 100000 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 100 1 100 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 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25737673 grid = 32 32 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0035513047 estimated relative force accuracy = 1.0694649e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8464 3072 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.999407 0.606424 10323 2 100.38 15.4573 3441 Per MPI rank memory allocation (min/avg/max) = 13.23 | 13.5 | 13.68 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 984081.82 164285.93 1.4452783 414.31516 288.32315 408.15406 0 0 820592.52 -189734.99 -442.69341 -420695.04 210858.97 10943.289 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.2697e-06 10323 2 103.7 0.000102621 3441 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.12359e-06 10323 2 103.7 9.76419e-05 3441 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.33251e-06 10323 2 103.7 9.77199e-05 3441 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.56308e-06 10323 2 103.7 9.79708e-05 3441 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.19402e-06 10323 2 103.7 9.44309e-05 3441 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.30682e-06 10323 2 103.7 0.00010372 3441 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20309e-06 10323 2 103.7 8.44864e-05 3441 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.44966e-06 10323 2 103.7 0.00011004 3441 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.40356e-06 10323 2 103.7 0.000101953 3441 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.31846e-06 10323 2 103.7 9.41087e-05 3441 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.35559e-06 10323 2 103.7 9.99473e-05 3441 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.26089e-06 10323 2 103.7 9.54783e-05 3441 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11892e-06 10323 2 103.7 9.40728e-05 3441 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.26579e-06 10323 2 103.7 0.000100049 3441 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.24078e-06 10323 2 103.7 9.40954e-05 3441 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.31843e-06 10323 2 103.7 9.81778e-05 3441 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.2893e-06 10323 2 103.7 0.000105089 3441 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.49089e-06 10323 2 103.7 9.71706e-05 3441 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.18546e-06 10323 2 103.7 9.78055e-05 3441 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.09248e-06 10323 2 103.7 8.95998e-05 3441 1000000 1000000 984533.79 164285.93 1.4452783 296.84954 234.26692 415.20831 0 0 817742.73 -178253.81 -442.69341 -422538.91 217599.49 7840.6744 Loop time of 10929.2 on 32 procs for 1000000 steps with 14171 atoms Performance: 7.905 ns/day, 3.036 hours/ns, 91.498 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5243.1 | 6143.7 | 6826.2 | 601.9 | 56.21 Bond | 1.529 | 6.6423 | 17.98 | 216.7 | 0.06 Kspace | 2495.7 | 3184.3 | 4080.9 | 834.9 | 29.14 Neigh | 389.52 | 389.89 | 390.28 | 1.0 | 3.57 Comm | 512.34 | 535.63 | 551.81 | 43.1 | 4.90 Output | 0.01691 | 0.019948 | 0.022833 | 1.3 | 0.00 Modify | 628.35 | 639.39 | 659.28 | 34.8 | 5.85 Other | | 29.59 | | | 0.27 Nlocal: 442.844 ave 472 max 408 min Histogram: 2 0 8 1 3 4 4 4 0 6 Nghost: 7656.03 ave 7875 max 7487 min Histogram: 4 7 0 4 3 2 4 4 2 2 Neighs: 219660 ave 241563 max 193019 min Histogram: 4 3 1 3 3 0 6 3 3 6 Total # of neighbors = 7029124 Ave neighs/atom = 496.02173 Ave special neighs/atom = 1.685555 Neighbor list builds = 50501 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25737673 grid = 32 32 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0035513047 estimated relative force accuracy = 1.0694649e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8464 3072 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.09248e-06 10323 2 103.7 8.95998e-05 3441 Per MPI rank memory allocation (min/avg/max) = 13.59 | 13.66 | 13.75 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 1000000 1000000 984534.47 164285.93 1.4452783 296.84954 234.26692 415.20831 0 0 817742.73 -178253.81 -442.69341 -422538.91 217599.49 7840.6744 Loop time of 8.34431e-06 on 32 procs for 0 steps with 14171 atoms 107.1% 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 | | 8.344e-06 | | |100.00 Nlocal: 442.844 ave 472 max 408 min Histogram: 2 0 8 1 3 4 4 4 0 6 Nghost: 7656.03 ave 7875 max 7487 min Histogram: 4 7 0 4 3 2 4 4 2 2 Neighs: 219660 ave 241563 max 193019 min Histogram: 4 3 1 3 3 0 6 3 3 6 Total # of neighbors = 7029124 Ave neighs/atom = 496.02173 Ave special neighs/atom = 1.685555 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out