#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (30 30 66.477992) with tilt (0 0 0) kspace_style pppm 0.00001 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (30 30 66.477992) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25669611 grid = 24 24 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0023816765 estimated relative force accuracy = 7.1723479e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 5 5 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.50351e-13 6000 1 103.7 1.08528e-10 2000 Per MPI rank memory allocation (min/avg/max) = 9.993 | 10.02 | 10.06 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 36.413039 59830.193 1.0000033 301.67629 0 0 0 0 5110.1383 78960.864 -104.25214 -105652.95 -21581.949 3596.0596 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970006 1.75957e-05 6000 1 103.7 0.00195305 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969973 8.15149e-05 6000 1 103.7 0.00928387 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970003 9.15213e-06 6000 1 103.7 0.000983394 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969986 4.36766e-05 6000 1 103.7 0.00495477 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97005 0.000151256 6000 1 103.7 0.0173398 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969982 5.65444e-05 6000 1 103.7 0.0064355 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970032 9.6585e-05 6000 1 103.7 0.0110166 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969999 5.79948e-06 6000 1 103.7 0.000542521 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969975 7.53313e-05 6000 1 103.7 0.00860302 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970038 0.000113433 6000 1 103.7 0.0129742 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969979 6.62238e-05 6000 1 103.7 0.00755088 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970031 9.25077e-05 6000 1 103.7 0.01056 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969995 1.59299e-05 6000 1 103.7 0.00175602 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969899 0.000302729 6000 1 103.7 0.0346227 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969999 5.72247e-06 6000 1 103.7 0.000626095 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969961 0.000119382 6000 1 103.7 0.0136047 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969971 8.94293e-05 6000 1 103.7 0.010212 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970066 0.000200327 6000 1 103.7 0.0230149 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969996 1.31357e-05 6000 1 103.7 0.00144958 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970008 2.41014e-05 6000 1 103.7 0.00272478 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970006 1.81305e-05 6000 1 103.7 0.00202979 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969998 9.34665e-06 6000 1 103.7 0.000986094 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97003 8.97514e-05 6000 1 103.7 0.0103083 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969972 8.53105e-05 6000 1 103.7 0.00971412 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969992 2.44132e-05 6000 1 103.7 0.0027575 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969988 3.66433e-05 6000 1 103.7 0.00413554 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970003 1.00417e-05 6000 1 103.7 0.00107143 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.96992 0.000244273 6000 1 103.7 0.0279688 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97004 0.000119654 6000 1 103.7 0.0137002 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969905 0.000284104 6000 1 103.7 0.0325267 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969973 8.05782e-05 6000 1 103.7 0.00913891 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970016 4.83154e-05 6000 1 103.7 0.0055288 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970009 2.691e-05 6000 1 103.7 0.00303894 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969998 8.09475e-06 6000 1 103.7 0.00086969 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969953 0.00014271 6000 1 103.7 0.0162467 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969935 0.000197264 6000 1 103.7 0.0224473 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969991 2.90494e-05 6000 1 103.7 0.00326701 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970064 0.00019285 6000 1 103.7 0.0221886 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969968 9.70088e-05 6000 1 103.7 0.0111176 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970039 0.000117381 6000 1 103.7 0.0135182 2000 2000000 2000000 180.16774 60142.271 0.99481431 305.07227 0 0 0 0 5178.0731 78920.286 -103.71117 -105652.63 -21554.268 3636.5406 Loop time of 11295.5 on 32 procs for 2000000 steps with 6000 atoms Performance: 15.298 ns/day, 1.569 hours/ns, 177.062 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 | 6204.3 | 6275.9 | 6356.4 | 37.1 | 55.56 Bond | 2.0445 | 2.377 | 3.4314 | 16.4 | 0.02 Kspace | 2232.6 | 2311.5 | 2387.3 | 61.9 | 20.46 Neigh | 493.82 | 494.66 | 495.54 | 2.9 | 4.38 Comm | 845.79 | 856.74 | 868.88 | 20.0 | 7.58 Output | 0.0075471 | 0.0093673 | 0.011067 | 1.1 | 0.00 Modify | 1069.7 | 1175.2 | 1303.7 | 286.5 | 10.40 Other | | 179.1 | | | 1.59 Nlocal: 187.5 ave 202 max 171 min Histogram: 1 1 5 4 2 5 5 6 1 2 Nghost: 6502 ave 6645 max 6409 min Histogram: 3 4 6 4 6 0 5 1 2 1 Neighs: 107428 ave 119027 max 96941 min Histogram: 1 2 7 3 3 6 3 5 1 1 Total # of neighbors = 3437682 Ave neighs/atom = 572.947 Ave special neighs/atom = 2 Neighbor list builds = 107090 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.25660463 grid = 24 24 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0023916069 estimated relative force accuracy = 7.2022531e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970039 0.000117381 6000 1 103.7 0.0135182 2000 Per MPI rank memory allocation (min/avg/max) = 9.995 | 10.02 | 10.06 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 446.38246 60142.271 0.99481431 305.07227 0 0 0 0 5178.0731 78882.684 -103.71117 -105615.02 -21554.268 3636.5406 Loop time of 7.31866e-06 on 32 procs for 0 steps with 6000 atoms 113.6% 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 | | 7.319e-06 | | |100.00 Nlocal: 187.5 ave 202 max 171 min Histogram: 1 1 5 4 2 5 5 6 1 2 Nghost: 6502 ave 6645 max 6409 min Histogram: 3 4 6 4 6 0 5 1 2 1 Neighs: 107428 ave 119027 max 96941 min Histogram: 1 2 7 3 3 6 3 5 1 1 Total # of neighbors = 3437682 Ave neighs/atom = 572.947 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:00:21