#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 68.468566) 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 (36.8271 36.8271 68.468566) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 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 ... WARNING: System is not charge neutral, net charge = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25652083 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0032092625 estimated relative force accuracy = 9.6645988e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8712 2700 generated 0 of 36 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 = 6 6 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 2 0.99141 0.711463 8304 2 96.7412 45.5755 2768 Per MPI rank memory allocation (min/avg/max) = 13.68 | 14.13 | 14.3 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 27001.825 92859.486 1.3074059 428.55654 103.90131 299.37784 0 0 26935.097 55145.334 -225.64506 -212309.1 -129825.39 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970014 4.15562e-05 8304 2 103.7 0.00471549 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969951 0.00014854 8304 2 103.7 0.0169412 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970025 7.54685e-05 8304 2 103.7 0.00865259 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969999 4.85605e-06 8304 2 103.7 0.000500634 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969969 9.58896e-05 8304 2 103.7 0.0109148 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970045 0.000133316 8304 2 103.7 0.0152551 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970031 9.3307e-05 8304 2 103.7 0.0106833 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969972 8.74666e-05 8304 2 103.7 0.00999297 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969991 2.76749e-05 8304 2 103.7 0.00305336 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970031 9.32925e-05 8304 2 103.7 0.0106402 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97003 8.94017e-05 8304 2 103.7 0.0102105 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969979 6.36032e-05 8304 2 103.7 0.00721904 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969983 5.28077e-05 8304 2 103.7 0.00602108 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970032 9.66544e-05 8304 2 103.7 0.011043 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969999 3.36409e-06 8304 2 103.7 0.000330449 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969936 0.000192113 8304 2 103.7 0.0219726 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969988 3.66103e-05 8304 2 103.7 0.00412191 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969956 0.000131706 8304 2 103.7 0.0149773 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97005 0.000151428 8304 2 103.7 0.0173284 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970041 0.000122365 8304 2 103.7 0.0139864 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969992 2.63566e-05 8304 2 103.7 0.00297794 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969992 2.55585e-05 8304 2 103.7 0.00285028 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969977 7.10674e-05 8304 2 103.7 0.00810242 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969982 5.49722e-05 8304 2 103.7 0.00626886 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970015 4.60837e-05 8304 2 103.7 0.00525917 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969998 7.31827e-06 8304 2 103.7 0.000793121 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970061 0.000181641 8304 2 103.7 0.0207945 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97002 5.98303e-05 8304 2 103.7 0.00682268 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970018 5.41263e-05 8304 2 103.7 0.00616644 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969986 4.19464e-05 8304 2 103.7 0.00476083 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969938 0.00018781 8304 2 103.7 0.0214929 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970043 0.000130014 8304 2 103.7 0.0148687 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970025 7.48021e-05 8304 2 103.7 0.00854246 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970055 0.000163741 8304 2 103.7 0.018736 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969943 0.000171252 8304 2 103.7 0.0196203 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969995 1.51926e-05 8304 2 103.7 0.00171397 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969947 0.000159773 8304 2 103.7 0.0182226 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969969 9.4297e-05 8304 2 103.7 0.0107465 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969962 0.000114127 8304 2 103.7 0.0130038 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970003 8.39148e-06 8304 2 103.7 0.000949915 2768 2000000 2000000 183.26156 97458.422 1.2457111 295.40965 40.537244 65.790178 0 0 21371.6 32469.349 -214.99717 -215292.39 -161345.12 5575.7062 Loop time of 26247.8 on 16 procs for 2000000 steps with 9101 atoms Performance: 6.583 ns/day, 3.646 hours/ns, 76.197 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16900 | 17608 | 18505 | 318.7 | 67.09 Bond | 3.4151 | 8.7611 | 14.407 | 120.5 | 0.03 Kspace | 3685.2 | 4586.1 | 5295.6 | 627.9 | 17.47 Neigh | 1395.9 | 1396.4 | 1396.8 | 0.9 | 5.32 Comm | 594.86 | 601.87 | 608.35 | 15.0 | 2.29 Output | 0.013379 | 0.015208 | 0.016865 | 0.9 | 0.00 Modify | 1613.3 | 1868.1 | 1930.2 | 256.4 | 7.12 Other | | 178.1 | | | 0.68 Nlocal: 568.812 ave 602 max 541 min Histogram: 2 0 2 3 4 0 3 1 0 1 Nghost: 8673.81 ave 8805 max 8560 min Histogram: 2 0 1 4 2 3 1 1 1 1 Neighs: 305058 ave 325062 max 286627 min Histogram: 1 1 2 4 1 2 1 3 0 1 Total # of neighbors = 4880933 Ave neighs/atom = 536.30733 Ave special neighs/atom = 1.8929788 Neighbor list builds = 105868 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) = 0.25709324 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0030015141 estimated relative force accuracy = 9.0389705e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970003 8.39148e-06 8304 2 103.7 0.000949915 2768 Per MPI rank memory allocation (min/avg/max) = 14.1 | 14.24 | 14.32 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 199.05123 97458.422 1.2457111 295.40965 40.537244 65.790178 0 0 21371.6 32945.83 -214.99717 -215768.86 -161345.1 5575.7062 Loop time of 3.88756e-06 on 16 procs for 0 steps with 9101 atoms 138.3% CPU use with 16 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 | | 3.888e-06 | | |100.00 Nlocal: 568.812 ave 602 max 541 min Histogram: 2 0 2 3 4 0 3 1 0 1 Nghost: 8673.81 ave 8805 max 8560 min Histogram: 2 0 1 4 2 3 1 1 1 1 Neighs: 305058 ave 325062 max 286627 min Histogram: 1 1 2 4 1 2 1 3 0 1 Total # of neighbors = 4880933 Ave neighs/atom = 536.30733 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 7:17:30