#------------------------------------------------------------------------------- # Stage 2.5: 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 2699 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (45.402 32.1502 62.648044) 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 (45.402 32.1502 62.648044) 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 2.5_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 ... WARNING: System is not charge neutral, net charge = 0.024 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 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 = 7 5 9 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 0.97 9.05276e-13 8097 2 103.7 1.03583e-10 2699 Per MPI rank memory allocation (min/avg/max) = 14.11 | 14.25 | 14.36 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 2976.1901 91446.309 1.3291045 298.73426 40.533371 71.948456 0 0 24083.729 19876.872 -226.3957 -220285.27 -176212.19 5554.7525 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969972 8.44485e-05 8097 2 103.7 0.00961053 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970038 0.000113513 8097 2 103.7 0.0129333 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970013 3.84742e-05 8097 2 103.7 0.00440138 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.96999 3.10853e-05 8097 2 103.7 0.00351997 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969994 1.79484e-05 8097 2 103.7 0.00202511 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970021 6.30613e-05 8097 2 103.7 0.0072342 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970025 7.52433e-05 8097 2 103.7 0.00860795 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969973 8.11789e-05 8097 2 103.7 0.00920305 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969982 5.41771e-05 8097 2 103.7 0.00616208 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969979 6.52313e-05 8097 2 103.7 0.0073947 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969964 0.000109449 8097 2 103.7 0.0124974 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 2.49886e-06 8097 2 103.7 0.00023105 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969997 1.16152e-05 8097 2 103.7 0.00128624 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969948 0.000156303 8097 2 103.7 0.017857 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969981 5.67222e-05 8097 2 103.7 0.00643299 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969985 4.59388e-05 8097 2 103.7 0.00520133 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970016 4.86071e-05 8097 2 103.7 0.00555664 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970018 5.37751e-05 8097 2 103.7 0.0061612 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969939 0.000185401 8097 2 103.7 0.0211906 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970036 0.000108567 8097 2 103.7 0.0124652 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969998 6.95558e-06 8097 2 103.7 0.000769924 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969986 4.28517e-05 8097 2 103.7 0.00483126 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.96999 3.22162e-05 8097 2 103.7 0.00364745 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969986 4.41836e-05 8097 2 103.7 0.00502856 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970002 6.64531e-06 8097 2 103.7 0.000751836 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969982 5.42368e-05 8097 2 103.7 0.00618395 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969969 9.52019e-05 8097 2 103.7 0.0108626 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970031 9.25948e-05 8097 2 103.7 0.0106155 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970026 7.72137e-05 8097 2 103.7 0.00884538 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970004 1.27251e-05 8097 2 103.7 0.00145117 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969972 8.59153e-05 8097 2 103.7 0.00975297 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970047 0.000141086 8097 2 103.7 0.016128 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97002 6.00328e-05 8097 2 103.7 0.0068262 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969996 1.34907e-05 8097 2 103.7 0.00148131 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969984 4.95003e-05 8097 2 103.7 0.00562188 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969967 9.90109e-05 8097 2 103.7 0.0112891 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969987 3.85411e-05 8097 2 103.7 0.00435602 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970064 0.000193653 8097 2 103.7 0.0221481 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969983 5.15937e-05 8097 2 103.7 0.00585774 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.67601e-05 8097 2 103.7 0.00299336 2699 2000000 2000000 203.9491 96839.051 1.2550898 298.12309 41.539621 49.527824 0 0 23031.82 21283.405 -213.78825 -220289.26 -175882.97 5543.3881 Loop time of 26189.9 on 16 procs for 2000000 steps with 8938 atoms Performance: 6.598 ns/day, 3.637 hours/ns, 76.365 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 | 16396 | 17158 | 17704 | 260.3 | 65.51 Bond | 4.2021 | 8.6967 | 12.984 | 62.4 | 0.03 Kspace | 4367.1 | 4911.4 | 5675.6 | 486.6 | 18.75 Neigh | 1428.8 | 1429.9 | 1430.9 | 2.3 | 5.46 Comm | 566.37 | 569.49 | 572.33 | 8.1 | 2.17 Output | 0.013693 | 0.015462 | 0.017012 | 0.9 | 0.00 Modify | 1631 | 1904.7 | 1997.2 | 272.5 | 7.27 Other | | 207.7 | | | 0.79 Nlocal: 558.625 ave 581 max 530 min Histogram: 1 1 0 3 0 3 4 1 1 2 Nghost: 8657.06 ave 8730 max 8553 min Histogram: 1 0 1 2 3 1 0 6 0 2 Neighs: 296162 ave 313908 max 277609 min Histogram: 1 1 0 0 8 1 2 1 0 2 Total # of neighbors = 4738595 Ave neighs/atom = 530.16279 Ave special neighs/atom = 1.8722309 Neighbor list builds = 104884 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) = 0.25733258 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030292656 estimated relative force accuracy = 9.1225434e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.67601e-05 8097 2 103.7 0.00299336 2699 Per MPI rank memory allocation (min/avg/max) = 14.11 | 14.28 | 14.36 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 253.6509 96839.051 1.2550898 298.12309 41.539621 49.527824 0 0 23031.82 20135.635 -213.78825 -219141.49 -175882.97 5543.3881 Loop time of 5.32756e-06 on 16 procs for 0 steps with 8938 atoms 103.2% 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 | | 5.328e-06 | | |100.00 Nlocal: 558.625 ave 581 max 530 min Histogram: 1 1 0 3 0 3 4 1 1 2 Nghost: 8657.06 ave 8730 max 8553 min Histogram: 1 0 1 2 3 1 0 6 0 2 Neighs: 296162 ave 313908 max 277609 min Histogram: 1 1 0 0 8 1 2 1 0 2 Total # of neighbors = 4738595 Ave neighs/atom = 530.16279 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:28:05