#------------------------------------------------------------------------------- # 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 2812 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) 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 69.281874) 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 = 0.0151 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25615969 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031432339 estimated relative force accuracy = 9.4657554e-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 0.99594 0.661671 8436 2 97.0955 30.2664 2812 Per MPI rank memory allocation (min/avg/max) = 14.05 | 14.15 | 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 13631.893 93962.523 1.2789064 429.73544 125.4983 256.8254 0 0 21680.644 56519.708 -220.49494 -206132.57 -127549.89 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969925 0.000224194 8436 2 103.7 0.0256793 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969997 1.06642e-05 8436 2 103.7 0.00114365 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970043 0.000128388 8436 2 103.7 0.0146712 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970031 9.19065e-05 8436 2 103.7 0.0104928 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970012 3.6026e-05 8436 2 103.7 0.00416266 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969994 1.90345e-05 8436 2 103.7 0.00215916 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969974 7.96601e-05 8436 2 103.7 0.00899703 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969969 9.61988e-05 8436 2 103.7 0.0109403 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970001 4.77918e-06 8436 2 103.7 0.000509107 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969973 8.23127e-05 8436 2 103.7 0.00939887 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970038 0.0001134 8436 2 103.7 0.0129789 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970079 0.000239225 8436 2 103.7 0.0274256 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969948 0.000155235 8436 2 103.7 0.0177402 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970004 1.25259e-05 8436 2 103.7 0.00145553 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969992 2.53386e-05 8436 2 103.7 0.00284503 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969965 0.000106673 8436 2 103.7 0.0121704 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969976 7.36881e-05 8436 2 103.7 0.00840533 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970015 4.67962e-05 8436 2 103.7 0.00531701 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969993 2.13526e-05 8436 2 103.7 0.00237029 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970045 0.000137326 8436 2 103.7 0.0157415 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969933 0.000201689 8436 2 103.7 0.0230875 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970008 2.62192e-05 8436 2 103.7 0.00298121 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970034 0.000103233 8436 2 103.7 0.0118138 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969947 0.000157631 8436 2 103.7 0.0180202 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969962 0.000116064 8436 2 103.7 0.0132296 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97006 0.000179724 8436 2 103.7 0.0206209 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970014 4.15023e-05 8436 2 103.7 0.00469981 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970022 6.74246e-05 8436 2 103.7 0.00770051 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97001 2.98966e-05 8436 2 103.7 0.0034282 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97004 0.000119765 8436 2 103.7 0.0137217 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969982 5.67323e-05 8436 2 103.7 0.00644946 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970023 7.01464e-05 8436 2 103.7 0.00802356 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970032 9.51541e-05 8436 2 103.7 0.0109054 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969995 1.67885e-05 8436 2 103.7 0.00187052 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969992 2.45086e-05 8436 2 103.7 0.00279348 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970015 4.44435e-05 8436 2 103.7 0.00510341 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969995 1.74244e-05 8436 2 103.7 0.00192656 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970007 2.17379e-05 8436 2 103.7 0.00248725 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970065 0.000193183 8436 2 103.7 0.0221254 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.57316e-05 8436 2 103.7 0.00172049 2812 2000000 2000000 -10.323501 98358.394 1.221749 297.74662 38.71324 91.612537 0 0 18751.645 47628.138 -210.64049 -207239.69 -140729.58 5657.979 Loop time of 26368.1 on 16 procs for 2000000 steps with 9188 atoms Performance: 6.553 ns/day, 3.662 hours/ns, 75.849 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 | 17554 | 17922 | 18481 | 189.5 | 67.97 Bond | 4.4973 | 8.9071 | 14.131 | 91.0 | 0.03 Kspace | 3760.3 | 4324.1 | 4690.6 | 387.7 | 16.40 Neigh | 1413.3 | 1414.1 | 1414.8 | 1.2 | 5.36 Comm | 606.32 | 608.85 | 611.72 | 7.1 | 2.31 Output | 0.018842 | 0.020766 | 0.02241 | 0.8 | 0.00 Modify | 1608.6 | 1876.9 | 2023.2 | 267.7 | 7.12 Other | | 213.7 | | | 0.81 Nlocal: 574.25 ave 603 max 537 min Histogram: 2 0 0 3 0 2 4 2 2 1 Nghost: 8715.12 ave 8824 max 8600 min Histogram: 1 2 3 1 0 2 0 5 1 1 Neighs: 308116 ave 325883 max 284437 min Histogram: 2 0 2 1 1 1 3 3 1 2 Total # of neighbors = 4929851 Ave neighs/atom = 536.55322 Ave special neighs/atom = 1.9037875 Neighbor list builds = 106257 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) = 0.25684942 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0029179597 estimated relative force accuracy = 8.7873491e-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 0.969995 1.57316e-05 8436 2 103.7 0.00172049 2812 Per MPI rank memory allocation (min/avg/max) = 14.11 | 14.26 | 14.33 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 -38.056447 98358.394 1.221749 297.74662 38.71324 91.612537 0 0 18751.645 48181.761 -210.64049 -207793.37 -140729.64 5657.979 Loop time of 4.90562e-06 on 16 procs for 0 steps with 9188 atoms 119.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.906e-06 | | |100.00 Nlocal: 574.25 ave 603 max 537 min Histogram: 2 0 0 3 0 2 4 2 2 1 Nghost: 8715.12 ave 8824 max 8600 min Histogram: 1 2 3 1 0 2 0 5 1 1 Neighs: 308116 ave 325883 max 284437 min Histogram: 2 0 2 1 1 1 3 3 1 2 Total # of neighbors = 4929851 Ave neighs/atom = 536.55322 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 7:19:31