#------------------------------------------------------------------------------- # 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 = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 56.180783) 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 (33.78995 48.916 56.180783) 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) = 0.25757039 grid = 30 36 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0029678301 estimated relative force accuracy = 8.9375323e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9350 3240 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 = 5 7 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 0.994396 0.923068 8304 2 96.7365 40.0666 2768 Per MPI rank memory allocation (min/avg/max) = 14.18 | 14.29 | 14.44 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 15862.668 92859.486 1.3074059 428.55654 57.479 196.54332 0 0 25548.385 46964.117 -225.64506 -214419.59 -141653.07 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970019 5.56891e-05 8304 2 103.7 0.00635169 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970006 1.89252e-05 8304 2 103.7 0.00215422 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.72889e-06 8304 2 103.7 0.000133375 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970039 0.00011502 8304 2 103.7 0.0132118 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969971 8.77809e-05 8304 2 103.7 0.0100025 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970061 0.000181747 8304 2 103.7 0.0207807 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970026 7.78895e-05 8304 2 103.7 0.00889801 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969941 0.000180781 8304 2 103.7 0.0207132 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970037 0.000112558 8304 2 103.7 0.012877 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969992 2.45177e-05 8304 2 103.7 0.00276381 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970004 1.20649e-05 8304 2 103.7 0.00135458 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970013 3.87514e-05 8304 2 103.7 0.00438874 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970003 1.07271e-05 8304 2 103.7 0.00118521 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969964 0.000110179 8304 2 103.7 0.0125591 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970023 6.93154e-05 8304 2 103.7 0.0078932 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969967 0.000101421 8304 2 103.7 0.011597 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969989 3.3378e-05 8304 2 103.7 0.00375819 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970015 4.68615e-05 8304 2 103.7 0.0053374 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970016 4.88302e-05 8304 2 103.7 0.00556945 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969972 8.54596e-05 8304 2 103.7 0.00971344 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969973 7.96439e-05 8304 2 103.7 0.00907542 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970034 0.000103223 8304 2 103.7 0.0118122 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970056 0.000167958 8304 2 103.7 0.0192285 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970012 3.6268e-05 8304 2 103.7 0.00413022 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970047 0.000139378 8304 2 103.7 0.0159404 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970001 4.7914e-06 8304 2 103.7 0.000473032 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969993 2.37379e-05 8304 2 103.7 0.00265498 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970058 0.000174815 8304 2 103.7 0.0199786 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970038 0.000112592 8304 2 103.7 0.012906 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970017 5.23852e-05 8304 2 103.7 0.0059857 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970054 0.000162631 8304 2 103.7 0.0186507 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970029 8.60732e-05 8304 2 103.7 0.00981767 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970001 3.12649e-06 8304 2 103.7 0.000350942 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970014 4.32326e-05 8304 2 103.7 0.00495913 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970024 7.22177e-05 8304 2 103.7 0.00824204 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969946 0.000162199 8304 2 103.7 0.0184949 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969998 7.82376e-06 8304 2 103.7 0.000858002 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969951 0.000146267 8304 2 103.7 0.0166811 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969995 1.6926e-05 8304 2 103.7 0.00191209 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970001 5.06879e-06 8304 2 103.7 0.000476868 2768 2000000 2000000 163.99159 97500.24 1.2451768 297.58713 47.820637 78.315997 0 0 21344.168 33321.197 -214.90495 -216142.46 -161350.95 5616.805 Loop time of 23249.3 on 16 procs for 2000000 steps with 9101 atoms Performance: 7.432 ns/day, 3.229 hours/ns, 86.024 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 | 13520 | 15011 | 16450 | 770.0 | 64.57 Bond | 3.27 | 6.9748 | 8.895 | 53.2 | 0.03 Kspace | 3100.4 | 4542.9 | 6041.3 |1403.8 | 19.54 Neigh | 1430 | 1430.6 | 1430.9 | 0.6 | 6.15 Comm | 462.9 | 470.9 | 478.97 | 22.3 | 2.03 Output | 0.013372 | 0.015034 | 0.016516 | 0.8 | 0.00 Modify | 1387.3 | 1567.4 | 1746 | 389.7 | 6.74 Other | | 219.2 | | | 0.94 Nlocal: 568.812 ave 603 max 551 min Histogram: 1 2 5 3 4 0 0 0 0 1 Nghost: 8847.44 ave 8908 max 8785 min Histogram: 2 1 1 2 3 1 2 1 1 2 Neighs: 304898 ave 324550 max 293328 min Histogram: 2 1 5 2 2 1 2 0 0 1 Total # of neighbors = 4878361 Ave neighs/atom = 536.02472 Ave special neighs/atom = 1.8929788 Neighbor list builds = 104592 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) = 0.25885735 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026279522 estimated relative force accuracy = 7.9139999e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9900 3240 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970001 5.06879e-06 8304 2 103.7 0.000476868 2768 Per MPI rank memory allocation (min/avg/max) = 14.26 | 14.42 | 14.47 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 171.78034 97500.24 1.2451768 297.58713 47.820637 78.315997 0 0 21344.168 34391.788 -214.90495 -217213.06 -161350.97 5616.805 Loop time of 4.06369e-06 on 16 procs for 0 steps with 9101 atoms 123.0% 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 | | 4.064e-06 | | |100.00 Nlocal: 568.812 ave 603 max 551 min Histogram: 1 2 5 3 4 0 0 0 0 1 Nghost: 8847.44 ave 8908 max 8785 min Histogram: 2 1 1 2 3 1 2 1 1 2 Neighs: 304898 ave 324550 max 293328 min Histogram: 2 1 5 2 2 1 2 0 0 1 Total # of neighbors = 4878361 Ave neighs/atom = 536.02472 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out