#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 3 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 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 (40.919 40.919 112.8) 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 (40.919 40.919 112.8) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000 fix 2 movable ave/time 1 299999 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 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) = 0.25881757 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028926595 estimated relative force accuracy = 8.7111581e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 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 17 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 1.00059 0.0794367 8304 2 97.7051 10.4246 2768 Per MPI rank memory allocation (min/avg/max) = 12.7 | 13.48 | 14.41 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 -2473.5902 188868.32 1.5677036 381.30689 5.5210083 20.520222 0 0 52147.665 -165200.79 -449.41339 -391845.93 -504873.02 11288.745 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969965 0.000108764 8304 2 103.7 0.0123987 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970022 6.80176e-05 8304 2 103.7 0.00776759 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970001 2.41819e-06 8304 2 103.7 0.000223373 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969977 6.98941e-05 8304 2 103.7 0.00793176 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970007 2.22931e-05 8304 2 103.7 0.00255175 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969945 0.000165437 8304 2 103.7 0.0189659 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970019 5.70592e-05 8304 2 103.7 0.00655161 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969985 4.61583e-05 8304 2 103.7 0.00524379 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970029 8.77882e-05 8304 2 103.7 0.0100652 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969994 1.82363e-05 8304 2 103.7 0.00204185 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969975 7.51636e-05 8304 2 103.7 0.00855628 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97002 5.99649e-05 8304 2 103.7 0.00688332 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970008 2.52575e-05 8304 2 103.7 0.00287043 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969988 3.73287e-05 8304 2 103.7 0.00419153 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970026 7.84265e-05 8304 2 103.7 0.00894952 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970016 4.74119e-05 8304 2 103.7 0.00541802 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970011 3.23085e-05 8304 2 103.7 0.00370942 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97003 9.02171e-05 8304 2 103.7 0.0103565 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969996 1.48077e-05 8304 2 103.7 0.00162197 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970043 0.000129826 8304 2 103.7 0.0148715 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969999 4.26516e-06 8304 2 103.7 0.000425881 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970024 7.13354e-05 8304 2 103.7 0.00817571 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970011 3.32194e-05 8304 2 103.7 0.0038092 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969985 4.65619e-05 8304 2 103.7 0.00528785 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970018 5.50918e-05 8304 2 103.7 0.00632878 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970041 0.000123939 8304 2 103.7 0.0142034 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970005 1.57254e-05 8304 2 103.7 0.00177818 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970028 8.43349e-05 8304 2 103.7 0.0096595 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970047 0.000140712 8304 2 103.7 0.0161611 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969939 0.000183635 8304 2 103.7 0.0209905 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970028 8.49676e-05 8304 2 103.7 0.00971619 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970029 8.61379e-05 8304 2 103.7 0.00990698 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970024 7.13337e-05 8304 2 103.7 0.00813831 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970018 5.47483e-05 8304 2 103.7 0.00627185 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970024 7.21362e-05 8304 2 103.7 0.00827244 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970007 2.00845e-05 8304 2 103.7 0.0022868 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970039 0.000117025 8304 2 103.7 0.0133658 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969987 3.92371e-05 8304 2 103.7 0.00446665 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969996 1.4132e-05 8304 2 103.7 0.00157907 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970047 0.000140244 8304 2 103.7 0.0160675 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.96999 3.19827e-05 8304 2 103.7 0.00360385 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970015 4.66193e-05 8304 2 103.7 0.00531828 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970018 5.29238e-05 8304 2 103.7 0.00605001 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970009 2.77464e-05 8304 2 103.7 0.00319693 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97001 2.95593e-05 8304 2 103.7 0.00335953 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969994 1.86694e-05 8304 2 103.7 0.00209047 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.969977 7.0081e-05 8304 2 103.7 0.00799157 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.969996 1.23737e-05 8304 2 103.7 0.00133808 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.970038 0.000115012 8304 2 103.7 0.0131805 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.970028 8.36105e-05 8304 2 103.7 0.00955026 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970002 6.76543e-06 8304 2 103.7 0.000736739 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97004 0.000120729 8304 2 103.7 0.0138503 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970011 3.19475e-05 8304 2 103.7 0.00361892 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.969981 5.90113e-05 8304 2 103.7 0.00665947 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970015 4.62256e-05 8304 2 103.7 0.00528407 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.970027 8.09765e-05 8304 2 103.7 0.00919655 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.970019 5.84443e-05 8304 2 103.7 0.00669329 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.96997 9.20698e-05 8304 2 103.7 0.0104361 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969991 2.77736e-05 8304 2 103.7 0.00312698 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.96998 6.14822e-05 8304 2 103.7 0.00697476 2768 3000000 3000000 2062.9353 186830.8 1.5848005 301.43157 44.987807 53.952563 0 0 52383.209 -149045.58 -454.31456 -391678.91 -488242.34 8924.0038 Loop time of 41284.8 on 32 procs for 3000000 steps with 12701 atoms Performance: 6.278 ns/day, 3.823 hours/ns, 72.666 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4356.4 | 15242 | 25903 |7247.7 | 36.92 Bond | 2.9968 | 7.9928 | 18.966 | 178.4 | 0.02 Kspace | 7880.6 | 18566 | 29454 |6583.5 | 44.97 Neigh | 2236.1 | 2241.6 | 2249.9 | 9.0 | 5.43 Comm | 895.62 | 1163.4 | 1309.2 | 412.1 | 2.82 Output | 0.01503 | 0.017755 | 0.020418 | 1.2 | 0.00 Modify | 3226.1 | 3463.6 | 3900.5 | 389.4 | 8.39 Other | | 599.2 | | | 1.45 Nlocal: 396.906 ave 574 max 204 min Histogram: 4 8 1 3 0 0 0 0 9 7 Nghost: 6237.78 ave 8651 max 3612 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 173502 ave 310066 max 46582 min Histogram: 12 0 0 3 1 3 1 0 3 9 Total # of neighbors = 5552073 Ave neighs/atom = 437.13668 Ave special neighs/atom = 1.3564286 Neighbor list builds = 160423 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25914364 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028379227 estimated relative force accuracy = 8.5463198e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.96998 6.14822e-05 8304 2 103.7 0.00697476 2768 Per MPI rank memory allocation (min/avg/max) = 12.71 | 13.59 | 14.42 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 3000000 3000000 2001.1723 186830.8 1.5848005 301.43157 44.987807 53.952563 0 0 52383.209 -148554.85 -454.31456 -392169.7 -488242.4 8924.0038 Loop time of 1.06913e-05 on 32 procs for 0 steps with 12701 atoms 106.4% 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 | | 1.069e-05 | | |100.00 Nlocal: 396.906 ave 574 max 204 min Histogram: 4 8 1 3 0 0 0 0 9 7 Nghost: 6237.78 ave 8651 max 3612 min Histogram: 4 4 0 4 4 4 0 4 0 8 Neighs: 173502 ave 310066 max 46582 min Histogram: 12 0 0 3 1 3 1 0 3 9 Total # of neighbors = 5552073 Ave neighs/atom = 437.13668 Ave special neighs/atom = 1.3564286 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out