#------------------------------------------------------------------------------- # 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 3728 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (39.00424 48.916 72.5) 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 (39.00424 48.916 72.5) 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 = 0.0366 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25775833 grid = 32 40 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0032019347 estimated relative force accuracy = 9.6425313e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 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 7 11 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 1.00534 0.106167 11184 2 97.6389 14.6849 3728 Per MPI rank memory allocation (min/avg/max) = 13.14 | 13.48 | 13.76 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 -1954.4371 138325.03 1.3164891 418.87842 52.735252 200.95777 0 0 39546.37 -2471.2797 -339.81325 -344479.12 -307150.34 11502.076 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969984 4.81121e-05 11184 2 103.7 0.00543658 3728 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969972 8.28143e-05 11184 2 103.7 0.00943059 3728 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970019 5.6918e-05 11184 2 103.7 0.00650579 3728 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970002 5.66019e-06 11184 2 103.7 0.000619922 3728 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970012 3.56327e-05 11184 2 103.7 0.00409123 3728 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969964 0.00010814 11184 2 103.7 0.0123395 3728 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970007 2.06723e-05 11184 2 103.7 0.00233668 3728 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969977 7.01332e-05 11184 2 103.7 0.00796956 3728 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969997 1.04887e-05 11184 2 103.7 0.00114732 3728 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970018 5.29798e-05 11184 2 103.7 0.00605637 3728 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969967 9.78633e-05 11184 2 103.7 0.0111346 3728 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969997 1.05716e-05 11184 2 103.7 0.00114079 3728 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969989 3.40619e-05 11184 2 103.7 0.00384614 3728 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969975 7.6601e-05 11184 2 103.7 0.00873843 3728 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970009 2.80672e-05 11184 2 103.7 0.00316375 3728 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969976 7.08562e-05 11184 2 103.7 0.00809889 3728 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970001 2.29396e-06 11184 2 103.7 0.000223286 3728 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969993 2.23585e-05 11184 2 103.7 0.00251284 3728 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969958 0.000123644 11184 2 103.7 0.0140961 3728 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969969 9.18539e-05 11184 2 103.7 0.0104922 3728 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97001 3.09794e-05 11184 2 103.7 0.00353326 3728 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970029 8.7351e-05 11184 2 103.7 0.0100146 3728 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969982 5.4177e-05 11184 2 103.7 0.00614688 3728 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969982 5.3317e-05 11184 2 103.7 0.00605484 3728 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970025 7.28475e-05 11184 2 103.7 0.00834331 3728 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970007 2.24204e-05 11184 2 103.7 0.0025144 3728 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970003 9.18417e-06 11184 2 103.7 0.000970324 3728 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970033 9.80547e-05 11184 2 103.7 0.0112602 3728 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969981 5.82115e-05 11184 2 103.7 0.00663277 3728 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969954 0.0001377 11184 2 103.7 0.0157379 3728 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.96781e-06 11184 2 103.7 0.000181302 3728 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969983 5.25618e-05 11184 2 103.7 0.00594914 3728 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97005 0.000148177 11184 2 103.7 0.0169868 3728 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970007 1.96591e-05 11184 2 103.7 0.00226186 3728 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969964 0.000108739 11184 2 103.7 0.0124253 3728 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969981 5.8019e-05 11184 2 103.7 0.00658428 3728 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969987 3.83323e-05 11184 2 103.7 0.00429753 3728 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.96998 6.02618e-05 11184 2 103.7 0.00683027 3728 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970039 0.000115143 11184 2 103.7 0.0132321 3728 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969964 0.000107663 11184 2 103.7 0.0122851 3728 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.970059 0.000174844 11184 2 103.7 0.0200688 3728 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970029 8.58583e-05 11184 2 103.7 0.00986741 3728 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970015 4.45549e-05 11184 2 103.7 0.00513379 3728 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.96994 0.000179203 11184 2 103.7 0.0205349 3728 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970007 2.03258e-05 11184 2 103.7 0.00229832 3728 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969971 8.84175e-05 11184 2 103.7 0.010039 3728 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.969972 8.38335e-05 11184 2 103.7 0.00957613 3728 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.970028 8.23086e-05 11184 2 103.7 0.00943706 3728 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.970048 0.000142451 11184 2 103.7 0.0163537 3728 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969964 0.0001059 11184 2 103.7 0.0120931 3728 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.969997 9.84818e-06 11184 2 103.7 0.00107718 3728 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969956 0.000130277 11184 2 103.7 0.0148779 3728 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970044 0.000131059 11184 2 103.7 0.014985 3728 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.969955 0.000134448 11184 2 103.7 0.015358 3728 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970002 6.19836e-06 11184 2 103.7 0.000671867 3728 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.970017 5.24773e-05 11184 2 103.7 0.0059685 3728 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97003 8.85078e-05 11184 2 103.7 0.0101204 3728 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.969975 7.75074e-05 11184 2 103.7 0.00881362 3728 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97003 8.83503e-05 11184 2 103.7 0.010119 3728 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969979 6.42252e-05 11184 2 103.7 0.00730137 3728 3000000 3000000 471.90865 130061.67 1.4001311 299.49429 295.56647 375.58239 0 0 34739.737 21693.127 -361.40299 -344350.16 -287246.15 8223.8803 Loop time of 38559.1 on 32 procs for 3000000 steps with 12941 atoms Performance: 6.722 ns/day, 3.570 hours/ns, 77.803 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17370 | 19940 | 25176 |2055.7 | 51.71 Bond | 4.4834 | 21.479 | 58.385 | 421.1 | 0.06 Kspace | 5838.4 | 11112 | 13712 |2782.1 | 28.82 Neigh | 1955.9 | 1960 | 1964.2 | 5.6 | 5.08 Comm | 1651.2 | 1748.5 | 1848.1 | 142.0 | 4.53 Output | 0.015262 | 0.01811 | 0.020764 | 1.2 | 0.00 Modify | 2756.4 | 3247.2 | 3576.8 | 559.4 | 8.42 Other | | 530.6 | | | 1.38 Nlocal: 404.406 ave 474 max 361 min Histogram: 3 7 13 1 0 0 0 0 2 6 Nghost: 8119.53 ave 8388 max 7591 min Histogram: 7 1 0 0 0 0 0 3 14 7 Neighs: 232328 ave 299794 max 191430 min Histogram: 5 11 5 2 1 0 0 0 0 8 Total # of neighbors = 7434486 Ave neighs/atom = 574.49084 Ave special neighs/atom = 2.0236458 Neighbor list builds = 156870 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) = 0.25822755 grid = 32 40 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0031888792 estimated relative force accuracy = 9.6032151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969979 6.42252e-05 11184 2 103.7 0.00730137 3728 Per MPI rank memory allocation (min/avg/max) = 13.49 | 13.68 | 14.08 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 347.58469 130061.67 1.4001311 299.49429 295.56647 375.58239 0 0 34739.737 22315.156 -361.40299 -344972.17 -287246.13 8223.8803 Loop time of 9.25197e-06 on 32 procs for 0 steps with 12941 atoms 109.8% 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 | | 9.252e-06 | | |100.00 Nlocal: 404.406 ave 474 max 361 min Histogram: 3 7 13 1 0 0 0 0 2 6 Nghost: 8119.53 ave 8388 max 7591 min Histogram: 7 1 0 0 0 0 0 3 14 7 Neighs: 232328 ave 299794 max 191430 min Histogram: 5 11 5 2 1 0 0 0 0 8 Total # of neighbors = 7434486 Ave neighs/atom = 574.49084 Ave special neighs/atom = 2.0236458 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out