#------------------------------------------------------------------------------- # 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 (36.8271 36.8271 68.468566) 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 68.468566) 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) = 0.25652083 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0032092625 estimated relative force accuracy = 9.6645988e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 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 0.995484 0.911408 8304 2 97.25 48.6188 2768 Per MPI rank memory allocation (min/avg/max) = 12.86 | 12.96 | 13.16 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 8423.4831 92859.486 1.3074059 428.55654 45.053176 208.7426 0 0 23641.169 38122.874 -225.64506 -214531.62 -152513.78 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969973 7.99111e-05 8304 2 103.7 0.00908975 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969965 0.000104357 8304 2 103.7 0.0119075 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969962 0.000113639 8304 2 103.7 0.0128963 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970016 4.72054e-05 8304 2 103.7 0.00537725 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969999 4.84846e-06 8304 2 103.7 0.000509715 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970045 0.000134196 8304 2 103.7 0.0154276 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969997 1.14541e-05 8304 2 103.7 0.00126729 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.77013e-06 8304 2 103.7 0.000138208 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969932 0.000204389 8304 2 103.7 0.0233448 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969987 3.89276e-05 8304 2 103.7 0.00439076 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969978 6.83492e-05 8304 2 103.7 0.00778548 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970065 0.000193434 8304 2 103.7 0.0221519 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969966 0.000104189 8304 2 103.7 0.0118853 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970018 5.5749e-05 8304 2 103.7 0.00638234 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970012 3.50521e-05 8304 2 103.7 0.00399625 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969974 7.86392e-05 8304 2 103.7 0.00896004 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969996 1.28811e-05 8304 2 103.7 0.0013762 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969984 5.08355e-05 8304 2 103.7 0.00575245 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970012 3.54231e-05 8304 2 103.7 0.00405696 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97001 3.09274e-05 8304 2 103.7 0.00346814 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.96998 6.2008e-05 8304 2 103.7 0.00708202 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 2.27805e-06 8304 2 103.7 0.000170108 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969943 0.000171744 8304 2 103.7 0.0196 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970026 7.73842e-05 8304 2 103.7 0.00881948 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969941 0.000181652 8304 2 103.7 0.0207507 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969977 6.99748e-05 8304 2 103.7 0.00794564 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969934 0.000199126 8304 2 103.7 0.0227417 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970037 0.00011318 8304 2 103.7 0.0129447 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969998 6.07275e-06 8304 2 103.7 0.000646062 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969952 0.000147322 8304 2 103.7 0.0168043 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970001 4.27866e-06 8304 2 103.7 0.000472714 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969987 3.98121e-05 8304 2 103.7 0.00453392 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969992 2.5935e-05 8304 2 103.7 0.00292563 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970096 0.000289261 8304 2 103.7 0.033109 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970082 0.000242798 8304 2 103.7 0.0279596 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.96997 9.03577e-05 8304 2 103.7 0.0102933 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.96997 8.91038e-05 8304 2 103.7 0.010148 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970002 6.49872e-06 8304 2 103.7 0.000747364 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970023 6.89942e-05 8304 2 103.7 0.00783769 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969947 0.000159987 8304 2 103.7 0.0183115 2768 2000000 2000000 208.12519 97258.15 1.2482762 292.55143 39.214126 89.770846 0 0 21395.692 32290.547 -215.43988 -215296.13 -161480.91 5521.7589 Loop time of 16103.4 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.731 ns/day, 2.237 hours/ns, 124.197 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8388.6 | 8899.3 | 9278.2 | 238.9 | 55.26 Bond | 2.3561 | 5.6528 | 9.2434 | 95.8 | 0.04 Kspace | 3206.2 | 3589.8 | 4100.4 | 380.5 | 22.29 Neigh | 695.31 | 695.82 | 696.75 | 1.3 | 4.32 Comm | 992.68 | 1009 | 1024.1 | 28.3 | 6.27 Output | 0.012105 | 0.014362 | 0.016485 | 1.1 | 0.00 Modify | 1436.2 | 1603.3 | 1809.7 | 380.0 | 9.96 Other | | 300.5 | | | 1.87 Nlocal: 284.406 ave 309 max 254 min Histogram: 2 1 0 4 5 6 5 4 4 1 Nghost: 7134.91 ave 7200 max 7079 min Histogram: 2 4 4 4 5 1 3 6 2 1 Neighs: 152802 ave 165007 max 136004 min Histogram: 3 0 0 4 3 8 3 4 5 2 Total # of neighbors = 4889667 Ave neighs/atom = 537.267 Ave special neighs/atom = 1.8929788 Neighbor list builds = 105839 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) = 0.2571449 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0029930625 estimated relative force accuracy = 9.0135189e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5852 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969947 0.000159987 8304 2 103.7 0.0183115 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13.07 | 13.17 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 -99.50328 97258.15 1.2482762 292.55143 39.214126 89.770846 0 0 21395.692 32810.065 -215.43988 -215815.66 -161480.92 5521.7589 Loop time of 1.64134e-05 on 32 procs for 0 steps with 9101 atoms 103.0% 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 | | 1.641e-05 | | |100.00 Nlocal: 284.406 ave 309 max 254 min Histogram: 2 1 0 4 5 6 5 4 4 1 Nghost: 7134.91 ave 7200 max 7079 min Histogram: 2 4 4 4 5 1 3 6 2 1 Neighs: 152802 ave 165007 max 136004 min Histogram: 3 0 0 4 3 8 3 4 5 2 Total # of neighbors = 4889667 Ave neighs/atom = 537.267 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