#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 84.1) 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 84.1) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 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 = 0.0406 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 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 13 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 1 1.00266 0.969541 11904 2 97.607 23.8685 3968 Per MPI rank memory allocation (min/avg/max) = 13.22 | 13.71 | 14.16 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 5276.969 139006.3 1.4192018 417.33588 128.09957 494.98117 0 0 42701.815 15197.087 -396.67289 -379296.13 -320774.14 12355.398 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970018 5.11759e-05 11904 2 103.7 0.00585008 3968 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969994 1.94559e-05 11904 2 103.7 0.00220626 3968 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970069 0.000197273 11904 2 103.701 0.0226578 3968 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969994 1.8795e-05 11904 2 103.7 0.00212146 3968 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969953 0.000135842 11904 2 103.7 0.0154928 3968 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969994 1.9853e-05 11904 2 103.7 0.00221253 3968 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969997 8.80012e-06 11904 2 103.7 0.000966049 3968 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970017 4.89495e-05 11904 2 103.7 0.00560259 3968 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969966 9.80921e-05 11904 2 103.7 0.0111902 3968 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970032 9.25596e-05 11904 2 103.7 0.0106333 3968 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970028 7.96903e-05 11904 2 103.7 0.00911947 3968 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970022 6.22197e-05 11904 2 103.7 0.00707523 3968 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969995 1.63566e-05 11904 2 103.7 0.00182573 3968 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969997 8.56813e-06 11904 2 103.7 0.000935534 3968 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969972 8.28095e-05 11904 2 103.7 0.00945563 3968 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969995 1.41816e-05 11904 2 103.7 0.00159097 3968 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969962 0.000112545 11904 2 103.7 0.0128283 3968 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970034 9.58392e-05 11904 2 103.7 0.0109961 3968 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970005 1.45545e-05 11904 2 103.7 0.00164553 3968 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.96998 5.81246e-05 11904 2 103.7 0.00663859 3968 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970016 4.70377e-05 11904 2 103.7 0.00541414 3968 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970023 6.73832e-05 11904 2 103.7 0.00771329 3968 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.96996 0.000115751 11904 2 103.7 0.0132146 3968 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969995 1.4606e-05 11904 2 103.7 0.00160168 3968 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97005 0.00014522 11904 2 103.701 0.0166279 3968 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970024 6.90019e-05 11904 2 103.7 0.0078529 3968 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970042 0.000121855 11904 2 103.7 0.013941 3968 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970042 0.000120691 11904 2 103.7 0.013792 3968 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969981 5.652e-05 11904 2 103.7 0.00645691 3968 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970005 1.45964e-05 11904 2 103.7 0.00164582 3968 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970003 9.58127e-06 11904 2 103.7 0.00109245 3968 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969999 4.66299e-06 11904 2 103.7 0.000490146 3968 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969991 2.57128e-05 11904 2 103.7 0.00289667 3968 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969991 2.58501e-05 11904 2 103.7 0.00288839 3968 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97001 2.97434e-05 11904 2 103.7 0.0033941 3968 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970005 1.40043e-05 11904 2 103.7 0.00159236 3968 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969982 5.388e-05 11904 2 103.7 0.00612484 3968 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969969 9.0303e-05 11904 2 103.7 0.0102994 3968 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969947 0.000151606 11904 2 103.699 0.0172947 3968 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969986 4.1705e-05 11904 2 103.7 0.00470628 3968 2000000 2000000 282.53313 139046.86 1.4187877 302.9462 330.093 522.13337 0 0 37715.188 22817.407 -396.55717 -380029.32 -318644.49 8968.845 Loop time of 27564.6 on 32 procs for 2000000 steps with 13901 atoms Performance: 6.269 ns/day, 3.828 hours/ns, 72.557 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12235 | 14385 | 17888 |1696.1 | 52.19 Bond | 2.9649 | 16.652 | 38.945 | 312.6 | 0.06 Kspace | 4350.7 | 7883.3 | 10057 |2314.3 | 28.60 Neigh | 1440.3 | 1442.5 | 1444.9 | 3.4 | 5.23 Comm | 1147.9 | 1223.6 | 1297.3 | 134.0 | 4.44 Output | 0.014967 | 0.017939 | 0.02076 | 1.3 | 0.00 Modify | 1887.8 | 2345.1 | 2442.4 | 334.0 | 8.51 Other | | 268.3 | | | 0.97 Nlocal: 434.406 ave 506 max 388 min Histogram: 5 7 6 4 1 1 0 0 2 6 Nghost: 8395.97 ave 8864 max 7761 min Histogram: 7 1 0 0 0 7 4 5 0 8 Neighs: 251036 ave 326623 max 206656 min Histogram: 7 7 8 2 0 0 0 0 1 7 Total # of neighbors = 8033153 Ave neighs/atom = 577.8831 Ave special neighs/atom = 2.0450327 Neighbor list builds = 105825 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) = 0.26028729 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027853376 estimated relative force accuracy = 8.3879615e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969986 4.1705e-05 11904 2 103.7 0.00470628 3968 Per MPI rank memory allocation (min/avg/max) = 13.56 | 13.73 | 14.16 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 2000000 2000000 198.98019 139046.86 1.4187877 302.9462 330.093 522.13337 0 0 37715.188 22809.059 -396.55717 -380020.97 -318644.5 8968.845 Loop time of 7.91331e-06 on 32 procs for 0 steps with 13901 atoms 113.7% 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 | | 7.913e-06 | | |100.00 Nlocal: 434.406 ave 506 max 388 min Histogram: 5 7 6 4 1 1 0 0 2 6 Nghost: 8395.97 ave 8864 max 7761 min Histogram: 7 1 0 0 0 7 4 5 0 8 Neighs: 251036 ave 326623 max 206656 min Histogram: 7 7 8 2 0 0 0 0 1 7 Total # of neighbors = 8033153 Ave neighs/atom = 577.8831 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out