#------------------------------------------------------------------------------- # Stage 2.5: 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 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 (45.28372 45.28372 45.28372) 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 (45.28372 45.28372 45.28372) 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25979226 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0025175327 estimated relative force accuracy = 7.5814749e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 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 = 7 7 7 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 0.97 7.62279e-13 8304 2 103.7 7.28733e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.11 | 13.27 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 2310.104 92859.489 1.3074058 300.56167 42.687475 59.823023 0 0 21930.048 34465.445 -225.64505 -218033.74 -161535.74 5672.948 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969974 7.95516e-05 8304 2 103.7 0.00903183 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970035 0.000104265 8304 2 103.7 0.0119164 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969946 0.000163543 8304 2 103.7 0.0186707 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969989 3.38984e-05 8304 2 103.7 0.00383683 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969992 2.51175e-05 8304 2 103.7 0.0028289 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970067 0.00020191 8304 2 103.7 0.0232018 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969987 4.0828e-05 8304 2 103.7 0.004623 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969954 0.000140239 8304 2 103.7 0.016013 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970016 4.81431e-05 8304 2 103.7 0.00548382 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969953 0.000142395 8304 2 103.7 0.0163077 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969948 0.000156232 8304 2 103.7 0.0178955 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969957 0.00013073 8304 2 103.7 0.0149377 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969984 4.84663e-05 8304 2 103.7 0.00549255 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969967 0.000100563 8304 2 103.7 0.0114813 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969992 2.67594e-05 8304 2 103.7 0.00298975 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969918 0.000246812 8304 2 103.7 0.0282677 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969973 8.17947e-05 8304 2 103.7 0.00930864 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969975 7.41008e-05 8304 2 103.7 0.00844096 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970005 1.40978e-05 8304 2 103.7 0.00162957 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970006 1.84628e-05 8304 2 103.7 0.00209534 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970011 3.34025e-05 8304 2 103.7 0.0038004 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969956 0.000130633 8304 2 103.7 0.0149203 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 2.04342e-06 8304 2 103.7 0.000205034 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969988 3.73851e-05 8304 2 103.7 0.00426238 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.96996 0.000120713 8304 2 103.7 0.0138263 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970039 0.000115544 8304 2 103.7 0.0131672 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969993 2.28026e-05 8304 2 103.7 0.00254454 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970012 3.57388e-05 8304 2 103.7 0.00405375 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969983 5.16941e-05 8304 2 103.7 0.00587943 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969961 0.000116773 8304 2 103.7 0.0133771 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969996 1.2644e-05 8304 2 103.7 0.00140678 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970047 0.000141585 8304 2 103.7 0.0162398 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970028 8.34737e-05 8304 2 103.7 0.00953974 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97003 8.78411e-05 8304 2 103.7 0.0100261 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970002 7.51587e-06 8304 2 103.7 0.000852553 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969992 2.60526e-05 8304 2 103.7 0.00292926 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969992 2.48917e-05 8304 2 103.7 0.00281313 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969954 0.000137795 8304 2 103.7 0.0157436 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969942 0.000175387 8304 2 103.7 0.0200599 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.87036e-05 8304 2 103.7 0.00326393 2768 2000000 2000000 202.13868 97162.661 1.249503 294.80367 40.711303 62.6585 0 0 21354.495 35260.865 -215.65161 -218012.15 -161293.42 5564.2688 Loop time of 16455.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.501 ns/day, 2.285 hours/ns, 121.540 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 | 8457.4 | 8891.9 | 9350.1 | 261.7 | 54.04 Bond | 2.4102 | 5.664 | 10.122 | 100.4 | 0.03 Kspace | 3160 | 3618.3 | 4051.1 | 410.1 | 21.99 Neigh | 710.64 | 711.66 | 712.95 | 2.9 | 4.32 Comm | 1048.7 | 1066.1 | 1081.2 | 22.8 | 6.48 Output | 0.010294 | 0.012512 | 0.014582 | 1.2 | 0.00 Modify | 1559.4 | 1678.8 | 2107.2 | 370.9 | 10.20 Other | | 483.1 | | | 2.94 Nlocal: 284.406 ave 302 max 258 min Histogram: 1 0 2 2 7 4 4 4 5 3 Nghost: 7155.53 ave 7198 max 7110 min Histogram: 2 4 0 5 4 4 4 5 1 3 Neighs: 153032 ave 166028 max 137427 min Histogram: 2 0 2 6 5 3 4 5 2 3 Total # of neighbors = 4897026 Ave neighs/atom = 538.0756 Ave special neighs/atom = 1.8929788 Neighbor list builds = 103450 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.2587397 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.002656158 estimated relative force accuracy = 7.9989409e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.87036e-05 8304 2 103.7 0.00326393 2768 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.12 | 13.27 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 257.27603 97162.661 1.249503 294.80367 40.711303 62.6585 0 0 21354.495 34384.991 -215.65161 -217136.28 -161293.42 5564.2688 Loop time of 8.37153e-06 on 32 procs for 0 steps with 9101 atoms 110.5% 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 | | 8.372e-06 | | |100.00 Nlocal: 284.406 ave 302 max 258 min Histogram: 1 0 2 2 7 4 4 4 5 3 Nghost: 7155.53 ave 7198 max 7110 min Histogram: 2 4 0 5 4 4 4 5 1 3 Neighs: 153032 ave 166028 max 137427 min Histogram: 2 0 2 6 5 3 4 5 2 3 Total # of neighbors = 4897026 Ave neighs/atom = 538.0756 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:53:28