#------------------------------------------------------------------------------- # 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 8.03468e-13 8304 2 103.7 7.7975e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.93 | 13.08 | 13.26 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 2733.3 92859.489 1.3074058 301.39993 50.557891 63.35363 0 0 22333.357 33658.496 -225.64505 -218001.62 -161895.86 5688.7697 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969991 2.90358e-05 8304 2 103.7 0.00326243 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970046 0.000139511 8304 2 103.7 0.0159558 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970017 4.99771e-05 8304 2 103.7 0.0057031 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969991 2.74964e-05 8304 2 103.7 0.00312103 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969992 2.59963e-05 8304 2 103.7 0.002922 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970009 2.75881e-05 8304 2 103.7 0.00312259 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969957 0.000128048 8304 2 103.7 0.0146502 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970009 2.66808e-05 8304 2 103.7 0.00303422 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969991 2.70341e-05 8304 2 103.7 0.00303699 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969991 2.7156e-05 8304 2 103.7 0.00307472 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969978 6.63393e-05 8304 2 103.7 0.00753095 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969988 3.66921e-05 8304 2 103.7 0.00413472 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970065 0.000197004 8304 2 103.7 0.022506 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969956 0.00013346 8304 2 103.7 0.0152784 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969942 0.000177723 8304 2 103.7 0.0203322 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970007 2.26569e-05 8304 2 103.7 0.00257568 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.96996 0.000120386 8304 2 103.7 0.013743 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97006 0.000181553 8304 2 103.7 0.0208243 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969993 2.39025e-05 8304 2 103.7 0.00268251 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969964 0.000110681 8304 2 103.7 0.0125829 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969971 8.80711e-05 8304 2 103.7 0.0100932 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970012 3.64678e-05 8304 2 103.7 0.00417016 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970039 0.00011599 8304 2 103.7 0.0132577 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970019 5.74221e-05 8304 2 103.7 0.00655685 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970035 0.000104317 8304 2 103.7 0.0119765 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970016 4.7598e-05 8304 2 103.7 0.00542658 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970027 8.26528e-05 8304 2 103.7 0.0094244 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.96993 0.000212507 8304 2 103.7 0.0243224 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970009 2.61239e-05 8304 2 103.7 0.0029567 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970004 1.22511e-05 8304 2 103.7 0.00139886 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970047 0.000139115 8304 2 103.7 0.0159007 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970032 9.59311e-05 8304 2 103.7 0.0110143 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969971 8.90143e-05 8304 2 103.7 0.0101533 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969979 6.29386e-05 8304 2 103.7 0.00719219 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970055 0.000163956 8304 2 103.7 0.0187486 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969971 9.10702e-05 8304 2 103.7 0.0103802 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970051 0.000152728 8304 2 103.7 0.0174646 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969984 4.99946e-05 8304 2 103.7 0.00566817 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969984 4.85316e-05 8304 2 103.7 0.00554066 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970027 8.14312e-05 8304 2 103.7 0.00934259 2768 2000000 2000000 490.73225 97527.211 1.2448324 296.82273 45.511168 69.586044 0 0 21560.481 34870.951 -214.84552 -218009.15 -161462.62 5602.3774 Loop time of 16511.3 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.466 ns/day, 2.293 hours/ns, 121.129 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 | 8486.9 | 8902 | 9393.5 | 227.2 | 53.91 Bond | 2.5566 | 5.6457 | 10.196 | 90.4 | 0.03 Kspace | 3186.5 | 3677.5 | 4096.3 | 355.4 | 22.27 Neigh | 711.42 | 711.93 | 712.34 | 1.0 | 4.31 Comm | 1060.3 | 1071.3 | 1081.3 | 17.0 | 6.49 Output | 0.0095277 | 0.011755 | 0.013843 | 1.2 | 0.00 Modify | 1572 | 1686.5 | 2090.3 | 364.0 | 10.21 Other | | 456.4 | | | 2.76 Nlocal: 284.406 ave 304 max 270 min Histogram: 2 8 2 6 2 4 2 1 3 2 Nghost: 7101.72 ave 7152 max 7040 min Histogram: 3 0 2 1 4 12 2 3 1 4 Neighs: 152389 ave 164457 max 142815 min Histogram: 4 2 4 5 5 5 2 0 2 3 Total # of neighbors = 4876446 Ave neighs/atom = 535.81431 Ave special neighs/atom = 1.8929788 Neighbor list builds = 103346 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) = 0.25864868 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0026694472 estimated relative force accuracy = 8.0389611e-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 0.970027 8.14312e-05 8304 2 103.7 0.00934259 2768 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.1 | 13.26 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 650.15306 97527.211 1.2448324 296.82273 45.511168 69.586044 0 0 21560.481 33919.643 -214.84552 -217057.84 -161462.62 5602.3774 Loop time of 8.7755e-06 on 32 procs for 0 steps with 9101 atoms 116.8% 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 | | 8.776e-06 | | |100.00 Nlocal: 284.406 ave 304 max 270 min Histogram: 2 8 2 6 2 4 2 1 3 2 Nghost: 7101.72 ave 7152 max 7040 min Histogram: 3 0 2 1 4 12 2 3 1 4 Neighs: 152389 ave 164457 max 142815 min Histogram: 4 2 4 5 5 5 2 0 2 3 Total # of neighbors = 4876446 Ave neighs/atom = 535.81431 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: 8:56:33