#------------------------------------------------------------------------------- # 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 4018 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (49.10328 49.10328 55.645058) 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 (49.10328 49.10328 55.645058) 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 = 0.0216 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32585793 grid = 48 48 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0030893499 estimated relative force accuracy = 9.3034856e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11780 4608 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 9 9 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 0.97 9.03944e-13 12054 2 103.7 8.1684e-11 4018 Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.52 | 13.63 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 1983.1364 134167.59 1.2789064 299.26712 52.800425 100.30325 0 0 27778.14 146303.24 -626.09682 -375554.97 -201320.49 8123.9763 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970014 4.28136e-05 12054 2 103.7 0.00492638 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969964 0.000108025 12054 2 103.7 0.0123423 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970017 5.21127e-05 12054 2 103.7 0.00593878 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969999 3.78967e-06 12054 2 103.7 0.000402804 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969945 0.000164596 12054 2 103.7 0.0188067 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970028 8.41247e-05 12054 2 103.7 0.0096514 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970037 0.000109956 12054 2 103.7 0.0125585 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970032 9.66601e-05 12054 2 103.7 0.0110335 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969977 7.06997e-05 12054 2 103.7 0.00805266 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969982 5.66058e-05 12054 2 103.7 0.00644797 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969978 6.64449e-05 12054 2 103.7 0.00757533 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969957 0.000127896 12054 2 103.7 0.0145558 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969983 5.13426e-05 12054 2 103.7 0.00584147 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969963 0.000111804 12054 2 103.7 0.0127399 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969941 0.000176721 12054 2 103.7 0.020229 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970047 0.000140979 12054 2 103.7 0.0161553 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969995 1.81514e-05 12054 2 103.7 0.00202684 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969972 8.58007e-05 12054 2 103.7 0.00979258 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969977 7.14075e-05 12054 2 103.7 0.00812521 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969969 9.48871e-05 12054 2 103.7 0.0108063 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970021 6.29546e-05 12054 2 103.7 0.00719272 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970044 0.00012998 12054 2 103.7 0.0148886 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969979 6.30971e-05 12054 2 103.7 0.00715024 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969998 7.75473e-06 12054 2 103.7 0.000847641 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970002 7.42279e-06 12054 2 103.7 0.000824653 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970028 8.3928e-05 12054 2 103.7 0.00958414 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970006 1.7184e-05 12054 2 103.7 0.00192367 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.96998 6.17451e-05 12054 2 103.7 0.00701533 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969957 0.000131277 12054 2 103.7 0.0149849 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970002 6.82475e-06 12054 2 103.7 0.000760477 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969995 1.64773e-05 12054 2 103.7 0.00182993 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970012 3.6457e-05 12054 2 103.7 0.004172 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970023 6.86469e-05 12054 2 103.7 0.00784858 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969944 0.000169725 12054 2 103.7 0.0193939 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97002 5.93913e-05 12054 2 103.7 0.0068207 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969999 5.44513e-06 12054 2 103.7 0.000559241 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969972 8.39226e-05 12054 2 103.7 0.0095945 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969976 7.32963e-05 12054 2 103.7 0.00835666 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969999 4.1554e-06 12054 2 103.7 0.000426097 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969999 5.62649e-06 12054 2 103.7 0.000613478 4018 2000000 2000000 -387.81315 139896.95 1.2265299 299.53206 64.869483 89.521213 0 0 26455.291 147920.71 -600.45556 -375465.61 -200935.22 8131.1682 Loop time of 17492.4 on 32 procs for 2000000 steps with 13126 atoms Performance: 9.879 ns/day, 2.430 hours/ns, 114.335 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 | 6608.2 | 6815.3 | 7148.2 | 158.9 | 38.96 Bond | 3.4229 | 7.1888 | 12.952 | 82.0 | 0.04 Kspace | 5953.6 | 6296.4 | 6503.6 | 169.2 | 36.00 Neigh | 621.58 | 622.97 | 624.42 | 3.4 | 3.56 Comm | 860.65 | 889.84 | 907.68 | 50.1 | 5.09 Output | 0.012386 | 0.015181 | 0.017826 | 1.3 | 0.00 Modify | 1929.4 | 2476.4 | 2716.9 | 632.7 | 14.16 Other | | 384.3 | | | 2.20 Nlocal: 410.188 ave 434 max 384 min Histogram: 2 0 4 4 6 3 3 5 2 3 Nghost: 5515.91 ave 5570 max 5446 min Histogram: 2 2 3 1 3 7 4 2 6 2 Neighs: 122446 ave 133062 max 113814 min Histogram: 1 3 5 5 6 3 5 2 1 1 Total # of neighbors = 3918288 Ave neighs/atom = 298.51348 Ave special neighs/atom = 1.9037026 Neighbor list builds = 106888 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) = 0.32484445 grid = 48 48 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032116641 estimated relative force accuracy = 9.671831e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11780 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969999 5.62649e-06 12054 2 103.7 0.000613478 4018 Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.54 | 13.63 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 -396.33562 139896.95 1.2265299 299.53206 64.869483 89.521213 0 0 26455.291 146774.32 -600.45556 -374319.22 -200935.22 8131.1682 Loop time of 7.41916e-06 on 32 procs for 0 steps with 13126 atoms 123.0% 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 | | 7.419e-06 | | |100.00 Nlocal: 410.188 ave 434 max 384 min Histogram: 2 0 4 4 6 3 3 5 2 3 Nghost: 5515.91 ave 5570 max 5446 min Histogram: 2 2 3 1 3 7 4 2 6 2 Neighs: 122446 ave 133062 max 113814 min Histogram: 1 3 5 5 6 3 5 2 1 1 Total # of neighbors = 3918288 Ave neighs/atom = 298.51348 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:58:11