#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1943 = # of frozen angles find clusters CPU = 0.000 seconds 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 fix 1 movable npt temp 298.2 298.2 100 iso 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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25570193 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0027808674 estimated relative force accuracy = 8.3744995e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999617 0.0497013 5829 1 97.8137 10.5457 1943 Per MPI rank memory allocation (min/avg/max) = 11.96 | 11.97 | 11.98 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 2930.1943 65736.674 1.1942357 432.78829 0 0 0 0 12252.647 42076.819 -133.90447 -122303.89 -67974.428 5553.707 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969973 1.17595e-06 5829 1 103.7 0.000102753 1943 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969993 1.87294e-06 5829 1 103.7 0.000137371 1943 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969987 1.28199e-06 5829 1 103.7 0.000103479 1943 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970061 1.18424e-06 5829 1 103.7 9.62058e-05 1943 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969991 1.25931e-06 5829 1 103.7 0.00010323 1943 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970043 1.46472e-06 5829 1 103.7 0.000107072 1943 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969983 1.1618e-06 5829 1 103.7 9.26081e-05 1943 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970046 1.61544e-06 5829 1 103.7 0.000125362 1943 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969937 1.33227e-06 5829 1 103.7 0.000130213 1943 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970085 1.64969e-06 5829 1 103.7 0.000114293 1943 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969892 1.14343e-06 5829 1 103.7 8.66067e-05 1943 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969908 1.42551e-06 5829 1 103.7 0.00012386 1943 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970029 1.16243e-06 5829 1 103.7 9.08296e-05 1943 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969886 1.73638e-06 5829 1 103.7 0.000171095 1943 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970072 1.97373e-06 5829 1 103.7 0.000151982 1943 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969987 1.19587e-06 5829 1 103.7 9.65349e-05 1943 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970101 1.23129e-06 5829 1 103.7 9.30075e-05 1943 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97004 1.13969e-06 5829 1 103.7 9.79808e-05 1943 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969931 1.16899e-06 5829 1 103.7 9.0457e-05 1943 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.9699 1.33599e-06 5829 1 103.7 0.000112446 1943 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970018 1.24912e-06 5829 1 103.7 0.000100197 1943 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969966 1.33492e-06 5829 1 103.7 0.00012003 1943 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97002 1.81438e-06 5829 1 103.7 0.000135677 1943 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970028 1.71067e-06 5829 1 103.7 0.000121249 1943 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970048 1.03482e-06 5829 1 103.7 9.7343e-05 1943 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970057 1.52402e-06 5829 1 103.7 0.000121 1943 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970033 2.4031e-06 5829 1 103.7 0.000169907 1943 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970081 1.68355e-06 5829 1 103.7 0.000105397 1943 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970052 1.5911e-06 5829 1 103.7 0.000128869 1943 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969902 1.16463e-06 5829 1 103.7 0.000103454 1943 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97002 1.72194e-06 5829 1 103.7 0.000113531 1943 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970008 1.0192e-06 5829 1 103.7 8.94665e-05 1943 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.96992 1.1929e-06 5829 1 103.7 0.000107897 1943 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.96998 1.28633e-06 5829 1 103.7 9.45995e-05 1943 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970043 1.12848e-06 5829 1 103.7 9.2718e-05 1943 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969996 1.72115e-06 5829 1 103.7 0.000113379 1943 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969999 1.37289e-06 5829 1 103.7 0.000131017 1943 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970112 1.67407e-06 5829 1 103.7 0.000124005 1943 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970045 1.40319e-06 5829 1 103.7 9.81676e-05 1943 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970086 1.57778e-06 5829 1 103.7 0.000114017 1943 2000000 2000000 525.26687 67248.857 1.1673817 297.48162 0 0 0 0 8550.3449 54607.45 -130.89344 -122256.09 -59098.298 3817.3993 Loop time of 51695.8 on 8 procs for 2000000 steps with 6249 atoms Performance: 3.343 ns/day, 7.180 hours/ns, 38.688 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33484 | 36364 | 38994 |1053.5 | 70.34 Bond | 6.8695 | 7.7189 | 9.015 | 22.0 | 0.01 Kspace | 6728.1 | 9359.7 | 12246 |2074.3 | 18.11 Neigh | 2206.9 | 2208.5 | 2210.1 | 3.0 | 4.27 Comm | 709.77 | 719.7 | 731.57 | 34.9 | 1.39 Output | 0.02464 | 0.02587 | 0.026844 | 0.5 | 0.00 Modify | 2349.6 | 2720.7 | 2898.1 | 380.6 | 5.26 Other | | 315.6 | | | 0.61 Nlocal: 781.125 ave 797 max 765 min Histogram: 2 0 0 1 1 2 0 0 0 2 Nghost: 9731.25 ave 9782 max 9680 min Histogram: 1 0 0 1 1 3 1 0 0 1 Neighs: 416832 ave 443704 max 386842 min Histogram: 1 1 0 0 2 1 0 1 1 1 Total # of neighbors = 3334654 Ave neighs/atom = 533.63002 Ave special neighs/atom = 1.8655785 Neighbor list builds = 102006 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) = 0.25524483 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0028442241 estimated relative force accuracy = 8.5652963e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970086 1.57778e-06 5829 1 103.7 0.000114017 1943 Per MPI rank memory allocation (min/avg/max) = 11.96 | 11.97 | 11.98 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 1033.1296 67248.857 1.1673817 297.48162 0 0 0 0 8550.3449 54390.002 -130.89344 -122038.64 -59098.296 3817.3993 Loop time of 4.27225e-06 on 8 procs for 0 steps with 6249 atoms 122.9% CPU use with 8 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 | | 4.272e-06 | | |100.00 Nlocal: 781.125 ave 797 max 765 min Histogram: 2 0 0 1 1 2 0 0 0 2 Nghost: 9731.25 ave 9782 max 9680 min Histogram: 1 0 0 1 1 3 1 0 0 1 Neighs: 416832 ave 443704 max 386842 min Histogram: 1 1 0 0 2 1 0 1 1 1 Total # of neighbors = 3334654 Ave neighs/atom = 533.63002 Ave special neighs/atom = 1.8655785 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:22:27