#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 2109 = # of frozen angles find clusters CPU = 0.001 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension 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_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension 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) = 0.24386748 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0036780491 estimated relative force accuracy = 1.1076336e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 7.79821e-13 6327 1 103.7 8.48956e-11 2109 Per MPI rank memory allocation (min/avg/max) = 9.396 | 11.96 | 14.26 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 -92.402763 199228.71 0.34683261 297.95317 0 0 0 0 8014.1016 63790.839 -39.419859 -116167.02 -44362.081 3846.5421 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.08686e-06 6327 1 103.7 9.03448e-05 2109 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.25457e-06 6327 1 103.7 0.00010059 2109 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.46293e-06 6327 1 103.7 0.000115017 2109 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.353e-06 6327 1 103.7 0.000109401 2109 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.44503e-06 6327 1 103.7 0.000115656 2109 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.36108e-06 6327 1 103.7 0.000102392 2109 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.24512e-06 6327 1 103.7 9.1294e-05 2109 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.25387e-06 6327 1 103.7 9.31765e-05 2109 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.32966e-06 6327 1 103.7 9.35662e-05 2109 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.4471e-06 6327 1 103.7 0.000114044 2109 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.42661e-06 6327 1 103.7 0.000117806 2109 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.21079e-06 6327 1 103.7 9.8562e-05 2109 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.5056e-06 6327 1 103.7 9.13163e-05 2109 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.66309e-06 6327 1 103.7 0.000140246 2109 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.19628e-06 6327 1 103.7 0.00010751 2109 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.12103e-06 6327 1 103.7 9.61006e-05 2109 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.10535e-06 6327 1 103.7 9.07409e-05 2109 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.32562e-06 6327 1 103.7 9.13394e-05 2109 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.22692e-06 6327 1 103.7 9.44726e-05 2109 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.19193e-06 6327 1 103.7 0.000101938 2109 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.41107e-06 6327 1 103.7 9.91904e-05 2109 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.41757e-06 6327 1 103.7 8.96432e-05 2109 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.06765e-06 6327 1 103.7 8.72403e-05 2109 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.18518e-06 6327 1 103.7 0.000108907 2109 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.45548e-06 6327 1 103.7 0.000126792 2109 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.99292e-06 6327 1 103.7 0.000120002 2109 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.75776e-06 6327 1 103.7 0.000162043 2109 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.42954e-06 6327 1 103.7 9.748e-05 2109 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.24318e-06 6327 1 103.7 9.44301e-05 2109 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.19903e-06 6327 1 103.7 9.88689e-05 2109 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.14543e-06 6327 1 103.7 0.000104821 2109 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.197e-06 6327 1 103.7 9.089e-05 2109 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.23615e-06 6327 1 103.7 9.28824e-05 2109 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.20948e-06 6327 1 103.7 0.000119646 2109 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.13073e-06 6327 1 103.7 9.39163e-05 2109 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.2651e-06 6327 1 103.7 0.000100434 2109 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.20573e-06 6327 1 103.7 9.08286e-05 2109 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.36274e-06 6327 1 103.7 0.000104208 2109 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.19794e-06 6327 1 103.7 0.000132255 2109 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.20218e-06 6327 1 103.7 0.000103481 2109 2000000 2000000 -173.35689 199228.71 0.34683261 291.85255 0 0 0 0 7961.9965 63848.791 -39.419859 -116169.29 -44358.5 3767.7838 Loop time of 52160.2 on 8 procs for 2000000 steps with 6441 atoms Performance: 3.313 ns/day, 7.244 hours/ns, 38.343 timesteps/s 98.2% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8479 | 19626 | 39893 |14006.7 | 37.63 Bond | 1.6728 | 2.4679 | 3.0994 | 36.3 | 0.00 Kspace | 8397.2 | 28724 | 48448 |11609.3 | 55.07 Neigh | 2270.7 | 2281.3 | 2298.3 | 21.7 | 4.37 Comm | 142.48 | 383.74 | 582.22 | 932.1 | 0.74 Output | 0.028985 | 0.031238 | 0.032873 | 0.7 | 0.00 Modify | 955.28 | 1080.3 | 1196.6 | 339.8 | 2.07 Other | | 62.71 | | | 0.12 Nlocal: 805.125 ave 1801 max 0 min Histogram: 4 0 0 0 0 0 0 0 2 2 Nghost: 5283.25 ave 9884 max 585 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 388868 ave 788941 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 4 Total # of neighbors = 3110947 Ave neighs/atom = 482.99131 Ave special neighs/atom = 1.9646018 Neighbor list builds = 99011 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) = 0.24386748 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0036780491 estimated relative force accuracy = 1.1076336e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.20218e-06 6327 1 103.7 0.000103481 2109 Per MPI rank memory allocation (min/avg/max) = 9.372 | 11.85 | 14.26 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 -173.08591 199228.71 0.34683261 291.85255 0 0 0 0 7961.9965 63848.791 -39.419859 -116169.29 -44358.5 3767.7838 Loop time of 3.04675e-06 on 8 procs for 0 steps with 6441 atoms 123.1% 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 | | 3.047e-06 | | |100.00 Nlocal: 805.125 ave 1801 max 0 min Histogram: 4 0 0 0 0 0 0 0 2 2 Nghost: 5283.25 ave 9884 max 585 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 388868 ave 788941 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 4 Total # of neighbors = 3110947 Ave neighs/atom = 482.99131 Ave special neighs/atom = 1.9646018 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 20:58:28