#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2812 = # 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 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 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996905 0.675589 8436 2 96.5543 51.378 2812 Per MPI rank memory allocation (min/avg/max) = 13.92 | 14 | 14.18 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 13860.07 93962.523 1.2789064 429.73544 31.372196 227.67343 0 0 23065.331 56541.657 -220.49494 -205249.27 -125383.23 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23681e-06 8436 2 103.7 9.45588e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.47139e-06 8436 2 103.7 9.63494e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.3037e-06 8436 2 103.7 0.000114865 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.17592e-06 8436 2 103.7 9.15414e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.07789e-06 8436 2 103.7 0.000114361 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32519e-06 8436 2 103.7 9.26914e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.25061e-06 8436 2 103.7 0.000101614 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.42088e-06 8436 2 103.7 0.000101698 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.3622e-06 8436 2 103.7 9.69387e-05 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.14841e-06 8436 2 103.7 0.000106732 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.46947e-06 8436 2 103.7 0.000112177 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.35559e-06 8436 2 103.7 0.000107811 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.16211e-06 8436 2 103.7 9.29976e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.71988e-06 8436 2 103.7 0.00013317 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.80492e-06 8436 2 103.7 0.000117965 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18892e-06 8436 2 103.7 0.000120604 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.23052e-06 8436 2 103.7 0.000102803 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10633e-06 8436 2 103.7 9.0474e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.45935e-06 8436 2 103.7 0.00010151 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.44151e-06 8436 2 103.7 9.78846e-05 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.30622e-06 8436 2 103.7 9.59635e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.75604e-06 8436 2 103.7 0.000115049 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.20215e-06 8436 2 103.7 9.37014e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.44145e-06 8436 2 103.7 0.000105184 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.22382e-06 8436 2 103.7 0.000100607 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.22149e-06 8436 2 103.7 0.000105778 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.70455e-06 8436 2 103.7 0.000108728 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.33359e-06 8436 2 103.7 9.65547e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12638e-06 8436 2 103.7 9.64328e-05 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.27966e-06 8436 2 103.7 9.47091e-05 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.74021e-06 8436 2 103.7 0.000111381 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.46953e-06 8436 2 103.7 9.82169e-05 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.12522e-06 8436 2 103.7 9.44729e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.24555e-06 8436 2 103.7 9.02555e-05 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.47976e-06 8436 2 103.7 9.77698e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10099e-06 8436 2 103.7 9.36148e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.37782e-06 8436 2 103.7 0.000102426 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.4799e-06 8436 2 103.7 0.000112941 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.4349e-06 8436 2 103.7 0.000110706 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18405e-06 8436 2 103.7 0.000105313 2812 2000000 2000000 1878.8926 93962.523 1.2789064 296.94898 45.728986 57.317938 0 0 19524.715 46197.537 -220.49494 -206929.03 -141103.73 5642.8218 Loop time of 24336 on 16 procs for 2000000 steps with 9188 atoms Performance: 7.101 ns/day, 3.380 hours/ns, 82.183 timesteps/s 99.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16489 | 16888 | 17389 | 197.6 | 69.40 Bond | 3.7576 | 8.8812 | 11.649 | 70.2 | 0.04 Kspace | 4177 | 4679.4 | 5086.6 | 376.7 | 19.23 Neigh | 976.43 | 976.83 | 977.3 | 0.8 | 4.01 Comm | 776.68 | 786.51 | 795.46 | 22.0 | 3.23 Output | 0.016342 | 0.018074 | 0.019634 | 0.8 | 0.00 Modify | 934.07 | 940.47 | 946.72 | 15.0 | 3.86 Other | | 55.82 | | | 0.23 Nlocal: 574.25 ave 590 max 543 min Histogram: 2 0 1 0 1 1 1 3 2 5 Nghost: 9021.12 ave 9081 max 8950 min Histogram: 2 0 2 0 3 1 2 3 1 2 Neighs: 322446 ave 336670 max 300087 min Histogram: 1 1 1 0 3 0 2 4 1 3 Total # of neighbors = 5159132 Ave neighs/atom = 561.50762 Ave special neighs/atom = 1.9037875 Neighbor list builds = 98863 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18405e-06 8436 2 103.7 0.000105313 2812 Per MPI rank memory allocation (min/avg/max) = 13.99 | 14.13 | 14.18 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 1879.7601 93962.523 1.2789064 296.94898 45.728986 57.317938 0 0 19524.715 46197.537 -220.49494 -206929.03 -141103.73 5642.8218 Loop time of 5.59913e-06 on 16 procs for 0 steps with 9188 atoms 117.2% CPU use with 16 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 | | 5.599e-06 | | |100.00 Nlocal: 574.25 ave 590 max 543 min Histogram: 2 0 1 0 1 1 1 3 2 5 Nghost: 9021.12 ave 9081 max 8950 min Histogram: 2 0 2 0 3 1 2 3 1 2 Neighs: 322446 ave 336670 max 300087 min Histogram: 1 1 1 0 3 0 2 4 1 3 Total # of neighbors = 5159132 Ave neighs/atom = 561.50762 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out