#------------------------------------------------------------------------------- # 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) = 0.24383926 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0037486683 estimated relative force accuracy = 1.1289003e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 1.07536e-12 6327 1 103.7 9.34506e-11 2109 Per MPI rank memory allocation (min/avg/max) = 11.96 | 14.7 | 18.29 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 -282.01652 199494.69 0.36118278 303.94829 54.268523 80.036408 0 0 6214.4646 72251.604 -42.647801 -119676.16 -41075.786 4061.6523 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.11984e-06 6327 1 103.7 9.32494e-05 2109 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.52824e-06 6327 1 103.7 0.000106103 2109 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.47005e-06 6327 1 103.7 0.000144854 2109 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.4251e-06 6327 1 103.7 0.00012464 2109 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.17629e-06 6327 1 103.7 9.71878e-05 2109 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.26536e-06 6327 1 103.7 0.000105256 2109 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.11373e-06 6327 1 103.7 0.000100148 2109 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.45348e-06 6327 1 103.7 0.000122969 2109 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.24133e-06 6327 1 103.7 9.42631e-05 2109 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.34821e-06 6327 1 103.7 0.000131116 2109 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.28575e-06 6327 1 103.7 0.000105992 2109 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.23081e-06 6327 1 103.7 9.73771e-05 2109 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.29761e-06 6327 1 103.7 8.98615e-05 2109 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.11441e-06 6327 1 103.7 9.01013e-05 2109 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.16024e-06 6327 1 103.7 0.000101711 2109 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.36185e-06 6327 1 103.7 0.000142095 2109 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.28255e-06 6327 1 103.7 0.000103467 2109 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.28122e-06 6327 1 103.7 9.76645e-05 2109 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.29535e-06 6327 1 103.7 0.000107235 2109 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.34664e-06 6327 1 103.7 9.91936e-05 2109 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.19889e-06 6327 1 103.7 0.000107349 2109 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.66547e-06 6327 1 103.7 0.000124866 2109 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.52286e-06 6327 1 103.7 0.000112539 2109 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.75092e-06 6327 1 103.7 9.41799e-05 2109 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.23436e-06 6327 1 103.7 9.51558e-05 2109 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.603e-06 6327 1 103.7 0.000104586 2109 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.87671e-06 6327 1 103.7 0.000128285 2109 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.21609e-06 6327 1 103.7 9.94305e-05 2109 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.30937e-06 6327 1 103.7 9.39489e-05 2109 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.21494e-06 6327 1 103.7 9.25808e-05 2109 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.38048e-06 6327 1 103.7 0.000107471 2109 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.68077e-06 6327 1 103.7 0.000102922 2109 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.33463e-06 6327 1 103.7 9.71105e-05 2109 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.25909e-06 6327 1 103.7 0.000116977 2109 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.31459e-06 6327 1 103.7 0.000103129 2109 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.29102e-06 6327 1 103.7 0.000104397 2109 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.23274e-06 6327 1 103.7 9.12009e-05 2109 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.32871e-06 6327 1 103.7 9.12531e-05 2109 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.18346e-06 6327 1 103.7 0.000117879 2109 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.52421e-06 6327 1 103.7 0.000121572 2109 2000000 2000000 -183.29492 199494.69 0.36118278 296.67502 62.149629 80.071213 0 0 6086.4027 72420.723 -42.647801 -119687.17 -41037.825 3964.4598 Loop time of 74354.5 on 8 procs for 2000000 steps with 6593 atoms Performance: 2.324 ns/day, 10.327 hours/ns, 26.898 timesteps/s 97.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3625 | 22635 | 60816 |16309.2 | 30.44 Bond | 1.7071 | 11.889 | 38.648 | 369.4 | 0.02 Kspace | 8343.2 | 46590 | 69277 |11394.7 | 62.66 Neigh | 3467.2 | 3476.6 | 3490.1 | 15.5 | 4.68 Comm | 212.77 | 407.94 | 598.26 | 898.1 | 0.55 Output | 0.032648 | 0.034802 | 0.036169 | 0.6 | 0.00 Modify | 1037.5 | 1162.3 | 1287 | 348.3 | 1.56 Other | | 70.86 | | | 0.10 Nlocal: 824.125 ave 1935 max 0 min Histogram: 4 0 0 0 0 0 0 2 0 2 Nghost: 5494.62 ave 10567 max 314 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 411536 ave 1.08667e+06 max 0 min Histogram: 4 0 0 0 0 2 0 0 0 2 Total # of neighbors = 3292290 Ave neighs/atom = 499.36144 Ave special neighs/atom = 2.0345821 Neighbor list builds = 99432 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) = 0.24383926 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0037486683 estimated relative force accuracy = 1.1289003e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.52421e-06 6327 1 103.7 0.000121572 2109 Per MPI rank memory allocation (min/avg/max) = 11.98 | 14.71 | 18.28 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 -183.04648 199494.69 0.36118278 296.67502 62.149629 80.071213 0 0 6086.4027 72420.723 -42.647801 -119687.17 -41037.825 3964.4598 Loop time of 3.952e-06 on 8 procs for 0 steps with 6593 atoms 123.4% 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 | | 3.952e-06 | | |100.00 Nlocal: 824.125 ave 1935 max 0 min Histogram: 4 0 0 0 0 0 0 2 0 2 Nghost: 5494.62 ave 10567 max 314 min Histogram: 2 2 0 0 0 0 0 0 2 2 Neighs: 411536 ave 1.08667e+06 max 0 min Histogram: 4 0 0 0 0 2 0 0 0 2 Total # of neighbors = 3292290 Ave neighs/atom = 499.36144 Ave special neighs/atom = 2.0345821 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 32:05:49