#------------------------------------------------------------------------------- # Stage 2.5: 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 2768 = # 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 2.5_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_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension 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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.19709e-13 8304 2 103.7 8.15561e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.74 | 13.05 | 13.13 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 2715.144 92859.489 1.3074058 299.63314 37.159931 71.164264 0 0 22401.935 86648.068 -448.40969 -271003.07 -161844.74 5655.4224 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.11427e-06 8304 2 103.7 8.60138e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19058e-06 8304 2 103.7 9.23745e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36099e-06 8304 2 103.7 9.18311e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.24525e-06 8304 2 103.7 0.000105239 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.12548e-06 8304 2 103.7 9.33092e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.6613e-06 8304 2 103.7 9.8573e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.32937e-06 8304 2 103.7 9.89873e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.13227e-06 8304 2 103.7 9.33228e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.39879e-06 8304 2 103.7 0.00010446 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.43501e-06 8304 2 103.7 0.00010807 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2866e-06 8304 2 103.7 9.64275e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.55092e-06 8304 2 103.7 0.000116266 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.36856e-06 8304 2 103.7 0.000108302 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.35912e-06 8304 2 103.7 8.89319e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26567e-06 8304 2 103.7 9.2532e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.28128e-06 8304 2 103.7 9.95759e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.27976e-06 8304 2 103.7 0.000101805 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.37702e-06 8304 2 103.7 9.87695e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.18798e-06 8304 2 103.7 9.39447e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.05149e-06 8304 2 103.7 8.85947e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.49956e-06 8304 2 103.7 0.000115792 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.37221e-06 8304 2 103.7 0.000113001 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.24417e-06 8304 2 103.7 9.79894e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.24647e-06 8304 2 103.7 9.5643e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.21436e-06 8304 2 103.7 0.00011328 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.31727e-06 8304 2 103.7 0.000104241 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.37088e-06 8304 2 103.7 0.000105118 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29952e-06 8304 2 103.7 0.000104895 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.16398e-06 8304 2 103.7 8.76656e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.71199e-06 8304 2 103.7 9.24763e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.15242e-06 8304 2 103.7 0.000103244 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.42793e-06 8304 2 103.7 0.000105091 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.41648e-06 8304 2 103.7 0.000125779 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.23087e-06 8304 2 103.7 9.28158e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.36303e-06 8304 2 103.7 9.60141e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.39645e-06 8304 2 103.7 9.76163e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.41049e-06 8304 2 103.7 0.000111411 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.21194e-06 8304 2 103.7 0.000116923 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.53306e-06 8304 2 103.7 9.96606e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.24574e-06 8304 2 103.7 9.64539e-05 2768 2000000 2000000 2704.2011 92859.489 1.3074058 295.75204 43.700435 68.861732 0 0 22338.911 86753.138 -448.40969 -270980.76 -161776.15 5582.1687 Loop time of 9611.93 on 32 procs for 2000000 steps with 9101 atoms Performance: 17.978 ns/day, 1.335 hours/ns, 208.075 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4327.7 | 4666.6 | 4942.3 | 207.5 | 48.55 Bond | 2.0143 | 5.0732 | 10.475 | 97.9 | 0.05 Kspace | 3440.8 | 3723 | 4065.3 | 232.6 | 38.73 Neigh | 305.93 | 306.59 | 307.23 | 1.9 | 3.19 Comm | 285.38 | 319.33 | 338.21 | 74.8 | 3.32 Output | 0.0096022 | 0.01188 | 0.013991 | 1.2 | 0.00 Modify | 544.03 | 556.47 | 574.3 | 34.9 | 5.79 Other | | 34.88 | | | 0.36 Nlocal: 284.406 ave 309 max 262 min Histogram: 1 2 3 4 6 9 2 2 2 1 Nghost: 4924.03 ave 5041 max 4776 min Histogram: 1 3 2 1 4 7 3 5 4 2 Neighs: 88654.1 ave 98638 max 78576 min Histogram: 1 1 3 5 9 5 3 2 1 2 Total # of neighbors = 2836932 Ave neighs/atom = 311.71651 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98304 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) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.24574e-06 8304 2 103.7 9.64539e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.74 | 13.05 | 13.13 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 2705.2067 92859.489 1.3074058 295.75204 43.700435 68.861732 0 0 22338.911 86753.138 -448.40969 -270980.76 -161776.15 5582.1687 Loop time of 6.78287e-06 on 32 procs for 0 steps with 9101 atoms 120.7% 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 | | 6.783e-06 | | |100.00 Nlocal: 284.406 ave 309 max 262 min Histogram: 1 2 3 4 6 9 2 2 2 1 Nghost: 4924.03 ave 5041 max 4776 min Histogram: 1 3 2 1 4 7 3 5 4 2 Neighs: 88654.1 ave 98638 max 78576 min Histogram: 1 1 3 5 9 5 3 2 1 2 Total # of neighbors = 2836932 Ave neighs/atom = 311.71651 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 9:20:40