#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24997142 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035792785 estimated relative force accuracy = 1.0778891e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.20868e-13 8304 2 103.7 7.51896e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.91 | 14.14 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 -441.72913 194193.27 0.62517633 297.54375 40.821029 46.122139 0 0 20808.634 28503.523 -107.89913 -209815.1 -160416 5615.9863 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.47945e-06 8304 2 103.7 0.000116139 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.3926e-06 8304 2 103.7 0.000127387 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.20025e-06 8304 2 103.7 9.43105e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.12514e-06 8304 2 103.7 8.87305e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.35511e-06 8304 2 103.7 0.000106959 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.57051e-06 8304 2 103.7 0.000137789 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.58547e-06 8304 2 103.7 0.000101883 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.23374e-06 8304 2 103.7 9.77991e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.131e-06 8304 2 103.7 0.000102487 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15416e-06 8304 2 103.7 9.45802e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33821e-06 8304 2 103.7 0.000108086 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.36354e-06 8304 2 103.7 0.000106696 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25335e-06 8304 2 103.7 9.9362e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.18388e-06 8304 2 103.7 9.8811e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.32432e-06 8304 2 103.7 0.000114972 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16333e-06 8304 2 103.7 9.35752e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.60172e-06 8304 2 103.7 0.000109803 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.33084e-06 8304 2 103.7 0.000102537 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.40839e-06 8304 2 103.7 0.000100616 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.2893e-06 8304 2 103.7 8.98252e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.54359e-06 8304 2 103.7 0.000111909 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.32162e-06 8304 2 103.7 0.000107736 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22201e-06 8304 2 103.7 9.75929e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.13261e-06 8304 2 103.7 9.46592e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.16075e-06 8304 2 103.7 9.14451e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.45589e-06 8304 2 103.7 0.000102711 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.39056e-06 8304 2 103.7 0.00010027 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28138e-06 8304 2 103.7 0.000101004 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.1726e-06 8304 2 103.7 0.00011815 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26944e-06 8304 2 103.7 0.00010781 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.4395e-06 8304 2 103.7 9.62618e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.25149e-06 8304 2 103.7 9.34601e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.17091e-06 8304 2 103.7 9.94349e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.7789e-06 8304 2 103.7 0.000124878 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.82328e-06 8304 2 103.7 0.000177918 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10367e-06 8304 2 103.7 9.69287e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.30736e-06 8304 2 103.7 9.71656e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.40617e-06 8304 2 103.7 0.000104801 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.49932e-06 8304 2 103.7 9.18118e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.33371e-06 8304 2 103.7 9.89108e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.33751e-06 8304 2 103.7 0.000104172 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.31261e-06 8304 2 103.7 0.000119816 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.53127e-06 8304 2 103.7 0.000103447 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.22255e-06 8304 2 103.7 0.000109341 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.35991e-06 8304 2 103.7 0.000119766 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.34297e-06 8304 2 103.7 9.97327e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.23048e-06 8304 2 103.7 0.000100242 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.20303e-06 8304 2 103.7 9.60501e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.79614e-06 8304 2 103.7 0.000148773 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.34808e-06 8304 2 103.7 9.39437e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.20926e-06 8304 2 103.7 0.000101359 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.74164e-06 8304 2 103.7 0.000126276 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.10564e-06 8304 2 103.7 0.000104311 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.14619e-06 8304 2 103.7 0.000100996 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.4643e-06 8304 2 103.7 9.54552e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.10676e-06 8304 2 103.7 9.03033e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.1935e-06 8304 2 103.7 9.58477e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.49038e-06 8304 2 103.7 0.000111692 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.21009e-06 8304 2 103.7 0.000102881 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.09435e-06 8304 2 103.7 9.19667e-05 2768 3000000 3000000 -150.57575 194193.27 0.62517633 296.88399 48.441178 75.322497 0 0 21168.416 27979.565 -107.89913 -209816.27 -160544.53 5603.5336 Loop time of 34120.1 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.597 ns/day, 3.159 hours/ns, 87.925 timesteps/s 98.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.784 | 10939 | 24305 |10196.1 | 32.06 Bond | 2.5623 | 7.152 | 16.434 | 169.9 | 0.02 Kspace | 5922.5 | 19344 | 30399 |7703.2 | 56.69 Neigh | 1711.4 | 1719.2 | 1730.8 | 13.9 | 5.04 Comm | 319.41 | 665.57 | 880.25 | 801.5 | 1.95 Output | 0.013985 | 0.016073 | 0.017868 | 0.9 | 0.00 Modify | 1208.2 | 1364.2 | 1589 | 418.6 | 4.00 Other | | 81.51 | | | 0.24 Nlocal: 284.406 ave 578 max 0 min Histogram: 14 2 0 0 0 0 0 0 3 13 Nghost: 4527.88 ave 8651 max 365 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 133250 ave 306930 max 0 min Histogram: 16 0 0 0 0 1 3 0 4 8 Total # of neighbors = 4264002 Ave neighs/atom = 468.52016 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149968 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24997142 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035792785 estimated relative force accuracy = 1.0778891e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.09435e-06 8304 2 103.7 9.19667e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.91 | 14.14 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 3000000 3000000 -150.14425 194193.27 0.62517633 296.88399 48.441178 75.322497 0 0 21168.416 27979.565 -107.89913 -209816.27 -160544.53 5603.5336 Loop time of 7.51356e-06 on 32 procs for 0 steps with 9101 atoms 111.0% 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 | | 7.514e-06 | | |100.00 Nlocal: 284.406 ave 578 max 0 min Histogram: 14 2 0 0 0 0 0 0 3 13 Nghost: 4527.88 ave 8651 max 365 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 133250 ave 306930 max 0 min Histogram: 16 0 0 0 0 1 3 0 4 8 Total # of neighbors = 4264002 Ave neighs/atom = 468.52016 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: 25:26:50