#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00065 0.109283 8304 2 97.7022 8.98285 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.1 | 14.71 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 -3652.8901 140505.98 1.42352 406.71708 6.4052887 22.552087 0 0 36250.537 -67024.873 -315.99625 -291765.78 -322511.16 9247.778 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.2318e-06 8304 2 103.7 9.15711e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26131e-06 8304 2 103.7 9.75003e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.55714e-06 8304 2 103.7 0.000109884 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.09386e-06 8304 2 103.7 9.86141e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.32767e-06 8304 2 103.7 0.000104702 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.21462e-06 8304 2 103.7 9.58319e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.03672e-06 8304 2 103.7 9.77447e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.15255e-06 8304 2 103.7 9.86204e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.18558e-06 8304 2 103.7 0.000100101 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.1849e-06 8304 2 103.7 8.8541e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.35808e-06 8304 2 103.7 9.33664e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.09351e-06 8304 2 103.7 9.16418e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.39315e-06 8304 2 103.7 9.18675e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.16763e-06 8304 2 103.7 9.44269e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.82828e-06 8304 2 103.7 0.00010902 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16123e-06 8304 2 103.7 0.000101678 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.55408e-06 8304 2 103.7 0.000111472 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.28346e-06 8304 2 103.7 0.000100841 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.39025e-06 8304 2 103.7 9.21469e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.67339e-06 8304 2 103.7 0.000132835 2768 1000000 1000000 114.20098 140505.98 1.42352 299.67324 56.758096 63.551762 0 0 34600.501 -51036.702 -315.99625 -291945.2 -308261.09 6813.8559 Loop time of 14251.4 on 16 procs for 1000000 steps with 10721 atoms Performance: 6.063 ns/day, 3.959 hours/ns, 70.169 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2264.8 | 8129.8 | 10834 |3713.5 | 57.05 Bond | 1.0726 | 3.6066 | 6.4892 | 93.8 | 0.03 Kspace | 2087.7 | 4797.5 | 10672 |4840.9 | 33.66 Neigh | 563.35 | 564.48 | 565.85 | 3.3 | 3.96 Comm | 264.28 | 314.93 | 339.19 | 161.3 | 2.21 Output | 0.016223 | 0.018183 | 0.019991 | 0.9 | 0.00 Modify | 399.44 | 418.32 | 461.82 | 122.4 | 2.94 Other | | 22.75 | | | 0.16 Nlocal: 670.062 ave 815 max 351 min Histogram: 4 0 0 0 0 0 0 0 4 8 Nghost: 8253.06 ave 9759 max 7010 min Histogram: 4 0 0 2 6 0 0 0 0 4 Neighs: 312619 ave 410014 max 88797 min Histogram: 4 0 0 0 0 0 0 2 1 9 Total # of neighbors = 5001908 Ave neighs/atom = 466.55237 Ave special neighs/atom = 1.6069397 Neighbor list builds = 49608 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25549962 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035283362 estimated relative force accuracy = 1.062548e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.67339e-06 8304 2 103.7 0.000132835 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 14.19 | 14.79 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 1000000 1000000 114.91738 140505.98 1.42352 299.67324 56.758096 63.551762 0 0 34600.501 -51036.702 -315.99625 -291945.2 -308261.09 6813.8559 Loop time of 3.9585e-06 on 16 procs for 0 steps with 10721 atoms 121.6% 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 | | 3.958e-06 | | |100.00 Nlocal: 670.062 ave 815 max 351 min Histogram: 4 0 0 0 0 0 0 0 4 8 Nghost: 8253.06 ave 9759 max 7010 min Histogram: 4 0 0 2 6 0 0 0 0 4 Neighs: 312619 ave 410014 max 88797 min Histogram: 4 0 0 0 0 0 0 2 1 9 Total # of neighbors = 5001908 Ave neighs/atom = 466.55237 Ave special neighs/atom = 1.6069397 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out