#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 100 ps 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 10000 10000 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 10 1 10 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 100000 2.4.restart dump sci all custom 10000 2.4.xyz id mol type q xs ys zs timestep 1 run 100000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997787 0.555628 8304 2 97.0045 27.0134 2768 Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.69 | 12.81 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 9982.6851 92859.489 1.3074058 428.55654 76.607836 328.42011 0 0 23858.099 -179486.14 -291.74384 0 -155223.01 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33866e-06 8304 2 103.7 9.94689e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.41756e-06 8304 2 103.7 0.000133928 2768 100000 100000 -417.79805 92859.489 1.3074058 296.00634 31.74667 122.2988 0 0 21483.784 -182905.43 -291.74384 0 -161267.6 5586.9684 Loop time of 760.044 on 16 procs for 100000 steps with 9101 atoms Performance: 11.368 ns/day, 2.111 hours/ns, 131.571 timesteps/s 99.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 589.43 | 634.62 | 676.19 | 87.5 | 83.50 Bond | 0.11923 | 0.36119 | 0.53761 | 18.8 | 0.05 Neigh | 36.925 | 36.971 | 37.008 | 0.3 | 4.86 Comm | 15.144 | 48.514 | 81.907 | 292.4 | 6.38 Output | 0.013312 | 0.015037 | 0.016567 | 0.9 | 0.00 Modify | 28.914 | 37.368 | 60.271 | 153.6 | 4.92 Other | | 2.198 | | | 0.29 Nlocal: 568.812 ave 585 max 539 min Histogram: 1 1 0 0 2 1 4 1 5 1 Nghost: 7830.25 ave 7927 max 7674 min Histogram: 1 0 1 0 4 2 2 1 2 3 Neighs: 255765 ave 270317 max 234249 min Histogram: 1 0 1 2 1 2 3 4 0 2 Total # of neighbors = 4092241 Ave neighs/atom = 449.6474 Ave special neighs/atom = 1.8929788 Neighbor list builds = 4837 Dangerous builds = 0 undump sci restart 0 dump sci all custom 100000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.41756e-06 8304 2 103.7 0.000133928 2768 Per MPI rank memory allocation (min/avg/max) = 12.61 | 12.71 | 12.81 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 100000 100000 -416.83107 92859.489 1.3074058 296.00634 31.74667 122.2988 0 0 21483.784 -182905.43 -291.74384 0 -161267.6 5586.9684 Loop time of 4.83544e-06 on 16 procs for 0 steps with 9101 atoms 103.4% 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 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 | | 4.835e-06 | | |100.00 Nlocal: 568.812 ave 585 max 539 min Histogram: 1 1 0 0 2 1 4 1 5 1 Nghost: 7830.25 ave 7927 max 7674 min Histogram: 1 0 1 0 4 2 2 1 2 3 Neighs: 255765 ave 270317 max 234249 min Histogram: 1 0 1 2 1 2 3 4 0 2 Total # of neighbors = 4092241 Ave neighs/atom = 449.6474 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out