#------------------------------------------------------------------------------- # 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 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.33e-13 8304 2 103.7 8.57199e-11 2768 Per MPI rank memory allocation (min/avg/max) = 13.09 | 13.16 | 13.3 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 -636.03249 92859.489 1.3074058 298.95808 38.230578 97.982653 0 0 21091.784 -180203.08 -225.64506 0 -158975.08 5642.6811 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.62903e-06 8304 2 103.7 0.000112388 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.36769e-06 8304 2 103.7 0.000110796 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.23853e-06 8304 2 103.7 9.29158e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.35087e-06 8304 2 103.7 0.000100965 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.37661e-06 8304 2 103.7 0.000102453 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.34485e-06 8304 2 103.7 9.86936e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.41671e-06 8304 2 103.7 0.00010769 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.27801e-06 8304 2 103.7 0.000106822 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.74044e-06 8304 2 103.7 0.000156149 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.26614e-06 8304 2 103.7 9.44006e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.156e-06 8304 2 103.7 0.000106347 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.15796e-06 8304 2 103.7 9.33515e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.18928e-06 8304 2 103.7 9.11118e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.30724e-06 8304 2 103.7 0.000122307 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.25155e-06 8304 2 103.7 8.83956e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.11008e-06 8304 2 103.7 9.44829e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 2.0505e-06 8304 2 103.7 0.000150838 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.73364e-06 8304 2 103.7 0.000121516 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.9977e-06 8304 2 103.7 0.000116809 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.55044e-06 8304 2 103.7 0.000105187 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.31239e-06 8304 2 103.7 0.000124299 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.42314e-06 8304 2 103.7 0.000103569 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.63672e-06 8304 2 103.7 0.000106567 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.65153e-06 8304 2 103.7 0.000103175 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.22701e-06 8304 2 103.7 0.000104863 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.51965e-06 8304 2 103.7 0.000114639 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.40263e-06 8304 2 103.7 0.000105029 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.17624e-06 8304 2 103.7 0.000105063 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.24276e-06 8304 2 103.7 9.49734e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26574e-06 8304 2 103.7 9.81607e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.20468e-06 8304 2 103.7 0.000103075 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.30424e-06 8304 2 103.7 0.000128259 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.27287e-06 8304 2 103.7 0.000128674 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.94844e-06 8304 2 103.7 0.000122602 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.75845e-06 8304 2 103.7 0.000109835 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.32062e-06 8304 2 103.7 0.000117767 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.56263e-06 8304 2 103.7 0.000109265 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.1144e-06 8304 2 103.7 0.000103144 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.13892e-06 8304 2 103.7 9.66083e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.14799e-06 8304 2 103.7 0.00010756 2768 2000000 2000000 469.70791 92859.489 1.3074058 297.86052 50.10034 107.80329 0 0 21081.229 -175629.75 -225.64506 0 -154390.62 5621.9652 Loop time of 19008.6 on 16 procs for 2000000 steps with 9101 atoms Performance: 9.091 ns/day, 2.640 hours/ns, 105.215 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 | 14248 | 15906 | 17080 | 581.9 | 83.68 Bond | 2.2597 | 7.6841 | 10.74 | 74.5 | 0.04 Neigh | 875.95 | 876.81 | 878.26 | 2.5 | 4.61 Comm | 352.21 | 1403.4 | 3165 |2069.5 | 7.38 Output | 0.012791 | 0.014541 | 0.016107 | 0.9 | 0.00 Modify | 648.39 | 768.28 | 1205.9 | 527.7 | 4.04 Other | | 46.9 | | | 0.25 Nlocal: 568.812 ave 597 max 532 min Histogram: 1 0 0 2 3 3 2 3 0 2 Nghost: 9037.12 ave 9143 max 8920 min Histogram: 3 0 0 3 1 1 1 4 1 2 Neighs: 319424 ave 346947 max 283516 min Histogram: 1 0 0 4 2 3 1 2 1 2 Total # of neighbors = 5110777 Ave neighs/atom = 561.56214 Ave special neighs/atom = 1.8929788 Neighbor list builds = 96638 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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 2000000 2 0.97 1.14799e-06 8304 2 103.7 0.00010756 2768 Per MPI rank memory allocation (min/avg/max) = 13.09 | 13.18 | 13.3 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 470.70728 92859.489 1.3074058 297.86052 50.10034 107.80329 0 0 21081.229 -175629.75 -225.64506 0 -154390.62 5621.9652 Loop time of 4.16744e-06 on 16 procs for 0 steps with 9101 atoms 118.5% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.167e-06 | | |100.00 Nlocal: 568.812 ave 597 max 532 min Histogram: 1 0 0 2 3 3 2 3 0 2 Nghost: 9037.12 ave 9143 max 8920 min Histogram: 3 0 0 3 1 1 1 4 1 2 Neighs: 319424 ave 346947 max 283516 min Histogram: 1 0 0 4 2 3 1 2 1 2 Total # of neighbors = 5110777 Ave neighs/atom = 561.56214 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: 5:32:50