#------------------------------------------------------------------------------- # 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 8.21676e-13 8304 2 103.7 7.96234e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.86 | 12.21 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 -1919.4842 92859.489 1.3074058 299.47351 43.492839 120.27629 0 0 21169.383 -184046.43 -448.40969 0 -162713.28 5652.4095 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.38714e-06 8304 2 103.7 0.000112791 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26018e-06 8304 2 103.7 0.000117909 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.54365e-06 8304 2 103.7 9.98248e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.42256e-06 8304 2 103.7 0.000120761 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.9551e-06 8304 2 103.7 0.000131558 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.4562e-06 8304 2 103.7 0.000107055 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.42377e-06 8304 2 103.7 9.48517e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.54658e-06 8304 2 103.7 0.000109495 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.3999e-06 8304 2 103.7 0.000113658 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.57234e-06 8304 2 103.7 0.000108928 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33839e-06 8304 2 103.7 9.67116e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 2.24692e-06 8304 2 103.7 0.000125743 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46297e-06 8304 2 103.7 0.000106877 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.77413e-06 8304 2 103.7 0.000121994 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.49158e-06 8304 2 103.7 9.51366e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.32306e-06 8304 2 103.7 9.7069e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.10075e-06 8304 2 103.7 0.000110897 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.86521e-06 8304 2 103.7 0.00011797 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.21512e-06 8304 2 103.7 9.93845e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36019e-06 8304 2 103.7 0.00010716 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.72799e-06 8304 2 103.7 0.000105854 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.42794e-06 8304 2 103.7 0.000105624 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.44145e-06 8304 2 103.7 0.000103704 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.43876e-06 8304 2 103.7 0.000131369 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.66468e-06 8304 2 103.7 0.000131947 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.29284e-06 8304 2 103.7 0.000100263 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.42579e-06 8304 2 103.7 0.000106314 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.46587e-06 8304 2 103.7 0.000141862 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.92171e-06 8304 2 103.7 0.000119809 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.34131e-06 8304 2 103.7 9.14876e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.41079e-06 8304 2 103.7 0.000124031 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 2.23474e-06 8304 2 103.7 0.000116074 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.33287e-06 8304 2 103.7 9.97174e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.55677e-06 8304 2 103.7 0.000114324 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.56241e-06 8304 2 103.7 0.000120573 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.49746e-06 8304 2 103.7 9.12524e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.95207e-06 8304 2 103.7 0.000110174 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.45542e-06 8304 2 103.7 9.92949e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.25771e-06 8304 2 103.7 8.95921e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.89334e-06 8304 2 103.7 0.000116894 2768 2000000 2000000 -1630.0377 92859.489 1.3074058 301.58557 38.286828 99.613275 0 0 21068.46 -181663.78 -448.40969 0 -160457.42 5692.2736 Loop time of 6598.77 on 32 procs for 2000000 steps with 9101 atoms Performance: 26.187 ns/day, 0.916 hours/ns, 303.087 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3989.1 | 4482.6 | 5128.1 | 402.3 | 67.93 Bond | 1.596 | 3.9665 | 10.409 | 92.3 | 0.06 Neigh | 320.82 | 321.99 | 323.01 | 5.0 | 4.88 Comm | 514.58 | 1136.3 | 1603.9 | 757.6 | 17.22 Output | 0.0089763 | 0.011173 | 0.013235 | 1.2 | 0.00 Modify | 601.55 | 626.95 | 649.94 | 76.0 | 9.50 Other | | 26.99 | | | 0.41 Nlocal: 284.406 ave 310 max 267 min Histogram: 2 5 3 6 5 6 1 3 0 1 Nghost: 4982.12 ave 5051 max 4943 min Histogram: 4 4 9 4 3 2 3 1 0 2 Neighs: 88296.5 ave 101226 max 80968 min Histogram: 7 3 5 4 4 2 4 1 1 1 Total # of neighbors = 2825489 Ave neighs/atom = 310.45918 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95455 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 1.89334e-06 8304 2 103.7 0.000116894 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.87 | 12.21 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 -1628.8051 92859.489 1.3074058 301.58557 38.286828 99.613275 0 0 21068.46 -181663.78 -448.40969 0 -160457.42 5692.2736 Loop time of 1.47199e-05 on 32 procs for 0 steps with 9101 atoms 102.3% 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 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 | | 1.472e-05 | | |100.00 Nlocal: 284.406 ave 310 max 267 min Histogram: 2 5 3 6 5 6 1 3 0 1 Nghost: 4982.12 ave 5051 max 4943 min Histogram: 4 4 9 4 3 2 3 1 0 2 Neighs: 88296.5 ave 101226 max 80968 min Histogram: 7 3 5 4 4 2 4 1 1 1 Total # of neighbors = 2825489 Ave neighs/atom = 310.45918 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: 6:22:24