#------------------------------------------------------------------------------- # 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 1.1191e-12 8304 2 103.7 7.62839e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.18 | 12.29 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 -555.09741 92859.489 1.3074058 299.02513 37.315355 127.0309 0 0 21443.361 -183089.24 -448.40969 0 -161481.53 5643.9466 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.66373e-06 8304 2 103.7 0.000140082 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.9572e-06 8304 2 103.7 0.000110745 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 2.02347e-06 8304 2 103.7 0.000122596 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.51862e-06 8304 2 103.7 0.000111019 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.38262e-06 8304 2 103.7 9.74349e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.53511e-06 8304 2 103.7 0.000100964 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.25712e-06 8304 2 103.7 9.8126e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.44584e-06 8304 2 103.7 0.000135533 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.58882e-06 8304 2 103.7 0.00011187 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.3436e-06 8304 2 103.7 0.000111027 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.59063e-06 8304 2 103.7 0.000106151 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.40684e-06 8304 2 103.7 0.000101954 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.34264e-06 8304 2 103.7 0.000111463 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.86149e-06 8304 2 103.7 0.000116289 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.34837e-06 8304 2 103.7 0.000113522 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.44344e-06 8304 2 103.7 0.000102024 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.48258e-06 8304 2 103.7 0.000110926 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 2.02686e-06 8304 2 103.7 0.000116229 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.73158e-06 8304 2 103.7 0.000111601 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.11435e-06 8304 2 103.7 0.000116829 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.81291e-06 8304 2 103.7 0.000113 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.81273e-06 8304 2 103.7 0.000116108 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.45097e-06 8304 2 103.7 0.000115535 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.81817e-06 8304 2 103.7 0.000133413 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.3622e-06 8304 2 103.7 9.81733e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.40299e-06 8304 2 103.7 0.00012826 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.63535e-06 8304 2 103.7 0.00010782 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.38712e-06 8304 2 103.7 0.000115586 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.19843e-06 8304 2 103.7 0.000113995 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.34705e-06 8304 2 103.7 0.000118881 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.16369e-06 8304 2 103.7 9.41746e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.85215e-06 8304 2 103.7 0.000138993 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.67251e-06 8304 2 103.7 0.000106563 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.50888e-06 8304 2 103.7 0.000117148 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.49524e-06 8304 2 103.7 0.000111495 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.39342e-06 8304 2 103.7 0.000116219 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.37158e-06 8304 2 103.7 9.33324e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.69296e-06 8304 2 103.7 0.000111474 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.92e-06 8304 2 103.7 0.000133366 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.14379e-06 8304 2 103.7 0.000105574 2768 2000000 2000000 -1323.0093 92859.489 1.3074058 301.05491 49.542853 118.56042 0 0 21313.288 -181753.84 -448.40969 0 -160272.45 5682.2576 Loop time of 10279.1 on 16 procs for 2000000 steps with 9101 atoms Performance: 16.811 ns/day, 1.428 hours/ns, 194.569 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 | 7579.4 | 8394.9 | 8922.3 | 355.3 | 81.67 Bond | 1.9812 | 6.5136 | 9.8138 | 83.1 | 0.06 Neigh | 547.06 | 548.08 | 548.67 | 1.8 | 5.33 Comm | 238.72 | 689.01 | 1483.8 |1199.0 | 6.70 Output | 0.013783 | 0.015501 | 0.017014 | 0.8 | 0.00 Modify | 532.18 | 609.85 | 766.95 | 277.8 | 5.93 Other | | 30.78 | | | 0.30 Nlocal: 568.812 ave 590 max 542 min Histogram: 1 0 0 6 1 1 2 1 2 2 Nghost: 6220.56 ave 6327 max 6059 min Histogram: 1 0 0 0 3 4 4 2 0 2 Neighs: 176562 ave 187011 max 162783 min Histogram: 1 0 0 3 4 0 3 2 1 2 Total # of neighbors = 2824988 Ave neighs/atom = 310.40413 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95434 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 1.14379e-06 8304 2 103.7 0.000105574 2768 Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.18 | 12.29 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 -1321.9349 92859.489 1.3074058 301.05491 49.542853 118.56042 0 0 21313.288 -181753.84 -448.40969 0 -160272.45 5682.2576 Loop time of 4.84588e-06 on 16 procs for 0 steps with 9101 atoms 112.2% 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 | | 4.846e-06 | | |100.00 Nlocal: 568.812 ave 590 max 542 min Histogram: 1 0 0 6 1 1 2 1 2 2 Nghost: 6220.56 ave 6327 max 6059 min Histogram: 1 0 0 0 3 4 4 2 0 2 Neighs: 176562 ave 187011 max 162783 min Histogram: 1 0 0 3 4 0 3 2 1 2 Total # of neighbors = 2824988 Ave neighs/atom = 310.40413 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: 2:59:24