#------------------------------------------------------------------------------- # 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 1.76426e-12 8304 2 103.7 8.03766e-11 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 12.05 | 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-06 189.08833 92859.489 1.3074058 302.64407 46.110376 113.18707 0 0 21681.82 -180946.67 -386.0007 0 -159105.56 5712.2523 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.29088e-06 8304 2 103.7 0.000100124 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.45243e-06 8304 2 103.7 0.000100581 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.2886e-06 8304 2 103.7 9.86013e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.33351e-06 8304 2 103.7 9.85887e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.64684e-06 8304 2 103.7 0.000103625 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.53857e-06 8304 2 103.7 0.000122358 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.08917e-06 8304 2 103.7 9.61703e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.47284e-06 8304 2 103.7 0.000109137 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.15738e-06 8304 2 103.7 9.22627e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39496e-06 8304 2 103.7 0.000110662 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.30703e-06 8304 2 103.7 9.94575e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.83655e-06 8304 2 103.7 0.000113867 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.27638e-06 8304 2 103.7 9.45078e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.89953e-06 8304 2 103.7 0.000124692 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.18487e-06 8304 2 103.7 0.000122929 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.21467e-06 8304 2 103.7 0.0001056 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.25623e-06 8304 2 103.7 9.79582e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.32787e-06 8304 2 103.7 0.000100343 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.72889e-06 8304 2 103.7 0.000112979 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.60334e-06 8304 2 103.7 9.93199e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.39097e-06 8304 2 103.7 0.000110212 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.44381e-06 8304 2 103.7 9.87671e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.77285e-06 8304 2 103.7 0.000107807 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.5372e-06 8304 2 103.7 0.000111103 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.65303e-06 8304 2 103.7 0.000129386 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.33626e-06 8304 2 103.7 9.29637e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.2116e-06 8304 2 103.7 0.00011895 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 2.12863e-06 8304 2 103.7 0.000115199 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.32763e-06 8304 2 103.7 0.000104431 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.72695e-06 8304 2 103.7 0.000101928 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.49613e-06 8304 2 103.7 0.000100454 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.29576e-06 8304 2 103.7 0.000117466 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.291e-06 8304 2 103.7 9.52124e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.41473e-06 8304 2 103.7 9.2669e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.62685e-06 8304 2 103.7 0.000104576 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.47035e-06 8304 2 103.7 0.000130595 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.25859e-06 8304 2 103.7 0.000117656 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.66415e-06 8304 2 103.7 0.000102196 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.47296e-06 8304 2 103.7 0.000104667 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.61026e-06 8304 2 103.7 0.000121583 2768 2000000 2000000 2122.4278 92859.489 1.3074058 295.26599 37.497175 99.999244 0 0 21447.592 -170002.19 -386.0007 0 -148417.11 5572.9948 Loop time of 6822.17 on 32 procs for 2000000 steps with 9101 atoms Performance: 25.329 ns/day, 0.948 hours/ns, 293.162 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4447.5 | 5023.8 | 5777 | 441.6 | 73.64 Bond | 1.5309 | 3.9581 | 7.1976 | 82.6 | 0.06 Neigh | 326.41 | 327.53 | 328.39 | 2.9 | 4.80 Comm | 239.5 | 822.84 | 1510.5 |1076.1 | 12.06 Output | 0.009198 | 0.011432 | 0.01355 | 1.2 | 0.00 Modify | 441.68 | 617.3 | 846.63 | 578.7 | 9.05 Other | | 26.73 | | | 0.39 Nlocal: 284.406 ave 308 max 257 min Histogram: 2 2 2 2 3 8 3 6 2 2 Nghost: 5374.41 ave 5517 max 5218 min Histogram: 2 1 3 3 7 5 3 3 2 3 Neighs: 100464 ave 115950 max 85691 min Histogram: 2 1 4 4 4 7 7 2 0 1 Total # of neighbors = 3214847 Ave neighs/atom = 353.24107 Ave special neighs/atom = 1.8929788 Neighbor list builds = 95531 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 1.61026e-06 8304 2 103.7 0.000121583 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 12.06 | 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 2123.5615 92859.489 1.3074058 295.26599 37.497175 99.999244 0 0 21447.592 -170002.19 -386.0007 0 -148417.11 5572.9948 Loop time of 7.54313e-06 on 32 procs for 0 steps with 9101 atoms 107.7% 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 | | 7.543e-06 | | |100.00 Nlocal: 284.406 ave 308 max 257 min Histogram: 2 2 2 2 3 8 3 6 2 2 Nghost: 5374.41 ave 5517 max 5218 min Histogram: 2 1 3 3 7 5 3 3 2 3 Neighs: 100464 ave 115950 max 85691 min Histogram: 2 1 4 4 4 7 7 2 0 1 Total # of neighbors = 3214847 Ave neighs/atom = 353.24107 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: 6:34:34