#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 1 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 100000 100000 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 2.6_averages.txt off 1 fix 3 movable ave/time 100 1 100 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 2.6_instantaneous.txt restart 1000000 2.6.restart dump sci all custom 100000 2.6.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 5.97855e-13 8304 2 103.7 7.80886e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.42 | 13.88 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 -769.38695 120303.9 1.009153 296.46642 44.690241 69.4521 0 0 21042.89 86976.025 -346.11593 -269047.14 -160914.09 5595.6522 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.14058e-06 8304 2 103.7 9.71851e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.09499e-06 8304 2 103.7 9.57954e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27679e-06 8304 2 103.7 9.01656e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39596e-06 8304 2 103.7 0.000109571 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.196e-06 8304 2 103.7 0.000106257 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.60796e-06 8304 2 103.7 9.75367e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.13068e-06 8304 2 103.7 9.91138e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.33866e-06 8304 2 103.7 0.000120998 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.14027e-06 8304 2 103.7 9.47699e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 2.0728e-06 8304 2 103.7 0.000118565 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.29992e-06 8304 2 103.7 0.000115367 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.73766e-06 8304 2 103.7 0.000132427 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11583e-06 8304 2 103.7 8.67347e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.12285e-06 8304 2 103.7 9.52695e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.76912e-06 8304 2 103.7 0.000128499 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16227e-06 8304 2 103.7 8.6887e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.22278e-06 8304 2 103.7 9.77227e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16646e-06 8304 2 103.7 0.000108141 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.54594e-06 8304 2 103.7 0.000112653 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.26883e-06 8304 2 103.7 8.80537e-05 2768 1000000 1000000 -505.08693 120303.9 1.009153 298.48664 48.98907 68.999145 0 0 21138.761 86837.351 -346.11593 -269038.9 -160944.8 5633.7828 Loop time of 5735.09 on 32 procs for 1000000 steps with 9101 atoms Performance: 15.065 ns/day, 1.593 hours/ns, 174.365 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 522.52 | 2052 | 2783.2 |1835.3 | 35.78 Bond | 0.99228 | 2.4956 | 4.3966 | 79.4 | 0.04 Kspace | 2104.9 | 2833.3 | 4371.2 |1569.2 | 49.40 Neigh | 161.17 | 161.97 | 162.96 | 5.0 | 2.82 Comm | 238.49 | 298.69 | 326.79 | 195.8 | 5.21 Output | 0.0097812 | 0.011942 | 0.014029 | 1.2 | 0.00 Modify | 346.52 | 367.43 | 419.21 | 151.5 | 6.41 Other | | 19.23 | | | 0.34 Nlocal: 284.406 ave 373 max 70 min Histogram: 4 3 1 0 0 0 0 0 11 13 Nghost: 4145.78 ave 5096 max 3600 min Histogram: 8 8 8 0 0 0 0 0 0 8 Neighs: 76888.6 ave 107660 max 14422 min Histogram: 6 2 0 0 0 0 1 3 10 10 Total # of neighbors = 2460435 Ave neighs/atom = 270.34776 Ave special neighs/atom = 1.8929788 Neighbor list builds = 49796 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.6.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.26883e-06 8304 2 103.7 8.80537e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.43 | 13.88 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 1000000 1000000 -504.39186 120303.9 1.009153 298.48664 48.98907 68.999145 0 0 21138.761 86837.351 -346.11593 -269038.9 -160944.8 5633.7828 Loop time of 7.86147e-06 on 32 procs for 0 steps with 9101 atoms 113.7% 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 Kspace | 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 | | 7.861e-06 | | |100.00 Nlocal: 284.406 ave 373 max 70 min Histogram: 4 3 1 0 0 0 0 0 11 13 Nghost: 4145.78 ave 5096 max 3600 min Histogram: 8 8 8 0 0 0 0 0 0 8 Neighs: 76888.6 ave 107660 max 14422 min Histogram: 6 2 0 0 0 0 1 3 10 10 Total # of neighbors = 2460435 Ave neighs/atom = 270.34776 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: 4:47:39