#------------------------------------------------------------------------------- # Stage 2.4: 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 file 2.4_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 file 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00088 0.0704157 8304 2 97.6595 9.8462 2768 Per MPI rank memory allocation (min/avg/max) = 12.42 | 13.2 | 13.76 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 -2989.9456 143908.11 1.3942094 410.14353 6.7571064 28.334897 0 0 32424.626 -37472.532 -320.88394 -277806.09 -282818.91 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.59658e-06 8304 2 103.7 0.000123927 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.13393e-06 8304 2 103.7 8.71874e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14764e-06 8304 2 103.7 0.000123231 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.11727e-06 8304 2 103.7 9.36909e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.63078e-06 8304 2 103.7 0.000119973 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.39024e-06 8304 2 103.7 9.6286e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22954e-06 8304 2 103.7 9.19944e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1324e-06 8304 2 103.7 9.45212e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.16014e-06 8304 2 103.7 9.77075e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39145e-06 8304 2 103.7 0.000117193 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.12756e-06 8304 2 103.7 9.1904e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.57353e-06 8304 2 103.7 9.66499e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46323e-06 8304 2 103.7 0.000100931 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.29673e-06 8304 2 103.7 9.07544e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.28576e-06 8304 2 103.7 9.66937e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.15029e-06 8304 2 103.7 9.39539e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13844e-06 8304 2 103.7 0.000102239 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.10983e-06 8304 2 103.7 9.29646e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.36119e-06 8304 2 103.7 9.81763e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.34306e-06 8304 2 103.7 0.000112888 2768 1000000 1000000 -848.38676 143908.11 1.3942094 302.35034 48.233812 75.604521 0 0 29166.191 -19738.779 -320.88394 -277689.38 -268138.13 6629.5871 Loop time of 9556.54 on 32 procs for 1000000 steps with 10381 atoms Performance: 9.041 ns/day, 2.655 hours/ns, 104.640 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 903.85 | 4209.5 | 6117.4 |3089.9 | 44.05 Bond | 0.98632 | 2.6534 | 4.8943 | 77.5 | 0.03 Kspace | 2025.7 | 3942.5 | 7269.1 |3205.5 | 41.25 Neigh | 432.5 | 433.12 | 434.03 | 2.6 | 4.53 Comm | 302.42 | 427.02 | 478.7 | 274.6 | 4.47 Output | 0.015033 | 0.017442 | 0.01976 | 1.1 | 0.00 Modify | 477.37 | 519.78 | 627.85 | 217.5 | 5.44 Other | | 21.91 | | | 0.23 Nlocal: 324.406 ave 418 max 128 min Histogram: 8 0 0 0 0 0 1 4 8 11 Nghost: 6031.81 ave 7559 max 3887 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 148376 ave 222871 max 26595 min Histogram: 8 0 0 0 0 2 5 1 5 11 Total # of neighbors = 4748042 Ave neighs/atom = 457.37809 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49606 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.34306e-06 8304 2 103.7 0.000112888 2768 Per MPI rank memory allocation (min/avg/max) = 12.43 | 13.23 | 13.75 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 -847.89476 143908.11 1.3942094 302.35034 48.233812 75.604521 0 0 29166.191 -19738.779 -320.88394 -277689.38 -268138.13 6629.5871 Loop time of 8.19138e-06 on 32 procs for 0 steps with 10381 atoms 117.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.191e-06 | | |100.00 Nlocal: 324.406 ave 418 max 128 min Histogram: 8 0 0 0 0 0 1 4 8 11 Nghost: 6031.81 ave 7559 max 3887 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 148376 ave 222871 max 26595 min Histogram: 8 0 0 0 0 2 5 1 5 11 Total # of neighbors = 4748042 Ave neighs/atom = 457.37809 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out