#------------------------------------------------------------------------------- # 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 = 12100 4500 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00088 0.0714329 8304 2 97.661 10.0798 2768 Per MPI rank memory allocation (min/avg/max) = 12.81 | 14.08 | 14.85 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 -3037.1238 143908.11 1.3942094 410.14353 6.549388 28.744611 0 0 32414.215 -37461.334 -320.88394 -277806.33 -282818.16 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33427e-06 8304 2 103.7 9.98561e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.48244e-06 8304 2 103.7 0.000106944 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.29443e-06 8304 2 103.7 9.88736e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13314e-06 8304 2 103.7 8.99433e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.1009e-06 8304 2 103.7 9.77773e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.1766e-06 8304 2 103.7 0.00010296 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.10786e-06 8304 2 103.7 9.32009e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1092e-06 8304 2 103.7 9.76691e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.19881e-06 8304 2 103.7 8.98328e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.36634e-06 8304 2 103.7 9.85685e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.18631e-06 8304 2 103.7 9.35058e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.52889e-06 8304 2 103.7 0.000102724 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.36402e-06 8304 2 103.7 0.000123812 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.28791e-06 8304 2 103.7 8.78344e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.0543e-06 8304 2 103.7 8.86331e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.2297e-06 8304 2 103.7 9.44949e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.1409e-06 8304 2 103.7 9.83063e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14123e-06 8304 2 103.7 9.85761e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31576e-06 8304 2 103.7 0.00010392 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13016e-06 8304 2 103.7 9.09982e-05 2768 1000000 1000000 -1178.9079 143908.11 1.3942094 299.37969 48.316107 63.912815 0 0 29025.583 -19477.452 -320.88394 -277700.96 -268040.6 6564.4503 Loop time of 15178.3 on 16 procs for 1000000 steps with 10381 atoms Performance: 5.692 ns/day, 4.216 hours/ns, 65.884 timesteps/s 99.0% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1535.8 | 7796.9 | 11450 |4139.1 | 51.37 Bond | 1.0286 | 3.6529 | 6.9477 | 90.2 | 0.02 Kspace | 2333.6 | 5997.9 | 12273 |4731.8 | 39.52 Neigh | 566.75 | 567.89 | 569.14 | 3.4 | 3.74 Comm | 262.54 | 331.39 | 365.68 | 220.9 | 2.18 Output | 0.01655 | 0.018586 | 0.020413 | 0.9 | 0.00 Modify | 434.18 | 457.99 | 509.99 | 142.0 | 3.02 Other | | 22.52 | | | 0.15 Nlocal: 648.812 ave 826 max 278 min Histogram: 4 0 0 0 0 0 0 0 6 6 Nghost: 7818.5 ave 9840 max 6044 min Histogram: 4 0 0 1 7 0 0 0 0 4 Neighs: 297450 ave 433761 max 55322 min Histogram: 4 0 0 0 0 0 0 4 5 3 Total # of neighbors = 4759202 Ave neighs/atom = 458.45314 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49674 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 = 12100 4500 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13016e-06 8304 2 103.7 9.09982e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.81 | 14.18 | 14.85 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 -1178.3123 143908.11 1.3942094 299.37969 48.316107 63.912815 0 0 29025.583 -19477.452 -320.88394 -277700.96 -268040.6 6564.4503 Loop time of 4.82087e-06 on 16 procs for 0 steps with 10381 atoms 118.0% 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 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 | | 4.821e-06 | | |100.00 Nlocal: 648.812 ave 826 max 278 min Histogram: 4 0 0 0 0 0 0 0 6 6 Nghost: 7818.5 ave 9840 max 6044 min Histogram: 4 0 0 1 7 0 0 0 0 4 Neighs: 297450 ave 433761 max 55322 min Histogram: 4 0 0 0 0 0 0 4 5 3 Total # of neighbors = 4759202 Ave neighs/atom = 458.45314 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