#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 300000 300000 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 300 1 300 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 restart 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24992822 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035847612 estimated relative force accuracy = 1.0795402e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00138 0.0823326 8304 2 97.6433 10.6908 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.62 | 14.13 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 1491.7475 194808.45 0.62320209 428.55654 7.7796492 20.122405 0 0 26022.059 9036.6725 -107.55839 -209848.26 -174761.63 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.36045e-06 8304 2 103.7 0.000110657 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.57454e-06 8304 2 103.7 0.000111673 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.15563e-06 8304 2 103.7 9.90275e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.353e-06 8304 2 103.7 0.000103293 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.26698e-06 8304 2 103.7 9.5021e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.40392e-06 8304 2 103.7 8.69186e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.26094e-06 8304 2 103.7 9.81045e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.79709e-06 8304 2 103.7 0.00011727 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25444e-06 8304 2 103.7 0.000106453 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24334e-06 8304 2 103.7 8.76372e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.22215e-06 8304 2 103.7 9.00842e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.39784e-06 8304 2 103.7 0.000110015 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.16887e-06 8304 2 103.7 9.20761e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25212e-06 8304 2 103.7 8.74651e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.20598e-06 8304 2 103.7 0.000102317 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.22955e-06 8304 2 103.7 0.000111068 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.18017e-06 8304 2 103.7 9.36086e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.1269e-06 8304 2 103.7 9.72349e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.30666e-06 8304 2 103.7 9.76192e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.54254e-06 8304 2 103.7 0.000116026 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.22699e-06 8304 2 103.7 9.74645e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.07788e-06 8304 2 103.7 0.000106203 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.27741e-06 8304 2 103.7 0.000103603 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.29826e-06 8304 2 103.7 0.000100226 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17919e-06 8304 2 103.7 9.44508e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.24277e-06 8304 2 103.7 9.66739e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.52109e-06 8304 2 103.7 0.000113105 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.17092e-06 8304 2 103.7 9.4722e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.05898e-06 8304 2 103.7 0.000106581 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.38846e-06 8304 2 103.7 9.58623e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27868e-06 8304 2 103.7 9.98477e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.23075e-06 8304 2 103.7 9.49139e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.02841e-06 8304 2 103.7 9.8236e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.09053e-06 8304 2 103.7 9.86731e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27136e-06 8304 2 103.7 9.02147e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.66032e-06 8304 2 103.7 0.000126231 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.10675e-06 8304 2 103.7 9.24681e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.66741e-06 8304 2 103.7 0.000117688 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.06954e-06 8304 2 103.7 9.14212e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13565e-06 8304 2 103.7 8.98411e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.50883e-06 8304 2 103.7 0.000109015 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.16695e-06 8304 2 103.7 9.3431e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.40056e-06 8304 2 103.7 0.000118422 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.42223e-06 8304 2 103.7 0.000102582 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.9902e-06 8304 2 103.7 0.000115309 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.38358e-06 8304 2 103.7 0.000102427 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.26971e-06 8304 2 103.7 0.000103244 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.18997e-06 8304 2 103.7 0.000141189 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.06838e-06 8304 2 103.7 9.18601e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.09378e-06 8304 2 103.7 9.65052e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.28255e-06 8304 2 103.7 0.000105776 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.91363e-06 8304 2 103.7 0.000145438 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.32025e-06 8304 2 103.7 9.04217e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.35975e-06 8304 2 103.7 0.00012063 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.50115e-06 8304 2 103.7 9.54184e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.38737e-06 8304 2 103.7 0.00010429 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18512e-06 8304 2 103.7 9.54178e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.40146e-06 8304 2 103.7 0.000105479 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.69248e-06 8304 2 103.7 0.000111795 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.2319e-06 8304 2 103.7 9.4121e-05 2768 3000000 3000000 -288.43211 194808.45 0.62320209 300.27613 35.95419 56.857996 0 0 20936.766 28299.547 -107.55839 -209789.54 -160460.41 5667.5585 Loop time of 34812.4 on 32 procs for 3000000 steps with 9101 atoms Performance: 7.446 ns/day, 3.223 hours/ns, 86.176 timesteps/s 98.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7202 | 10940 | 25063 |9822.5 | 31.43 Bond | 2.6487 | 7.1277 | 16.014 | 165.2 | 0.02 Kspace | 5731.3 | 19938 | 31073 |7320.7 | 57.27 Neigh | 1857.6 | 1864.8 | 1879.1 | 15.4 | 5.36 Comm | 213.64 | 657.04 | 906.01 | 950.1 | 1.89 Output | 0.014602 | 0.016912 | 0.018993 | 1.0 | 0.00 Modify | 1153.1 | 1338.7 | 1588.9 | 473.4 | 3.85 Other | | 66.71 | | | 0.19 Nlocal: 284.406 ave 585 max 0 min Histogram: 12 0 0 0 3 5 0 0 0 12 Nghost: 4488.75 ave 8859 max 5 min Histogram: 4 0 8 0 2 6 0 4 4 4 Neighs: 133051 ave 312510 max 0 min Histogram: 12 4 0 0 1 3 0 0 4 8 Total # of neighbors = 4257619 Ave neighs/atom = 467.81881 Ave special neighs/atom = 1.8929788 Neighbor list builds = 149846 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.24992822 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035847612 estimated relative force accuracy = 1.0795402e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.2319e-06 8304 2 103.7 9.4121e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.05 | 12.75 | 14.13 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 3000000 3000000 -288.00961 194808.45 0.62320209 300.27613 35.95419 56.857996 0 0 20936.766 28299.547 -107.55839 -209789.54 -160460.41 5667.5585 Loop time of 7.48753e-06 on 32 procs for 0 steps with 9101 atoms 114.8% 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 | | 7.488e-06 | | |100.00 Nlocal: 284.406 ave 585 max 0 min Histogram: 12 0 0 0 3 5 0 0 0 12 Nghost: 4488.75 ave 8859 max 5 min Histogram: 4 0 8 0 2 6 0 4 4 4 Neighs: 133051 ave 312510 max 0 min Histogram: 12 4 0 0 1 3 0 0 4 8 Total # of neighbors = 4257619 Ave neighs/atom = 467.81881 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out