#------------------------------------------------------------------------------- # Stage 2.4: 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 file 2.4_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 file 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2567886 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031460223 estimated relative force accuracy = 9.4741527e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.993872 0.768093 8304 2 97.1212 28.3129 2768 Per MPI rank memory allocation (min/avg/max) = 12.85 | 12.93 | 13.09 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 13387.995 92859.486 1.3074058 428.55654 181.61275 290.06848 0 0 25074.284 40897.417 -225.64506 -214466.22 -148022.84 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.19598e-06 8304 2 103.7 9.70824e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.45954e-06 8304 2 103.7 0.000100674 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.30811e-06 8304 2 103.7 9.38968e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.15153e-06 8304 2 103.7 0.000106503 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.12739e-06 8304 2 103.7 9.5501e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.28899e-06 8304 2 103.7 9.80289e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.47542e-06 8304 2 103.7 8.98444e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16053e-06 8304 2 103.7 9.96595e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.39568e-06 8304 2 103.7 0.000118783 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.10371e-06 8304 2 103.7 9.56568e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.30702e-06 8304 2 103.7 9.89861e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.2514e-06 8304 2 103.7 0.000116236 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.14192e-06 8304 2 103.7 8.94272e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19642e-06 8304 2 103.7 9.11368e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.1566e-06 8304 2 103.7 8.74556e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.61325e-06 8304 2 103.7 0.000112947 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.52851e-06 8304 2 103.7 0.000125574 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.31097e-06 8304 2 103.7 9.26126e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.14974e-06 8304 2 103.7 8.95521e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.4139e-06 8304 2 103.7 0.000102967 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.10809e-06 8304 2 103.7 8.88297e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.28765e-06 8304 2 103.7 0.000102554 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21995e-06 8304 2 103.7 0.000108361 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.14236e-06 8304 2 103.7 9.3947e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.08778e-06 8304 2 103.7 0.000111541 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.20791e-06 8304 2 103.7 0.00012651 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.32974e-06 8304 2 103.7 9.81768e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.62612e-06 8304 2 103.7 0.000118021 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.24386e-06 8304 2 103.7 0.000101019 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.55811e-06 8304 2 103.7 0.000104807 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27558e-06 8304 2 103.7 9.88709e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.13535e-06 8304 2 103.7 0.000100727 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.42958e-06 8304 2 103.7 0.000113226 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26568e-06 8304 2 103.7 0.000110236 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.07935e-06 8304 2 103.7 9.21782e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.20009e-06 8304 2 103.7 9.6041e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.64333e-06 8304 2 103.7 0.000118782 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.20876e-06 8304 2 103.7 0.000105609 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.28817e-06 8304 2 103.7 9.62684e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29066e-06 8304 2 103.7 0.000112719 2768 2000000 2000000 2926.8871 92859.486 1.3074058 302.14172 43.869149 71.409597 0 0 22399.092 31256.786 -225.64506 -215522.16 -161751.01 5702.7706 Loop time of 14799.7 on 32 procs for 2000000 steps with 9101 atoms Performance: 11.676 ns/day, 2.056 hours/ns, 135.138 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 | 8381.4 | 8885 | 9593.3 | 309.4 | 60.03 Bond | 2.4544 | 5.5186 | 11.572 | 84.2 | 0.04 Kspace | 2707.2 | 3411.3 | 3919.8 | 499.7 | 23.05 Neigh | 494.76 | 495.45 | 496.12 | 1.6 | 3.35 Comm | 965.24 | 986 | 1003.5 | 33.0 | 6.66 Output | 0.011792 | 0.014071 | 0.016193 | 1.1 | 0.00 Modify | 961.47 | 973.6 | 986.84 | 18.6 | 6.58 Other | | 42.83 | | | 0.29 Nlocal: 284.406 ave 302 max 249 min Histogram: 1 0 0 1 2 4 9 6 5 4 Nghost: 7324.47 ave 7396 max 7237 min Histogram: 1 1 2 5 3 7 6 3 2 2 Neighs: 160075 ave 172461 max 139604 min Histogram: 1 1 1 1 4 5 7 5 2 5 Total # of neighbors = 5122411 Ave neighs/atom = 562.84046 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98388 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.2567886 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031460223 estimated relative force accuracy = 9.4741527e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29066e-06 8304 2 103.7 0.000112719 2768 Per MPI rank memory allocation (min/avg/max) = 12.85 | 13.03 | 13.13 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 2000000 2000000 2927.7554 92859.486 1.3074058 302.14172 43.869149 71.409597 0 0 22399.092 31256.786 -225.64506 -215522.16 -161751.01 5702.7706 Loop time of 7.78122e-06 on 32 procs for 0 steps with 9101 atoms 116.1% 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 | | 7.781e-06 | | |100.00 Nlocal: 284.406 ave 302 max 249 min Histogram: 1 0 0 1 2 4 9 6 5 4 Nghost: 7324.47 ave 7396 max 7237 min Histogram: 1 1 2 5 3 7 6 3 2 2 Neighs: 160075 ave 172461 max 139604 min Histogram: 1 1 1 1 4 5 7 5 2 5 Total # of neighbors = 5122411 Ave neighs/atom = 562.84046 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_NPT.out