#------------------------------------------------------------------------------- # 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) = 0.25609786 grid = 30 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0033114692 estimated relative force accuracy = 9.972391e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5632 2160 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.995217 0.814214 8304 2 97.3375 26.0433 2768 Per MPI rank memory allocation (min/avg/max) = 12.85 | 12.92 | 13.14 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 9820.7758 92859.485 1.3074059 428.55654 129.21805 200.34649 0 0 23718.774 36209.855 -225.64506 -214276.43 -154018.23 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.42358e-06 8304 2 103.7 0.000103944 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.38454e-06 8304 2 103.7 9.82499e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.47475e-06 8304 2 103.7 0.000111523 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.50211e-06 8304 2 103.7 9.91136e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.24535e-06 8304 2 103.7 0.000108593 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.19154e-06 8304 2 103.7 9.28929e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.12957e-06 8304 2 103.7 9.11177e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10315e-06 8304 2 103.7 9.6106e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.39831e-06 8304 2 103.7 9.98983e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21228e-06 8304 2 103.7 9.41299e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.29389e-06 8304 2 103.7 0.000100085 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.16616e-06 8304 2 103.7 9.45653e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.33504e-06 8304 2 103.7 8.81462e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.43349e-06 8304 2 103.7 9.98758e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.19586e-06 8304 2 103.7 9.10409e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.19218e-06 8304 2 103.7 9.96402e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 2.3492e-06 8304 2 103.7 0.000157624 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.49103e-06 8304 2 103.7 0.000123647 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25731e-06 8304 2 103.7 0.000108942 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.41553e-06 8304 2 103.7 0.000112753 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.10636e-06 8304 2 103.7 0.000112258 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.1664e-06 8304 2 103.7 9.96654e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.3684e-06 8304 2 103.7 0.000100039 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.85706e-06 8304 2 103.7 0.000132783 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.27314e-06 8304 2 103.7 9.63789e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.149e-06 8304 2 103.7 9.37051e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.59531e-06 8304 2 103.7 0.000107205 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.24598e-06 8304 2 103.7 9.51884e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.29902e-06 8304 2 103.7 0.000118009 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.2107e-06 8304 2 103.7 0.00011798 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.2946e-06 8304 2 103.7 9.87167e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.70615e-06 8304 2 103.7 0.000115158 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.42943e-06 8304 2 103.7 0.000101261 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.67204e-06 8304 2 103.7 0.000106379 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.23733e-06 8304 2 103.7 0.000101561 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.15402e-06 8304 2 103.7 9.28996e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.18401e-06 8304 2 103.7 9.96512e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.23645e-06 8304 2 103.7 9.83762e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.2553e-06 8304 2 103.7 9.54674e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.58199e-06 8304 2 103.7 0.000107804 2768 2000000 2000000 2424.3001 92859.485 1.3074059 291.10797 46.948292 89.333506 0 0 22144.538 30931.547 -225.64506 -214942.52 -161730.15 5494.5143 Loop time of 15459.8 on 32 procs for 2000000 steps with 9101 atoms Performance: 11.177 ns/day, 2.147 hours/ns, 129.368 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 | 7947.6 | 9104 | 10193 | 649.2 | 58.89 Bond | 2.291 | 5.3462 | 9.6072 | 93.3 | 0.03 Kspace | 2684 | 3775.5 | 4939 |1007.9 | 24.42 Neigh | 539.88 | 540.54 | 541.07 | 1.7 | 3.50 Comm | 1014.7 | 1022 | 1032 | 13.5 | 6.61 Output | 0.012881 | 0.015138 | 0.017255 | 1.1 | 0.00 Modify | 960.5 | 967.38 | 976.99 | 12.3 | 6.26 Other | | 44.97 | | | 0.29 Nlocal: 284.406 ave 301 max 267 min Histogram: 1 3 4 3 1 8 6 2 2 2 Nghost: 7251.28 ave 7296 max 7192 min Histogram: 1 2 3 2 5 5 2 5 3 4 Neighs: 160072 ave 181627 max 140725 min Histogram: 3 1 4 6 3 4 6 1 3 1 Total # of neighbors = 5122299 Ave neighs/atom = 562.82815 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98289 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) = 0.25609786 grid = 30 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0033114692 estimated relative force accuracy = 9.972391e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5632 2160 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.58199e-06 8304 2 103.7 0.000107804 2768 Per MPI rank memory allocation (min/avg/max) = 12.86 | 13.11 | 13.53 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 2425.3868 92859.485 1.3074059 291.10797 46.948292 89.333506 0 0 22144.538 30931.547 -225.64506 -214942.52 -161730.15 5494.5143 Loop time of 9.18862e-06 on 32 procs for 0 steps with 9101 atoms 112.2% 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 | | 9.189e-06 | | |100.00 Nlocal: 284.406 ave 301 max 267 min Histogram: 1 3 4 3 1 8 6 2 2 2 Nghost: 7251.28 ave 7296 max 7192 min Histogram: 1 2 3 2 5 5 2 5 3 4 Neighs: 160072 ave 181627 max 140725 min Histogram: 3 1 4 6 3 4 6 1 3 1 Total # of neighbors = 5122299 Ave neighs/atom = 562.82815 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