#------------------------------------------------------------------------------- # 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 = 0.002 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) = 0.25784211 grid = 30 32 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028657894 estimated relative force accuracy = 8.6302397e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5796 1920 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.992893 0.741664 8304 2 96.6151 42.8439 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13 | 13.18 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 18280.18 95589.251 1.27007 428.55654 31.54534 225.68736 0 0 25166.926 49253.496 -219.20126 -214470.59 -139792.93 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.2662e-06 8304 2 103.7 0.000101846 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19132e-06 8304 2 103.7 0.000101972 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.3937e-06 8304 2 103.7 0.000101231 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.3211e-06 8304 2 103.7 0.000107692 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.69424e-06 8304 2 103.7 0.000125413 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.13054e-06 8304 2 103.7 0.00010254 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.17887e-06 8304 2 103.7 8.98714e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16959e-06 8304 2 103.7 8.90371e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.24463e-06 8304 2 103.7 9.98272e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.12144e-06 8304 2 103.7 9.34411e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.3051e-06 8304 2 103.7 9.26583e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.07862e-06 8304 2 103.7 9.05559e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.32967e-06 8304 2 103.7 9.55649e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.69634e-06 8304 2 103.7 0.000113528 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.13452e-06 8304 2 103.7 9.68411e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.37136e-06 8304 2 103.7 0.000100279 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.2181e-06 8304 2 103.7 9.28732e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.20764e-06 8304 2 103.7 9.87817e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.18952e-06 8304 2 103.7 0.000100555 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.19367e-06 8304 2 103.7 9.54325e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.31011e-06 8304 2 103.7 0.000100459 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.20098e-06 8304 2 103.7 9.9581e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.13201e-06 8304 2 103.7 9.15075e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.26324e-06 8304 2 103.7 0.000104678 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.44448e-06 8304 2 103.7 0.0001096 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.12279e-06 8304 2 103.7 9.24412e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.31813e-06 8304 2 103.7 9.87429e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.79533e-06 8304 2 103.7 0.000130754 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.3179e-06 8304 2 103.7 8.85347e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.24083e-06 8304 2 103.7 9.72111e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.46059e-06 8304 2 103.7 9.73139e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.28862e-06 8304 2 103.7 0.000103031 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.53461e-06 8304 2 103.7 0.000104922 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.30839e-06 8304 2 103.7 8.97877e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.1119e-06 8304 2 103.7 0.000106325 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.21553e-06 8304 2 103.7 0.000106516 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.31956e-06 8304 2 103.7 0.000110852 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.23971e-06 8304 2 103.7 0.000103768 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.03438e-06 8304 2 103.7 0.000111454 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3855e-06 8304 2 103.7 8.92479e-05 2768 2000000 2000000 788.94678 95589.251 1.27007 298.92 44.39004 59.101249 0 0 21654.593 32956.105 -219.20126 -216373.41 -161659.22 5641.9623 Loop time of 15279.8 on 32 procs for 2000000 steps with 9101 atoms Performance: 11.309 ns/day, 2.122 hours/ns, 130.892 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8761.8 | 9118.7 | 9528.8 | 242.0 | 59.68 Bond | 2.465 | 5.6475 | 10.098 | 88.3 | 0.04 Kspace | 3086.8 | 3498.7 | 3861.1 | 391.1 | 22.90 Neigh | 653.9 | 654.81 | 655.51 | 1.9 | 4.29 Comm | 969.17 | 987.64 | 1000.7 | 32.0 | 6.46 Output | 0.010473 | 0.012783 | 0.015349 | 1.2 | 0.00 Modify | 964.15 | 971.62 | 986.01 | 18.8 | 6.36 Other | | 42.66 | | | 0.28 Nlocal: 284.406 ave 299 max 262 min Histogram: 1 2 2 1 3 7 2 5 7 2 Nghost: 7202.62 ave 7259 max 7160 min Histogram: 1 5 4 6 6 2 3 2 1 2 Neighs: 155518 ave 164889 max 139991 min Histogram: 1 1 1 4 1 3 9 3 4 5 Total # of neighbors = 4976562 Ave neighs/atom = 546.81486 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98616 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) = 0.25784211 grid = 30 32 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028657894 estimated relative force accuracy = 8.6302397e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5796 1920 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.3855e-06 8304 2 103.7 8.92479e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13.07 | 13.18 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 789.84256 95589.251 1.27007 298.92 44.39004 59.101249 0 0 21654.593 32956.105 -219.20126 -216373.41 -161659.22 5641.9623 Loop time of 1.3438e-05 on 32 procs for 0 steps with 9101 atoms 100.7% 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 | | 1.344e-05 | | |100.00 Nlocal: 284.406 ave 299 max 262 min Histogram: 1 2 2 1 3 7 2 5 7 2 Nghost: 7202.62 ave 7259 max 7160 min Histogram: 1 5 4 6 6 2 3 2 1 2 Neighs: 155518 ave 164889 max 139991 min Histogram: 1 1 1 4 1 3 9 3 4 5 Total # of neighbors = 4976562 Ave neighs/atom = 546.81486 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