#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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) = 0.30192074 grid = 27 27 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0037881537 estimated relative force accuracy = 1.1407912e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5200 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999236 0.0471827 6000 1 98.0043 9.22797 2000 Per MPI rank memory allocation (min/avg/max) = 9.579 | 9.608 | 9.635 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 1880.1109 59830.193 1.0000033 447.33728 0 0 0 0 8751.7256 84557.958 -178.76427 -124284.9 -30975.218 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.32953e-06 6000 1 103.7 0.000102359 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.26945e-06 6000 1 103.7 0.000104554 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.16616e-06 6000 1 103.7 9.36633e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.49318e-06 6000 1 103.7 0.00010504 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.33949e-06 6000 1 103.7 0.000101667 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.55456e-06 6000 1 103.7 0.000111666 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.40189e-06 6000 1 103.7 0.00013266 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.25747e-06 6000 1 103.7 0.000101204 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.28921e-06 6000 1 103.7 9.51713e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.28453e-06 6000 1 103.7 9.60228e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.32947e-06 6000 1 103.7 0.000126012 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.64951e-06 6000 1 103.7 0.000101523 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.19559e-06 6000 1 103.7 8.87068e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.13739e-06 6000 1 103.7 0.0001054 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.24304e-06 6000 1 103.7 0.000107297 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.46761e-06 6000 1 103.7 0.000134728 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.52297e-06 6000 1 103.7 0.000106451 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.75707e-06 6000 1 103.7 0.000121788 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.48326e-06 6000 1 103.7 0.000123904 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.77302e-06 6000 1 103.7 0.000133115 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.29524e-06 6000 1 103.7 9.85502e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.42226e-06 6000 1 103.7 0.000106028 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.07947e-06 6000 1 103.7 9.19837e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.38786e-06 6000 1 103.7 9.84076e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.40516e-06 6000 1 103.7 0.000115025 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.08092e-06 6000 1 103.7 9.59449e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.34339e-06 6000 1 103.7 9.99127e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.2404e-06 6000 1 103.7 0.000117533 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.44889e-06 6000 1 103.7 0.000125587 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.53746e-06 6000 1 103.7 8.99813e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.19448e-06 6000 1 103.7 9.5253e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.23047e-06 6000 1 103.7 9.60094e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.32926e-06 6000 1 103.7 0.000105444 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.06534e-06 6000 1 103.7 9.03109e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.19363e-06 6000 1 103.7 0.000112583 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.13676e-06 6000 1 103.7 8.94383e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.29358e-06 6000 1 103.7 9.38286e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.56115e-06 6000 1 103.7 0.000114996 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.37767e-06 6000 1 103.7 0.000103831 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.21379e-06 6000 1 103.7 9.06586e-05 2000 2000000 2000000 -248.50655 59830.193 1.0000033 290.72933 0 0 0 0 5070.6196 97512.651 -178.76427 -124232.25 -21648.978 3465.5691 Loop time of 7587.71 on 32 procs for 2000000 steps with 6000 atoms Performance: 22.774 ns/day, 1.054 hours/ns, 263.584 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 | 3437.2 | 3726.4 | 3978.7 | 208.4 | 49.11 Bond | 1.7109 | 2.0013 | 3.125 | 16.9 | 0.03 Kspace | 2161.9 | 2417.2 | 2707.1 | 258.9 | 31.86 Neigh | 209.88 | 210.58 | 211.22 | 3.1 | 2.78 Comm | 609.71 | 619.82 | 629.43 | 18.3 | 8.17 Output | 0.0094775 | 0.011311 | 0.013021 | 1.0 | 0.00 Modify | 578.93 | 583.48 | 587.1 | 8.6 | 7.69 Other | | 28.21 | | | 0.37 Nlocal: 187.5 ave 198 max 174 min Histogram: 4 2 2 2 3 3 3 3 4 6 Nghost: 4719.66 ave 4823 max 4637 min Histogram: 4 2 2 6 6 2 5 3 1 1 Neighs: 67985.1 ave 78138 max 59011 min Histogram: 1 1 3 7 8 4 4 3 0 1 Total # of neighbors = 2175523 Ave neighs/atom = 362.58717 Ave special neighs/atom = 2 Neighbor list builds = 98481 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) = 0.30192074 grid = 27 27 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0037881537 estimated relative force accuracy = 1.1407912e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5200 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.21379e-06 6000 1 103.7 9.06586e-05 2000 Per MPI rank memory allocation (min/avg/max) = 9.58 | 9.609 | 9.635 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 -247.82776 59830.193 1.0000033 290.72933 0 0 0 0 5070.6196 97512.651 -178.76427 -124232.25 -21648.978 3465.5691 Loop time of 8.33384e-06 on 32 procs for 0 steps with 6000 atoms 111.0% 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 | | 8.334e-06 | | |100.00 Nlocal: 187.5 ave 198 max 174 min Histogram: 4 2 2 2 3 3 3 3 4 6 Nghost: 4719.66 ave 4823 max 4637 min Histogram: 4 2 2 6 6 2 5 3 1 1 Neighs: 67985.1 ave 78138 max 59011 min Histogram: 1 1 3 7 8 4 4 3 0 1 Total # of neighbors = 2175523 Ave neighs/atom = 362.58717 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out