#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 1949 = # of frozen angles find clusters CPU = 0.000 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 npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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) = 0.25064772 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0038579523 estimated relative force accuracy = 1.1618109e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999423 0.0519776 5847 1 97.8147 9.74609 1949 Per MPI rank memory allocation (min/avg/max) = 11.77 | 11.8 | 11.83 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 -2055.0971 61383.024 1.0542115 440.68389 0 0 0 0 10498.023 50006.526 -112.69358 -109073.94 -48569.391 5358.1539 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969982 1.08167e-06 5847 1 103.7 0.000110293 1949 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97001 1.33331e-06 5847 1 103.7 9.0062e-05 1949 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970028 1.49685e-06 5847 1 103.7 0.000124933 1949 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970033 1.58775e-06 5847 1 103.7 0.000115016 1949 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969989 1.48261e-06 5847 1 103.7 9.1957e-05 1949 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970064 2.21806e-06 5847 1 103.7 0.000160787 1949 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969812 1.48233e-06 5847 1 103.7 0.00014203 1949 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969992 1.20424e-06 5847 1 103.7 0.000101932 1949 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970107 1.78383e-06 5847 1 103.7 0.000122725 1949 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970012 1.28235e-06 5847 1 103.7 9.95833e-05 1949 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969963 1.27318e-06 5847 1 103.7 8.95494e-05 1949 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970001 1.25743e-06 5847 1 103.7 9.45804e-05 1949 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969995 1.29229e-06 5847 1 103.7 8.8257e-05 1949 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970001 1.10124e-06 5847 1 103.7 9.68049e-05 1949 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969987 1.36989e-06 5847 1 103.7 0.000102035 1949 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970097 2.05067e-06 5847 1 103.7 0.000145788 1949 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970001 1.06679e-06 5847 1 103.7 9.20595e-05 1949 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969893 1.3814e-06 5847 1 103.7 0.00012222 1949 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969967 1.40802e-06 5847 1 103.7 0.000140793 1949 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969998 1.24961e-06 5847 1 103.7 9.21727e-05 1949 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970014 1.34631e-06 5847 1 103.7 0.000140917 1949 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969995 1.63398e-06 5847 1 103.7 0.000136977 1949 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969812 1.10093e-06 5847 1 103.7 0.000103039 1949 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969874 1.92593e-06 5847 1 103.7 0.000139216 1949 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969856 1.41587e-06 5847 1 103.7 0.000145341 1949 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969964 1.23247e-06 5847 1 103.7 8.98934e-05 1949 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970133 1.4596e-06 5847 1 103.7 0.000122162 1949 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970022 1.21253e-06 5847 1 103.7 0.000105116 1949 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969904 1.53549e-06 5847 1 103.7 0.00014063 1949 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969917 1.17154e-06 5847 1 103.7 0.000124988 1949 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970004 1.24865e-06 5847 1 103.7 9.57978e-05 1949 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970135 1.56733e-06 5847 1 103.7 0.00010553 1949 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970006 1.4698e-06 5847 1 103.7 9.66091e-05 1949 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970027 1.6386e-06 5847 1 103.7 0.000125949 1949 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970013 1.50873e-06 5847 1 103.7 9.90188e-05 1949 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970086 1.31435e-06 5847 1 103.7 9.47181e-05 1949 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970018 1.53949e-06 5847 1 103.7 0.000120122 1949 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969928 1.68674e-06 5847 1 103.7 0.000114842 1949 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970039 1.14514e-06 5847 1 103.7 9.71384e-05 1949 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970047 1.58129e-06 5847 1 103.7 0.000125852 1949 2000000 2000000 236.66004 62404.932 1.0369483 298.41481 0 0 0 0 7086.2196 62585.518 -110.84817 -109057.65 -39385.911 3628.3433 Loop time of 30892.7 on 8 procs for 2000000 steps with 6029 atoms Performance: 5.594 ns/day, 4.291 hours/ns, 64.740 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21440 | 22506 | 23597 | 523.9 | 72.85 Bond | 2.8095 | 3.4669 | 4.462 | 23.5 | 0.01 Kspace | 3649.1 | 4739.6 | 5800.3 |1139.1 | 15.34 Neigh | 1373.6 | 1373.9 | 1374.3 | 0.6 | 4.45 Comm | 495.83 | 497.8 | 501.66 | 9.3 | 1.61 Output | 0.014738 | 0.015793 | 0.016735 | 0.6 | 0.00 Modify | 1484.3 | 1586.2 | 1713 | 245.6 | 5.13 Other | | 186.1 | | | 0.60 Nlocal: 753.625 ave 782 max 730 min Histogram: 1 2 0 1 0 2 0 0 0 2 Nghost: 9814.25 ave 9930 max 9725 min Histogram: 2 0 0 2 1 1 0 1 0 1 Neighs: 418227 ave 443648 max 385626 min Histogram: 2 0 0 1 1 0 1 0 0 3 Total # of neighbors = 3345815 Ave neighs/atom = 554.95356 Ave special neighs/atom = 1.9396251 Neighbor list builds = 102624 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) = 0.25030454 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0039221722 estimated relative force accuracy = 1.1811505e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970047 1.58129e-06 5847 1 103.7 0.000125852 1949 Per MPI rank memory allocation (min/avg/max) = 11.77 | 11.8 | 11.83 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 534.92433 62404.932 1.0369483 298.41481 0 0 0 0 7086.2196 62436.525 -110.84817 -108908.66 -39385.911 3628.3433 Loop time of 3.18238e-06 on 8 procs for 0 steps with 6029 atoms 129.6% CPU use with 8 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 | | 3.182e-06 | | |100.00 Nlocal: 753.625 ave 782 max 730 min Histogram: 1 2 0 1 0 2 0 0 0 2 Nghost: 9814.25 ave 9930 max 9725 min Histogram: 2 0 0 2 1 1 0 1 0 1 Neighs: 418227 ave 443648 max 385626 min Histogram: 2 0 0 1 1 0 1 0 0 3 Total # of neighbors = 3345815 Ave neighs/atom = 554.95356 Ave special neighs/atom = 1.9396251 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:36:16