#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 3275 = # 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00148 0.0774694 9825 1 97.5257 11.6128 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.26 | 13.65 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 -8884.2294 143340.91 1.3114365 420.87983 5.8820453 38.386046 0 0 40023.03 -92447.214 -319.55737 -317381.09 -369761.01 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.17372e-06 9825 1 103.7 0.000100391 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.49976e-06 9825 1 103.7 0.000116299 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.32215e-06 9825 1 103.7 9.72775e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 9.999e-07 9825 1 103.7 8.95539e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.11827e-06 9825 1 103.7 9.17128e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.17723e-06 9825 1 103.7 0.000100517 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.12215e-06 9825 1 103.7 0.00011 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.06495e-06 9825 1 103.7 9.31583e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.45165e-06 9825 1 103.7 9.44921e-05 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 2.00874e-06 9825 1 103.7 0.000104861 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.27913e-06 9825 1 103.7 9.67702e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.16385e-06 9825 1 103.7 9.37123e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.18085e-06 9825 1 103.7 9.40166e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.27982e-06 9825 1 103.7 0.000104569 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.34691e-06 9825 1 103.7 0.000108105 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.54597e-06 9825 1 103.7 0.000106275 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.11192e-06 9825 1 103.7 0.000107733 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.1815e-06 9825 1 103.7 0.000113004 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.11971e-06 9825 1 103.7 8.93861e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.03938e-06 9825 1 103.7 9.92509e-05 3275 1000000 1000000 -7072.2753 143340.91 1.3114365 297.88406 43.773539 70.988266 0 0 37155.357 -73116.325 -319.55737 -317448.18 -353294.39 7030.6757 Loop time of 9232.88 on 32 procs for 1000000 steps with 12250 atoms Performance: 9.358 ns/day, 2.565 hours/ns, 108.309 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 | 4249.6 | 5184.5 | 5760.2 | 630.8 | 56.15 Bond | 1.1183 | 2.6642 | 4.7708 | 68.1 | 0.03 Kspace | 2011 | 2585.7 | 3526.2 | 897.8 | 28.00 Neigh | 313.69 | 314.23 | 315 | 2.0 | 3.40 Comm | 507.85 | 543.71 | 566.01 | 81.2 | 5.89 Output | 0.01329 | 0.016072 | 0.018653 | 1.3 | 0.00 Modify | 557.55 | 576.24 | 608.06 | 71.4 | 6.24 Other | | 25.89 | | | 0.28 Nlocal: 382.812 ave 421 max 347 min Histogram: 3 0 5 2 4 6 9 2 0 1 Nghost: 7263.12 ave 7509 max 6974 min Histogram: 7 1 2 2 4 0 2 1 6 7 Neighs: 188060 ave 208870 max 153437 min Histogram: 3 1 4 0 0 2 2 9 7 4 Total # of neighbors = 6017914 Ave neighs/atom = 491.25829 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49842 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.03938e-06 9825 1 103.7 9.92509e-05 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.42 | 13.65 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 1000000 1000000 -7071.4377 143340.91 1.3114365 297.88406 43.773539 70.988266 0 0 37155.357 -73116.325 -319.55737 -317448.18 -353294.39 7030.6757 Loop time of 1.11544e-05 on 32 procs for 0 steps with 12250 atoms 114.6% 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 | | 1.115e-05 | | |100.00 Nlocal: 382.812 ave 421 max 347 min Histogram: 3 0 5 2 4 6 9 2 0 1 Nghost: 7263.12 ave 7509 max 6974 min Histogram: 7 1 2 2 4 0 2 1 6 7 Neighs: 188060 ave 208870 max 153437 min Histogram: 3 1 4 0 0 2 2 9 7 4 Total # of neighbors = 6017914 Ave neighs/atom = 491.25829 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out