#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 200 ps with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 npt temp 298.2 298.2 100 iso 1 1 100 drag 0 mtk yes nreset 4000 fix 2 movable ave/time 1 19999 20000 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 2.5_averages.txt off 1 fix 3 movable ave/time 20 1 20 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 2.5_instantaneous.txt restart 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.56901e-13 8304 2 103.7 7.50902e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.64 | 12.98 | 13.33 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 2451.5757 92859.489 1.3074058 297.68012 40.563187 82.868926 0 0 22236.995 89776.188 -448.40969 -273796.57 -161659.96 5618.5602 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970128 1.53557e-06 8304 2 103.7 0.000112121 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969967 1.06107e-06 8304 2 103.7 0.000104413 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.96996 1.59721e-06 8304 2 103.7 0.000114521 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969987 1.21272e-06 8304 2 103.7 9.41549e-05 2768 200000 200000 71.508109 97527.271 1.2448317 295.70074 40.487057 90.150361 0 0 21254.167 91224.31 -426.94822 -273790.81 -161181.69 5581.2005 Loop time of 1249.73 on 32 procs for 200000 steps with 9101 atoms Performance: 13.827 ns/day, 1.736 hours/ns, 160.034 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 424.84 | 450.38 | 483.52 | 72.4 | 36.04 Bond | 0.21249 | 0.5523 | 1.1173 | 35.6 | 0.04 Kspace | 432.27 | 465.47 | 491 | 71.1 | 37.25 Neigh | 34.395 | 34.451 | 34.52 | 0.6 | 2.76 Comm | 72.486 | 73.498 | 74.316 | 5.0 | 5.88 Output | 0.010491 | 0.012687 | 0.014746 | 1.2 | 0.00 Modify | 148.54 | 181.28 | 217.26 | 207.3 | 14.51 Other | | 44.1 | | | 3.53 Nlocal: 284.406 ave 305 max 267 min Histogram: 2 3 2 7 2 6 5 3 1 1 Nghost: 4827.12 ave 4877 max 4766 min Histogram: 1 2 2 3 6 3 6 3 3 3 Neighs: 84435.3 ave 91094 max 78869 min Histogram: 3 4 2 6 5 2 4 1 2 3 Total # of neighbors = 2701931 Ave neighs/atom = 296.88287 Ave special neighs/atom = 1.8929788 Neighbor list builds = 10253 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 2.5.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) = 0.32610766 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.003114396 estimated relative force accuracy = 9.3789111e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.969987 1.21272e-06 8304 2 103.7 9.41549e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.62 | 12.99 | 13.32 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 200000 200000 -2.6813812 97527.271 1.2448317 295.70074 40.487057 90.150361 0 0 21254.167 90214.653 -426.94822 -272781.15 -161181.7 5581.2005 Loop time of 1.16867e-05 on 32 procs for 0 steps with 9101 atoms 112.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.169e-05 | | |100.00 Nlocal: 284.406 ave 305 max 267 min Histogram: 2 3 2 7 2 6 5 3 1 1 Nghost: 4827.12 ave 4877 max 4766 min Histogram: 1 2 2 3 6 3 6 3 3 3 Neighs: 84435.3 ave 91094 max 78869 min Histogram: 3 4 2 6 5 2 4 1 2 3 Total # of neighbors = 2701931 Ave neighs/atom = 296.88287 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 0:40:09