#------------------------------------------------------------------------------- # 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 = 18700 7776 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00147 0.0780296 9825 1 97.5233 11.6143 3275 Per MPI rank memory allocation (min/avg/max) = 16.16 | 16.72 | 17.08 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 -8955.3724 143340.91 1.3114365 420.87983 5.8520294 38.473088 0 0 39994.656 -92412.022 -319.55737 -317378.35 -369751.4 9933.6285 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.20113e-06 9825 1 103.7 0.000105586 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.22346e-06 9825 1 103.7 8.91809e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.16755e-06 9825 1 103.7 0.000100206 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.25158e-06 9825 1 103.7 9.14866e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.18858e-06 9825 1 103.7 9.7943e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.12286e-06 9825 1 103.7 9.12515e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.30517e-06 9825 1 103.7 0.000103404 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.18182e-06 9825 1 103.7 9.66162e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.45124e-06 9825 1 103.7 0.000118579 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.44067e-06 9825 1 103.7 9.40342e-05 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.36079e-06 9825 1 103.7 9.89092e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.22265e-06 9825 1 103.7 0.000119612 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.26885e-06 9825 1 103.7 9.25499e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.35855e-06 9825 1 103.7 9.71121e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.23915e-06 9825 1 103.7 9.05919e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.25497e-06 9825 1 103.7 0.000103788 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.16939e-06 9825 1 103.7 9.45447e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.21151e-06 9825 1 103.7 0.000103875 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.29662e-06 9825 1 103.7 9.56842e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.29119e-06 9825 1 103.7 0.000116562 3275 1000000 1000000 -7326.5107 143340.91 1.3114365 301.42215 42.503336 58.081086 0 0 36999.911 -73193.627 -319.55737 -317454.18 -353547.31 7114.1818 Loop time of 26381.3 on 8 procs for 1000000 steps with 12250 atoms Performance: 3.275 ns/day, 7.328 hours/ns, 37.906 timesteps/s 99.1% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15905 | 19107 | 20813 |1148.5 | 72.43 Bond | 1.5054 | 6.0648 | 8.521 | 109.0 | 0.02 Kspace | 3679.6 | 5386.2 | 8594.6 |2166.6 | 20.42 Neigh | 1090.6 | 1091.4 | 1092.1 | 1.5 | 4.14 Comm | 258.27 | 261.45 | 264.12 | 12.6 | 0.99 Output | 0.028341 | 0.031412 | 0.03437 | 1.1 | 0.00 Modify | 489.4 | 490.72 | 492.81 | 4.6 | 1.86 Other | | 38.19 | | | 0.14 Nlocal: 1531.25 ave 1621 max 1431 min Histogram: 2 0 0 0 1 1 1 2 0 1 Nghost: 12153 ave 12507 max 11995 min Histogram: 3 2 1 0 0 0 0 1 0 1 Neighs: 752635 ave 819431 max 639267 min Histogram: 2 0 0 0 0 1 0 1 1 3 Total # of neighbors = 6021080 Ave neighs/atom = 491.51673 Ave special neighs/atom = 1.6481633 Neighbor list builds = 49845 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 = 18700 7776 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.29119e-06 9825 1 103.7 0.000116562 3275 Per MPI rank memory allocation (min/avg/max) = 16.17 | 16.94 | 17.27 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 -7325.6393 143340.91 1.3114365 301.42215 42.503336 58.081086 0 0 36999.911 -73193.627 -319.55737 -317454.18 -353547.31 7114.1818 Loop time of 3.194e-06 on 8 procs for 0 steps with 12250 atoms 125.2% 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 | | 3.194e-06 | | |100.00 Nlocal: 1531.25 ave 1621 max 1431 min Histogram: 2 0 0 0 1 1 1 2 0 1 Nghost: 12153 ave 12507 max 11995 min Histogram: 3 2 1 0 0 0 0 1 0 1 Neighs: 752635 ave 819431 max 639267 min Histogram: 2 0 0 0 0 1 0 1 1 3 Total # of neighbors = 6021080 Ave neighs/atom = 491.51673 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