#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2009 = # 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 300000 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25058007 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003281826 estimated relative force accuracy = 9.8831215e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00107 0.0913488 6027 2 97.6769 10.0712 2009 Per MPI rank memory allocation (min/avg/max) = 11.02 | 12.33 | 13.54 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-06 442.27685 139013.56 0.61716203 429.78001 6.5736717 31.143332 0 0 17068.541 17710.285 -75.986356 -144854.95 -110038.4 5832.8145 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23866e-06 6027 2 103.7 9.15709e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.31358e-06 6027 2 103.7 9.94e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.3236e-06 6027 2 103.7 8.80936e-05 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16656e-06 6027 2 103.7 0.00010426 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.69161e-06 6027 2 103.7 0.000130471 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.24354e-06 6027 2 103.7 0.000110311 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.78379e-06 6027 2 103.7 0.000126162 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.18849e-06 6027 2 103.7 9.37606e-05 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.11526e-06 6027 2 103.7 9.08739e-05 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34547e-06 6027 2 103.7 0.000112248 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.29168e-06 6027 2 103.7 9.45097e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.33149e-06 6027 2 103.7 9.57629e-05 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.49734e-06 6027 2 103.7 0.000104818 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 2.04497e-06 6027 2 103.7 0.000165479 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.08558e-06 6027 2 103.7 0.000100413 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.06711e-06 6027 2 103.7 9.62123e-05 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.76775e-06 6027 2 103.7 0.000123274 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14447e-06 6027 2 103.7 8.55847e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.37855e-06 6027 2 103.7 0.000106644 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.02671e-06 6027 2 103.7 0.000109035 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.09556e-06 6027 2 103.7 8.91837e-05 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.0713e-06 6027 2 103.7 9.47501e-05 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.05905e-06 6027 2 103.7 8.93587e-05 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.15893e-06 6027 2 103.7 9.11046e-05 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.18859e-06 6027 2 103.7 8.98349e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.29365e-06 6027 2 103.7 0.000107511 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.20218e-06 6027 2 103.7 9.12154e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.7068e-06 6027 2 103.7 0.00014061 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.63693e-06 6027 2 103.7 0.000120409 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33825e-06 6027 2 103.7 0.000106834 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.15125e-06 6027 2 103.7 9.56947e-05 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.41325e-06 6027 2 103.7 9.50949e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.19217e-06 6027 2 103.7 0.000104654 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.75937e-06 6027 2 103.7 0.000118364 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.43749e-06 6027 2 103.7 9.82227e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10193e-06 6027 2 103.7 9.89447e-05 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.26453e-06 6027 2 103.7 9.8837e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.29855e-06 6027 2 103.7 9.9801e-05 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.09061e-06 6027 2 103.7 9.23298e-05 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.48446e-06 6027 2 103.7 0.000123523 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.18775e-06 6027 2 103.7 9.12096e-05 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.24571e-06 6027 2 103.7 9.70213e-05 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.67085e-06 6027 2 103.7 0.000120545 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.13818e-06 6027 2 103.7 9.88759e-05 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.27577e-06 6027 2 103.7 0.000104652 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.08104e-06 6027 2 103.7 0.00010731 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.2639e-06 6027 2 103.7 0.000103231 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.27228e-06 6027 2 103.7 9.82714e-05 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.27158e-06 6027 2 103.7 9.8373e-05 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.68445e-06 6027 2 103.7 0.000133815 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.4634e-06 6027 2 103.7 9.79743e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.21618e-06 6027 2 103.7 9.22241e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.19071e-06 6027 2 103.7 0.000111207 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.12406e-06 6027 2 103.7 9.12383e-05 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.36715e-06 6027 2 103.7 0.000109432 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.24338e-06 6027 2 103.7 0.000151844 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.22486e-06 6027 2 103.7 9.70257e-05 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.23342e-06 6027 2 103.7 0.000102913 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.04161e-06 6027 2 103.7 9.7518e-05 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18459e-06 6027 2 103.7 0.000100911 2009 3000000 3000000 -6.849667 139013.56 0.61716203 301.83191 22.369986 42.49659 0 0 13351.425 31742.926 -75.986356 -144791.13 -99631.913 4096.3504 Loop time of 26706.5 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.706 ns/day, 2.473 hours/ns, 112.332 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.044 | 8051 | 19192 |8825.2 | 30.15 Bond | 2.5262 | 5.8491 | 13.808 | 142.1 | 0.02 Kspace | 4266.9 | 15460 | 23587 |6403.6 | 57.89 Neigh | 1306.9 | 1313.1 | 1322.7 | 14.2 | 4.92 Comm | 352.6 | 684.93 | 902.19 | 794.6 | 2.56 Output | 0.012746 | 0.014597 | 0.016282 | 0.8 | 0.00 Modify | 979.48 | 1143.4 | 1374.1 | 463.9 | 4.28 Other | | 48.29 | | | 0.18 Nlocal: 205.094 ave 410 max 0 min Histogram: 16 0 0 0 0 0 0 0 0 16 Nghost: 4058.38 ave 7334 max 781 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 95378 ave 234476 max 0 min Histogram: 16 0 0 0 0 4 0 1 7 4 Total # of neighbors = 3052095 Ave neighs/atom = 465.04571 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146364 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25058007 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003281826 estimated relative force accuracy = 9.8831215e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18459e-06 6027 2 103.7 0.000100911 2009 Per MPI rank memory allocation (min/avg/max) = 11.04 | 12.55 | 13.54 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 3000000 3000000 -6.4710633 139013.56 0.61716203 301.83191 22.369986 42.49659 0 0 13351.425 31742.926 -75.986356 -144791.13 -99631.913 4096.3504 Loop time of 7.59287e-06 on 32 procs for 0 steps with 6563 atoms 115.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.593e-06 | | |100.00 Nlocal: 205.094 ave 410 max 0 min Histogram: 16 0 0 0 0 0 0 0 0 16 Nghost: 4058.38 ave 7334 max 781 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 95378 ave 234476 max 0 min Histogram: 16 0 0 0 0 4 0 1 7 4 Total # of neighbors = 3052095 Ave neighs/atom = 465.04571 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out