#------------------------------------------------------------------------------- # Stage 2.5: 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 3000000 2.5.restart dump sci all custom 300000 2.5.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) = 0.22644817 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036818993 estimated relative force accuracy = 1.108793e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 7.95586e-13 6000 1 103.7 7.7307e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.252 | 9.866 | 11.07 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 -116.72564 119700 0.49983619 300.80388 0 0 0 0 5105.6669 66836.168 -41.077287 -93208.705 -21266.87 3585.6603 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.36367e-06 6000 1 103.7 0.000116235 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.38474e-06 6000 1 103.7 9.99656e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.15457e-06 6000 1 103.7 8.78815e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.18146e-06 6000 1 103.7 9.94948e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.59084e-06 6000 1 103.7 0.000108149 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.35629e-06 6000 1 103.7 0.000104374 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.06481e-06 6000 1 103.7 0.000101814 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.34544e-06 6000 1 103.7 0.000102265 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.24899e-06 6000 1 103.7 9.70791e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.30568e-06 6000 1 103.7 9.30692e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.86168e-06 6000 1 103.7 0.000126688 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.1857e-06 6000 1 103.7 9.35622e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.32884e-06 6000 1 103.7 9.29149e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.70949e-06 6000 1 103.7 0.000120673 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.27622e-06 6000 1 103.7 0.00012341 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.13516e-06 6000 1 103.7 0.000117219 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.65922e-06 6000 1 103.7 0.000110418 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.25645e-06 6000 1 103.7 9.7626e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.29216e-06 6000 1 103.7 9.15913e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.09611e-06 6000 1 103.7 8.9089e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.13192e-06 6000 1 103.7 8.91218e-05 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.23377e-06 6000 1 103.7 9.42834e-05 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.19408e-06 6000 1 103.7 0.000118255 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.92248e-06 6000 1 103.7 0.000128528 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.29229e-06 6000 1 103.7 0.000113626 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.21719e-06 6000 1 103.7 9.65316e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.26415e-06 6000 1 103.7 9.97572e-05 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.71554e-06 6000 1 103.7 0.000105279 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.55702e-06 6000 1 103.7 0.000105969 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.54509e-06 6000 1 103.7 9.86316e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.19221e-06 6000 1 103.7 0.000122971 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.4547e-06 6000 1 103.7 9.25828e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.1667e-06 6000 1 103.7 9.14736e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.25604e-06 6000 1 103.7 0.000100006 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.18614e-06 6000 1 103.7 0.000111083 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.38362e-06 6000 1 103.7 0.000106162 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.08536e-06 6000 1 103.7 9.53127e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.42462e-06 6000 1 103.7 0.000114698 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.88574e-06 6000 1 103.7 0.000125377 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.86789e-06 6000 1 103.7 0.000136074 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.20473e-06 6000 1 103.7 9.87346e-05 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.26856e-06 6000 1 103.7 0.00010758 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.13653e-06 6000 1 103.7 0.000101188 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.22432e-06 6000 1 103.7 9.7715e-05 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.32896e-06 6000 1 103.7 9.39843e-05 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.22337e-06 6000 1 103.7 9.4079e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.15231e-06 6000 1 103.7 8.97479e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.28092e-06 6000 1 103.7 0.000106673 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.30859e-06 6000 1 103.7 9.93513e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.51841e-06 6000 1 103.7 0.000103956 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.59426e-06 6000 1 103.7 0.000121305 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.22971e-06 6000 1 103.7 0.000100945 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.32498e-06 6000 1 103.7 9.78932e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.57815e-06 6000 1 103.7 0.000108859 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.2487e-06 6000 1 103.7 0.000136675 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.09109e-06 6000 1 103.7 9.12994e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.14584e-06 6000 1 103.7 8.84403e-05 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.60119e-06 6000 1 103.7 0.000100775 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.11752e-06 6000 1 103.7 9.67482e-05 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.3843e-06 6000 1 103.7 9.40925e-05 2000 3000000 3000000 -316.55006 119700 0.49983619 301.90244 0 0 0 0 4958.1816 66978.616 -41.077287 -93204.124 -21267.327 3598.7554 Loop time of 27724.3 on 32 procs for 3000000 steps with 6000 atoms Performance: 9.349 ns/day, 2.567 hours/ns, 108.208 timesteps/s 98.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4088 | 9976 | 21338 |9774.4 | 35.98 Bond | 2.0642 | 3.2565 | 5.0292 | 32.6 | 0.01 Kspace | 3692 | 15152 | 25356 |8003.2 | 54.65 Neigh | 1042.7 | 1054 | 1082.4 | 39.2 | 3.80 Comm | 59.062 | 483.42 | 709.97 |1104.4 | 1.74 Output | 0.011381 | 0.012964 | 0.014312 | 0.8 | 0.00 Modify | 861.35 | 994.42 | 1172.8 | 385.5 | 3.59 Other | | 61.64 | | | 0.22 Nlocal: 187.5 ave 385 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 4534.97 ave 9016 max 0 min Histogram: 8 0 0 8 0 0 5 3 0 8 Neighs: 120126 ave 274592 max 0 min Histogram: 16 0 0 0 0 0 2 2 4 8 Total # of neighbors = 3844024 Ave neighs/atom = 640.67067 Ave special neighs/atom = 2 Neighbor list builds = 148504 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.22644817 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036818993 estimated relative force accuracy = 1.108793e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.3843e-06 6000 1 103.7 9.40925e-05 2000 Per MPI rank memory allocation (min/avg/max) = 8.252 | 9.866 | 11.07 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 -316.26995 119700 0.49983619 301.90244 0 0 0 0 4958.1816 66978.616 -41.077287 -93204.124 -21267.327 3598.7554 Loop time of 1.25557e-05 on 32 procs for 0 steps with 6000 atoms 107.8% 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 | | 1.256e-05 | | |100.00 Nlocal: 187.5 ave 385 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 4534.97 ave 9016 max 0 min Histogram: 8 0 0 8 0 0 5 3 0 8 Neighs: 120126 ave 274592 max 0 min Histogram: 16 0 0 0 0 0 2 2 4 8 Total # of neighbors = 3844024 Ave neighs/atom = 640.67067 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 20:30:24