#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 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 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 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 2.5_averages.txt off 1 fix 3 movable ave/time 200 1 200 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.74794e-13 8304 2 103.7 7.24754e-11 2768 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.42 | 17.76 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 -983.86615 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.267 -320.88394 -277671.63 -268045.9 6482.7542 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.37948e-06 8304 2 103.7 0.000101475 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11935e-06 8304 2 103.7 9.93627e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32366e-06 8304 2 103.7 0.000100653 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13757e-06 8304 2 103.7 9.64525e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.21001e-06 8304 2 103.7 9.71364e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.402e-06 8304 2 103.7 0.000102671 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.11903e-06 8304 2 103.7 0.000113941 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10036e-06 8304 2 103.7 9.36466e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.30144e-06 8304 2 103.7 9.07179e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2601e-06 8304 2 103.7 9.71951e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2477e-06 8304 2 103.7 9.62525e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.06858e-06 8304 2 103.7 9.7842e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.42337e-06 8304 2 103.7 9.83287e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.48307e-06 8304 2 103.7 0.000111011 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23654e-06 8304 2 103.7 0.000110676 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.27105e-06 8304 2 103.7 9.53511e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30781e-06 8304 2 103.7 0.000100221 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15506e-06 8304 2 103.7 9.09363e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31547e-06 8304 2 103.7 9.40702e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.0335e-06 8304 2 103.7 9.42096e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2405e-06 8304 2 103.7 9.71176e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.24573e-06 8304 2 103.7 0.000108016 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.18251e-06 8304 2 103.7 9.40945e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20939e-06 8304 2 103.7 9.63414e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.71743e-06 8304 2 103.7 0.000109494 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.41897e-06 8304 2 103.7 0.000107 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.20532e-06 8304 2 103.7 9.05077e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.24133e-06 8304 2 103.7 9.54376e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.11718e-06 8304 2 103.7 8.89834e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.22438e-06 8304 2 103.7 9.5757e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.13144e-06 8304 2 103.7 0.000121617 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15793e-06 8304 2 103.7 9.62541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.4359e-06 8304 2 103.7 0.000102096 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.15989e-06 8304 2 103.7 9.23426e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.10184e-06 8304 2 103.7 0.000100673 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.30244e-06 8304 2 103.7 8.66762e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.30564e-06 8304 2 103.7 9.72739e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.22687e-06 8304 2 103.7 9.75737e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.28625e-06 8304 2 103.7 9.72527e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.14012e-06 8304 2 103.7 9.39181e-05 2768 2000000 2000000 -882.55982 143908.11 1.3942094 297.54551 58.318921 81.23566 0 0 29105.349 -19628.816 -320.88394 -277695.78 -268079.69 6524.2324 Loop time of 50327.3 on 8 procs for 2000000 steps with 10381 atoms Performance: 3.434 ns/day, 6.990 hours/ns, 39.740 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5287.4 | 26914 | 39705 |7711.0 | 53.48 Bond | 2.2055 | 10.742 | 18.558 | 164.1 | 0.02 Kspace | 7068.5 | 19879 | 41530 |8982.3 | 39.50 Neigh | 1995.7 | 1998.4 | 2001.3 | 4.4 | 3.97 Comm | 467.23 | 552.17 | 606 | 216.3 | 1.10 Output | 0.025472 | 0.028225 | 0.030959 | 1.1 | 0.00 Modify | 874.78 | 914.23 | 974.67 | 123.2 | 1.82 Other | | 58.59 | | | 0.12 Nlocal: 1297.62 ave 1613 max 566 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10470.1 ave 13058 max 8339 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593734 ave 831352 max 112581 min Histogram: 2 0 0 0 0 0 0 1 2 3 Total # of neighbors = 4749869 Ave neighs/atom = 457.55409 Ave special neighs/atom = 1.6595704 Neighbor list builds = 99271 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.14012e-06 8304 2 103.7 9.39181e-05 2768 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.45 | 17.76 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 2000000 2000000 -881.96211 143908.11 1.3942094 297.54551 58.318921 81.23566 0 0 29105.349 -19628.816 -320.88394 -277695.78 -268079.69 6524.2324 Loop time of 7.05062e-06 on 8 procs for 0 steps with 10381 atoms 122.3% 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 | | 7.051e-06 | | |100.00 Nlocal: 1297.62 ave 1613 max 566 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10470.1 ave 13058 max 8339 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593734 ave 831352 max 112581 min Histogram: 2 0 0 0 0 0 0 1 2 3 Total # of neighbors = 4749869 Ave neighs/atom = 457.55409 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out