#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 4 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 400000 400000 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 400 1 400 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 4000000 2.5.restart dump sci all custom 400000 2.5.xyz id mol type q xs ys zs timestep 1 run 4000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.09051e-13 11184 2 103.7 9.04379e-11 3728 Per MPI rank memory allocation (min/avg/max) = 17.84 | 20.77 | 29.38 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 336054.86 143799.62 1.371895 300.02436 285.30279 377.29377 0 0 271586.02 -52622.164 -383.45046 -378998.54 -159372.09 8238.4355 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.57921e-06 11184 2 103.7 0.000121986 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.49798e-06 11184 2 103.7 9.5447e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.44372e-06 11184 2 103.7 9.52718e-05 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.38824e-06 11184 2 103.7 9.12637e-05 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.21294e-06 11184 2 103.7 9.44598e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.34339e-06 11184 2 103.7 9.42393e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.17615e-06 11184 2 103.7 9.14384e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.27323e-06 11184 2 103.7 0.000117779 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.51481e-06 11184 2 103.7 9.53781e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.20207e-06 11184 2 103.7 8.68317e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.38616e-06 11184 2 103.7 0.000103448 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2785e-06 11184 2 103.7 9.30702e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.21125e-06 11184 2 103.7 9.63043e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.32417e-06 11184 2 103.7 9.83762e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.43144e-06 11184 2 103.7 0.000102644 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 2.00977e-06 11184 2 103.7 0.000124889 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.78616e-06 11184 2 103.7 0.000102901 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.24102e-06 11184 2 103.7 9.8891e-05 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.08473e-06 11184 2 103.7 0.000102625 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.34566e-06 11184 2 103.7 9.43273e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.30865e-06 11184 2 103.7 9.96901e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.32486e-06 11184 2 103.7 9.31825e-05 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.45236e-06 11184 2 103.7 0.000142977 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.17752e-06 11184 2 103.7 8.87785e-05 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.42886e-06 11184 2 103.7 0.000110814 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.26985e-06 11184 2 103.7 0.000114178 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.31911e-06 11184 2 103.7 9.44319e-05 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.07155e-06 11184 2 103.7 9.91584e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.3093e-06 11184 2 103.7 9.62095e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.61031e-06 11184 2 103.7 9.38779e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.4661e-06 11184 2 103.7 9.88216e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.10232e-06 11184 2 103.7 9.40938e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.10895e-06 11184 2 103.7 9.55432e-05 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.07166e-06 11184 2 103.7 9.26467e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.25954e-06 11184 2 103.7 8.99749e-05 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.6397e-06 11184 2 103.7 9.64887e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.25273e-06 11184 2 103.7 9.3846e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.15933e-06 11184 2 103.7 9.97886e-05 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.35709e-06 11184 2 103.7 0.000100553 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.75829e-06 11184 2 103.7 9.72127e-05 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.34013e-06 11184 2 103.7 9.22845e-05 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.30229e-06 11184 2 103.7 9.31121e-05 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.2527e-06 11184 2 103.7 9.50503e-05 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.06019e-06 11184 2 103.7 9.32544e-05 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.69287e-06 11184 2 103.7 0.000114996 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.16543e-06 11184 2 103.7 9.20679e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.17181e-06 11184 2 103.7 8.84621e-05 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.271e-06 11184 2 103.7 9.96002e-05 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.10795e-06 11184 2 103.7 9.72287e-05 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 2.05341e-06 11184 2 103.7 0.00011563 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.25203e-06 11184 2 103.7 0.000106608 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.38702e-06 11184 2 103.7 9.48401e-05 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.81834e-06 11184 2 103.7 9.60048e-05 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.20017e-06 11184 2 103.7 9.55776e-05 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.13422e-06 11184 2 103.7 8.96569e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.20078e-06 11184 2 103.7 9.97003e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.14909e-06 11184 2 103.7 9.4941e-05 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.13179e-06 11184 2 103.7 8.84366e-05 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.06818e-06 11184 2 103.7 9.72376e-05 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.35184e-06 11184 2 103.7 0.000118982 3728 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.29525e-06 11184 2 103.7 0.00010269 3728 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.10341e-06 11184 2 103.7 9.92315e-05 3728 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.32775e-06 11184 2 103.7 0.00010037 3728 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.07128e-06 11184 2 103.7 9.96816e-05 3728 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.29754e-06 11184 2 103.7 0.000104688 3728 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.4891e-06 11184 2 103.7 9.79826e-05 3728 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.1754e-06 11184 2 103.7 9.19951e-05 3728 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.32036e-06 11184 2 103.7 9.79263e-05 3728 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.06596e-06 11184 2 103.7 9.16647e-05 3728 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.12771e-06 11184 2 103.7 9.66364e-05 3728 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.15873e-06 11184 2 103.7 9.02374e-05 3728 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.68034e-06 11184 2 103.7 9.93856e-05 3728 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.14527e-06 11184 2 103.7 9.89035e-05 3728 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.60153e-06 11184 2 103.7 0.000129921 3728 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.43281e-06 11184 2 103.7 0.000110598 3728 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.20323e-06 11184 2 103.7 9.70482e-05 3728 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.38335e-06 11184 2 103.7 0.000114008 3728 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.18886e-06 11184 2 103.7 9.22465e-05 3728 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.18346e-06 11184 2 103.7 8.92521e-05 3728 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.26496e-06 11184 2 103.7 9.43256e-05 3728 4000000 4000000 335589.14 143799.62 1.371895 295.91765 290.74343 379.7459 0 0 271398.51 -52169.42 -383.45046 -379001.14 -159101.56 8125.6685 Loop time of 139286 on 8 procs for 4000000 steps with 13901 atoms Performance: 2.481 ns/day, 9.673 hours/ns, 28.718 timesteps/s 98.5% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 66816 | 81502 | 1.1502e+05 |6077.6 | 58.51 Bond | 24.623 | 74.742 | 195.81 | 776.5 | 0.05 Kspace | 14593 | 48255 | 63019 |7932.8 | 34.64 Neigh | 6202.7 | 6207.3 | 6211.6 | 3.6 | 4.46 Comm | 1047.3 | 1119.3 | 1187.7 | 138.7 | 0.80 Output | 0.030503 | 0.033938 | 0.037068 | 1.2 | 0.00 Modify | 1947.7 | 1978.5 | 2016.9 | 55.6 | 1.42 Other | | 149 | | | 0.11 Nlocal: 1737.62 ave 2079 max 1576 min Histogram: 3 2 1 0 0 0 0 0 0 2 Nghost: 13836 ave 14538 max 12618 min Histogram: 2 0 0 0 0 0 0 3 1 2 Neighs: 975664 ave 1.34717e+06 max 804850 min Histogram: 3 3 0 0 0 0 0 0 0 2 Total # of neighbors = 7805310 Ave neighs/atom = 561.4927 Ave special neighs/atom = 1.8838932 Neighbor list builds = 200126 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 21978 9600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.26496e-06 11184 2 103.7 9.43256e-05 3728 Per MPI rank memory allocation (min/avg/max) = 17.84 | 20.77 | 29.38 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 4000000 4000000 335590.13 143799.62 1.371895 295.91765 290.74343 379.7459 0 0 271398.51 -52169.42 -383.45046 -379001.14 -159101.56 8125.6685 Loop time of 3.24175e-06 on 8 procs for 0 steps with 13901 atoms 135.0% 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 | | 3.242e-06 | | |100.00 Nlocal: 1737.62 ave 2079 max 1576 min Histogram: 3 2 1 0 0 0 0 0 0 2 Nghost: 13836 ave 14538 max 12618 min Histogram: 2 0 0 0 0 0 0 3 1 2 Neighs: 975664 ave 1.34717e+06 max 804850 min Histogram: 3 3 0 0 0 0 0 0 0 2 Total # of neighbors = 7805310 Ave neighs/atom = 561.4927 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out