#------------------------------------------------------------------------------- # 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 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 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 2.5_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 file 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25741609 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 = 12100 4500 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.2109e-13 8304 2 103.7 7.55165e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.81 | 14.18 | 14.85 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 -1178.3069 143908.11 1.3942094 299.37969 48.316107 63.912815 0 0 29025.582 -19477.43 -320.88394 -277700.96 -268040.58 6564.4503 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.12081e-06 8304 2 103.7 9.23573e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.4142e-06 8304 2 103.7 0.000109565 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.10375e-06 8304 2 103.7 0.000100498 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.43945e-06 8304 2 103.7 0.000103905 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16928e-06 8304 2 103.7 9.39571e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.39881e-06 8304 2 103.7 9.05805e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20163e-06 8304 2 103.7 0.000102123 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.11829e-06 8304 2 103.7 9.61969e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.32819e-06 8304 2 103.7 0.000102582 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34523e-06 8304 2 103.7 0.000101477 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.26906e-06 8304 2 103.7 8.58777e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.08826e-06 8304 2 103.7 9.24868e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.63063e-06 8304 2 103.7 0.000112908 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20361e-06 8304 2 103.7 0.000108385 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.11656e-06 8304 2 103.7 9.46441e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.57794e-06 8304 2 103.7 0.000103332 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.19189e-06 8304 2 103.7 9.53158e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14687e-06 8304 2 103.7 9.09857e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25929e-06 8304 2 103.7 0.000103024 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.16354e-06 8304 2 103.7 0.000110327 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.5334e-06 8304 2 103.7 0.00010261 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.13894e-06 8304 2 103.7 9.87008e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22659e-06 8304 2 103.7 0.000102781 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.36434e-06 8304 2 103.7 9.79496e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.25857e-06 8304 2 103.7 0.000103117 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.26808e-06 8304 2 103.7 8.99423e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.38458e-06 8304 2 103.7 9.81555e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.10942e-06 8304 2 103.7 8.97422e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.56024e-06 8304 2 103.7 0.000130493 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.35655e-06 8304 2 103.7 0.000106654 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.61443e-06 8304 2 103.7 9.36837e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.6099e-06 8304 2 103.7 0.000100646 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.11586e-06 8304 2 103.7 9.79479e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.27693e-06 8304 2 103.7 9.43378e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.16285e-06 8304 2 103.7 0.000108164 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.20492e-06 8304 2 103.7 9.99229e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.43682e-06 8304 2 103.7 0.00010748 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.48023e-06 8304 2 103.7 9.92835e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.18187e-06 8304 2 103.7 0.000102903 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.23997e-06 8304 2 103.7 9.14255e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.19307e-06 8304 2 103.7 9.78527e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.58311e-06 8304 2 103.7 0.000110844 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.17869e-06 8304 2 103.7 0.000108068 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.40678e-06 8304 2 103.7 0.00012081 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.29151e-06 8304 2 103.7 9.881e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.22322e-06 8304 2 103.7 0.000104401 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.54392e-06 8304 2 103.7 0.000107207 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.14542e-06 8304 2 103.7 9.20616e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.45921e-06 8304 2 103.7 0.000110621 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.16818e-06 8304 2 103.7 9.49811e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.19205e-06 8304 2 103.7 9.29146e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.47721e-06 8304 2 103.7 0.000121427 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.35243e-06 8304 2 103.7 0.000153712 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.07085e-06 8304 2 103.7 8.91495e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.17128e-06 8304 2 103.7 0.00012457 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.27188e-06 8304 2 103.7 9.4968e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.19684e-06 8304 2 103.7 9.44104e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.46939e-06 8304 2 103.7 9.9942e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.16376e-06 8304 2 103.7 8.72014e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10993e-06 8304 2 103.7 9.62132e-05 2768 3000000 3000000 -597.10002 143908.11 1.3942094 305.43348 42.191988 71.759045 0 0 29315.932 -19811.083 -320.88394 -277692.67 -268073.87 6697.1906 Loop time of 45129.2 on 16 procs for 3000000 steps with 10381 atoms Performance: 5.744 ns/day, 4.179 hours/ns, 66.476 timesteps/s 99.0% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4620.8 | 23246 | 34103 |7105.6 | 51.51 Bond | 3.293 | 11.004 | 20.422 | 149.7 | 0.02 Kspace | 6853.1 | 17747 | 36418 |8155.2 | 39.32 Neigh | 1690.7 | 1694.1 | 1698 | 5.8 | 3.75 Comm | 786.56 | 998.04 | 1101.5 | 395.4 | 2.21 Output | 0.016144 | 0.018111 | 0.019912 | 0.9 | 0.00 Modify | 1291.3 | 1365.5 | 1526.2 | 255.1 | 3.03 Other | | 67.69 | | | 0.15 Nlocal: 648.812 ave 830 max 277 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 7814.38 ave 9817 max 6043 min Histogram: 4 0 0 1 7 0 0 0 0 4 Neighs: 297143 ave 428535 max 55784 min Histogram: 4 0 0 0 0 0 0 3 5 4 Total # of neighbors = 4754286 Ave neighs/atom = 457.97958 Ave special neighs/atom = 1.6595704 Neighbor list builds = 149033 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) = 0.25741609 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 = 12100 4500 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10993e-06 8304 2 103.7 9.62132e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.81 | 14.22 | 14.85 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 -596.48302 143908.11 1.3942094 305.43348 42.191988 71.759045 0 0 29315.932 -19811.083 -320.88394 -277692.67 -268073.87 6697.1906 Loop time of 4.44244e-06 on 16 procs for 0 steps with 10381 atoms 121.0% CPU use with 16 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 | | 4.442e-06 | | |100.00 Nlocal: 648.812 ave 830 max 277 min Histogram: 4 0 0 0 0 0 0 0 7 5 Nghost: 7814.38 ave 9817 max 6043 min Histogram: 4 0 0 1 7 0 0 0 0 4 Neighs: 297143 ave 428535 max 55784 min Histogram: 4 0 0 0 0 0 0 3 5 4 Total # of neighbors = 4754286 Ave neighs/atom = 457.97958 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