#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 npt temp 298.2 298.2 100 iso 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.0902e-13 8304 2 103.7 7.24043e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.68 | 13.15 | 13.34 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 3189.9806 92859.489 1.3074058 304.93285 40.384506 89.498931 0 0 22450.437 89562.698 -448.40969 -273843.15 -161700.14 5755.4518 SHAKE stats (type/ave/delta/count) on step 50000 2 0.96992 1.19221e-06 8304 2 103.7 0.000100904 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970007 1.3088e-06 8304 2 103.7 0.000118649 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970016 1.81697e-06 8304 2 103.7 9.33139e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970051 1.81734e-06 8304 2 103.7 0.000107604 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970053 1.28215e-06 8304 2 103.7 9.03627e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969953 1.38135e-06 8304 2 103.7 9.14498e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970087 1.25338e-06 8304 2 103.7 9.50563e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969925 1.48884e-06 8304 2 103.7 0.000123538 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970072 1.46627e-06 8304 2 103.7 0.000107389 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970021 1.60549e-06 8304 2 103.7 0.000119087 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969969 1.1705e-06 8304 2 103.7 0.000114763 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970032 1.55243e-06 8304 2 103.7 0.000112175 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969956 1.15351e-06 8304 2 103.7 9.13794e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970005 1.44735e-06 8304 2 103.7 0.00010073 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969988 1.57868e-06 8304 2 103.7 9.65651e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970048 2.10954e-06 8304 2 103.7 0.000163504 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969982 1.17805e-06 8304 2 103.7 0.000119955 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969983 1.21765e-06 8304 2 103.7 9.78633e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969988 1.23925e-06 8304 2 103.7 0.00010189 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970006 1.30696e-06 8304 2 103.7 9.64809e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969969 1.43784e-06 8304 2 103.7 0.000103313 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.96989 1.394e-06 8304 2 103.7 0.000106493 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970066 1.99186e-06 8304 2 103.7 0.000125102 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970087 1.42712e-06 8304 2 103.7 0.000113293 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97003 1.1503e-06 8304 2 103.7 8.81575e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969922 1.25393e-06 8304 2 103.7 0.000112396 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969924 1.40368e-06 8304 2 103.7 0.000110887 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970036 1.50655e-06 8304 2 103.7 0.000100314 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970015 1.2688e-06 8304 2 103.7 9.29546e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969962 1.23807e-06 8304 2 103.7 9.54249e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970083 1.0833e-06 8304 2 103.7 9.23067e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970035 1.16104e-06 8304 2 103.7 9.59157e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969973 1.31922e-06 8304 2 103.7 0.000108397 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970003 1.52786e-06 8304 2 103.7 0.000108923 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969975 1.36488e-06 8304 2 103.7 0.000109049 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970024 1.53026e-06 8304 2 103.7 0.000110805 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969937 1.50745e-06 8304 2 103.7 0.00011046 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.96999 1.29602e-06 8304 2 103.7 0.00010649 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969925 1.33032e-06 8304 2 103.7 0.000121968 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969945 1.22546e-06 8304 2 103.7 0.000111273 2768 2000000 2000000 144.19121 97572.733 1.2442517 298.52463 38.650993 77.552568 0 0 21285.569 91158.425 -426.74929 -273790.94 -161230.74 5634.5 Loop time of 12333.1 on 32 procs for 2000000 steps with 9101 atoms Performance: 14.011 ns/day, 1.713 hours/ns, 162.165 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4238.4 | 4463.2 | 4749.7 | 175.2 | 36.19 Bond | 2.4534 | 5.6288 | 10.191 | 79.4 | 0.05 Kspace | 4309.4 | 4596 | 4821.4 | 174.0 | 37.27 Neigh | 316.47 | 317.16 | 317.79 | 2.4 | 2.57 Comm | 718.26 | 728.93 | 735.04 | 15.7 | 5.91 Output | 0.0096478 | 0.011928 | 0.014049 | 1.2 | 0.00 Modify | 1460.9 | 1791.1 | 2145.1 | 659.3 | 14.52 Other | | 431.1 | | | 3.50 Nlocal: 284.406 ave 296 max 266 min Histogram: 1 0 2 3 3 6 5 3 3 6 Nghost: 4828.06 ave 4865 max 4787 min Histogram: 4 1 2 1 4 4 7 4 4 1 Neighs: 84348.5 ave 89520 max 77135 min Histogram: 1 1 2 2 5 6 5 5 1 4 Total # of neighbors = 2699152 Ave neighs/atom = 296.57752 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102694 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) = 0.3260959 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031158348 estimated relative force accuracy = 9.383244e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969945 1.22546e-06 8304 2 103.7 0.000111273 2768 Per MPI rank memory allocation (min/avg/max) = 12.66 | 13.17 | 13.33 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 -174.71249 97572.733 1.2442517 298.52463 38.650993 77.552568 0 0 21285.569 90138.93 -426.74929 -272771.43 -161230.73 5634.5 Loop time of 7.47319e-06 on 32 procs for 0 steps with 9101 atoms 107.0% 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 | | 7.473e-06 | | |100.00 Nlocal: 284.406 ave 296 max 266 min Histogram: 1 0 2 3 3 6 5 3 3 6 Nghost: 4828.06 ave 4865 max 4787 min Histogram: 4 1 2 1 4 4 7 4 4 1 Neighs: 84348.5 ave 89520 max 77135 min Histogram: 1 1 2 2 5 6 5 5 1 4 Total # of neighbors = 2699152 Ave neighs/atom = 296.57752 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:35:26