#------------------------------------------------------------------------------- # 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 2699 = # 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 8.71414e-13 8097 2 103.7 7.4408e-11 2699 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.25 | 17.24 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 64.139529 138878.49 1.4411859 296.66873 38.049249 51.2144 0 0 36216.235 -63623.759 -317.08001 -295427.35 -322745.61 6662.4151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.21295e-06 8097 2 103.7 9.27689e-05 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.33861e-06 8097 2 103.7 0.000107709 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.87273e-06 8097 2 103.7 0.000124028 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.15067e-06 8097 2 103.7 9.53282e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.27116e-06 8097 2 103.7 0.000110814 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.37131e-06 8097 2 103.7 0.000100073 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.18408e-06 8097 2 103.7 9.48013e-05 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.40238e-06 8097 2 103.7 9.29198e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.34542e-06 8097 2 103.7 0.000100513 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.10016e-06 8097 2 103.7 8.95024e-05 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.40548e-06 8097 2 103.7 0.000109585 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.34524e-06 8097 2 103.7 0.00010807 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13993e-06 8097 2 103.7 9.88163e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25582e-06 8097 2 103.7 0.000103587 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.34923e-06 8097 2 103.7 9.56532e-05 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16916e-06 8097 2 103.7 9.65119e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.31014e-06 8097 2 103.7 9.46209e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14624e-06 8097 2 103.7 8.83635e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.46576e-06 8097 2 103.7 0.000104976 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.33945e-06 8097 2 103.7 9.351e-05 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.26973e-06 8097 2 103.7 0.000110009 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.69188e-06 8097 2 103.7 0.000121198 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.40965e-06 8097 2 103.7 9.04749e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.0486e-06 8097 2 103.7 9.07806e-05 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.09195e-06 8097 2 103.7 9.39543e-05 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.19393e-06 8097 2 103.7 8.92445e-05 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.61143e-06 8097 2 103.7 9.43236e-05 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.14752e-06 8097 2 103.7 0.000114168 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.26698e-06 8097 2 103.7 8.45308e-05 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.28959e-06 8097 2 103.7 9.57115e-05 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.36111e-06 8097 2 103.7 9.95217e-05 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15305e-06 8097 2 103.7 9.39894e-05 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.34081e-06 8097 2 103.7 0.000106535 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.05655e-06 8097 2 103.7 9.17044e-05 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.42835e-06 8097 2 103.7 0.000104199 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.74804e-06 8097 2 103.7 0.000125944 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.40744e-06 8097 2 103.7 0.00010034 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.13748e-06 8097 2 103.7 9.59769e-05 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.11972e-06 8097 2 103.7 0.000103755 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.28148e-06 8097 2 103.7 9.54423e-05 2699 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.15885e-06 8097 2 103.7 9.1105e-05 2699 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.31414e-06 8097 2 103.7 9.98598e-05 2699 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.42147e-06 8097 2 103.7 0.000111091 2699 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.74128e-06 8097 2 103.7 0.000114877 2699 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.31116e-06 8097 2 103.7 0.000105827 2699 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.16209e-06 8097 2 103.7 9.61012e-05 2699 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.27935e-06 8097 2 103.7 0.000102763 2699 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.18316e-06 8097 2 103.7 8.69182e-05 2699 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.42084e-06 8097 2 103.7 9.3831e-05 2699 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.59505e-06 8097 2 103.7 0.000105659 2699 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.19761e-06 8097 2 103.7 9.01833e-05 2699 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.5091e-06 8097 2 103.7 0.000117413 2699 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.17657e-06 8097 2 103.7 0.000101938 2699 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.29629e-06 8097 2 103.7 0.000104135 2699 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.35118e-06 8097 2 103.7 9.69793e-05 2699 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.16308e-06 8097 2 103.7 9.56528e-05 2699 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.17072e-06 8097 2 103.7 9.34693e-05 2699 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.05324e-06 8097 2 103.7 0.000106593 2699 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.08309e-06 8097 2 103.7 9.5586e-05 2699 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35433e-06 8097 2 103.7 0.000103181 2699 3000000 3000000 -13.979932 138878.49 1.4411859 303.59551 43.838458 39.982205 0 0 36130.55 -63644.976 -317.08001 -295424.07 -322854.67 6817.9728 Loop time of 65246.7 on 8 procs for 3000000 steps with 10558 atoms Performance: 3.973 ns/day, 6.041 hours/ns, 45.979 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11453 | 38636 | 51829 |8032.4 | 59.21 Bond | 3.3535 | 12.715 | 20.745 | 180.2 | 0.02 Kspace | 8643 | 21855 | 49065 |10689.9 | 33.50 Neigh | 2677.8 | 2681.6 | 2686.3 | 5.4 | 4.11 Comm | 691.97 | 767.97 | 841.46 | 181.7 | 1.18 Output | 0.023203 | 0.026009 | 0.028619 | 1.1 | 0.00 Modify | 1159.1 | 1216.5 | 1261.5 | 104.2 | 1.86 Other | | 76.89 | | | 0.12 Nlocal: 1319.75 ave 1589 max 711 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 11033.5 ave 13114 max 9475 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 614162 ave 824682 max 178299 min Histogram: 2 0 0 0 0 0 0 1 1 4 Total # of neighbors = 4913296 Ave neighs/atom = 465.36238 Ave special neighs/atom = 1.5849593 Neighbor list builds = 148395 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.35433e-06 8097 2 103.7 0.000103181 2699 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.25 | 17.24 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 -13.425848 138878.49 1.4411859 303.59551 43.838458 39.982205 0 0 36130.55 -63644.976 -317.08001 -295424.07 -322854.67 6817.9728 Loop time of 1.90281e-05 on 8 procs for 0 steps with 10558 atoms 105.1% 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 | | 1.903e-05 | | |100.00 Nlocal: 1319.75 ave 1589 max 711 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 11033.5 ave 13114 max 9475 min Histogram: 2 0 0 4 0 0 0 0 0 2 Neighs: 614162 ave 824682 max 178299 min Histogram: 2 0 0 0 0 0 0 1 1 4 Total # of neighbors = 4913296 Ave neighs/atom = 465.36238 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out