#------------------------------------------------------------------------------- # 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 8.68305e-13 8304 2 103.7 7.76481e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.64 | 13.09 | 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 2578.7219 92859.489 1.3074058 294.98121 49.533279 62.375248 0 0 22308.023 89590.939 -448.40969 -273804.51 -161793.64 5567.6197 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970018 1.33381e-06 8304 2 103.7 0.000115714 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970023 1.14439e-06 8304 2 103.7 9.33542e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969926 1.29134e-06 8304 2 103.7 0.000126253 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969965 1.27046e-06 8304 2 103.7 8.80688e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970001 1.51295e-06 8304 2 103.7 0.000108301 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969911 1.16783e-06 8304 2 103.7 0.00010015 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969962 1.16191e-06 8304 2 103.7 9.97717e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97003 1.71383e-06 8304 2 103.7 0.000169043 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970003 1.68852e-06 8304 2 103.7 0.000113069 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970022 1.41407e-06 8304 2 103.7 9.97426e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970114 1.71705e-06 8304 2 103.7 0.000130872 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970015 1.48294e-06 8304 2 103.7 9.56719e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17269e-06 8304 2 103.7 0.000104667 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970057 1.21189e-06 8304 2 103.7 9.46065e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969995 1.27919e-06 8304 2 103.7 0.000103843 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969929 1.55077e-06 8304 2 103.7 0.000109112 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970084 1.47115e-06 8304 2 103.7 0.000107011 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970037 1.18807e-06 8304 2 103.7 9.44937e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969937 1.50115e-06 8304 2 103.7 0.000140834 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.1699e-06 8304 2 103.7 0.000121405 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970031 2.02782e-06 8304 2 103.7 0.000137191 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970105 1.69262e-06 8304 2 103.7 0.000121203 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969937 1.47246e-06 8304 2 103.7 9.84345e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969965 1.25538e-06 8304 2 103.7 0.000105966 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969916 1.14717e-06 8304 2 103.7 0.000102649 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97008 1.60858e-06 8304 2 103.7 0.000135409 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969977 1.42223e-06 8304 2 103.7 9.28524e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970128 2.12972e-06 8304 2 103.7 0.000140018 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969968 1.29509e-06 8304 2 103.7 9.42524e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970044 1.42582e-06 8304 2 103.7 0.00010633 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970041 1.33479e-06 8304 2 103.7 9.35018e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969956 1.50062e-06 8304 2 103.7 0.000117164 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97007 1.63613e-06 8304 2 103.7 0.000107255 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969976 1.26636e-06 8304 2 103.7 9.52143e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969934 1.47492e-06 8304 2 103.7 0.000110711 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970015 1.13625e-06 8304 2 103.7 8.59763e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970017 1.24762e-06 8304 2 103.7 9.0644e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969995 1.1043e-06 8304 2 103.7 0.000123635 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970047 1.3235e-06 8304 2 103.7 0.000102134 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969999 1.1619e-06 8304 2 103.7 9.1667e-05 2768 2000000 2000000 423.12562 97314.035 1.2475594 295.22712 46.515356 64.279087 0 0 21413.633 90814.616 -427.88376 -273790.86 -161451.82 5572.2611 Loop time of 12280.5 on 32 procs for 2000000 steps with 9101 atoms Performance: 14.071 ns/day, 1.706 hours/ns, 162.860 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 | 4135.5 | 4452.4 | 4654.4 | 175.7 | 36.26 Bond | 2.1164 | 5.5456 | 12.389 | 106.8 | 0.05 Kspace | 4349.3 | 4555.1 | 4878 | 175.8 | 37.09 Neigh | 312.18 | 313.09 | 313.98 | 3.4 | 2.55 Comm | 719.51 | 732.76 | 746.87 | 28.1 | 5.97 Output | 0.0083397 | 0.010615 | 0.012736 | 1.3 | 0.00 Modify | 1463.4 | 1791.5 | 2156 | 659.3 | 14.59 Other | | 430.1 | | | 3.50 Nlocal: 284.406 ave 299 max 268 min Histogram: 4 1 1 4 5 4 2 5 4 2 Nghost: 4835.47 ave 4892 max 4771 min Histogram: 2 0 3 1 7 6 7 4 1 1 Neighs: 84583.4 ave 93819 max 79384 min Histogram: 6 6 3 4 3 4 2 1 1 2 Total # of neighbors = 2706669 Ave neighs/atom = 297.40347 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102600 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) = 0.32616287 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031076479 estimated relative force accuracy = 9.3585894e-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 0.969999 1.1619e-06 8304 2 103.7 9.1667e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.78 | 13.16 | 13.35 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 420.04977 97314.035 1.2475594 295.22712 46.515356 64.279087 0 0 21413.633 89850.066 -427.88376 -272826.31 -161451.82 5572.2611 Loop time of 7.68862e-06 on 32 procs for 0 steps with 9101 atoms 113.0% 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 | | 7.689e-06 | | |100.00 Nlocal: 284.406 ave 299 max 268 min Histogram: 4 1 1 4 5 4 2 5 4 2 Nghost: 4835.47 ave 4892 max 4771 min Histogram: 2 0 3 1 7 6 7 4 1 1 Neighs: 84583.4 ave 93819 max 79384 min Histogram: 6 6 3 4 3 4 2 1 1 2 Total # of neighbors = 2706669 Ave neighs/atom = 297.40347 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: 6:35:25