#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2220 = # 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 0.9869233 0.9869233 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 2.4_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 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.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) = 0.25538038 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0026185817 estimated relative force accuracy = 7.8857811e-06 using double precision KISS FFT 3d grid and FFT values/proc = 17908 7200 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999133 0.0492608 6660 1 98.0265 9.28324 2220 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15.11 | 15.32 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 -1625.4297 66726.301 1.0011033 447.0653 0 0 0 0 9614.2969 72305.84 -116.031 -117087.06 -35166.922 5926.1467 SHAKE stats (type/ave/delta/count) on step 50000 1 0.9701 2.31311e-06 6660 1 103.7 0.000173253 2220 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969941 1.69646e-06 6660 1 103.7 0.000113026 2220 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970107 1.65386e-06 6660 1 103.7 0.000130311 2220 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970013 1.45586e-06 6660 1 103.7 0.000103983 2220 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969866 1.3386e-06 6660 1 103.7 0.000147164 2220 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970044 1.45426e-06 6660 1 103.7 9.95712e-05 2220 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969983 1.29759e-06 6660 1 103.7 9.52805e-05 2220 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970014 9.80855e-07 6660 1 103.7 9.27602e-05 2220 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969891 1.41756e-06 6660 1 103.7 0.000122362 2220 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970025 1.10497e-06 6660 1 103.7 0.000110444 2220 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969966 1.10245e-06 6660 1 103.7 0.00011073 2220 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970056 1.33632e-06 6660 1 103.7 0.000103357 2220 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969967 1.53498e-06 6660 1 103.7 9.77879e-05 2220 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970036 1.84396e-06 6660 1 103.7 0.000152475 2220 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969988 1.18666e-06 6660 1 103.7 9.69958e-05 2220 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970062 1.321e-06 6660 1 103.7 9.76961e-05 2220 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969963 1.25326e-06 6660 1 103.7 0.000119227 2220 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969988 1.27701e-06 6660 1 103.7 0.000117237 2220 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969959 1.4551e-06 6660 1 103.7 0.000114598 2220 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969903 1.31358e-06 6660 1 103.7 0.000119481 2220 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969909 1.40606e-06 6660 1 103.7 0.000140621 2220 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969997 1.15698e-06 6660 1 103.7 0.000101995 2220 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969995 1.67721e-06 6660 1 103.7 0.000113053 2220 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.96992 1.72466e-06 6660 1 103.7 0.00013342 2220 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970051 1.47392e-06 6660 1 103.7 0.000102936 2220 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969916 1.35303e-06 6660 1 103.7 0.000116011 2220 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970028 1.24503e-06 6660 1 103.7 0.000103208 2220 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.969979 1.11117e-06 6660 1 103.7 9.59678e-05 2220 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969997 1.19723e-06 6660 1 103.7 9.61416e-05 2220 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970016 1.14935e-06 6660 1 103.7 0.000102965 2220 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970071 1.52137e-06 6660 1 103.7 0.000118263 2220 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969872 1.91219e-06 6660 1 103.7 0.000158285 2220 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969979 1.243e-06 6660 1 103.7 0.00011547 2220 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970013 1.19729e-06 6660 1 103.7 8.67286e-05 2220 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970023 1.3459e-06 6660 1 103.7 9.73373e-05 2220 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969929 1.61554e-06 6660 1 103.7 0.000111569 2220 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970028 1.34228e-06 6660 1 103.7 0.000106039 2220 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970004 1.53833e-06 6660 1 103.7 0.000103507 2220 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969942 1.29906e-06 6660 1 103.7 9.73313e-05 2220 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969994 1.19618e-06 6660 1 103.7 0.000104436 2220 2000000 2000000 241.79261 66415.107 1.0057941 295.10554 0 0 0 0 5905.2216 86361.459 -116.57467 -117058.66 -24791.978 3911.8194 Loop time of 77982.8 on 4 procs for 2000000 steps with 6668 atoms Performance: 2.216 ns/day, 10.831 hours/ns, 25.647 timesteps/s 99.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51949 | 55917 | 59016 |1205.6 | 71.70 Bond | 4.0943 | 4.2668 | 4.439 | 5.9 | 0.01 Kspace | 11226 | 14323 | 18290 |2381.2 | 18.37 Neigh | 3579.2 | 3579.5 | 3579.8 | 0.4 | 4.59 Comm | 637.51 | 638.97 | 640.28 | 4.6 | 0.82 Output | 0.03563 | 0.037068 | 0.038241 | 0.5 | 0.00 Modify | 3007.9 | 3172.5 | 3355.1 | 261.4 | 4.07 Other | | 347.1 | | | 0.45 Nlocal: 1667 ave 1683 max 1645 min Histogram: 1 0 0 0 0 1 0 1 0 1 Nghost: 14379.5 ave 14439 max 14348 min Histogram: 2 0 1 0 0 0 0 0 0 1 Neighs: 961102 ave 1.00864e+06 max 921409 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 3844408 Ave neighs/atom = 576.54589 Ave special neighs/atom = 1.9976005 Neighbor list builds = 103826 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.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) = 0.2554738 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0026065207 estimated relative force accuracy = 7.8494595e-06 using double precision KISS FFT 3d grid and FFT values/proc = 17908 7200 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969994 1.19618e-06 6660 1 103.7 0.000104436 2220 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15.2 | 15.32 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 202.22882 66415.107 1.0057941 295.10554 0 0 0 0 5905.2216 86404.221 -116.57467 -117101.42 -24791.978 3911.8194 Loop time of 3.78325e-06 on 4 procs for 0 steps with 6668 atoms 125.6% CPU use with 4 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 | | 3.783e-06 | | |100.00 Nlocal: 1667 ave 1683 max 1645 min Histogram: 1 0 0 0 0 1 0 1 0 1 Nghost: 14379.5 ave 14439 max 14348 min Histogram: 2 0 1 0 0 0 0 0 0 1 Neighs: 961102 ave 1.00864e+06 max 921409 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 3844408 Ave neighs/atom = 576.54589 Ave special neighs/atom = 1.9976005 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 21:41:49