#------------------------------------------------------------------------------- # 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 2151 = # of frozen angles find clusters CPU = 0.000 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) = 0.25606163 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0024979572 estimated relative force accuracy = 7.5225239e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.99942 0.0512949 6453 1 97.9585 9.41374 2151 Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.02 | 12.03 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 -2515.9347 64686.415 1.0002033 446.98873 0 0 0 0 9626.4146 69770.179 -112.43299 -113858.5 -34461.905 5743.9268 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969961 1.32312e-06 6453 1 103.7 9.84159e-05 2151 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970018 1.26092e-06 6453 1 103.7 0.00011073 2151 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969922 1.25048e-06 6453 1 103.7 0.000134794 2151 SHAKE stats (type/ave/delta/count) on step 200000 1 0.96997 1.39711e-06 6453 1 103.7 0.000100122 2151 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970096 1.25148e-06 6453 1 103.7 9.2011e-05 2151 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970061 1.62772e-06 6453 1 103.7 0.000109944 2151 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970021 1.14901e-06 6453 1 103.7 9.31833e-05 2151 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969875 1.316e-06 6453 1 103.7 0.000109061 2151 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970001 1.26191e-06 6453 1 103.7 0.000100094 2151 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969993 1.61124e-06 6453 1 103.7 0.000121349 2151 SHAKE stats (type/ave/delta/count) on step 550000 1 0.96993 1.31063e-06 6453 1 103.7 9.28627e-05 2151 SHAKE stats (type/ave/delta/count) on step 600000 1 0.96994 1.14104e-06 6453 1 103.7 9.68189e-05 2151 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970039 1.04226e-06 6453 1 103.7 0.000100828 2151 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970007 1.63015e-06 6453 1 103.7 0.000109564 2151 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970057 1.06818e-06 6453 1 103.7 0.000112269 2151 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969989 1.46506e-06 6453 1 103.7 9.61551e-05 2151 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969911 1.64443e-06 6453 1 103.7 0.000121052 2151 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970047 1.21011e-06 6453 1 103.7 9.30064e-05 2151 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970048 1.67381e-06 6453 1 103.7 0.000122554 2151 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969949 1.20949e-06 6453 1 103.7 0.000104266 2151 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969959 1.23975e-06 6453 1 103.7 9.9524e-05 2151 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969989 1.36012e-06 6453 1 103.7 9.45869e-05 2151 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970008 1.14957e-06 6453 1 103.7 0.000107143 2151 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970023 1.31411e-06 6453 1 103.7 9.07186e-05 2151 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970038 1.8669e-06 6453 1 103.7 0.000103992 2151 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969969 1.4411e-06 6453 1 103.7 0.00011373 2151 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970008 1.24141e-06 6453 1 103.7 9.4733e-05 2151 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970032 1.44791e-06 6453 1 103.7 0.00010007 2151 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970063 1.23414e-06 6453 1 103.7 8.87784e-05 2151 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970061 1.09503e-06 6453 1 103.7 9.19421e-05 2151 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969978 1.26304e-06 6453 1 103.7 0.000119863 2151 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970027 1.1647e-06 6453 1 103.7 0.000104675 2151 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969955 1.20013e-06 6453 1 103.7 9.64332e-05 2151 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970021 1.30734e-06 6453 1 103.7 0.000121309 2151 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.96996 1.29827e-06 6453 1 103.7 9.16912e-05 2151 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970017 1.07412e-06 6453 1 103.7 9.43397e-05 2151 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970052 1.05947e-06 6453 1 103.7 9.17236e-05 2151 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970081 1.6064e-06 6453 1 103.7 0.000123064 2151 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970003 1.41565e-06 6453 1 103.7 9.59251e-05 2151 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970022 1.2761e-06 6453 1 103.7 0.000100998 2151 2000000 2000000 54.159271 64451.638 1.0038467 293.42363 0 0 0 0 5696.8712 83818.173 -112.84255 -113829.86 -24314.812 3770.5735 Loop time of 34221.6 on 8 procs for 2000000 steps with 6463 atoms Performance: 5.049 ns/day, 4.753 hours/ns, 58.443 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23229 | 24580 | 25873 | 609.1 | 71.82 Bond | 3.0132 | 3.4105 | 3.7067 | 10.7 | 0.01 Kspace | 4289.5 | 5584.4 | 6935.6 |1276.0 | 16.32 Neigh | 1539.6 | 1539.9 | 1540.2 | 0.6 | 4.50 Comm | 520.98 | 524.01 | 526.93 | 10.8 | 1.53 Output | 0.016117 | 0.01715 | 0.018019 | 0.5 | 0.00 Modify | 1642.1 | 1836.4 | 1914.5 | 245.1 | 5.37 Other | | 153.8 | | | 0.45 Nlocal: 807.875 ave 840 max 786 min Histogram: 1 1 1 1 1 2 0 0 0 1 Nghost: 10367.2 ave 10399 max 10330 min Histogram: 1 0 1 1 1 1 0 0 2 1 Neighs: 465261 ave 495590 max 437654 min Histogram: 2 0 1 0 1 1 0 1 1 1 Total # of neighbors = 3722091 Ave neighs/atom = 575.90763 Ave special neighs/atom = 1.9969055 Neighbor list builds = 103658 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) = 0.25613538 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0024889281 estimated relative force accuracy = 7.495333e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970022 1.2761e-06 6453 1 103.7 0.000100998 2151 Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.26 | 12.41 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 202.5024 64451.638 1.0038467 293.42363 0 0 0 0 5696.8712 83850.911 -112.84255 -113862.59 -24314.812 3770.5735 Loop time of 2.995e-06 on 8 procs for 0 steps with 6463 atoms 125.2% 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 | | 2.995e-06 | | |100.00 Nlocal: 807.875 ave 840 max 786 min Histogram: 1 1 1 1 1 2 0 0 0 1 Nghost: 10367.2 ave 10399 max 10330 min Histogram: 1 0 1 1 1 1 0 0 2 1 Neighs: 465261 ave 495590 max 437654 min Histogram: 2 0 1 0 1 1 0 1 1 1 Total # of neighbors = 3722091 Ave neighs/atom = 575.90763 Ave special neighs/atom = 1.9969055 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 9:31:31