#------------------------------------------------------------------------------- # 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) = 0.25466625 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0028494316 estimated relative force accuracy = 8.5809786e-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 0.999591 0.0509763 6660 1 97.8537 8.9982 2220 Per MPI rank memory allocation (min/avg/max) = 14.88 | 15.1 | 15.31 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-06 259.32638 69186.83 1.0721042 442.14521 0 0 0 0 11221.644 63725.315 -128.19243 -123974.27 -49027.312 6061.2561 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969906 1.31669e-06 6660 1 103.7 0.000108464 2220 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970047 1.87932e-06 6660 1 103.7 0.000141258 2220 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969969 1.1193e-06 6660 1 103.7 9.57963e-05 2220 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969998 1.08645e-06 6660 1 103.7 9.12679e-05 2220 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969939 1.20041e-06 6660 1 103.7 0.000103292 2220 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970082 1.17578e-06 6660 1 103.7 9.39796e-05 2220 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970068 1.46351e-06 6660 1 103.7 0.000135774 2220 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969949 1.23042e-06 6660 1 103.7 0.000106722 2220 SHAKE stats (type/ave/delta/count) on step 450000 1 0.96982 1.52793e-06 6660 1 103.7 0.000152024 2220 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970019 1.24363e-06 6660 1 103.7 9.49573e-05 2220 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969957 1.33579e-06 6660 1 103.7 0.000116977 2220 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969887 1.25906e-06 6660 1 103.7 0.000113311 2220 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969916 1.14023e-06 6660 1 103.7 9.57278e-05 2220 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969911 1.3337e-06 6660 1 103.7 0.000116937 2220 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970001 1.41638e-06 6660 1 103.7 0.000101494 2220 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969978 1.44101e-06 6660 1 103.7 0.000108674 2220 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969982 1.23652e-06 6660 1 103.7 9.27745e-05 2220 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969915 1.28789e-06 6660 1 103.7 0.000101344 2220 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969891 1.09694e-06 6660 1 103.7 9.05968e-05 2220 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970106 1.88191e-06 6660 1 103.7 0.000164925 2220 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970002 1.0868e-06 6660 1 103.7 9.87822e-05 2220 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970017 1.17843e-06 6660 1 103.7 9.96077e-05 2220 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970079 1.48225e-06 6660 1 103.7 0.000106738 2220 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969996 1.29529e-06 6660 1 103.7 9.54884e-05 2220 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970046 1.46207e-06 6660 1 103.7 0.000115895 2220 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970036 1.29324e-06 6660 1 103.7 9.64981e-05 2220 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.96986 1.29668e-06 6660 1 103.7 0.000120759 2220 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970069 1.5659e-06 6660 1 103.7 0.000122529 2220 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970057 1.51705e-06 6660 1 103.7 0.000123914 2220 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970015 1.09494e-06 6660 1 103.7 9.52503e-05 2220 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970134 1.35834e-06 6660 1 103.7 9.67502e-05 2220 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970109 2.30905e-06 6660 1 103.7 0.000140653 2220 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969983 1.16941e-06 6660 1 103.7 0.000117924 2220 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97004 1.12347e-06 6660 1 103.7 9.87239e-05 2220 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.96997 1.80993e-06 6660 1 103.7 0.000109993 2220 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969942 1.34817e-06 6660 1 103.7 0.000101066 2220 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970065 1.27618e-06 6660 1 103.7 0.000100721 2220 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969952 1.15488e-06 6660 1 103.7 9.50212e-05 2220 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970018 1.13286e-06 6660 1 103.7 0.000103776 2220 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.05732e-06 6660 1 103.7 9.37297e-05 2220 2000000 2000000 13.118836 69828.79 1.062248 302.29955 0 0 0 0 6960.4803 78547.149 -127.01391 -123939.08 -38431.45 4144.1475 Loop time of 79302.3 on 4 procs for 2000000 steps with 6820 atoms Performance: 2.179 ns/day, 11.014 hours/ns, 25.220 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 | 54828 | 57571 | 62636 |1297.4 | 72.60 Bond | 4.4458 | 4.6114 | 5.016 | 10.9 | 0.01 Kspace | 8764.8 | 13829 | 16571 |2646.4 | 17.44 Neigh | 3742.6 | 3743.4 | 3744.4 | 1.2 | 4.72 Comm | 573.31 | 575.02 | 577.65 | 6.8 | 0.73 Output | 0.03644 | 0.037997 | 0.039276 | 0.5 | 0.00 Modify | 3065.4 | 3232.6 | 3477.8 | 298.0 | 4.08 Other | | 347 | | | 0.44 Nlocal: 1705 ave 1722 max 1690 min Histogram: 1 0 1 0 0 0 1 0 0 1 Nghost: 14253.5 ave 14298 max 14214 min Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 956424 ave 988033 max 921461 min Histogram: 1 1 0 0 0 0 0 0 0 2 Total # of neighbors = 3825695 Ave neighs/atom = 560.95235 Ave special neighs/atom = 1.9530792 Neighbor list builds = 103610 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) = 0.25447964 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0028756556 estimated relative force accuracy = 8.6599516e-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 0.97 1.05732e-06 6660 1 103.7 9.37297e-05 2220 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15.19 | 15.31 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 14.450778 69828.79 1.062248 302.29955 0 0 0 0 6960.4803 78456.564 -127.01391 -123848.49 -38431.451 4144.1475 Loop time of 3.77775e-06 on 4 procs for 0 steps with 6820 atoms 119.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 3.778e-06 | | |100.00 Nlocal: 1705 ave 1722 max 1690 min Histogram: 1 0 1 0 0 0 1 0 0 1 Nghost: 14253.5 ave 14298 max 14214 min Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 956424 ave 988033 max 921461 min Histogram: 1 1 0 0 0 0 0 0 0 2 Total # of neighbors = 3825695 Ave neighs/atom = 560.95235 Ave special neighs/atom = 1.9530792 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 22:04:02