#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 ps 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 8303 = # 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 20000 20000 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 v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 20 1 20 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 v_surfacetension file 2.5_instantaneous.txt restart 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32364737 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035984908 estimated relative force accuracy = 1.0836748e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 5.03901e-11 24909 2 103.7 2.94378e-09 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.58 | 15.01 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 4.8381848 292483.1 1.2451553 295.71562 133.85813 308.00082 0 0 63380.528 264807.1 -1280.9966 -811898.68 -483269.2 16744.444 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.4107e-06 24909 2 103.7 9.39084e-05 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.30233e-06 24909 2 103.7 0.000104724 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.41036e-06 24909 2 103.7 9.96459e-05 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.35926e-06 24909 2 103.7 9.8327e-05 8303 200000 200000 302.6465 292483.1 1.2451553 297.8846 140.63313 360.29708 0 0 63962.217 264355.64 -1280.9966 -811883.7 -483064.91 16867.259 Loop time of 2902.92 on 32 procs for 200000 steps with 27300 atoms Performance: 5.953 ns/day, 4.032 hours/ns, 68.896 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1198.2 | 1267.1 | 1350.1 | 98.7 | 43.65 Bond | 0.46002 | 1.124 | 1.908 | 29.7 | 0.04 Kspace | 1173.3 | 1255.9 | 1322.2 | 98.2 | 43.26 Neigh | 81.915 | 82.123 | 82.411 | 1.5 | 2.83 Comm | 127.62 | 129.47 | 132.67 | 12.9 | 4.46 Output | 0.023151 | 0.027945 | 0.032573 | 1.7 | 0.00 Modify | 156.1 | 157.45 | 158.46 | 4.3 | 5.42 Other | | 9.719 | | | 0.33 Nlocal: 853.125 ave 898 max 819 min Histogram: 3 2 5 5 3 5 5 2 1 1 Nghost: 7042.31 ave 7122 max 6948 min Histogram: 2 1 3 3 3 3 9 5 1 2 Neighs: 253395 ave 271370 max 233663 min Histogram: 2 1 4 4 3 5 1 8 3 1 Total # of neighbors = 8108650 Ave neighs/atom = 297.02015 Ave special neighs/atom = 1.892967 Neighbor list builds = 10752 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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) = 0.32364737 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035984908 estimated relative force accuracy = 1.0836748e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.35926e-06 24909 2 103.7 9.8327e-05 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.58 | 15.01 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 200000 200000 303.55348 292483.1 1.2451553 297.8846 140.63313 360.29708 0 0 63962.217 264355.64 -1280.9966 -811883.7 -483064.91 16867.259 Loop time of 1.18885e-05 on 32 procs for 0 steps with 27300 atoms 136.4% 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 | | 1.189e-05 | | |100.00 Nlocal: 853.125 ave 898 max 819 min Histogram: 3 2 5 5 3 5 5 2 1 1 Nghost: 7042.31 ave 7122 max 6948 min Histogram: 2 1 3 3 3 3 9 5 1 2 Neighs: 253395 ave 271370 max 233663 min Histogram: 2 1 4 4 3 5 1 8 3 1 Total # of neighbors = 8108650 Ave neighs/atom = 297.02015 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 1:42:46