#------------------------------------------------------------------------------- # 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) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-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 8.36886e-13 24909 2 103.7 8.13287e-11 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.65 | 15.19 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 2763.7752 278556.86 1.3074059 299.53628 120.77847 270.05382 0 0 66907.42 263259.37 -1345.0391 -815039.38 -484481.76 16960.783 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.7591e-06 24909 2 103.7 0.000113402 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.47338e-06 24909 2 103.7 0.000104775 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.15791e-06 24909 2 103.7 0.000105185 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.36948e-06 24909 2 103.7 0.000115217 8303 200000 200000 2779.6919 278556.86 1.3074059 298.94069 128.50362 214.10354 0 0 67069.441 263048.5 -1345.0391 -815081.04 -484620.49 16927.058 Loop time of 3031.77 on 32 procs for 200000 steps with 27300 atoms Performance: 5.700 ns/day, 4.211 hours/ns, 65.968 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 | 1246.8 | 1346.3 | 1443 | 130.2 | 44.41 Bond | 0.61203 | 1.1231 | 1.9933 | 29.2 | 0.04 Kspace | 1181.8 | 1276.2 | 1372.5 | 131.5 | 42.09 Neigh | 89.491 | 89.654 | 89.816 | 1.1 | 2.96 Comm | 137.4 | 142.2 | 146.27 | 25.3 | 4.69 Output | 0.022546 | 0.027393 | 0.032038 | 1.7 | 0.00 Modify | 162.92 | 164.64 | 168.2 | 13.3 | 5.43 Other | | 11.62 | | | 0.38 Nlocal: 853.125 ave 890 max 808 min Histogram: 2 0 1 5 4 7 6 4 1 2 Nghost: 7276.66 ave 7368 max 7196 min Histogram: 4 3 1 6 0 8 2 6 0 2 Neighs: 265965 ave 287147 max 239216 min Histogram: 1 1 2 4 5 5 4 7 1 2 Total # of neighbors = 8510869 Ave neighs/atom = 311.75344 Ave special neighs/atom = 1.892967 Neighbor list builds = 10711 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) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-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 1.36948e-06 24909 2 103.7 0.000115217 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.66 | 15.19 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 2780.7277 278556.86 1.3074059 298.94069 128.50362 214.10354 0 0 67069.441 263048.5 -1345.0391 -815081.04 -484620.49 16927.058 Loop time of 8.58372e-06 on 32 procs for 0 steps with 27300 atoms 113.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.584e-06 | | |100.00 Nlocal: 853.125 ave 890 max 808 min Histogram: 2 0 1 5 4 7 6 4 1 2 Nghost: 7276.66 ave 7368 max 7196 min Histogram: 4 3 1 6 0 8 2 6 0 2 Neighs: 265965 ave 287147 max 239216 min Histogram: 1 1 2 4 5 5 4 7 1 2 Total # of neighbors = 8510869 Ave neighs/atom = 311.75344 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: 1:41:27