#------------------------------------------------------------------------------- # 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 2812 = # 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 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 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 group rdfgroup_1 union subset_Li subset_Li 7 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 100 4 4 fix rdf_1 rdfgroup_1 ave/time 1 20000 20000 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 5 5 13 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.70828e-13 8436 2 103.7 7.55733e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.92 | 14.06 | 14.17 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 1891.1015 93962.523 1.2789064 302.0573 41.655454 74.396805 0 0 19536.945 46190.335 -220.49494 -206927.8 -141084.47 5739.8934 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.33343e-06 8436 2 103.7 0.000109283 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.48053e-06 8436 2 103.7 9.34206e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.13809e-06 8436 2 103.7 8.91066e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.24699e-06 8436 2 103.7 9.82058e-05 2812 200000 200000 2720.1093 93962.523 1.2789064 295.45011 49.45404 71.161752 0 0 19848.06 45980.461 -220.49494 -206910.86 -140961.72 5614.3391 Loop time of 2457.25 on 16 procs for 200000 steps with 9188 atoms Performance: 7.032 ns/day, 3.413 hours/ns, 81.392 timesteps/s 99.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1651.4 | 1713.7 | 1756.2 | 68.5 | 69.74 Bond | 0.32695 | 0.94126 | 1.3555 | 23.1 | 0.04 Kspace | 408.09 | 450.27 | 513.06 | 134.8 | 18.32 Neigh | 97.463 | 97.572 | 97.652 | 0.6 | 3.97 Comm | 80.271 | 82.401 | 84.176 | 11.5 | 3.35 Output | 0.015514 | 0.017277 | 0.01896 | 0.8 | 0.00 Modify | 103.45 | 104.78 | 105.76 | 6.8 | 4.26 Other | | 7.554 | | | 0.31 Nlocal: 574.25 ave 596 max 554 min Histogram: 1 4 0 0 3 3 1 1 1 2 Nghost: 9042.38 ave 9090 max 9017 min Histogram: 3 4 0 5 0 2 0 0 1 1 Neighs: 322477 ave 336433 max 310268 min Histogram: 2 2 1 2 2 1 2 1 2 1 Total # of neighbors = 5159632 Ave neighs/atom = 561.56204 Ave special neighs/atom = 1.9037875 Neighbor list builds = 9880 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.24699e-06 8436 2 103.7 9.82058e-05 2812 Per MPI rank memory allocation (min/avg/max) = 15.45 | 15.62 | 15.7 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 2720.9273 93962.523 1.2789064 295.45011 49.45404 71.161752 0 0 19848.06 45980.461 -220.49494 -206910.86 -140961.72 5614.3391 Loop time of 4.18438e-06 on 16 procs for 0 steps with 9188 atoms 122.5% CPU use with 16 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 | | 4.184e-06 | | |100.00 Nlocal: 574.25 ave 596 max 554 min Histogram: 1 4 0 0 3 3 1 1 1 2 Nghost: 9042.38 ave 9090 max 9017 min Histogram: 3 4 0 5 0 2 0 0 1 1 Neighs: 322477 ave 336433 max 310268 min Histogram: 2 2 1 2 2 1 2 1 2 1 Total # of neighbors = 5159632 Ave neighs/atom = 561.56204 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 1:22:02