318 lines
14 KiB
Groff
318 lines
14 KiB
Groff
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# SRD diffusion demo - poydisperse spheres
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units lj
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atom_style sphere
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atom_modify first big
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dimension 2
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# create big particles with 3 different types and diameters
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lattice sq 0.3
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Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region box
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
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create_atoms CPU = 0.000 seconds
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group big type 1
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100 atoms in group big
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set group big type/fraction 2 0.33 394895
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Setting atom values ...
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35 settings made for type/fraction
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set group big type/fraction 3 0.5 989894
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Setting atom values ...
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57 settings made for type/fraction
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group big type 2 3
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100 atoms in group big
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set type 1*3 mass 1.0
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Setting atom values ...
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100 settings made for mass
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles, repulsive only to prevent aggregation
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 big nve
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.poly.equil
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run 1000
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Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.54
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ghost atom cutoff = 2.54
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binsize = 1.27, bins = 15 15 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -0.16013916 0 1.2654608 1.1298975
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1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
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Loop time of 0.00622873 on 1 procs for 1000 steps with 100 atoms
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Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 Matom-step/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0015709 | 0.0015709 | 0.0015709 | 0.0 | 25.22
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Neigh | 0.0014016 | 0.0014016 | 0.0014016 | 0.0 | 22.50
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Comm | 0.0012066 | 0.0012066 | 0.0012066 | 0.0 | 19.37
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Output | 6.169e-06 | 6.169e-06 | 6.169e-06 | 0.0 | 0.10
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Modify | 0.0013508 | 0.0013508 | 0.0013508 | 0.0 | 21.69
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Other | | 0.0006926 | | | 11.12
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Nlocal: 100 ave 100 max 100 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 60 ave 60 max 60 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 152 ave 152 max 152 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 152
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Ave neighs/atom = 1.52
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Neighbor list builds = 115
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Dangerous builds = 0
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#undump 1
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unfix 1
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unfix 2
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# add small particles as hi density lattice
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region plane block INF INF INF INF -0.001 0.001 units box
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lattice sq 250.0
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Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
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create_atoms 4 region plane
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Created 83521 atoms
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using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
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create_atoms CPU = 0.016 seconds
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set type 4 mass 0.1
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Setting atom values ...
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83521 settings made for mass
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group small type 4
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83521 atoms in group small
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set *-4 cutoffs to non-zero values
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 1 4 0.0 1.0 0.5
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pair_coeff 2 4 0.0 1.0 1.0
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pair_coeff 3 4 0.0 1.0 0.75
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pair_coeff 4 4 0.0 1.0 0.0
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delete_atoms overlap 1.0 small big
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System init for delete_atoms ...
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Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 14 14 2
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) command delete_atoms, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/2d
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bin: standard
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(2) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d
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bin: standard
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WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
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Deleted 63410 atoms, new total = 20211
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# SRD run
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reset_timestep 0
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neighbor 0.3 multi
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neigh_modify delay 0 every 1 check yes
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comm_modify mode multi group big vel yes
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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# use fix SRD to push small particles out from inside big ones
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# if comment out, big particles won't see SRD particles
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timestep 0.001
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fix 1 big nve
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
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fix 3 all enforce2d
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# diagnostics
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
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thermo_modify temp tbig
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
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thermo 1000
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#dump 1 all atom 1000 dump.poly
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#dump 1 all image 1000 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
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@Article{Intveld08,
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author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
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title = {Accurate and Efficient Methods for Modeling Colloidal
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Mixtures in an Explicit Solvent using Molecular Dynamics},
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journal = {Comput.\ Phys.\ Commut.},
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year = 2008,
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volume = 179,
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pages = {320--329}
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}
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@article{Shire2020,
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author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
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title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
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Detection Applied to Investigate the Quasi-Static Limit},
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journal = {Computational Particle Mechanics},
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year = {2020}
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@article{Monti2022,
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author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
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Ishan and Silbert, Leonardo E. and Grest, Gary S.
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and Lechman, Jeremy B.},
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title = {Large-scale frictionless jamming with power-law particle
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size distributions},
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journal = {Phys. Rev. E},
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volume = {106}
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issue = {3}
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year = {2022}
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}
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- fix srd command: doi:10.1063/1.3419070
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@Article{Petersen10,
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author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
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G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
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title = {Mesoscale Hydrodynamics via Stochastic Rotation
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Dynamics: Comparison with {L}ennard-{J}ones Fluid},
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journal = {J.~Chem.\ Phys.},
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year = 2010,
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volume = 132,
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pages = 174106
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
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SRD info:
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SRD/big particles = 20111 100
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big particle diameter max/min = 1 1
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SRD temperature & lamda = 1 0.063245553
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SRD max distance & max velocity = 0.25298221 12.649111
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SRD grid counts: 73 73 1
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SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
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SRD per actual grid cell = 4.9371727
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SRD viscosity = 0.23321983
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big/SRD mass density ratio = 0.16131131
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WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
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# of rescaled SRD velocities = 0
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ave/max small velocity = 4.1934421 7.74495
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ave/max big velocity = 1.4399093 3.5724039
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.54
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ghost atom cutoff = 2.54
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binsize = 18.257419, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/multi/atomonly/newton
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stencil: half/multi/2d
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
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Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
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0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
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1000 1.0181191 3924 0.0076572255 0.030604433 1.5476019 3.7992573 7242 26 26 0 635 15876 5329 3924 0.98110339 0 3
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2000 0.69783736 3992 0.0027817464 -0.47755891 0.56221876 1.9887267 7740 34 34 1 1186 15876 5329 3992 1.0611575 0 24
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3000 0.89084297 3981 0.004323119 -0.45361044 0.87374558 1.7342893 7775 24 24 0 1923 15876 5329 3981 1.1207371 0 24
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4000 0.84391846 4036 0.0045581483 -0.33619115 0.92124735 1.8456288 8060 43 43 0 2734 15876 5329 4036 1.1481354 0 24
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5000 0.69548234 4056 0.0030033315 -0.42926535 0.60700333 1.6113509 8260 33 33 0 3638 15876 5329 4056 1.148749 0 24
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6000 0.71729125 4023 0.0035318938 -0.35493291 0.71383106 1.673491 8224 29 29 0 4528 15876 5329 4023 1.1602572 0 24
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7000 0.90145513 4032 0.0047423524 -0.38469129 0.95847685 1.7537778 8382 31 31 0 5395 15876 5329 4032 1.1543513 0 24
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8000 0.6739295 4026 0.0029910322 -0.39963744 0.60451751 1.646528 8409 35 35 0 6293 15876 5329 4026 1.1540519 0 24
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9000 0.80563959 4041 0.0042947965 -0.33238166 0.86802133 1.6597032 8429 29 29 0 7164 15876 5329 4041 1.1880521 0 24
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10000 0.90407954 4022 0.0046865656 -0.39987673 0.94720178 1.445708 8349 30 30 0 8189 15876 5329 4022 1.171667 0 24
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Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms
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Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 Matom-step/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.019832 | 0.019832 | 0.019832 | 0.0 | 0.35
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Neigh | 0.020738 | 0.020738 | 0.020738 | 0.0 | 0.37
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Comm | 0.056875 | 0.056875 | 0.056875 | 0.0 | 1.01
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Output | 0.00083247 | 0.00083247 | 0.00083247 | 0.0 | 0.01
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Modify | 5.4828 | 5.4828 | 5.4828 | 0.0 | 97.05
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Other | | 0.06854 | | | 1.21
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Nlocal: 20211 ave 20211 max 20211 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 49 ave 49 max 49 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 160 ave 160 max 160 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 160
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Ave neighs/atom = 0.0079164811
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:11
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