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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2 by 2 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) = 4.172 | 4.172 | 4.172 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 0.00891987 on 4 procs for 1000 steps with 100 atoms
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Performance: 48431181.463 tau/day, 112109.216 timesteps/s, 11.211 Matom-step/s
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98.2% CPU use with 4 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 | 0.00039835 | 0.00043547 | 0.00047558 | 0.0 | 4.88
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Neigh | 0.00033856 | 0.00036829 | 0.00038548 | 0.0 | 4.13
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Comm | 0.0065535 | 0.0065882 | 0.0066353 | 0.0 | 73.86
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Output | 1.0991e-05 | 1.2359e-05 | 1.4677e-05 | 0.0 | 0.14
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Modify | 0.00043639 | 0.00045662 | 0.00050811 | 0.0 | 5.12
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Other | | 0.001059 | | | 11.87
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Nlocal: 25 ave 29 max 23 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Nghost: 33.75 ave 35 max 31 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Neighs: 38 ave 46 max 34 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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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 = 0.006 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) = 19.17 | 19.17 | 19.18 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 0.98459665 3968 0.0086216557 0.27547381 1.7425228 4.4010488 7403 34 34 0 663 25600 5329 3968 0.98292304 0 5
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2000 0.74381104 4003 0.0041077507 -0.27806095 0.8302175 2.6170187 7746 32 32 0 1272 25600 5329 4003 1.0631936 0 5
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3000 0.86305095 3969 0.0048953507 -0.29654658 0.98939933 2.1215334 7834 35 35 0 1974 25600 5329 3969 1.1209619 0 5
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4000 0.8262932 4022 0.0049907905 -0.2224882 1.0086887 2.079935 8196 27 27 0 2753 25600 5329 4022 1.1040604 0 5
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5000 0.85908819 4038 0.0043301633 -0.40487209 0.87516931 1.7917343 8347 28 28 0 3622 25600 5329 4038 1.1575336 0 5
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6000 0.8048766 4024 0.0047529981 -0.2386377 0.96062844 1.8195477 8103 26 26 0 4536 25600 5329 4024 1.1818796 0 5
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7000 0.84561126 4047 0.0039459142 -0.46245206 0.79750871 1.4432235 8154 20 20 0 5483 25600 5329 4047 1.1817402 0 5
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8000 0.81543891 4037 0.0037591562 -0.45524091 0.75976306 1.7501338 8377 27 27 0 6472 25600 5329 4037 1.168956 0 5
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9000 0.71960112 4045 0.0035243955 -0.3598901 0.71231557 1.7333111 8440 30 30 0 7386 25600 5329 4045 1.1765277 0 5
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10000 1.0831334 4043 0.0053045911 -0.54175788 1.0721109 1.7434822 8283 33 33 0 8331 25600 5329 4043 1.1696048 0 5
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Loop time of 1.82855 on 4 procs for 10000 steps with 20211 atoms
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Performance: 472504.837 tau/day, 5468.806 timesteps/s, 110.530 Matom-step/s
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99.3% CPU use with 4 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 | 0.0057481 | 0.0069625 | 0.0087051 | 1.3 | 0.38
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Neigh | 0.0067658 | 0.0070766 | 0.0076303 | 0.4 | 0.39
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Comm | 0.10613 | 0.10693 | 0.10786 | 0.2 | 5.85
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Output | 0.00053606 | 0.00059075 | 0.00063891 | 0.0 | 0.03
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Modify | 1.6117 | 1.6525 | 1.6763 | 1.9 | 90.37
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Other | | 0.05449 | | | 2.98
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Nlocal: 5052.75 ave 5483 max 4509 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 27 ave 28 max 26 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 39.5 ave 55 max 26 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Total # of neighbors = 158
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Ave neighs/atom = 0.0078175251
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:03
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