319 lines
14 KiB
Groff
319 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 viscosity 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 0.00883083 on 4 procs for 1000 steps with 100 atoms
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Performance: 48919544.759 tau/day, 113239.687 timesteps/s, 11.324 Matom-step/s
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99.6% 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 | 0.00040021 | 0.00044336 | 0.00050371 | 0.0 | 5.02
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Neigh | 0.00033682 | 0.00036617 | 0.00038566 | 0.0 | 4.15
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Comm | 0.006519 | 0.0065578 | 0.0066015 | 0.0 | 74.26
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Output | 1.1215e-05 | 1.2252e-05 | 1.4089e-05 | 0.0 | 0.14
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Modify | 0.00043326 | 0.00044482 | 0.00046058 | 0.0 | 5.04
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Other | | 0.001006 | | | 11.40
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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 small viscosity 10 x y 50
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fix 4 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 500 dump.poly.mp
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#dump 1 all image 500 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 0.83735494 3964 0.0071370659 0.19481352 1.4424724 3.9770741 7472 25 25 0 603 25600 5329 3964 0.96475118 0 2
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2000 0.89694821 3981 0.0057098818 -0.18242861 1.1540242 3.1251883 7672 28 28 0 1238 25600 5329 3981 1.0589985 0 2
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3000 0.99778172 3975 0.0051822049 -0.43931933 1.0473754 1.8970896 7814 24 24 0 1968 25600 5329 3975 1.1192504 0 3
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4000 0.90067439 4030 0.0045096255 -0.43056442 0.91144042 1.8769981 8104 33 33 0 2911 25600 5329 4030 1.1382082 0 3
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5000 0.90625848 4018 0.0055622776 -0.22613322 1.1241919 2.1866405 8287 26 26 0 3900 25600 5329 4018 1.1429442 0 3
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6000 1.1284139 4022 0.0065653291 -0.354418 1.3269187 2.0312152 8268 35 35 0 5013 25600 5329 4022 1.1559733 0 3
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7000 1.0073477 4043 0.0063924548 -0.2089691 1.291979 2.3332058 8433 39 39 0 6093 25600 5329 4043 1.1308958 0 3
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8000 1.0621801 4050 0.00731979 -0.10324558 1.4794028 2.6610716 8353 40 40 0 7194 25600 5329 4050 1.1539521 0 3
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9000 1.3173319 4046 0.0085268497 -0.23946297 1.7233616 2.4074596 8290 33 33 0 8498 25600 5329 4046 1.1601502 0 3
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10000 1.1754738 4009 0.0074264713 -0.25049186 1.5009641 2.4237351 8305 30 30 0 9811 25600 5329 4009 1.1489476 0 43
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Loop time of 1.85719 on 4 procs for 10000 steps with 20211 atoms
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Performance: 465218.852 tau/day, 5384.477 timesteps/s, 108.826 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 | 0.0056791 | 0.0069765 | 0.0089852 | 1.6 | 0.38
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Neigh | 0.006991 | 0.0073805 | 0.0079507 | 0.4 | 0.40
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Comm | 0.10756 | 0.10836 | 0.10942 | 0.2 | 5.83
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Output | 0.00052479 | 0.0005511 | 0.00062567 | 0.0 | 0.03
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Modify | 1.6443 | 1.6772 | 1.7031 | 1.7 | 90.31
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Other | | 0.0567 | | | 3.05
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Nlocal: 5052.75 ave 5381 max 4651 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 28.5 ave 30 max 26 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Neighs: 34.75 ave 55 max 26 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Total # of neighbors = 139
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Ave neighs/atom = 0.006877443
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Neighbor list builds = 501
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Dangerous builds = 0
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Total wall time: 0:00:03
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