364 lines
16 KiB
Groff
364 lines
16 KiB
Groff
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
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using 1 OpenMP thread(s) per MPI task
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# Aspherical shear demo - 2d line boxes, solvated by SRD particles
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units lj
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atom_style line
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atom_modify first big
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dimension 2
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read_data data.line.srd
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Reading data file ...
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orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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400 atoms
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400 lines
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read_data CPU = 0.003 seconds
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# add small particles as hi density lattice
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lattice sq 0.4
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Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
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region plane block INF INF INF INF -0.001 0.001
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lattice sq 10.0
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Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
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create_atoms 2 region plane
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Created 33489 atoms
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using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
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create_atoms CPU = 0.003 seconds
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group big type 1
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400 atoms in group big
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group small type 2
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33489 atoms in group small
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set group small mass 0.01
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Setting atom values ...
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33489 settings made for mass
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# delete overlaps
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# must set 1-2 cutoff to non-zero value
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pair_style lj/cut 1.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 1.0 1.0
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delete_atoms overlap 1.5 small big
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System init for delete_atoms ...
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Generated 0 of 1 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 = 1.8
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ghost atom cutoff = 1.8
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binsize = 0.9, bins = 64 64 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:313)
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Deleted 13605 atoms, new total = 20284
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# SRD run
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reset_timestep 0
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velocity small create 1.44 87287 loop geom
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neighbor 0.8 multi
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule/intra big include big
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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 line/lj 2.5
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pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
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pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
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pair_coeff 1 2 1.0 0.2 1.0 0.2 2.5
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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 0.0001
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fix 1 big rigid molecule
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100 rigid bodies with 400 atoms
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fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
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fix 3 all deform 1 x scale 1.25 y scale 1.25
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fix 4 all enforce2d
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# diagnostics
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compute tsmall small temp/deform
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compute tbig big temp
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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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compute_modify tbig extra/dof -350
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compute 1 big erotate/asphere
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compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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thermo 1000
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thermo_style custom step c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
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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:533)
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compute 10 big property/atom end1x end1y end2x end2y
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#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
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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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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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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 0 of 1 mixed pair_coeff terms from geometric mixing rule
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WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
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WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
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SRD info:
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SRD/big particles = 19884 400
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big particle diameter max/min = 1.9988171 0.50330564
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SRD temperature & lamda = 1 0.02
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SRD max distance & max velocity = 0.08 40
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SRD grid counts: 230 230 1
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SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
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SRD per actual grid cell = 0.45503978
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SRD viscosity = 0.92062623
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big/SRD mass density ratio = 12.298053
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WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
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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 = 15.906001 29.105426
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ave/max big velocity = 0 0
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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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 35 35 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair line/lj, 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) = 43.18 | 43.18 | 43.18 Mbytes
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Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
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0 1.6084386 0 0 0 0 0 0
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1000 1.4566787 1.2042825 0.00015900089 0.0011955837 0 0.060628048 0.75322967
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2000 1.3561018 1.2092936 0.00026739313 0.0020783306 0 0.10539215 0.53247025
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3000 1.3327447 1.1696777 0.0003215116 0.0024935719 0 0.12644903 0.32024668
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4000 1.3031273 1.1385596 0.00037337107 0.0031214473 0 0.15828859 0.64066244
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5000 1.28204 1.0983763 0.00047966362 0.0033295434 0 0.16884114 0.32103666
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6000 1.2654396 1.0969562 0.00049917373 0.0037382387 0 0.18956609 0.16211614
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7000 1.2401503 1.1232046 0.00045137168 0.0037522201 0 0.19027508 0.014071672
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8000 1.2349025 1.059008 0.00056648801 0.0039664742 0 0.20113991 0.24483817
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9000 1.2272907 1.0371006 0.00056271544 0.0037847074 0 0.19192251 0.032968056
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10000 1.2153817 1.0209113 0.00053291164 0.0037197691 0 0.18862949 0.3237698
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Loop time of 6.0346 on 1 procs for 10000 steps with 20284 atoms
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Performance: 14317.424 tau/day, 1657.109 timesteps/s, 33.613 Matom-step/s
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96.2% 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 | 0.10636 | 0.10636 | 0.10636 | 0.0 | 1.76
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Neigh | 0.01905 | 0.01905 | 0.01905 | 0.0 | 0.32
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Comm | 0.041223 | 0.041223 | 0.041223 | 0.0 | 0.68
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Output | 0.0017015 | 0.0017015 | 0.0017015 | 0.0 | 0.03
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Modify | 5.8165 | 5.8165 | 5.8165 | 0.0 | 96.39
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Other | | 0.04976 | | | 0.82
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Nlocal: 20284 ave 20284 max 20284 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 84 ave 84 max 84 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Neighbor list builds = 500
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Dangerous builds = 0
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#undump 1
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#undump 2
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unfix 3
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change_box all triclinic
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Changing box ...
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triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
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fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip #tstat yes
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#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
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fix 3 all deform 1 xy erate 0.0002 units box remap v
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run 30000
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
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SRD info:
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SRD/big particles = 19884 400
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big particle diameter max/min = 1.9988171 0.50330564
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SRD temperature & lamda = 1 0.02
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SRD max distance & max velocity = 0.08 40
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SRD grid counts: 288 288 1
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SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
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SRD per actual grid cell = 0.26976265
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SRD viscosity = 1.0312189
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big/SRD mass density ratio = 20.672578
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WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
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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 = 12.805429 40
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ave/max big velocity = 0.50400801 2.1697856
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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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 44 44 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair line/lj, perpetual
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attributes: half, newton on
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pair build: half/multi/atomonly/newton/tri
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stencil: half/multi/2d/tri
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 58.85 | 58.85 | 58.85 Mbytes
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Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
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10000 1.0423767 0 0.00053289774 0.0037197858 0 0.18863034 0.014558088
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11000 1.0333923 1.0309908 0.00058283908 0.0042336078 0 0.21468625 0.13036048
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12000 1.0268543 1.0290122 0.00055294944 0.0044278861 0 0.2245381 0.53275676
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13000 1.0257856 1.0140434 0.00051520803 0.0042888387 0 0.21748701 0.2066835
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14000 1.0239497 1.0321558 0.00054742053 0.004259664 0 0.21600756 0.24430097
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15000 1.0194475 1.0119806 0.00053619565 0.0041113765 0 0.2084879 0.18420434
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16000 1.016421 1.0309991 0.00049553642 0.0041338645 0 0.20962827 0.18298406
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17000 1.0088527 0.99723694 0.00049824173 0.0044777581 0 0.22706711 0.65557023
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18000 1.0073877 1.0136962 0.00058327835 0.0045355884 0 0.22999969 0.13700737
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19000 1.0026916 1.0253129 0.00056760151 0.0045138437 0 0.22889701 0.16443344
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20000 1.0024042 0.98988084 0.00057568118 0.0048644983 0 0.24667871 0.060864322
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21000 0.99500641 0.99075324 0.00062187543 0.0050480594 0 0.25598709 0.18428384
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22000 0.99286446 0.98642266 0.00061024492 0.0050497174 0 0.25607117 0.18499738
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23000 0.99204086 0.98869005 0.00064013575 0.0052921112 0 0.26836296 0.046987646
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24000 0.98768375 1.0110613 0.00065868636 0.0049285304 0 0.24992578 0.22623751
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25000 0.98763308 0.98752678 0.00067070463 0.0049364253 0 0.25032613 0.022819382
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26000 0.9844889 1.0059918 0.00075364589 0.0053381778 0 0.270699 0.089735771
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27000 0.98574608 0.99094039 0.00080711088 0.0054137233 0 0.27452991 0.14477885
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28000 0.98139419 0.97487219 0.00071242405 0.0053315389 0 0.27036234 -0.016357088
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29000 0.98458705 0.98600894 0.00068355573 0.0050157315 0 0.25434775 0.015749835
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30000 0.98440759 1.0010793 0.00067594666 0.0048121267 0 0.24402295 0.20422918
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31000 0.98060632 0.9825933 0.00069529947 0.0050649881 -0.00010700206 0.25684555 0.0014601267
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32000 0.97616624 0.94976641 0.00067682494 0.0052111319 -0.00013230279 0.2642565 0.013738873
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33000 0.97926122 0.95756794 0.00071774059 0.0053716513 -0.00024804252 0.27239644 0.10643895
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34000 0.97227771 0.94365547 0.00080885359 0.0055744144 -0.00063217879 0.28267856 0.12472959
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35000 0.97295679 0.98103625 0.0008130852 0.0057598371 -0.00097218501 0.29208134 0.88422099
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36000 0.97131919 0.97164636 0.0008345433 0.0062212675 -0.001543055 0.31548048 0.22389401
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37000 0.96988732 0.98589058 0.00083271625 0.0062999411 -0.0026064482 0.31947001 0.11797226
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38000 0.97135512 0.96486494 0.00076943974 0.0057397763 -0.0041174109 0.29106406 0.072790492
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39000 0.97386738 0.95218062 0.00079594844 0.0056308358 -0.0069006312 0.28553968 0.12417837
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40000 0.97914045 1.0033941 0.000830798 0.0055952714 -0.0086705514 0.28373621 0.1976663
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Loop time of 15.944 on 1 procs for 30000 steps with 20284 atoms
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Performance: 16256.931 tau/day, 1881.589 timesteps/s, 38.166 Matom-step/s
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99.5% 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 | 0.31871 | 0.31871 | 0.31871 | 0.0 | 2.00
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Neigh | 0.082974 | 0.082974 | 0.082974 | 0.0 | 0.52
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Comm | 0.16092 | 0.16092 | 0.16092 | 0.0 | 1.01
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Output | 0.0047257 | 0.0047257 | 0.0047257 | 0.0 | 0.03
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Modify | 15.189 | 15.189 | 15.189 | 0.0 | 95.27
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Other | | 0.1871 | | | 1.17
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Nlocal: 20284 ave 20284 max 20284 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 76 ave 76 max 76 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 38 ave 38 max 38 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 38
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Ave neighs/atom = 0.0018733978
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Neighbor list builds = 1500
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Dangerous builds = 0
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Total wall time: 0:00:22
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