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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2 by 2 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 = 0.001 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) = 13.44 | 13.45 | 13.47 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 1.4539924 1.2578325 0.0001679809 0.0010497614 0 0.053233399 0.69841607
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2000 1.3516746 1.1693535 0.00031932331 0.0021450754 0 0.10877677 0.058141137
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3000 1.3294093 1.1539986 0.00032558495 0.0022345521 0 0.11331414 0.085892255
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4000 1.3049311 1.1174444 0.00039637116 0.0026520968 0 0.13448783 0.10574422
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5000 1.2790124 1.1209176 0.0004519172 0.0032635257 0 0.16549339 0.59225702
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6000 1.2631214 1.0868777 0.00052274216 0.003527049 0 0.17885666 0.26093936
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7000 1.2520054 1.0780954 0.00051683183 0.0038111141 0 0.1932616 -0.0014733978
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8000 1.2412037 1.0587149 0.00056620143 0.0038329297 0 0.19436786 0.31576462
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9000 1.2242125 1.0699712 0.00065335672 0.0039948578 0 0.20257924 0.19755012
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10000 1.2155758 1.0279682 0.00059730828 0.004142635 0 0.21007302 0.30022953
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Loop time of 1.92412 on 4 procs for 10000 steps with 20284 atoms
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Performance: 44903.607 tau/day, 5197.177 timesteps/s, 105.420 Matom-step/s
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97.6% 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 | 0.026855 | 0.027529 | 0.028377 | 0.4 | 1.43
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Neigh | 0.0073723 | 0.007433 | 0.0075693 | 0.1 | 0.39
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Comm | 0.062837 | 0.065574 | 0.066747 | 0.6 | 3.41
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Output | 0.00072894 | 0.00076558 | 0.00083361 | 0.0 | 0.04
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Modify | 1.7861 | 1.7926 | 1.8 | 0.4 | 93.16
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Other | | 0.03026 | | | 1.57
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Nlocal: 5071 ave 5096 max 5051 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Nghost: 44 ave 51 max 40 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 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 = 12.826666 40
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ave/max big velocity = 0.53469722 1.7415554
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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) = 17.6 | 17.6 | 17.61 Mbytes
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Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
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10000 1.0416233 0 0.0005972922 0.0041426543 0 0.210074 0.016213064
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11000 1.0366852 1.0236717 0.00066926382 0.004404743 0 0.22336452 0.097686059
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12000 1.028695 1.0023004 0.00065323121 0.0043971164 0 0.22297777 0.30007875
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13000 1.0223214 1.0296267 0.00060201395 0.0041815724 0 0.21204754 0.17307062
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14000 1.0210601 1.0092227 0.00057020066 0.0041936718 0 0.2126611 0.13379405
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15000 1.0169223 1.003359 0.00060818329 0.0046120335 0 0.23387622 0.39144341
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16000 1.012222 0.99937463 0.00060471571 0.004533278 0 0.22988253 0.16026051
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17000 1.0087993 0.98937449 0.00061843646 0.0048888197 0 0.24791205 0.095507016
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18000 1.0030288 0.94092316 0.00054252694 0.0046740839 0 0.2370228 -0.070838649
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19000 1.0010739 0.99759814 0.00054041829 0.0045481798 0 0.2306382 0.1944996
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20000 1.004189 1.0157285 0.00053330893 0.0044999261 0 0.22819125 0.14452619
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21000 0.99601133 1.003771 0.00053282188 0.0048954851 0 0.24825005 0.20196263
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22000 0.99445408 1.0163465 0.00059954941 0.0051668276 0 0.26200983 0.21332194
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23000 0.99663947 0.94920707 0.00057729723 0.0051052499 0 0.25888722 0.19282224
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24000 0.99500015 1.0021742 0.00064312956 0.0053430656 0 0.27094686 0.18044164
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25000 0.99388189 0.98446723 0.00060150964 0.0054017824 0 0.27392438 0.18844037
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26000 0.99632932 0.94670024 0.00052479857 0.004905147 0 0.24874 0.17961314
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27000 0.99112962 1.0247118 0.00053159824 0.004752248 0 0.2409865 0.12037737
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28000 0.98887153 0.97734068 0.00052255365 0.0050199491 0 0.25456162 0.29110866
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29000 0.98938025 0.99467239 0.00053095044 0.0050303107 0 0.25508706 0.59776339
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30000 0.99081592 0.98822122 0.00056693985 0.0052452228 0 0.26598525 0.0150843
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31000 0.99050903 1.0184912 0.00056742049 0.0056515686 0 0.28659104 0.07877756
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32000 0.98929926 0.99257634 0.00058111732 0.005740055 0 0.29107819 0.19146041
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33000 0.98698723 0.94872564 0.00056547335 0.0057628447 0 0.29223385 0.076755599
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34000 0.98967998 0.98777081 0.00056045905 0.0055645603 0 0.28217885 0.095025284
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35000 0.98777734 0.95746323 0.00050104756 0.0055630681 -4.7847642e-05 0.28210318 0.25667997
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36000 0.98661597 0.98801246 0.00047074618 0.0054500805 -5.8956193e-05 0.27637358 0.18221607
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37000 0.98390111 0.9837894 0.00044581144 0.0054703357 -7.4197741e-05 0.27740072 0.11959303
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38000 0.98092646 1.0142057 0.0004945556 0.0056372628 -8.6736668e-05 0.2858656 0.017325263
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39000 0.98125957 0.94219822 0.00059691168 0.0060914156 -9.9726556e-05 0.30889569 0.0081217281
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40000 0.98362942 0.9649582 0.00062286697 0.0063736358 -0.00010700337 0.32320707 0.293121
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Loop time of 5.08621 on 4 procs for 30000 steps with 20284 atoms
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Performance: 50961.296 tau/day, 5898.298 timesteps/s, 119.641 Matom-step/s
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98.8% 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 | 0.084321 | 0.084948 | 0.086233 | 0.3 | 1.67
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Neigh | 0.027521 | 0.029247 | 0.030632 | 0.7 | 0.58
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Comm | 0.19101 | 0.20262 | 0.2068 | 1.5 | 3.98
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Output | 0.0019581 | 0.0020369 | 0.0022544 | 0.3 | 0.04
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Modify | 4.681 | 4.6884 | 4.7051 | 0.4 | 92.18
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Other | | 0.07891 | | | 1.55
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Nlocal: 5071 ave 5197 max 4951 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 44 ave 50 max 41 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 5.75 ave 12 max 0 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Total # of neighbors = 23
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Ave neighs/atom = 0.0011338986
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Neighbor list builds = 1500
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Dangerous builds = 0
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Total wall time: 0:00:07
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