323 lines
14 KiB
Groff
323 lines
14 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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4 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 = 0.002 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 0.0002
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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 0.04
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SRD max distance & max velocity = 0.16 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 = 1.0732692
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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) = 9.752 | 9.762 | 9.781 Mbytes
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Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
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0 1.4809886 0 0 0 0 0 0
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1000 1.2265081 1.1522909 0.00027866069 0.0022427232 0 0.1137285 0.58262976
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2000 1.1757141 1.1251323 0.00040597152 0.003287261 0 0.16669701 0.27109853
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3000 1.126304 1.0646585 0.00050542958 0.0040748897 0 0.20663766 0.36959653
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4000 1.1140297 1.0761435 0.00060430927 0.0052863645 0 0.26807154 0.35099205
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5000 1.0823307 1.0256814 0.00066557681 0.0051213284 0 0.25970256 0.28491631
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6000 1.0656188 1.0387091 0.00066454105 0.005213537 0 0.26437846 0.2150581
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7000 1.0600108 1.0099931 0.0007238719 0.005470459 0 0.27740698 0.21846568
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8000 1.0464374 1.0049819 0.00061068366 0.0053702582 0 0.27232579 0.1326171
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9000 1.0381097 1.0126049 0.00057318728 0.0055976321 0 0.28385592 0.16797796
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10000 1.0312982 1.0018962 0.00050597007 0.0051153126 0 0.2593975 0.15281043
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Loop time of 1.2997 on 8 procs for 10000 steps with 20284 atoms
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Performance: 132953.355 tau/day, 7694.060 timesteps/s, 156.066 Matom-step/s
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96.7% CPU use with 8 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 | 0.01406 | 0.014495 | 0.01532 | 0.3 | 1.12
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Neigh | 0.0051916 | 0.0053424 | 0.0054386 | 0.1 | 0.41
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Comm | 0.062053 | 0.065305 | 0.069014 | 0.9 | 5.02
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Output | 0.00062289 | 0.00065254 | 0.00077243 | 0.0 | 0.05
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Modify | 1.169 | 1.178 | 1.1905 | 0.6 | 90.64
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Other | | 0.03589 | | | 2.76
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Nlocal: 2535.5 ave 2637 max 2476 min
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Histogram: 1 3 1 1 0 0 0 0 1 1
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Nghost: 31.125 ave 42 max 25 min
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Histogram: 3 0 1 2 0 0 0 0 1 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 8 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 40000
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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 0.04
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SRD max distance & max velocity = 0.16 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 = 1.5799049
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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 = 1
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ave/max small velocity = 12.481632 40
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ave/max big velocity = 0.58815233 1.5489134
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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) = 11.95 | 11.95 | 11.95 Mbytes
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Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
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10000 0.98889306 0 0.00050595647 0.0051153289 0 0.25939833 0.020019811
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11000 0.98995417 0.99721412 0.0005166709 0.0054320552 0 0.27545952 0.03376188
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12000 0.99401168 0.95502319 0.00053659416 0.0054974426 0 0.27877531 0.056856034
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13000 0.98790692 0.96488357 0.00061076364 0.0053196554 0 0.26975972 0.2677228
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14000 0.98939233 0.98809694 0.00052317779 0.0050536922 0 0.25627273 0.20381427
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15000 0.99046365 0.97048828 0.00056914402 0.0053274908 0 0.27015706 0.082163088
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16000 0.99743447 1.0111983 0.00053706165 0.0048068384 0 0.24375478 0.06429569
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17000 0.99622359 1.0124982 0.0005905197 0.0055966416 -7.4541903e-05 0.2838057 0.25418037
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18000 0.99283929 0.99581721 0.00061730878 0.0059098964 -0.00014754106 0.29969084 0.12701702
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19000 0.99175517 1.0115581 0.0005128714 0.0059214809 -0.00046203987 0.30027829 0.2640506
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20000 0.98895811 0.97731528 0.00052294314 0.0055670021 -0.0016029702 0.28230268 0.26239209
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21000 0.98904093 0.98120258 0.00054169978 0.0052762731 -0.0026834879 0.26755981 0.15432481
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22000 0.98773149 0.99217218 0.00056091602 0.0052754729 -0.0044093345 0.26751923 0.2208051
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23000 0.98802862 0.96564549 0.00062226338 0.0053263454 -0.008790914 0.27009898 0.18058977
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24000 0.98754002 1.024015 0.00057178953 0.0054083382 -0.0094859317 0.27425683 0.01598147
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25000 0.98656341 0.94647246 0.00066215791 0.0053555849 -0.014877058 0.27158171 0.28794628
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26000 0.98750471 1.0077626 0.00058955769 0.0057081639 -0.013151869 0.28946099 0.20814911
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27 |