487 lines
25 KiB
Groff
487 lines
25 KiB
Groff
LAMMPS (27 Jun 2024)
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# ------ 2D oxidizing bar ------ #
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dimension 2
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units lj
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atom_style hybrid rheo/thermal bond
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boundary m m p
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comm_modify vel yes
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newton off
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region box block -60 60 0 80 -0.01 0.01 units box
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create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
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Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
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2 by 2 by 1 MPI processor grid
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region lbar block -15 0 3 80 EDGE EDGE units box
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region rbar block 0 15 3 80 EDGE EDGE units box
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region bar union 2 lbar rbar
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region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
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lattice hex 1.0
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Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
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create_atoms 1 region bar
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Created 2255 atoms
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using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
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create_atoms CPU = 0.004 seconds
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create_atoms 3 region floor
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Created 446 atoms
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using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
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create_atoms CPU = 0.000 seconds
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set region rbar type 2
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Setting atom values ...
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1148 settings made for type
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group bar type 1 2
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2255 atoms in group bar
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group rbar type 2
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1148 atoms in group rbar
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group floor type 3
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446 atoms in group floor
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set group all sph/e 0.0
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Setting atom values ...
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2701 settings made for sph/e
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set group all rheo/status 1
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Setting atom values ...
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2701 settings made for rheo/status
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# ------ Model parameters ------#
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variable cut equal 3.0
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variable n equal 1.0
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variable rho0 equal 1.0
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variable cs equal 1.0
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variable mp equal ${rho0}/${n}
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variable mp equal 1/${n}
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variable mp equal 1/1
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variable zeta equal 0.05
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variable kappa equal 0.1*${rho0}/${mp}
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variable kappa equal 0.1*1/${mp}
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variable kappa equal 0.1*1/1
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variable dt_max equal 0.1*${cut}/${cs}/3
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variable dt_max equal 0.1*3/${cs}/3
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variable dt_max equal 0.1*3/1/3
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variable eta equal 0.05
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variable Cv equal 1.0
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variable L equal 0.1
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variable Tf equal 1.0
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mass * ${mp}
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mass * 1
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timestep 0.1
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pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
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pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
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pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
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pair_coeff * * rheo
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pair_coeff * * rheo/solid 1.0 1.0 1.0
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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0 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds many bar bar 1 0 1.5
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Generated 0 of 3 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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 73 49 1
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3 neighbor lists, perpetual/occasional/extra = 2 1 0
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(1) command create_bonds, occasional
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attributes: full, newton off
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pair build: full/bin
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stencil: full/bin/2d
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bin: standard
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(2) pair rheo, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/2d
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bin: standard
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(3) pair rheo/solid, perpetual, trim from (2)
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attributes: half, newton off, cut 1.3
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pair build: trim
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stencil: none
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bin: none
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Added 6547 bonds, new total = 6547
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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6 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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bond_style hybrid bpm/spring rheo/shell t/form 100
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bond_coeff 1 bpm/spring 1.0 1.0 1.0
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bond_coeff 2 rheo/shell 0.2 0.2 0.1
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# ------ Apply dynamics ------#
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# Note: surface detection is not performed on solid bodies, so cannot use surface property
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compute coord all rheo/property/atom coordination
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variable surf atom c_coord<22
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group surf dynamic all var surf every 10
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dynamic group surf defined
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fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
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fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
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fix 2 all rheo/viscosity * constant ${eta}
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fix 2 all rheo/viscosity * constant 0.05
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fix 3 all rheo/pressure * linear
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fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
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fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
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fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
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fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
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fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1
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fix 5 rbar rheo/oxidation 1.5 2 1.0
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fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
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fix 7 all gravity 5e-5 vector 0 -1 0
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fix 8 floor setforce 0.0 0.0 0.0
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fix 9 surf add/heat linear 1.1 0.5
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fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
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fix 11 all enforce2d
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compute surf all rheo/property/atom surface
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compute rho all rheo/property/atom rho
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compute phase all rheo/property/atom phase
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compute temp all rheo/property/atom temperature
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compute eng all rheo/property/atom energy
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compute nbond_shell all rheo/property/atom nbond/shell
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compute nbond_solid all nbond/atom bond/type 1
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# ------ Output & Run ------ #
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thermo 200
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thermo_style custom step time ke press atoms
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#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
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run 40000
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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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- BPM bond style: doi:10.1039/D3SM01373A
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@Article{Clemmer2024,
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author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
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title = {A soft departure from jamming: the compaction of deformable
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granular matter under high pressures},
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journal = {Soft Matter},
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year = 2024,
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volume = 20,
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number = 8,
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pages = {1702--1718}
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}
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- @article{PalermoInPrep,
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journal = {in prep},
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title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
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year = {2024},
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author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
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}
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- @article{ApplMathModel.130.310,
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title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
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journal = {Applied Mathematical Modelling},
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volume = {130},
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pages = {310-326},
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year = {2024},
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issn = {0307-904X},
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doi = {https://doi.org/10.1016/j.apm.2024.02.027},
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author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
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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 3 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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 73 49 1
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8 neighbor lists, perpetual/occasional/extra = 7 1 0
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(1) pair rheo, perpetual, half/full from (3)
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attributes: half, newton off
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pair build: halffull/newtoff
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stencil: none
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bin: none
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(2) pair rheo/solid, perpetual, trim from (4)
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attributes: half, newton off, cut 1.3
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pair build: trim
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stencil: none
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bin: none
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(3) compute RHEO/KERNEL, perpetual
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attributes: full, newton off
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pair build: full/bin
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stencil: full/bin/2d
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bin: standard
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(4) compute RHEO/GRAD, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(5) compute RHEO/VSHIFT, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(6) compute RHEO/SURFACE, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(7) fix rheo/thermal, occasional, trim from (4)
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attributes: half, newton off, cut 3
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pair build: trim
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stencil: none
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bin: none
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(8) fix rheo/oxidation, perpetual, trim from (3)
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attributes: full, newton off, cut 1.8
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pair build: trim
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
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Step Time KinEng Press Atoms
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0 0 0 0 2701
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200 20 4.1737457e-07 1.298459e-07 2701
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400 40 1.6692448e-06 4.9223021e-07 2701
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600 60 3.7115752e-06 1.0476692e-05 2701
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800 80 4.678922e-06 0.00015017477 2701
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1000 100 4.7534549e-06 0.00027967322 2701
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1200 120 3.4532974e-06 0.00045908503 2701
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1400 140 1.4159611e-06 0.00055855688 2701
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1600 160 4.5151976e-07 0.00058351591 2701
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1800 180 5.1656107e-07 0.00055163637 2701
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2000 200 1.882995e-06 0.00048349046 2701
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2200 220 3.3481991e-06 0.00037790487 2701
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2400 240 3.8173347e-06 0.00023972848 2701
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2600 260 3.1832818e-06 9.5696995e-05 2701
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2800 280 1.5994934e-06 -2.7484809e-05 2701
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3000 300 3.573403e-07 -8.56391e-05 2701
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3200 320 1.6485893e-07 -5.6974248e-05 2701
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3400 340 8.5665044e-07 3.473389e-06 2701
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3600 360 2.0801421e-06 5.7938582e-05 2701
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3800 380 3.1934959e-06 0.00016746888 2701
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4000 400 3.2540476e-06 0.00026471904 2701
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4200 420 2.5603544e-06 0.00037699521 2701
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4400 440 1.4309318e-06 0.00047456272 2701
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4600 460 6.5231009e-07 0.00050551979 2701
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4800 480 6.9010626e-07 0.00048100816 2701
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5000 500 1.2663499e-06 0.00042166061 2701
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5200 520 2.0653769e-06 0.00033547376 2701
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5400 540 2.2709253e-06 0.00023015884 2701
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5600 560 1.7864994e-06 0.00013378564 2701
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5800 580 9.5638493e-07 4.4666688e-05 2701
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6000 600 3.0331342e-07 -1.884252e-06 2701
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6200 620 3.451498e-07 8.3090163e-07 2701
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6400 640 9.5098597e-07 4.7759688e-05 2701
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6600 660 1.8169765e-06 0.00011801205 2701
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6800 680 2.3723951e-06 0.00019823562 2701
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7000 700 2.3542553e-06 0.00028873701 2701
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7200 720 1.9132157e-06 0.00036386547 2701
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7400 740 1.4123115e-06 0.00040731263 2701
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7600 760 1.2422941e-06 0.00041151319 2701
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7800 780 1.4355275e-06 0.00038364583 2701
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8000 800 1.7835754e-06 0.00032724239 2701
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8200 820 1.961321e-06 0.00025932051 2701
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8400 840 1.8005786e-06 0.00018763659 2701
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8600 860 1.4274768e-06 0.00012392727 2701
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8800 880 1.075959e-06 8.1241673e-05 2701
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9000 900 1.014674e-06 7.0104531e-05 2701
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9200 920 1.3155353e-06 8.7991534e-05 2701
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9400 940 1.815649e-06 0.00012975516 2701
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9600 960 2.2699387e-06 0.0001861001 2701
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9800 980 2.4916284e-06 0.00024375475 2701
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10000 1000 2.4741893e-06 0.00029466715 2701
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10200 1020 2.3835838e-06 0.00032733587 2701
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10400 1040 2.3816351e-06 0.00033659466 2701
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10600 1060 2.5177605e-06 0.00032136429 2701
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10800 1080 2.6973866e-06 0.00028678114 2701
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11000 1100 2.8219278e-06 0.00023889501 2701
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11200 1120 2.794743e-06 0.00019226876 2701
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11400 1140 2.667182e-06 0.00015100316 2701
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11600 1160 2.5918212e-06 0.00012484649 2701
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11800 1180 2.6802845e-06 0.00011912201 2701
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12000 1200 2.9620111e-06 0.00013336302 2701
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12200 1220 3.3281225e-06 0.00016262605 2701
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12400 1240 3.6587842e-06 0.00020175308 2701
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12600 1260 3.8696418e-06 0.00023984351 2701
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12800 1280 3.9774608e-06 0.00026981166 2701
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13000 1300 4.0621923e-06 0.00028706126 2701
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13200 1320 4.2118368e-06 0.00028639136 2701
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13400 1340 4.4229032e-06 0.00026844105 2701
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13600 1360 4.6415059e-06 0.00023789752 2701
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13800 1380 4.8106868e-06 0.00020524655 2701
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14000 1400 4.9343741e-06 0.00017392428 2701
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14200 1420 5.0835921e-06 0.00015013775 2701
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14400 1440 5.3365604e-06 0.0001413941 2701
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14600 1460 5.7248817e-06 0.00014521418 2701
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14800 1480 6.2145391e-06 0.00016109563 2701
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15000 1500 6.7347576e-06 0.00018481456 2701
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15200 1520 7.221694e-06 0.00020956545 2701
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15400 1540 7.6762698e-06 0.0002293694 2701
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15600 1560 8.1313425e-06 0.00024058679 2701
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15800 1580 8.6053324e-06 0.00024015877 2701
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16000 1600 9.1091988e-06 0.00022927412 2701
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16200 1620 9.6165964e-06 0.00021035982 2701
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16400 1640 1.0093906e-05 0.00018782673 2701
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16600 1660 1.0561165e-05 0.00016863993 2701
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16800 1680 1.1066274e-05 0.00015693261 2701
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17000 1700 1.1661861e-05 0.00015221008 2701
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17200 1720 1.236148e-05 0.00015781879 2701
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17400 1740 1.3124872e-05 0.00017008789 2701
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17600 1760 1.3924606e-05 0.00018628888 2701
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17800 1780 1.4733479e-05 0.0002011741 2701
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18000 1800 1.5558838e-05 0.00021115187 2701
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18200 1820 1.6415631e-05 0.00021314897 2701
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18400 1840 1.7287377e-05 0.00020793654 2701
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18600 1860 1.8202577e-05 0.00019550685 2701
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18800 1880 1.9126239e-05 0.00018102715 2701
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19000 1900 2.0074716e-05 0.0001684831 2701
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19200 1920 2.1090982e-05 0.00015956926 2701
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19400 1940 2.2180303e-05 0.00015805759 2701
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19600 1960 2.3330404e-05 0.00016157807 2701
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19800 1980 2.4557652e-05 0.00017047221 2701
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20000 2000 2.5841568e-05 0.00018216972 2701
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20200 2020 2.7188233e-05 0.00018953358 2701
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20400 2040 2.8576958e-05 0.00019304182 2701
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20600 2060 2.999218e-05 0.00019239757 2701
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20800 2080 3.1437794e-05 0.00018759619 2701
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21000 2100 3.2938831e-05 0.00017863274 2701
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21200 2120 3.4506515e-05 0.00016911647 2701
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21400 2140 3.6126713e-05 0.00016161126 2701
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21600 2160 3.7812343e-05 0.0001583968 2701
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21800 2180 3.9564996e-05 0.00016178647 2701
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22000 2200 4.1406387e-05 0.00016872633 2701
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22200 2220 4.3340255e-05 0.00017435061 2701
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22400 2240 4.5333317e-05 0.00017910049 2701
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22600 2260 4.7311785e-05 0.0001800877 2701
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22800 2280 4.9303605e-05 0.00017728464 2701
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23000 2300 5.1334424e-05 0.00017486007 2701
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23200 2320 5.3402091e-05 0.00016867905 2701
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23400 2340 5.5505853e-05 0.00016402807 2701
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23600 2360 5.7679415e-05 0.00016343865 2701
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23800 2380 5.9920078e-05 0.00016623374 2701
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24000 2400 6.2239328e-05 0.00017028032 2701
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24200 2420 6.4624902e-05 0.00017371561 2701
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24400 2440 6.7054046e-05 0.00017565916 2701
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24600 2460 6.9522453e-05 0.00017545566 2701
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24800 2480 7.2079202e-05 0.00017437049 2701
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25000 2500 7.4716585e-05 0.00017043497 2701
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25200 2520 7.7415627e-05 0.00016579093 2701
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25400 2540 8.0169507e-05 0.00016268419 2701
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25600 2560 8.3001779e-05 0.00016233687 2701
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25800 2580 8.5921287e-05 0.00016275719 2701
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26000 2600 8.8880908e-05 0.00016425339 2701
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26200 2620 9.1881788e-05 0.00016478504 2701
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26400 2640 9.4969348e-05 0.00016371806 2701
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26600 2660 9.817611e-05 0.00016339555 2701
|
|
26800 2680 0.00010146396 0.00015937569 2701
|
|
27000 2700 0.00010485972 0.0001562082 2701
|
|
27200 2720 0.00010837565 0.00015181198 2701
|
|
27400 2740 0.00011187666 0.00015162336 2701
|
|
27600 2760 0.00011543324 0.0001606148 2701
|
|
27800 2780 0.00011905739 0.00016161123 2701
|
|
28000 2800 0.00012280117 0.00016267347 2701
|
|
28200 2820 0.00012665753 0.00016393863 2701
|
|
28400 2840 0.00013061568 0.00016168097 2701
|
|
28600 2860 0.00013469542 0.00015439793 2701
|
|
28800 2880 0.00013889392 0.00014870639 2701
|
|
29000 2900 0.00014307887 0.00015020156 2701
|
|
29200 2920 0.00014714875 0.00015727801 2701
|
|
29400 2940 0.0001510796 0.00016230922 2701
|
|
29600 2960 0.0001551489 0.00016725059 2701
|
|
29800 2980 0.00015918695 0.0001556229 2701
|
|
30000 3000 0.00016145717 0.00015704562 2701
|
|
30200 3020 0.00016164704 0.00015902669 2701
|
|
30400 3040 0.00016250791 0.00017587854 2701
|
|
30600 3060 0.0001639094 0.00016958759 2701
|
|
30800 3080 0.00016479103 0.00016810892 2701
|
|
31000 3100 0.00016521873 0.00016027053 2701
|
|
31200 3120 0.00016540216 0.00015397865 2701
|
|
31400 3140 0.00016690063 0.00015955009 2701
|
|
31600 3160 0.00016832002 0.00015593907 2701
|
|
31800 3180 0.00016948949 0.00015690982 2701
|
|
32000 3200 0.0001700061 0.00016199222 2701
|
|
32200 3220 0.00017122936 0.00016220019 2701
|
|
32400 3240 0.00017198531 0.00015194229 2701
|
|
32600 3260 0.00017286097 0.00014880433 2701
|
|
32800 3280 0.00017395847 0.00014887179 2701
|
|
33000 3300 0.00017527125 0.00015338612 2701
|
|
33200 3320 0.00017667877 0.00014965389 2701
|
|
33400 3340 0.00017944144 0.00014195087 2701
|
|
33600 3360 0.0001807053 0.00014509998 2701
|
|
33800 3380 0.00018242869 0.00014683629 2701
|
|
34000 3400 0.00018415985 0.00014295872 2701
|
|
34200 3420 0.00018635902 0.00013823794 2701
|
|
34400 3440 0.00018885401 0.00013629126 2701
|
|
34600 3460 0.00019106836 0.000138816 2701
|
|
34800 3480 0.00019256787 0.00014358744 2701
|
|
35000 3500 0.00019410016 0.0001420669 2701
|
|
35200 3520 0.00019563657 0.0001340349 2701
|
|
35400 3540 0.00019734994 0.00012994197 2701
|
|
35600 3560 0.00019880477 0.00013331695 2701
|
|
35800 3580 0.00020014422 0.00013848097 2701
|
|
36000 3600 0.00020165626 0.00013796434 2701
|
|
36200 3620 0.00020297057 0.0001346407 2701
|
|
36400 3640 0.00020432584 0.00012838525 2701
|
|
36600 3660 0.00020530152 0.00012848442 2701
|
|
36800 3680 0.00020709012 0.0001296875 2701
|
|
37000 3700 0.00020939979 0.00017016832 2701
|
|
37200 3720 0.00021026158 0.00017388254 2701
|
|
37400 3740 0.00021203076 0.00012169741 2701
|
|
37600 3760 0.00021407912 0.00012467048 2701
|
|
37800 3780 0.00021652866 0.000129545 2701
|
|
38000 3800 0.00021927979 0.00013537464 2701
|
|
38200 3820 0.00022175274 0.00014124275 2701
|
|
38400 3840 0.00022431717 0.0001456533 2701
|
|
38600 3860 0.00022586947 0.00015646735 2701
|
|
38800 3880 0.00021974508 0.0001467496 2701
|
|
39000 3900 0.00021270891 0.0001291023 2701
|
|
39200 3920 0.00020709839 0.00014468038 2701
|
|
39400 3940 0.00020138943 0.000156103 2701
|
|
39600 3960 0.00019579027 0.00015207179 2701
|
|
39800 3980 0.00019219602 0.0001548601 2701
|
|
40000 4000 0.00018931715 0.00013543387 2701
|
|
Loop time of 169.513 on 4 procs for 40000 steps with 2701 atoms
|
|
|
|
Performance: 2038784.562 tau/day, 235.970 timesteps/s, 637.356 katom-step/s
|
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 16.279 | 22.828 | 28 | 98.9 | 13.47
|
|
Bond | 0.88503 | 1.4645 | 2.0916 | 36.3 | 0.86
|
|
Neigh | 29.832 | 29.954 | 30.069 | 1.5 | 17.67
|
|
Comm | 1.2274 | 1.3406 | 1.4623 | 7.3 | 0.79
|
|
Output | 0.0041506 | 0.0054325 | 0.0062685 | 1.1 | 0.00
|
|
Modify | 107.8 | 113.27 | 120.23 | 47.8 | 66.82
|
|
Other | | 0.6549 | | | 0.39
|
|
|
|
Nlocal: 675.25 ave 1362 max 1 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 94.75 ave 154 max 45 min
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
Neighs: 10485 ave 21200 max 18 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 20408.5 ave 41306 max 18 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 81634
|
|
Ave neighs/atom = 30.223621
|
|
Ave special neighs/atom = 1.7304702
|
|
Neighbor list builds = 39994
|
|
Dangerous builds = 0
|
|
Total wall time: 0:02:50
|