380 lines
20 KiB
Groff
380 lines
20 KiB
Groff
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
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# ------ 2D Ice Cube Pour ------ #
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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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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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region box block -25 25 0 100 -0.01 0.01 units box
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create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
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Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
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2 by 2 by 1 MPI processor grid
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region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
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region fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
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region fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
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region fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
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region fluid block -24 24 1 30 EDGE EDGE units box
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lattice sq 1.0
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Lattice spacing in x,y,z = 1 1 1
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create_atoms 1 region fluid
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Created 1470 atoms
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using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
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create_atoms CPU = 0.001 seconds
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set group all sph/e 8.0
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Setting atom values ...
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1470 settings made for sph/e
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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/${n}
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variable mp equal 1/1
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variable zeta equal 0.05
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variable kappa equal 0.01*${rho0}/${mp}
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variable kappa equal 0.01*1/${mp}
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variable kappa equal 0.01*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 1.0
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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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bond_style bpm/spring
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bond_coeff 1 1.0 1.0 1.0
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# ------ Pour particles ------#
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molecule my_mol "square.mol"
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Read molecule template my_mol:
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#Made with create_mol.py
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1 molecules
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0 fragments
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100 atoms with max type 1
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342 bonds with max type 1
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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# Wall region extends far enough in z to avoid contact
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region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
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region drop block -16 16 70 90 EDGE EDGE side in units box
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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 0.01 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 0.01 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 0.01 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 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 1 react 1.5 1
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fix 5 all wall/region wall harmonic 1.0 1.0 1.0
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fix 6 all gravity 5e-4 vector 0 -1 0
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fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
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WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
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fix 8 all enforce2d
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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 all nbond/atom
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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 c_rho
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run 30000
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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 0 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 = 31 61 1
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7 neighbor lists, perpetual/occasional/extra = 6 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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Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
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Step Time KinEng Press Atoms
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0 0 0 0 1470
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200 20 5.6002982e-05 3.4434234e-05 1570
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400 40 8.2173099e-05 8.6171768e-05 1570
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600 60 8.019018e-05 0.00010750355 1570
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800 80 0.00013866953 0.00010265608 1570
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1000 100 0.00018965028 8.1985605e-05 1570
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1200 120 0.00022033242 7.4736443e-05 1670
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1400 140 0.00030767062 0.00011264333 1670
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1600 160 0.00040770127 0.00018779992 1670
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1800 180 0.00047476332 0.00023153009 1670
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2000 200 0.00059116774 0.00027200445 1670
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2200 220 0.0007151733 0.0002919963 1770
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2400 240 0.00083392135 0.00029757889 1770
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2600 260 0.00099653466 0.00036547269 1770
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2800 280 0.0011964069 0.00045983458 1770
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3000 300 0.0013716953 0.00055013647 1770
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3200 320 0.0015174096 0.00064203572 1870
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3400 340 0.0016539743 0.00086671622 1870
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3600 360 0.0015887858 0.00066353749 1870
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3800 380 0.0016451684 0.00070551483 1870
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4000 400 0.0017330971 0.00080722283 1870
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4200 420 0.001812193 0.00073573903 1970
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4400 440 0.001755871 0.0010621909 1970
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4600 460 0.0016190772 0.00072913706 1970
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4800 480 0.0015741931 0.00073524088 1970
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5000 500 0.0016488815 0.00088684275 1970
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5200 520 0.0017213288 0.00077042378 2070
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5400 540 0.0018509598 0.0010219434 2070
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5600 560 0.0020251064 0.00083182483 2070
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5800 580 0.0022473255 0.00095076144 2070
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6000 600 0.0024843519 0.0011247014 2070
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6200 620 0.0022282321 0.0018105932 2170
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6400 640 0.0020289063 0.0014158497 2170
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6600 660 0.002145241 0.0011359383 2170
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6800 680 0.0024313937 0.0016475504 2170
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7000 700 0.0021000599 0.0020983745 2170
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7200 720 0.0019137235 0.0010439152 2270
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7400 740 0.0018801367 0.00095436448 2270
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7600 760 0.0017979449 0.0011184039 2270
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7800 780 0.0018005205 0.0009243205 2270
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8000 800 0.0017827073 0.0013671228 2270
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8200 820 0.0018387108 0.0015426012 2270
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8400 840 0.0016000788 0.0016751514 2270
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8600 860 0.0013954964 0.0016884335 2270
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8800 880 0.0013283728 0.0012399398 2270
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9000 900 0.001389385 0.0012968496 2270
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9200 920 0.0012295438 0.0012995821 2270
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9400 940 0.0010522655 0.00082245528 2270
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9600 960 0.00097085496 0.00053833131 2270
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9800 980 0.0009398987 0.00063467387 2270
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10000 1000 0.00092710392 0.00059494446 2270
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10200 1020 0.00095545471 0.00074560644 2270
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10400 1040 0.0009645841 0.00085429807 2270
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10600 1060 0.00064037148 0.0017222246 2270
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10800 1080 0.00046790978 0.00088204234 2270
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11000 1100 0.00030106229 0.00074950209 2270
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11200 1120 0.00027746016 0.00052831745 2270
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11400 1140 0.0002533348 0.0006272715 2270
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11600 1160 0.00021825085 0.00029691552 2270
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11800 1180 0.0001451308 0.00015037478 2270
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12000 1200 0.0001314823 0.00017227174 2270
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12200 1220 0.00013693632 0.00017791384 2270
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12400 1240 0.00014987347 0.0002286677 2270
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12600 1260 0.00015092598 0.0003698436 2270
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12800 1280 0.0001291653 0.00047229532 2270
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13000 1300 0.00011949988 0.00049560375 2270
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13200 1320 0.00011694665 0.00057542084 2270
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13400 1340 9.6164519e-05 0.00062714755 2270
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13600 1360 8.4517591e-05 0.00044156913 2270
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13800 1380 0.00019140516 0.0003264745 2270
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14000 1400 0.00013868599 0.00037753497 2270
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14200 1420 9.3701636e-05 0.00031517848 2270
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14400 1440 6.7389077e-05 0.0002946861 2270
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14600 1460 5.3640086e-05 0.00026650711 2270
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14800 1480 4.2699992e-05 0.00023789279 2270
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15000 1500 5.3012016e-05 0.00019933234 2270
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15200 1520 5.8834197e-05 0.00022407007 2270
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15400 1540 5.0899982e-05 0.00029695531 2270
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15600 1560 3.0476742e-05 0.00039119066 2270
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15800 1580 1.6633264e-05 0.00033770401 2270
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16000 1600 1.098906e-05 0.00036684894 2270
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16200 1620 1.464848e-05 0.00036449759 2270
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16400 1640 1.9598429e-05 0.00021056689 2270
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16600 1660 1.2644955e-05 0.00020781781 2270
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16800 1680 8.8428553e-06 0.000165 2270
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17000 1700 8.8971439e-06 0.00012266475 2270
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17200 1720 1.7032781e-05 0.00019873443 2270
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17400 1740 1.9448563e-05 0.00025661663 2270
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17600 1760 1.3714713e-05 0.000324022 2270
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17800 1780 9.1326468e-06 0.00031392513 2270
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18000 1800 9.2464802e-06 0.00029729527 2270
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18200 1820 1.5553042e-05 0.00027488475 2270
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18400 1840 1.4132933e-05 0.00019565459 2270
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18600 1860 9.4734832e-06 0.00016716988 2270
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18800 1880 5.5115145e-06 0.00013728033 2270
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19000 1900 8.268812e-06 0.00015119605 2270
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19200 1920 1.2470136e-05 0.00020222131 2270
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19400 1940 9.9387775e-06 0.00024503373 2270
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19600 1960 5.4241999e-06 0.00026921858 2270
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19800 1980 2.7987348e-06 0.00026201267 2270
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20000 2000 6.272538e-06 0.00025626323 2270
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20200 2020 8.0157781e-06 0.000220139 2270
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20400 2040 6.1652093e-06 0.00017089058 2270
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20600 2060 2.9967592e-06 0.00014582864 2270
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20800 2080 3.016678e-06 0.000148629 2270
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21000 2100 7.287645e-06 0.00016486102 2270
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21200 2120 8.6905277e-06 0.00020276916 2270
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21400 2140 6.8453018e-06 0.00023156153 2270
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21600 2160 3.3853799e-06 0.0002432462 2270
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21800 2180 4.1241209e-06 0.00022829024 2270
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22000 2200 7.0802396e-06 0.00020784823 2270
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22200 2220 7.3361691e-06 0.00018114134 2270
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22400 2240 5.0764593e-06 0.00014351106 2270
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22600 2260 2.7487537e-06 0.00012919872 2270
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22800 2280 4.620167e-06 0.00013746218 2270
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23000 2300 6.9819357e-06 0.00015985102 2270
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23200 2320 6.8923916e-06 0.00018713045 2270
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23400 2340 4.1795088e-06 0.00019846682 2270
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23600 2360 2.2871028e-06 0.00021068421 2270
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23800 2380 3.862046e-06 0.00019553306 2270
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24000 2400 5.2448555e-06 0.00017398041 2270
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24200 2420 4.7565441e-06 0.00015008142 2270
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24400 2440 2.2952135e-06 0.00012747106 2270
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24600 2460 2.1575617e-06 0.00012516996 2270
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24800 2480 4.1777868e-06 0.0001331902 2270
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25000 2500 5.5679133e-06 0.00015504562 2270
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25200 2520 4.5758741e-06 0.00017146032 2270
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25400 2540 2.3403277e-06 0.00017611666 2270
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25600 2560 2.7029302e-06 0.00016850788 2270
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25800 2580 4.3601102e-06 0.00015884642 2270
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26000 2600 5.2244249e-06 0.00013793898 2270
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26200 2620 3.4577672e-06 0.00012395875 2270
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26400 2640 2.361577e-06 0.00011600057 2270
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26600 2660 2.8515644e-06 0.00011277063 2270
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26800 2680 4.0851213e-06 0.0001290832 2270
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27000 2700 4.2579644e-06 0.0001476495 2270
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27200 2720 2.6593858e-06 0.00015977745 2270
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27400 2740 1.990115e-06 0.00015612787 2270
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27600 2760 2.6756835e-06 0.00014913772 2270
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27800 2780 3.9032806e-06 0.00014014763 2270
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28000 2800 3.2729446e-06 0.00012216846 2270
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28200 2820 1.9357278e-06 0.00011078621 2270
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28400 2840 1.7094832e-06 0.00010910509 2270
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28600 2860 2.8731406e-06 0.00011179644 2270
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28800 2880 3.7062354e-06 0.00012254091 2270
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29000 2900 2.7844262e-06 0.00013060331 2270
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29200 2920 1.7680655e-06 0.00013797514 2270
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29400 2940 1.706873e-06 0.0001350685 2270
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29600 2960 2.8764562e-06 0.00012428508 2270
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29800 2980 3.1502029e-06 0.00011456718 2270
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30000 3000 2.1833409e-06 0.00010317469 2270
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Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
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Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/s
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99.7% CPU use with 4 MPI tasks x no 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 | 0.63183 | 21.226 | 42.266 | 444.6 | 12.82
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Bond | 0.095073 | 0.17799 | 0.27877 | 17.0 | 0.11
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Neigh | 2.0745 | 2.0781 | 2.0822 | 0.2 | 1.25
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Comm | 0.32024 | 0.38703 | 0.45564 | 8.1 | 0.23
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Output | 0.60459 | 0.76798 | 0.93724 | 18.6 | 0.46
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Modify | 119.85 | 140.76 | 161.36 | 172.2 | 85.00
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Other | | 0.2124 | | | 0.13
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Nlocal: 567.5 ave 1139 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 75.5 ave 152 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 9238.25 ave 18490 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 17945 ave 35917 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 71780
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Ave neighs/atom = 31.621145
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Ave special neighs/atom = 0.22026432
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Neighbor list builds = 2071
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Dangerous builds = 0
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Total wall time: 0:02:45
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