489 lines
25 KiB
Groff
489 lines
25 KiB
Groff
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
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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 = 0.001 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 0.05
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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 status all rheo/property/atom status
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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 c_status
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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 4.1743799e-07 1.1743617e-07 2701
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400 40 1.6697519e-06 4.6974469e-07 2701
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600 60 3.7127333e-06 1.0646825e-05 2701
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800 80 4.6683656e-06 0.00015182605 2701
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1000 100 4.7368707e-06 0.00028128761 2701
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1200 120 3.4384322e-06 0.00045913378 2701
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1400 140 1.4119866e-06 0.00055627091 2701
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1600 160 4.4114517e-07 0.00058247308 2701
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1800 180 4.8289229e-07 0.0005510948 2701
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2000 200 1.8494183e-06 0.00048386222 2701
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2200 220 3.3319816e-06 0.00037903264 2701
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2400 240 3.8128922e-06 0.00024115906 2701
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2600 260 3.1943401e-06 9.727407e-05 2701
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2800 280 1.6172816e-06 -2.632162e-05 2701
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3000 300 3.6100709e-07 -8.5761867e-05 2701
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3200 320 1.4745502e-07 -5.9204127e-05 2701
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3400 340 8.3369782e-07 8.8312464e-07 2701
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3600 360 2.0484052e-06 5.8521477e-05 2701
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3800 380 3.1639387e-06 0.0001685663 2701
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4000 400 3.1692907e-06 0.00026875988 2701
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4200 420 2.391933e-06 0.00038621787 2701
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4400 440 1.1964404e-06 0.00048901286 2701
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4600 460 4.0508824e-07 0.00051863639 2701
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4800 480 5.4908507e-07 0.00049263754 2701
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5000 500 1.3139665e-06 0.00041984264 2701
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5200 520 2.1939161e-06 0.00033095351 2701
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5400 540 2.3687031e-06 0.00022422981 2701
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5600 560 1.8280882e-06 0.00011544328 2701
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5800 580 8.8610517e-07 2.9307791e-05 2701
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6000 600 2.0989359e-07 -1.7340941e-05 2701
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6200 620 2.8658301e-07 -8.1237835e-06 2701
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6400 640 9.7636239e-07 4.3755922e-05 2701
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6600 660 1.891303e-06 0.0001185719 2701
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6800 680 2.4149904e-06 0.00020830273 2701
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7000 700 2.3174953e-06 0.00030114767 2701
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7200 720 1.7918612e-06 0.00037821537 2701
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7400 740 1.2114987e-06 0.0004233475 2701
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7600 760 9.9661553e-07 0.00042958263 2701
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7800 780 1.1552559e-06 0.00039944618 2701
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8000 800 1.5249138e-06 0.00034034478 2701
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8200 820 1.7453861e-06 0.00026826463 2701
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8400 840 1.6259021e-06 0.00019131768 2701
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8600 860 1.2612805e-06 0.0001162957 2701
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8800 880 8.6964518e-07 7.1771506e-05 2701
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9000 900 7.6892472e-07 5.6170687e-05 2701
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9200 920 1.0780045e-06 7.1925995e-05 2701
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9400 940 1.6514902e-06 0.00011635293 2701
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9600 960 2.1891377e-06 0.00017599885 2701
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9800 980 2.4551701e-06 0.00024127934 2701
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10000 1000 2.4277051e-06 0.00029918622 2701
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10200 1020 2.2655987e-06 0.00034067996 2701
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10400 1040 2.1767207e-06 0.00035598133 2701
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10600 1060 2.2796719e-06 0.00034359076 2701
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10800 1080 2.4884225e-06 0.00030749714 2701
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11000 1100 2.6387215e-06 0.00025725198 2701
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11200 1120 2.5968908e-06 0.00020170699 2701
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11400 1140 2.4108931e-06 0.00015185858 2701
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11600 1160 2.2375166e-06 0.00011800349 2701
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11800 1180 2.2407196e-06 0.00010646971 2701
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12000 1200 2.4845263e-06 0.00011817498 2701
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12200 1220 2.8733204e-06 0.00015013186 2701
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12400 1240 3.2437087e-06 0.00019211975 2701
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12600 1260 3.4732728e-06 0.00023620276 2701
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12800 1280 3.5836611e-06 0.00027352269 2701
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13000 1300 3.6592211e-06 0.00029533734 2701
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13200 1320 3.782506e-06 0.00030032559 2701
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13400 1340 3.9807086e-06 0.00028395722 2701
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13600 1360 4.2023176e-06 0.00025390325 2701
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13800 1380 4.3559781e-06 0.00021794236 2701
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14000 1400 4.4273371e-06 0.00018026034 2701
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14200 1420 4.49867e-06 0.0001526569 2701
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14400 1440 4.6591574e-06 0.00013707051 2701
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14600 1460 4.9589583e-06 0.00013803875 2701
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14800 1480 5.3859375e-06 0.00015455425 2701
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15000 1500 5.8639557e-06 0.00017954785 2701
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15200 1520 6.3075561e-06 0.0002084257 2701
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15400 1540 6.7022179e-06 0.0002347669 2701
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15600 1560 7.0789688e-06 0.00025020766 2701
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15800 1580 7.4734777e-06 0.00025394845 2701
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16000 1600 7.8884743e-06 0.00024571725 2701
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16200 1620 8.3224059e-06 0.00022706648 2701
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16400 1640 8.7337783e-06 0.00020320706 2701
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16600 1660 9.1454649e-06 0.00017824346 2701
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16800 1680 9.5948793e-06 0.00015961835 2701
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17000 1700 1.0106407e-05 0.00015135471 2701
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17200 1720 1.0707273e-05 0.00015166884 2701
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17400 1740 1.1392597e-05 0.0001645916 2701
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17600 1760 1.2118829e-05 0.00018119729 2701
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17800 1780 1.2846056e-05 0.0002003616 2701
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18000 1800 1.3555288e-05 0.00021585952 2701
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18200 1820 1.4301024e-05 0.00022290158 2701
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18400 1840 1.5089217e-05 0.00021970192 2701
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18600 1860 1.5902351e-05 0.00020911128 2701
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18800 1880 1.6753175e-05 0.00019278718 2701
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19000 1900 1.7602996e-05 0.00017584076 2701
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19200 1920 1.8479378e-05 0.00016206226 2701
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19400 1940 1.9421603e-05 0.00015575677 2701
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19600 1960 2.0477421e-05 0.00015687558 2701
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19800 1980 2.1617288e-05 0.00016424998 2701
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20000 2000 2.2814347e-05 0.00017466664 2701
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20200 2020 2.4029097e-05 0.00018647149 2701
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20400 2040 2.5255953e-05 0.00019516077 2701
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20600 2060 2.649418e-05 0.00019906384 2701
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20800 2080 2.7755897e-05 0.00019630586 2701
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21000 2100 2.9067854e-05 0.00018674721 2701
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21200 2120 3.0396477e-05 0.0001758048 2701
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21400 2140 3.1759719e-05 0.00016782801 2701
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21600 2160 3.3193597e-05 0.00016324138 2701
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21800 2180 3.4729384e-05 0.00016124274 2701
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22000 2200 3.6367594e-05 0.00016437457 2701
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22200 2220 3.8095131e-05 0.00017015573 2701
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22400 2240 3.9867003e-05 0.00017649465 2701
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22600 2260 4.169511e-05 0.00018111374 2701
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22800 2280 4.3566134e-05 0.00018104136 2701
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23000 2300 4.5461538e-05 0.00017822707 2701
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23200 2320 4.7377333e-05 0.00017285066 2701
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23400 2340 4.9354403e-05 0.00016826524 2701
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23600 2360 5.1399791e-05 0.00016517913 2701
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23800 2380 5.3510931e-05 0.00016299649 2701
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24000 2400 5.5681048e-05 0.00016256674 2701
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24200 2420 5.7902429e-05 0.00016513449 2701
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24400 2440 6.0216049e-05 0.00016895109 2701
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24600 2460 6.270982e-05 0.00016946227 2701
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24800 2480 6.5390117e-05 0.00016589426 2701
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25000 2500 6.8121899e-05 0.00016241676 2701
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25200 2520 7.0947331e-05 0.00015624292 2701
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25400 2540 7.4304148e-05 0.0001449537 2701
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25600 2560 7.7745077e-05 0.00013179658 2701
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25800 2580 8.0739829e-05 0.00013098838 2701
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26000 2600 8.3827874e-05 0.00014278841 2701
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26200 2620 8.7060677e-05 0.00015381649 2701
|
|
26400 2640 9.0266508e-05 0.00016130999 2701
|
|
26600 2660 9.3339049e-05 0.00016908268 2701
|
|
26800 2680 9.6347013e-05 0.00016771087 2701
|
|
27000 2700 9.9294711e-05 0.00016577315 2701
|
|
27200 2720 0.00010230007 0.0001670893 2701
|
|
27400 2740 0.00010547172 0.00016569077 2701
|
|
27600 2760 0.00010872426 0.00016506303 2701
|
|
27800 2780 0.00011201844 0.00016482702 2701
|
|
28000 2800 0.00011532129 0.00016694886 2701
|
|
28200 2820 0.00011869854 0.00016163005 2701
|
|
28400 2840 0.00012209747 0.00015339281 2701
|
|
28600 2860 0.00012549322 0.00014765883 2701
|
|
28800 2880 0.00012898685 0.00014241765 2701
|
|
29000 2900 0.00013259039 0.00014215724 2701
|
|
29200 2920 0.00013628209 0.00014881155 2701
|
|
29400 2940 0.00014001213 0.00015671333 2701
|
|
29600 2960 0.00014379216 0.00016446215 2701
|
|
29800 2980 0.00014764687 0.0001639602 2701
|
|
30000 3000 0.00015142301 0.00015664816 2701
|
|
30200 3020 0.00015496407 0.00015545099 2701
|
|
30400 3040 0.00015797338 0.00015368625 2701
|
|
30600 3060 0.00016042141 0.00015679918 2701
|
|
30800 3080 0.00016244716 0.00016093678 2701
|
|
31000 3100 0.00016202247 0.00016066954 2701
|
|
31200 3120 0.0001613312 0.00015932059 2701
|
|
31400 3140 0.00016274961 0.00015988567 2701
|
|
31600 3160 0.00016541518 0.00015724809 2701
|
|
31800 3180 0.00016809362 0.00015498827 2701
|
|
32000 3200 0.00017067801 0.00014830489 2701
|
|
32200 3220 0.00017333906 0.00014371345 2701
|
|
32400 3240 0.0001759011 0.00014421259 2701
|
|
32600 3260 0.00017849952 0.00014228443 2701
|
|
32800 3280 0.00017801812 0.00014117391 2701
|
|
33000 3300 0.00017718857 0.00014644675 2701
|
|
33200 3320 0.00017833666 0.0001291286 2701
|
|
33400 3340 0.000178576 0.00014878558 2701
|
|
33600 3360 0.00017846711 0.00013905481 2701
|
|
33800 3380 0.00017822937 0.00015535996 2701
|
|
34000 3400 0.00017899663 0.00016094303 2701
|
|
34200 3420 0.00017924661 0.00015017553 2701
|
|
34400 3440 0.00018024855 0.00014723549 2701
|
|
34600 3460 0.00018143865 0.00013903131 2701
|
|
34800 3480 0.00018258173 0.00013722112 2701
|
|
35000 3500 0.00018404873 0.00014675949 2701
|
|
35200 3520 0.00018538521 0.00015108242 2701
|
|
35400 3540 0.00018669649 0.00014564852 2701
|
|
35600 3560 0.00018814608 0.00013762161 2701
|
|
35800 3580 0.00018967415 0.00014602307 2701
|
|
36000 3600 0.00019146735 0.000126909 2701
|
|
36200 3620 0.00019414036 0.00012384379 2701
|
|
36400 3640 0.00019613057 0.00011059573 2701
|
|
36600 3660 0.00019897104 0.00013621801 2701
|
|
36800 3680 0.00020169688 0.00013665462 2701
|
|
37000 3700 0.00020447655 0.00013929258 2701
|
|
37200 3720 0.00020711105 0.0001363895 2701
|
|
37400 3740 0.00021077854 0.00013610672 2701
|
|
37600 3760 0.00021303084 0.00015051235 2701
|
|
37800 3780 0.00021619561 0.00012664801 2701
|
|
38000 3800 0.0002194018 0.00012808247 2701
|
|
38200 3820 0.00022242646 0.0001360174 2701
|
|
38400 3840 0.00022531568 0.00013311221 2701
|
|
38600 3860 0.00022821731 0.00013523939 2701
|
|
38800 3880 0.000231228 0.00014090695 2701
|
|
39000 3900 0.00023404038 0.00013661835 2701
|
|
39200 3920 0.00023755044 0.00013659469 2701
|
|
39400 3940 0.00024009059 0.00012097907 2701
|
|
39600 3960 0.0002432098 9.7877876e-05 2701
|
|
39800 3980 0.00024475294 0.0001164688 2701
|
|
40000 4000 0.00024171274 0.00012432219 2701
|
|
Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms
|
|
|
|
Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s
|
|
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 16.881 | 24.402 | 30.74 | 114.6 | 12.67
|
|
Bond | 1.1126 | 1.8917 | 2.6935 | 43.3 | 0.98
|
|
Neigh | 35.387 | 35.508 | 35.625 | 1.5 | 18.43
|
|
Comm | 1.5499 | 1.6694 | 1.8006 | 7.4 | 0.87
|
|
Output | 0.99755 | 1.0072 | 1.0165 | 0.8 | 0.52
|
|
Modify | 120.6 | 127.43 | 135.54 | 54.8 | 66.14
|
|
Other | | 0.7553 | | | 0.39
|
|
|
|
Nlocal: 675.25 ave 1373 max 7 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 103 ave 163 max 50 min
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
Neighs: 10509 ave 21592 max 126 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 20367 ave 41981 max 141 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 81468
|
|
Ave neighs/atom = 30.162162
|
|
Ave special neighs/atom = 1.6593854
|
|
Neighbor list builds = 39932
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:03:12
|