Atoms‐to‐Confinuum (AtC) user package for LAMMPS
Atoms‐to‐Confinuum (AtC) user package for LAMMPS
Atoms‐to‐Confinuum (AtC) user package for LAMMPS
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Atoms‐to‐Con)nuum(<strong>AtC</strong>)<strong>user</strong><strong>package</strong><strong>for</strong><br />
<strong>LAMMPS</strong><br />
ReeseJones,JeremyTempleton,<br />
GregoryWagner,JonathanZimmerman<br />
SandiaNa)onalLaboratories,Livermore,CA<br />
<strong>LAMMPS</strong>Workshop<br />
Albuquerque,NewMexico<br />
February24‐26,2010<br />
Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company,<br />
<strong>for</strong> the United States Department of Energyʼs National Nuclear Security Administration<br />
under contract DE-AC04-94AL85000.
2<br />
ObjecMves<strong>for</strong>Package<br />
• CalculaMonofconMnuummechanicalvariablesfrom<br />
atomisMcsimulaMondatausingtheHardy’sEulerian<br />
<strong>for</strong>mulaMonandourLagrangian<strong>for</strong>mulaMon.<br />
• CouplingofatomisMc(MD,MS)andconMnuum(finite<br />
element)regions<strong>for</strong>rigorousthermaland<br />
mechanicalboundarycondiMons.<br />
• Couplingtoemulateelectronictemperatureeffects<br />
inmetalsviathetwotemperaturemodel(TTM).<br />
Electron-transport enhanced simulation of<br />
heating and de<strong>for</strong>mation of a metallic CNT<br />
Compressive stress field <strong>for</strong> an atomic<br />
simulation of shock loading
3<br />
fixatc<br />
fix ID groupID atc type paramfile<br />
• ID,group‐IDaredocumentedinfixcommand<br />
• type=thermalortwo_temperatureorhardy<br />
– thermal=thermalcouplingwithfield:temperature<br />
– two_temperature=electron‐phononcouplingwithfield,temperatureand<br />
electron_temperature<br />
– hardy=Hardyon‐the‐flypost‐processing<br />
• paramfile=filewithmaterialparameters(notspecified<strong>for</strong><br />
hardytype)
4<br />
Theatcpicture:mesh,boxandatoms<br />
Saltwater-electrode-CNT<br />
system: mesh overlaps exactly<br />
with water-CNT atom region<br />
Circular hole in plate: mesh<br />
overlaps exactly with box,<br />
but atom region is subset<br />
Elastic inclusion problem:<br />
mesh overlaps exactly with<br />
box and atoms
5<br />
Hardyon‐the‐flypost‐processing<br />
Hardy(JournalofChemicalPhysics,1982)<br />
Zimmermanetal.(MSMSE,2004)<br />
Zimmermanetal.(JournalofComputa)onalPhysics,2010)<br />
# …create and initialize the MD system <br />
fix <strong>AtC</strong> internal atc hardy <br />
x<br />
ψ = 0<br />
ψ > 0<br />
fix_modify <strong>AtC</strong> fem create mesh 1 1 1 box p p p<br />
fix_modify <strong>AtC</strong> atom_element_map eulerian 100<br />
fix_modify <strong>AtC</strong> transfer fields none <br />
fix_modify <strong>AtC</strong> transfer fields add density energy<br />
stress temperature <br />
fix_modify <strong>AtC</strong> transfer output nvtFE 100 text<br />
run 1000
6<br />
Commonfix_modifycommands<strong>for</strong>atc‐hardy<br />
Setup:<br />
fix_modify <strong>AtC</strong> fem create mesh <br />
fix_modify <strong>AtC</strong> transfer internal <br />
ControlandMmefiltering:<br />
fix_modify <strong>AtC</strong> transfer filter <br />
fix_modify <strong>AtC</strong> transfer filter scale<br />
fix_modify <strong>AtC</strong> transfer atom_element_map<br />
fix_modify <strong>AtC</strong> transfer neighbor_reset_frequency<br />
fix_modify <strong>AtC</strong> transfer kernel<br />
Output:textandEnSight<br />
fix_modify <strong>AtC</strong> transfer output <br />
fix_modify <strong>AtC</strong> transfer atomic_output <br />
fix_modify <strong>AtC</strong> mesh output
7<br />
Commonfix_modifycommands<strong>for</strong>atc‐hardy<br />
ComputaMonoffields:<br />
fix_modify <strong>AtC</strong> transfer fields <br />
fix_modify <strong>AtC</strong> transfer gradients <br />
fix_modify <strong>AtC</strong> transfer rates <br />
fix_modify <strong>AtC</strong> transfer computes <br />
fix_modify <strong>AtC</strong> set <br />
fix_modify <strong>AtC</strong> transfer on_the_fly <br />
fix_modify <strong>AtC</strong> boundary_integral <br />
fix_modify <strong>AtC</strong> contour_integral
8<br />
Examplesofusingatc‐hardy<br />
u 1<br />
Tensile stretching of<br />
plate with circular hole<br />
P 11 P 22<br />
eam_unistrain_qsphere<br />
Uniaxial stretching of homogeneous bar,<br />
1D elements
9<br />
Thermalcouplingusingatc<br />
• CoupledFEM/MDequaMons<br />
2<br />
M N V K<br />
3k<br />
θ<br />
∑ = ∑ α ( vα ⋅fα ) Δ<br />
α<br />
+ ∑<br />
J<br />
fem<br />
IJ J I IJ J<br />
B α<br />
J<br />
m<br />
v<br />
∂U<br />
= − −<br />
∑<br />
α α Iα I α<br />
∂xα<br />
I<br />
• CombinedMD/FEMsystem<br />
hastwo‐waycoupling:<br />
HeatatnodesaffectsMDenergy<br />
throughthermostat<br />
N<br />
λ v<br />
Couplingparameter<br />
(temperature/fluxconstraint)<br />
AtomscontributetonodalheatequaMon<br />
θ
10<br />
Two‐Temperaturecouplingusingatc<br />
Explicit representation<br />
of phonons by MD<br />
Electron effects solved<br />
<strong>for</strong> on overlaid mesh<br />
Energy exchange handled<br />
though thermostats as in<br />
the thermal-only problem
11<br />
2Ddiffusionproblem<br />
Exampleofusingatc‐thermal<br />
• Platewith<br />
embeddedMD<br />
region(~33,000<br />
atoms)<br />
• IniMalizedto<br />
temperaturefield<br />
withgaussian<br />
profile<br />
• AdiabaMc<br />
boundary<br />
condiMonsat<br />
edges
12<br />
Exampleofusingatc‐two_temperature<br />
JouleheaMnginnanodevices<br />
CNT used as a nanowire<br />
reservoirs of hot electrons<br />
CNT heating<br />
through<br />
exchange with<br />
electrons<br />
Thermalinduced<br />
mechanical<br />
oscillations
13<br />
Futurework:otherphysicalmodels<br />
• Elasto‐dynamicresponseatthenano‐scale<br />
• Fluidicspeciestransport<br />
o TransportofsaltwaterintoNTs<br />
o Energystoragedevices<br />
o Long‐rangeelectrostaMcinteracMons<br />
onFEmesh
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