A Brief User’s Guide and Developer’s Introduction to...

R. S. Elliott

Start from thebeginning(Linux setup)

Building KIMand LAMMPS

Test the setupwith the KIMexample inLAMMPS

Setup toexecute anOpenKIMTest with thelocalLAMMPS

Prepare andrun the Testslocally

Compare theresults

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A Brief User’s Guide and Developer’sIntroduction to OpenKIM

Ryan S. Elliott and Ellad B. Tadmor

[email protected]

University of Minnesota, Minneapolis, MN, USA

Funding from NSF: CDI & CDS&E

LAMMPS Workshop and SymposiumAlbuquerque, NM — Aug. 1–3, 2017

R. S. Elliott






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Outline

1 Start from the beginning (Linux setup)

2 Building KIM and LAMMPS

3 Test the setup with the KIM example in LAMMPS

4 Setup to execute an OpenKIM Test with the local LAMMPS

5 Prepare and run the Tests locallyJohnson ModelMishin–Mehl Model

6 Compare the results

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Initial filesThis version of Install.py will be included in the next stable release of LAMMPS

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Vagrant fileVagrant (http://www.vagrantup.com) and Virtual Box (http://www.virtualbox.org) are not necessary.

This demonstration should work on most Linux systems.

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Boot the VM

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Login to the VM

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Install the compilers

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Unpack LAMMPS

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The KIM Install.py script

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OpenKIM Cu Models

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The Mishin–Mehl EAM Model

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Build KIM with example Models and Mishin–Mehl

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Locally available Model listing

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Build LAMMPS with KIM support

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Find the KIM example provided with LAMMPS

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Run the KIM example in LAMMPS

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Put LAMMPS (temporally) on the system PATH

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Find OpenKIM.org Test Drivers that use LAMMPS

Nearly all OpenKIM.org Test Drivers use either:Atomic Simulation Environment (ASE) OR LAMMPS

The Test Drivers that use LAMMPS are:

• ClusterEnergyAndForces TD 000043093022 001

• CohesiveEnergyVsLatticeConstant TD 554653289799 001

• Grain Boundary Symmetric Tilt Relaxed Energy vs Angle Cubic Crystal TD 410381120771 000

• LammpsExample2 TD 887699523131 002

• LammpsExample TD 567444853524 003

• LatticeConstant2DHexagonalEnergy TD 034540307932 000

• LatticeConstantHexagonalEnergy TD 942334626465 002

• LinearThermalExpansionCoeffCubic TD 522633393614 000

• TriclinicPBCEnergyAndForces TD 892847239811 001

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OpenKIM.org Test Drivers

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OpenKIM.org LAMMPS Test Driver

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Cu FCC Test from OpenKIM.org

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Download the Test and Test Driver

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Johnson Model

Mishin–Mehl Model

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Unpack the Test and Test Driver

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Johnson Model

Mishin–Mehl Model

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Listing of Test files and pipeline.stdin.tpl

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Johnson Model

Mishin–Mehl Model

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Preparing the ex model Cu PF Johnson Test

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Johnson Model

Mishin–Mehl Model

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Running the ex model Cu PF Johnson Test

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Johnson Model

Mishin–Mehl Model

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Results from the ex model Cu PF Johnson Test

R. S. Elliott






Johnson Model

Mishin–Mehl Model

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Preparing and running the Mishin–Mehl Test

R. S. Elliott






Johnson Model

Mishin–Mehl Model

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Results from the Mishin–Mehl Test

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Listing of results directories

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Plot of Energy vs. Lattice Constant results

Using your favorite edn parser and visualization packages,we can visualize and compare the results

-4

-3.5

-3

-2.5

-2

-1.5

-1

-0.5

0

0.5

1

1.5

2.5 3 3.5 4 4.5 5 5.5

Energ

y (e

V)

Lattice spacing (angstrom)

Cohesive energy relation cubic crystal

Mishin-MehlJohnson

A Brief User’s Guide and Developer’s Introduction to...

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