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EAM_Dynamo_AgrawalMishraWard_2013_Be__MO_404563086984_000

Interatomic potential for Beryllium (Be).
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Title
A single sentence description.
EAM potential (LAMMPS cubic hermite tabulation) for Be developed by Agrawal et al. (2013) v000
Description
A short description of the Model describing its key features including for example: type of model (pair potential, 3-body potential, EAM, etc.), modeled species (Ac, Ag, ..., Zr), intended purpose, origin, and so on.
We present an embedded atom method (EAM) potential for hexagonal beryllium, with a pair function in the form of a Morse potential and a Johnson embedding function with exponential electron density. The cohesive energy, elastic constants, lattice parameters and relaxed vacancy formation energy were used to fit the potential. The fitted-potential was validated by a comparison to first-principles and, wherever available, experimental results for the lattice energies of various crystal structures: vacancy cluster, interstitial formation and surface. Using a large cutoff distance of 5 Angstroms, which includes interactions to approximately the eighth neighbor shell of beryllium, allows our potential to reproduce these quantities considerably better than previous EAM potentials. The accuracy obtained by our potential is similar to or in some cases even better than available modified EAM potentials, while being computationally less intensive.
Species
The supported atomic species.
Be
Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
None
Content Origin NIST IPRP (https://www.ctcms.nist.gov/potentials/Be.html)
Content Other Locations http://atomistics.osu.edu/
Contributor tadmor
Maintainer tadmor
Creator Ellad Tadmor
Publication Year 2018
Item Citation

This Model originally published in [1-2] is archived in OpenKIM [3-6].

[1] Agrawal A, Mishra R, Ward L, Flores KM, Windl W. An embedded atom method potential of beryllium. Modelling and Simulation in Materials Science and Engineering [Internet]. 2013;21(8):085001. Available from: http://stacks.iop.org/0965-0393/21/i=8/a=085001 doi:10.1088/0965-0393/21/8/085001 — (Primary Source) A primary source is a reference directly related to the item documenting its development, as opposed to other sources that are provided as background information.

[2] Agrawal A, Mishra R, Ward L, Flores KM, Windl W. Corrigendum: An embedded atom method potential of beryllium ( Modelling Simul. Mater. Sci. Eng . 21 085001). Modelling and Simulation in Materials Science and Engineering [Internet]. 2015;23(6):069501. Available from: http://stacks.iop.org/0965-0393/23/i=6/a=069501 doi:10.1088/0965-0393/23/6/069501

[3] EAM potential (LAMMPS cubic hermite tabulation) for Be developed by Agrawal et al. (2013) v000. OpenKIM; 2018. doi:10.25950/a2e624ea

[4] EAM Model Driver for tabulated potentials with cubic Hermite spline interpolation as used in LAMMPS v005. OpenKIM; 2018. doi:10.25950/68defa36

[5] Tadmor EB, Elliott RS, Sethna JP, Miller RE, Becker CA. The potential of atomistic simulations and the Knowledgebase of Interatomic Models. JOM. 2011;63(7):17. doi:10.1007/s11837-011-0102-6

[6] Elliott RS, Tadmor EB. Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API). OpenKIM; 2011. doi:10.25950/ff8f563a

Click here to download the above citation in BibTeX format.
Funding Not available
Short KIM ID
The unique KIM identifier code.
MO_404563086984_000
Extended KIM ID
The long form of the KIM ID including a human readable prefix (100 characters max), two underscores, and the Short KIM ID. Extended KIM IDs can only contain alpha-numeric characters (letters and digits) and underscores and must begin with a letter.
EAM_Dynamo_AgrawalMishraWard_2013_Be__MO_404563086984_000
DOI 10.25950/a2e624ea
https://doi.org/10.25950/a2e624ea
https://search.datacite.org/works/10.25950/a2e624ea
KIM Item Type
Specifies whether this is a Portable Model (software implementation of an interatomic model); Portable Model with parameter file (parameter file to be read in by a Model Driver); Model Driver (software implementation of an interatomic model that reads in parameters).
Portable Model using Model Driver EAM_Dynamo__MD_120291908751_005
DriverEAM_Dynamo__MD_120291908751_005
KIM API Version2.0
Potential Type eam

Verification Check Dashboard

(Click here to learn more about Verification Checks)

Grade Name Category Brief Description Full Results Aux File(s)
P vc-species-supported-as-stated mandatory
The model supports all species it claims to support; see full description.
Results Files
P vc-periodicity-support mandatory
Periodic boundary conditions are handled correctly; see full description.
Results Files
P vc-permutation-symmetry mandatory
Total energy and forces are unchanged when swapping atoms of the same species; see full description.
Results Files
A vc-forces-numerical-derivative consistency
Forces computed by the model agree with numerical derivatives of the energy; see full description.
Results Files
F vc-dimer-continuity-c1 informational
The energy versus separation relation of a pair of atoms is C1 continuous (i.e. the function and its first derivative are continuous); see full description.
Results Files
P vc-objectivity informational
Total energy is unchanged and forces transform correctly under rigid-body translation and rotation; see full description.
Results Files
P vc-inversion-symmetry informational
Total energy is unchanged and forces change sign when inverting a configuration through the origin; see full description.
Results Files
P vc-memory-leak informational
The model code does not have memory leaks (i.e. it releases all allocated memory at the end); see full description.
Results Files
P vc-thread-safe mandatory
The model returns the same energy and forces when computed in serial and when using parallel threads for a set of configurations. Note that this is not a guarantee of thread safety; see full description.
Results Files
F vc-unit-conversion mandatory
The model is able to correctly convert its energy and/or forces to different unit sets; see full description.
Results Files

Visualizers (in-page)


BCC Lattice Constant

This bar chart plot shows the mono-atomic body-centered cubic (bcc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Be


Cohesive Energy Graph

This graph shows the cohesive energy versus volume-per-atom for the current mode for four mono-atomic cubic phases (body-centered cubic (bcc), face-centered cubic (fcc), simple cubic (sc), and diamond). The curve with the lowest minimum is the ground state of the crystal if stable. (The crystal structure is enforced in these calculations, so the phase may not be stable.) Graphs are generated for each species supported by the model.

Species: Be


Diamond Lattice Constant

This bar chart plot shows the mono-atomic face-centered diamond lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Be


FCC Elastic Constants

This bar chart plot shows the mono-atomic face-centered cubic (fcc) elastic constants predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Be


FCC Lattice Constant

This bar chart plot shows the mono-atomic face-centered cubic (fcc) lattice constant predicted by the current model (shown in red) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Be


FCC Stacking Fault Energies

This bar chart plot shows the intrinsic and extrinsic stacking fault energies as well as the unstable stacking and unstable twinning energies for face-centered cubic (fcc) predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

(No matching species)

FCC Surface Energies

This bar chart plot shows the mono-atomic face-centered cubic (fcc) relaxed surface energies predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

(No matching species)

SC Lattice Constant

This bar chart plot shows the mono-atomic simple cubic (sc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Be


Cubic Crystal Basic Properties Table

Species: Be



Tests



Cohesive energy versus lattice constant curve for monoatomic cubic lattices v003

Creators: Daniel S. Karls
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/64cb38c5

This Test Driver uses LAMMPS to compute the cohesive energy of a given monoatomic cubic lattice (fcc, bcc, sc, or diamond) at a variety of lattice spacings. The lattice spacings range from a_min (=a_min_frac*a_0) to a_max (=a_max_frac*a_0) where a_0, a_min_frac, and a_max_frac are read from stdin (a_0 is typically approximately equal to the equilibrium lattice constant). The precise scaling and number of lattice spacings sampled between a_min and a_0 (a_0 and a_max) is specified by two additional parameters passed from stdin: N_lower and samplespacing_lower (N_upper and samplespacing_upper). Please see README.txt for further details.
Test Test Results Link to Test Results page Benchmark time
Usertime muliplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run.

Measured in Millions of Whetstone Instructions (MWI)
Cohesive energy versus lattice constant curve for bcc Be v003 view 4414
Cohesive energy versus lattice constant curve for diamond Be v003 view 4606
Cohesive energy versus lattice constant curve for fcc Be v003 view 4670
Cohesive energy versus lattice constant curve for sc Be v003 view 4638


Elastic constants for cubic crystals at zero temperature and pressure v006

Creators: Junhao Li and Ellad Tadmor
Contributor: tadmor
Publication Year: 2019
DOI: https://doi.org/10.25950/5853fb8f

Computes the cubic elastic constants for some common crystal types (fcc, bcc, sc, diamond) by calculating the hessian of the energy density with respect to strain. An estimate of the error associated with the numerical differentiation performed is reported.
Test Test Results Link to Test Results page Benchmark time
Usertime muliplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run.

Measured in Millions of Whetstone Instructions (MWI)
Elastic constants for bcc Be at zero temperature v006 view 1823
Elastic constants for diamond Be at zero temperature v001 view 11580
Elastic constants for fcc Be at zero temperature v006 view 5886
Elastic constants for sc Be at zero temperature v006 view 1408


Elastic constants for hexagonal crystals at zero temperature v004

Creators: Junhao Li
Contributor: jl2922
Publication Year: 2019
DOI: https://doi.org/10.25950/d794c746

Computes the elastic constants for hcp crystals by calculating the hessian of the energy density with respect to strain. An estimate of the error associated with the numerical differentiation performed is reported.
Test Test Results Link to Test Results page Benchmark time
Usertime muliplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run.

Measured in Millions of Whetstone Instructions (MWI)
Elastic constants for hcp Be at zero temperature v004 view 1496


Equilibrium lattice constant and cohesive energy of a cubic lattice at zero temperature and pressure v007

Creators: Daniel S. Karls and Junhao Li
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/2765e3bf

Equilibrium lattice constant and cohesive energy of a cubic lattice at zero temperature and pressure.
Test Test Results Link to Test Results page Benchmark time
Usertime muliplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run.

Measured in Millions of Whetstone Instructions (MWI)
Equilibrium zero-temperature lattice constant for bcc Be v007 view 2143
Equilibrium zero-temperature lattice constant for diamond Be v007 view 2655
Equilibrium zero-temperature lattice constant for fcc Be v007 view 3455
Equilibrium zero-temperature lattice constant for sc Be v007 view 2527


Equilibrium lattice constants for hexagonal bulk structures at zero temperature and pressure v005

Creators: Daniel S. Karls and Junhao Li
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/c339ca32

Calculates lattice constant of hexagonal bulk structures at zero temperature and pressure by using simplex minimization to minimize the potential energy.
Test Test Results Link to Test Results page Benchmark time
Usertime muliplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run.

Measured in Millions of Whetstone Instructions (MWI)
Equilibrium lattice constants for hcp Be v005 view 15918





Download Dependency

This Model requires a Model Driver. Archives for the Model Driver EAM_Dynamo__MD_120291908751_005 appear below.


EAM_Dynamo__MD_120291908751_005.txz Tar+XZ Linux and OS X archive
EAM_Dynamo__MD_120291908751_005.zip Zip Windows archive

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