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Sim_LAMMPS_ModifiedTersoff_ByggmastarHodilleFerro_2018_BeO__SM_305223021383_000

Interatomic potential for Beryllium (Be), Oxygen (O).
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Title
A single sentence description.
LAMMPS Modified Tersoff potential for Be-O developed by Byggmästar et al. (2018) v000
Description An analytical interatomic bond order potential for the Be–O system is presented. The potential is fitted and compared to a large database of bulk BeO and point defect properties obtained using density functional theory. Its main applications include simulations of plasma-surface interactions involving oxygen or oxide layers on beryllium, as well as simulations of BeO nanotubes and nanosheets. We apply the potential in a study of oxygen irradiation of Be surfaces, and observe the early stages of an oxide layer forming on the Be surface. Predicted thermal and elastic properties of BeO nanotubes and nanosheets are simulated and compared with published ab initio data.

Notes:
J. Byggmästar (University of Helsinki) noted that the pure elemental potentials for Be-Be and O-O are from the following references:

Be-Be: Björkas, C., Juslin, N., Timko, H., Vörtler, K., Nordlund, K., Henriksson, K., & Erhart, P. (2009). Interatomic potentials for the Be–C–H system. Journal of Physics: Condensed Matter, 21(44), 445002. DOI: 10.1088/0953-8984/21/44/445002

O-O: Erhart, P., Juslin, N., Goy, O., Nordlund, K., Müller, R., & Albe, K. (2006). Analytic bond-order potential for atomistic simulations of zinc oxide. Journal of Physics: Condensed Matter, 18(29), 6585–6605. DOI: https://doi.org/10.1088/0953-8984/18/29/003

which should be cited if only the Be-Be or O-O parts are used.
Species
The supported atomic species.
Be, O
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)
Contributor karls
Maintainer karls
Creator
Publication Year 2019
Item Citation

This Simulator Model originally published in [1-3] is archived in OpenKIM [4-6].

[1] Byggmästar J, Hodille EA, Ferro Y, Nordlund K. Analytical bond order potential for simulations of BeO 1D and 2D nanostructures and plasma-surface interactions. Journal of Physics: Condensed Matter [Internet]. 2018Mar;30(13):135001. Available from: https://doi.org/10.1088%2F1361-648x%2Faaafb3 doi:10.1088/1361-648x/aaafb3

[2] Björkas C, Juslin N, Timko H, Vörtler K, Nordlund K, Henriksson K, et al. Interatomic potentials for the Be–C–H system. Journal of Physics: Condensed Matter [Internet]. 2009Oct;21(44):445002. Available from: https://doi.org/10.1088%2F0953-8984%2F21%2F44%2F445002 doi:10.1088/0953-8984/21/44/445002

[3] Erhart P, Juslin N, Goy O, Nordlund K, Müller R, Albe K. Analytic bond-order potential for atomistic simulations of zinc oxide. Journal of Physics: Condensed Matter [Internet]. 2006Jun;18(29):6585–605. Available from: https://doi.org/10.1088%2F0953-8984%2F18%2F29%2F003 doi:10.1088/0953-8984/18/29/003

[4] LAMMPS Modified Tersoff potential for Be-O developed by Byggmästar et al. (2018) v000. OpenKIM; 2019. doi:10.25950/8e6fb85e

[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.
SM_305223021383_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.
Sim_LAMMPS_ModifiedTersoff_ByggmastarHodilleFerro_2018_BeO__SM_305223021383_000
DOI 10.25950/8e6fb85e
https://doi.org/10.25950/8e6fb85e
https://search.datacite.org/works/10.25950/8e6fb85e
KIM Item TypeSimulator Model
KIM API Version2.1
Simulator Name
The name of the simulator as defined in kimspec.edn.
LAMMPS
Potential Type tersoff
Simulator Potential tersoff/zbl

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
N/A 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

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: O
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: O
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
Species: O


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
Species: O


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: O
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: O
Species: Be


Cubic Crystal Basic Properties Table

Species: Be

Species: O



Tests



Cohesive energy versus lattice constant curve for monoatomic cubic lattices v002

Creators:
Contributor: karls
Publication Year: 2018
DOI: https://doi.org/10.25950/c6746c52

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 Oxygen view 2342
Cohesive energy versus lattice constant curve for diamond Oxygen view 2438
Cohesive energy versus lattice constant curve for fcc Oxygen view 2471
Cohesive energy versus lattice constant curve for sc Oxygen view 2631


Cohesive energy versus lattice constant curve for monoatomic cubic lattices v003

Creators:
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 1855
Cohesive energy versus lattice constant curve for diamond Be v003 view 1951
Cohesive energy versus lattice constant curve for fcc Be v003 view 1951
Cohesive energy versus lattice constant curve for sc Be v003 view 1919


Elastic constants for cubic crystals at zero temperature and pressure v005

Creators:
Contributor: tadmor
Publication Year: 2019
DOI: https://doi.org/10.25950/49c5c255

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 O at zero temperature v005 view 4749
Elastic constants for diamond O at zero temperature v000 view 5583
Elastic constants for fcc O at zero temperature v005 view 5358
Elastic constants for sc O at zero temperature v005 view 4428


Elastic constants for cubic crystals at zero temperature and pressure v006

Creators:
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 3359
Elastic constants for diamond Be at zero temperature v001 view 7613
Elastic constants for fcc Be at zero temperature v006 view 6750
Elastic constants for sc Be at zero temperature v006 view 2975


Elastic constants for hexagonal crystals at zero temperature v003

Creators:
Contributor: jl2922
Publication Year: 2018
DOI: https://doi.org/10.25950/2e4b93d9

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 O at zero temperature view 3401


Elastic constants for hexagonal crystals at zero temperature v004

Creators:
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 2706


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

Creators:
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 2847
Equilibrium zero-temperature lattice constant for bcc O v007 view 6750
Equilibrium zero-temperature lattice constant for diamond Be v007 view 7645
Equilibrium zero-temperature lattice constant for diamond O v007 view 6750
Equilibrium zero-temperature lattice constant for fcc Be v007 view 7965
Equilibrium zero-temperature lattice constant for fcc O v007 view 6526
Equilibrium zero-temperature lattice constant for sc Be v007 view 5886
Equilibrium zero-temperature lattice constant for sc O v007 view 6910


Equilibrium lattice constants for hexagonal bulk structures at zero temperature and pressure v004

Creators:
Contributor: jl2922
Publication Year: 2018
DOI: https://doi.org/10.25950/25bcc28b

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 O view 9914


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

Creators:
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 19452




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