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SW_MX2_KurniawanPetrieWilliams_2021_MoS__MO_677328661525_000

Interatomic potential for Molybdenum (Mo), Sulfur (S).
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Title
A single sentence description.
Modified Stillinger-Weber potential (MX2) for monolayer MoS2 by Kurniawan et al. (2022) 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.
This is a Stillinger-Weber (SW) parameterization for molybdenum disulfide. The parameters were calibrated to atomic forces from a DFT calculation of a molybdenum disulfide monolayer at 750K, as explained in Wen et al. (2017). Parameters $q_{IJ}$ are set to be zero for all pair-wise interactions and $\gamma$ to be the same for all three-body interactions. Additionally, to explore the full parameter space, $p_{IJ}$ are allowed to take any positive real value. This also allows the two-body interaction term to be a continuous function in $p_{IJ}$, which is needed in the information geometry analysis. The relation between $\sigma_{IJ}$ and the equilibrium lattice constants of the system is also eliminated. Further, we don't require $d\phi_2/dr|_{r=d}=0$ at the equilibrium bond length $d$, i.e., the atoms are not required to be in a pair-wise equilibrium state, which removes the constraint on $B_{IJ}$. Potential fitting was done to minimize the weighted least-squares loss function. We set the tolerance for the force components corresponding to each atom to be 10\% of the force magnitude acting on the same atom, a reasonable choice of fractional tolerance. We use these values as the non-uniform error bars, i.e., inverse weights, in the loss function.
Species
The supported atomic species.
Mo, S
Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
As with the original model by Wen et al. (2017) (or reference the model), this model is designed for two-dimensional (2D) monolayer molybdenum disulfide (MoS2), and is not appropriate for bulk MoS2 or other compounds of Mo and/or S.
Contributor Yonatan Kurniawan
Maintainer Yonatan Kurniawan
Developer Yonatan Kurniawan
Cody Petrie
Kinamo Williams
Mark K. Transtrum
Ryan S. Elliott
Ellad B. Tadmor
Daniel S. Karls
Mingjian Wen
Published on KIM 2022
How to Cite

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

[1] Kurniawan Y, Petrie CL, Williams KJ, Transtrum MK, Tadmor EB, Elliott RS, et al. Bayesian, Frequentist, and Information Geometry approaches to parametric uncertainty quantification of classical empirical interatomic potentials. 2021Dec; Available from: https://arxiv.org/abs/2112.10851v1 — (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] Wen M, Shirodkar SN, Plecháč P, Kaxiras E, Elliott RS, Tadmor EB. A force-matching Stillinger-Weber potential for MoS2: Parameterization and Fisher information theory based sensitivity analysis. Journal of Applied Physics. 2017Dec;122(24):244301. doi:10.1063/1.5007842

[3] Modified Stillinger-Weber potential (MX2) for monolayer MoS2 by Kurniawan et al. (2022) v000. OpenKIM; 2022. doi:10.25950/328bfabb

[4] Stillinger-Weber Model Driver for Monolayer MX2 systems v001. OpenKIM; 2018. doi:10.25950/7d664757

[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 Award Title: Reliable Materials Simulation based on the Knowledgebase of Interatomic Models (KIM)
Award Number: CMMT-1834332
Award URI: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1834332
Funder: National Science Foundation

Short KIM ID
The unique KIM identifier code.
MO_677328661525_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.
SW_MX2_KurniawanPetrieWilliams_2021_MoS__MO_677328661525_000
DOI 10.25950/328bfabb
https://doi.org/10.25950/328bfabb
https://search.datacite.org/works/10.25950/328bfabb
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 SW_MX2__MD_242389978788_001
DriverSW_MX2__MD_242389978788_001
KIM API Version2.2
Potential Type swmx2

(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
P 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
N/A 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
P 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


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: Mo


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: Mo


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: Mo


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: Mo


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: Mo


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: Mo


Cubic Crystal Basic Properties Table

Species: Mo

Species: S



Disclaimer From Model Developer

As with the original model by Wen et al. (2017) (or reference the model), this model is designed for two-dimensional (2D) monolayer molybdenum disulfide (MoS2), and is not appropriate for bulk MoS2 or other compounds of Mo and/or S.



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 multiplied 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 Mo v004 view 2138
Cohesive energy versus lattice constant curve for diamond Mo v004 view 2208
Cohesive energy versus lattice constant curve for fcc Mo v004 view 2944
Cohesive energy versus lattice constant curve for sc Mo v004 view 2609


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 multiplied 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 Mo at zero temperature v006 view 7343
Elastic constants for diamond Mo at zero temperature v001 view 18375
Elastic constants for fcc Mo at zero temperature v006 view 15227
Elastic constants for sc Mo at zero temperature v006 view 14014


Relaxed energy as a function of tilt angle for a symmetric tilt grain boundary within a cubic crystal v003

Creators:
Contributor: brunnels
Publication Year: 2022
DOI: https://doi.org/10.25950/2c59c9d6

Computes grain boundary energy for a range of tilt angles given a crystal structure, tilt axis, and material.
Test Test Results Link to Test Results page Benchmark time
Usertime multiplied 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)
Relaxed energy as a function of tilt angle for a 100 symmetric tilt grain boundary in bcc Mo v001 view 36131391
Relaxed energy as a function of tilt angle for a 110 symmetric tilt grain boundary in bcc Mo v001 view 167660190
Relaxed energy as a function of tilt angle for a 111 symmetric tilt grain boundary in bcc Mo v001 view 163589492
Relaxed energy as a function of tilt angle for a 112 symmetric tilt grain boundary in bcc Mo v001 view 452418494


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 multiplied 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 Mo v007 view 3727
Equilibrium zero-temperature lattice constant for diamond Mo v007 view 4734
Equilibrium zero-temperature lattice constant for fcc Mo v007 view 3764
Equilibrium zero-temperature lattice constant for sc Mo v007 view 3429


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 multiplied 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 Mo v005 view 65487





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