Efficient "universal" shifted Lennard-Jones model for all KIM API supported species
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 "Universal" parameterization for the LennardJones612 model driver for all species types supported by the KIM API. The parameterization uses a shifted cutoff so that all interactions have a continuous energy function at the cutoff radius. See the README and params files for more details.
Species
The supported atomic species.
Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Ni, No, Np, O, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, U, Uuh, Uuo, Uup, Uuq, Uus, Uut, V, W, Xe, Y, Yb, Zn, Zr, electron, user01, user02, user03, user04, user05, user06, user07, user08, user09, user10, user11, user12, user13, user14, user15, user16, user17, user18, user19, user20
Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
This model was automatically fit using Lorentz-Berthelot mixing rules. It reproduces the dimer equilibrium separation (covalent radii) and the bond dissociation energies. It has not been fitted to other physical properties and its ability to model structures other than dimers is unknown.
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.
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).
The letter grade C was assigned because the normalized error in the computation was 9.76349e-06 compared with a machine precision of 2.22045e-16. The letter grade was based on 'score=log10(error/eps)', with ranges A=[0, 7.5], B=(7.5, 10.0], C=(10.0, 12.5], D=(12.5, 15.0), F>15.0. 'A' is the best grade, and 'F' indicates failure.
vc-forces-numerical-derivative
consistency
Forces computed by the model agree with numerical derivatives of the energy; see full description.
Unable to perform verification check due to an error.
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.
Model energy and forces are invariant with respect to rigid-body motion (translation and rotation) for all configurations the model was able to compute.
vc-objectivity
informational
Total energy is unchanged and forces transform correctly under rigid-body translation and rotation; see full description.
Unable to perform verification check due to an error.
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.
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.
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.
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.
This graph shows the dislocation core energy of a cubic crystal at zero temperature and pressure for a specific set of dislocation core cutoff radii. After obtaining the total energy of the system from conjugate gradient minimizations, non-singular, isotropic and anisotropic elasticity are applied to obtain the dislocation core energy for each of these supercells with different dipole distances. Graphs are generated for each species supported by the model.
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.
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.
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.
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.
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.
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
This model was automatically fit using Lorentz-Berthelot mixing rules. It reproduces the dimer equilibrium separation (covalent radii) and the bond dissociation energies. It has not been fitted to other physical properties and its ability to model structures other than dimers is unknown.
Creators: Daniel Karls
Contributor: karls
Publication Year: 2016
DOI: https://doi.org/
Given an xyz file corresponding to a finite cluster of atoms, create a LAMMPS
file with the given positions/species and compute the total potential energy
and atomic forces.
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 monoatomic cubic lattice
Creators: Daniel Karls
Contributor: karls
Publication Year: 2016
DOI: https://doi.org/
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)
Measures the cubic elastic constants for some common crystal types (fcc, bcc, sc) by calculating the hessian of the energy density with respect to strain. Error estimate is reported due to the numerical differentiation.
This version fixes the number of repeats in the species key.
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)
The isothermal classical and first strain gradient elastic constants for a crystal at 0 K and zero stress.
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)
Measures the hexagonal elastic constants for hcp structure by calculating the hessian of the energy density with respect to strain. Error estimate is reported due to the numerical differentiation.
This version fixes the number of repeats in the species key and the coordinate of the 2nd atom in the normed basis.
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)
LammpsExample2: energy-volume curve for monoatomic cubic lattice
Creators: Daniel Karls
Contributor: karls
Publication Year: 2014
DOI: https://doi.org/
This example Test Driver illustrates the use of LAMMPS in the openkim-pipeline
to compute an energy-volume curve (more specifically, a cohesive energy-lattice
constant curve) for a given cubic lattice (fcc, bcc, sc, diamond) of a single given
species. The curve is computed for lattice constants ranging from a_min to a_max,
with most samples being about a_0 (a_min, a_max, and a_0 are specified via stdin.
a_0 is typically approximately equal to the equilibrium lattice constant.). The precise
scaling of sample points going from a_min to a_0 and from a_0 to a_max is specified
by two separate parameters passed from stdin. 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)
LammpsExample: cohesive energy and equilibrium lattice constant of fcc argon
Creators: Daniel Karls
Contributor: karls
Publication Year: 2018
DOI: https://doi.org/
This example Test Driver illustrates the use of LAMMPS to compute the equilibrium lattice spacing and cohesive energy of fcc argon using Polak-Ribiere conjugate gradient minimization in LAMMPS and an initial guess at the equilibrium lattice spacing supplied by the user through pipeline.stdin.tpl.
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 and equilibrium lattice constant of hexagonal 2D crystalline layers
Creators: Ilia Nikiforov
Contributor: ilia
Publication Year: 2016
DOI: https://doi.org/
This Test Driver computes the equilibrium lattice spacing and cohesive energy of a 2D hexagonal monolayer crystal using Polak-Ribiere conjugate gradient minimization in LAMMPS. Through pipeline.stdin.tpl, the user supplies the choice of structure type, an initial guess at the equilibrium lattice spacing and the two atomic species comprising the crystal.
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 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)
Calculates lattice constant by minimizing energy function.
This version fixes the output format problems in species and stress, and adds support for PURE and OPBC neighbor lists. The cell used for calculation is switched from a hexagonal one to an orthorhombic one to comply with the requirement of OPBC.
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)
This Test Driver uses LAMMPS to compute the linear thermal expansion coefficient at a finite temperature under a given pressure for cubic lattice (fcc, bcc, sc, diamond) of a single given species.
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)
Calculates the phonon dispersion relations for fcc lattices and records the results as curves.
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)
Intrinsic and extrinsic stacking fault energies, unstable stacking fault energy, unstable twinning energy, stacking fault energy as a function of fractional displacement, and gamma surface for a monoatomic FCC 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)
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)
Potential energy and atomic forces of periodic, non-orthogonal cell of atoms
Creators: Daniel Karls
Contributor: karls
Publication Year: 2014
DOI: https://doi.org/
Given an extended xyz file corresponding to a non-orthogonal periodic box of
atoms, create a LAMMPS file with the given positions/species and compute the
total potential energy and atomic forces.
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)
Computes the monovacancy formation energy and relaxation volume for cubic and hcp monoatomic crystals.
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)
Computes the monovacancy formation and migration energies for cubic and hcp monoatomic crystals.
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)
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)
LennardJones612_UniversalShifted__MO_959249795837_002