Jump to: Tests | Visualizers | Files | Wiki

SW_MX2_WenShirodkarPlechac_2017_MoS__MO_201919462778_001

Title
A single sentence description.
Modified Stillinger-Weber potential (MX2) for monolayer MoS2 developed by Wen et al. (2017) v001
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.
Two-dimensional molybdenum disulfide (MoS2) is a promising material
for the next generation of switchable transistors and
photodetectors. In order to perform large-scale molecular simulations
of the mechanical and thermal behavior of MoS2-based devices, an
accurate interatomic potential is required. To this end, we have
developed a Stillinger-Weber potential for monolayer MoS2. The
potential parameters are optimized to reproduce the geometry (bond
lengths and bond angles) of MoS2 in its equilibrium state and to match
as closely as possible the forces acting on the atoms along a
dynamical trajectory obtained from ab initio molecular
dynamics. Verification calculations indicate that the new potential
accurately predicts important material properties including the strain
dependence of the cohesive energy, the elastic constants, and the
linear thermal expansion coefficient. The uncertainty in the potential
parameters is determined using a Fisher information theory
analysis. It is found that the parameters are fully identified, and
none are redundant. In addition, the Fisher information matrix
provides uncertainty bounds for predictions of the potential for new
properties. As an example, bounds on the average vibrational thickness
of a MoS2 monolayer at finite temperature are computed and found to be
consistent with the results from a molecular dynamics simulation.
Species
The supported atomic species.
Mo, S
Contributor Mwen
Maintainer Mwen
Author Mingjian Wen
Publication Year 2018
Source Citations
A citation to primary published work(s) that describe this KIM Item.

Wen M, et al. (2017) A force-matching Stillinger-Weber potential for MoS_2: Parameterization and Fisher information theory based sensitivity analysis. Journal of Applied Physics 122(24):244301. doi:10.1063/1.5007842

Item Citation Click here to download a citation in BibTeX format.
Short KIM ID
The unique KIM identifier code.
MO_201919462778_001
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_WenShirodkarPlechac_2017_MoS__MO_201919462778_001
DOI 10.25950/eeedbbc4
https://doi.org/10.25950/eeedbbc4
https://search.datacite.org/works/10.25950/eeedbbc4
KIM Item Type
Specifies whether this is a Stand-alone Model (software implementation of an interatomic model); Parameterized Model (parameter file to be read in by a Model Driver); Model Driver (software implementation of an interatomic model that reads in parameters).
Parameterized Model using Model Driver SW_MX2__MD_242389978788_001
DriverSW_MX2__MD_242389978788_001
KIM API Version2.0
Previous Version SW_MX2_WenShirodkarPlechac_2017_MoS__MO_201919462778_000

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
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
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

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: Mo
Species: S

Click on any thumbnail to get a full size image.



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
Species: S

Click on any thumbnail to get a full size image.



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
Species: S

Click on any thumbnail to get a full size image.



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
Species: S

Click on any thumbnail to get a full size image.



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
Species: S

Click on any thumbnail to get a full size image.



Cubic Crystal Basic Properties Table

Species: Mo

Species: S



Tests

CohesiveEnergyVsLatticeConstant__TD_554653289799_002
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)
CohesiveEnergyVsLatticeConstant_bcc_Mo__TE_903593174145_002 view 1576
CohesiveEnergyVsLatticeConstant_bcc_S__TE_236749031642_002 view 1649
CohesiveEnergyVsLatticeConstant_diamond_Mo__TE_332233266787_002 view 1576
CohesiveEnergyVsLatticeConstant_diamond_S__TE_690800658487_002 view 1246
CohesiveEnergyVsLatticeConstant_fcc_Mo__TE_408532402297_002 view 1796
CohesiveEnergyVsLatticeConstant_fcc_S__TE_562587649704_002 view 1833
CohesiveEnergyVsLatticeConstant_sc_Mo__TE_951306870292_002 view 1833
CohesiveEnergyVsLatticeConstant_sc_S__TE_085816116079_002 view 1906
ElasticConstantsCubic__TD_011862047401_004
Computes the cubic elastic constants for some common crystal types (fcc, bcc, sc) 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)
ElasticConstantsCubic_bcc_Mo__TE_454217749882_004 view 3189
ElasticConstantsCubic_bcc_S__TE_949083098829_004 view 2566
ElasticConstantsCubic_fcc_Mo__TE_425639580159_004 view 3995
ElasticConstantsCubic_fcc_S__TE_711736518885_004 view 3482
ElasticConstantsCubic_sc_Mo__TE_959738251850_004 view 3225
ElasticConstantsCubic_sc_S__TE_258290086299_004 view 3006
ElasticConstantsHexagonal__TD_612503193866_003
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)
ElasticConstantsHexagonal_hcp_Mo__TE_040254693124_003 view 3922
ElasticConstantsHexagonal_hcp_S__TE_647103039326_003 view 3335
LatticeConstantCubicEnergy__TD_475411767977_005
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)
LatticeConstantCubicEnergy_bcc_Mo__TE_279386991452_005 view 1320
LatticeConstantCubicEnergy_bcc_S__TE_130588168329_005 view 1429
LatticeConstantCubicEnergy_diamond_Mo__TE_055175214741_005 view 1686
LatticeConstantCubicEnergy_diamond_S__TE_582794783472_005 view 1320
LatticeConstantCubicEnergy_fcc_Mo__TE_434577360861_005 view 1613
LatticeConstantCubicEnergy_fcc_S__TE_531894700060_005 view 1356
LatticeConstantCubicEnergy_sc_Mo__TE_877374933970_005 view 1503
LatticeConstantCubicEnergy_sc_S__TE_361985763049_005 view 1210
LatticeConstantHexagonalEnergy__TD_942334626465_004
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)
LatticeConstantHexagonalEnergy_hcp_Mo__TE_965423669120_004 view 19170
LatticeConstantHexagonalEnergy_hcp_S__TE_237886957846_004 view 11326
SurfaceEnergyCubicCrystalBrokenBondFit__TD_955413365818_003
Calculates the surface energy of several high symmetry surfaces and produces a broken-bond model fit. In latex form, the fit equations are given by:

E_{FCC} (\vec{n}) = p_1 (4 \left( |x+y| + |x-y| + |x+z| + |x-z| + |z+y| +|z-y|\right)) + p_2 (8 \left( |x| + |y| + |z|\right)) + p_3 (2 ( |x+ 2y + z| + |x+2y-z| + |x-2y + z| + |x-2y-z| + |2x+y+z| + |2x+y-z| +|2x-y+z| +|2x-y-z| +|x+y+2z| +|x+y-2z| +|x-y+2z| +|x-y-2z| ) + c

E_{BCC} (\vec{n}) = p_1 (6 \left( | x+y+z| + |x+y-z| + |-x+y-z| + |x-y+z| \right)) + p_2 (8 \left( |x| + |y| + |z|\right)) + p_3 (4 \left( |x+y| + |x-y| + |x+z| + |x-z| + |z+y| +|z-y|\right)) +c.

In Python, these two fits take the following form:

def BrokenBondFCC(params, index):

import numpy
x, y, z = index
x = x / numpy.sqrt(x**2.+y**2.+z**2.)
y = y / numpy.sqrt(x**2.+y**2.+z**2.)
z = z / numpy.sqrt(x**2.+y**2.+z**2.)

return params[0]*4* (abs(x+y) + abs(x-y) + abs(x+z) + abs(x-z) + abs(z+y) + abs(z-y)) + params[1]*8*(abs(x) + abs(y) + abs(z)) + params[2]*(abs(x+2*y+z) + abs(x+2*y-z) +abs(x-2*y+z) +abs(x-2*y-z) + abs(2*x+y+z) +abs(2*x+y-z) +abs(2*x-y+z) +abs(2*x-y-z) + abs(x+y+2*z) +abs(x+y-2*z) +abs(x-y+2*z) +abs(x-y-2*z))+params[3]

def BrokenBondBCC(params, x, y, z):


import numpy
x, y, z = index
x = x / numpy.sqrt(x**2.+y**2.+z**2.)
y = y / numpy.sqrt(x**2.+y**2.+z**2.)
z = z / numpy.sqrt(x**2.+y**2.+z**2.)

return params[0]*6*(abs(x+y+z) + abs(x-y-z) + abs(x-y+z) + abs(x+y-z)) + params[1]*8*(abs(x) + abs(y) + abs(z)) + params[2]*4* (abs(x+y) + abs(x-y) + abs(x+z) + abs(x-z) + abs(z+y) + abs(z-y)) + params[3]
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)
SurfaceEnergyCubicCrystalBrokenBondFit_bcc_Mo__TE_336897536534_003 view 39055


Errors

  • No Errors associated with this Model




Download Dependency

This Model requires a Model Driver. Archives for the Model Driver SW_MX2__MD_242389978788_001 appear below.


SW_MX2__MD_242389978788_001.txz Tar+XZ Linux and OS X archive
SW_MX2__MD_242389978788_001.zip Zip Windows archive

Wiki

Wiki is ready to accept new content.

Login to edit Wiki content