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Sim_LAMMPS_BOP_ZhouWardFoster_2015_CCu__SM_784926969362_000

Title
A single sentence description.
LAMMPS BOP potential for the C-Cu system developed by Zhou, Ward, and Foster (2015) v000
Description Mainly a Carbon potential. The Cu is added to allow modeling of growth of C on Cu substrate. Abstract from paper:

Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, the potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. Most importantly, the potential must predict the crystalline growth of the correct phases during direct MD simulations of
synthesis to achieve a predictive simulation of defect formation. Because an unlimited number of structures not included in the potential parameterization are encountered, the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We demonstrate that our potential reasonably captures the property trends of important carbon phases. Stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure.
Species
The supported atomic species.
C, Cu
Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
None
Content Origin LAMMPS package 22-Sep-2017
Contributor ronmiller
Maintainer ronmiller
Author Ronald E. Miller
Publication Year 2019
Item Citation

This Simulator Model originally published in [1] is archived in OpenKIM [2-4].

[1] Zhou XW, Ward DK, Foster ME. An analytical bond-order potential for carbon. Journal of Computational Chemistry [Internet]. 2015May;36(23):1719–35. Available from: https://doi.org/10.1002/jcc.23949 doi:10.1002/jcc.23949

[2] Miller RE. LAMMPS BOP potential for the C-Cu system developed by Zhou, Ward, and Foster (2015) v000. OpenKIM; 2019. doi:10.25950/4e29e7d2

[3] 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

[4] 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.
Short KIM ID
The unique KIM identifier code.
SM_784926969362_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_BOP_ZhouWardFoster_2015_CCu__SM_784926969362_000
DOI 10.25950/4e29e7d2
https://doi.org/10.25950/4e29e7d2
https://search.datacite.org/works/10.25950/4e29e7d2
KIM Item TypeSimulator Model
KIM API Version2.1
Simulator Name
The name of the simulator as defined in kimspec.edn.
LAMMPS
Potential Type bop
Simulator Potential bop

Verification Check Dashboard

(Click here to learn more about Verification Checks)

Grade Name Category Brief Description Full Results Aux File(s)
F 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
F 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: C
Species: Cu


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: C
Species: Cu


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: Cu
Species: C


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: Cu
Species: C


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: C
Species: Cu


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.

Species: Cu


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.

Species: Cu


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: C
Species: Cu


Cubic Crystal Basic Properties Table

Species: C

Species: Cu



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_C__TE_381992859743_002 view 5262
CohesiveEnergyVsLatticeConstant_diamond_C__TE_609752483801_002 view 4716
CohesiveEnergyVsLatticeConstant_fcc_C__TE_004682584752_002 view 5326
CohesiveEnergyVsLatticeConstant_sc_C__TE_095514597201_002 view 4460
CohesiveEnergyVsLatticeConstant__TD_554653289799_003
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_Cu__TE_864632638496_003 view 2751
CohesiveEnergyVsLatticeConstant_diamond_Cu__TE_596332570306_003 view 2591
CohesiveEnergyVsLatticeConstant_fcc_Cu__TE_311348891940_003 view 2815
CohesiveEnergyVsLatticeConstant_sc_Cu__TE_767437873249_003 view 2815
ElasticConstantsCubic__TD_011862047401_005
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)
ElasticConstantsCubic_bcc_C__TE_658794163909_005 view 20342
ElasticConstantsCubic_diamond_C__TE_266299090062_000 view 258701
ElasticConstantsCubic_fcc_C__TE_000146156270_005 view 23262
ElasticConstantsCubic_sc_C__TE_994329625827_005 view 16877
ElasticConstantsCubic__TD_011862047401_006
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)
ElasticConstantsCubic_bcc_Cu__TE_091603841600_006 view 5342
ElasticConstantsCubic_diamond_Cu__TE_330878926469_001 view 38483
ElasticConstantsCubic_fcc_Cu__TE_188557531340_006 view 7293
ElasticConstantsCubic_sc_Cu__TE_319353354686_006 view 7166
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_C__TE_638600582934_003 view 6481
ElasticConstantsHexagonal__TD_612503193866_004
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_Cu__TE_198002759922_004 view 177454
LatticeConstant2DHexagonalEnergy__TD_034540307932_002
Given atomic species and structure type (graphene-like, 2H, or 1T) of a 2D hexagonal monolayer crystal, as well as an initial guess at the lattice spacing, this Test Driver calculates the equilibrium lattice spacing and cohesive energy using Polak-Ribiere conjugate gradient minimization in LAMMPS
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)
LatticeConstant2DHexagonalEnergy_graphene_C__TE_638394465817_002 view 2527
LatticeConstantCubicEnergy__TD_475411767977_007
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_C__TE_035231992677_007 view 10109
LatticeConstantCubicEnergy_bcc_Cu__TE_873531926707_007 view 5246
LatticeConstantCubicEnergy_diamond_C__TE_072855742236_007 view 22744
LatticeConstantCubicEnergy_diamond_Cu__TE_939141232476_007 view 13787
LatticeConstantCubicEnergy_fcc_C__TE_200775201868_007 view 11996
LatticeConstantCubicEnergy_fcc_Cu__TE_387272513402_007 view 12572
LatticeConstantCubicEnergy_sc_C__TE_515273288513_007 view 10396
LatticeConstantCubicEnergy_sc_Cu__TE_904717264736_007 view 6302
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_C__TE_698171651321_004 view 169152
LatticeConstantHexagonalEnergy__TD_942334626465_005
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_Cu__TE_344176839725_005 view 11144797
LinearThermalExpansionCoeffCubic__TD_522633393614_001
This Test Driver uses LAMMPS to compute the linear thermal expansion coefficient at a finite temperature under a given pressure for a cubic lattice (fcc, bcc, sc, diamond) of a single given species.
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)
LinearThermalExpansionCoeffCubic_fcc_Cu__TE_335019190158_001 view 457751394
PhononDispersionCurve__TD_530195868545_004
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 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)
PhononDispersionCurve_fcc_Cu__TE_575177044018_004 view 66057
StackingFaultFccCrystal__TD_228501831190_002
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 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)
StackingFaultFccCrystal_0bar_Cu__TE_090810770014_002 view 564429111
SurfaceEnergyCubicCrystalBrokenBondFit__TD_955413365818_004
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_fcc_Cu__TE_689904280697_004 view 567869


Errors

ElasticConstantsFirstStrainGradient__TD_361847723785_000
Test Error Categories Link to Error page
ElasticConstantsFirstStrainGradientNumerical_fcc_Cu__TE_948689877911_000 mismatch view

LatticeConstantCubicEnergy__TD_475411767977_007

LatticeConstantHexagonalEnergy__TD_942334626465_005
Test Error Categories Link to Error page
LatticeConstantHexagonalEnergy_hcp_C__TE_698171651321_005 other view

LatticeInvariantShearPathCubicCrystalCBKIM__TD_083627594945_001

LinearThermalExpansionCoeffCubic__TD_522633393614_000

StackingFaultFccCrystal__TD_228501831190_001
Test Error Categories Link to Error page
StackingFaultFccCrystal_Cu_0bar__TE_090810770014_001 other view

VacancyFormationEnergyRelaxationVolume__TD_647413317626_000
Test Error Categories Link to Error page
VacancyFormationEnergyRelaxationVolume_fcc_Cu__TE_864259611541_000 mismatch view

VacancyFormationMigration__TD_554849987965_000
Test Error Categories Link to Error page
VacancyFormationMigration_fcc_Cu__TE_038488899376_000 mismatch view

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