Sim_LAMMPS_ReaxFF_XiaoShiHao_2017_PHOC__SM_424780295507_000
| Title
A single sentence description.
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LAMMPS ReaxFF transferable potential for P/H/O/C systems with application to phosphorene developed by Xiao et al. (2017) v000 |
|---|---|
| Citations
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| Description | We developed ReaxFF parameters for phosphorus and hydrogen to give a good description of the chemical and mechanical properties of pristine and defected black phosphorene. ReaxFF for P/H is transferable to a wide range of phosphorus- and hydrogen-containing systems including bulk black phosphorus, blue phosphorene, edge-hydrogenated phosphorene, and phosphorus hydride molecules. The potential parameters were obtained by conducting global optimization with respect to a set of reference data generated by extensive ab initio calculations. Emphasis was placed on the mechanical response of black phosphorene with different types of defects. Compared to the nonreactive SW potential (Jiang, J.-W. Nanotechnology 2015, 26, 315706), ReaxFF for P/H systems provides a significant improvement in describing the mechanical properties of the pristine and defected black phosphorene, as well as the thermal stability of phosphorene nanotubes. A counterintuitive phenomenon is observed that single vacancies weaken the black phosphorene more than double vacancies with higher formation energy. Our results also showed that the mechanical response of black phosphorene is more sensitive to defects in the zigzag direction than that in the armchair direction. In addition, we developed a preliminary set of ReaxFF parameters for P/H/O/C to demonstrate that the ReaxFF parameters developed in this work could be generalized to oxidized phosphorene and P-containing 2D van der Waals heterostructures. That is, the proposed ReaxFF parameters for P/H systems establish a solid foundation for modeling of a wide range of P-containing materials. In addition, we extended ReaxFF in LAMMPS by adding a 60° correction term, which significantly improved the description of phosphorus clusters (need to use modified "reaxc_valence_angles.cpp" file in building the LAMMPS package). |
| Species
The supported atomic species.
| C, H, O, P |
| Disclaimer
A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.
|
Using these forcefields for systems they have not been explicitly trained against may produce unrealistic results. Please see the full manuscripts for more detailed information. In addition, the P-O and P-C parameters of P/H/O/C ReaxFF are designed to demonstrate that the ReaxFF parameters developed in this work could be generalized to oxidized phosphorene and P-containing 2D van der Waals heterostructures. That is, the P-O and P-C parts of this ReaxFF force field are not production ready. |
| Content Origin | ReaxFF file for P/H systems with or without 60° angle correction (reaxc_valence_angles.cpp) and the modified source file and preliminary version of the ReaxFF file for P/H/O/C systems are provided in the SI at http://dx.doi.org/10.1021/acs.jpca.7b05257 |
| Contributor |
Xiao Hang |
| Maintainer |
Xiao Hang |
| Developer |
Xiao Hang Xiaoyang Shi Feng Hao Xiangbiao Liao Yayun Zhang Xi Chen |
| Published on KIM | 2021 |
| How to Cite |
This Simulator Model originally published in [1] is archived in OpenKIM [2-4]. [1] Xiao H, Shi X, Hao F, Liao X, Zhang Y, Chen X. Development of a Transferable Reactive Force Field of P/H Systems: Application to the Chemical and Mechanical Properties of Phosphorene. Journal of Physical Chemistry A. 2017;121(32):6135–49. doi:10.1021/acs.jpca.7b05257 — (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] Hang X, Shi X, Hao F, Liao X, Zhang Y, Chen X. LAMMPS ReaxFF transferable potential for P/H/O/C systems with application to phosphorene developed by Xiao et al. (2017) v000. OpenKIM; 2021. doi:10.25950/7546cc95 [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. |
| Funding | Not available |
| Short KIM ID
The unique KIM identifier code.
| SM_424780295507_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_ReaxFF_XiaoShiHao_2017_PHOC__SM_424780295507_000 |
| DOI |
10.25950/7546cc95 https://doi.org/10.25950/7546cc95 https://commons.datacite.org/doi.org/10.25950/7546cc95 |
| KIM Item Type | Simulator Model |
| KIM API Version | 2.2 |
| Simulator Name
The name of the simulator as defined in kimspec.edn.
| LAMMPS |
| Potential Type | reax |
| Simulator Potential | reax/c |
| Run Compatibility | portable-models |
| 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 |
| F | vc-periodicity-support | mandatory | Periodic boundary conditions are handled correctly; see full description. |
Results | Files |
| F | 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 |
| F | 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 |
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.
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.
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.
Dislocation Core Energies
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.
(No matching species)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.
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.
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.
Cubic Crystal Basic Properties Table
Species: CSpecies: H
Species: O
Species: P
Disclaimer From Model Developer
Using these forcefields for systems they have not been explicitly trained against may produce unrealistic results. Please see the full manuscripts for more detailed information. In addition, the P-O and P-C parameters of P/H/O/C ReaxFF are designed to demonstrate that the ReaxFF parameters developed in this work could be generalized to oxidized phosphorene and P-containing 2D van der Waals heterostructures. That is, the P-O and P-C parts of this ReaxFF force field are not production ready.
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 diamond O v004 | view | 32374 | |
| Cohesive energy versus lattice constant curve for fcc C v004 | view | 55657 | |
| Cohesive energy versus lattice constant curve for fcc O v004 | view | 67657 | |
| Cohesive energy versus lattice constant curve for fcc P v004 | view | 25412 | |
| Cohesive energy versus lattice constant curve for sc C v004 | view | 5669 | |
| Cohesive energy versus lattice constant curve for sc O v004 | view | 10012 | |
| Cohesive energy versus lattice constant curve for sc P v004 | view | 8424 |
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.
Creators:
Contributor: ilia
Publication Year: 2024
DOI: https://doi.org/10.25950/2f2c4ad3
Computes the equilibrium crystal structure and energy for an arbitrary crystal at zero temperature and applied stress by performing symmetry-constrained relaxation. The crystal structure is specified using the AFLOW prototype designation. Multiple sets of free parameters corresponding to the crystal prototype may be specified as initial guesses for structure optimization. No guarantee is made regarding the stability of computed equilibria, nor that any are the ground state.
Creators: Ilia Nikiforov
Contributor: ilia
Publication Year: 2019
DOI: https://doi.org/10.25950/dd36239b
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 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 graphene v002 | view | 345 |
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.
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 H v005 | view | 1072317 | |
| Equilibrium lattice constants for hcp O v005 | view | 1803318 |
ElasticConstantsCubic__TD_011862047401_006
| Test | Error Categories | Link to Error page |
|---|---|---|
| Elastic constants for bcc P at zero temperature v006 | other | view |
| Elastic constants for fcc P at zero temperature v006 | other | view |
| Elastic constants for sc P at zero temperature v006 | other | view |
ElasticConstantsHexagonal__TD_612503193866_004
| Test | Error Categories | Link to Error page |
|---|---|---|
| Elastic constants for hcp H at zero temperature v004 | other | view |
| Elastic constants for hcp O at zero temperature v004 | other | view |
EquilibriumCrystalStructure__TD_457028483760_000
EquilibriumCrystalStructure__TD_457028483760_001
| Test | Error Categories | Link to Error page |
|---|---|---|
| Equilibrium crystal structure and energy for CHO in AFLOW crystal prototype A2BC2_mP20_11_4e_2e_4e v000 | other | view |
EquilibriumCrystalStructure__TD_457028483760_002
LatticeConstantCubicEnergy__TD_475411767977_007
| Test | Error Categories | Link to Error page |
|---|---|---|
| Equilibrium zero-temperature lattice constant for diamond P v007 | other | view |
LatticeConstantHexagonalEnergy__TD_942334626465_005
| Test | Error Categories | Link to Error page |
|---|---|---|
| Equilibrium lattice constants for hcp C v005 | other | view |
| Equilibrium lattice constants for hcp P v005 | other | view |
LinearThermalExpansionCoeffCubic__TD_522633393614_001
| Test | Error Categories | Link to Error page |
|---|---|---|
| Linear thermal expansion coefficient of diamond C at 293.15 K under a pressure of 0 MPa v001 | other | view |
VacancyFormationEnergyRelaxationVolume__TD_647413317626_001
| Test | Error Categories | Link to Error page |
|---|---|---|
| Monovacancy formation energy and relaxation volume for sc O | other | view |
VacancyFormationMigration__TD_554849987965_001
| Test | Error Categories | Link to Error page |
|---|---|---|
| Vacancy formation and migration energy for sc O | other | view |
| Sim_LAMMPS_ReaxFF_XiaoShiHao_2017_PHOC__SM_424780295507_000.txz | Tar+XZ | Linux and OS X archive |
| Sim_LAMMPS_ReaxFF_XiaoShiHao_2017_PHOC__SM_424780295507_000.zip | Zip | Windows archive |