EAM potential (LAMMPS cubic hermite tabulation) for the Pd-H system developed by Zhou et al. (2008) v000

Xiaowang Zhou; Jonathan A. Zimmerman; Bryan M. Wong; J. J. Hoyt

doi:10.25950/c577c984

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EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000

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Interatomic potential for Hydrogen (H), Palladium (Pd).
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Title A single sentence description.	EAM potential (LAMMPS cubic hermite tabulation) for the Pd-H system developed by Zhou et al. (2008) 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.	Palladium hydrides have important applications. However, the complex Pd–H alloy system presents a formidable challenge to developing accurate computational models. In particular, the separation of a Pd–H system to dilute (α) and concentrated (β) phases is a central phenomenon, but the capability of interatomic potentials to display this phase miscibility gap has been lacking. We have extended an existing palladium embedded-atom method potential to construct a new Pd–H embedded-atom method potential by normalizing the elemental embedding energy and electron density functions. The developed Pd–H potential reasonably well predicts the lattice constants, cohesive energies, and elastic constants for palladium, hydrogen, and PdHx phases with a variety of compositions. It ensures the correct hydrogen interstitial sites within the hydrides and predicts the phase miscibility gap. Preliminary molecular dynamics simulations using this potential show the correct phase stability, hydrogen diffusion mechanism, and mechanical response of the Pd–H system.
Species The supported atomic species.	H, Pd
Disclaimer A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.	None
Content Origin	NIST IPRP (https://www.ctcms.nist.gov/potentials/Pd.html#Pd-H)

Contributor	Ellad B. Tadmor
Maintainer	Ellad B. Tadmor
Developer	Xiaowang Zhou Jonathan A. Zimmerman Bryan M. Wong J. J. Hoyt
Published on KIM	2018
How to Cite	Click here to download this citation in BibTeX format.
Citations This panel presents information regarding the papers that have cited the interatomic potential (IP) whose page you are on. The OpenKIM machine learning based Deep Citation framework is used to determine whether the citing article actually used the IP in computations (denoted by "USED") or only provides it as a background citation (denoted by "NOT USED"). For more details on Deep Citation and how to work with this panel, click the documentation link at the top of the panel. The word cloud to the right is generated from the abstracts of IP principle source(s) (given below in "How to Cite") and the citing articles that were determined to have used the IP in order to provide users with a quick sense of the types of physical phenomena to which this IP is applied. The bar chart shows the number of articles that cited the IP per year. Each bar is divided into green (articles that USED the IP) and blue (articles that did NOT USE the IP). Users are encouraged to correct Deep Citation errors in determination by clicking the speech icon next to a citing article and providing updated information. This will be integrated into the next Deep Citation learning cycle, which occurs on a regular basis. OpenKIM acknowledges the support of the Allen Institute for AI through the Semantic Scholar project for providing citation information and full text of articles when available, which are used to train the Deep Citation ML algorithm.	This panel provides information on past usage of this interatomic potential (IP) powered by the OpenKIM Deep Citation framework. The word cloud indicates typical applications of the potential. The bar chart shows citations per year of this IP (bars are divided into articles that used the IP (green) and those that did not (blue)). The complete list of articles that cited this IP is provided below along with the Deep Citation determination on usage. See the Deep Citation documentation for more information. 78 Citations (51 used) Show Model Used Show All Help us to determine which of the papers that cite this potential actually used it to perform calculations. If you know, click the . M. Ponga and D. Sun, “A unified framework for heat and mass transport at the atomic scale,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 15 Abstract: We present a unified framework to simulate heat and mass tra… read more Abstract: We present a unified framework to simulate heat and mass transport in systems of particles. The proposed framework is based on kinematic mean field theory and uses a phenomenological master equation to compute effective transport rates between particles without the need to evaluate operators. We exploit this advantage and apply the model to simulate transport phenomena at the nanoscale. We demonstrate that, when calibrated to experimentally-measured transport coefficients, the model can accurately predict transient and steady state temperature and concentration profiles even in scenarios where the length of the device is comparable to the mean free path of the carriers. Through several example applications, we demonstrate the validity of our model for all classes of materials, including ones that, until now, would have been outside the domain of computational feasibility. read less X. W. Zhou and S. Foiles, “Uncertainty Quantification and Reduction of Molecular Dynamics Models.” 2017. link Times cited: 9 Abstract: Molecular dynamics (MD) is an important method underlying th… read more Abstract: Molecular dynamics (MD) is an important method underlying the modern field of Computational Materials Science. Without requiring prior knowledge as inputs, MD simulations have been used to study a variety of material problems. However, results of molecular dynamics simulations are often associated with errors as compared with experimental observations. These errors come from a variety of sources, including inac- curacy of interatomic potentials, short length and time scales, idealized problem description and statistical uncertainties of MD simulations themselves. This chapter specifically devotes to the statistical uncertainties of MD simulations. In particular, methods to quantify and reduce such statistical uncertainties are demonstrated using a variety of exemplar cases, including calculations of finite temperature static properties such as lattice constants, cohesive energies, elastic constants, dislocation energies, ther- mal conductivities, surface segregation and calculations of kinetic properties such as diffusion parameters. We also demonstrate that when the statistical uncertainties are reduced to near zero, MD can be used to validate and improve widely used theories. read less C. Tang, G. Sun, and Y. Liu, “Impact of host phonons on interstitial diffusion,” Scientific Reports. 2022. link Times cited: 0 J. Bian, L. Yang, W. Yuan, and G. Wang, “Influence of hydrogenation on the mechanical properties of Pd nanoparticles,” RSC Advances. 2021. link Times cited: 1 Abstract: Atomic simulations are conducted to investigate the influenc… read more Abstract: Atomic simulations are conducted to investigate the influence of hydrogenation on the mechanical properties of Pd nanoparticles. It is found that with an increase in the H atom content both the elastic modulus and the yield stress decrease approximately linearly. Moreover, the H atom content evidently alters the atomic deformation mechanisms in Pd nanoparticles. When the H atom content is in the range of 0–0.3, yield initiates from dislocation nucleating beneath surface steps and then a pyramid hillock is formed. Subsequently, dislocation nucleation and exhaustion at the surface will govern the plastic deformation. However, when the H atom content is in the range of 0.3–0.4, massive initial defects are introduced by hydrogenation, which partially suppress the dislocation nucleation around the surface steps, and no pyramid dislocation hillock is formed. Dislocation multiplication will dominate the subsequent plastic deformation. Moreover, as the H atom content increases to 0.4–0.5, the recoverable phase transition plays a key role in the plastic deformation. This study enriches our understanding of the impact of hydrogenation on the mechanical properties and deformation mechanisms of Pd nanoparticles. read less K. Sytwu et al., “Driving energetically unfavorable dehydrogenation dynamics with plasmonics,” Science. 2020. link Times cited: 36 Abstract: Coaxing unreactive sites Optical excitation of localized sur… read more Abstract: Coaxing unreactive sites Optical excitation of localized surface plasmon resonances can confine light and create electromagnetic (EM) “hotspots” that can increase catalytic reaction rates. Sytwu et al. show how optical excited plasmons can also control the location of the active site. A crossed-bar gold-palladium hydride (Au-PdHx) plasmonic antenna-reactor system localized EM radiation away from the more reactive PdHx tips. Using in situ environmental transmission electron microscopy, the authors show that changing the illumination wavelength and intensity, along with the surrounding hydrogen gas pressure, could shift dehydrogenation away from the sharp PdHx nanorod tips to the flat middle faces. Science, this issue p. 280 Plasmon excitation can initiate hydrogen dissociation at normally unreactive palladium nanorod crystal faces. Nanoparticle surface structure and geometry generally dictate where chemical transformations occur, with higher chemical activity at sites with lower activation energies. Here, we show how optical excitation of plasmons enables spatially modified phase transformations, activating otherwise energetically unfavorable sites. We have designed a crossed-bar Au-PdHx antenna-reactor system that localizes electromagnetic enhancement away from the innately reactive PdHx nanorod tips. Using optically coupled in situ environmental transmission electron microscopy, we track the dehydrogenation of individual antenna-reactor pairs with varying optical illumination intensity, wavelength, and hydrogen pressure. Our in situ experiments show that plasmons enable new catalytic sites, including dehydrogenation at the nanorod faces. Molecular dynamics simulations confirm that these new nucleation sites are energetically unfavorable in equilibrium and only accessible through tailored plasmonic excitation. read less R. B. Schwarz, A. Khachaturyan, A. Caro, M. Baskes, and E. Martinez, “Coherent phase decomposition in the Pd–H system,” Journal of Materials Science. 2020. link Times cited: 6 J. Méndez and M. Ponga, “MXE: A package for simulating long-term diffusive mass transport phenomena in nanoscale systems,” Comput. Phys. Commun. 2019. link Times cited: 8 A. M. Igoshkin, “Molecular Dynamics Study of the Deposition of Palladium-Silver Films on a Silver Substrate,” Journal of Structural Chemistry. 2019. link Times cited: 0 X. Sun, M. P. Ariza, M. Ortiz, and K. G. Wang, “Atomistic modeling and analysis of hydride phase transformation in palladium nanoparticles,” Journal of the Mechanics and Physics of Solids. 2019. link Times cited: 11 G. Bonny et al., “Classical interatomic potential for quaternary Ni–Fe–Cr–Pd solid solution alloys,” Modelling and Simulation in Materials Science and Engineering. 2018. link Times cited: 9 Abstract: In this paper, we present a new quaternary interatomic poten… read more Abstract: In this paper, we present a new quaternary interatomic potential for the NiFeCrPd system, which is an extension on the previous NiFeCr potential. Density functional theory is used to calculate the quantities to be fitted, with particular focus on the energetics of point defects with solutes, for the potential to be used towards understanding radiation damage properties. The potential thus will enable the modeling of multi-elemental solid solution alloys consisting of up to four elements. To test the potential, we have performed atomistic kinetic Monte Carlo simulations to investigate the effect of configurational entropy on the self-diffusion coefficients. The self-diffusion coefficients are found to increase with chemical complexity, contrary to the common postulation of sluggish diffusion in high entropy alloys (HEAs). In addition, we have performed molecular dynamics simulations to elucidate the effect of Pd on vacancy diffusion and clustering in pure Ni and binary alloys. In agreement with recent irradiation experiments, our simulations show that while large vacancy clusters, such as stacking fault tetrahedra, are formed in pure Ni, Ni–Fe and Ni–Cr systems, negligible vacancy clustering is observed in Ni–Pd systems, indicating a possible effect of Pd in reducing cluster sizes. We suggest that this potential will be useful for studying the defect evolution in multi-component HEAs. read less X. Zhou, T. W. Heo, B. C. Wood, V. Stavila, S. Kang, and M. Allendorf, “Molecular dynamics studies of fundamental bulk properties of palladium hydrides for hydrogen storage,” Journal of Applied Physics. 2018. link Times cited: 7 Abstract: Solid-state hydrogen storage materials undergo complex phase… read more Abstract: Solid-state hydrogen storage materials undergo complex phase transformations whose behavior are collectively determined by thermodynamic (e.g., Gibbs free energy), mechanical (e.g., lattice and elastic constants), and mass transport (e.g., diffusivity) properties. These properties depend on the reaction conditions and evolve continuously during (de)hydrogenation. Thus, they are difficult to measure in experiments. Because of this, past progress to improve solid-state hydrogen storage materials has been prolonged. Using PdHx as a representative example for interstitial metal hydride, we have recently applied molecular dynamics simulations to quantify hydrogen diffusion in the entire reaction space of temperature and composition. Here, we have further applied molecular dynamics simulations to obtain well-converged expressions for lattice constants, Gibbs free energies, and elastic constants of PdHx at various stages of the reaction. Our studies confirm significant dependence of elastic constants on temperature and composition. Specifically, a new dynamic effect of hydrogen diffusion on elastic constants is discovered and discussed.Solid-state hydrogen storage materials undergo complex phase transformations whose behavior are collectively determined by thermodynamic (e.g., Gibbs free energy), mechanical (e.g., lattice and elastic constants), and mass transport (e.g., diffusivity) properties. These properties depend on the reaction conditions and evolve continuously during (de)hydrogenation. Thus, they are difficult to measure in experiments. Because of this, past progress to improve solid-state hydrogen storage materials has been prolonged. Using PdHx as a representative example for interstitial metal hydride, we have recently applied molecular dynamics simulations to quantify hydrogen diffusion in the entire reaction space of temperature and composition. Here, we have further applied molecular dynamics simulations to obtain well-converged expressions for lattice constants, Gibbs free energies, and elastic constants of PdHx at various stages of the reaction. Our studies confirm significant dependence of elastic constants on temperat... read less G. Venturini, K. G. Wang, I. Romero, M. P. Ariza, and M. Ortiz, “Atomistic long-term simulation of heat and mass transport,” Journal of The Mechanics and Physics of Solids. 2014. link Times cited: 38 J. H. He, D. Knies, G. Hubler, K. Grabowski, R. J. Tonucci, and L. Dechiaro, “Hydrogen segregation and lattice reorientation in palladium hydride nanowires,” Applied Physics Letters. 2012. link Times cited: 7 Abstract: We study palladium hydride nanowires of different sizes and … read more Abstract: We study palladium hydride nanowires of different sizes and hydrogen concentrations at 300 K using molecular dynamic simulations. Strong surface segregation of hydrogen with a depletion zone behind is observed in the palladium hydride nanowires. We also show that lattice reorientation is controlled by the hydrogen concentration as well as the nanowire size. The interplay of surface stresses and hydrogen induced stresses is responsible for the observations. read less H. Pham, B. Arman, S. Luo, and T. Çagin, “Shock compression and spallation of palladium bicrystals with a Σ5 grain boundary,” Journal of Applied Physics. 2011. link Times cited: 9 Abstract: We investigate an elementary process of shock response of gr… read more Abstract: We investigate an elementary process of shock response of grain boundaries (GBs) using molecular dynamics simulations: shock compression and spallation in Pd bicrystals with a symmetric Σ5/(210)/〈100〉 GB. The loading direction is normal to GB. An elastic shock may induce the elastic-plastic or two-wave structure at the GB. The GB serves as a wave scattering center for the transverse motion perpendicular to the GB rotation axis and the shock direction: it induces a phase shift of 180∘, an increase in the amplitude of the particle velocity, GB sliding and grain orientation distortion. The GB is the preferred nucleation site both for dislocations and voids. Our results suggest that both microstructure and the loading geometry contribute to dynamic response of a solid. read less M. Ceriotti, M. Parrinello, T. Markland, and D. Manolopoulos, “Efficient stochastic thermostatting of path integral molecular dynamics.,” The Journal of chemical physics. 2010. link Times cited: 255 Abstract: The path integral molecular dynamics (PIMD) method provides … read more Abstract: The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nosé-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations. read less X. Sun, “Exploring solute-defect interactions in nanosized palladium hydrides across multiple time scales,” Computational Materials Science. 2023. link Times cited: 0 D. Chow, N. Burns, E. Boateng, J. van der Zalm, S. Kycia, and A. Chen, “Mechanical Exfoliation of Expanded Graphite to Graphene-Based Materials and Modification with Palladium Nanoparticles for Hydrogen Storage,” Nanomaterials. 2023. link Times cited: 0 Abstract: Hydrogen is a promising green fuel carrier that can replace … read more Abstract: Hydrogen is a promising green fuel carrier that can replace fossil fuels; however, its storage is still a challenge. Carbon-based materials with metal catalysts have recently been the focus of research for solid-state hydrogen storage due to their efficacy and low cost. Here, we report on the exfoliation of expanded graphite (EG) through high shear mixing and probe tip sonication methods to form graphene-based nanomaterial ShEG and sEG, respectively. The exfoliation processes were optimized based on electrochemical capacitance measurements. The exfoliated EG was further functionalized with palladium nanoparticles (Pd-NP) for solid-state hydrogen storage. The prepared graphene-based nanomaterials (ShEG and sEG) and the nanocomposites (Pd-ShEG and Pd-sEG) were characterized with various traditional techniques (e.g., SEM, TEM, EDX, XPS, Raman, XRD) and the advanced high-resolution pair distribution function (HRPDF) analysis. Electrochemical hydrogen uptake and release (QH) were measured, showing that the sEG decorated with Pd-NP (Pd-sEG, 31.05 mC cm−2) and ShEG with Pd-NP (Pd-ShEG, 24.54 mC cm−2) had a notable improvement over Pd-NP (9.87 mC cm−2) and the composite of Pd-EG (14.7 mC cm−2). QH showed a strong linear relationship with an effective surface area to volume ratio, indicating nanoparticle size as a determining factor for hydrogen uptake and release. This work is a promising step toward the design of the high-performance solid-state hydrogen storage devices through mechanical exfoliation of the substrate EG to control nanoparticle size and dispersion. read less Z. Dong et al., “Efficient Pd on Carbon Catalyst for Ammonium Formate Dehydrogenation: Effect of Surface Oxygen Functional Groups,” SSRN Electronic Journal. 2022. link Times cited: 4 J. Hong et al., “Metastable hexagonal close-packed palladium hydride in liquid cell TEM,” Nature. 2022. link Times cited: 21 C. Tang, G. Sun, and Y. Liu, “Is hydrogen diffusion in amorphous metals non-Arrhenian?,” International Journal of Hydrogen Energy. 2022. link Times cited: 3 A. Landers et al., “Dynamics and Hysteresis of Hydrogen Intercalation and Deintercalation in Palladium Electrodes: A Multimodal In Situ X-ray Diffraction, Coulometry, and Computational Study,” Chemistry of Materials. 2021. link Times cited: 7 S. Paul, D. Schwen, M. Short, and K. Momeni, “Effect of Irradiation on Ni-Inconel/Incoloy Heterostructures in Multimetallic Layered Composites,” Journal of Nuclear Materials. 2021. link Times cited: 12 X. W. Zhou, N. Bartelt, and R. Sills, “Enabling simulations of helium bubble nucleation and growth: A strategy for interatomic potentials,” Physical Review B. 2021. link Times cited: 5 Abstract: Helium bubbles are a severe form of radiation damage that ha… read more Abstract: Helium bubbles are a severe form of radiation damage that has been frequently observed. It would be possible to understand the complex processes that cause bubble formation if suitable interatomic potentials were available to enable molecular dynamics simulations. In this paper, Pd-H-He embedded-atom method potentials based on both Daw-Baskes and Finnis-Sinclair formalisms have been developed to enable modeling of He bubbles formed by the radioactive decay of tritium in Pd. Our potentials incorporate helium into an existing Pd-H potential while addressing two challenging paradoxes: (a) Interstitial He atoms can dramatically lower their energies by forming dimers and larger clusters in Pd but are only bound by weak van der Waals forces in the gas phase. (b) He atoms diffuse readily in Pd yet significantly distort the Pd lattice with large volume expansions. We demonstrate that both of our potentials reproduce density functional theory results for (b). However, the Daw-Baskes formalism fails to resolve paradox (a) because it cannot reproduce the experimental helium equation of state. We resolved this problem through a modification of the Finnis-Sinclair formalism in which a (fictitious) negative embedding charge density is produced by Pd at the He binding sites. In addition to molecular statics validation of static properties, molecular dynamics simulation tests establish that our Finnis-Sinclair potential leads to the nucleation of helium bubbles from an initial random distribution of helium interstitial atoms. read less D. Chun et al., “Metastable Hexagonal Close-Packed Palladium Hydride in Liquid Cell Transmission Electron Microscopy.” 2020. link Times cited: 0 Abstract: Metastable phases—kinetically favored structures—are ubiqu… read more Abstract: Metastable phases—kinetically favored structures—are ubiquitous in nature. Rather than forming thermodynamically stable ground-state structures, crystals grown from high-energy precursors often initially adopt metastable structures depending on the initial conditions such as temperature, pressure, or crystal size. As the crystals grow further, they typically undergo a series of transformations from metastable to lower-energy phases and ultimately energetically stable phases, as described by Wilhelm Ostwald. Metastable phases, however, sometimes provide superior chemical and physical properties, and hence, discovering and synthesizing novel metastable phases are promising avenues for achieving innovations in materials science. The most common strategy for synthesizing a metastable material involves manipulating thermodynamic conditions such as temperature and pressure during the course of synthesis. However, the search for metastable materials has mainly been heuristic, on the basis of experiences, intuitions, or even speculative predictions. This limitation necessitates the advent of a new paradigm to discover novel metastable phases, i.e., by “rational design and synthesis” instead of a “rule of thumb,” and based on ab initio methods, i.e., the calculation of thermodynamic and kinetic properties of materials with various compositions, crystal structures, and crystal sizes. The design rule is embodied in the discovery of a metastable hexagonal close-packed (HCP) palladium hydride (PdHx), synthesized in a liquid cell environment using a transmission electron microscope (TEM). The metastable HCP structure is stabilized through a unique interplay among the precursor concentrations in the solution: a sufficient supply of hydrogen (H) favors the HCP structure on the sub-nanometer scale, and an insufficient supply of Pd inhibits further growth and subsequent transition toward the thermodynamically stable face-centered cubic (FCC) structure. The crystal structure was modulated (HCP or FCC) by adjusting the H concentration inside the TEM liquid cell, providing strong evidence for the crucial role of the H concentration. Monte Carlo simulations reveal that an unexpected inhomogeneous distribution of interstitial H atoms, distinct from the predominant occupation at the octahedral interstitial sites, is key to stabilizing nanoscale HCP PdHx. Furthermore, insufficient Pd brings a multi-step nucleation and growth pathway, deduced from in situ liquid cell TEM combined with atomic electron tomography, which maintains the metastable phase intact. These findings provide new thermodynamic insights into metastability-engineering strategy to be deployed in discovering new metastable phases. read less M. Alí, E. A. Crespo, M. Ruda, E. Bringa, and S. B. Ramos, “Hydrogen effects on the mechanical properties of nanocrystalline free-standing Palladium thin films,” International Journal of Hydrogen Energy. 2020. link Times cited: 3 V. Dubinko, D. Laptiev, D. Terentyev, S. Dmitriev, and K. Irwin, “Symmetry transformation in Pd quasicrystals upon heating and hydrogenation,” Computational Materials Science. 2020. link Times cited: 0 A. Tehranchi and W. Curtin, “The role of atomistic simulations in probing hydrogen effects on plasticity and embrittlement in metals,” Engineering Fracture Mechanics. 2019. link Times cited: 43 H. N. Pishkenari, F. S. Yousefi, and A. Taghibakhshi, “Determination of surface properties and elastic constants of FCC metals: a comparison among different EAM potentials in thin film and bulk scale,” Materials Research Express. 2018. link Times cited: 22 Abstract: Three independent elastic constants C11, C12, and C44 were c… read more Abstract: Three independent elastic constants C11, C12, and C44 were calculated and compared using available potentials of eight different metals with FCC crystal structure; Gold, Silver, Copper, Nickel, Platinum, Palladium, Aluminum and Lead. In order to calculate the elastic constants, the second derivative of the energy density of each system was calculated with respect to different directions of strains. Each set of the elastic constants of the metals in bulk scale was compared with experimental results, and the average relative error was for each was calculated and compared with other available potentials. Then, using the Voigt-Reuss-Hill method, approximated values for Young and shear moduli and Poisson’s ratio of the FCC metals in the bulk scale were found for each potential. Furthermore, to observe the surface effects on the metals in nanoscale, surface elastic constants of the thin films of the metals have been calculated. In the study of the thin films of materials in nanoscale, the number of surface atoms is considerable compared to all atoms of the object. This leads to an increase in the surface effects, which influence the elastic properties. By considering this fact and employing related definitions and equations, the properties of the thin films of the metals were calculated, and the surface effects for different crystallographic directions were compared. Subsequently, in some cases, comparisons among characteristics of the metals in the thin film and bulk material were made. read less X. W. Zhou, T. Heo, B. Wood, V. Stavila, S. Kang, and M. Allendorf, “Temperature- and concentration-dependent hydrogen diffusivity in palladium from statistically-averaged molecular dynamics simulations,” Scripta Materialia. 2018. link Times cited: 19 X. Sun, P. Ariza, M. Ortiz, and K. G. Wang, “Long-term atomistic simulation of hydrogen absorption in palladium nanocubes using a diffusive molecular dynamics method,” International Journal of Hydrogen Energy. 2018. link Times cited: 11 X. Sun, M. P. Ariza, M. Ortiz, and K. G. Wang, “Acceleration of diffusive molecular dynamics simulations through mean field approximation and subcycling time integration,” J. Comput. Phys. 2017. link Times cited: 9 X. Zhou and J. Song, “Effect of local stress on hydrogen segregation at grain boundaries in metals,” Materials Letters. 2017. link Times cited: 19 X. W. Zhou, V. Stavila, M. Allendorf, T. Heo, B. Wood, and S. Kang, “Molecular Dynamics Studies of Finite-Temperature Elastic Constants of PdHx.,” MRS Advances. 2017. link Times cited: 3 X. Zhou, B. Ouyang, W. Curtin, and J. Song, “Atomistic investigation of the influence of hydrogen on dislocation nucleation during nanoindentation in Ni and Pd,” Acta Materialia. 2016. link Times cited: 29 G. Xu and M. Demkowicz, “Crack healing in nanocrystalline palladium,” Extreme Mechanics Letters. 2016. link Times cited: 7 K. G. Wang, P. Ariza, and M. Ortiz, “Long-term atomistic simulation of hydrogen diffusion in metals,” International Journal of Hydrogen Energy. 2015. link Times cited: 9 S. Debiaggi, E. Crespo, F. U. Braschi, E. Bringa, M. Alí, and M. Ruda, “Hydrogen absorption in Pd thin-films,” International Journal of Hydrogen Energy. 2014. link Times cited: 18 C. Wei, F. Kong, and H. Gong, “Phase stability and elastic property of PdH and PdCuH phases,” International Journal of Hydrogen Energy. 2013. link Times cited: 27 A. Caravella, S. Hara, E. Drioli, and G. Barbieri, “Sieverts law pressure exponent for hydrogen permeation through Pd-based membranes: Coupled influence of non-ideal diffusion and multicomponent external mass transfer,” International Journal of Hydrogen Energy. 2013. link Times cited: 41 H. Ren, X. Yang, Y. Gao, and T.-Y. Zhang, “Solute concentrations and stresses in nanograined H–Pd solid solution,” Acta Materialia. 2013. link Times cited: 9 F. Ma, K. Xu, and P. Chu, “Surface-induced structural transformation in nanowires,” Materials Science & Engineering R-reports. 2013. link Times cited: 24 E. Crespo, M. Ruda, S. Debiaggi, E. Bringa, F. U. Braschi, and G. Bertolino, “Hydrogen absorption in Pd nanoparticles of different shapes,” International Journal of Hydrogen Energy. 2012. link Times cited: 27 B. M. Wong and J. Cordaro, “Electronic Properties of Vinylene-Linked Heterocyclic Conducting Polymers: Predictive Design and Rational Guidance from DFT Calculations,” The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 2011. link Times cited: 57 Abstract: The band structure and electronic properties in a series of … read more Abstract: The band structure and electronic properties in a series of vinylene-linked heterocyclic conducting polymers are investigated using density functional theory (DFT). In order to accurately calculate electronic band gaps, we utilize hybrid functionals with fully periodic boundary conditions to understand the effect of chemical functionalization on the electronic structure of these materials. The use of predictive first-principles calculations coupled with simple chemical arguments highlights the critical role that aromaticity plays in obtaining a low band gap polymer. Contrary to some approaches which erroneously attempt to lower the band gap by increasing the aromaticity of the polymer backbone, we show that being aromatic (or quinoidal) in itself does not ensure a low band gap. Rather, an iterative approach which destabilizes the ground state of the parent polymer toward the aromatic ↔ quinoidal level crossing on the potential energy surface is a more effective way of lowering the band gap in these conjugated systems. Our results highlight the use of predictive calculations guided by rational chemical intuition for designing low band gap polymers in photovoltaic materials. read less X. W. Zhou, F. Doty, and P. Yang, “Atomistic simulation study of atomic size effects on B1 (NaCl), B2 (CsCl), and B3 (zinc-blende) crystal stability of binary ionic compounds,” Computational Materials Science. 2011. link Times cited: 15 E. Crespo, S. Claramonte, M. Ruda, and S. Debiaggi, “Thermodynamics of hydrogen in Pd nanoparticles,” International Journal of Hydrogen Energy. 2010. link Times cited: 18 M. Ruda, E. Crespo, and S. Debiaggi, “Atomistic modeling of H absorption in Pd nanoparticles,” Journal of Alloys and Compounds. 2010. link Times cited: 22 C.-K. Chen and S. Chang, “An investigation of the internal temperature dependence of Pd–Pt cluster beam deposition: A molecular dynamics study,” Applied Surface Science. 2010. link Times cited: 7 H. Kimizuka, B. Thomsen, and M. Shiga, “Artificial neural network-based path integral simulations of hydrogen isotope diffusion in palladium,” Journal of Physics: Energy. 2022. link Times cited: 7 Abstract: The contribution of nuclear quantum effects (NQEs) to the ki… read more Abstract: The contribution of nuclear quantum effects (NQEs) to the kinetics and dynamics of interstitial H isotopes in face-centered cubic Pd was intensively investigated using several path-integral techniques, along with a newly developed machine-learning interatomic potential based on artificial neural networks for Pd–H alloys. The diffusion coefficients (D) of protium, deuterium, and tritium in Pd were predicted over a wide temperature range (50–1500 K) based on quantum transition-state theory (QTST) combined with path-integral molecular-dynamics simulations. The importance of NQEs even at high temperatures was illustrated in terms of the characteristic temperature dependence of the activation free energies for H-isotope migration in Pd. This illuminates the overall picture of anomalous D crossovers among the three H isotopes in Pd. In addition, the D of protium in Pd was directly computed using two approximate quantum-dynamics methods based on Feynman’s path-integral theory, i.e. centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD), in the temperature range 370–1500 K. The D values obtained from the CMD and RPMD simulations were very similar and agreed better with the reported experimental values than the QTST results in this temperature range. Our machine learning-based path-integral calculations elucidate the underlying quantum nature of the ‘reversed S’-type nonlinear behavior of D for the three H isotopes in Pd on the Arrhenius plots. read less K. Nishimura and K. Miyake, “Molecular Dynamics Study on Hydrogen Diffusion in Pd and Pd-Ag Alloys,” Journal of The Society of Materials Science, Japan. 2018. link Times cited: 0 Abstract: Hydrogen diffusion in Pd with various H concentrations and P… read more Abstract: Hydrogen diffusion in Pd with various H concentrations and Pd-Ag alloys with various Ag and H concentrations is investigated using molecular dynamics simulations. At H concentration of 0.5 in Pd, the miscibility gap caused by the spinodal decomposition is observed. The diffusion coefficient of H in Pd is kept constant at H concentration less than 0.1, then increases with increasing H concentration until the phase transition occurs, and after reaching a maximum it decreases with increasing H concentration. The simulations of varying a temperature predict the activation energy for H diffusion of 0.163 eV at H concentration of 0.05, which agrees well with that reported in the literature, and minimum activation energy of 0.144 eV at H concentration of 0.5. Moreover, our results indicate that the addition of Ag to Pd leads to the dissipation of the miscibility gap. The diffusion coefficient of H in Pd-Ag alloys significantly decreases with increasing Ag concentration. The minimum activation energy for H diffusion in Pd-Ag alloys is estimated to be 0.135 eV when Ag and H concentration are 0.1 and 0.5, respectively. read less K. Nishimura and K. Miyake, “The Influence of Dislocations on Hydrogen Diffusion in Palladium,” Journal of The Society of Materials Science, Japan. 2016. link Times cited: 2 Abstract: Understanding the diffusion properties of hydrogen in metals… read more Abstract: Understanding the diffusion properties of hydrogen in metals, especially interactions between hydrogen and lattice defects such as dislocations, is essential in order to improve the performance and reliability of equipment associated with hydrogen. We investigate the effect of edge dislocations on hydrogen diffusion in face-centered-cubic (fcc) metals using molecular dynamics simulations of palladium-hydrogen as a model system. We find that the hydrogen diffusion in a perfect crystal without the dislocations is isotropic, whereas that in a system with the dislocations has anisotropy. In addition, our results predict high hydrogen diffusivity along the dislocation lines in high hydrostatic stress region with high hydrogen density after hydrogen accumulation caused by the interactions between hydrogen atoms and the dislocations. The activation energy of the hydrogen diffusivity in the system with the dislocations is estimated to be 0.10 eV, which is 38 % smaller than that in the perfect crystal. read less K. Nishimura, “Molecular Dynamics Study on Hydrogen Diffusion in Palladium,” Journal of The Society of Materials Science, Japan. 2014. link Times cited: 3 Abstract: 1 緒言近年,化石燃料に依存しない再生可能エネルギーの利用が注目を集めており,実用化を目指して多くの研究開発が行… read more Abstract: 1 緒言近年,化石燃料に依存しない再生可能エネルギーの利用が注目を集めており,実用化を目指して多くの研究開発が行われている.各種の再生可能エネルギーが検討されている中で,水素は電気エネルギーとの等価変換が可能であり,最も有力な候補の一つである.水素の製造・輸送・貯蔵・供給に用いられる水素利用機器の開発において,その性能および信頼性の向上のためには材料中の水素特性の理解が必要不可欠である.特に,金属材料中の水素拡散特性の解明が重要となる.本研究ではパラジウムに着目する.パラジウムおよびパラジウム合金は, 水素利用機器で用いられる水素貯蔵材料 1), 2)や水素透過膜 3), 4)などへの適用が期待されている. しかし,金属材料中の水素の特性に関する基礎的な理解は進んでいない.その一因として,水素は原子半径および質量が小さいために実験による直接観察が難しいことが考えられる.そこで,原子モデルを用いたシミュレーションによる研究が期待されており,いくつかの研究成果が報告されている.分子動力学法によるニッケル中の水素の拡散に関する研究,5), 6)分子静力学法を用いた鉄中の転位と水素の相互作用に関する研究,7), 8)さらに経路積分分子動力学法による鉄中の転位が水素拡散に及ぼす影響に関する研究 9), 10)などが報告されている.本研究で着目するパラジウムについても分子動力学法,11), 12)モンテカルロ法,13), 14)第一原理計算 15)を用いて水素に関連する特性の評価が行われている.Kamakotiらは,第一原理計算によりパラジウムおよびパラジウム合金中の水素拡散の活性化エネルギーを評価し,水素に関連するエネルギーについて議論する際には零点エネルギー補正が重要であることを指摘している.16)しかしながら,パラジウム中の水素拡散に及ぼす圧力およびせん断等の外部負荷応力の影響を調べた研究は少なく,水素利用機器にパラジウムを適用する際に必要となる情報が十分に得られているわけではない. そこで,本研究では,材料中の水素挙動を動的に解析することができる分子動力学シミュレーションを用いて, パラジウム中の水素拡散特性を詳細に検討する.まず, 水素の拡散係数の温度依存性を明らかにし,水素拡散の活性化エネルギーを評価する.次に,水素拡散に及ぼす圧力および純粋せん断の影響を評価する.さらに,系内に存在する格子欠陥が水素の拡散係数に及ぼす影響について検討する. 2 解析方法 2・1 原子間ポテンシャル分子動力学法では,材料は原子の集合体としてモデル化される.それぞれの原子について Newtonの運動方程式を解くことにより,原子運動の時間発展を求めることができる.材料固有の性質は原子間ポテンシャルによって記述される.本研究では,Zhouらによって開発されたパラジウム-水素系の原子埋込み法に基づく原子間ポテンシャル 17)を採用する.本ポテンシャルは,パラジウムの結晶構造(面心立方格子構造),格子定数 (0.389nm), 凝集エネルギー,弾性定数等を再現するようにポテンシャル・パラメータがフィッティングされている.さらに, 様々な組成のパラジウム水素化物 (PdHx) の諸特性も再現できる.Table 1に Zhouらのポテンシャルを用いて算パラジウム中の水素拡散に関する分子動力学シミュレーション西村憲治 Molecular Dynamics Study on Hydrogen Diffusion in Palladium read less B. Yao, Z. R. Liu, and R. F. Zhang, “EAPOTc: An integrated empirical interatomic potential optimization platform for compound solids,” Computational Materials Science. 2022. link Times cited: 1 J.-ping Du, W.-T. Geng, K. Arakawa, J. Li, and S. Ogata, “Hydrogen-Enhanced Vacancy Diffusion in Metals.,” The journal of physical chemistry letters. 2020. link Times cited: 23 Abstract: Vacancy diffusion is fundamental to materials science. Hydro… read more Abstract: Vacancy diffusion is fundamental to materials science. Hydrogen atoms bind strongly to vacancies and are often believed to retard vacancy diffusion. Here, we use a potential-of-mean-force method to study the diffusion of vacancies in Cu and Pd. We find H atoms, instead of dragging, enhance the diffusivity of vacancies due to a positive hydrogen Gibbs excess at the saddle-point: that is, the migration saddle attracts more H than the vacancy ground state, characterized by an activation excess ΓHm ≈ 1 H, together with also-positive migration activation volume Ωm and activation entropy Sm. Thus, according to the Gibbs adsorption isotherm generalized to the activation path, a higher μH significantly lowers the migration free-energy barrier. This is verified by ab initio grand canonical Monte Carlo simulations and direct molecular dynamics simulations. This trend is believed to be generic for migrating dislocations, grain boundaries, and so on that also have a higher capacity for attracting H atoms due to a positive activation volume at the migration saddles. read less I. Hijazi, Y. Zhang, and R. Fuller, “A Simple Palladium Hydride Embedded Atom Method Potential for Hydrogen Energy Applications,” Journal of Energy Resources Technology. 2019. link Times cited: 3 Abstract: When hydrogen is produced from a biomass or coal gasifier, i… read more Abstract: When hydrogen is produced from a biomass or coal gasifier, it is necessary to purify it from syngas streams containing components such as CO, CO2, N2, CH4, and other products. Therefore, a challenge related to hydrogen purification is the development of hydrogen-selective membranes that can operate at elevated temperatures and pressures, provide high fluxes, long operational lifetime, and resistance to poisoning while still maintaining reasonable cost. Palladium-based membranes have been shown to be well suited for these types of high-temperature applications and have been widely utilized for hydrogen separation. Palladium's unique ability to absorb a large quantity of hydrogen can also be applied in various clean energy technologies, like hydrogen fuel cells. In this paper, a fully analytical interatomic embedded atom method (EAM) potential for the Pd-H system has been developed, that is easily extendable to ternary Palladium-based hydride systems, such as Pd-Cu-H and Pd-Ag-H. The new potential has fewer fitting parameters than previously developed EAM Pd-H potentials and is able to accurately predict the cohesive energy, lattice constant, bulk modulus, elastic constants, melting temperature, and the stable Pd-H structures in molecular dynamics (MD) simulations with various hydrogen concentrations. The EAM potential also well predicts the miscibility gap, the segregation of the palladium hydride system into dilute (α), and concentrated (β) phases. read less H. Chauke, M. Mashamaite, R. Modiba, and P. Ngoepe, “Advances in Ti-Based Systems as High Temperature Shape Memory Alloys,” Key Engineering Materials. 2018. link Times cited: 3 Abstract: In this study, we investigate the effect of ternary addition… read more Abstract: In this study, we investigate the effect of ternary addition on the structural, mechanical properties and temperature dependence of Ti-based as potential shape memory alloys using molecular dynamics approach. We found that binary Ti-Pt alloys exhibit shape memory properties and display possible martensitic transformation from B2 to B19 phases. Partial addition with Zr, Co, Pd, Ir showed preferential ternary high temperature shape memory alloys formation of 6.25 at. % X composition (Ti-Pt-X). We found that the equilibrium lattice constants are in better agreement with the available experimental values. The heats of formation and elastic properties reveal possible composition and phases at temperature above 900 K with good shape memory properties. Their structures were confirmed using the X-ray diffraction patterns at different temperatures. read less X. Zhang, M. Wang, R. He, W.-yi Li, and B. Y. Zong, “A phase field model to simulate competitive precipitation of Mg2Sn along the basal or pyramidal habit planes in Mg-2.2Sn-0.1Zn alloy,” Computational Materials Science. 2017. link Times cited: 3 N. V. Ilawe, J. Zimmerman, and B. M. Wong, “Breaking Badly: DFT-D2 Gives Sizeable Errors for Tensile Strengths in Palladium-Hydride Solids.,” Journal of chemical theory and computation. 2015. link Times cited: 72 Abstract: Dispersion interactions play a crucial role in noncovalently… read more Abstract: Dispersion interactions play a crucial role in noncovalently bound molecular systems, and recent studies have shown that dispersion effects are also critical for accurately describing covalently bound solids. While most studies on bulk solids have solely focused on equilibrium properties (lattice constants, bulk moduli, and cohesive energies), there has been little work on assessing the importance of dispersion effects for solid-state properties far from equilibrium. In this work, we present a detailed analysis of both equilibrium and highly nonequilibrium properties (tensile strengths leading to fracture) of various palladium-hydride systems using representative DFT methods within the LDA, GGA, DFT-D2, DFT-D3, and nonlocal vdw-DFT families. Among the various DFT methods, we surprisingly find that the empirically constructed DFT-D2 functional gives extremely anomalous and qualitatively incorrect results for tensile strengths in palladium-hydride bulk solids. We present a detailed analysis of these effects and discuss the ramifications of using these methods for predicting solid-state properties far from equilibrium. Most importantly, we suggest caution in using DFT-D2 (or other coarse-grained parametrizations obtained from DFT-D2) for computing material properties under large stress/strain loads or for evaluating solid-state properties under extreme structural conditions. read less X. W. Zhou and F. Doty, “Embedded-ion method: An analytical energy-conserving charge-transfer interatomic potential and its application to the La-Br system,” Physical Review B. 2008. link Times cited: 30 N. V. Ilawe, M. Groulx, and B. M. Wong, “Density Functional Theory Methods for Computing and Predicting Mechanical Properties.” 2016. link Times cited: 0 C. Zhang, R. Fuller, and I. Hijazi, “Quaternary Hydrides Pd1-y-zAgyCuzHx Embedded Atom Method Potentials for Hydrogen Energy Applications,” Journal of Energy and Power Technology. 2021. link Times cited: 0 Abstract: The Pd-H system has attracted extensive attention. Pd can ab… read more Abstract: The Pd-H system has attracted extensive attention. Pd can absorb considerable amount of H at room temperature, this ability is reversible, so it is suitable for multiple energy applications. Pd-Ag alloys possess higher H permeability, solubility and narrower miscibility gap with better mechanical properties than pure Pd, but sulfur poisoning remains an issue. Pd-Cu alloys have excellent resistance to sulfur and carbon monoxide poisoning and hydrogen embrittlement, good mechanical properties, and broader temperature working environments over pure Pd, but relatively lower hydrogen permeability and solubility than pure Pd and Pd-Ag alloys. This suggests that alloying Pd with Ag and Cu to create Pd-Ag-Cu ternary alloys can optimize the overall performance and substantially lowers the cost. Thus, in this paper, we provide the first embedded atom method potentials for the quaternary hydrides Pd1-y-zAgyCuzHx. The fully analytical potentials are fitted utilizing the central atom method without performing time-consuming molecular dynamics simulations. read less R. A. Ciufo and G. Henkelman, “Embedded atom method potential for hydrogen on palladium surfaces,” Journal of Molecular Modeling. 2020. link Times cited: 3 B. Ma et al., “Effects of Monovacancy and Divacancies on Hydrogen Solubility, Trapping and Diffusion Behaviors in fcc-Pd by First Principles,” Materials. 2020. link Times cited: 5 Abstract: The hydrogen blistering phenomenon is one of the key issues … read more Abstract: The hydrogen blistering phenomenon is one of the key issues for the target station of the accelerator-based neutron source. In the present study, the effect of monovacancies and divacancies defects on the solution, clustering and diffusion behaviors of H impurity in fcc-Pd were studied through first principles calculations. Our calculations prove that vacancies behave as an effective sink for H impurities. We found that, although the H-trap efficiency of the larger vacancy defect was reduced, its H-trap ability strengthened. There is a short-ranged area around the vacancy defects in which H impurities tend to diffuse to vacancy defects, gather and form hydrogen bubbles. Therefore, the characteristic of large vacancy defects formation in materials should be considered when screening anti-blistering materials for neutron-producing targets or when designing radiation resistant composite materials. read less W. Yuan et al., “Atomic-scale selectivity of hydrogen for storage sites in Pd nanoparticles at atmospheric pressure.,” Nanoscale. 2019. link Times cited: 5 Abstract: Hydrogen-storage materials are important carriers for a viab… read more Abstract: Hydrogen-storage materials are important carriers for a viable hydrogen economy. Despite palladium being the most studied storage material, the hydrogen-storage mechanism of Pd remains ambiguous owing to the lack of atomic-scale evidence of the diffusion and storage of H atoms in its lattice. In the study reported here, this classical process was investigated on the atomic scale using an in situ transmission electron microscope equipped with an atmospheric-pressure sample holder. The expansion of the Pd interplanar spacings was found to comprise three distinct stages during the diffusion of H atoms. Moreover, the expansion in d-spacing of Pd{111} was markedly different from that of Pd{220}. First-principles calculations indicate that H atoms mainly occupy the centers of the tetrahedral cages in the Pd unit cells during the diffusion stage, and they eventually occupy the octahedral cage centers in the equilibrium state. Moreover, H atoms were detected in substantially high densities in defects such as stacking faults and twin boundaries. These observations on the preferred hydrogen-storage domains can help clarify the hydrogen-storage mechanism and offer guidelines on the future design of higher-capacity hydrogen-storage materials. read less V. Dubinko, D. Laptev, D. Terentyev, S. Dmitriev, and K. Irwin, “Assessment of discrete breathers in the metallic hydrides,” Computational Materials Science. 2019. link Times cited: 12 X. W. Zhou, M. E. Foster, and R. Sills, “An Fe‐Ni‐Cr embedded atom method potential for austenitic and ferritic systems,” Journal of Computational Chemistry. 2018. link Times cited: 65 Abstract: Fe‐Ni‐Cr stainless‐steels are important structural materials… read more Abstract: Fe‐Ni‐Cr stainless‐steels are important structural materials because of their superior strength and corrosion resistance. Atomistic studies of mechanical properties of stainless‐steels, however, have been limited by the lack of high‐fidelity interatomic potentials. Here using density functional theory as a guide, we have developed a new Fe‐Ni‐Cr embedded atom method potential. We demonstrate that our potential enables stable molecular dynamics simulations of stainless‐steel alloys at high temperatures, accurately reproduces the stacking fault energy—known to strongly influence the mode of plastic deformation (e.g., twinning vs. dislocation glide vs. cross‐slip)—of these alloys over a range of compositions, and gives reasonable elastic constants, energies, and volumes for various compositions. The latter are pertinent for determining short‐range order and solute strengthening effects. Our results suggest that our potential is suitable for studying mechanical properties of austenitic and ferritic stainless‐steels which have vast implementation in the scientific and industrial communities. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. read less I. Hijazi, Y. Zhang, and R. Fuller, “A simple embedded atom potential for Pd-H alloys,” Molecular Simulation. 2018. link Times cited: 3 Abstract: ABSTRACT Metal Hydride systems are an important research top… read more Abstract: ABSTRACT Metal Hydride systems are an important research topic in material science because of their many practical, industrial, and scientific applications. Therefore, the development of reliable and efficient interatomic potentials for metal hydrides systems, to be utilised in molecular simulations, can be of great value in accelerating the research in this field. In this paper, a fully analytical interatomic Embedded Atom Potential (EAM) for the Pd-H system has been developed, that can be easily extended to ternary Palladium-based hydride systems. The new potential has fewer fitting parameters than previously developed EAM Pd-H potentials and can better predict the cohesive energy, lattice constant, bulk modulus, elastic constants, and the stable alloy crystal structures during molecular dynamics (MD) simulations for various hydrogen concentrations. The EAM potential also predicts the miscibility gap, the separation of a Pd-H system to dilute (α) and concentrated (β) phases. read less Y. H. Park and I. Hijazi, “Development of physics based analytical interatomic potential for palladium-hydride,” Journal of Molecular Modeling. 2017. link Times cited: 6 F. Valencia et al., “Hydrogen Storage in Palladium Hollow Nanoparticles,” Journal of Physical Chemistry C. 2016. link Times cited: 26 Abstract: The potential and properties of palladium hollow nanoparticl… read more Abstract: The potential and properties of palladium hollow nanoparticles (hNPs) as a possible H storage material are explored by means of classical molecular dynamics (MD) simulations. First, we study the stability of pure Pd hNPs for different sizes and thicknesses, obtaining good agreement with experimental results for nanometer size Pd hNP. Next we add, every 100 fs, single H atoms into the NP cavity. During the first stages of the simulation, our results show hydride formation on the inner surface, similar to what has been observed in experiments on Pd surfaces and NPs. Formation of the Pd hydride decreases the absorption rate, and H gas is formed inside the cavity. The maximum H gas pressure that is reached is of 7 GPa, before fractures appear in the hNP, and consequently the hNP breaks up. We obtain a maximum H/Pd ratio of 1.21 when H is introduced only inside the cavity. However, when H is deposited both on the inside and outside surfaces, this ratio reaches 1.70, which is 25% larger than previous reports. B... read less L. Hale, J. Zimmerman, and B. M. Wong, “Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys.,” The Journal of chemical physics. 2016. link Times cited: 11 Abstract: Palladium is an attractive material for hydrogen and hydroge… read more Abstract: Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material's structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of material defects, and we compare the material behavior displayed with expectations from experiment and theory. We also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations. read less J. Baker et al., “Hydrogen Effect on Creation of Nanoporous Palladium by Palladium Hydride Wire Explosion.” 2015. link Times cited: 1 Abstract: Nanoporous palladium was created using highly loaded palladi… read more Abstract: Nanoporous palladium was created using highly loaded palladium hydride wires subjected to a fast electrical pulse of energy. The delivered energy was insufficient to melt an unloaded palladium wire. Electrical explosion experiments of palladium hydride wires were performed on single samples at the loading ratios ranging from 0.5 up to 0.96, approaching the highest experimentally achieved loading ratio of 1. It was found that nanoporous palladium was created by pulsing of palladium hydride wires at loading ratios higher than the threshold of 0.6. Each additional increase in the hydrogen loading ratio caused an accompanying increase in the surface area. In contrast, when the hydrogen loading ratio was below 0.6 the wire remained intact and there was no nanoporosity produced. This novel method used a low energy, but high power, fast rise time pulsed power system which is effective in creating nanoporous palladium. read less K.-H. Lin, B. Liao, S. Ju, J.-S. Lin, and J. Hsieh, “Mechanical properties and thermal stability of ultrathin molybdenum nanowires,” RSC Advances. 2015. link Times cited: 2 Abstract: The most stable structures of three ultrathin molybdenum (Mo… read more Abstract: The most stable structures of three ultrathin molybdenum (Mo) nanowires were predicted by the simulated annealing basin-hopping method (SABH) with the penalty algorithm. The predicted structures of Mo nanowires indicate that, at this small scale, they do not possess the BCC configuration found in bulk Mo material. Mechanical properties including the Young's modulus, yielding stress, and strength of these wires were determined by a tensile test after the analysis of the stress–strain profiles. In addition, in order to understand the feasibility of application of these Mo nanowires in nano-devices, their thermal stability was also investigated at room temperature (300 K) by MD simulation. read less J. Baker et al., “Production of nanoporous palladium from a deuterium loaded wire driven by a low energy, fast pulser,” 2014 IEEE International Power Modulator and High Voltage Conference (IPMHVC). 2014. link Times cited: 2 Abstract: A low energy, fast rise time system for pulsing low mass wir… read more Abstract: A low energy, fast rise time system for pulsing low mass wires is presented. The system was used to pulse a deuterium loaded wire using a fast pulse not sufficiently energetic to drive an unloaded wire into vaporization. An element such as palladium, which was studied in these experiments, has the capacity to store deuterium to extremely high concentrations. The pulsed power system will be described, and results will be presented showing the production of nanoporous palladium using a low energy pulsed power system. read less P. Kowalczyk, A. Terzyk, P. A. Gauden, S. Furmaniak, and K. Kaneko, “Toward in silico modeling of palladium-hydrogen-carbon nanohorn nanocomposites.,” Physical chemistry chemical physics : PCCP. 2014. link Times cited: 3 Abstract: We present the first in silico modeling of the Pd-H-single-w… read more Abstract: We present the first in silico modeling of the Pd-H-single-walled carbon nanohorn nanocomposites. Temperature-quench Monte Carlo simulations are used to generate the most stable morphologies of Pd81 clusters (cluster sizes of ∼2 nm) deposited inside the morphologically defective single-walled carbon nanohorns (S. Furmaniak, A. P. Terzyk, K. Kaneko, P. A. Gauden, P. Kowalczyk, T. Itoh, Phys. Chem. Chem. Phys., 2013, 15, 1232-1240). The optimized Pd81-single-walled carbon nanohorn nanocomposites are next used in calculating the H binding energy distributions at 300 K. The most stable positions of H impurity in confined Pd81 clusters are identified, showing subsurface character of H absorption from the dilute H2 gas at 300 K. The H binding energy distribution on the Pd(100) open surface at 300 K is computed and compared with those corresponding to Pd81-single-walled carbon nanohorn nanocomposites. Finally, the impact of the Pd-H short-range order on the H binding energy is explored and critically discussed. read less K.-H. Lin, J.-Y. Li, J.-S. Lin, S. Ju, J.-M. Lu, and J. Hsieh, “Mechanical properties and thermal stability of ultrathin tungsten nanowires,” RSC Advances. 2014. link Times cited: 10 Abstract: The most stable structures of three ultrathin tungsten nanow… read more Abstract: The most stable structures of three ultrathin tungsten nanowires were predicted by the simulated annealing basin-hopping method (SABH) with the penalty algorithm. The predicted structures of tungsten nanowires indicate the tungsten nanowires at this small scale do not possess the B.C.C. configuration in bulk tungsten material. By molecular dynamics (MD) simulation, the mechanical properties including the Young's modulus, yielding stress, and strength of these wires were determined by the tensile test after the analysis of the stress–strain profiles. Besides, in order to understand the feasibility of application of tungsten nanowire on nanodevices, the thermal stability of these ultrathin tungsten nanowires was also investigated at room temperature (300 K) by molecular dynamics (MD). read less L. Hale, B. M. Wong, J. Zimmerman, and X. Zhou, “Atomistic potentials for palladium–silver hydrides,” Modelling and Simulation in Materials Science and Engineering. 2012. link Times cited: 27 Abstract: New embedded-atom method potentials for the ternary palladiu… read more Abstract: New embedded-atom method potentials for the ternary palladium–silver–hydrogen system are developed by extending a previously developed palladium–hydrogen potential. The ternary potentials accurately capture the heat of mixing and structural properties associated with solid solution alloys of palladium–silver. Stable hydrides are produced with properties that smoothly transition across the compositions. Additions of silver to palladium are predicted to alter the properties of the hydrides by decreasing the miscibility gap and increasing the likelihood of hydrogen atoms occupying tetrahedral interstitial sites over octahedral interstitial sites. read less X. Sun, P. Ariza, and K. G. Wang, “DEFORMATION-DIFFUSION COUPLED ANALYSIS OF LONG-TERM HYDROGEN DIFFUSION IN NANOFILMS.” 2016. link Times cited: 4 Abstract: The absorption and desorption of hydrogen in nanomaterials c… read more Abstract: The absorption and desorption of hydrogen in nanomaterials can be characterized by an atomic, deformation-diffusion coupled process with a time scale of the order of seconds to hours. This time scale is beyond the time windows of conventional atomistic computational models such as molecular dynamics (MD) and transition state theory based accelerated MD. In this paper, we present a novel, deformation-diffusion coupled computational model basing on non-equilibrium statistical mechanics, which allows long-term simulation of hydrogen absorption and desorption at atomic scale. Specifically, we propose a carefully designed trial Hamiltonian in order to construct our meanfield based approximation, then apply it to investigate the palladium-hydrogen (Pd-H) system. Specifically, here we combine the meanfield model with a discrete kinetic law for hydrogen diffusion in palladium nanofilms. This combination in practice defines the evolution of hydrogen atomic fractions and lattice constants, which facilitates the characterization of the deformation-diffusion process of hydrogen over both space and time. Using the embedded atom model (EAM) potential, we investigate the deformation-diffusion problem of hydrogen desorption and absorption in palladium nanofilms and compare our results with experiments both in equilibrium and non-equilibrium cases. read less M. Ceriotti, “A novel framework for enhanced molecular dynamics based on the generalized Langevin equation.” 2010. link Times cited: 18 Abstract: The modeling of Brownian motion by Einstein and Langevin, at… read more Abstract: The modeling of Brownian motion by Einstein and Langevin, at the beginning of the past century, can be regarded as start point of the systematic use of stochastic methods in physics and chemistry. Besides the theory of Brownian motion, stochastic methods have been applied to countless applications, including the sampling of canonical, constant-temperature ensemble in molecular dynamics simulations. In the vast majority of cases, the stochastic differential equations which are used as a physical model or as a computational tool are assumed to be Markovian, i.e. they are able to predict the stochastic evolution of the system based on a knowledge of its state at a single instant. On the other hand, many important developments can be derived by removing this assumption. In the Mori-Zwanzig theory, for instance, when one integrates out part of the dynamical variables from a Hamiltonian system, a non-Markovian stochastic equation for the remaining degrees of freedom arises, which contains finite-memory friction and noise. By changing the properties of the memory in this generalized Langevin equation (GLE), one can greatly influence the static and dynamic properties. In this thesis we developed a robust and flexible framework for exploiting this class of stochastic differential equations in order to enhance and modify almost at will the properties of a molecular dynamics trajectory. We begin by mapping the non-Markovian dynamics onto a Markovian one in an extended phase-space, as this is more convenient for both simulations and analytical derivations. We then show how a number of static and dynamic properties can be computed exactly in the case of a harmonic oscillator and how the predictions in this limit compare with the behavior of a real system. By performing a fitting procedure, we can then generate sets of parameters that impart to the stochastic dynamics the properties which are best suited to the sampling problem. When a set of independent GLEs is applied to the Cartesian coordinates of an ensemble of coupled oscillators, the response is as if the stochastic terms had been applied in normal mode representation. This is a consequence of the linear nature of the generalized Langevin equation we employ. This feature allows us to tune the properties as a function of the vibrational frequency of the (quasi-)harmonic modes, without the need to know any frequency and displacement pattern explicitly. This property has allowed us to develop and demonstrate many different applications. For instance, one can either enhance or degrade the efficiency of sampling of selected normal modes in constant-temperature simulations. One can then increase read less S. Winczewski, J. Dziedzic, and J. Rybicki, “Central-force decomposition of spline-based modified embedded atom method potential,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 0 Abstract: Central-force decompositions are fundamental to the calculat… read more Abstract: Central-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in systems treated with this novel class of empirical potentials. We briefly discuss the properties of the obtained decomposition and highlight further computational techniques that can be expected to benefit from the results of this work. To demonstrate the practicability of the derived expressions, we apply them to calculate stress fields due to an edge dislocation in bcc Mo, comparing their predictions to those of linear elasticity theory. read less
Funding	Not available

Short KIM ID The unique KIM identifier code.	MO_114797992931_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.	EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000
DOI	10.25950/c577c984 https://doi.org/10.25950/c577c984 https://commons.datacite.org/doi.org/10.25950/c577c984
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 EAM_Dynamo__MD_120291908751_005
Driver	EAM_Dynamo__MD_120291908751_005
KIM API Version	2.0
Potential Type	eam

Verification Check Dashboard

(Click here to learn more about Verification Checks)

Grade	Name	Category	Brief Description	Full Results	Aux File(s)
P All elements claimed by model are supported in at least one of the tested configurations.	vc-species-supported-as-stated	mandatory	The model supports all species it claims to support; see full description.	Results	Files
P Periodic boundary conditions were correctly supported for all configurations that the model was able to compute.	vc-periodicity-support	mandatory	Periodic boundary conditions are handled correctly; see full description.	Results	Files
P Model energy has permutation symmetry for all configurations the model was able to compute.	vc-permutation-symmetry	mandatory	Total energy and forces are unchanged when swapping atoms of the same species; see full description.	Results	Files
B The letter grade B was assigned because the normalized error in the computation was 2.05015e-07 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.	Results	Files
F The model is C^0 continuous. This means that the model has continuous energy, but a discontinuous first derivative.	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 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.	Results	Files
P Model energy has inversion symmetry for all configurations the model was able to compute.	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 No memory leak detected.	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 All threads give identical results for tested case. Model appears to be thread-safe.	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 Unit conversion successful	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

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: Pd

Species: H

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: Pd

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: H

Species: Pd

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.

Species: Pd

Species: H

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: H

Species: Pd

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: Pd

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: Pd

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: Pd

Species: H

Cubic Crystal Basic Properties Table

Species: H

Species: Pd

Tests

CohesiveEnergyVsLatticeConstant__TD_554653289799_003

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	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 Pd v004	view	2715
Cohesive energy versus lattice constant curve for diamond Pd v004	view	2871
Cohesive energy versus lattice constant curve for fcc Pd v004	view	2646
Cohesive energy versus lattice constant curve for sc Pd v004	view	2805

ElasticConstantsCubic__TD_011862047401_006

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	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 H at zero temperature v006	view	2239
Elastic constants for bcc Pd at zero temperature v006	view	6590
Elastic constants for fcc H at zero temperature v006	view	1919
Elastic constants for fcc Pd at zero temperature v006	view	1855
Elastic constants for sc H at zero temperature v006	view	6462
Elastic constants for sc Pd at zero temperature v006	view	1599

ElasticConstantsHexagonal__TD_612503193866_004

Elastic constants for hexagonal crystals at zero temperature v004

Creators: Junhao Li
Contributor: jl2922
Publication Year: 2019
DOI: https://doi.org/10.25950/d794c746

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 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 hcp H at zero temperature v004		view	2101
Elastic constants for hcp Pd at zero temperature v004		view	1401

EquilibriumCrystalStructure__TD_457028483760_002

Equilibrium structure and energy for a crystal structure at zero temperature and pressure v002

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.

Test	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 crystal structure and energy for H in AFLOW crystal prototype A_cI2_229_a v002	view	55595
Equilibrium crystal structure and energy for H in AFLOW crystal prototype A_hP2_194_c v002	view	149450
Equilibrium crystal structure and energy for H in AFLOW crystal prototype A_hP4_194_f v002	view	53894
Equilibrium crystal structure and energy for HPd in AFLOW crystal prototype AB_cF8_225_a_b v002	view	81719

EquilibriumCrystalStructure__TD_457028483760_003

Equilibrium structure and energy for a crystal structure at zero temperature and pressure v003

Creators:
Contributor: ilia
Publication Year: 2025
DOI: https://doi.org/10.25950/866c7cfa

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.

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 crystal structure and energy for Pd in AFLOW crystal prototype A_cF4_225_a v003		view	180238

GrainBoundaryCubicCrystalSymmetricTiltRelaxedEnergyVsAngle__TD_410381120771_003

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	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 fcc Pd v000	view	5175742
Relaxed energy as a function of tilt angle for a 110 symmetric tilt grain boundary in fcc Pd v000	view	14128952
Relaxed energy as a function of tilt angle for a 111 symmetric tilt grain boundary in fcc Pd v000	view	8406651
Relaxed energy as a function of tilt angle for a 112 symmetric tilt grain boundary in fcc Pd v000	view	32252258

LatticeConstantCubicEnergy__TD_475411767977_007

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	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 H v007	view	1759
Equilibrium zero-temperature lattice constant for bcc Pd v007	view	1823
Equilibrium zero-temperature lattice constant for diamond H v007	view	2975
Equilibrium zero-temperature lattice constant for diamond Pd v007	view	2239
Equilibrium zero-temperature lattice constant for fcc H v007	view	2975
Equilibrium zero-temperature lattice constant for fcc Pd v007	view	1823
Equilibrium zero-temperature lattice constant for sc H v007	view	2175
Equilibrium zero-temperature lattice constant for sc Pd v007	view	1823

LatticeConstantHexagonalEnergy__TD_942334626465_005

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 H v005		view	22604
Equilibrium lattice constants for hcp Pd v005		view	18178

LinearThermalExpansionCoeffCubic__TD_522633393614_002

Linear thermal expansion coefficient of cubic crystal structures v002

Creators:
Contributor: mjwen
Publication Year: 2024
DOI: https://doi.org/10.25950/9d9822ec

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 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)
Linear thermal expansion coefficient of fcc Pd at 293.15 K under a pressure of 0 MPa v002		view	306777

PhononDispersionCurve__TD_530195868545_004

Phonon dispersion relations for an fcc lattice v004

Creators: Matt Bierbaum
Contributor: mattbierbaum
Publication Year: 2019
DOI: https://doi.org/10.25950/64f4999b

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)
Phonon dispersion relations for fcc Pd v004		view	53198

StackingFaultFccCrystal__TD_228501831190_002

Stacking and twinning fault energies of an fcc lattice at zero temperature and pressure v002

Creators:
Contributor: SubrahmanyamPattamatta
Publication Year: 2019
DOI: https://doi.org/10.25950/b4cfaf9a

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)
Stacking and twinning fault energies for fcc Pd v002		view	3040043

SurfaceEnergyCubicCrystalBrokenBondFit__TD_955413365818_004

High-symmetry surface energies in cubic lattices and broken bond model v004

Creators: Matt Bierbaum
Contributor: mattbierbaum
Publication Year: 2019
DOI: https://doi.org/10.25950/6c43a4e6

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 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)
Broken-bond fit of high-symmetry surface energies in fcc Pd v004		view	26199

VacancyFormationEnergyRelaxationVolume__TD_647413317626_001

Monovacancy formation energy and relaxation volume for cubic and hcp monoatomic crystals v001

Creators:
Contributor: efuem
Publication Year: 2023
DOI: https://doi.org/10.25950/fca89cea

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)
Monovacancy formation energy and relaxation volume for fcc Pd		view	374581

VacancyFormationMigration__TD_554849987965_001

Vacancy formation and migration energies for cubic and hcp monoatomic crystals v001

Creators:
Contributor: efuem
Publication Year: 2023
DOI: https://doi.org/10.25950/c27ba3cd

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)
Vacancy formation and migration energy for fcc Pd		view	2594681

Errors

ElasticConstantsCubic__TD_011862047401_006

Test	Error Categories	Link to Error page
Elastic constants for diamond H at zero temperature v001	other	view
Elastic constants for diamond Pd at zero temperature v001	other	view

EquilibriumCrystalStructure__TD_457028483760_002

Test	Error Categories	Link to Error page
Equilibrium crystal structure and energy for H in AFLOW crystal prototype A_tP1_123_a v002	other	view

LatticeConstantCubicEnergy__TD_475411767977_006

Test	Error Categories	Link to Error page
Equilibrium zero-temperature lattice constant for diamond H	other	view

No Driver

Verification Check	Error Categories	Link to Error page
MemoryLeak__VC_561022993723_004	other	view

Files

CMakeLists.txt
LICENSE
PdH_Zhou_June29_2007_2.eam.alloy
kimprovenance.edn
kimspec.edn

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EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000.txz	Tar+XZ	Linux and OS X archive
EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000.zip	Zip	Windows archive

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This Model requires a Model Driver. Archives for the Model Driver EAM_Dynamo__MD_120291908751_005 appear below.

EAM_Dynamo__MD_120291908751_005.txz	Tar+XZ	Linux and OS X archive
EAM_Dynamo__MD_120291908751_005.zip	Zip	Windows archive

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EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000

Verification Check Dashboard

Visualizers (in-page)

BCC Lattice Constant

Cohesive Energy Graph

Diamond Lattice Constant

Dislocation Core Energies

FCC Elastic Constants

FCC Lattice Constant

FCC Stacking Fault Energies

FCC Surface Energies

SC Lattice Constant

Cubic Crystal Basic Properties Table

Tests

Errors

Files

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