AndreaBozzo/ceres-open-data-index huggingface dataset:
Solute strengthening of prism edge dislocations in Mg alloys

The poor ductility of hcp Mg is attributed to the low activity of non-basal slip systems and so activation of prismatic slip can aid ductility in rolled sheets by providing three additional  Burgers vector slip systems.  Experimental studies show that dilute additions of alloying elements such as Zn and Al leads to softening of prismatic slip at low temperatures but strengthening at higher temperatures.  Here, the role of solute strengthening of prismatic edge dislocations is investigated as a possible explanation for the higher-T strengthening.  Mg-Zn is studied using first-principles inputs in a parameter-free solute strengthening theory.  First-principles DFT is necessary to accurately assess the strong solute chemical interaction energies in the core of the compact edge dislocation.   Such calculations are subtle due to motion of the dislocation in the presence of the solute, and methods to obtain reliable results with acceptable computational cost are discussed.   While interaction energies of Zn in the prism edge core can be quite large (+/- 0.34 eV), the edge solute strengthening of prismatic slip in dilute Mg-Zn remains well below experiments at high temperatures.  However, the large difference (0.68 eV) in Zn/dislocation interaction energies across the core of the edge dislocation suggests strengthening by dynamic strain aging as an explanation for the higher-T strengthening.

Tags: dft, edge-solute-strengthening, marvel, mg-zn, prismatic-slip, solutedislocation-interaction-energy
Learning a reactive potential for silica-water through uncertainty attribution

The reactivity of silicates in aqueous solution is relevant to various chemistries ranging from silicate minerals in geology, to the C-S-H phase in cement, nanoporous zeolite catalysts, or highly porous precipitated silica. While simulations of chemical reactions can provide insight at the molecular level, balancing accuracy and scale in reactive simulations in the condensed phase is a challenge. Here, we demonstrate how a machine-learning reactive interatomic potential can accurately capture silicate-water reactivity. The model was trained on a new dataset comprising 400,000 energies and forces of molecular clusters at the 𝜔-B97XD\def2-TVZP level. To ensure the robustness of the model, we introduce a new and general active learning strategy based on the attribution of the model uncertainty, that automatically isolates uncertain regions of bulk simulations to be calculated as small-sized clusters. Our trained potential is found to reproduce static and dynamic properties of liquid water and solid crystalline silicates, despite having been trained exclusively on cluster data. Furthermore, we utilize enhanced sampling simulations to recover the self-ionization reactivity of water accurately, and the acidity of silicate oligomers, and lastly study the silicate dimerization reaction in a water solution at neutral conditions and find that the reaction occurs through a flanking mechanism.

Tags: active-learning, chemical-reactions, free-energy, neural-network-potential, silicates
Auxetic polymer networks: The role of crosslinking, density, and disorder

Low-crosslinked polymer networks have recently been found to behave auxetically when subjected to small tensions, that is, their Poisson's ratio ν becomes negative. In addition, for specific state points, numerical simulations revealed that diamond-like networks reach the limit of mechanical stability, exhibiting values of ν = −1, a condition that we define as hyper-auxeticity. This behavior is interesting per se for its consequences in materials science but is also appealing for fundamental physics because the mechanical instability is accompanied by evidence of criticality. In this work, we deepen our understanding of this phenomenon by performing a large set of equilibrium and stress–strain simulations in combination with phenomenological elasticity theory. The two approaches are found to be in good agreement, confirming the above results. We also extend our investigations to disordered polymer networks and find that the hyper-auxetic behavior also holds in this case, still manifesting a similar critical-like behavior as in the diamond one. Finally, we highlight the role of the number density, which is found to be a relevant control parameter determining the elastic properties of the system. The validity of the results under disordered conditions paves the way for an experimental investigation of this phenomenon in real systems, such as hydrogels.

Tags: auxetic-materials, elasticity, hydrogels
Identifying the structure of supported metal catalysts using vibrational fingerprints from ab initio nanoscale models

The anharmonic infrared spectrum of adsorbed CO is simulated using density functional theory (DFT) to gain insight into the nature of Pd nanoparticles (NPs) supported on ceria. The authors systematically determine how the simulated infrared spectra are affected by CO coverage, NP size (0.5–1.5 nm), NP morphology (octahedral, icosahedral), and metal-support contact angle, by exploring a diversity of realistic models inspired by ab initio molecular dynamics.

Tags: carbon-monoxide, ceria, infrarred, palladium, spectroscopy
Oxidation of interfacial cobalt controls the pH-dependence of the oxygen evolution reaction

Transition metal oxides (e.g., cobalt oxides) often undergo a dynamic surface reconstruction under oxygen evolution reaction (OER) conditions to form the active state, which differs in response to the electrolyte pH. The resulting pH-dependency of OER activity is commonly observed but poorly understood. Herein, we demonstrate that operando X-ray absorption spectroscopy (XAS) characterization enables tracking of the Co oxidation transformation at different pH-directed (hydr)oxide/electrolyte interfaces. Combined with in situ electrochemical analyses, correlations between Co redox dynamics, flat band potential and Co oxidation transformations are established to explain the pH-dependency of OER activity. In alkaline environments, the low flat band potential allows a low-potential Co redox transformation, which in turns favors surface reconstruction. In neutral and acidic environments, an anodic shift of the Co redox transformation increases the OER overpotential, particularly in an acidic environment. The largest OER overpotential, in a neutral environment, is further attributable to the poor polarizability of Co atoms and the slowest Co oxidation transformation with respect to the change in applied potential (or OER current). These findings reveal that the Co oxidation transformation at the interface is the factor directly determining the pH-dependency of OER activity, therefore providing insight into designing efficient OER catalysts in different pH environments.

Tags: cobalt-oxides, electrocatalytic-interface, operando-x-ray-adsorption-spectroscopy, oxygen-evolution-reaction
Machine learning enables the discovery of 2D Invar and anti-Invar monolayers

Materials demonstrating positive thermal expansion (PTE) or negative thermal expansion (NTE) are quite common, whereas those exhibiting zero thermal expansion (ZTE) are notably scarce. In this work, we identify the mechanical descriptors, namely in-plane tensile stiffness and out-of-plane bending stiffness, that can effectively classify PTE and NTE 2D crystals. By utilizing high throughput calculations and the state-of-the-art symbolic regression method, these descriptors aid in the discovery of ZTE or 2D Invar monolayers with the linear thermal expansion coefficient (LTEC) within ±2×10⁻⁶ K⁻¹ in the middle range of temperatures. Additionally, the descriptors assist the discovery of large PTE and NTE 2D monolayers with the LTEC larger than ±15×10⁻⁶ K⁻¹, which are so-called 2D anti-Invar monolayers. Advancing our understanding of materials with exceptionally low or high thermal expansion is of substantial scientific and technological interest, particularly in developing next-generation electronics at the nanometer even Ångstrom scale.

Tags: 2d-materials, bending-stiffness, linear-coefficient-of-thermal-expansion, machine-learning, symbolic-regression, thermal-expansion, zero-thermal-expansion
Comparative study of defects in graphene flake grown on amorphous and crystalline copper surfaces

We performed a computational study using Density Functional Theory calculations on a copper-graphene system. A global minima search was performed using the Minima Hopping algorithm to find multiple graphene isomers that can appear on different substrates. As a model of copper substrate, we used a 112 copper atom cluster and as a model of graphene flake, we used 40 carbon atoms on top of the copper surface. The system was placed in vacuum to guarantee no interaction between images.

The dataset contains coordinates of graphene flake isomers on crystalline and amorphous Cu substrates.

Tags: copper, density-functional-theory, graphene, graphene-growth, metal-substrate
Ge(110) c(8×10) reconstructions stabilized by vibrations

Determining the atomic structure of a surface is essential for reliable simulations and in-depth exploration of chemical and atomic-scale physical processes. Using Ge(110) c(8×10) as a case study, this work employs Density Functional Theory (DFT) calculations to examine the role of vibrational entropy in surface reconstruction stability. The Ge(110) c(8×10) unit cell consists of interstitial-based pentamers (Universal Building Block model, UBB) interspersed with regions appearing in STM images as unreconstructed. DFT calculations predict that adding more pentamers lowers the surface energy, contradicting experimental findings. This discrepancy is resolved when vibrational entropy is accounted for and sur-face divacancies are introduced in addition to the UBB pentamers. These divacancies are similar to those proposed earlier in the Tetramer-Heptagonal and Tetragonal Ring (THTR) reconstruction model. The nearest neighbors of the vacancy sites are rebonded as on monatomic step edges. The differences in the vibrational entropy contributed by pentamers, divacancies, and unreconstructed surface stabilize Ge(110) c(8×10) reconstructions with the pentamer density observed experimentally. The presence of divacancies is conceptually consistent with the presence of monatomic steps in Ge(110) "16×2", the most stable reconstruction of this surface.

Tags: dft, ge110-surface-reconstruction, pbe, rvv10
Spin-dependent interactions in orbital-density-dependent functionals: non-collinear Koopmans spectral functionals

The presence of spin-orbit coupling or non-collinear magnetic spin states can have dramatic effects on the ground-state and spectral properties of materials, in particular on the band structure. Here, we develop non-collinear Koopmans-compliant functionals based on Wannier functions and density-functional perturbation theory, targeting accurate spectral properties in the quasiparticle approximation. Our non-collinear Koopmans-compliant theory involves functionals of four-component orbitals densities, that can be obtained from the charge and spin-vector densities of Wannier functions. We validate our approach on four emblematic non-magnetic and magnetic semiconductors where the effect of spin-orbit coupling goes from small to very large: the III-IV semiconductor GaAs, the transition-metal dichalcogenide WSe₂, the cubic perovskite CsPbBr₃, and the ferromagnetic semiconductor CrI₃. 
The predicted band gaps are comparable in accuracy to state-of-the-art many-body perturbation theory and include spin-dependent interactions and screening effects that are missing in standard diagrammatic approaches based on the random phase approximation. While the inclusion of orbital- and spin-dependent interactions in many-body perturbation theory requires self-screening or vertex corrections, they emerge naturally in the Koopmans-functionals framework.

Tags: marvelp4, metal-halide-perovskite, non-collinear-magnetism, snsf, spectral-functionals, spin-dependent-interactions, spin-orbit-coupling, spin-torque, transition-metal-dichalcogenide
From Methane to Methanol: Pd-iC-CeO2 Catalysts Engineered for High Selectivity via Mechano-Chemical Synthesis

In the pursuit of selective conversion of methane directly to methanol in the liquid phase, a common challenge is the concurrent formation of undesirable liquid oxygenates or combustion byproducts. However, we demonstrate that monometallic Pd-CeO2 catalysts, modified by carbon, created by a simple mechanochemical synthesis method exhibit 100% selectivity towards methanol at 75°C, using hydrogen peroxide as oxidizing agent. The solvent-free synthesis yields a distinctive Pd-iC-CeO2 interface, where interfacial carbon (iC) modulates metal-oxide interactions and facilitates tandem methane activation and peroxide decomposition, thus resulting in an exclusive methanol selectivity of 100% with a rate of 117 µmol/gcat at 75°C. Notably, solvent interactions of H2O2 (aq) were found to be critical for methanol selectivity through a DFT-simulated Eley-Rideal-like mechanism. This mechanism uniquely enables the direct conversion of methane into methanol via a solid-liquid-gas process.

Tags: ch3oh, ch4, eley-rideal-mechanism, h2o2, pdcceo2, pdceo2
Evolving scattering networks for material classification, stealthy hyperuniform shielding, and preferential attachment

The design of stealthy hyperuniform (SHU) materials has been a critical topic in realizing bandgap materials without crystalline order. Most previous approaches to constructing SHU materials, such as the collective coordinate method, have assumed the closed system, maintaining the number of particles inside a system during the design process. Here, I develop the concept of evolving wave networks, allowing for the open-system design of disordered materials based on the evolution process. The programs are applied to introduce the concept of evolving wave networks (Code_Set_Fig_2), classify material states according to network parameters (Code_Set_Fig_3), generate the stealthy hyperuniformity (SHU) shielding of existing materials (Code_Set_Fig_4), and realize preferential attachment in evolving wave networks (Code_Set_Fig_5).

Tags: disordered-material, evolution, network, scattering
Evolving scattering networks for material classification, stealthy hyperuniform shielding, preferential attachment, and material phase diagram

The design of stealthy hyperuniform (SHU) materials has been a critical topic in realizing bandgap materials without crystalline order. Most previous approaches to constructing SHU materials, such as the collective coordinate method, have assumed the closed system, maintaining the number of particles inside a system during the design process. Here, I develop the concept of evolving wave networks, allowing for the open-system design of disordered materials based on the evolution process. The programs are applied to introduce the concept of evolving wave networks (Code_Set_Fig_2), classify material states according to network parameters (Code_Set_Fig_3), generate the stealthy hyperuniformity (SHU) shielding of existing materials (Code_Set_Fig_4), realize preferential attachment in evolving wave networks (Code_Set_Fig_5), and obtain the following phase diagram of disordered materials (Code_Set_Fig_6).

Tags: disordered-material, evolution, network, scattering
Single-site DFT+DMFT for vanadium dioxide using bond-centered orbitals

We present a combined density-functional theory and single-site dynamical mean-field theory (DMFT) study of vanadium dioxide (VO₂) using an unconventional set of bond-centered orbitals as the basis of the correlated subspace. VO₂ is a prototypical material undergoing a metal-insulator transition (MIT), hosting both intriguing physical phenomena and the potential for industrial applications. With our choice of correlated subspace basis, we investigate the interplay of structural dimerization and electronic correlations in VO₂ in a computationally cheaper way compared to other state-of-the-art methods, such as cluster DMFT. Our approach allows us to treat the rutile and M1 monoclinic VO₂ phases on an equal footing and to vary the dimerizing distortion continuously, exploring the energetics of the transition between the two phases. The choice of basis presented in this work hence offers a complementary view on the long-standing discussion of the MIT in VO₂ and suggests possible future extensions to other similar materials hosting molecular-orbital-like states.

Tags: dft, dftdmft, vo2
Topological magnons driven by the Dzyaloshinskii-Moriya interaction in the centrosymmetric ferromagnet Mn₅Ge₃

The phase of the quantum-mechanical wave function can encode a topological structure with wide-ranging physical consequences, such as anomalous transport effects and the existence of edge states robust against perturbations. While this has been exhaustively demonstrated for electrons, properties associated with the elementary quasiparticles in magnetic materials are still underexplored. Here, we show theoretically and via inelastic neutron scattering experiments that the bulk ferromagnet Mn₅Ge₃ hosts gapped topological Dirac magnons. Although inversion symmetry prohibits a net Dzyaloshinskii-Moriya interaction in the unit cell, it is locally allowed and is responsible for the gap opening in the magnon spectrum. This gap is predicted and experimentally verified to close by rotating the magnetization away from the c-axis. Hence, Mn₅Ge₃ is the first realization of a gapped Dirac magnon material in three dimensions. Its tunability by chemical doping or by thin film nanostructuring defines an exciting new platform to explore and design topological magnons.

Tags: dzyaloshinskii-moriya-interaction, inelastic-neutron-scattering, marvel, spin-waves, topological-magnon
Expanding density-correlation machine learning representations for anisotropic coarse-grained particles

This record contains three datasets and the scripts used to generate figures in "Expanding density-correlation machine learning representations for anisotropic coarse-grained particles." This paper explores the theory and implementation of machine-learning descriptors for ellipsoidal bodies, extending the popular "Smooth Overlap of Atomic Positions" (SOAP) formalism. These case studies serve to demonstrate the different use cases of this technology.  The three datasets are:
- Generated configurations of nematic and smectic liquid crystal systems, with a range of orientational order, characterized by the nematic order parameter
- Dimers of (1, 1.5, 2) ellipsoids at different interaction cutoffs and rotations, with computed Gay-Berne type energies
- Crystalline configurations of planar benzene molecules, with energetics computed  using QuantumEspresso v7.046 using Perdew–Burke–Ernzerhof (PBE) pseudopotentials and cutoff parameters reported by Prandini et al.,  Grimme D3-dispersion correction, and a 3 × 3 Monkhorst–Pack k-point grid.

Tags: benzene, liquid-crystals, machine-learning, methods, quantum-espresso
Understanding imidazolium-based ionic liquids role in the CO₂ electroreduction reaction: experimental and theoretical study

Seven imidazolium-based ionic liquids (ILs) with different anions and cations were investigated as catholytes for the CO₂ electrocatalytic reduction to CO over silver. A significant activity and stability, but different selectivities for CO₂ reduction or the side H₂ evolution were observed. Density functional theory results show that the role of the IL anions is to tune the ratio between the CO₂ captured and electrochemically converted. Acetate anions (being strong Lewis bases) are more prone to CO₂ capture, enhancing H₂ evolution, while fluorinated anions (being weaker Lewis bases) favour the CO₂ electroreduction. Differently from the hydrolytically unstable 1-butyl-3-methylimidazolium tetrafluoroborate, 1-Butyl-3-Methylimidazolium Triflate was the most promising IL showing the highest Faradaic efficiency to CO (>95%), up to 8h of stable operation at high current rates (-20mA & -60 mA).  
These results open the way for a strategic selection of the most suitable IL for the CO₂ electroreduction and its future process scale-up.

Tags: dft, experimental, free-energy, quantum-espresso
Principles of isomer stability in small clusters

In this work we study isomers of several representative small clusters to find principles for their stability. Our conclusions about the principles underlying the structure of clusters are based on a huge database of 44'000 isomers generated for 59 different clusters on the density functional theory level by Minima Hopping. We explore the potential energy surface of small neutral, anionic and cationic isomers, moving left to right across the third period of the periodic table and varying the number of atoms n and the cluster charge state q (X^q_n, with X={Na, Mg, Al, Si, Ge}, q=-1,0,1,2). We use structural descriptors such as bond lengths and atomic coordination numbers, the surface to volume ratios and the shape factor as well as electronic descriptors such as shell filling and hardness to detect correlations with the stability of clusters. The isomers of metallic clusters are found to be structure seekers with a strong tendency to adopt compact  shapes. However certain numbers of atoms can suppress the formation of a nearly spherical metallic clusters. Small non-metallic clusters typically also do not adopt compact spherical shapes for their lowest energy structures. In both cases spherical jellium models are not any more applicable. Nevertheless for many  structures, that have frequently a high degree of symmetry, the Kohn-Sham eigenvalues are bunched into shells and if the available electrons can completely fill such shells, a particularly stable structure can result. We call such a cluster whose shape gives rise to shells that can be completely filled by the number of available electrons an optimally matched cluster, since both the structure and the number of electrons must be special and match. In this way we can also explain the stability trends for covalent silicon and germanium cluster isomers, whose stability was previously explained by the presence of certain structural motifs. Thus we propose a unified framework to explain trends in the stability of isomers and to predict their structure for a wide range of small clusters.

This data record contains structure coordinates (compressed file all_minima_xyz_structures.tar.gz) of all minima found by the minima hopping method for all neutral and charged clusters, that are 43606 different structures. The python dictionary all_minima_names.npy stores all minima names. The python dictionary all_minima_data.npy stores all structural and electronic properties calculated for all minima. The jupyter notebook all_minima_data_analysis.ipynb helps the reading of the all_minima_names.npy and all_minima_data.npy python dictionaries.

Tags: atomic-clusters, cscs, dft, snsf