AndreaBozzo/ceres-open-data-index huggingface dataset:
From organic fragments to photoswitchable catalysts: the off-on structural repository for transferable kernel-based potentials

Structurally and conformationally diverse databases are needed to train accurate neural networks or kernel-based potentials capable of exploring the complex free energy landscape of flexible functional organic molecules. Curating such databases for species beyond "simple" drug-like compounds or molecules comprised of well-defined building blocks (e.g., peptides) is challenging, as it requires thorough chemical space mapping and evaluation of both chemical and conformational diversity. Here, we introduce the OFF–ON (Organic Fragments From Organocatalysts that are Non-modular) database, a repository of 7,869 equilibrium and 67,457 non--equilibrium geometries of organic compounds and dimers aimed at describing conformationally flexible functional organic molecules, with an emphasis on photoswitchable organocatalysts. The relevance of this database is then demonstrated by training a Local Kernel Regression model on a low-cost semiempirical baseline and comparing it with a PBE0-D3 reference for several known catalysts, notably the free energy surfaces of exemplary photoswitchable organocatalysts. Our results demonstrate that the OFF–ON dataset offers reliable predictions for simulating the conformational behavior of virtually any (photoswitchable) organocatalyst or organic compound comprised of H, C, N, O, F, and S atoms, thereby opening a computationally feasible route to explore complex free energy surfaces in order to rationalize and predict catalytic behavior.

Tags: free-energy, machine-learning, photoswitchable-organocatalyst
Hydrodynamic finite-size scaling of the thermal conductivity in glasses

In the past few years, the theory of thermal transport in amorphous solids has been substantially extended beyond the Allen-Feldman model. The resulting formulation, based on the Green-Kubo linear response or the Wigner-transport equation, bridges this model for glasses with the traditional Boltzmann kinetic approach for crystals. The computational effort required by these methods usually scales as the cube of the number of atoms, thus severely limiting the size range of computationally affordable glass models. Leveraging hydrodynamic arguments, we show how this issue can be overcome through a simple formula to extrapolate a reliable estimate of the bulk thermal conductivity of glasses from finite models of moderate size. We showcase our findings for realistic models of paradigmatic glassy materials.
This repository contains example inputs to compute the hydrodynamic extrapolation of the thermal conductivity of glasses.
Explicit examples are for amorphous silicon. Optimized atomic configurations are provided also for amorphous silica and silicon carbide.

Tags: amorphous-solids, glasses, max, size-effects, thermal-transport
Incompleteness of graph neural networks for points clouds in three dimensions

Graph neural networks are a popular deep-learning architecture in applications to materials and molecules, and the most widespread implementations rely on interatomic distances as geometric descriptors. Unfortunately, GNNs based on distances are not complete, i.e. there are geometries, corresponding to molecules and/or periodic structures, that are indistinguishable by the GNN. For these, the corresponding machine-learning models will be unable to learn differences in the properties of the "degenerate" structures. This dataset contains a collection of molecular and solid structures that cannot be discriminated by distance-based graph neural networks, together with example code showing how to parse them and use to demonstrate the shortcomings of this class of machine-learning algorithms.

Tags: graph-neural-networks, machine-learning, marvel, point-clouds
Dipolar spin wave packet transport in a van der Waals antiferromagnet

Antiferromagnets are promising platforms for transduction and transmission of quantum information via magnons — the quanta of spin waves — and they offer advantages over ferromagnets in regard to dissipation, speed of response, and robustness to external fields. Recently, transduction was shown in a van der Waals antiferromagnets, where strong spin-exciton coupling enables readout of the amplitude and phase of coherent magnons by photons of visible light. This discovery shifts the focus of research to transmission, specifically to exploring the nonlocal interactions that enable magnon wave packets to propagate. Here we demonstrate that magnon propagation is mediated by the long-range dipole-dipole interaction. This coupling is an inevitable consequence of fundamental electrodynamics, and as such, will likely mediate the propagation of spin at long wavelengths in the entire class of van der Waals magnets currently under investigation. Successfully identifying the mechanism of spin propagation provides a set of optimization rules, as well as caveats, that are essential for any future applications of these promising systems.

Tags: antiferromagnets, magnetostatic-spin-waves, spin-transport, time-resolved-kerr-microscopy
Conical spin order with chiral quadrupole helix in CsCuCl₃

Here we report a resonant x-ray diffraction (RXD) study at the Cu L₃ edge on the multichiral system CsCuCl₃, exhibiting helical magnetic order in a chiral crystal structure. RXD is a powerful technique to disentangle electronic degrees of freedom due to its sensitivity to electric monopoles (charge), magnetic dipoles (spin), and electric quadrupoles (orbital). We characterize electric quadrupole moments around Cu ascribed to the unoccupied Cu 3d orbital, whose quantization axis is off the basal plane. Detailed investigation of magnetic reflections reveals additional sinusoidal modulations along the principal axis superimposed on the reported helical structure, i.e., a longitudinal conical (helical-butterfly) structure. The out-of-plane modulations imply significant spin-orbit interaction despite S=1/2 of Cu²⁺.

Tags: experimental, h2020, marvel
Evolving wave networks for 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 generate the datasets for the SHU shielding of existing materials (Code_Set_Fig_4) and the realization of preferential attachment in evolving wave networks (Code_Set_Fig_5).

Tags: disordered-material, evolution, network, scattering
Machine learning on multiple topological materials datasets

A dataset of 35,608 materials with their topological properties is constructed by combining the density functional theory (DFT) results of Materiae and the Topological Materials Database. Thanks to this, machine-learning approaches are developed to categorize materials into five distinct topological types, with the XGBoost model achieving an impressive 85.2% classification accuracy. By conducting generalization tests on different sub-datasets, differences are identified between the original datasets in terms of topological types, chemical elements, unknown magnetic compounds, and feature space coverage. Their impact on model performance is analyzed.
Turning to the simpler binary classification between trivial insulators and nontrivial topological materials, three different approaches are also tested. Key characteristics influencing material topology are identified, with the maximum packing efficiency and the fraction of p valence electrons being highlighted as critical features

Tags: database, machine-learning, topological-materials
Synchronized crystallization in tin-lead perovskite solar cells

Tin-lead halide perovskites with a bandgap near 1.2 electron-volt hold great promise for thin-film photovoltaics. However, the film quality of solution-processed Sn-Pb perovskites is compromised by the asynchronous crystallization behavior between Sn and Pb components, where the crystallization of Sn-based perovskites tends to occur faster than that of Pb. Here we show that the rapid crystallization of Sn is rooted in its stereochemically active lone pair, which impedes coordination between the metal ion and Lewis base ligands in the perovskite precursor. From this perspective, we introduce a noncovalent binding agent targeting the open metal site of coordinatively unsaturated Sn(II) solvates, thereby synchronizing crystallization kinetics and homogenizing Sn-Pb alloying. The resultant single-junction Sn-Pb perovskite solar cells achieve a certified power conversion efficiency of 24.13 per cent. The encapsulated device retains 90 per cent of the initial efficiency after 795 hours of maximum power point operation under simulated one-sun illumination. 
We conducted DFT and AIMD simulations to study the structure and interactions of metal iodide-solvent ligand complexes. This archive contains the optimized atomic coordinates of PbI2/SnI2-ligands complexes and the initial and final configurations of AIMD trajectories.

Tags: halide-perovskite, lead-iodide, tin-iodide
Lattice energies and relaxed geometries for 2'707 organic molecular crystals and their 3'242 molecular components.

This data record contains the xyz-style files for 2'707 organic molecular crystals and their 3'202 molecular components. The crystals were initially taken directly from the Cambridge Structure Database, and the relaxations were computed and reported by [1]. This record contains an augmentation of a subset of this data, where we have identified the molecular constituents of each crystal, performed geometric relaxations using the same computational parameters, and identified the constituent functional groups. A full detail of methodology and provenance is included in the ESI of [2].
Each crystal and molecule has been relaxed using Quantum Espresso with the following parameters: the PBE exchange-correlation functional, the D2 dispersion correction, ultrasoft pseudopotentials with GIPAW reconstruction, and an equivalent plane-wave energy cutoff of 60 Ryd. We converged the energies within 1E-4 Ryd and forces below 1E-3 Ryd/Bohr, respectively, using MT-decoupling for the molecules to ensure no self-interaction. Furthermore, we compute the binding energy based on the lowest energy conformed represented in the dataset, ensuring comparability between crystals and co-crystals of similar stoichiometries without needing to obtain the global minimum conformation of each molecule.

Tags: marvel, marveldd1, snsf, trinity-college
Zero-point renormalization of the bandgap, mass enhancement, and spectral functions: Validation of methods and verification of first-principles codes

Verification and validation of methods and first-principles software are at the core of computational solid-state physics but are too rarely addressed. We compare four first-principles codes: Abinit, Quantum ESPRESSO, EPW, ZG, and three methods: (i) the Allen-Heine-Cardona theory using density functional perturbation theory (DFPT), (ii)  the Allen-Heine-Cardona theory using Wannier function perturbation theory (WFPT), and (iii) an adiabatic non-perturbative frozen-phonon method. For these cases, we compute the real and imaginary parts of the electron-phonon self-energy in diamond and BAs, including dipoles and quadrupoles when interpolating. We find excellent agreement between software that implements the same formalism as well as good agreement between the DFPT and WFPT methods. Importantly, we find that the Deybe-Waller term is momentum dependent which impacts the mass enhancement, yielding approximate results when using the Luttinger approximations. Finally, we compare the electron-phonon spectral functions between Abinit and EPW and find excellent agreement even away from the band edges.

Tags: ab-initio, electron-phonon-coupling, first-principles, verification-and-validation, zero-point-renormalization
Proximity-induced Cooper pairing at low and finite energies in the gold Rashba surface state

Multi-band effects in superconducting heterostructures provide a rich playground for unconventional physics. We combine two complementary approaches based on density-functional theory (DFT) and effective low-energy model theory in order to investigate the proximity effect in a gold overlayer on the s-wave superconductor aluminium. We explain both theoretical approaches and intertwine the effective model and DFT analysis. This allows us to predict finite energy superconducting avoided crossings due to the interplay of the Rashba surface state of Au, and hybridization with the electronic structure of superconducting Al. We investigate the nature of the induced superconducting pairing and analyze their mixed singlet-triplet character. Our findings demonstrate the general recipes to explore material systems that exhibit novel finite-energy pairings.

This dataset accompanies a publication where the data is presented and discussed in detail.

Tags: ab-initio, bogoliubov-de-gennes, jukkr, spin-orbit-coupling, superconductivity
Machine learning on multiple topological materials datasets

A dataset of 35,608 materials with their topological properties is constructed by combining the density functional theory (DFT) results of Materiae and the Topological Materials Database. Thanks to this, machine-learning approaches are developed to categorize materials into five distinct topological types, with the XGBoost model achieving an impressive 85.2% classification accuracy. By conducting generalization tests on different sub-datasets, differences are identified between the original datasets in terms of topological types, chemical elements, unknown magnetic compounds, and feature space coverage. Their impact on model performance is analyzed.
Turning to the simpler binary classification between trivial insulators and nontrivial topological materials, three different approaches are also tested. Key characteristics influencing material topology are identified, with the maximum packing efficiency and the fraction of p valence electrons being highlighted as critical features.

Tags: database, machine-learning, topological-materials
Scaling relations and dynamical predictiveness of electric dipole strength on 2e- ORR catalytic property

Efficient O₂ reduction to H₂O₂, vital for energy conversion and environmental cleanup, relies on precise control of heterogeneous catalysts interacting with reaction species. Through high-throughput density functional theory calculations, consisting of 369 single atom catalysts, we identified the polarized descriptor (electric dipole strength) on two-dimensional carbon materials, revealing insights into the catalytic effect of support polarization. Surprisingly, this descriptor exhibits advanced scaling relationships towards H₂O₂ synthesis, incorporating factors such as active metals, coordination environments, and surface curvatures, highlighting its widespread significance. Furthermore, it demonstrates reliable predictability for O₂ adsorption in dynamic water environments, with optimal reactivity observed within the range of -1.40 to -1.00 e·Å, as confirmed by dynamic and static simulations of the 2e- pathway of O₂ reduction. In essence, these findings offer valuable insights for the rational design of electrocatalysts tailored for selective O₂ reduction.

Tags: density-functional-theory-calculations, electric-dipole-strength, oxygen-reduction-reaction, support-polarization
FINALES (06/2022) – Electrolyte Optimization for Minimum Density and Maximum Viscosity

This study presents the initial implementation of the Fast INtention-Agnostic LEarning Server (FINALES) in a demonstration of a distributed Materials Acceleration Platform (MAP) including experimental and computational methods and a machine learning (ML)-based optimizer. In this demonstration, the optimizer was configured to minimize the density of the electrolyte solutions while maximizing the viscosity by exploiting experimental and computational results. The tenants (the units connected to FINALES in the MAP) are shortly described in the following:

- Autonomous Synthesis and Analysis of Battery electrolytes (ASAB) setup: an experimental tenant providing density and viscosity data using a densimeter of the type DMA 4100M and a viscometer of type Lovis 2000 both by Anton Paar Germany
- Molecular dynamics tenant: a computational tenant capable of providing radial distribution functions, diffusion coefficients, ionic conductivity, transference numbers, heat capacity and density data to the MAP
- Optimizer: the tenant guiding the optimization by processing the available data and generating requests for electrolyte formulations to be tested subsequently

This dataset accompanies the publication:
Vogler, M., Busk, J., Hajiyani, H., Jørgensen, P. B., Safaei, N., Castelli, I. E., Ramirez, F. F., Carlsson, J., Pizzi, G., Clark, S., Hanke, F., Bhowmik, A. & Stein, H. S. Brokering between tenants for an international materials acceleration platform. Matter 6, 2647–2665 (2023). DOI: https://doi.org/10.1016/j.matt.2023.07.016

Tags: battery-electrolyte, big-map, conductivity, density, marvelp3, materials-acceleration-platform-map, polis, radial-distribution-function-rdf, viscosity
Engineering epitaxial interfaces for topological insulator – superconductor hybrid devices with Al electrodes

Proximity-induced superconductivity in hybrid devices of topological insulators and superconductors offers a promising platform for the pursuit of elusive topological superconductivity and its anticipated applications, such as fault-tolerant quantum computing. To study and harness such hybrid devices, a key challenge is the realization of highly functional material interfaces with a suitable superconductor featuring 2e-periodic parity-conserving transport to ensure a superconducting hard-gap free of unpaired electrons, which is important for Majorana physics. A superconductor well-known for this characteristic is Al, however, its direct integration into devices based on tetradymite topological insulators has so far been found to yield non-transparent interfaces. By focusing on Bi₂Te₃-Al heterostructures, this study identifies detrimental interdiffusion processes at the interface through atomically resolved structural and chemical analysis, and showcase their mitigation by leveraging different interlayers – namely Nb, Ti, Pd, and Pt – between Bi₂Te₃ and Al. Through structural transformation of the interlayer materials (X) into their respective tellurides (XTe₂) atomically-sharp epitaxial interfaces are engineered and further characterized in low-temperature transport experiments on Al-X-Bi₂Te₃-X-Al Josephson junctions and in complementary density functional theory calculations. By demonstrating functional interfaces between Bi₂Te₃ and Al, this work provides key insights and paves the way for the next generation of sophisticated topological devices.

Tags: dft, epitaxial-interfaces, fleur, hybrid-devices, interface-engineering, josephson-junctions, jukkr, majorana-platform, superconductors, tmdc, topological-insulator, topological-materials, topological-superconductivity
First-principles study of the gap in the spin excitation spectrum of the CrI₃ honeycomb ferromagnet

The nature of the gap observed at the zone border in the spin excitation spectrum of CrI₃ quasi-two-dimensional single crystals is still controversial. We perform first-principles calculations based on time-dependent density functional perturbation theory, which indicate that the observed gap results from a combination of spin-orbit and interlayer interaction effects. The former give rise to the anisotropic spin-spin interactions that are responsible for its very existence, while the latter determine both its displacement from the K point of the Brillouin zone, due to the in-plane lattice distortions induced by them, and an enhancement of its magnitude, in agreement with experiments and previous theoretical work based on a lattice model.

Tags: cri3, dirac-cone, magnons, marvel, quantum-espresso, tddft
Electronic excited states from physically-constrained machine learning

Data-driven techniques are increasingly used to replace electronic-structure calculations of matter. In this context, a relevant question is whether machine learning (ML) should be applied directly to predict the desired properties or be combined explicitly with physically-grounded operations. We present an example of an integrated modeling approach, in which a symmetry-adapted ML model of an effective Hamiltonian is trained to reproduce electronic excitations from a quantum-mechanical calculation. The resulting model can make predictions for molecules that are much larger and more complex than those that it is trained on, and allows for dramatic computational savings by indirectly targeting the outputs of well-converged calculations while using a parameterization corresponding to a minimal atom-centered basis. Our results on a comprehensive dataset of hydrocarbons emphasize the merits of intertwining data-driven techniques with physical approximations, improving the transferability and interpretability of ML models without affecting their accuracy and computational efficiency, and providing a blueprint for developing ML-augmented electronic-structure methods.
Here we include the dataset, accompanying the paper linked below, of hydrocarbons including ethane, ethene, butadiene, hexane, hexatriene, isoprene, styrene, polyalkenes (dodecahexaene, tetradecaheptaene, hexadecaoctaene, octadecanonaene, eicosadecaene), aromatics (benzene, azulene, naphthalene, biphenyl), anthracene, beta-carotene, fullerene. We also provide scripts to generate the Fock and overlap matrices in this dataset. The code for machine learning can be found at the Software reference below.

Tags: epfl, erc, excited-states, fiamma, hamiltonian, lifetimes, machine-learning
Radicals in aqueous solution: Assessment of density-corrected SCAN functional

We study self-interaction effects in solvated and strongly-correlated cationic molecular clusters, with a focus on the solvated hydroxyl radical. To address the self-interaction issue, we apply the DC-r²SCAN method, with the auxiliary density matrix approach. Validating our method through simulations of bulk liquid water, we demonstrate that DC-r²SCAN maintains the structural accuracy of r²SCAN while effectively addressing spin density localization issues. Extending our analysis to solvated cationic molecular clusters, we find that the hemibonded motif in the [CH₃S∴CH₃SH]⁺ cluster is disrupted in the DC-r²SCAN simulation, in contrast to r²SCAN that preserves the (three-electron-two-center)-bonded motif. Similarly, for the [SH∴SH₂]⁺ cluster, r²SCAN restores the hemibonded motif through spin leakage, while DC-r²SCAN predicts a weaker hemibond formation influenced by solvent-solute interactions. Our findings demonstrate the potential of DC-r²SCAN combined with the auxiliary density matrix method to improve electronic structure calculations, providing insights into the properties of solvated cationic molecular clusters. This work contributes to the advancement of self-interaction corrected electronic structure theory and offers a computational framework for modeling condensed phase systems with intricate correlation effects.

Tags: aqueous-hydroxyl-radical, aqueous-sulfanyl-radical, density-corrected-dft, density-functional-theory, hydrogen-sulfide, methanethiol, r2scan