AndreaBozzo/ceres-open-data-index huggingface dataset:
The dynamic diversity and invariance of ab-initio water

Comprehending water dynamics is crucial in various fields such as water desalination, ion separation, electrocatalysis, and biochemical processes. While ab-initio molecular dynamics (AIMD) accurately portray water's structure, computing its dynamic properties over nanosecond timescales proves cost-prohibitive. This study employs machine learning potentials (MLPs) to accurately determine the dynamical properties of liquid water with ab-initio accuracy. Our findings reveal diversity in the calculated diffusion coefficient (D) and viscosity of water (η) across different methodologies. Specifically, while the GGA, meta-GGA, and hybrid functional methods struggle to predict dynamic properties under ambient conditions, whereas methods on the higher level of Jacob's ladder of DFT approximation perform significantly better. Intriguingly, we discovered that all D and η adhere to the established Stokes-Einstein (SE) relation for all the ab-initio water. The diversity observed among different methods can be attributed to distinct structural entropy, affirming the applicability of excess entropy scaling relations across all functionals. The correlation between D and η provides valuable insights for identifying the ideal temperature to accurately replicate liquid water's dynamic properties. Furthermore, our findings can validate the rationale behind employing artificially high temperatures in the simulation of water via AIMD. These outcomes not only pave the path toward designing better functionals for water but also underscore the significance of water's many-body characteristics.

Tags: aimd, density-functional-theory, diffusion, dynamical-properties, machine-learning-potential, water
First-principles Hubbard parameters with automated and reproducible workflows

We introduce an automated, flexible framework (aiida-hubbard) to self-consistently calculate Hubbard U and V parameters from first-principles. By leveraging density-functional perturbation theory, the computation of the Hubbard parameters is efficiently parallelized using multiple concurrent and inexpensive primitive cell calculations. Furthermore, the intersite V parameters are defined on-the-fly during the iterative procedure to account for atomic relaxations and diverse coordination environments. We devise a novel, code-agnostic data structure to store Hubbard related information together with the atomistic structure, to enhance the reproducibility of Hubbard-corrected calculations. We demonstrate the scalability and reliability of the framework by computing in high-throughput fashion the self-consistent onsite U and intersite V parameters for 115 Li-containing bulk solids with up to 32 atoms in the unit cell. Our analysis of the Hubbard parameters calculated reveals a significant correlation of the onsite U values on the oxidation state and coordination environment of the atom on which the Hubbard manifold is centered, while intersite V values exhibit a general decay with increasing interatomic distance. We find, e.g., that the numerical values of U for the 3d orbitals of Fe and Mn can vary up to 3 eV and 6 eV, respectively; their distribution is characterized by typical shifts of about 0.5 eV and 1.0 eV upon change in oxidation state, or local coordination environment. For the intersite V a narrower spread is found, with values ranging between 0.2 eV and 1.6 eV when considering transition metal and oxygen interactions. This framework paves the way for the exploration of redox materials chemistry and high-throughput screening of d and f compounds across diverse research areas, including the discovery and design of novel energy storage materials, as well as other technologically-relevant applications.

Tags: aiida, dftu, dftuv, hubbard, oxidation-state
Machine learning potential for the Cu-W system

Combining the excellent thermal and electrical properties of Cu with the high abrasion resistance and thermal stability of W, Cu-W nanoparticle-reinforced metal matrix composites and nano-multilayers (NMLs) are finding applications as brazing fillers and shielding material for plasma and radiation.  Due to the large lattice mismatch between fcc Cu and bcc W, these systems have complex interfaces that are beyond the scales suitable for ab initio methods, thus motivating the development of chemically accurate interatomic potentials. Here, a neural network potential (NNP) for Cu-W is developed within the Behler-Parrinello framework using a curated training dataset that captures metallurgically-relevant local atomic environments. The Cu-W NNP accurately predicts (i) the metallurgical properties (elasticity, stacking faults, dislocations, thermodynamic behavior) in elemental Cu and W, (ii) energies and structures of Cu-W intermetallics and solid solutions, and (iii) a range of fcc Cu/bcc W  interfaces, and exhibits physically-reasonable behavior for solid W/liquid Cu systems.  As will be demonstrated in forthcoming work, this near-ab initio-accurate NNP can be applied to understand complex phenomena involving interface-driven processes and properties in Cu-W composites.

Tags: copper-tungsten, marvel, molecular-dynamics-simulation, nanomultilayer, neural-network-potentials
Stacking of charge-density waves in 2H-NbSe₂ bilayers

We employ ab-initio electronic-structure calculations to investigate the charge-density waves and periodic lattice distortions in bilayer 2⁢H-NbSe₂. We demonstrate that the vertical stacking can give rise to a variety of patterns that may lower the symmetry of the charge-density waves exhibited separately by the two composing 1⁢H-NbSe₂ monolayers. The general tendency to a spontaneous symmetry breaking observed in the ground state and the first excited states is shown to originate from a non-negligible interlayer coupling. Simulated images for scanning tunneling microscopy as well as geometric structure factors show signatures of the different stacking orders. This may not only be useful to reinterpret past experiments on surfaces and thin films, but it may also be exploited to devise ad hoc experiments for the investigation of the stacking order in 2H-NbSe₂. We anticipate that our analysis not only applies to the 2H-NbSe₂, but is also relevant for thin films and bulk, whose smallest centrosymmetric component is indeed the bilayer. Finally, our results illustrate clearly that the vertical stacking is not only important for 1T structures, as exemplified by the metal-to-insulator transition observed in 1⁢T-TaS₂, but seems to be a general feature of metallic layered transition metal dichalcogenides as well. The dataset includes the fully relaxed atomic positions of the most favorable charge-density waves, as well as the main output files of the electronic structure calculations. Selected files for the charge densities are also included.

Tags: charge-density-waves, dft, h2020, marie-curie-fellowship, stacking-order, transition-metal-dichalcogenides
Automated prediction of ground state spin for transition metal complexes

Predicting the ground state spin of transition metal complexes is a challenging task. Previous attempts have been focused on specific regions of chemical space, whereas a more general automated approach is required to process crystallographic structures for high-throughput quantum chemistry computations. In this work, we developed a method to predict ground state spins of transition metal complexes. We started by constructing a dataset which contains 2,063 first row transition metal complexes taken from experimental crystal structures and their computed ground state spins. This dataset showed large chemical diversity in terms of metals, metal oxidation states, coordination geometries, and ligands. Then, we analyzed the trends between structural and electronic features of the complexes and their ground state spins, and put forward an empirical spin state assignment model. We also used simple descriptors to build a statistical model with >95% predictive accuracy across the board. With this, we provide a practical and automated way to determine the ground state spin of transition metal complex from structure, enabling the high-throughput exploration of crystallographic repositories.

Tags: machine-learning, marvel, marvelp2, spin-state, transition-metal, transition-metal-complex
Automated prediction of ground state spin for transition metal complexes

Predicting the ground state spin of transition metal complexes is a challenging task. Previous attempts have been focused on specific regions of chemical space, whereas a more general automated approach is required to process crystallographic structures for high-throughput quantum chemistry computations. In this work, we developed a method to predict ground state spins of transition metal complexes. We started by constructing a dataset which contains 2,032 first row transition metal complexes taken from experimental crystal structures and their computed ground state spins. This dataset showed large chemical diversity in terms of metals, metal oxidation states, coordination geometries, and ligands. Then, we analyzed the trends between structural and electronic features of the complexes and their ground state spins, and put forward an empirical spin state assignment model. We also used simple descriptors to build a statistical model with 97% predictive accuracy across the board. With this, we provide a practical and automated way to determine the ground state spin of transition metal complex from structure, enabling the high-throughput exploration of crystallographic repositories.

Tags: machine-learning, marvel, spin-state, transition-metal, transition-metal-complex
Atomic-level structure of the amorphous drug Atuliflapon via NMR crystallography

We determine the complete atomic-level structure of the amorphous form of the drug atuliflapon, a 5-lipooxygenase activating protein (FLAP) inhibitor, via chemical-shift-driven NMR crystallography. The ensemble of preferred structures allows us to identify a number of specific conformations and interactions that stabilize the amorphous structure. These include preferred hydrogen-bonding motifs with water and with other drug molecules, as well as conformations of the cyclohexane and pyrazole rings that stabilize structure by indirectly allowing for optimization of hydrogen bonding.

Tags: atuliflapon, nmr-crystallography, solid-state-nmr
DFT calculations of surface binding and interstitial hydrogen formation energies for plasma-facing materials

This dataset contains the results of density functional theory (DFT) calculations performed using Quantum ESPRESSO to study surface binding energies (SBE) and the formation energies of interstitial hydrogen (H-IFE) in various plasma-facing materials (PFMs). These calculations support the findings reported in the article Comprehensive Screening of Plasma-Facing Materials for Nuclear Fusion, where a combination of peer-reviewed data from the PAULING FILE database and first-principles calculations are used to evaluate potential PFM candidates. Key results include a detailed comparison of tungsten and alternative refractory materials, focusing on their behavior under intense neutron bombardment and plasma interactions in nuclear fusion reactors. The dataset includes input and output files from the Quantum ESPRESSO simulations, offering valuable insight into defect energetics in candidate materials.

Tags: dft, eurofusion, interstitial-formation-energy, marvel, nuclear-fusion, plasma-facing-materials, surface-binding-energy
Dataset of tensile properties for sub-sized specimens of nuclear structural materials

The dataset provides records of tensile properties of nuclear structural materials. The focus is on studying the influence of specimen dimensions and geometry on mechanical properties such as yield strength, ultimate tensile strength, uniform elongation, and total elongation. The dataset was created through an extensive literature review of scientific articles and databases. The search inclusion criteria targeted peer-reviewed studies on tensile testing of sub-sized specimens, providing quantitative data on tensile properties relative to specimen size. The extracted data points from the literature review were organized into a tabular format database containing 1,070 tensile testing records with 54 parameters, including material type and composition, manufacturing information, irradiation conditions, specimen size and dimensions, and tensile properties. Materials science experts conducted systematic checks to validate the collected data, ensuring accuracy in the material type, manufacturing processes and treatment methods, and testing conditions, as well as verifying the chemical composition and other pertinent information. Our team performed statistical analyses to identify and address data outliers, ensuring the reliability of the dataset.

Tags: nuclear-structural-materials, specimen-size-effect, sub-sized-specimens, tensile-properties
Extensive band gap tunability in covalent organic frameworks via metal intercalation and high pressure

Covalent organic frameworks (COFs) are materials of growing interest for electronic applications due to their tunable structures, chemical stability, and layered architectures that support extended π-systems and directional charge transport. While their electronic properties are strongly influenced by the choice of molecular building blocks and the stacking arrangement, experimental control over these features remains limited, and the number of well-characterized COFs is still relatively small. Here, we explore two alternative strategies, hydrostatic pressure and metal intercalation, to tune the electronic structure of COFs. Using periodic density functional theory (DFT) calculations, we show that the band gap of pristine COF-1 decreases by ∼1 eV under compression up to 10 GPa. Metal intercalation induces an even greater reduction, in some cases leading to metallic behavior. We demonstrate that pressure and intercalation offer effective, continuous control over COF electronic properties, providing powerful means to complement and extend conventional design approaches.

Tags: band-gap, covalent-organic-frameworks, dft, electronic-bands, high-pressure, intercalation, marvel, swiss-national-supercomputing-center-cscs
Glassy dynamics and crystalline local order in two-dimensional amorphous silica

We reassess the modeling of amorphous silica bilayers as a two-dimensional classical system whose particles interact with an effective pairwise potential. We show that it is possible to reparameterize the potential developed by Roy, Heyde, and Heuer to quantitatively match the structural details of the experimental samples. We then study the glassy dynamics of the reparameterized model at low temperatures.  Using appropriate cage-relative correlation functions, which suppress the effect of Mermin-Wagner fluctuations, we highlight the presence of two well-defined Arrhenius regimes separated by a narrow crossover region, which we connect to the thermodynamic anomalies and the changes in the local structure. We find that the bond-orientational order grows steadily below the crossover temperature and is associated to transient crystalline domains of nanometric size.  These findings raise fundamental questions about the nature of glass structure in two dimensions and provide guidelines to interpret the experimental data.

This dataset is associated with "Glassy dynamics and crystalline local order in two-dimensional amorphous silica", Marco Dirindin and Daniele Coslovich (2024) [arXiv:2410.10500].
It includes scripts and data files to allow for the replication of the figures. The EPS figures in the Figures folder were generated using gnuplot version 5.4.

Tags: 2d-materials, glass-transition, silica-bilayer
The initial stages of cement hydration at the molecular level

Cement hydration is crucial for the strength development of cement-based materials; however, the mechanism that underlies this complex reaction remains poorly understood at the molecular level. An in-depth understanding of cement hydration is required for the development of environmentally friendly cement and consequently the reduction of carbon emissions in the cement industry. Here, we use molecular dynamics simulations with a reactive force field to investigate the initial hydration processes of tricalcium silicate (C₃S) and dicalcium silicate (C₂S) up to 40 ns. Our simulations provide theoretical support for the rapid initial hydration of C₃S compared to C₂S at the molecular level. The dissolution pathways of calcium ions in C₃S and C₂S are revealed, showing that, two dissolution processes are required for the complete dissolution of calcium ions in C₃S. Our findings promote the understanding of the calcium dissolution stage and serve as a valuable reference for the investigation of the initial cement hydration.

Tags: cement-hydration, molecular-dynamics-simulation, reaxff-reactive-force-field
From operando investigations to implementation of Ni-MOF-74 oxygen evolution electrocatalysts

Metal-organic frameworks (MOFs) as electrocatalysts for the alkaline oxygen evolution reaction (OER) show promising catalytic activity by offering great variability and high surface areas, enabling performance optimization and mechanistic studies. However, their stability during reaction and the structure-performance relationship defining the origin of the high OER activity, are still vigorously debated. Herein, we leverage operando X-ray absorption spectroscopy and operando X-ray diffraction to unveil the structural and electronic transformations of Ni-MOF-74 during OER. We identify the irreversible destruction of the MOF-74 crystal into a highly OER active, amorphous NiOOH-metal organic compound. Based on these findings, we propose an amorphous Ni metal organic compound (Ni-MOC*) for achieving high current densities both in a three-electrode cell (14 A gNi-1 at 1.5 VRHE) and in an anion exchange membrane water electrolyzer (AEM-WE) with a stable AEM-WE performance exceeding 100 h at 500 mA cm-2.

Tags: alkalineaem-water-electrolysis, electrocatalysis, marvel, ni-mof-74, oer, operando-xasxrd
High-throughput screening of Weyl semimetals

Topological Weyl semimetals represent a novel class of non-trivial materials, where band crossings with linear dispersions take place at generic momenta across reciprocal space. These crossings give rise to low-energy properties akin to those of Weyl fermions, and are responsible for several exotic phenomena. Up to this day, only a handful of Weyl semimetals have been discovered, and the search for new ones remains a very active area. The main challenge on the computational side arises from the fact that many of the tools used to identify the topological class of a material do not provide a complete picture in the case of Weyl semimetals. In this work, we propose an alternative and inexpensive, criterion to screen for possible Weyl fermions, based on the analysis of the band structure along high-symmetry directions in the absence of spin-orbit coupling. We test the method by running a high-throughput screening on a set of 6000 inorganic bulk materials and identify 49 possible candidates for topological properties. A further analysis, carried out by identifying and characterizing the crossings in the Brillouin zone, shows us that 3 of these candidates are Weyl semimetals. Interestingly, while these 3 materials underwent other high-throughput screenings, none had revealed their topological behavior before.

Tags: high-throughput, marvelp3, topological-materials, weyl-semimetal
High-throughput screening of Weyl semimetals

Topological Weyl semimetals represent a novel class of non-trivial materials, where band crossings with linear dispersions take place at generic momenta across reciprocal space. These crossings give rise to low-energy properties akin to those of Weyl fermions, and are responsible for several exotic phenomena. Up to this day, only a handful of Weyl semimetals have been discovered, and the search for new ones remains a very active area. The main challenge on the computational side arises from the fact that many of the tools used to identify the topological class of a material do not provide a complete picture in the case of Weyl semimetals. In this work, we propose an alternative and inexpensive, criterion to screen for possible Weyl fermions, based on the analysis of the band structure along high-symmetry directions in the absence of spin-orbit coupling. We test the method by running a high-throughput screening on a set of 6000 inorganic bulk materials and identify 49 possible candidates for topological properties. A further analysis, carried out by identifying and characterizing the crossings in the Brillouin zone, shows us that 3 of these candidates are Weyl semimetals. Interestingly, while these 3 materials underwent other high-throughput screenings, none had revealed their topological behavior before.

Tags: high-throughput, topological-materials, weyl-semimetal
Analysis of bootstrap and subsampling in high-dimensional regularized regression (code)

We investigate popular resampling methods for estimating the uncertainty of statistical models, such as subsampling, bootstrap and the jackknife, and their performance in high-dimensional supervised regression tasks. We provide a tight asymptotic description of the biases and variances estimated by these methods in the context of generalized linear models, such as ridge and logistic regression, taking the limit where the number of samples n and dimension d of the covariates grow at a comparable fixed rate α = n/d. Our findings are three-fold: i) resampling methods are fraught with problems in high dimensions and exhibit the double-descent-like behavior typical of these situations; ii) only when α is large enough do they provide consistent and reliable error estimations (we give convergence rates); iii) in the over-parametrized regime α < 1 relevant to modern machine learning practice, their predictions are not consistent, even with optimal regularization.
This record provides the code to reproduce the numerical experiments of the related paper "Analysis of bootstrap and subsampling in high-dimensional regularized regression".

Tags: marvelp2, neural-networks, numerical-simulation, uncertainty-quantification
Reduced graphene oxide membrane models for hydrogen storage

A database of 600 atomistic models of reduced graphene oxide (rGO) and hydrogenated rGO (H-rGO) was constructed, comprising 120 rGO and 480 H-rGO structures. The dataset spans a broad range of oxygen concentrations, –O–:–OH (epoxy/ether to hydroxyl) ratios, and hydrogenation levels. The database is designed for applications in computational modeling, machine learning, and structure–property analyses. The models were generated following a three-step simulation protocol:
 – Step 1 | Generation of Pseudo-GO Models: Graphene sheets were functionalized with oxygen groups (–O– or –OH), randomly distributed according to three –O–:–OH ratios (25:75, 50:50, and 75:25). Functionalization was applied symmetrically on both sides of the sheet, avoiding adjacent carbon atoms.
 – Step 2 | Thermal Reduction: Each pseudo-GO structure was subjected to annealing at four different temperatures (1000, 1500, 2000, and 2500 K). After initial relaxation at 300 K, the models were heated, equilibrated, annealed back to room temperature, and re-optimized. This step produced 120 rGO models exhibiting a range of oxygen contents, functional group distributions, and defect patterns.
 – Step 3 | Hydrogenation of rGO Models: rGO models were exposed to atomic hydrogen using a combined Grand Canonical Monte Carlo and molecular dynamics (GCMC/MD) scheme at 300 K and four hydrogen pressures (1, 2, 4, and 8 bar). Hydrogenation was performed with 50 GCMC exchange steps every 1 ps of MD, followed by relaxation and removal of unstable species. This step generated 480 H-rGO models with varying hydrogen coverage and bonding configurations.
All simulations were performed using the LAMMPS software package with the ReaxFF reactive force field.

Tags: functionalized-carbon-nanostructures, graphene-oxide-models, hydrogenated-graphene-oxide, reduced-graphene-oxide