AndreaBozzo/ceres-open-data-index huggingface dataset:
Zeo-1: A computational data set of zeolite structures

Fast, empirical potentials are gaining increased popularity in the computational fields of materials science, physics and chemistry. With it, there is a rising demand for high-quality reference data for the training and validation of such models. In contrast to research that is mainly focused on small organic molecules, this work presents a data set of geometry-optimized bulk phase zeolite structures. Covering a majority of framework types from the Database of Zeolite Structures, this set includes over thirty thousand geometries. Calculated properties include system energies, nuclear gradients and stress tensors at each point, making the data suitable for model development, validation or referencing applications focused on periodic silica systems.

Tags: bulk-phase, density-functional-theory, dft, h2020, horizon-europe, machine-learning, marie-curie-fellowship, silica, zeolite
Effect of density, phonon scattering and nanoporosity on the thermal conductivity of anisotropic cellulose nanocrystal foams

Ice templated anisotropic foams based on cellulose nanocrystals (CNC) with densities ranging between 25 to 130 kg.m-3 were prepared from aqueous CNC dispersions. The thermal conductivities perpendicular to the columnar macropores direction increased in a non-monotonous way with the increasing CNC foam density while the thermal conductivity reached a minimum value for the CNC foam with the highest nanoporosity. Theoretical calculations including the solid and gas conduction within the foams as well as the thermal conductivity of water showed that phonon scattering at the solid-solid interfaces is responsible for reaching low thermal conductivity values. The foam wall nanoporosity, the particle alignment, the macropores orientation and the foam wall thickness seem to have a minimal effect on the thermal conductivity but can explain the deviations between the theoretical estimates and the experimental data. To this end the identification of the important influencing factors and the great importance of phonon scattering paves the way to design new fossil-free nanofibrillar foams with superinsulating properties.

Tags: cellulose-nanocrystals, cellulose-nanomaterials, foams, moisture-uptake, thermal-conductivity
On-surface activation of benzylic C–H bonds for the synthesis of pentagon-fused graphene nanoribbons

In this record we provide data to support our recent findings related to the fabrication of pentagon-fused graphene nanoribbons. Graphene nanoribbons (GNRs) have potential for applications in electronic devices. A key issue, thereby, is the fine-tuning of their electronic characteristics, which can be achieved through subtle structural modifications. These are not limited to the conventional armchair, zigzag, and cove edges, but also possible through incorporation of non-hexagonal rings. On-surface synthesis enables the fabrication and visualization of GNRs with atomically precise chemical structures, but strategies for the incorporation of non-hexagonal rings have been underexplored. In the publication, we describe the on-surface synthesis of armchair-edged GNRs with incorporated five-membered rings through the C-H activation and cyclization of benzylic methyl groups. Ortho-Tolyl-substituted dibromobianthryl was employed as the precursor monomer, and visualization of the resulting structures after annealing at 300 °C on a gold surface by high-resolution noncontact atomic force microscopy clearly revealed the formation of methylene-bridged pentagons at the GNR edges. These persisted after annealing at 340 °C, along with a few fully conjugated pentagons having singly-hydrogenated apexes. The benzylic methyl groups could also migrate or cleave-off, resulting in defects lacking the five-membered rings. Moreover, unexpected and unique structural rearrangements, including the formation of embedded heptagons, were observed. Despite the coexistence of different reaction pathways that hamper selective synthesis of a uniform structure, our results provide novel insights into on-surface reactions en route to functional, non-benzenoid carbon nanomaterials.

Tags: ab-initio, cscs, graphene-nanoribbons, marveldd3, on-surface-synthesis, snsf
Characterization of chemisorbed species and active adsorption sites in Mg-Al mixed metal oxides for high temperature CO2 capture

Mg-Al mixed metal oxides (MMOs), derived from the decomposition of layered double hydroxides (LDHs), have been purposed as a material for CO2 capture of industrial plant emissions. In order to aid in the design and optimization of these materials for CO2 capture at 200 °C, we have used the combination of solid-state nuclear magnetic resonance (ssNMR) and density functional theory (DFT) to characterize the CO2 gas sorption products and determine the various sorption sites in the Mg-Al MMOs. Comparison of DFT cluster calculations with 13C chemical shift of the chemisorbed products indicates that mono and bi-dentate carbonate are formed at the Mg-O site with an adjacent Al substitution of an Mg atom, while bicarbonate is formed at Mg-OH sites without adjacent Al substitution. Quantitative 13C NMR shows an increase in the relative amount of strongly basic sites, where the monodentate carbonate product is formed, with increasing Al mole % in the MMO. This detailed understanding of the various basic Mg-O sites presents in the MMO material, and the formation of the carbonate, bidentate carbonate and bicarbonate chemisorbed species yields new insight into the mechanism of CO2 adsorption at 200 °C which can further aid in the design and capture capacity optimization of the materials.

Tags: carbon-capture, dft, epfl, marvel, nmr
A dataset for beta-glycine with Wannier centers

The beta-glycine dataset is created with the purpose of validating the electron machine learning potential (eMLP) on crystalline beta glycine. It contains 25,676 configurations with normal mode perturbations for the nuclei and unit cell and electric field perturbations. Energies, forces and Wannier centers are computed using density functional theory (DFT) with the PBE functional and a Plane-Wave basis set in the ab-initio quantum chemistry code QuantumESPRESSO.

Tags: beta-glycine, density-functional-theory, machine-learning, wannier-centers
Data-driven simulation and characterisation of gold nanoparticles melting

We develop efficient, accurate, transferable, and interpretable machine learning force fields for Au nanoparticles, based on data gathered from Density Functional Theory calculations. We then use them to investigate the thermodynamic stability of Au nanoparticles of different sizes (1 to 6 nm), containing up to 6266 atoms, with respect to a solid-liquid phase change through molecular dynamics simulations. We predict nanoparticle melting temperatures in good agreement with respect to available experimental data. Furthermore, we characterize in detail the solid to liquid phase change mechanism employing an unsupervised learning scheme to categorize local atomic environments. We thus provide a rigorous and data-driven definition of liquid atomic arrangements in the inner and surface regions of a nanoparticle, and employ it to show that melting initiates at the outer layers. 

The record contains all the MD simulation trajectories carried out using mapped machine learning force fields in LAMMPS, the machine learning force fields as LAMMPS pair potentials, and the ab initio training data used to construct such force fields.

Tags: erc, gold, h2020, machine-learning, max, molecular-dynamics-simulation, nanoparticle
Density functional Bogoliubov-de Gennes analysis of superconducting Nb and Nb(110) surfaces

Material-specific calculations based on density functional theory play a major role in understanding and designing the properties of quantum matter. In the field of topological quantum computing there is an intense search for material systems that have the ability to realize Majorana zero modes. The ability to combine the accurate electronic structure, that is accessible from density functional theory, with superconductivity can help gaining material-specific insights and may contribute to the understanding and realization of Majorana zero modes in solid state systems. In this work we report on our implementation of the Bogoliubov-de Gennes method into the JuKKR code [https://jukkr.fz-juelich.de], an implementation of the all-electron, full-potential Korringa-Kohn-Rostoker Green function method, which allows a material-specific description of inhomogeneous superconductors and heterostructures on the basis of density functional theory. We describe the formalism and report on calculations for the s-wave superconductor Nb. We compare the properties of the superconducting state both in the bulk and for (110) thin films of different thickness. We comment on the importance of spin-orbit coupling, the effect of surface relaxations and the influence of a softening of phonon modes on the surface for the resulting superconducting gap.

This dataset contains the Fleur and KKR calculations that were done in this study using the AiiDA-Fleur and AiiDA-KKR plugins and a tutorial that introduces the practical use of AiiDA-KKR for BdG calculations.

Tags: aiida-kkr, bogoliubov-de-gennes, density-functional-theory, jukkr, nb, superconductivity, surface
On-surface synthesis of π-conjugated ladder-type polymers comprising nonbenzenoid moieties

In this record we provide data to support our recent findings related to the fabrication of π-conjugated ladder-type polymers comprising nonbenzenoid moieties. On-surface synthesis provides a powerful approach toward the atomically precise fabrication of π-conjugated ladder polymers (CLPs). In the manuscript we report the surface-assisted synthesis of nonbenzenoid CLPs from cyclopenta-annulated anthracene monomers on Au(111) under ultrahigh vacuum conditions. Successive thermal annealing steps reveal the dehalogenative homocoupling to yield an intermediate 1D polymer and the subsequent cyclodehydrogenation to form the fully conjugated ladder polymer. Notably, neighbouring monomers may fuse in two different ways, resulting in six- and five-membered rings, respectively. The structure and electronic properties of the reaction products have been investigated via low-temperature scanning tunneling microscopy and spectroscopy, complemented by density-functional theory calculations. Our results provide perspectives for the on-surface synthesis of nonbenzenoid CLPs with the potential to be used for organic electronic devices.

Tags: ab-initio, cscs, horizon-2020, marveldd3, nonbenzenoid, on-surface-synthesis, polymers, snsf
The importance of nuclear quantum effects for NMR crystallography

The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of the computational prediction of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy surface.
To test the limits of this approximation, we perform a systematic study of the role of finite-temperature and quantum nuclear fluctuations on 1H, 13C, and 15N chemical shieldings in molecular crystals -- considering the paradigmatic examples of the different polymorphs of benzene, glycine, and succinic acid.
We find the effect of quantum fluctuations to be comparable in size to the typical errors of predictions of chemical shieldings for static nuclei with respect to experimental measurements, and to improve the match between experiments and theoretical predictions, translating to more reliable assignment of the NMR spectra to the correct candidate structure.
Thanks to the use of integrated machine-learning models trained on both first-principles configurational energies and chemical shieldings, the accurate sampling of thermal and quantum fluctuations of the structures can be achieved at an affordable cost, setting a new standard for the calculations that underlie solid-state structural determination by NMR.

This archive contains the machine-learning potentials and shielding models, sample inputs, and scripts to reproduce the results discussed in the manuscript. It further contains the reference data and scripts to reconstruct the shielding models.

Tags: first-principles-gipaw-dft, machine-learning, marvel, molecular-crystals, nmr-chemical-shielding, nuclear-quantum-effects, snsf
Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine

Structure prediction for molecular crystals is a longstanding challenge, as often minuscule free energy differences between polymorphs are sensitively affected by the description of electronic structure, the statistical mechanics of the nuclei and the cell, and thermal expansion. The importance of these effects has been individually established, but rigorous free energy calculations, which simultaneously account for all terms, have not been computationally viable.
Here we reproduce the experimental stabilities of polymorphs of prototypical compounds -- benzene, glycine, and succinic acid -- by computing rigorous first-principles Gibbs free energies, at a fraction of the cost of conventional methods. This is achieved by a bottom-up approach, which involves generating machine-learning potentials to calculate surrogate free energies and subsequently calculating true first-principles free energies using inexpensive free energy perturbations.
Accounting for all relevant physical effects is no longer a daunting task and provides the foundation for structure predictions for more complex systems of industrial importance.

This Materials Cloud archive contains first-principles training, validation, and test data for polymorphs of benzene, succinic acid, and glycine underlying the above-mentioned machine-learning potentials. 
For each compound the archive provides two sets of data: the first based on DFT calculations with the semi-local PBE functional and the Tkatchenko-Scheffler dispersion correction, and the second based on DFT calculations with the hybrid PBE0 functional and the many-body dispersion correction of Tkatchenko et al. For each compound and both levels of electronic-structure theory, structure datasets in libatom extended-xyz format provide representative, thermalised configurations and the associated configurational energies, atomic forces, and stresses on the simulation cell. The configurations are extracted from a combination of classical temperature replica exchange molecular dynamics simulations and path-integral molecular dynamics for a representative set of perturbed unit cells based on the experimental structures of: forms I, II, Ihp and V' of benzene, alpha- and beta-succinic acid, and alpha-, beta-, gamma-, and delta-glycine. The detailed data provenance and dataset architecture is described in the attached README file.

Tags: first-principles, hybrid-functional-dft, marvel, molecular-crystals, snsf
Coherent energy exchange between carriers and phonons in Peierls-distorted bismuth unveiled by broadband XUV pulses

In Peierls-distorted materials, photoexcitation leads to a strongly coupled transient response between structural and electronic degrees of freedom, always measured independently of each other. Here we use transient reflectivity in the extreme ultraviolet to quantify both responses in photoexcited bismuth in a single measurement. With the help of first-principles calculations based on density-functional theory (DFT) and time-dependent DFT, the real-space atomic motion and the temperature of both electrons and holes as a function of time are captured simultaneously, retrieving an anticorrelation between the A1g phonon dynamics and carrier temperature. The results reveal a coherent, bi-directional energy exchange between carriers and phonons, which is a dynamical counterpart of the static Peierls-Jones distortion, providing first-time validation of previous theoretical predictions.

Tags: absorption-spectrum, bismuth, cscs, density-functional-theory, density-of-states, extreme-ultraviolet, investissements-davenir, marvelosp, photoexcitation, real-space-atomic-motion, snsf, time-dependent-density-functional-theory, transient-reflectivity
Molecular dynamics based cohesive law for epoxy-graphene interfaces

Molecular dynamics (MD) simulations are performed to obtain mode I and II fracture energies and cohesive laws for bulk epoxy and interfaces formed between epoxy and single-layer graphene (SLG), multilayer graphene (MLG), and multilayer graphene oxide (MLGO). The elastic moduli and ultimate tensile and shear strengths of epoxy--graphene interfaces are calculated from uniaxial tension and simple shear loadings. The results show that Young's modulus and the ultimate tensile strength increase relative to bulk epoxy, whereas the shear modulus and ultimate shear strength are reduced. Failure of epoxy--graphene interfaces in tension occurs due to the formation of voids in the epoxy. Failure in shear is due to tangential slipping at the interface. Under mixed mode conditions, the shear modulus and shear strength decrease with increasing tensile load. The critical energy release rate G_c for the studied epoxy--SLG/MLG/MLGO systems are obtained using a continuum fracture mechanics approach and are found to be significantly lower than for bulk epoxy. All of the results are combined to define mode I and II cohesive laws for bulk epoxy and epoxy--SLG/MLG/MLGO interfaces that can be used in theoretical models and numerical methods, such as finite elements, that employ cohesive zones.

Tags: cohesive-law, graphene-reinforced-epoxy-composite, molecular-dynamics-simulation
Oxygen vacancies in strontium titanate: a DFT+DMFT study

We address the long-standing question of the nature of oxygen vacancies in strontium titanate, using a combination of density functional theory and dynamical mean-field theory (DFT+DMFT) to investigate in particular the effect of vacancy-site correlations on the electronic properties. Our approach uses a minimal low-energy electronic subspace including the Ti-t2g orbitals plus an additional vacancy-centered Wannier function, and it provides an intuitive and physically transparent framework to study the effect of the local electron-electron interactions on the excess charge introduced by the oxygen vacancies. We estimate the strength of the screened interaction parameters using the constrained random phase approximation, and we find a sizable Hubbard U parameter for the vacancy orbital. Our main finding, which reconciles previous experimental and computational results, is that the ground state is either a state with double occupation of the localized defect state or a state with a singly occupied vacancy and one electron transferred to the conduction band. The balance between these two competing states is determined by the strength of the interaction both on the vacancy and the Ti sites, and on the Ti-Ti distance across the vacancy. Finally, we contrast the case of vacancy doping in SrTiO3 with doping via La substitution, and we show that the latter is well described by a simple rigid-band picture.

Tags: cscs, dftdmft, electronic-structure, marveldd5, oxygen-vacancies
The nature of the active sites on Ni/CeO2 catalysts for methane conversions

Effective catalysts for the direct conversion of methane to methanol and for methane's dry reforming to syngas are Holy Grails of catalysis research toward clean energy technologies. It has recently been discovered that Ni at low loadings on CeO2 is very reactive towards reactants CH4, H2O and CO2 and active for both of these reactions. Revealing the nature of the active sites in such systems is paramount to a rational design of improved catalysts. Here, using a combination of experimental measurements and density functional theory calculations, we show that the most active sites are cationic Ni atoms in clusters at step edges on the CeO2 surface, using the activation of CH4 as an example . We show that the size and morphology of the supported nanoparticles together with strong Ni−support bonding and charge transfer at the step edge are key to the high catalytic activity towards these methane conversions. We anticipate that this knowledge will inspire the development of more efficient catalysts for these reactions.

Tags: ch4-dissociation, dftuv, ni-clusters-on-ceo2
Revealing hidden magneto-electric multipoles using Compton scattering

Magneto-electric multipoles, which are odd under both space-inversion 𝓘 and time-reversal 𝓣 symmetries, are fundamental in understanding and characterizing magneto-electric materials. However, the detection of these magneto-electric multipoles is often not straightforward as they remain "hidden" in conventional experiments in part since many magneto-electrics exhibit combined 𝓘𝓣 symmetry. In the present work, we show that the anti-symmetric Compton profile is a unique signature for all the magneto-electric multipoles, since the asymmetric magnetization density of the magneto-electric multipoles couples to space via spin-orbit coupling, resulting in an anti-symmetric Compton profile. We develop the key physics of the anti-symmetric Compton scattering using symmetry analysis and demonstrate it using explicit first-principles calculations for two well-known representative materials with magneto-electric multipoles, insulating LiNiPO₄ and metallic Mn₂Au. Our work emphasizes the crucial roles of the orientation of the spin moments, the spin-orbit coupling, and the band structure in generating the anti-symmetric Compton profile in magneto-electric materials.

Tags: compton-scattering, density-functional-theory, erc, h2020, horizon-europe, linipo4, magneto-electric-multipoles, mn2au
Assessment of approximate methods for anharmonic free energies

Quantitative evaluation of the thermodynamic properties of materials—most notably their stability, as measured by the free energy—must take into account the role of thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic nature of the interatomic potential are often crucial and require computationally costly path integral simulations to obtain results that are essentially exact for a given potential. Consequently, different approximate frameworks for computing affordable estimates of the anharmonic free energies have been developed over the years. Understanding which of the approximations involved are justified for a given system, and therefore choosing the most suitable method, is complicated by the lack of comparative benchmarks. To facilitate this choice we assess the accuracy and efficiency of some of the most commonly used approximate methods: the independent mode framework, the vibrational self-consistent field, and self-consistent phonons. We compare the anharmonic correction to the Helmholtz free energy against reference path integral calculations. These benchmarks are performed for a diverse set of systems, ranging from simple weakly anharmonic solids to flexible molecular crystals with freely rotating units. The results suggest that, for simple solids such as allotropes of carbon, these methods yield results that are in excellent agreement with the reference calculations, at a considerably lower computational cost. For more complex molecular systems such as polymorphs of ice and paracetamol the methods do not consistently provide a reliable approximation of the anharmonic correction. Despite substantial cancellation of errors when comparing the stability of different phases, we do not observe a systematic improvement over the harmonic approximation even for relative free energies. We conclude that, at least for the classes of materials considered here, efforts toward obtaining computationally feasible anharmonic free energies should therefore be directed toward reducing the expense of path integral methods.

Tags: crystal-structure-prediction, erc, marvel, nuclear-quantum-effects, quantum-statistics, snsf