arXiv subjects

Kristjan Eimre

Publications and source records attributed to Kristjan Eimre.

18 recordsLinked to original sources

arXiv2026

optimade-maker: Automated generation of interoperable materials APIs from static datasets

Atomistic structural data are central to materials science, condensed matter physics, and chemistry, and are increasingly digitised across diverse repositories and databases. Interoperable access to these heterogeneous data sources enables reusable clients and tools, and is essential for cross-database analyses and data-driven materials discovery. Toward this aim, the OPTIMADE (Open Databases Integration for Materials Design) specification defines a standard REST API for atomistic structures and related properties. However, deploying and maintaining compliant services remains technically demanding and poses a significant barrier for many data providers. Here, we present optimade-maker, a lightweight toolkit for the automated generation of OPTIMADE-compliant APIs directly from raw atomistic structure and property data. The toolkit supports a wide range of raw datasets, enables conversion to a standardised OPTIMADE data representation, and allows for rapid deployment of APIs in both local and production environments. We further demonstrate it through an automated service on the Materials Cloud Archive, which automatically creates and publishes OPTIMADE APIs for contributed datasets, enabling immediate discoverability and interoperability. In addition, we implement data transformation pipelines for the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD), enabling unified access to these curated resources through the OPTIMADE framework. By lowering the technical barriers to interoperable data publication, optimade-maker represents an important step toward a scalable, FAIR materials data ecosystem integrating both community-contributed and curated databases.

cs.DB↗

arXiv2025

MC3D: The Materials Cloud computational database of experimentally known stoichiometric inorganics

DFT is a widely used method to compute properties of materials, which are often collected in databases and serve as valuable starting points for further studies. In this article, we present the Materials Cloud Three-Dimensional Structure Database (MC3D), an online database of computed three-dimensional (3D) inorganic crystal structures. Close to a million experimentally reported structures were imported from the COD, ICSD and MPDS databases; these were parsed and filtered to yield a collection of 72589 unique and stoichiometric structures, of which 95% are, to date, classified as experimentally known. The geometries of structures with up to 64 atoms were then optimized using density-functional theory (DFT) with automated workflows and curated input protocols. The procedure was repeated for different functionals (and computational protocols), with the latest version (MC3D PBEsol-v2) comprising 32013 unique structures. All versions of the MC3D are made available on the Materials Cloud portal, which provides a graphical interface to explore and download the data. The database includes the full provenance graph of all the calculations driven by the automated workflows, thus establishing full reproducibility of the results and more-than-FAIR procedures.

cond-mat.mtrl-sci↗

arXiv2024

Jupyter widgets and extensions for education and research in computational physics and chemistry

Interactive notebooks are a precious tool for creating graphical user interfaces and teaching materials. Python and Jupyter are becoming increasingly popular in this context, with Jupyter widgets at the core of the interactive functionalities. However, while packages and libraries which offer a broad range of general-purpose widgets exist, there is limited development of specialized widgets for computational physics, chemistry and materials science. This deficiency implies significant time investments for the development of effective Jupyter notebooks for research and education in these domains. Here, we present custom Jupyter widgets that we have developed to target the needs of these communities. These widgets constitute high-quality interactive graphical components and can be employed, for example, to visualize and manipulate data, or to explore different visual representations of concepts, clarifying the relationships existing between them. In addition, we discuss with one example how similar functionality can be exposed in the form of JupyterLab extensions, modifying the JupyterLab interface for an enhanced user experience when working with applications within the targeted scientific domains.

physics.ed-ph↗

arXiv2024

Electronic decoupling and hole-doping of graphene nanoribbons on metal substrates by chloride intercalation

Atomically precise graphene nanoribbons (GNRs) have a wide range of electronic properties that depend sensitively on their chemical structure. Several types of GNRs have been synthesized on metal surfaces through selective surface-catalyzed reactions. The resulting GNRs are adsorbed on the metal surface, which may lead to hybridization between the GNR orbitals and those of the substrate. This makes investigation of the intrinsic electronic properties of GNRs more difficult, and also rules out capacitive gating. Here we demonstrate the formation of a dielectric gold chloride adlayer that can intercalate underneath GNRs on the Au(111) surface. The intercalated gold chloride adlayer electronically decouples the GNRs from the metal and leads to a substantial hole doping of the GNRs. Our results introduce an easily accessible tool in the in situ characterization of GNRs grown on Au(111) that allows for exploration of their electronic properties in a heavily hole-doped regime.

cond-mat.mtrl-sci↗

arXiv2024

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the upcoming v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development.

cond-mat.mtrl-sci↗

arXiv2023

Tailoring magnetism of nanographenes via tip-controlled dehydrogenation

Atomically precise graphene nanoflakes, called nanographenes, have emerged as a promising platform to realize carbon magnetism. Their ground state spin configuration can be anticipated by Ovchinnikov-Lieb rules based on the mismatch of π-electrons from two sublattices. While rational geometrical design achieves specific spin configurations, further direct control over the π-electrons offers a desirable extension for efficient spin manipulations and potential quantum device operations. To this end, we apply a site-specific dehydrogenation using a scanning tunneling microscope tip to nanographenes deposited on a Au(111) substrate, which shows the capability of precisely tailoring the underlying π-electron system and therefore efficiently manipulating their magnetism. Through first-principles calculations and tight-binding mean-field-Hubbard modelling, we demonstrate that the dehydrogenation-induced Au-C bond formation along with the resulting hybridization between frontier π-orbitals and Au substrate states effectively eliminate the unpaired π-electron. Our results establish an efficient technique for controlling the magnetism of nanographenes.

cond-mat.mtrl-sci↗

arXiv2023

How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

In the past decades many density-functional theory methods and codes adopting periodic boundary conditions have been developed and are now extensively used in condensed matter physics and materials science research. Only in 2016, however, their precision (i.e., to which extent properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. We discuss here general recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z=1 to 96 and characterizing 10 prototypical cubic compounds for each element: 4 unaries and 6 oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Such effort is facilitated by deploying AiiDA common workflows that perform automatic input parameter selection, provide identical input/output interfaces across codes, and ensure full reproducibility. Finally, we discuss the extent to which the current results for total energies can be reused for different goals (e.g., obtaining formation energies).

cond-mat.mtrl-sci↗

arXiv2021

Synthesis and characterization of super-nonazethrene

Beginning with the early work of Clar et al. in 1955, zethrenes and their laterally-extended homologues, super-zethrenes, have been intensively studied in the solution phase, and are widely investigated as optical and charge transport materials. Super-zethrenes are also considered to exhibit an open-shell ground state. Zethrenes may thus serve as model compounds to investigate nanoscale pi-magnetism. However, their synthesis is extremely challenging due to their high reactivity. We report here a combined in-solution and on-surface synthesis of the hitherto largest zethrene homologue - super-nonazethrene - on Au(111). Using single-molecule scanning tunneling microscopy and spectroscopy, we show that super-nonazethrene exhibits an open-shell singlet ground state featuring a large spin polarization-driven electronic gap of 1 eV. We obtain real-space maps of the frontier molecular orbitals, and find that they correspond to singly occupied molecular orbitals. In consistence with the emergence of an open-shell ground state, high-resolution tunneling spectroscopy reveals inelastic singlet-triplet spin excitations in super-nonazethrene, characterized by a strong intramolecular magnetic exchange coupling of 51 meV. Further insights are gained by mean-field and many-body perturbation theory calculations. Given the paucity of zethrene chemistry on surfaces, our results therefore provide unprecedented access to large open-shell zethrene compounds amenable to scanning probe measurements, with potential application in molecular spintronics.

cond-mat.mes-hall↗

arXiv2021

Observation of fractional edge excitations in nanographene spin chains

Fractionalization is a phenomenon in which strong interactions in a quantum system drive the emergence of excitations with quantum numbers that are absent in the building blocks. Outstanding examples are excitations with charge e/3 in the fractional quantum Hall effect, solitons in one-dimensional conducting polymers and Majorana states in topological superconductors. Fractionalization is also predicted to manifest itself in low-dimensional quantum magnets, such as one-dimensional antiferromagnetic S = 1 chains. The fundamental features of this system are gapped excitations in the bulk and, remarkably, S = 1/2 edge states at the chain termini, leading to a four-fold degenerate ground state that reflects the underlying symmetry-protected topological order. Here, we use on-surface synthesis to fabricate one-dimensional spin chains that contain the S = 1 polycyclic aromatic hydrocarbon triangulene as the building block. Using scanning tunneling microscopy and spectroscopy at 4.5 K, we probe length-dependent magnetic excitations at the atomic scale in both open-ended and cyclic spin chains, and directly observe gapped spin excitations and fractional edge states therein. Exact diagonalization calculations provide conclusive evidence that the spin chains are described by the S = 1 bilinear-biquadratic Hamiltonian in the Haldane symmetry-protected topological phase. Our results open a bottom-up approach to study strongly correlated quantum spin liquid phases in purely organic materials, with the potential for the realization of measurement-based quantum computation.

cond-mat.mes-hall↗

arXiv2021

Common workflows for computing material properties using different quantum engines

The prediction of material properties through electronic-structure simulations based on density-functional theory has become routinely common, thanks, in part, to the steady increase in the number and robustness of available simulation packages. This plurality of codes and methods aiming to solve similar problems is both a boon and a burden. While providing great opportunities for cross-verification, these packages adopt different methods, algorithms, and paradigms, making it challenging to choose, master, and efficiently use any one for a given task. Leveraging recent advances in managing reproducible scientific workflows, we demonstrate how developing common interfaces for workflows that automatically compute material properties can tackle the challenge mentioned above, greatly simplifying interoperability and cross-verification. We introduce design rules for reproducible and reusable code-agnostic workflow interfaces to compute well-defined material properties, which we implement for eleven different quantum engines and use to compute three different material properties. Each implementation encodes carefully selected simulation parameters and workflow logic, making the implementer's expertise of the quantum engine directly available to non-experts. Full provenance and reproducibility of the workflows is guaranteed through the use of the AiiDA infrastructure. All workflows are made available as open-source and come pre-installed with the Quantum Mobile virtual machine, making their use straightforward.

cond-mat.mtrl-sci↗

arXiv2020

AiiDAlab -- an ecosystem for developing, executing, and sharing scientific workflows

Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited experience in (and time for) user interface design, which can make research software difficult to install and use for novices. When combined with the increasing complexity of scientific workflows (involving many steps and software packages), setting up a computational research environment becomes a major entry barrier. AiiDAlab is a web platform that enables computational scientists to package scientific workflows and computational environments and share them with their collaborators and peers. By leveraging the AiiDA workflow manager and its plugin ecosystem, developers get access to a growing range of simulation codes through a python API, coupled with automatic provenance tracking of simulations for full reproducibility. Computational workflows can be bundled together with user-friendly graphical interfaces and made available through the AiiDAlab app store. Being fully compatible with open-science principles, AiiDAlab provides a complete infrastructure for automated workflows and provenance tracking, where incorporating new capabilities becomes intuitive, requiring only Python knowledge.

cond-mat.mtrl-sci↗

arXiv2020

Coupled spin states in armchair graphene nanoribbons with asymmetric zigzag edge extensions

Carbon-based magnetic structures promise significantly longer coherence times than traditional magnetic materials, which is of fundamental importance for spintronic applications. An elegant way of achieving carbon-based magnetic moments is the design of graphene nanostructures with an imbalanced occupation of the two sublattices forming the carbon honeycomb lattice. According to Lieb's theorem, this induces local magnetic moments that are proportional to the sublattice imbalance. Exact positioning of sublattice imbalanced nanostructures in graphene nanomaterials hence offers a route to control interactions between induced local magnetic moments and to obtain graphene nanomaterials with magnetically non-trivial ground states. Here, we show that such sublattice imbalanced nanostructures can be incorporated along a large band gap armchair graphene nanoribbon on the basis of asymmetric zigzag edge extensions, which is achieved by incorporating specifically designed precursor monomers during the bottom-up fabrication of the graphene nanoribbons. Scanning tunneling spectroscopy of an isolated and electronically decoupled zigzag edge extension reveals Hubbard-split states in accordance with theoretical predictions. Investigation of pairs of such zigzag edge extensions reveals ferromagnetic, antiferromagnetic or quenching of the magnetic interactions depending on the relative alignment of the asymmetric edge extensions. Moreover, a ferromagnetic spin chain is demonstrated for a periodic pattern of zigzag edge extensions along the nanoribbon axis. This work opens a route towards the design and fabrication of graphene nanoribbon-based spin chains with complex magnetic ground states.

cond-mat.mes-hall↗

arXiv2020

Giant magnetic exchange coupling in rhombus-shaped nanographenes with zigzag periphery

Nanographenes with zigzag edges are predicted to manifest non-trivial pi-magnetism resulting from the interplay of hybridization of localized frontier states and Coulomb repulsion between valence electrons. This provides a chemically tunable platform to explore quantum magnetism at the nanoscale and opens avenues toward organic spintronics. The magnetic stability in nanographenes is thus far limited by the weak magnetic exchange coupling which remains below the room temperature thermal energy. Here, we report the synthesis of large rhombus-shaped nanographenes with zigzag periphery on gold and copper surfaces. Single-molecule scanning probe measurements unveil an emergent magnetic spin-singlet ground state with increasing nanographene size. The magnetic exchange coupling in the largest nanographene, determined by inelastic electron tunneling spectroscopy, exceeds 100 meV or 1160 K, which outclasses most inorganic nanomaterials and remarkably survives on a metal electrode.

cond-mat.mes-hall↗

arXiv2020

Collective All-Carbon Magnetism in Triangulene Dimers

Triangular zigzag nanographenes, such as triangulene and its pi-extended homologues, have received widespread attention as organic nanomagnets for molecular spintronics, and may serve as building blocks for high-spin networks with long-range magnetic order - of immense fundamental and technological relevance. As a first step toward these lines, we present the on-surface synthesis and a proof-of-principle experimental study of magnetism in covalently bonded triangulene dimers. On-surface reactions of rationally-designed precursor molecules on Au(111) lead to the selective formation of triangulene dimers in which the triangulene units are either directly connected through their minority sublattice atoms, or are separated via a 1,4-phenylene spacer. The chemical structures of the dimers have been characterized by bond-resolved scanning tunneling microscopy. Scanning tunneling spectroscopy and inelastic electron tunneling spectroscopy measurements reveal collective singlet-triplet spin excitations in the dimers, demonstrating efficient inter-triangulene magnetic coupling.

cond-mat.mes-hall↗

arXiv2019

On-surface synthesis of polyazulene with 2,6-connectivity

Azulene, the smallest neutral nonalternant aromatic hydrocarbon, serves as not only a prototype for fundamental studies but also a versatile building block for functional materials because of its unique opto(electronic) properties. Here, we report the on-surface synthesis and characterization of the homopolymer of azulene connected exclusively at the 2,6-positions using 2,6-diiodoazulene as the monomer precursor. As an intermediate to the formation of polyazulene, a gold-(2,6-azulenylene) chain is observed.

cond-mat.mtrl-sci↗

arXiv2019

On-surface synthesis of antiaromatic and open-shell indeno[2,1-b]fluorene polymers and their lateral fusion into porous ribbons

Polycyclic hydrocarbons have received great attention due to their potential role in organic electronics and, for open-shell systems with unpaired electron densities, in spintronics and da-ta storage. However, the intrinsic instability of polyradical hydrocarbons severely limits de-tailed investigations of their electronic structure. Here, we report the on-surface synthesis of conjugated polymers consisting of indeno[2,1-b]fluorene units, which are antiaromatic and open-shell biradicaloids. The observed reaction products, which also include a non-benzenoid porous ribbon arising from lateral fusion of unprotected indeno[2,1-b]fluorene chains, have been characterized via low temperature scanning tunneling microscopy/spectroscopy and non-contact atomic force microscopy, complemented by density-functional theory calculations. These polymers present a low band gap when adsorbed on Au(111). Moreover, their pro-nounced antiaromaticity and radical character, elucidated by ab initio calculations, make them promising candidates for applications in electronics and spintronics. Further, they provide a rich playground to explore magnetism in low-dimensional organic nanomaterials.

cond-mat.mtrl-sci↗

arXiv2019

Ab Initio calculation of field emission from metal surfaces with atomic--scale defects

In this work we combine density functional theory and quantum transport calculations to study the influence of atomic--scale defects on the work function and field emission characteristics of metal surfaces. We develop a general methodology for the calculation of the field emitted current density from nano-featured surfaces, which is then used to study specific defects on a Cu(111) surface. Our results show that the inclusion of a defect can significantly locally enhance the field emitted current density. However, this increase is attributed solely to the decrease of the work function due to the defect, with the effective field enhancement being minute. Finally, the Fowler--Nordheim equation is found to be valid when the modified value for the work function is used, with only an approximately constant factor separating the computed currents from those predicted by the Fowler--Nordheim equation.

cond-mat.mes-hall↗

arXiv2018

Dynamic coupling of a finite element solver to large-scale atomistic simulations

We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that follows the geometry defined by atomistic data. On this mesh, different multiphysics problems can be solved to obtain distributions of physical quantities of interest, which can be fed back to the atomistic system. The simulation flow is optimized to maximize computational efficiency while maintaining good accuracy. This is achieved by providing the modules for a) optimization of the density of the generated mesh according to requirements of a specific geometry and b) efficient extension of the finite element domain without a need to extend the atomistic one. Our method is organized as an open-source C++ code. In the current implementation, an efficient Laplace equation solver for calculation of electric field distribution near rough atomistic surface demonstrates the capability of the suggested approach.

cs.CE↗