arXiv subjects

Marnik Bercx

Publications and source records attributed to Marnik Bercx.

15 recordsLinked to original sources

arXiv2026

Correcting DFT formation energies towards experimental accuracy using foundational MLIPs and latent-feature delta-learning

Crystal structure databases curated by high-throughput density functional theory calculations typically serve as the starting point for computational materials discovery efforts. Thermodynamic stability data, such as formation energies and the energy above the convex hull, are important quantities to guide the search for novel materials, enabling filtering for (meta)stable structures. Here, we present the thermodynamic stability of the fully open-source, reproducible, and experimentally focused Materials Cloud three-dimensional crystals database (MC3D). We compare against two other DFT databases, the Open Quantum Materials Database (OQMD) and the Materials Project (MP), as well as against experimental formation enthalpies. We then demonstrate how recent foundational machine learning interatomic potentials (MLIPs) trained at the r$^2$SCAN level (specifically, we test PET-OMATPES here) can be leveraged to improve the agreement of formation energies with experiment, reducing the mean absolute error by more than 40% relative to GGA without requiring any additional DFT calculation. Our results validate and extend the established practice of combining PBEsol geometries with meta-GGA energies to the era of foundational MLIPs. Finally, we train classical machine learning models to further correct the formation energies in a delta-learning framework, where we use the information-rich latent features of the foundational MLIP. These models further reduce the mean absolute error below 50 meV/atom, bringing it down to values comparable with the experimental uncertainty itself. Notably, compared to purely compositional features, the latent features (combined with carefully tuned regularization) simultaneously reduce the prediction error and limit the impact of the learned corrections on the relative phase stability.

cond-mat.mtrl-sci↗

arXiv2026

Score-based diffusion models for accurate crystal-structure inpainting and reconstruction of hydrogen positions

Generative AI models, such as score-based diffusion models, have recently advanced the field of computational materials science by enabling the generation of new materials with desired properties. In addition, these models could also be leveraged to reconstruct crystal structures for which partial information is available. One relevant example is the reliable determination of atomic positions occupied by hydrogen atoms in hydrogen-containing crystalline materials. While crucial to the analysis and prediction of many materials properties, the identification of hydrogen positions can however be difficult and expensive, as it is challenging in X-ray scattering experiments and often requires dedicated neutron scattering measurements. As a consequence, inorganic crystallographic databases frequently report lattice structures where hydrogen atoms have been either omitted or inserted with heuristics or by chemical intuition. Here, we combine diffusion models from the field of materials science with techniques originally developed in computer vision for image inpainting. We present how this knowledge transfer across domains enables a much faster and more accurate completion of host structures, compared to unconditioned diffusion models or previous approaches solely based on DFT. Overall, our approach exceeds a success rate of 97% in terms of finding a structural match or predicting a more stable configuration than the initial reference, when starting both from structures that were already relaxed with DFT, or directly from the experimentally determined host structures.

cond-mat.mtrl-sci↗

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↗

arXiv2025

Making atomistic materials calculations accessible with the AiiDAlab Quantum ESPRESSO app

Despite the wide availability of density functional theory (DFT) codes, their adoption by the broader materials science community remains limited due to challenges such as software installation, input preparation, high-performance computing setup, and output analysis. To overcome these barriers, we introduce the Quantum ESPRESSO app, an intuitive, web-based platform built on AiiDAlab that integrates user-friendly graphical interfaces with automated DFT workflows. The app employs a modular Input-Process-Output model and a plugin-based architecture, providing predefined computational protocols, automated error handling, and interactive results visualization. We demonstrate the app's capabilities through plugins for electronic band structures, projected density of states, phonon, infrared/Raman, X-ray and muon spectroscopies, Hubbard parameters (DFT+$U$+$V$), Wannier functions, and post-processing tools. By extending the FAIR principles to simulations, workflows, and analyses, the app enhances the accessibility and reproducibility of advanced DFT calculations and provides a general template to interface with other first-principles calculation codes.

cond-mat.mtrl-sci↗

arXiv2025

Massive Atomic Diversity: a compact universal dataset for atomistic machine learning

The development of machine-learning models for atomic-scale simulations has benefited tremendously from the large databases of materials and molecular properties computed in the past two decades using electronic-structure calculations. More recently, these databases have made it possible to train universal models that aim at making accurate predictions for arbitrary atomic geometries and compositions. The construction of many of these databases was however in itself aimed at materials discovery, and therefore targeted primarily to sample stable, or at least plausible, structures and to make the most accurate predictions for each compound - e.g. adjusting the calculation details to the material at hand. Here we introduce a dataset designed specifically to train machine learning models that can provide reasonable predictions for arbitrary structures, and that therefore follows a different philosophy. Starting from relatively small sets of stable structures, the dataset is built to contain massive atomic diversity (MAD) by aggressively distorting these configurations, with near-complete disregard for the stability of the resulting configurations. The electronic structure details, on the other hand, are chosen to maximize consistency rather than to obtain the most accurate prediction for a given structure, or to minimize computational effort. The MAD dataset we present here, despite containing fewer than 100k structures, has already been shown to enable training universal interatomic potentials that are competitive with models trained on traditional datasets with two to three orders of magnitude more structures. We describe in detail the philosophy and details of the construction of the MAD dataset. We also introduce a low-dimensional structural latent space that allows us to compare it with other popular datasets and that can be used as a general-purpose materials cartography tool.

cond-mat.mtrl-sci↗

arXiv2025

A Python workflow definition for computational materials design

Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow exchange format to share workflows between Python-based WfMS, currently AiiDA, jobflow, and pyiron. This development is motivated by the similarity of these three Python-based WfMS, that represent the different workflow steps and data transferred between them as nodes and edges in a graph. With the PWD, we aim at fostering the interoperability and reproducibility between the different WfMS in the context of Findable, Accessible, Interoperable, Reusable (FAIR) workflows. To separate the scientific from the technical complexity, the PWD consists of three components: (1) a conda environment that specifies the software dependencies, (2) a Python module that contains the Python functions represented as nodes in the workflow graph, and (3) a workflow graph stored in the JavaScript Object Notation (JSON). The first version of the PWD supports directed acyclic graph (DAG)-based workflows. Thus, any DAG-based workflow defined in one of the three WfMS can be exported to the PWD and afterwards imported from the PWD to one of the other WfMS. After the import, the input parameters of the workflow can be adjusted and computing resources can be assigned to the workflow, before it is executed with the selected WfMS. This import from and export to the PWD is enabled by the PWD Python library that implements the PWD in AiiDA, jobflow, and pyiron.

cs.SE↗

arXiv2025

Accurate and efficient protocols for high-throughput first-principles materials simulations

Advancements in theoretical and algorithmic approaches, workflow engines, and an ever-increasing computational power have enabled a novel paradigm for materials discovery through first-principles high-throughput simulations. A major challenge in these efforts is to automate the selection of parameters used by simulation codes to deliver numerical precision and computational efficiency. Here, we propose a rigorous methodology to assess the quality of self-consistent DFT calculations with respect to smearing and $k$-point sampling across a wide range of crystalline materials. For this goal, we develop criteria to reliably estimate average errors on total energies, forces, and other properties as a function of the desired computational efficiency, while consistently controlling $k$-point sampling errors. The present results provide automated protocols (named standard solid-state protocols or SSSP) for selecting optimized parameters based on different choices of precision and efficiency tradeoffs. These are available through open-source tools that range from interactive input generators for DFT codes to high-throughput workflows.

cond-mat.mtrl-sci↗

arXiv2025

Charting the landscape of Bardeen-Cooper-Schrieffer superconductors in experimentally known compounds

We perform a high-throughput computational search for novel phonon-mediated superconductors, starting from the Materials Cloud 3-dimensional structure database of experimentally known inorganic stoichiometric compounds. We first compute the Allen-Dynes critical temperature (T$_c$) for 4533 non-magnetic metals using a direct and progressively finer sampling of the electron-phonon couplings. For the candidates with the largest T$_c$, we use automated Wannierizations and electron-phonon interpolations to obtain a high-quality dataset for the most promising 250 dynamically stable structures, for which we calculate spectral functions, superconducting bandgaps, and isotropic Migdal-Eliashberg critical temperatures. For 140 of these, we also provide anisotropic Migdal-Eliashberg superconducting gaps and critical temperatures. The approach is remarkably successful in finding known superconductors, and we find 24 unknown ones with a predicted anisotropic T$_{\rm c}$ above 10~K. Among them, we identify a possible double gap superconductor (p-doped BaB$_2$), a non-magnetic half-Heusler ZrRuSb, and the perovskite TaRu$_3$C, all exhibiting significant T$_{\rm c}$. Finally, we introduce a sensitivity analysis to estimate the robustness of the predictions.

cond-mat.supr-con↗

arXiv2025

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 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. 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 Fe and Mn 3d orbitals 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.

cond-mat.mtrl-sci↗

arXiv2023

The rule of four: anomalous stoichiometries of inorganic compounds

Why are materials with specific characteristics more abundant than others? This is a fundamental question in materials science and one that is traditionally difficult to tackle, given the vastness of compositional and configurational space. We highlight here the anomalous abundance of inorganic compounds whose primitive unit cell contains a number of atoms that is a multiple of four. This occurrence - named here the 'rule of four' - has to our knowledge not previously been reported or studied. Here, we first highlight the rule's existence, especially notable when restricting oneself to experimentally known compounds, and explore its possible relationship with established descriptors of crystal structures, from symmetries to energies. We then investigate this relative abundance by looking at structural descriptors, both of global (packing configurations) and local (the smooth overlap of atomic positions) nature. Contrary to intuition, the overabundance does not correlate with low-energy or high-symmetry structures; in fact, structures which obey the 'rule of four' are characterized by low symmetries and loosely packed arrangements maximizing the free volume. We are able to correlate this abundance with local structural symmetries, and visualize the results using a hybrid supervised-unsupervised machine learning method.

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

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↗

arXiv2019

Accelerated Discovery of Efficient Solar-cell Materials using Quantum and Machine-learning Methods

Solar-energy plays an important role in solving serious environmental problems and meeting high-energy demand. However, the lack of suitable materials hinders further progress of this technology. Here, we present the largest inorganic solar-cell material search to date using density functional theory (DFT) and machine-learning approaches. We calculated the spectroscopic limited maximum efficiency (SLME) using Tran-Blaha modified Becke-Johnson potential for 5097 non-metallic materials and identified 1997 candidates with an SLME higher than 10%, including 934 candidates with suitable convex-hull stability and effective carrier mass. Screening for 2D-layered cases, we found 58 potential materials and performed G0W0 calculations on a subset to estimate the prediction-uncertainty. As the above DFT methods are still computationally expensive, we developed a high accuracy machine learning model to pre-screen efficient materials and applied it to over a million materials. Our results provide a general framework and universal strategy for the design of high-efficiency solar cell materials. The data and tools are publicly distributed at: https://www.ctcms.nist.gov/~knc6/JVASP.html, https://www.ctcms.nist.gov/jarvisml/, https://jarvis.nist.gov/ and https://github.com/usnistgov/jarvis .

cond-mat.mtrl-sci↗

arXiv2017

Exceeding the Shockley-Queisser limit within the detailed balance framework

The Shockley-Queisser limit is one of the most fundamental results in the field of photovoltaics. Based on the principle of detailed balance, it defines an upper limit for a single junction solar cell that uses an absorber material with a specific band gap. Although methods exist that allow a solar cell to exceed the Shockley-Queisser limit, here we show that it is possible to exceed the Shockley-Queisser limit without considering any of these additions. Merely by introducing an absorptivity that does not assume that every photon with an energy above the band gap is absorbed, efficiencies above the Shockley-Queisser limit are obtained. This is related to the fact that assuming optimal absorption properties also maximizes the recombination current within the detailed balance approach. We conclude that considering a finite thickness for the absorber layer allows the efficiency to exceed the Shockley-Queisser limit, and that this is more likely to occur for materials with small band gaps.

cond-mat.mtrl-sci↗

arXiv2016

First-principles analysis of the efficiency of photovoltaic layers for CuAu-like chalcogenides and silicon

Chalcopyrite semiconductors are of considerable interest for application as absorber layers in thin-film photovoltaic cells. When growing films of these compounds, however, they are often found to contain CuAu- like domains, a metastable phase of chalcopyrite. It has been reported that for CuInS2, the presence of the CuAu-like phase improves the short circuit current of the chalcopyrite-based photovoltaic cell. We investigate the thermodynamic stability of both phases for a selected list of I-III-VI2 materials using a first-principles density functional theory approach. For the CuIn-VI2 compounds, the difference in formation energy between the chalcopyrite and CuAu-like phase is found to be close to 2 meV/atom, indicating a high likelihood of the presence of CuAu-like domains. Next, we calculate the Spectroscopic Limited Maximum Efficiency (SLME) of the CuAu- like phase and compare the results with those of the corresponding chalcopyrite phase. We identify several candidates with a high efficiency, such as CuAu-like CuInS2, for which we obtain an SLME of 29% at a thickness of 500 nm. We observe that the SLME can have values above the Shockley-Queisser (SQ) limit, and show that this can occur because the SQ limit assumes the absorptivity to be a step function, thus overestimating the radiative recombination in the detailed balance approach. This means that it is possible to find higher theoretical efficiencies within this framework simply by calculating the J-V characteristic with an absorption spectrum. Finally, we expand our SLME analysis to indirect band gap absorbers by studying silicon, and find that the SLME quickly overestimates the reverse saturation current of indirect band gap materials, drastically lowering their calculated efficiency.

cond-mat.mtrl-sci↗