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Luigi Genovese

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Published work

29 published item(s)

preprint2026arXiv

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

preprint2022arXiv

Transition-Based Constrained DFT for the Robust and Reliable Treatment of Excitations in Supramolecular Systems

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and $Δ$SCF results for the low lying excited states (S$_{1}$ and T$_{1}$) of a set of gas phase acene molecules and OLED emitters, as well as with reference results from the literature. At the PBE level of theory, T-CDFT outperforms $Δ$SCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge-transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT. T-CDFT is designed for large systems and has been implemented in the linear scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

preprint2021arXiv

Exploring Metastable States in UO$_2$ using Hybrid Functionals and Dynamical Mean Field Theory

A detailed exploration of the $f$-atomic orbital occupancy space for UO$_2$ is performed using a first principles approach based on density functional theory (DFT), employing a full hybrid functional within a systematic basis set. Specifically, the PBE0 functional is combined with an occupancy biasing scheme implemented in a wavelet-based algorithm which is adapted to large supercells. The results are compared with previous DFT+U calculations reported in the literature, while dynamical mean field theory (DMFT) is also performed to provide a further base for comparison. This work shows that the computational complexity of the energy landscape of a correlated $f$-electron oxide is much richer than has previously been demonstrated. The resulting calculations provide evidence of the existence of multiple previously unexplored metastable electronic states of UO$_2$, including those with energies which are lower than previously reported ground states.

preprint2020arXiv

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments, and quantify inter-fragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems, and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

preprint2020arXiv

The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure programs and redesign them as free, open-source libraries. They include "heavy-duty" ones with a high degree of parallelisation, and potential for adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers.

preprint2016arXiv

A wavelet-based Projector Augmented-Wave (PAW) method: reaching frozen-core all-electron precision with a systematic, adaptive and localized wavelet basis set

We present a Projector Augmented-Wave~(PAW) method based on a wavelet basis set. We implemented our wavelet-PAW method as a PAW library in the ABINIT package [http://www.abinit.org] and into BigDFT [http://www.bigdft.org]. We test our implementation in prototypical systems to illustrate the potential usage of our code. By using the wavelet-PAW method, we can simulate charged and special boundary condition systems with frozen-core all-electron precision. Furthermore, our work paves the way to large-scale and potentially order-N simulations within a PAW method.

preprint2016arXiv

Challenges in Large Scale Quantum Mechanical Calculations

During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs and sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains.

preprint2016arXiv

Revisiting the domain model for lithium intercalated graphite

In this letter, we study the stability of the domain model for lithium intercalated graphite in stages III and II by means of Density Functional Theory and Kinetic Lattice Monte Carlo simulations. We find that the domain model is either thermodynamically or kinetically stable when compared to the standard model in stages III and II. The existence of domains in the intercalation sequence is well supported by recent high resolution transmission electron microscope observations in lithiated graphite. Moreover, we predict that such domain staging sequences leads to a wide range of diffusivity as reported in experiments.

preprint2015arXiv

Accurate and efficient linear scaling DFT calculations with universal applicability

Density Functional Theory calculations traditionally suffer from an inherent cubic scaling with respect to the size of the system, making big calculations extremely expensive. This cubic scaling can be avoided by the use of so-called linear scaling algorithms, which have been developed during the last few decades. In this way it becomes possible to perform ab-initio calculations for several tens of thousands of atoms or even more within a reasonable time frame. However, even though the use of linear scaling algorithms is physically well justified, their implementation often introduces some small errors. Consequently most implementations offering such a linear complexity either yield only a limited accuracy or, if one wants to go beyond this restriction, require a tedious fine tuning of many parameters. In our linear scaling approach within the BigDFT package, we were able to overcome this restriction. Using an ansatz based on localized support functions expressed in an underlying Daubechies wavelet basis -- which offers ideal properties for accurate linear scaling calculations -- we obtain an amazingly high accuracy and a universal applicability while still keeping the possibility of simulating large systems with only a moderate demand of computing resources.

preprint2015arXiv

Fragment Approach to Constrained Density Functional Theory Calculations using Daubechies Wavelets

In a recent paper we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions is optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e. without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.

preprint2015arXiv

Identification of Resonant States via the Generalized Virial Theorem

The numerical extraction of resonant states of open quantum systems is usually a difficult problem. Regularization techniques, such as the mapping to complex coordinates or the addition of Complex Absorbing Potentials are typically employed, as they render resonant wavefunctions localized and therefore normalizable. Physically relevant metastable states have energies that do not depend on the chosen regularization method. Their identification therefore involves cumbersome comparisons between multiple regularised calculations, often performed graphically, which require fine-tuning and specific intuition to avoid approximated, if not wrong, results. In this Letter, we define an operator that explicitly measures such invariance, valid for any arbitrary mapping of spatial coordinates. Resonant states of the system can eventually simply be identified evaluating the expectation value of this operator. Our method eases the extraction of resonant states even for numerical potentials that are difficult to scale to complex coordinates, and avoids the need for ad hoc complex absorbing potentials. We provide explicit evidence of our findings discussing one-dimensional case-studies,also in the presence of external electric fields.

preprint2015arXiv

Multipole-Preserving Quadratures for Discretization of Functions in Real-Space Electronic Structure Calculations

Discretizing an analytic function on a uniform real-space grid is often done via a straightforward collocation method. This is ubiquitous in all areas of computational physics and quantum chemistry. An example in Density Functional Theory (DFT) is given by the external potential or the pseudo-potential describing the interaction between ions and electrons. The accuracy of the collocation method used is therefore very important for the reliability of subsequent treatments like self-consistent field solutions of the electronic structure problems. By construction, the collocation method introduces numerical artifacts typical of real-space treatments, like the so-called egg-box error, that may spoil the numerical stability of the description when the real-space grid is too coarse. As the external potential is an input of the problem, even a highly precise computational treatment cannot cope this inconvenience. We present in this paper a new quadrature scheme that is able to exactly preserve the moments of a given analytic function even for large grid spacings, while reconciling with the traditional collocation method when the grid spacing is small enough. In the context of real-space electronic structure calculations, we show that this method improves considerably the stability of the results for large grid spacings, opening the path towards reliable low-accuracy DFT calculations with reduced number of degrees of freedom.

preprint2015arXiv

Phonon-limited carrier mobility and resistivity from carbon nanotubes to graphene

Under which conditions do the electrical transport properties of one-dimensional (1D) carbon nanotubes (CNTs) and 2D graphene become equivalent? We have performed atomistic calculations of the phonon-limited electrical mobility in graphene and in a wide range of CNTs of different types to address this issue. The theoretical study is based on a tight-binding method and a force-constant model from which all possible electron-phonon couplings are computed. The electrical resistivity of graphene is found in very good agreement with experiments performed at high carrier density. A common methodology is applied to study the transition from 1D to 2D by considering CNTs with diameter up to 16 nm. It is found that the mobility in CNTs of increasing diameter converges to the same value, the mobility in graphene. This convergence is much faster at high temperature and high carrier density. For small-diameter CNTs, the mobility strongly depends on chirality, diameter, and existence of a bandgap.

preprint2014arXiv

Daubechies Wavelets for Linear Scaling Density Functional Theory

We demonstrate that Daubechies wavelets can be used to construct a minimal set of optimized localized contracted basis functions in which the Kohn-Sham orbitals can be represented with an arbitrarily high, controllable precision. Ground state energies and the forces acting on the ions can be calculated in this basis with the same accuracy as if they were calculated directly in a Daubechies wavelets basis, provided that the amplitude of these contracted basis functions is sufficiently small on the surface of the localization region, which is guaranteed by the optimization procedure described in this work. This approach reduces the computational costs of DFT calculations, and can be combined with sparse matrix algebra to obtain linear scaling with respect to the number of electrons in the system. Calculations on systems of 10,000 atoms or more thus become feasible in a systematic basis set with moderate computational resources. Further computational savings can be achieved by exploiting the similarity of the contracted basis functions for closely related environments, e.g. in geometry optimizations or combined calculations of neutral and charged systems.

preprint2013arXiv

A Customized 3D GPU Poisson Solver for Free Boundary Conditions

A 3-dimensional GPU Poisson solver is developed for all possible combinations of free and periodic boundary conditions (BCs) along the three directions. It is benchmarked for various grid sizes and different BCs and a significant performance gain is observed for problems including one or more free BCs. The GPU Poisson solver is also benchmarked against two different CPU implementations of the same method and a significant amount of acceleration of the computation is observed with the GPU version.

preprint2013arXiv

Accurate Complex Scaling of Three Dimensional Numerical Potentials

The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scaling of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.

preprint2013arXiv

Boron aggregation in the ground states of boron-carbon fullerenes

We present novel structural motifs for boron-carbon nano-cages of the stochiometries B12C48 and B12C50, based on first principle calculations. These configurations are distinct from those proposed so far by the fact that the boron atoms are not isolated and distributed over the entire surface of the cages, but rather aggregate at one location to form a patch. Our putative ground state of B12C48 is 1.8 eV lower in energy than the previously proposed ground state and violates all the suggested empirical rules for constructing low energy fullerenes. The B12C50 configuration is energetically even more favorable than B12C48, showing that structures derived from the C60 Buckminsterfullerene are not necessarily magic sizes for heterofullerenes.

preprint2013arXiv

Norm-conserving pseudopotentials with chemical accuracy compared to all-electron calculations

By adding a non-linear core correction to the well established Dual Space Gaussian type pseudopotentials for the chemical elements up to the third period, we construct improved pseudopotentials for the Perdew Burke Ernzerhof (PBE) functional and demonstrate that they exhibit excellent accuracy. Our benchmarks for the G2-1 test set show average atomization energy errors of only half a kcal/mol. The pseudopotentials also remain highly reliable for high pressure phases of crystalline solids. When supplemented by empirical dispersion corrections the average error in the interaction energy between molecules is also about half a kcal/mol. The accuracy that can be obtained by these pseudopotentials in combination with a systematic basis set is well superior to the accuracy that can be obtained by commonly used medium size Gaussian basis sets in all-electron calculations.

preprint2013arXiv

Selecting Boron Fullerenes by Cage-Doping Mechanisms

So far, no boron fullerenes were synthesized: more compact sp3-bonded clusters are energetically preferred. To circumvent this, metallic clusters have been suggested by Pochet et al. [Phys. Rev. B 83, 081403(R) (2011)] as "seeds" for a possible synthesis which would topologically protect the sp2 sector of the configuration space. In this paper, we identify a basic pentagonal unit which allows a balance between the release of strain and the self-doping rule. We formulate a guiding principle for the stability of boron fullerenes, which takes the form of an isolated filled pentagon rule (IFPR). The role of metallic clusters is then reexamined. It is shown that the interplay of the IFPR and the seed-induced doping breaks polymorphism and its related problems: it can effectively select between different isomers and reduce the reactivity of the boron shells. The balance between self and exterior doping represents the best strategy for boron buckyball synthesis.

preprint2012arXiv

Efficient and accurate solver of the three-dimensional screened and unscreened Poisson's equation with generic boundary conditions

We present an explicit solver of the three-dimensional screened and unscreened Poisson's equation which combines accuracy, computational efficiency and versatility. The solver, based on a mixed plane-wave / interpolating scaling function representation, can deal with any kind of periodicity (along one, two, or three spatial axes) as well as with fully isolated boundary conditions. It can seamlessly accommodate a finite screening length, non-orthorhombic lattices and charged systems. This approach is particularly advantageous because convergence is attained by simply refining the real space grid, namely without any adjustable parameter. At the same time, the numerical method features O(N log N) scaling of the computational cost (N being the number of grid points) very much like plane-wave methods. The methodology, validated on model systems, is tailored for leading-edge computer simulations of materials (including ab initio electronic structure computations), but it might as well be beneficial for other research domains.

preprint2012arXiv

Tunable magnetic states in h-BN sheets

Magnetism in 2D atomic sheets has attracted considerable interest as its existence could allow the development of electronic and spintronic devices. The existence of magnetism is not sufficient for devices, however, as states must be addressable and modifiable through the application of an external drive. We show that defects in hexagonal boron nitride present a strong interplay between the the N-N distance in the edge and the magnetic moments of the defects. By stress-induced geometry modifications, we change the ground state magnetic moment of the defects. This control is made possible by the triangular shape of the defects as well as the strong spin localisation in the magnetic state.

preprint2011arXiv

The effect of ionization on the global minima of small and medium sized silicon and magnesium clusters

We re-examine the question of whether the geometrical ground state of neutral and ionized clusters are identical. Using a well defined criterion for being "identical" together, the extensive sampling methods on a potential energy surface calculated by density functional theory, we show that the ground states are in general different. This behavior is to be expected whenever there are metastable configurations which are close in energy to the ground state, but it disagrees with previous studies.

preprint2011arXiv

The energy landscape of fullerene materials: a comparison between boron, boron-nitride and carbon

Using the minima hopping global geometry optimization method on the density functional potential energy surface we study medium size and large boron clusters. Even though for isolated medium size clusters the ground state is a cage like structure they are unstable against external perturbations such as contact with other clusters. The energy landscape of larger boron clusters is glass like and has a large number of structures which are lower in energy than the cages. This is in contrast to carbon and boron nitride systems which can be clearly identified as structure seekers in our minima hopping runs. The differences in the potential energy landscape explain why carbon and boron nitride systems are found in nature whereas pure boron fullerenes have not been found.

preprint2011arXiv

Wavelet-Based Linear-Response Time-Dependent Density-Functional Theory

Linear-response time-dependent (TD) density-functional theory (DFT) has been implemented in the pseudopotential wavelet-based electronic structure program BigDFT and results are compared against those obtained with the all-electron Gaussian-type orbital program deMon2k for the calculation of electronic absorption spectra of N2 using the TD local density approximation (LDA). The two programs give comparable excitation energies and absorption spectra once suitably extensive basis sets are used. Convergence of LDA density orbitals and orbital energies to the basis-set limit is significantly faster for BigDFT than for deMon2k. However the number of virtual orbitals used in TD-DFT calculations is a parameter in BigDFT, while all virtual orbitals are included in TD-DFT calculations in deMon2k. As a reality check, we report the x-ray crystal structure and the measured and calculated absorption spectrum (excitation energies and oscillator strengths) of the small organic molecule N-cyclohexyl-2-(4-methoxyphenyl)imidazo[1,2-a]pyridin-3-amine.

preprint2011arXiv

Wavelets for Density-Functional Theory and Post-Density-Functional-Theory Calculations

We give a fairly comprehensive review of wavelets and of their application to density-functional theory (DFT) and to our recent application of a wavelet-based version of linear-response time-dependent DFT (LR-TD-DFT). Our intended audience is quantum chemists and theoretical solid-state and chemical physicists. Wavelets are a Fourier-transform-like approach which developed primarily in the latter half of the last century and which was rapidly adapted by engineers in the 1990s because of its advantages compared to standard Fourier transform techniques for multiresolution problems with complicated boundary conditions. High performance computing wavelet codes now also exist for DFT applications in quantum chemistry and solid-state physics, notably the BigDFT code described in this chapter. After briefly describing the basic equations of DFT and LR-TD-DFT, we discuss how they are solved in BigDFT and present new results on the small test molecule carbon monoxide to show how BigDFT results compare against those obtained with the quantum chemistry gaussian-type orbital (GTO) based code deMon2k. In general, the two programs give essentially the same orbital energies, but the wavelet basis of BigDFT converges to the basis set limit much more rapidly than does the GTO basis set of deMon2k. Wavelet-based LR-TD-DFT is still in its infancy, but our calculations confirm the feasibility of implementing LR-TD-DFT in a wavelet-based code.

preprint2010arXiv

Structural Metastability of Endohedral Silicon Fullerenes

Endohedrally doped Si20 fullerenes appear as appealing building blocks for nanoscale materials. We investigate their structural stability with an unbiased and systematic global geometry optimization method within density-functional theory. For a wide range of metal doping atoms, it was sufficient to explore the Born Oppenheimer surface for only a moderate number of local minima to find structures that clearly differ from the initial endohedral cages, but are considerably more favorable in terms of energy. Previously proposed structures are thus all metastable.

preprint2008arXiv

Daubechies wavelets as a basis set for density functional pseudopotential calculations

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances and an excellent efficiency for parallel calculations.

preprint2005arXiv

A wide class of four point functions of BPS operators in N=4 SYM at order g^4

The calculation of a large family of four point functions of general BPS operators in N=4 SYM is reduced to the evaluation of colour contractions. For 1/2 BPS operators O_Δthe explicit results at order g^4 for the function < O_n O_2 O_n O_2 > are given up to n=6. The OPE of the general result is performed up to the second order in the short distance expansion parameter. Two examples are given, in which the mixing of the operators in the intermediate channel can be resolved using four point functions computed by this method.

preprint2005arXiv

Rationality of the Anomalous Dimensions in N=4 SYM theory

We reconsider the general constraints on the perturbative anomalous dimensions in conformal invariant QFT and in particular in N=4 SYM with gauge group SU(N_c). We show that all the perturbative corrections to the anomalous dimension of a renormalized gauge invariant local operator can be written as polynomials in its one loop anomalous dimension. In the N=4 SYM theory the coefficients of these polynomials are rational functions of the number of colours N_c.