arXiv subjects

Sara Bonella

Publications and source records attributed to Sara Bonella.

At least 19 recordsLinked to original sources

arXiv2026

P3MaZe: a Mass-Zero constrained-dynamics formulation of particle-mesh electrostatics

We introduce P3MaZe, a real-space particle-mesh electrostatic method that combines the standard short-range/long-range decomposition of Particle-Particle Particle-Mesh (P3M) electrostatics with the Mass-Zero constrained dynamics (MaZe) framework. In this formulation, the smooth long-range electrostatic potential is represented on a mesh as a zero-inertia auxiliary field, while the discretized Poisson equation is enforced as a holonomic constraint during molecular dynamics. By retaining the standard P3M decomposition, P3MaZe preserves the systematic accuracy controls associated with the real-space cutoff, the Ewald splitting, the mesh spacing, and the charge-assignment procedure, while replacing the conventional multigrid Poisson solver by a constrained correction problem. The method is validated for molten NaCl and simple point-charge flexible water (SPC/Fw). Structural, translational, collective, and rotational dynamical observables are in quantitative agreement with those obtained with established electrostatic methods, including real-space P3M, and Ewald summation. The constrained formulation consistently requires fewer multigrid iterations than the corresponding real-space P3M solver while retaining the expected linear scaling with system size. These results establish P3MaZe as a promising new direction for scalable real-space electrostatics in large-scale molecular simulations.

physics.comp-ph↗

arXiv2026

Perspective on a challenge: predicting the photochemistry of cyclobutanone

This Perspective is part of a Special Topic that explored the maturity of nonadiabatic molecular dynamics for predicting photochemical processes. In 2023, a prediction challenge was issued to the community of computational photochemists to simulate the photochemistry of cyclobutanone, photoexcited at 200 nm, and the resulting time-resolved MeV-UED signal. The challenge attracted 15 theoretical predictions from more than 70 researchers, employing a wide range of strategies for electronic structure and nonadiabatic molecular dynamics to predict the time-resolved MeV-UED signal before the experiment had been conducted at SLAC (Stanford, USA). The MeV-UED instrument at Shanghai Jiao Tong University was also used to provide a second independent time-resolved MeV-UED signal for the photochemistry of cyclobutanone. This Perspective discusses the various approaches and strategies used by the participants to predict the photochemistry of cyclobutanone. This work also summarizes the strengths and weaknesses of various methods used for photoexcitation, electronic structure, nonadiabatic dynamics, and calculation of observables, as agreed by the participants during a CECAM workshop dedicated to the results of the challenge and organized in Lausanne in April 2025. This Perspective also collects all the predicted time-resolved MeV-UED signals into a single figure, together with the experimental signal. This challenge (i) demonstrated the qualitative predictive power of nonadiabatic molecular dynamics and (ii) underscore the impact of electronic-structure theory on the outcome of the excited-state dynamics and the need for its careful benchmarking. This effort allowed the community to share practical strategies to perform nonadiabatic dynamics (discussed in the present Perspective) and constitutes a 'calibration' exercise for computational photochemistry.

physics.chem-ph↗

arXiv2025

Electrically driven first-order phase transition of a 2D ionic crystal at the electrode/electrolyte interface

Liquid electrolytes adsorbed at the surface of metallic electrodes display a multitude of structures that can largely differ from the parent bulk system, both in terms of composition and local organization. In particular, the existence of disorder-order or order-order transitions has been increasingly reported in experimental and simulation studies, and the electrode potential identified as the corresponding driving force. The microscopic mechanisms and the stages of the process are, however, poorly understood, and the free energy variation during the transition remain insufficiently characterized. To fill this gap, we investigate the crystallization of the adsorbed layer in a prototypical molten salt-metal interface. We demonstrate that the transition from the disordered to ordered structures proceeds in two stages. Pre-ordering effects are observed across a wide range of potentials, resulting in the formation of a poly-crystalline structure on the electrode surface, before an abrupt ordering transition finally occurs. The pre-ordering displays signature of a continuous transition. On the other hand, finite-size effects analysis proves the first-order character of the transition towards the mono-crystalline state. Upon increasing the system size, a shift in the onset applied voltage is observed, accompanied by a dramatic increase in the free energy barrier. The latter reflects in the interfacial capacitance, which displays a peak that sharpens with increasing system size.

physics.chem-ph↗

arXiv2025

scicode-widgets: Bringing Computational Experiments to the Classroom with Jupyter Widgets

"Computational experiments" use code and interactive visualizations to convey mathematical and physical concepts in an intuitive way, and are increasingly used to support ex cathedra lecturing in scientific and engineering disciplines. Jupyter notebooks are particularly well-suited to implement them, but involve large amounts of ancillary code to process data and generate illustrations, which can distract students from the core learning outcomes. For a more engaging learning experience that only exposes relevant code to students, allowing them to focus on the interplay between code, theory and physical insights, we developed scicode-widgets (released as scwidgets), a Python package to build Jupyter-based applications. The package facilitates the creation of interactive exercises and demonstrations for students in any discipline in science, technology and engineering. Students are asked to provide pedagogically meaningful contributions in terms of theoretical understanding, coding ability, and analytical skills. The library provides the tools to connect custom pre- and post-processing of students' code, which runs seamlessly "behind the scenes", with the ability to test and verify the solution, as well as to convert it into live interactive visualizations driven by Jupyter widgets.

physics.ed-ph↗

arXiv2025

Anharmonic phonons via quantum thermal bath simulations

Lattice vibrations within crystalline solids, or phonons, provide information on a variety of important material characteristics, from thermal qualities to optical properties and phase transition behaviour. When the material contains light ions, or is subjected to sufficiently low temperatures and/or high pressures, anharmonic and nuclear quantum effects (NQEs) may significantly alter its phonon characteristics. Unfortunately, accurate inclusion of these two effects within numerical simulations typically incurs a substantial computational cost. In this work, we present a novel approach which promises to mitigate this problem. The scheme leverages the recently introduced quantum correlators approach for the extraction of anharmonic phonon frequencies from molecular dynamics data. To account for NQEs without excessive increase of the computational cost, we include nuclear quantum effects via the quantum thermal bath (QTB) method. This is the first full exploration of the use of QTB for the calculation of phonon dispersion relations. We demonstrate the noteworthy efficiency and accuracy of the scheme, and analyze its upsides and drawbacks by first considering 1-dimensional systems, and then the physically interesting case of solid neon.

physics.comp-ph↗

arXiv2025

Correcting systematic errors in the likelihood optimization of underdamped Langevin models of molecular dynamics trajectories

Since Kramers' pioneering work in 1940, significant efforts have been devoted to studying Langevin equations applied to physical and chemical reactions projected onto few collective variables, with particular focus on the inference of their parameters. While the inference for overdamped Langevin equations is well-established and widely applied, a notable gap remains in the literature for underdamped Langevin equation. This gap arises from the challenge of accessing velocities solely through finite differences of positions, resulting in spurious correlations. In this letter, we propose an analytical correction for these correlations, specifically designed for a likelihood-maximization algorithm that exploits short, non-ergodic trajectories that can be obtained at reasonable numerical cost. The accuracy and robustness of our approach are tested on a benchmark case and a realistic system. This work paves the way for applying generalized Langevin equation inference to activated phenomena, such as chemical reactions, in several scientific domains.

cond-mat.stat-mech↗

arXiv2025

Mass-Zero constrained molecular dynamics for electrostatic interactions

Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald sums and achieve semi-logarithmic scaling in the number of particles. These methods solve the problem in reciprocal space, requiring extensive use of Fast Fourier transforms (FFTs). While highly efficient in many contexts, FFTs may encounter scalability challenges at very large processor counts due to their communication requirements. To mitigate these problems, the development and scalable coding of real-space approaches to solve the Poisson equation on a grid is an active field of research. In this work, we introduce a novel real-space approach that provides some advantages over alternatives. Our method exploits an extended Lagrangian in which the values of the field at the grid points are treated as auxiliary variables of zero inertia and the discretized Poisson equation is enforced as a dynamical constraint. The solution of the constraints leads to a linear system - different from those appearing in other real-space approaches - that can be efficiently solved via state-of-the-art iterative methods. The method inherits the numerical scaling of the adopted iterative solver, e.g. linear with a multigrid (MG) approach, but converges with fewer cycles. We analyze this approach considering realistic simulations of molten NaCl that validate its ability to reproduce structural and transport properties. Using this non-trivial benchmark, we demonstrate linear scaling and illustrate some features of our algorithm.

physics.comp-ph↗

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↗

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↗

arXiv2022

Mass-Zero constrained dynamics for simulations based on orbital-free density functional theory

A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case the recently introduced Mass-Zero (MaZe) constrained dynamics. The formalism ensures that full adiabatic separation is enforced between nuclear and electronic degrees of freedom and, consequently, that the exact Born-Oppenheimer probability for the nuclei is sampled. Numerical integration of the MaZe dynamics combines standard molecular dynamics algorithms, e.g. Verlet or velocity Verlet, with the SHAKE method to impose the minimum conditions on the electronic degrees of freedom as a set of constraints. The developments presented in this work, that include a bespoke adaptation of the standard SHAKE algorithm, ensure that the quasilinear scaling of OFDFT is preserved by the new method for a broad range of kinetic and exchange-correlation functionals, including nonlocal ones. The efficiency and accuracy of the approach is demonstrated via calculations of static and dynamic properties of liquid sodium in the constant energy and constant temperature ensembles.

cond-mat.stat-mech↗

arXiv2022

OSSCAR, an open platform for collaborative development of computational tools for education in science

In this paper we present the Open Software Services for Classrooms and Research (OSSCAR) platform. OSSCAR provides an open collaborative environment to develop, deploy and access educational resources in the form of web applications. To minimize efforts in the creation and use of new educational material, it combines software tools that have emerged as standards with custom domain-specific ones. The technical solutions adopted to create and distribute content are described and motivated on the basis of reliability, sustainability, ease of uptake and use. Examples from courses in the domains of physics, chemistry, and materials science are shown to demonstrate the style and level of interactivity of typical applications. The tools presented are easy to use, and create a uniform and open environment exploitable by a large community of teachers, students, and researchers with the goal of facilitating learning and avoiding, when possible, duplication of efforts in creating teaching material. Contributions to expand the educational content of the OSSCAR project are welcome.

physics.ed-ph↗

arXiv2021

Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath

We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQE) in molecular simulations: the adaptive Quantum Thermal Bath (adQTB). In this method, zero point energy is introduced through a generalized Langevin thermostat designed to precisely enforce the quantum fluctuation-dissipation theorem. We propose a refined adQTB algorithm with improved accuracy and we report adQTB simulations of liquid water. Through extensive comparison with reference path integral calculations, we demonstrate that it provides excellent accuracy for a broad range of structural and thermodynamic observables as well as infrared vibrational spectra. The adQTB has a computational cost comparable to classical molecular dynamics, enabling simulations of up to millions of degrees of freedom.

physics.chem-ph↗

arXiv2021

Mass-Zero constrained dynamics and statistics for the shell model in magnetic field

In several domains of physics, including first principle simulations and classical models for polarizable systems, the minimization of an energy function with respect to a set of auxiliary variables must be performed to define the dynamics of physical degrees of freedom. In this paper, we discuss a recent algorithm proposed to efficiently and rigorously simulate this type of systems: the Mass-Zero (MaZe) Constrained Dynamics. In MaZe the minimum condition is imposed as a constraint on the auxiliary variables treated as degrees of freedom of zero inertia driven by the physical system. The method is formulated in the Lagrangian framework, enabling the properties of the approach to emerge naturally from a fully consistent dynamical and statistical viewpoint. We begin by presenting MaZe for typical minimization problems where the imposed constraints are holonomic and summarizing its key formal properties, notably the exact Born-Oppenheimer dynamics followed by the physical variables and the exact sampling of the corresponding physical probability density. We then generalize the approach to the case of conditions on the auxiliary variables that linearly involve their velocities. Such conditions occur, for example, when describing systems in external magnetic field and they require to adapt MaZe to integrate semiholonomic constraints. The new development is presented in the second part of this paper and illustrated via a proof-of-principle calculation of the charge transport properties of a simple classical polarizable model of NaCl.

physics.comp-ph↗

arXiv2020

Fluctuation relations for dissipative systems in constant external magnetic field: theory and molecular dynamics simulations

It has recently been pointed out that Hamiltonian particle systems in constant magnetic fields satisfy generalized time-reversal symmetries that enable to prove useful statistical relationships based on equilibrium phase-space probability distributions without the need to invert, as commonly considered necessary, the magnetic field. Among these relations, that hold without need of Casimir modifications, one finds the standard linear response Green-Kubo relations, and consequently the Onsager reciprocal relations. Going beyond linear response is also possible, for instance in terms of transient and steady state Fluctuation Relations (FRs). Here we highlight how the generalized time-reversal symmetries ensure that the (transient) FRs theory directly applies also for systems in external magnetic fields. Furthermore we show that transient FR can indeed be verified in nonequilibrium molecular dynamics simulations, for systems subjected to magnetic and electric fields, which are thermostatted à la Nosé-Hoover. The result is nontrivial because, since it is not immediate within which sizes and time scales the effects can actually be observable, it is not obvious what one may obtain by real molecular dynamics simulations.

cond-mat.stat-mech↗

arXiv2020

Fluctuation relations for systems in constant magnetic field

The validity of the Fluctuation Relations (FR) for systems in a constant magnetic field is investigated. Recently introduced time-reversal symmetries that hold in presence of static electric and magnetic fields and of deterministic thermostats are used to prove the transient FR without invoking, as commonly done, inversion of the magnetic field. Steady-state FR are also derived, under the t-mixing condition. These results extend the predictive power of important statistical mechanics relations. We illustrate this via the non-linear response for the cumulants of the dissipation, showing how the new FR enable to determine analytically null cumulants also for systems in a single magnetic field.

cond-mat.stat-mech↗

arXiv2020

Mass-zero constrained molecular dynamics for electrode charges in simulations of electrochemical systems

Classical molecular dynamics simulations have recently become a standard tool for the study of electrochemical systems. State-of-the-art approaches represent the electrodes as perfect conductors, modelling their responses to the charge distribution of electrolytes via the so-called fluctuating charge model. These fluctuating charges are additional degrees of freedom that, in a Born-Oppenheimer spirit, adapt instantaneously to changes in the environment to keep each electrode at a constant potential. Here we show that this model can be treated in the framework of constrained molecular dynamics, leading to a symplectic and time-reversible algorithm for the evolution of all the degrees of freedom of the system. The computational cost and the accuracy of the new method are similar to current alternative implementations of the model. The advantage lies in the accuracy and long term stability guaranteed by the formal properties of the algorithm and in the possibility to systematically introduce additional kinematic conditions of arbitrary number and form. We illustrate the performance of the constrained dynamics approach by enforcing the electroneutrality of the electrodes in a simple capacitor consisting of two graphite electrodes separated by a slab of liquid water.

cond-mat.stat-mech↗

arXiv2020

Adiabatic motion and statistical mechanics via mass zero constrained dynamics

In recent work [Coretti et al., The Journal of Chemical Physics, 2018, 149, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical variables, employs constrained molecular dynamics to strictly enforce the condition that the force on the fast degrees of freedom, modeled as having zero mass, is null at each time step. The algorithm is symplectic and fully time reversible, and results in stable and efficient propagation. In this paper we complete the discussion of the mechanics of mass zero constrained dynamics by showing how to adapt it to problems where the fast degrees of freedom must satisfy additional conditions. This extension includes, in particular, the important case of first principles molecular dynamics. We then consider the statistical mechanics of the mass zero constrained dynamical system demonstrating that the marginal probability sampled by the dynamics in the physical phase space recovers the form of the Born-Oppenheimer probability density.

cond-mat.stat-mech↗

arXiv2019

Charge fluctuations from molecular simulations in the constant-potential ensemble

We revisit the statistical mechanics of charge fluctuations in capacitors. In constant-potential classical molecular simulations, the atomic charge of electrode atoms are treated as additional degrees of freedom which evolve in time so as to satisfy the constraint of fixed electrostatic potential for each configuration of the electrolyte. The present work clarifies the role of the overall electroneutrality constraint, as well as the link between the averages computed within the Born-Oppenheimer approximation and that of the full constant-potential ensemble. This allows us in particular to derive a complete fluctuation-dissipation relation for the differential capacitance, that includes a contribution from the charge fluctuations (around the charges satisfying the constant-potential and electroneutrality constraints) also present in the absence of an electrolyte. We provide a simple expression for this contribution from the elements of the inverse of the matrix defining the quadratic form of the fluctuating charges in the energy. We then illustrate numerically the validity of our results, and recover the expected result for an empty capacitor with structureless electrodes at large inter-electrode distances. By considering a variety of liquids between graphite electrodes, we confirm that this contribution to the total differential capacitance is small compared to that induced by the thermal fluctuations of the electrolyte.

cond-mat.stat-mech↗