arXiv subjects

Guillaume Fraux

Publications and source records attributed to Guillaume Fraux.

15 recordsLinked to original sources

arXiv2025

Metatensor and metatomic: foundational libraries for interoperable atomistic machine learning

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own right, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, including low-level libraries, training utilities, and interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

physics.chem-ph↗

arXiv2025

PET-MAD, a lightweight universal interatomic potential for advanced materials modeling

Machine-learning interatomic potentials (MLIPs) have greatly extended the reach of atomic-scale simulations, offering the accuracy of first-principles calculations at a fraction of the cost. Leveraging large quantum mechanical databases and expressive architectures, recent ''universal'' models deliver qualitative accuracy across the periodic table but are often biased toward low-energy configurations. We introduce PET-MAD, a generally applicable MLIP trained on a dataset combining stable inorganic and organic solids, systematically modified to enhance atomic diversity. Using a moderate but highly-consistent level of electronic-structure theory, we assess PET-MAD's accuracy on established benchmarks and advanced simulations of six materials. Despite the small training set and lightweight architecture, PET-MAD is competitive with state-of-the-art MLIPs for inorganic solids, while also being reliable for molecules, organic materials, and surfaces. It is stable and fast, enabling the near-quantitative study of thermal and quantum mechanical fluctuations, functional properties, and phase transitions out of the box. It can be efficiently fine-tuned to deliver full quantum mechanical accuracy with a minimal number of targeted calculations.

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↗

arXiv2024

PLUMED Tutorials: a collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce ``PLUMED Tutorials'', a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

physics.ed-ph↗

arXiv2024

i-PI 3.0: a flexible and efficient framework for advanced atomistic simulations

Atomic-scale simulations have progressed tremendously over the past decade, largely due to the availability of machine-learning interatomic potentials. These potentials combine the accuracy of electronic structure calculations with the ability to reach extensive length and time scales. The i-PI package facilitates integrating the latest developments in this field with advanced modeling techniques, thanks to a modular software architecture based on inter-process communication through a socket interface. The choice of Python for implementation facilitates rapid prototyping but can add computational overhead. In this new release, we carefully benchmarked and optimized i-PI for several common simulation scenarios, making such overhead negligible when i-PI is used to model systems up to tens of thousands of atoms using widely adopted machine learning interatomic potentials, such as Behler-Parinello, DeePMD and MACE neural networks. We also present the implementation of several new features, including an efficient algorithm to model bosonic and fermionic exchange, a framework for uncertainty quantification to be used in conjunction with machine-learning potentials, a communication infrastructure that allows deeper integration with electronic-driven simulations, and an approach to simulate coupled photon-nuclear dynamics in optical or plasmonic cavities.

physics.chem-ph↗

arXiv2024

Surface segregation in high-entropy alloys from alchemical machine learning

High-entropy alloys (HEAs), containing several metallic elements in near-equimolar proportions, have long been of interest for their unique mechanical properties. More recently, they have emerged as a promising platform for the development of novel heterogeneous catalysts, because of the large design space, and the synergistic effects between their components. In this work we use a machine-learning potential that can model simultaneously up to 25 transition metals to study the tendency of different elements to segregate at the surface of a HEA. We use as a starting point a potential that was previously developed using exclusively crystalline bulk phases, and show that, thanks to the physically-inspired functional form of the model, adding a much smaller number of defective configurations makes it capable of describing surface phenomena. We then present several computational studies of surface segregation, including both a simulation of a 25-element alloy, that provides a rough estimate of the relative surface propensity of the various elements, and targeted studies of CoCrFeMnNi and IrFeCoNiCu, which provide further validation of the model, and insights to guide the modeling and design of alloys for heterogeneous catalysis.

cond-mat.mtrl-sci↗

arXiv2023

Fast evaluation of spherical harmonics with sphericart

Spherical harmonics provide a smooth, orthogonal, and symmetry-adapted basis to expand functions on a sphere, and they are used routinely in physical and theoretical chemistry as well as in different fields of science and technology, from geology and atmospheric sciences to signal processing and computer graphics. More recently, they have become a key component of rotationally equivariant models in geometric machine learning, including applications to atomic-scale modeling of molecules and materials. We present an elegant and efficient algorithm for the evaluation of the real-valued spherical harmonics. Our construction features many of the desirable properties of existing schemes and allows to compute Cartesian derivatives in a numerically stable and computationally efficient manner. To facilitate usage, we implement this algorithm in sphericart, a fast C++ library which also provides C bindings, a Python API, and a PyTorch implementation that includes a GPU kernel.

physics.chem-ph↗

arXiv2023

Modeling high-entropy transition-metal alloys with alchemical compression

Alloys composed of several elements in roughly equimolar composition, often referred to as high-entropy alloys, have long been of interest for their thermodynamics and peculiar mechanical properties, and more recently for their potential application in catalysis. They are a considerable challenge to traditional atomistic modeling, and also to data-driven potentials that for the most part have memory footprint, computational effort and data requirements which scale poorly with the number of elements included. We apply a recently proposed scheme to compress chemical information in a lower-dimensional space, which reduces dramatically the cost of the model with negligible loss of accuracy, to build a potential that can describe 25 d-block transition metals. The model shows semi-quantitative accuracy for prototypical alloys, and is remarkably stable when extrapolating to structures outside its training set. We use this framework to study element segregation in a computational experiment that simulates an equimolar alloy of all 25 elements, mimicking the seminal experiments by Cantor et al., and use our observations on the short-range order relations between the elements to define a data-driven set of Hume-Rothery rules that can serve as guidance for alloy design. We conclude with a study of three prototypical alloys, CoCrFeMnNi, CoCrFeMoNi and IrPdPtRhRu, determining their stability and the short-range order behavior of their constituents.

cond-mat.mtrl-sci↗

arXiv2022

Unified theory of atom-centered representations and message-passing machine-learning schemes

Data-driven schemes that associate molecular and crystal structures with their microscopic properties share the need for a concise, effective description of the arrangement of their atomic constituents. Many types of models rely on descriptions of atom-centered environments, that are associated with an atomic property or with an atomic contribution to an extensive macroscopic quantity. Frameworks in this class can be understood in terms of atom-centered density correlations (ACDC), that are used as a basis for a body-ordered, symmetry-adapted expansion of the targets. Several other schemes, that gather information on the relationship between neighboring atoms using "message-passing" ideas, cannot be directly mapped to correlations centered around a single atom. We generalize the ACDC framework to include multi-centered information, generating representations that provide a complete linear basis to regress symmetric functions of atomic coordinates, and provides a coherent foundation to systematize our understanding of both atom-centered and message-passing, invariant and equivariant machine-learning schemes.

stat.ML↗

arXiv2021

Efficient implementation of atom-density representations

Physically-motivated and mathematically robust atom-centred representations of molecular structures are key to the success of modern atomistic machine learning (ML) methods. They lie at the foundation of a wide range of methods to predict the properties of both materials and molecules as well as to explore and visualize the chemical compound and configuration space. Recently, it has become clear that many of the most effective representations share a fundamental formal connection: that they can all be expressed as a discretization of N-body correlation functions of the local atom density, suggesting the opportunity of standardizing and, more importantly, optimizing the calculation of such representations. We present an implementation, named librascal, whose modular design lends itself both to developing refinements to the density-based formalism and to rapid prototyping for new developments of rotationally equivariant atomistic representations. As an example, we discuss SOAP features, perhaps the most widely used member of this family of representations, to show how the expansion of the local density can be optimized for any choice of radial basis set. We discuss the representation in the context of a kernel ridge regression model, commonly used with SOAP features, and analyze how the computational effort scales for each of the individual steps of the calculation. By applying data reduction techniques in feature space, we show how to further reduce the total computational cost by at up to a factor of 4 or 5 without affecting the model's symmetry properties and without significantly impacting its accuracy.

physics.chem-ph↗

arXiv2020

The role of feature space in atomistic learning

Eficient, physically-inspired descriptors of the structure and composition of molecules and materials play a key role in the application of machine-learning techniques to atomistic simulations. The proliferation of approaches, as well as the fact that each choice of features can lead to very different behavior depending on how they are used, e.g. by introducing non-linear kernels and non-Euclidean metrics to manipulate them, makes it difficult to objectively compare different methods, and to address fundamental questions on how one feature space is related to another. In this work we introduce a framework to compare different sets of descriptors, and different ways of transforming them by means of metrics and kernels, in terms of the structure of the feature space that they induce. We define diagnostic tools to determine whether alternative feature spaces contain equivalent amounts of information, and whether the common information is substantially distorted when going from one feature space to another. We compare, in particular, representations that are built in terms of n-body correlations of the atom density, quantitatively assessing the information loss associated with the use of low-order features. We also investigate the impact of different choices of basis functions and hyperparameters of the widely used SOAP and Behler-Parrinello features, and investigate how the use of non-linear kernels, and of a Wasserstein-type metric, change the structure of the feature space in comparison to a simpler linear feature space.

physics.comp-ph↗

arXiv2020

Structure-Property Maps with Kernel Principal Covariates Regression

Data analyses based on linear methods constitute the simplest, most robust, and transparent approaches to the automatic processing of large amounts of data for building supervised or unsupervised machine learning models. Principal covariates regression (PCovR) is an underappreciated method that interpolates between principal component analysis and linear regression, and can be used to conveniently reveal structure-property relations in terms of simple-to-interpret, low-dimensional maps. Here we provide a pedagogic overview of these data analysis schemes, including the use of the kernel trick to introduce an element of non-linearity, while maintaining most of the convenience and the simplicity of linear approaches. We then introduce a kernelized version of PCovR and a sparsified extension, and demonstrate the performance of this approach in revealing and predicting structure-property relations in chemistry and materials science, showing a variety of examples including elemental carbon, porous silicate frameworks, organic molecules, amino acid conformers, and molecular materials.

stat.ML↗

arXiv2018

On the use of the IAST method for gas separation studies in porous materials with gate-opening behavior

Highly flexible nanoporous materials, exhibiting for instance gate opening or breathing behavior, are often presented as candidates for separation processes due to their supposed high adsorption selectivity. But this view, based on "classical" considerations of rigid materials and the use of the Ideal Adsorbed Solution Theory (IAST), does not necessarily hold in the presence of framework deformations. Here, we revisit some results from the published literature and show how proper inclusion of framework flexibility in the osmotic thermodynamic ensemble drastically changes the conclusions, in contrast to what intuition and standard IAST would yield. In all cases, the IAST method does not reproduce the gate-opening behavior in the adsorption of mixtures, and may overestimates the selectivity by up to two orders of magnitude.

physics.chem-ph↗

arXiv2018

Recent advances in the computational chemistry of soft porous crystals

Here we highlight recent progress in the field of computational chemistry of nanoporous materials, focusing on methods and studies that address the extraordinary dynamic nature of these systems: the high flexibility of their frameworks, the large-scale structural changes upon external physical or chemical stimulation, and the presence of defects and disorder. The wide variety of behavior demonstrated in soft porous crystals, including the topical class of metal-organic frameworks, opens new challenges for computational chemistry methods at all scales.

physics.chem-ph↗

arXiv2014

Heterogeneous ice nucleation on silver-iodide-like surfaces

We attempt to simulate the heterogeneous nucleation of ice at model silver-iodide surfaces and find relatively facile ice nucleation and growth at the Ag+ termi nated basal face, but never see nucleation at the I- terminated basal face or the prism and normal faces. Water molecules strongly adsorb onto the Ag+ terminate d face to give a well-ordered hexagonal ice-like bilayer that then acts as a template for further ice growth.

cond-mat.mtrl-sci↗