arXiv subjects

Juan C. Verduzco

Publications and source records attributed to Juan C. Verduzco.

7 recordsLinked to original sources

arXiv2026

Evaluating LLM-generated code for domain-specific languages: molecular dynamics with LAMMPS

Large language models (LLMs) are changing the way researchers interact with code and data in scientific computing. While their ability to generate general-purpose code is well established, their effectiveness in producing scientifically valid scripts for domain-specific language (DSLs) remains largely unexplored. We propose an evaluation procedure that enables domain experts to assess the validity of LLM-generated input files for LAMMPS, a widely used molecular dynamics (MD) code, without requiring deep familiarity with its syntax. The evaluation procedure combines a normalization step that produces canonical input files with an extensible parser for syntax analysis, followed by a reduced-cost execution stage and accuracy checks that isolate common errors before running costly simulations. We apply the pipeline to eight state-of-the-art LLMs across three prompts of increasing complexity. The parser pass rate has improved from 74% to 91% over the past year, but scientific accuracy on coupled multi-step workflows remains limited. Across all 80 scripts evaluated on the most complex prompt, only one was fully correct as generated. We further package the automated stages as a reusable agentic skill that LLMs can invoke during script generation; in a small-scale demonstration, this skill helped two models produce five fully correct scripts out of six across the same three prompts, including the hardest one. The pipeline highlights both the limitations of current LLMs in generating scientific DSLs and a practical path toward integrating them into domain-specific computational ecosystems.

cs.SE↗

arXiv2025

A collaborative digital twin built on FAIR data and compute infrastructure

The integration of machine learning with automated experimentation in self-driving laboratories (SDL) offers a powerful approach to accelerate discovery and optimization tasks in science and engineering applications. When supported by findable, accessible, interoperable, and reusable (FAIR) data infrastructure, SDLs with overlapping interests can collaborate more effectively. This work presents a distributed SDL implementation built on nanoHUB services for online simulation and FAIR data management. In this framework, geographically dispersed collaborators conducting independent optimization tasks contribute raw experimental data to a shared central database. These researchers can then benefit from analysis tools and machine learning models that automatically update as additional data become available. New data points are submitted through a simple web interface and automatically processed using a nanoHUB Sim2L, which extracts derived quantities and indexes all inputs and outputs in a FAIR data repository called ResultsDB. A separate nanoHUB workflow enables sequential optimization using active learning, where researchers define the optimization objective, and machine learning models are trained on-the-fly with all existing data, guiding the selection of future experiments. Inspired by the concept of ``frugal twin", the optimization task seeks to find the optimal recipe to combine food dyes to achieve the desired target color. With easily accessible and inexpensive materials, researchers and students can set up their own experiments, share data with collaborators, and explore the combination of FAIR data, predictive ML models, and sequential optimization. The tools introduced are generally applicable and can easily be extended to other optimization problems.

cs.AI↗

arXiv2024

Accelerating active learning materials discovery with FAIR data and workflows: a case study for alloy melting temperatures

Active learning (AL) is a powerful sequential optimization approach that has shown great promise in the discovery of new materials. However, a major challenge remains the acquisition of the initial data and the development of workflows to generate new data at each iteration. In this study, we demonstrate a significant speedup in an optimization task by reusing a published simulation workflow available for online simulations and its associated data repository, where the results of each workflow run are automatically stored. Both the workflow and its data follow FAIR (findable, accessible, interoperable, and reusable) principles using nanoHUB's infrastructure. The workflow employs molecular dynamics to calculate the melting temperature of multi-principal component alloys. We leveraged all prior data not only to develop an accurate machine learning model to start the sequential optimization but also to optimize the simulation parameters and accelerate convergence. Prior work showed that finding the alloy composition with the highest melting temperature required testing 15 alloy compositions, and establishing the melting temperature for each composition took, on average, 4 simulations. By developing a workflow that utilizes the FAIR data in the nanoHUB database, we reduced the number of simulations per composition to one and found the alloy with the lowest melting temperature testing only three compositions. This second optimization, therefore, shows a speedup of 10x as compared to models that do not access the FAIR databases.

cond-mat.mtrl-sci↗

arXiv2023

GPT-4 as an interface between researchers and computational software: improving usability and reproducibility

Large language models (LLMs) are playing an increasingly important role in science and engineering. For example, their ability to parse and understand human and computer languages makes them powerful interpreters and their use in applications like code generation are well-documented. We explore the ability of the GPT-4 LLM to ameliorate two major challenges in computational materials science: i) the high barriers for adoption of scientific software associated with the use of custom input languages, and ii) the poor reproducibility of published results due to insufficient details in the description of simulation methods. We focus on a widely used software for molecular dynamics simulations, the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), and quantify the usefulness of input files generated by GPT-4 from task descriptions in English and its ability to generate detailed descriptions of computational tasks from input files. We find that GPT-4 can generate correct and ready-to-use input files for relatively simple tasks and useful starting points for more complex, multi-step simulations. In addition, GPT-4's description of computational tasks from input files can be tuned from a detailed set of step-by-step instructions to a summary description appropriate for publications. Our results show that GPT-4 can reduce the number of routine tasks performed by researchers, accelerate the training of new users, and enhance reproducibility.

cond-mat.mtrl-sci↗

arXiv2023

Atomistic mechanisms underlying the maximum in diffusivity in doped Li$_7$La$_3$Zr$_2$O$_{12}$

Doped lithium lanthanum zirconium oxide (LLZO) is a promising class of solid electrolytes for lithium-ion batteries due to their good electrochemical stability and compatibility with Li metal anodes. Ionic diffusivity in these ceramics is known to occur via correlated, vacancy mediated, jumps of Li+ between alternating tetrahedral and octahedral sites. Aliovalent doping at the Zr-site increases the concentration of vacancies in the Li+ sublattice and cation diffusivity, but such an increase is universally followed by a decrease for Li+ concentration lower than 6.3 - 6.5 Li molar content. Molecular dynamics simulations based on density functional theory show that the maximum in diffusivity originates from competing effects between the increased vacancy concentration and the increasing occupancy of the low-energy tetrahedral sites by Li+, which increases the overall activation energy associated with diffusion. For the relatively high temperatures of our simulations, Li+ concentration plays a dominant role in transport as compared to dopant chemistry.

cond-mat.mtrl-sci↗

arXiv2021

Active learning and molecular dynamics simulations to find high melting temperature alloys

Active learning (AL) can drastically accelerate materials discovery; its power has been shown in various classes of materials and target properties. Prior efforts have used machine learning models for the optimal selection of physical experiments or physics-based simulations. However, the latter efforts have been mostly limited to the use of electronic structure calculations and properties that can be obtained at the unit cell level and with negligible noise. We couple AL with molecular dynamics simulations to identify multiple principal component alloys (MPCAs) with high melting temperatures. Building on cloud computing services through nanoHUB, we present a fully autonomous workflow for the efficient exploration of the high dimensional compositional space of MPCAs. We characterize how uncertainties arising from the stochastic nature of the simulations and the acquisition functions used to select simulations affect the convergence of the approach. Interestingly, we find that relatively short simulations with significant uncertainties can be used to efficiently find the desired alloys as the random forest models used for AL average out fluctuations.

cond-mat.mtrl-sci↗

arXiv2021

Hybrid Polymer-Garnet Materials for All-Solid-State Energy Storage Devices

Hybrid electrolyte materials comprising polymer-ionic salt matrixes embedded with garnet particles constitute a promising class of materials for the realization of all-solid-state batteries. In addition to providing solutions to the safety issues inherent to current liquid electrolytes, hybrid polymer electrolytes offer advantages over other solid-state electrolytes. This is because their functional properties such as ionic conductivity, electrochemical stability, mechanical and thermal properties can be tailored to a particular application by independently optimizing the properties of the constituent materials. Thereby, providing a rational approach to solving bottlenecks currently preventing solid-state electrolytes from practical implementation into battery devices. This review starts with a survey of solid-state electrolytes, focusing on their materials and ion transport limitations. Next, we summarize the current understanding of transport mechanisms in composite polymer electrolytes (CPEs) with the purpose of identifying materials solutions for further improving their properties. The overall goal of the review is to foster heightened research interest in these hybrid structures to rapidly advance development of future all-solid-state battery devices.

physics.app-ph↗