Evaluating LLM-based AI agents integrated with materials synthesis tools: the case of atomic layer deposition

Modern generative machine learning (ML) models can propose novel inorganic crystalline materials with targeted properties; however, synthesis planning of these materials remains difficult due to the complexity of the associated physical processes and limited availability of computational tools. We introduce a novel hybrid framework to evaluate Large Language Models (LLMs) in inorganic synthesis planning by combining thermodynamic databases with simplified kinetics models to approximate realistic synthesis conditions. As a case study, we focus on the niobium-oxygen system, which features multiple industrially relevant oxide phases with well-characterized data. In computational simulations, we compare LLM-generated synthesis routes with classical path-planning algorithms, showing that the implicit priors in LLMs can yield more viable strategies. In our evaluation setting, classical search methods serve primarily as a foil rather than a direct competitor. This illustrates the relative complexity of the problem and highlights where the LLM's implicit priors add value.

Evaluating AI agents on scientific research tasks is constrained by the time and resources required for the underlying experiments or calculations. In computational materials research, repeating the same expensive simulations across agents and trials can make evaluation impractical. We introduce CompMat-Bench, a benchmark of 94 tasks derived from recently published computational materials studies, each asking agents to complete a step toward achieving the study's scientific goal. We reproduce the research steps in advance and assess agents on preparing inputs and analyzing outputs for expensive simulations, so expensive simulations can be avoided during evaluation. The reproduced inputs and results serve as ground truth for grading agents with fixed rules, without an LLM judge. The benchmark supports four evaluation conditions: single tasks and workflows composed of related tasks, each with full or reduced methodological guidance. With full guidance on single tasks, agents based on three LLMs demonstrate the ability to complete individual materials research steps, with pass rates of 66.0-90.4% across 94 tasks. Both longer workflows and reduced guidance can limit agent performance, but in different ways for different agents: they lower the pass rates of the weaker agents, whereas the strongest agent falls only when a long workflow is combined with reduced guidance. Failure analysis attributes most failures to scientific errors rather than to errors in software usage. CompMat-Bench provides a basis for comparing agents on the steps of real materials research and for analyzing agent failure modes.

Agentic AI systems increasingly connect large language models (LLMs) to external scientific tools, yet whether and when tool access improves prediction accuracy remains uncharacterized. We present AGAPI (AtomGPT.org API), an open access platform integrating eight open-source LLMs with 18 REST endpoints (28 agent tools, 50 web apps) spanning materials databases, force fields, tight-binding band structures, X-ray diffraction, and protein structure. A three-evaluation residual decomposition on JARVIS-Leaderboard electronic-structure test sets separates agent pipeline fidelity from inherited density functional theory (DFT) functional bias. For bulk modulus and bandgap the agent reproduces JARVIS-DFT entries to numerical precision, so the experimental-reference degradation is functional bias, not agentic malfunction. On memorization-resistant test sets (57 defective supercells, 60 hypothetical compositions), tool-augmented mean absolute error (MAE) is below 0.005 eV versus 1.25 to 1.86 eV tool-free, confirming tools are indispensable where parametric knowledge is unavailable. We further demonstrate autonomous multi-step workflows including 10-operation defect-engineering pipelines. AGAPI is available at https://github.com/atomgptlab/agapi.