AtomWorld: A Benchmark for Evaluating Spatial Reasoning in Large Language Models on Crystalline Materials

Abstract

Large Language Models (LLMs) excel at textual reasoning and are beginning to develop spatial understanding, prompting the question of whether these abilities can be combined for complex, domain-specific tasks. This question is essential in fields like materials science, where deep understanding of 3D atomic structures is fundamental. While initial studies have successfully applied LLMs to tasks involving pure crystal generation or coordinate understandings, a standardized benchmark to systematically evaluate their core reasoning abilities across diverse atomic structures has been notably absent. To address this gap, we introduce the AtomWorld benchmark to evaluate LLMs on tasks based in Crystallographic Information Files (CIFs), a standard structure representation format. These tasks, including structural editing, CIF perception, and property-guided modeling, reveal a critical limitation: current models, despite establishing promising baselines, consistently fail in structural understanding and spatial reasoning. Our experiments show that these models make frequent errors on structure modification tasks, and even in the basic CIF format understandings, potentially leading to cumulative errors in subsequent analysis and materials insights. By defining these standardized tasks, AtomWorld lays the ground for advancing LLMs toward robust atomic-scale modeling, crucial for accelerating materials research and automating scientific workflows.