LATHE: LAnguage-driven Toolkit for Hypothesis-based crystal Editing

Abstract

Manipulating crystal structures towards targeted geometric properties or symmetry constraints is a longstanding challenge. Existing computational frameworks fall short: LLMs have poor spatial awareness and operate at coarse granularity in the token space, while diffusion- and gradient-based structure generation approaches generally produce complete structures \textit{de novo} rather allowing for fine-grained editing of a given input under arbitrary constraints. We present LATHE, a geometric toolkit that closes this gap by expressing seven classes of crystallographic properties --- bond length, bond angle, dihedral angle, coordination environment, lattice parameters, cell volume, and space group, as differentiable objectives to enable direct geometric editing of crystal structures. To demonstrate its usage in materials design, we further expose LATHE through a Model Context Protocol server and embed it in a closed-loop multi-agent system which translates hypotheses intogeometric modifications in natural language towards a given design objective. Across single-property benchmarks, LATHE attains near-perfect constraint satisfaction on all seven property types while keeping optimized structures close to local energy minima. The LATHE-equipped agent translates over 87.5\% of natural-language prompts into valid executable configurations and faithfully completes them. In a band-gap inverse-design case study, the multi-agent loop reaches the target tolerance window in nine of ten independent runs at a typical cost of thirteen hypothesis-evaluation cycles. By bridging natural-language hypothesis generation and physically grounded gradient-based structural editing, this work establishes a paradigm for interpretable, closed-loop computational materials discovery that is immediately applicable to a broad class of functional material design tasks.