The automated generation of three-dimensional atomic structures from natural-language descriptions remains a persistent challenge, as large language models lack intrinsic geometric reasoning. We introduce ATLAS, a holistic framework that integrates seven modular components-ranging from a density-based structure analyzer and a JSON-based semantic bridge to a deterministic build engine, physical validator, and intent-aware scorer-to translate user prompts into physically valid coordinates. The build engine executes a component algebra that encompasses named structures, unary and binary operations (supercell, resizing, rotation, translation, union, subtraction, intersection), and geometric variables, while the validator enforces periodic-boundary conditions and system-specific checks on bonding, coordination, vacuum, and composition. ATLAS supports nine major build categories, including heterojunctions, surfaces, nanoparticles, and defects, and is equipped with a score-driven automatic refinement loop that leverages a curated test suite for systematic component-level improvement.