SCALAR: Quantifying Structural Hallucination, Consistency, and Reasoning Gaps in Materials Foundation Models

Large language models are increasingly applied to materials science reasoning, yet their behavior under physically structured distribution shifts remains poorly understood. We introduce SCALAR (Structural Consistency And Logic Across Regimes), a benchmark for evaluating geometric scale generalization and its connection to structural hallucination, consistency, and reasoning in materials foundation models. Given canonical crystal representations, models must reason about derived nanoparticle structures obtained through supercell expansion and geometric truncation across length scales spanning a few atoms to over 18,000 atoms, totaling $\approx$100,000 structures from DFT-validated unit cells. SCALAR defines three tasks. (i) CIF to property prediction. (ii) A Chain-of-Thought variant with explicit physics-grounded reasoning. (iii) Inverse retrieval identifying crystals from candidates given target properties. Outputs are evaluated via structured metrics capturing numeric error, hallucination, cross-prompt consistency, monotonic reasoning, output validity, and retrieval regret. Experiments across diverse foundation models reveal large, model-dependent shifts under explicit reasoning, often reducing hallucination and error, but frequently destabilizing consistency or validity. These results demonstrate that geometric scale generalization cannot be inferred from accuracy alone. Supplementary materials are available at https://github.com/KurbanIntelligenceLab/SCALAR.

C2NP: A Benchmark for Learning Scale-Dependent Geometric Invariances in 3D Materials Generation

Generative models for materials have achieved strong performance on periodic bulk crystals, yet their ability to generalize across scale transitions to finite nanostructures remains largely untested. We introduce Crystal-to-Nanoparticle (C2NP), a systematic benchmark for evaluating generative models when moving between infinite crystalline unit cells and finite nanoparticles, where surface effects and size-dependent distortions dominate. C2NP defines two complementary tasks: (i) generating nanoparticles of specified radii from periodic unit cells, testing whether models capture surface truncation and geometric constraints; and (ii) recovering bulk lattice parameters and space-group symmetry from finite particle configurations, assessing whether models can infer underlying crystallographic order despite surface perturbations. Using diverse materials as a structurally consistent testbed, we construct over 170,000 nanoparticle configurations by carving particles from supercells derived from DFT-relaxed crystal unit cells, and introduce size-based splits that separate interpolation from extrapolation regimes. Experiments with state-of-the-art approaches, including diffusion, flow-matching, and variational models, show that even when losses are low, models often fail geometrically under distribution shift, yielding large lattice-recovery errors and near-zero joint accuracy on structure and symmetry. Overall, our results suggest that current methods rely on template memorization rather than scalable physical generalization. C2NP offers a controlled, reproducible framework for diagnosing these failures, with immediate applications to nanoparticle catalyst design, nanostructured hydrides for hydrogen storage, and materials discovery. Dataset and code are available at https://github.com/KurbanIntelligenceLab/C2NP.

Stress-Testing Multimodal Foundation Models for Crystallographic Reasoning

Evaluating foundation models for crystallographic reasoning requires benchmarks that isolate generalization behavior while enforcing physical constraints. This work introduces a multiscale multicrystal dataset with two physically grounded evaluation protocols to stress-test multimodal generative models. The Spatial-Exclusion benchmark withholds all supercells of a given radius from a diverse dataset, enabling controlled assessments of spatial interpolation and extrapolation. The Compositional-Exclusion benchmark omits all samples of a specific chemical composition, probing generalization across stoichiometries. Nine vision--language foundation models are prompted with crystallographic images and textual context to generate structural annotations. Responses are evaluated via (i) relative errors in lattice parameters and density, (ii) a physics-consistency index penalizing volumetric violations, and (iii) a hallucination score capturing geometric outliers and invalid space-group predictions. These benchmarks establish a reproducible, physically informed framework for assessing generalization, consistency, and reliability in large-scale multimodal models. Dataset and code are available at https://github.com/KurbanIntelligenceLab/StressTestingMMFMinCR.

Understanding the Capabilities of Molecular Graph Neural Networks in Materials Science Through Multimodal Learning and Physical Context Encoding

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that integrates textual descriptors, such as IUPAC names, molecular formulas, physicochemical properties, and synonyms, alongside molecular graphs. A gated fusion mechanism balances geometric and textual features, allowing models to exploit complementary information. Experiments on benchmark datasets indicate that adding textual data yields notable improvements for certain electronic properties, while gains remain limited for others. Furthermore, the GNN architectures display similar performance patterns (improving and deteriorating on analogous targets), suggesting they learn comparable representations rather than distinctly different physical insights.