PHREEQC-MCQ-200: A Diagnostic Benchmark for Tool-Augmented Scientific Simulator Agents

[Submitted on 1 Jul 2026]

View PDF HTML (experimental)

Abstract:Large language model agents are increasingly connected to scientific software, yet it remains unclear when tool access makes scientific computation more reliable rather than merely more complex. We introduce PHREEQC-MCQ-200, a benchmark for evaluating tool-augmented agents on deterministic aqueous-geochemistry simulations. The benchmark contains 200 multiple-choice questions derived from 21 validated PHREEQC scenarios, requiring agents to construct simulator inputs, execute PHREEQC, inspect structured outputs, and commit to final answers.
Across multiple frontier and mid-tier model families, simulator access substantially improves aggregate accuracy, confirming that grounded execution is necessary for many scientific-computation tasks. However, the gains are not monotonic: tool-augmented agents also lose items they answered correctly without tools, revealing regressions that average accuracy alone hides. We further show that output-access protocol matters. A table-of-contents interface can reduce token cost while preserving or improving accuracy for stronger models, but it degrades performance for mid-tier models that cannot reliably navigate structured simulator outputs.
PHREEQC-MCQ-200 therefore frames scientific tool use as an end-to-end diagnostic problem rather than a simple tool-calling capability. We argue that evaluations of scientific agents should report not only accuracy, but also item-level retention, output-access sensitivity, trajectory failures, and where the computation chain breaks.

Submission history

From: Ke Zhang [view email]
[v1] Wed, 1 Jul 2026 04:51:37 UTC (3,487 KB)