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jaguar_qm

Run quantum mechanics calculations on small molecules: optimize geometry, compute single-point energy, or predict vibrational frequencies. Accepts .mae, .pdb, .sdf, or prebuilt Jaguar .in files and returns a job ID for tracking.

Instructions

Run a Jaguar quantum-mechanics calculation on a small molecule. calculation is 'optimization', 'energy', or 'frequency'. Accepts a structure file (.mae/.pdb/.sdf) — a Jaguar input is built automatically — or a prebuilt Jaguar .in file. Long-running; returns a job_id. Keep systems small (a few dozen atoms) on CPU-only hardware.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
calculationNooptimization
basisNo6-31G**
functionalNoB3LYP
chargeNo
multiplicityNo
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description alone must disclose behavioral traits. It mentions that the tool is 'long-running' and 'returns a job_id,' indicating asynchronous execution, but it does not describe side effects, data modification, error behavior, or required permissions. This is insufficient for a complex computational tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is three sentences: first defines purpose, second details parameters, third gives behavioral note. Every sentence adds value with no redundancy. It is appropriately front-loaded with the tool's main function.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 6 parameters, no output schema, and no annotations, the description covers the tool's core purpose and key inputs but lacks details on return values beyond job_id, error handling, and output format. It does not fully compensate for the missing structured information.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so the description must compensate. It explains that 'calculation' is one of three options and that 'input_path' accepts structure files or .in files. Other parameters (basis, functional, charge, multiplicity) are listed with defaults but not elaborated. This provides partial but incomplete guidance.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it runs a Jaguar quantum-mechanics calculation on a small molecule. It specifies the calculation types ('optimization', 'energy', 'frequency') and accepted input formats (structure file or .in file). This distinguishes it from sibling tools like 'compute_descriptors' or 'epik' which have different purposes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description advises to 'keep systems small (a few dozen atoms) on CPU-only hardware,' providing explicit context for appropriate use. However, it does not explicitly state when not to use this tool or mention alternative tools for larger systems or different hardware, which would improve the score.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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