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lichman0405

raspa-mcp

by lichman0405

parse_rdf_output

Extract radial distribution function (RDF) data from RASPA2 simulation output, returning r(Å) and g(r) arrays for each atom pair and the first-peak position to identify adsorption sites and coordination shells.

Instructions

Parse RASPA2 radial distribution function (RDF) output files (3-3).

RASPA2 writes RDF data to RDF__.dat files when 'ComputeRDF yes' is set in simulation.input (requires NVT-MC or NVT-MD simulation).

Returns r(Å) and g(r) arrays per pair, plus first-peak position — useful for identifying preferred adsorption sites and coordination shells.

component_a / component_b: optional name filters (e.g. "CO2", "framework"). Leave empty to return all RDF datasets in the output directory.

Args: output_dir: Path to RASPA2 Output directory. component_a: Optional filter: only return pairs containing this name. component_b: Optional filter: only return pairs containing this name.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
output_dirYes
component_aNo
component_bNo
Behavior4/5

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

With no annotations provided, the description carries the full burden. It discloses return values (r(Å), g(r) arrays, first-peak position) and the source file naming convention. It does not explicitly state read-only behavior or failure modes, but 'parse' strongly implies non-modifying behavior. Overall, it gives solid insight into what to expect.

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

Conciseness4/5

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

The description is detailed but not bloated. The first sentence gives the purpose, followed by useful context on file generation and return values, then structured parameter explanations. Every sentence adds value, though it could be slightly more compact without losing information.

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

Completeness4/5

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

For a parser with no output schema, the description covers the essential context: what files are parsed, under what simulation conditions they are generated, what data is returned, and how filters work. It lacks an explicit example of the returned data structure, but the information provided is sufficient for an agent to invoke the tool and interpret the result.

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

Parameters5/5

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

The input schema has 0% description coverage, so the description must compensate. It does so thoroughly with an 'Args' section explaining output_dir as the path to the RASPA2 Output directory and component_a/component_b as optional name filters, including examples and the behavior when left empty.

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 explicitly states 'Parse RASPA2 radial distribution function (RDF) output files' with a specific verb and resource. It clearly distinguishes from sibling tools like parse_raspa_output, parse_msd_output, and parse_ti_output by focusing on RDF data.

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 provides clear context on when RASPA2 produces RDF files (ComputeRDF yes in NVT-MC or NVT-MD) and how to use optional filters. It does not explicitly compare to alternatives, but the context strongly implies when this tool is appropriate versus general parse_raspa_output.

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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