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christopher2lllp3t-cell

materials-studio-mcp-moc

md_build_clayff_spce_nacl_lammps

Generate an exact-count neutral quartz LAMMPS candidate using ClayFF, SPC/E, and Joung potentials for reliable molecular dynamics simulations.

Instructions

Generate an exact-count neutral quartz ClayFF/SPC/E/Joung LAMMPS candidate.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dry_runNo
max_atomsYes
output_slotYes
input_sha256Yes
idempotency_keyYes
clay_bonded_pathYes
project_directoryYes
clay_bonded_sha256Yes
confirmation_tokenNo
clay_nonbonded_pathYes
packing_receipt_pathYes
clay_nonbonded_sha256Yes
input_packed_structureYes
packing_receipt_sha256Yes
joung_cheatham_spce_pathYes
authenticated_methods_pathYes
joung_cheatham_spce_sha256Yes
supporting_information_pathYes
authenticated_methods_sha256Yes
supporting_information_sha256Yes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior1/5

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

No annotations are present, so the description must disclose side effects, validation behavior, and safety traits, but it only states the output type. It fails to mention dry_run defaulting, confirmation_token requirements, checksum validation, or that it writes to output_slot.

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 a single sentence with no fluff, and the core action and artifact are front-loaded. However, given tool complexity, a longer structured description would be more appropriate, so it doesn't earn a 5.

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

Completeness1/5

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

For a tool with 18 required parameters, no annotations, and sibling workflow dependencies, one sentence does not provide enough context. It doesn't indicate where this step fits in the pipeline, what the output candidate is used for, or how to handle the many integrity-related inputs.

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

Parameters1/5

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

Schema description coverage is 0% and the description names none of the 20 parameters. It does not explain required inputs such as input_packed_structure, packing_receipt_path, force field files, or idempotency_key, nor how they relate to each other.

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?

Description uses specific action 'Generate' with a precise artifact: an exact-count, neutral quartz ClayFF/SPC/E/Joung LAMMPS candidate. This distinguishes it from sibling packing/slab-building tools like ms_pack_periodic_aqueous_nacl and ms_geology_build_periodic_slab_cell.

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

Usage Guidelines2/5

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

No guidance on when to invoke this tool versus alternatives or in what workflow order (e.g., after packing, before LAMMPS run). With sibling tools for packing and building, the absence of explicit selection criteria leaves the agent to infer context.

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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