computational-chemistry-skill

Plans, reviews, and documents staged computational chemistry workflows with human-in-the-loop browser approval.

31|3|Updated Jul 19, 2026
One-click install
npx skills add https://github.com/jianzushen/Computational-chemistry-skill --skill computational-chemistry-skill-jianzushen
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: computational-chemistry-skill
Source: https://github.com/jianzushen/Computational-chemistry-skill
Command: npx skills add https://github.com/jianzushen/Computational-chemistry-skill --skill computational-chemistry-skill-jianzushen

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires Flask, jsonschema, PyYAML, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve? Computational chemistry projects often fail because plans, parameters, and conclusions lose traceability between the research question, the actual calculation inputs, and the final manuscript. This Skill turns research goals, structures, software constraints, and real calculation records into a reviewable, staged workflow with a complete provenance chain from scientific question to paper-ready methods section. ## Core Features & Use Cases - Progressive stage-1 intake: Confirms the calculation goal, structure files, software/version, run environment, deliverables, and key parameters before generating any files, then produces a single fixed .review/review.html for final browser approval. - Minimal calculation delivery: After approval, generates only the target program's required input/structure/parameter files plus one README with run commands and return-file instructions; scheduler scripts are created only on request. - Result validation and analysis: Checks returned inputs, outputs, logs, and final structures for completeness and comparability, provides numbered data-processing tutorials, and classifies conclusions as strongly supported, supported, partially supported, inconclusive, or contradicted. - Use Case: A researcher asks to optimize a structure with CP2K. The Skill asks targeted questions until the plan is complete, renders one review page, generates the minimal CP2K input set after approval, then later validates the returned outputs and drafts the manuscript methods section from the real run records. ## Quick Start Load the repository's SKILL.md into your AI tool and say: help me optimize this structure with CP2K, then answer the staged intake questions.

Frequently Asked Questions about computational-chemistry-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate CP2K or Quantum ESPRESSO input files with this workflow?▼

Describe your goal in natural language, such as optimizing a structure with CP2K. The Skill first asks about the goal, structure, software version, run environment, and key parameters, then generates the minimal input files plus one README only after you approve the browser review page.

What is the staged review process for computational chemistry plans?▼

After stage-1 intake is complete and consistent, the Skill renders a single fixed page at .review/review.html for your approval. Revisions overwrite the same file, and no calculation files are created before you confirm the plan.

Does the skill run calculations or submit Slurm jobs automatically?▼

No. All production calculations, scheduler submissions, and remote jobs are executed by the user. The Skill only plans, generates input files, validates returned results, and documents methods; it never connects via SSH or runs sbatch on your behalf.

Can I use it on Windows with PowerShell?▼

Yes, Windows automation optionally uses PowerShell 7 via pwsh with non-interactive flags, finite timeouts, and captured output. PowerShell failure never blocks analysis or file generation, and WSL or Linux routes use Bash instead.

Why did my simple request not create a review page or input files?▼

That is expected behavior. The default workflow collects the goal, structure, software version, environment, deliverables, and key parameters first, and only creates .review/review.html after the intake passes completeness and consistency checks.

How are commercial software results handled in manuscript methods?▼

The methods section truthfully records the actual commercial software and version used, based only on real run records. Open-source alternatives may be suggested for reproduction, but they are never described as the source of the original results.