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reacnetgenerator

Analyze LAMMPS reactive MD trajectories to generate reaction networks and reports.

124|25|Updated Feb 20, 2026
Search Tags:#data-analysis#trajectory-analysis#reacnetgenerator#reactive-md#network-generation#lammps#wrapper-cli
One-click install
npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill reacnetgenerator
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reacnetgenerator
Source: https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/main/analysis/reacnetgenerator
Command: npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill reacnetgenerator

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ReacNetGenerator processes reactive molecular dynamics trajectories to generate reaction networks and detailed reports, enabling users to decipher complex chemical pathways from MD data.

Core Features & Use Cases

  • Run ReacNetGenerator on bond, dump, xyz, or extxyz trajectories to extract species and reaction networks.
  • Handle common LAMMPS trajectory issues (e.g., coordinate conventions, PBC) and optionally use the wrapper rng-pipeline or the native CLI.
  • Infer atom name ordering from nearby data files and output results into out/<basename>/ with run logs and a summary.
  • Provide a choice between wrapper tooling and native CLI flags to suit advanced user needs such as --miso, --nopbc, or --use-ase.

Quick Start

Run the wrapper workflow to analyze a LAMMPS trajectory and inspect the generated outputs in out/.

Frequently Asked Questions about reacnetgenerator

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

FAQPage Schema
How do I generate reaction networks from reactive MD trajectories?▼

Generating reaction networks from reactive MD trajectories involves analyzing bond, dump, or XYZ trajectory files to extract chemical species and map reaction pathways into a structured network report.

Does ReacNetGenerator work with LAMMPS dump trajectories?▼

ReacNetGenerator works with LAMMPS dump trajectories by handling coordinate conventions and periodic boundary conditions to accurately extract species and generate reaction networks.

How do I handle periodic boundary conditions when analyzing trajectory data?▼

Handle periodic boundary conditions when analyzing trajectory data by applying the --nopbc flag to bypass PBC processing, ensuring accurate species extraction for your reactive MD simulation data.

Can I analyze extxyz trajectory files to extract chemical species?▼

Analyze extxyz trajectory files to extract chemical species by utilizing the --use-ase flag, which supports reading and processing extended XYZ format trajectory data for network generation.

What is the best way to run reaction network generation on large MD datasets?▼

Run reaction network generation on large MD datasets using the rng-pipeline wrapper or native CLI with the --miso flag, outputting structured logs and summaries to predictable result layouts for efficient analysis.

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