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Quick Start

This page walks you through a minimal, end-to-end ReaxKit workflow, and shows you how to use ReaxKit CLI commands. By the end, you will have parsed a ReaxFF output file and produced a simple result.

This guide assumes ReaxKit is already installed (If not, see Installation). Moreover, if you are not familiar with the data organization by ReaxFF, see ReaxFF File References.

Step 1: Check that ReaxKit works

Open a terminal and run:

reaxkit --help

You should see the ReaxKit CLI help message listing available workflows.

Step 2: Inspect available data and files

If you already know which file you should process, skip this step and go to step 3.

ReaxKit includes a built-in help system that knows which quantities appear in which ReaxFF files.

To explore this:

reaxkit help

or search for a specific quantity:

reaxkit help pressure

reaxkit help "electric field"

This helps you decide which file you need for a given analysis.

Moreover, if you prefer to work with CLI commands to know which files are available in a director or to know what that files is about, you can easily obtain this information without any need to check the online documentation.

For this purpose, 

reaxkit intspec --folder workflow

will show you what files are available in the workflow/ directory, while

reaxkit intspec --file fort7_analyzer

shows the explanations (i.e., docstrings) for a specific file and its public functions.

Step 3: Finding the supported tasks for a given ReaxFF file

If you want to know which task a specific file like xmolout supports, you can simply do:

reaxkit xmolout -h

which prints in the terminal a list of positional arguments (i.e., supported tasks) and options (i.e., supported flags). For example, the above CLI command will show you that xmolout workflow supports tasks like trajget, MSD, RDF, etc.

Later on, for a specific task like trajget you may request its supported flags simply by:

reaxkit xmolout trajget -h

which lists CLI examples and options (i.e. flags) such as --atoms, plot, etc.

Step 4: Run a simple analysis

Once you know the tasks and flags related to a specific ReaxFF output file, you can use the full, appropriate CLI command to extract data and generate a simple plot:

reaxkit xmolout trajget --atoms 1 --dims z --xaxis time --plot --export atom1_z.csv

This will show you the z-trajectory for atom 1 across time (not iteration), and then exports its data (i.e., z-coordination vs time) in a csv file.

Generally, depending on the workflow:

  • data may be printed to the terminal,

  • plots may appear interactively,

  • or files may be saved to a reaxkit_outputs/ directory (if you generate an input file such as tregime, it will be saved in reaxkit_generated_inputs/ by default).

What just happened?

Behind the scenes, ReaxKit:

  1. parsed the raw ReaxFF file using the xmolout_handler,

  2. processed the data using the xmolout_analyzer,

  3. exposed the result through the xmolout_workflow via the CLI.

You do not need to interact with these layers directly to use ReaxKit.

Where to go next

  • If you want a detailed explanation of what happened in this quick start, see 01_understanding_quickstart.md

  • More examples, specifically how to use/develop analyzers instead of workflows (i.e., CLI commands): see examples

  • Developer templates: see templates

  • Installation details: see Installation

  • CLI discovery: run reaxkit help

This quick start intentionally keeps things minimal. More advanced workflows (multi-file analysis, plotting options, video generation) are documented in the examples and tutorials.