Welcome to AlloMorph
====================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   usage
   api
   configuration

`AlloMorph` is a toolkit for generating monometallic to trimetallic nanoparticle structural datasets for machine learning.

Key Features
------------

- **Initial Structure Generation**: Generate monometallic (MNP), bimetallic (BNP), and trimetallic (TNP) nanoparticles with configurable shapes and atomic distributions.
- **Configurable Elements**: Support arbitrary metallic elements via an overridable element-property dictionary.
- **MD Simulation Orchestration**: Automatically set up and manage LAMMPS simulations for annealing nanoparticles.
- **Feature Extraction**: Extract structural features from nanoparticles using NCPac and MD outputs.
- **Modular Design**: Clean Python API and CLI for easy integration into workflows.

Quick Start
------------

.. code-block:: bash
   # Generate structures (all stages: MNP, BNP, CS, TNP)
   allomorph init-struct --stage all

   # Or generate only monometallic nanoparticles
   allomorph init-struct --stage mnp

   # Setup MD simulations
   allomorph md-sim setup --init-dir InitStruct/TNP --target-dir MDsim_runs

For more details, see the :doc:`installation` and :doc:`usage` guides.