magic-3-tools 0.1.0

A library for molecular dynamics analysis and RDF calculations

MagicTools

A Python library for molecular dynamics analysis and Radial Distribution Function (RDF) calculations.

Description

MagicTools provides a comprehensive set of tools for analyzing molecular dynamics simulations, with a focus on:

• Radial Distribution Functions (RDF): Calculate and analyze pair distribution functions
• Angular Distribution Functions (ADF): Analyze angular correlations
• Molecular System Manipulation: Build and modify molecular systems
• Trajectory Processing: Read and process molecular dynamics trajectories
• Visualization: Plot distribution functions with customizable settings

Installation

From PyPI

pip install magictools

From source

git clone https://github.com/mposysoev/MagicTools.git
cd magictools
pip install -e .

Requirements

• Python >= 3.10
• numpy >= 1.20.0
• pandas >= 1.3.0
• matplotlib >= 3.3.0

Optional dependencies

For trajectory reading support:

pip install magictools[trajectory]

Quick Start

Using as a Library

import magictools as mt

# Create a system
system = mt.System()

# Load data and calculate RDF
# ... your code here ...

# Plot results
mt.OnePlot(rdf_data, title="My RDF Analysis")

Using the Command-Line Tool

The package provides a magic-rdf command-line tool for RDF calculations:

magic-rdf -i input.inp

Command-line options:

• -i <file>: Input file (default: rdf.inp)
• -np <n>: Run in parallel using n cores
• --force: Skip trajectory checks
• --opt_memory_use: Enable memory optimization for large systems
• --notrim: Disable automatic trimming

Example:

# Run RDF calculation with custom input file
magic-rdf -i my_system.inp

# Run in parallel on 4 cores
magic-rdf -i my_system.inp -np 4

# Run with memory optimization
magic-rdf -i large_system.inp --opt_memory_use

Input File Format

The magic-rdf tool uses MagiC-2 RDF input format. See documentation for detailed format specification.

Example input file:

&PARAMETERS
TRAJECTORY = trajectory.xyz
FORMAT = XYZ
...
&ENDPARAMETERS

Main Classes

• System: Top-level object representing the entire molecular system
• MolType: Molecular type definitions and topology
• Atom, AtomType: Atom representations and atom type definitions
• Bond, BondType: Bond representations and bond type definitions
• DF, DFset: Distribution functions and sets of distribution functions
• Trajectory: Trajectory file handling and processing
• RDFCalculator: Main calculator for RDF analysis

Main Functions

• OnePlot(): Plot distribution functions on a single plot
• MultPlot(): Create multiple plots for distribution function analysis
• ReadMagic(): Read MagiC format files

License

This project is licensed under the GNU General Public License v3.0 (GPL-3.0). See the LICENSE file for details.

Citation

If you use MagicTools in your research, please cite:

TODO: Add citation information

Contact

• Author: Alexander Lyubartsev
• Email: [e-mail]
• GitHub: https://github.com/mposysoev/MagicTools