Lattice Microbes Documentation

Introduction

Welcome to the Lattice Microbes documentation. This project is a comprehensive whole-cell modeling platform that combines C++, CUDA, and Python to provide high-performance simulations.

Project Organization

Lattice Microbes Architecture and Organization

The diagram above illustrates the complete architecture and organization of the Lattice Microbes project, showing how different components interact across Python, C++, and CUDA layers.

Multi-Language Architecture

This codebase consists of three main language components:

• 🐍 Python Interface (Python Modules) - High-level API and user interface
• ⚡ CUDA Kernels (CUDA Kernels) - GPU-accelerated computation
• 🔧 C++ Core - Core simulation engine and data structures

Key Components

Python Modules

• pyLM - Core Lattice Microbes Python interface
• pySTDLM - Standard cell modeling tools
• jLM - Julia-inspired Python interface

CUDA Modules

• Particle size aware kernels (particle_size_kernels.cu)
• Diffusion solvers (byte_diffusion_*.cu)
• Reaction kernels
• Random number generation (XORWow.cu)

C++ Core

• RDME Solvers (MpdRdmeSolver)
• CME Solvers
• I/O and file handling
• Core data structures

Navigation Guide

File Type Legend

Files in the documentation are tagged by their language:

• [Python] Python source files (.py, .pyw)
• [CUDA] CUDA source/header files (.cu, .cuh)
• [C++] C++ source files (.cpp, .cc)
• [C++ Header] C++ header files (.h, .hpp)

Quick Links

• File List - Browse all source files organized by directory
• Namespaces - View Python modules and C++ namespaces
• Classes - Browse all classes and structures
• Functions - Index of all functions and methods

Version Information

• Project: Lattice Microbes
• Version: 2.5
• Documentation Generated:

  Date

• Doxygen Version: 1.14.0