# TUG Documentation

TUG is a Julia package that provides a framework for solving transport problems, notably diffusion, on uniform grids. It implements different numerical approaches, including implicit BTCS (Backward Time, Central Space) Euler and parallel 2D ADI (Alternating Direction Implicit).

```@contents
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## Introduction

TUG, originally developed as a C++ library, is now available as a Julia package. It aims to offer a comprehensive toolkit for solving transport problems, such as diffusion and advection, on uniform grids.

## Installation

If TUG is locally cloned on your machine, you can install it by pointing to the local path. Open Julia REPL and follow these steps:

```julia
using Pkg
Pkg.develop(path="path/to/tug/julia/TUG")  # Replace with the actual path to the TUG directory
using TUG
```

## Getting Started

Below are some basic examples of using TUG. For more detailed information, see the API section. For more advanced examples, see the test files in the `test` directory.

### Creating a Simulation

To create a simulation with TUG, you first need to set up a grid and boundary conditions. Here is an example of setting up a basic simulation:

```julia
using TUG

# Create a 1D grid
grid = TUG.Grid{Float64}(5, ones(1, 5))

# Define boundary conditions
boundary = TUG.Boundary{Float64}(grid)

# Initialize a simulation with default parameters
simulation = TUG.Simulation{Float64}(grid, boundary)
```

### Running a Simulation

After setting up the simulation, you can run it and analyze the results:

```julia
# Set initial concentrations
TUG.setConcentrations!(grid, [1.0, 1.0, 20.0, 1.0, 1.0])

# Run the simulation
TUG.run(simulation)

# Retrieve the concentrations after simulation
concentrations = TUG.getConcentrations(grid)
```

### Advanced Setup

You can also customize your simulation with different parameters:

```julia
# Create a simulation with custom parameters
simulation = TUG.Simulation{Float64}(
    grid,
    boundary;
    approach = TUG.FTCS,
    iterations = 2,
    timestep = 0.2,
    consoleOutput = TUG.CONSOLE_OUTPUT_ON,
    csvOutput = TUG.CSV_OUTPUT_ON
)
```

### Dynamic Simulation

For dynamic simulations where the concentration is manipulated externally during runtime:

```julia
# Initialize a dynamic simulation
dynamicSimulation = TUG.DynamicSimulation{Float64}(grid, boundary; timestep = 0.1)

# Create and update the grid over iterations
TUG.createGrid(dynamicSimulation)
for _ = 1:20
    TUG.next(dynamicSimulation)
    # Update the concentration
end
```

## API Reference

For a detailed reference of all functionalities, see the API section:

```@autodocs
Modules = [TUG]
```