From de034ef8a05b3dc2d1990debe724a66e1d7060d5 Mon Sep 17 00:00:00 2001
From: Americo Cunha <36556019+americocunhajr@users.noreply.github.com>
Date: Thu, 18 Jul 2024 16:08:44 -0300
Subject: [PATCH] Update README.md

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 ## Premixed Turbulent Combustion with Stochastic Mixing Models Simulator
 
-**PaSR-SDE: Premixed Turbulent Combustion with Stochastic Mixing Models Simulator** is a Matlab code to simulate premixed turbulent combustion in a partially stirred reactor using stochastic micro-mixing models.
+**PaSR-SDE: Premixed Turbulent Combustion with Stochastic Mixing Models Simulator** is a Matlab code designed to simulate premixed turbulent combustion in a partially stirred reactor using stochastic micro-mixing models.
 
 <p align="center">
 <img src="logo/PaSR.png" width="60%">
 </p>
 
-### Documentation
-
-**PaSR-SDE** routines are commented to explain their functionality to the final user. Each routine has a short description of its purpose and a list of inputs and/or outputs.
-
-### Software History
+## Table of Contents
+- [Overview](#overview)
+- [Features](#features)
+- [Usage](#usage)
+- [Documentation](#documentation)
+- [Reproducibility](#reproducibility)
+- [Authors](#authors)
+- [Citing PaSR-SDE](#citing-pasr-sde)
+- [License](#license)
+- [Institutional support](#institutional-support)
+- [Funding](#funding)
+
+## Overview
+**PaSR-SDE** provides a robust framework for simulating premixed turbulent combustion using stochastic mixing models in a partially stirred reactor. This simulator is useful for researchers studying combustion in turbulent flows.
 
 **PaSR-SDE** development started in the first author master thesis in 2007, under suppervision of the second author. The underlying results were disclosed in the following publication:
-- *E. M. Orbegoso and L. F. Figueira da Silva, Study of stochastic mixing models for combustion in turbulent flows, Proceedings of the Combustion Institute, v. 32, pp. 1595-1603, 2009 http://dx.doi.org/10.1016/j.proci.2008.06.008*
+- **E. M. Orbegoso and L. F. Figueira da Silva**, *Study of stochastic mixing models for combustion in turbulent flows*, Proceedings of the Combustion Institute, v. 32, pp. 1595-1603, 2009  <a href="http://dx.doi.org/10.1016/j.proci.2008.06.008" target="_blank">DOI</a>
 
 The development resumed in 2023, with the last author updating the code to make it compatible with newer versions of Matlab.
 
+## Features
+- Simulates premixed turbulent combustion using stochastic micro-mixing models
+- Well-documented code with detailed comments
+- Educational style for ease of use
+- Includes example scripts for representative benchmark tests
+
+## Usage
+To get started with **PaSR-SDE**, follow these steps:
+1. Clone the repository:
+   ```bash
+   git clone https://github.com/americocunhajr/PaSR-SDE.git
+   ```
+2. Navigate to the code directory:
+   ```bash
+   cd PaSR-SDE/PaSR-SDE-2.0
+   ```
+3. To simulate a PaSR reactor, execute:
+   ```bash
+   Main_PaSR_Simulation
+   ```
+
+### Documentation
+**PaSR-SDE** routines are commented to explain their functionality. Each routine includes a short description of its purpose and a list of inputs and outputs. Users can refer to the example scripts provided to understand how to set up and run their simulations.
+
 ### Reproducibility
 Simulations done with **PaSR-SDE** are fully reproducible, as can be seen on this <a href="https://codeocean.com/capsule/3034874/tree/v1" target="_blank">CodeOcean capsule</a>
 
@@ -26,8 +59,7 @@ Simulations done with **PaSR-SDE** are fully reproducible, as can be seen on thi
 - Americo Cunha Jr (UERJ)
 
 ### Citing PaSR-SDE
-
-We kindly ask users to cite the following references in any publications reporting work done with **CRFlowLib**:
+If you use **PaSR-SDE** in your research, please cite the following references:
 - *E. M. Orbegoso and L. F. Figueira da Silva, Study of stochastic mixing models for combustion in turbulent flows, Proceedings of the Combustion Institute, v. 32, pp. 1595-1603, 2009 http://dx.doi.org/10.1016/j.proci.2008.06.008*
 - *E. M. Orbegoso, L. F. Figueira da Silva and A. Cunha Jr, PaSR-SDE: A Matlab Package for Premixed Turbulent Combustion Stochastic Mixing Models, Software Impacts, v. 15, pp. 100480, 2023 http://dx.doi.org/10.1016/j.simpa.2023.100480*
 
@@ -56,7 +88,6 @@ We kindly ask users to cite the following references in any publications reporti
 ```
 
 ### License
-
 **PaSR-SDE** is released under the MIT license. See the LICENSE file for details. All new contributions must be made under the MIT license.
 
 <img src="logo/mit_license_red.png" width="10%">