# Data Archive

## Overview

This data archive accompanies the research paper "CFD Analysis of Mucus Bridge
Instability and Breakup in the Vocal Folds" by Heinrich et al. The archive
contains OpenFOAM case setups, simulation scripts, and extracted visualization
data for the multiphase Volume-of-Fluid CFD simulation of mucus bridge breakup
during vocal fold phonation.



## Repository Structure

The general repository structure is as follows:

```
├── README.md                       # This file
├── 1_source_code/                  # OpenFOAM source code for initialization
├── 2_case_setup/                   # OpenFOAM case files and scripts
└── 3_extracted_data/               # Processed visualization data
    ├── 1_dp_491Pa/                 # Data from 491 Pa case
    ├── 2_dp_981Pa/                 # Data from 981 Pa case
    └── 3_dp_1472Pa/                # Data from 1472 Pa case
```

The directory `1_source_code` contains the OpenFOAM source code for the tool
`vofperm`, which is able to initialize the mucus layer with a random,
stochastic disturbance.

The directory `2_case_setup` contains an OpenFOAM template for the base case
with a transglottal pressure difference of 491 Pa and a mesh resolution
resulting in a total of 80 mio cells.

The directory `3_extracted_data` contains the alpha iso-surfaces and
cutplanes with x- and y-normal vector in VTK format.



## System Requirements

### Software Dependencies
- **OpenFOAM**: v2412
- **Operating System**: Linux
- **Minimum Hardware**:
  - RAM: 4 GB RAM per cpu core
  - CPU: HPC cluster system with 2560 cores
  - Storage: ~300 GB free space per case



## Case Setup Description

### Physical Model
- **Geometry**: Simplified vocal folds based on Zhao et al. (2002)
- **Fluids**: Air (Newtonian) and mucus (non-Newtonian, Power Law model)
- **Multiphase method**: Volume-of-Fluid (VoF) with isoAdvector
- **Vocal fold motion**: Prescribed analytical motion

### Key Parameters
| Parameter | Value | Unit |
|-----------|-------|------|
| Vocal fold frequency | 142 | Hz |
| Maximum glottal opening | 4.0 | mm |
| Minimum glottal opening | 0.2 | mm |
| Mucus layer thickness | 100 | μm |
| Surface tension coefficient | 51.9e-3 | N/m |
| Air density | 1.186 | kg/m3 |
| Mucus density | 1000 | kg/m3 |

### Boundary Conditions
- **Inlet**: Total pressure (491/981/1472 Pa)
- **Outlet**: Static pressure (0 Pa)
- **Walls**: No-slip, perfectly wetting (0° contact angle)



## Running the Simulations

### Prerequisites
1. Install OpenFOAM v2412
2. Compile the initialization tool `vofperm`
3. Ensure sufficient computational resources

### Basic Execution
```bash
# Navigate to desired case directory
cd 2_case_setup/

# Prepare the case (mesh generation, initialization, etc.)
./Allpre

# Run simulation
./Allrun
```