Bursting Bubble Simulations

Computational fluid dynamics simulations for bursting bubble studies using the Basilisk C framework.

Basilisk (Required)

First-time install (or reinstall):

curl -sL https://raw.githubusercontent.com/comphy-lab/basilisk-C/main/reset_install_basilisk-ref-locked.sh | bash -s -- --ref=v2026-01-13 --hard

Subsequent runs (reuses existing basilisk/ if same ref):

curl -sL https://raw.githubusercontent.com/comphy-lab/basilisk-C/main/reset_install_basilisk-ref-locked.sh | bash -s -- --ref=v2026-01-13

Note: Replace v2026-01-13 with the latest release tag.

Overview

This repository contains axisymmetric two-phase flow simulations with adaptive mesh refinement for studying bubble bursting phenomena. The simulations use the Volume-of-Fluid (VOF) method to track the interface between the bubble and surrounding fluid, with automatic mesh refinement focused on regions of interest.

Quick Start

Single Simulation

# Edit parameters
vim default.params      # Set CaseNo, Oh, Bond, etc.

# Run simulation (serial)
./runSimulation.sh

# Run with MPI (4 cores)
./runSimulation.sh --mpi

Parameter Sweep

# Configure sweep
vim sweep.params        # Set CASE_START, CASE_END, sweep variables

# Run sweep (serial)
./runParameterSweep.sh

# Run sweep with MPI (4 cores per case)
./runParameterSweep.sh --mpi

Repository Structure

├── src-local/                     Modular helper files
│   ├── parse_params.sh            Parameter parsing utilities
│   ├── sweep_utils.sh             Sweep generation utilities
│   └── basilisk_version.sh        Centralized version pinning
├── postProcess/                   Post-processing tools and visualization
│   ├── getData.c                  Field extraction on structured grids
│   ├── getFacet.c                 Interface geometry extraction
│   └── Video.py                   Frame-by-frame visualization pipeline
├── simulationCases/               Case-based simulation outputs
│   ├── burstingBubble.c           Main simulation case
│   └── DataFiles/                 Input geometry data
├── runSimulation.sh               Single case runner
├── runParameterSweep.sh           Parameter sweep runner (local)
├── runSweepHamilton-serial.sbatch HPC Stage 1 runner (Durham Hamilton)
├── runSweepHamilton.sbatch        HPC sweep runner (Durham Hamilton)
├── runSweepSnellius-serial.sbatch HPC Stage 1 runner (SURF Snellius)
├── runSweepSnellius.sbatch        HPC sweep runner (SURF Snellius)
├── runPostProcess-Ncases.sh       Post-processing pipeline
├── default.params                 Single-case configuration
├── sweep.params                   Sweep configuration

Key Parameters

• Ohnesorge Number (Oh): Oh = mu/sqrt(rho*sigma*R) - ratio of viscous to inertial-capillary forces
• Bond Number (Bo): Bo = rho*g*R^2/sigma - ratio of gravitational to surface tension forces
• Maximum Refinement Level: Controls mesh resolution (e.g., level 10 = 1024 cells)
• tmax: Maximum simulation time (dimensionless, based on capillary time scale)

Requirements

• Basilisk Framework: Install via the ref-locked script above (upstream docs: basilisk.fr)
• MPI (optional): For parallel execution
  • macOS: brew install open-mpi
  • Linux: sudo apt-get install libopenmpi-dev

Two-Stage Execution

The simulation uses a two-stage execution model due to a Basilisk limitation (distance.h is incompatible with MPI):

1. Stage 1: Generate restart file (serial or OpenMP)
2. Stage 2: Run full simulation from restart (supports MPI)

# Run both stages (default)
./runSimulation.sh default.params

# Or separately:
./runSimulation.sh --stage1 default.params    # Generate restart
./runSimulation.sh --stage2 --mpi 8 default.params  # Full simulation

Troubleshooting

"restart file not found"

Stage 2 requires a restart file from Stage 1. Run Stage 1 first:

./runSimulation.sh --stage1 default.params

"restart file is empty"

Stage 1 may have failed silently. Check for:

• Compilation errors in the case directory
• Memory issues (reduce MAXlevel)
• Invalid parameters

"qcc not found"

Basilisk is not installed. Run the install script:

curl -sL https://raw.githubusercontent.com/comphy-lab/basilisk-C/main/reset_install_basilisk-ref-locked.sh | bash -s -- --ref=v2026-01-13

Parameters not updating on reruns

The scripts preserve existing case.params and source files for reruns. Use --force to overwrite:

./runSimulation.sh --force default.params

HPC jobs failing

1. Ensure Stage 1 completed locally before submitting Stage 2
2. Check that restart files exist in each case directory
3. Verify SLURM parameters match your allocation

License

Copyright (C) 2026 CoMPhy Lab.

This project is licensed under the GNU General Public License v3.0. See LICENSE for details.

Contact

For questions or collaboration inquiries, please contact the CoMPhy Lab.