Synopsis

rebl-AMR

This is an Open-Source Software for Binarized-Octree Mesh Generation around Immersed Geometries.
The main goal is to generate octrees for adaptive mesh refinement (AMR) of Cartesian domains with immersed complex geometries.

Features

• MPI parallelization
• User-friendly interface
• Geometry encoding

Configuration

rebl-AMR provides config.sh which can be used to automatically configure the code for Stampede2 (https://www.tacc.utexas.edu/systems/stampede2), Comet (https://www.sdsc.edu/services/hpc/hpc_systems.html) and Bridges (https://www.psc.edu/resources/computing/bridges) clusters

Linux

source config.sh 

Installation

rebl-AMR requires the following libraries

• CMAKE
• MPI (MPI 3.0 standard compliant version)
• Zoltan
• ParMetis
• HDF5

Build

rebl-AMR uses CMakeLists.txt and CMakeModules folder to detect the library paths.
These two components are crucial for complilation of rebl-AMR. Perform the following steps

  cd build
  cmake ..
  make 

The executable will be placed in the /bin folder

Run

mpirun -np Nprocessor ./bin/amrGem ./input/Geometry.stl procLevel meshLevel 

• NProcessor: Number of processes (squared number)
• proclevel : topology adaptation level
• meshlevel : gradient based adaptation level

Visualization

• The output is written to the /soln folder
• Paraview can be used to visualize the solution
• Simply open the file ending with xdmf in soln/

Paraview Visualization:

• Poisson solution with Neumann and Dirichlet Boundary conditions

Directory structure

rebl-AMR
│   README.md
│   CMakeLists.txt    
│   LICENSE
│   config.sh
│
└─── CMakeModules
│   │   FindMYMPI.cmake: cmake script to find MPI
│   │   FindMYHDF5.cmake: cmake script to find HDF5
|   |   FindParmetis.cmake
|   |   FindZoltan.cmake
|   |   ProcessorCount.cmake
|   |   ResolveCompilerPaths.cmake
|   |   CorrectWindowsPaths.cmake
└─── src
│   │   ReblAmr.cpp     
│   │   templateForest.cpp
│   │   communicate.cpp  
│   │   interpolate.cpp
│   │   solver.cpp
│   │   hdf5xmf.cpp
│   │   geomSTL.cpp
│   │   datatype.cpp
|   |   tree.cpp
│   │   templatePhdf5.cpp
│   │   params.cpp 
│   │   definitions.cpp 
│   │ 
│   └─── include (headers)
│       │   ReblAmr.hpp     
│       │   templateForest.hpp
│       │   communicate.hpp  
│       │   interpolate.hpp
│       │   solver.hpp
│       │   hdf5xmf.hpp
│       │   geomSTL.hpp
│       │   datatype.hpp
|       |   tree.hpp
│       │   templatePhdf5.hpp
│       │   params.hpp 
│       │   definitions.hpp 
│   
└─── bin
│       amrGem (executable)  
│  
│
└─── build   
│       Will be populated by cmake   
│  
│
└─── soln 
│   │   Pxdmf3d1.h5: outputs the file in hdf5 format 
│   │   Pxdmf3d1.xmf: meta data to be used by ParaView
│   
└─── archives
 

Details

For complete documentation visit www.reblamr.com

Notes

We welcome any feedbacks by the users and developers
Please read the LICENSE file for how to use this software

Acknowledgements

rebl-AMR is developed as part of the NSF-GEM3D Award No. 1440638.
It is developed at the Department of Mechanical Engineering at University Pittsburgh, PA, USA.

Contributors

• Jaber J. Hasbestan ([email protected])
• Shamsulhaq Basir ([email protected])
• Inanc Senocak ([email protected])