bigquantum / Anisotropic_cardiac_tissue-3D

This a reaction-diffusion PDE solver in 3D implemented with C/C++/CUDA and OpenGL interoperability. In addition, the media has rotational anisotropy to account for the tissue fiber effects.

Anisotropic cardiac tissue in 3D

This software was developerd by: Hector Augusto Velasco-Perez @CHAOS Lab@Georgia Institute of Technology

Special thanks to:

• Dr. @Flavio Fenton
• Dr. @Claire Yanyan Ji
• Dr. @Abouzar Kaboudian
• Dr. @Shahriar Iravanian

Software general decription

This software allows you to solve the Fenton-Karma (FK) model with a diffusive coupling in a 3D domain with a constant rotating conducting anisotropy. The software allows for input/output files and real time graphics for user interactivity. This software is implemented in C/CUDA.

Other features

• Time integration: first order explicit Euler method
• Spacial coupling: fourth order Laplacian with finite differences
• Filament tracking: pixel and subpixel resolution
• Zero-flux boundary conditions and optional periodic boundary conditions at the top and bottom of the domain
• Switch between anisotropic and isotropic tissue. The anisotropy is a constant rotating anisotropy
• Switch between single and double precision

Software requirements

• CUDA v7 or higher
• glew.h, glut.h, freeglut.h
• SOIL.h library (sudo apt-get install libsoil-dev)

Software use (in order of appearance)

• To run the eprogram, open a Linux terminal and type make
• globalVariables.cuh:
  • nx,ny,nz: Grid size
  • ITPERFRAME is the number of iterations it computes in the background without rendering an image.
  • Uth is the filament voltage treshold.
  • NN is the size of the array in floats (doubles) to save the tip filament trajectory.
  • DOUBLE_PRECISION: switch between double and single presicion (comment/uncomment).
  • ANISOTROPIC_TISSUE: switch between isotropic and anisotropic fibers (comment/uncomment).
  • LOAD_DATA: switch from loading an external file or initializing the simulation with a precoded initial condition (comment/uncomment).
  • SAVE_DATA: switch between saving data or not saving data (comment/uncomment).
  • SPIRAL_TIP_INTERPOLATION: Switch between subpixel resolution interpolating algorithm or pixel resolution algorithm for filament tracing (comment/uncomment).
  • Model parameters. Remember to modify the parameters for the floating point type selected.
• main3V-FK.cu:
  • strAdress: memory adress where the output data will be saved.
  • The structure param contains most of the physical parameters. To see which parameters it contains see typedef3V-FK.h.
  • pwdAdress contains the input-memory adress (if LOAD_DATA in not commented).
  • keyboard function: keyboard shortcuts. All names are self explanetory.
  • exitProgram function: comment/uncomment the functions inside the #ifdef SAVE_DATA.