diff --git a/README.org b/README.org index 33e33db..2ca7d2a 100644 --- a/README.org +++ b/README.org @@ -1,20 +1,88 @@ -#+TITLE: Diffusion module +#+TITLE: BTCSDiffusion -This is the according repository to the diffusion module we discussed earlier. -With this readme I will document all my steps I've done and will do. +#+BEGIN_CENTER +A framework solving diffusion problems using BTCS approach. +#+END_CENTER -* Current State +* About -- 1D diffusion is possible by setting bc at left/right end +by hand+ by =setBoundaryCondition()= or use the - default value (Neumann with gradient 0) -- +Always set concentrations/diffusion coefficients by using std::vecto+ -- Set concentrations of ghost zones by defining them via a list tuples. - + index 0 points to the left ghost zone - + index 1 to the right ghost zone -- simple datastructure, which is currently just a class called *BTCSDiffusion* +This project aims to provide a library for solving diffusion problems using the +backward Euler method (BTCS) implemented in C++. -* ToDos +The library is built on top of [[https://eigen.tuxfamily.org/index.php?title=Main_Page][Eigen]], providing easy access to data structures +and the linear equation solver. -- [X] keep sparse matrix in memory -- [-] allow different boundary conditions at the ends and also inside the grid -- [ ] implement 2D diffusion +We designed the API to be as much flexible as possible. Nearly every built-in, +framework or third-party data structure can be used to model a problem, as long +a pointer to continious memory can be providided. + +Also we provide basic parallelization by using [[https://www.openmp.org/][OpenMP]], which can be easily +turned on/off during generation of makefiles. + +At the current state, only 1D diffusion problems on a regular grid can be solved +reliably. The 2D solution is already implemented, but still returns wrong +values. This will be fixed in the future. + +* Getting started + +As this diffusion module is designed as a framework library and makefile +generation is done by [[https://cmake.org/][CMake]], you're good to go to also use CMake as your build +toolkit. If you decide to not use CMake, you need to manually link your +application/library to BTCSDiffusion. + +1. Create project directory. + + #+BEGIN_SRC + $ mkdir sample_project && cd sample_project + #+END_SRC + +2. Clone this repository into path of choice project directory + + #+BEGIN_SRC + $ git clone git@git.gfz-potsdam.de:mluebke/diffusion.git + #+END_SRC + +3. Add the following line into =CMakeLists.txt= file: + + #+BEGIN_SRC + add_subdirectory(path_to_diffusion_module EXCLUDE_FROM_ALL) + #+END_SRC + +4. Write application/library using API of =BTCSDiffusion=. + +5. Link target application/library against =BTCSDiffusion=. Do this by adding + into according =CMakeLists.txt= file: + + #+BEGIN_SRC + target_link_libraries(your_libapp BTCSDiffusion) + #+END_SRC + +6. Build your application/library with CMake. + + +* Usage + +Setting up an enviroment to use the =BTCSDiffusion= module is divided into the +following steps: + +1. Defining dimension of diffusion problem. +2. Set grid sizes in according dimensions. +3. Set the timestep to simulate. +4. Defining boundary conditions. +5. Run the simulation! + +This will run a simulation on the defined grid for one species. See the source +code documentation of =BTCSDiffusion= and the examples in the =app/= directory +for more information. + +* Roadmap + +- [X] 1D diffusion +- [ ] 2D diffusion +- [ ] 3D diffusion (?) +- [ ] R-API +- [ ] Python-API (?) +- [ ] Testing + +* License +TODO?