New read me

Doxyfile.in

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Parallel BEM Solver for deal.II"
+PROJECT_NAME           = "pi-BEM: a parallel BEM solver for deal.II"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version

README.md

@@ -1,8 +1,63 @@
-Parallel BEM Solver for deal.II
-===============================
+#Parallel BEM Solver for deal.II
 
 [![Build Status](https://travis-ci.org/mathLab/pi-BEM.svg?branch=master)](https://travis-ci.org/mathLab/pi-BEM)
 
+The library represents a parallel solver for the Laplace equation through Boundary Element Methods. We have developed the software in C++ on top of the [deal.II](https://github.com/dealii/dealii) library. 
+
+## Provided features
+
+We provide the following capabilities
+
+- Read of the grid through an external file in one of the following formats (.prm, .msh, .vtk), the files specifies the kind of boundary condition to be applied on the nodes.
+- Possibility of solving mixed Dirichlet Neumann boundary value problem.
+- Automatic treatment of sharp edges via the double nodes technique.
+- Usage of Lagrangian Finite Elements of arbitrary order. We also provide interfaces with discontinuous elements.
+- Distributed memory (MPI) parallelisation of the standard collocation BEM for the Laplace equation.
+- Coupling with a Fast Multiple Method (FMM) to get a performance improvement.
+- Hybrid Distributed (MPI) - Shared (Intel Threaded Building Block) memory parallelisation for the BEM-FMM code
+- Recovery of both primal (potential) and dual (potential normal derivative) unknowns.
+- L2 projection of the full 3D potential gradient for post processing.
+- Extensive tuning via parameter file using the [deal2lkit](https://github.com/mathLab/deal2lkit) library 
+
+
+## Code Structure
+We have subdivided the code in main classes to handle the many different aspects of a complete BEM simulation.
+
+- Driver. This class is in charge of organising the overall BEM simulation. It has interfaces with all the other classes in order to perform a complete simulation.
+- ComputationalDomain. This class handles, and provides to the other classes, ONLY the geometry of the problem. In particular
+ - it handles the domain decomposition using a graph partitioning tool (METIS);
+ - it reads the domain from an external file.
+- BoundaryCondition. The class handles the boundary conditions. In particular
+	- it reads the boundary conditions for the potential and its normal derivative; 
+	- given the peculiarities of the BEM, the boundary conditions represent the actual unknowns, thus it creates the vectors containing the two variables and fills them with the proper data;
+	- it performs the error analysis on both unknowns.
+
+- BEMProblem. This class is the core of the BEM simulation
+	- it receives the variables vector filled in with the proper boundary condition;
+	- it creates the codimension 1 functional space setting up the BEM;
+	- it solves the system using a preconditioned parallel GMRES solver;
+	- it eventually interacts with the FMM accelerator.
+- BEMFMA. This class handles the accelerator, in particular
+	- it sets up an hierarchical 3D space subdivision (octree);
+	- it receives two distributed vectors representing the unknowns and performs a full FMM matrix vector product.
+
+## Install Procedure
+In order to successfully compile the code you need 
+
+- to install the Trilinos and Metis wrappers of the library, see the official [instructions](https://www.dealii.org/developer/readme.html) 
+- to install the [deal.II](https://github.com/dealii/dealii) library allowing both for multiprocessors and multithreaded environment.
+- to install the [deal2lkit](https://github.com/mathLab/deal2lkit) library allowing both for multiprocessors and multithreaded environment.
+
+
+Then you can clone the repository and compile it
+
+	git clone https://github.com/mathLab/pi-BEM.git
+	cd pi-BEM
+	mkdir build
+	cd build
+	cmake ../
+	make -j4
+
 After you have compiled your application, you can run 
 
 	make test
@@ -17,8 +72,7 @@ Take a look at
 https://www.dealii.org/developer/developers/testsuite.html for more
 information on how to create tests and add categories of tests.
 
-Notice to developers
-====================
+#Notice to developers
 
 Before making a pull request, please make sure you run the script
 
@@ -30,10 +84,9 @@ white space changes are inserted in the repository.
 The script requires Artistic Style Version 2.04 (astyle) to work 
 properly.
 
-Licence
-=======
+#Licence
 
-Please see the file ./LICENSE for details
+Please see the file [./LICENSE](https://github.com/mathLab/pi-BEM/blob/master/LICENSE) for details
 
 
 

include/bem_fma.h

@@ -40,6 +40,13 @@ namespace Operator
 using namespace dealii;
 using namespace deal2lkit;
 
+/**
+* A class for the handling of the Fast Multiple Method coupled with the Bundary Element Method.
+* It is derived from ParameterAcceptor to have a common interface with parameter files. In
+* particular this class performs the matrix vector products approximating long range interactions
+* via Multipole and Local Expansions that are contained in dedicated classes.
+
+*/
 template <int dim>//, Type V>
 class BEMFMA : public ParameterAcceptor
 {

include/bem_problem.h

@@ -101,6 +101,13 @@ using namespace deal2lkit;
 //using namespace TrilinosWrappers;
 //using namespace TrilinosWrappers::MPI;
 
+/**
+* - BEMProblem. This class is the core of the BEM simulation
+*   - it receives the variables vector filled in with the proper boundary condition;
+*   - it creates the codimension 1 functional space setting up the BEM;
+*   - it solves the system using a preconditioned parallel GMRES solver;
+*   - it eventually interacts with the FMM accelerator.
+*/
 template <int dim>
 class BEMProblem : public ParameterAcceptor
 {

include/boundary_conditions.h

@@ -76,6 +76,12 @@
 #include <deal2lkit/parsed_data_out.h>
 #include <deal2lkit/utilities.h>
 
+/**
+* - BoundaryCondition. The class handles the boundary conditions. In particular
+*   - it reads the boundary conditions for the potential and its normal derivative;
+*   - given the peculiarities of the BEM, the boundary conditions represent the actual unknowns, thus it creates the vectors containing the variables and fills them with the proper data;
+*   - it performs the error analysis on both unknowns.
+*/
 template <int dim>
 class BoundaryConditions : public ParameterAcceptor
 {

include/computational_domain.h

@@ -67,6 +67,11 @@
 using namespace dealii;
 using namespace deal2lkit;
 
+/**
+* - ComputationalDomain. This class handles, and provides to the other classes, ONLY the geometry of the problem. In particular
+*  - it handles the domain decomposition using a graph partitioning tool (METIS);
+*  - it reads the domain from an external file.
+*/
 template <int dim>
 class ComputationalDomain : public ParameterAcceptor
 {

include/driver.h

@@ -69,7 +69,9 @@ using namespace dealii;
 //using namespace TrilinosWrappers::MPI::Vector;
 //using namespace TrilinosWrappers::MPI::SparseMatrix;
 
-
+/**
+* This class is in charge of organising the overall BEM simulation. It has interfaces with all the other classes in order to have a complete simulation.
+*/
 template <int dim>
 class Driver : public ParameterAcceptor
 {