Doc updated, I added a Main Example section, which contains what was in the...

Doc updated, I added a Main Example section, which contains what was in the mediawiki under Example Section

Doc/Site_dox/FDownload.dox

 /*! \page install Downloading, Building and Installing ScalFMM
 *
+* On this page, you will find all the requirements for building and installing ScalFMM.
+*
+* \tableofcontents
+*
 * \section download Download ScalFMM
 *
 * To download ScalFmm go on http://scalfmm-public.gforge.inria.fr/download.html.

Doc/Site_dox/FExamples.dox

+/*! \page mainexamples Main Examples
+
+ * \tableofcontents
+
+ * In the scalfmm directory, you can locate several folders. The
+ * sources folder called Src, the examples/tests folder Tests, the
+ * unit tests folders UTests, the Addons folder which contains one
+ * sub-folder per addon, the doc directory where you can find some
+ * documentation and the data folder which contains particles files or
+ * any other data needed per the simulation examples.
+
+ * Here we focus mainly on the Tests and UTests folders, and we
+ * encourage users to look directly in the code file to see how things
+ * are made.
+
+ * \section how How to use
+
+ * \subsection parameters The parameters system
+
+ * Most of the examples need some user parameters or let the user shows
+ * some values. This is done with the FParameters class. You can open
+ * an example and find the parameters directives, like in the
+ * Tests/Utils/testStatsTree.cpp:
+
+ \code{.cpp}
+ const int NbLevels = FParameters::getValue(argc,argv,"-h", 5);	
+
+ const int SizeSubLevels = FParameters::getValue(argc,argv,"-sh", 3);
+
+ const char* const filename = FParameters::getStr(argc,argv,"-f", "../Data/test20k.fma"); 
+ \endcode
+
+ * This means that in the console, you can tape: 
+
+ \code{.cpp}
+ ./Tests/Release/testStatsTree -h [an height] -sh [a sub height] -f [a file to load]
+ \endcode
+
+
+ * \subsection concrete A Concrete example : SH FMM
+
+ * In this part we will run a simulation with Spherical Harmonics :
+ * Tests/Kernels/testSphericalAlgorithm.cpp.
+
+ * \subsubsection create Create a particles file 
+
+ In the test file we can read: 
+
+ \code{.cpp}
+ * const char* const filename = FParameters::getStr(argc,argv,"-f", "../Data/test20k.fma"); 
+ * FFmaLoader<ParticleClass> loader(filename); 
+ \endcode
+
+ * It means, that the test file is reading FMA file (with FFmaLoader)
+ * which can be changed but here we still use this format. We can pass a
+ * file in parameter with the -f command. So let first create a 2.000.000
+ * particles file in the FMA test format:
+
+ \code{.cpp}
+ * ./Tests/Release/testLoaderFMACreate -nb 2000000 -f my2kkpartfile.fma 
+ \endcode
+
+ Which create a file called my2kkpartfile.fma. 
+
+ * \subsubsection running Running the Simulation
+
+ * With the SH kernel we can choose the P=4 accuracy parameter for this
+ * kernel.
+
+ \code{.cpp}
+ * ./Tests/Release/testSphericalAlgorithm -f my2kkpartfile.fma -h 5 -sh 3 -p 4 
+ \endcode
+
+ \section example_from_test Examples from Tests
+
+ \subsection tests_utils From Tests/Utils
+
+ <ul>
+ <li> testACA.cpp : this file the ACA matrix operation. </li>
+ <li> testLoaderCreate.cpp : this file creates a basic particles file in the basic format. </li>
+ <li> testBlas.cpp : this file tests the blas, it simply validate that the link was OK </li>
+ <li> testLoaderFMABinCreate.cpp : this file creates a particles file in binary in the FMA format.  </li>
+ <li> testChebBinaryM2L.cpp :  </li>
+ <li> testLoaderFMABinCreateSphere.cpp : this file creates particles file in binary and FMA format with a spherical distribution.  </li>
+ <li> testChebBinarySymM2L.cpp  </li>
+ <li> testLoaderFMA.cpp : this file illustrates how to load particles from a FMA file.  </li>
+ <li> testChebInterpolator.cpp :  </li>
+ <li> testLoaderFMACreate.cpp: this file creates a particles text-file in the FMA format.  </li>
+ <li> testChebM2Lprecomputation.cpp : </li>
+ <li> testLoaderFMACreateSphere.cpp : this file creates particles text file in the FMA format with a spherical distribution.  </li>
+ <li> testChebOctree.cpp : this file illustrates how to use the octree.  </li>
+ <li> testLoaderFMATsm.cpp : this load an FMA file with targets != sources.  </li>
+ <li> testChebSxUCBSy.cpp  </li>
+ <li> testLoaderFMATsmCreate.cpp : this create a particles text file with targets != sources </li>
+ <li> testChebSymmetries.cpp </li>
+ <li> testMemStats.cpp : this shows how to use the memory stats. </li>
+ <li> testChebTensorProduct.cpp:  </li>
+ <li> testMortonIndex.cpp: this is an example of the Morton index usage and conversion.  </li>
+ <li> testCompareIOTree.cpp : this loads two octrees and compare them.  </li>
+ <li> testDebug.cpp : to illustrate how to use the debug macro and controller </li>
+ <li> testOctree.cpp : to show how to use the octree.  </li>
+ <li> testFmmAlgorithm.cpp : this runs the FMM algorithm with the test set.  </li>
+ <li> testOctreeIter.cpp : shows how to iterate on the octree.  </li>
+ <li> testFmmAlgorithmPeriodic.cpp : this runs the FMM algorithm with the test set and periodic set to ON.  </li>
+ <li> testOctreePrintMorton.cpp : to knows every thing about the Morton index of an octree.  </li>
+ <li> testFmmAlgorithmProc.cpp : this runs the FMM algorithm with the test set and MPI.  </li>
+ <li> testOctreeRearrange.cpp : this runs the FMM algorithm with the test set and rearrange the particles.  </li>
+ <li> testFmmAlgorithmProcPeriodic.cpp : this runs the FMM algorithm with the test set, MPI and periodicity.  </li>
+ <li> testOctreeRearrangeProc.cpp : this runs the FMM algorithm with the test set and rearrange the data with MPI.  </li>
+ <li> testFmmAlgorithmTsm.cpp : this runs the FMM algorithm with the test set and sources != targets.  </li>
+ <li> testStatsTree.cpp : this gives some information about an octree.  </li>
+ <li> testFmmDemonstration.cpp:  </li>
+ <li> testTic.cpp: shows how to use the timer.  </li>
+ <li> testLoader.cpp : this uses a basic loader.  </li>
+ <li> testTreeIO.cpp : this stores and restore an octree on hard drive. </li>
+ </ul>
+
+ * \subsection tests_kernels From Tests/Kernels
+
+ <ul>
+ <li> testChebAlgorithm.cpp : this runs the Chebyshev FMM. </li>
+ <li> testFlopsChebAlgorithm.cpp : this counts the flops in the Chebyshev FMM. </li>
+ <li> testRotationAlgorithm.cpp : this runs the Rotation FMM.</li> 
+ <li> testSphericalBlockBlasAlgorithm.cpp : this runs the SH FMM with blocked blas. </li>
+ <li> testSphericalEwalAlgorithm.cpp : this runs the SH FMM and compare with an ewal summation. </li> 
+ <li> testSphericalGalaxyCsv.cpp : this runs the SH FMM output an csv file to visualize in Paraview. </li>
+ <li> testSphericalProcAlgorithm.cpp : this runs the SH FMM with MPI. </li>
+ <li> testSphericalRotationAlgorithm.cpp : this runs the SH FMM with rotation. </li>
+ <li> testSphericalTsmAlgorithm.cpp : this runs the SH FMM with targets != sources. </li>
+ <li> testSphericalAlgorithm.cpp : this runs the SH FMM. </li>
+ <li> testSphericalTsmNoTsm.cpp : this runs the SH FMM with targets != sources. </li>
+ <li> testSphericalBench.cpp : this runs the SH FMM and perform some bench. </li>
+ <li> testTuneSphericalBlockBlas.cpp : this runs the SH FMM and shows different results for the size of the block. </li>
+ <li> testSphericalBlasAlgorithm.cpp : this runs the SH FMM with blas. </li>
+ <li> testCompareKernels.cpp : this runs compare several kernels. </li>
+ </ul>
+
+ \section examples_from_Utest Examples from UTests
+
+ * In this folder you will find the unit tests. There are some related to
+ * data structures (like vector or list) and some others related to real
+ * FMM.
+
+ <ul>
+
+ <li> FUTester.hpp : this is the main class for unit test.  </li>
+ <li> utestParameters.cpp : this tests the FParameters class which allow a quick access to application command line parameter.  </li>
+ <li> utestQuicksort.cpp : this tests the quick sort in sequential and shared memory.  </li>
+ <li> utestRotationDirect.cpp : this tests the rotation FMM.  </li>
+ <li> utestBoolArray.cpp : this tests the boolean array which is a data structure that enable bit bool value.  </li>
+ <li> utestRotationDirectPeriodic.cpp : this tests the rotation kernel with periodicity.  </li>
+ <li> utestBuffer.cpp : this tests the buffer used in the serialization of data in the MPI FMM.  </li>
+ <li> utestSphericalDirect.cpp : this tests the Spherical Harmonic kernel.  </li>
+ <li> utestChebyshevDirect.cpp : this tests the Chebyshev kernel.  </li>
+ <li> utestSphericalDirectPeriodic.cpp : this tests the Chebyshev kernel with periodicity.  </li>
+ <li> utestChebyshevDirectPeriodic.cpp : this tests the Spherical Harmonic kernel with periodicity.  </li>
+ <li> utestSphericalWithPrevious.cpp : this tests the Spherical Harmonic kernel with a previous run.  </li>
+ <li> utestList.cpp : this tests our home made linked list.  </li>
+ <li> utestTest.cpp : this tests the unit test main class (this is just an example of how to use).  </li>
+ <li> utestMorton.cpp : this tests the Morton indexing tools.  </li>
+ <li> utestVector.cpp : this tests our home made vector.  </li>
+ <li> utestOctree.cpp : this tests the octree validation.	 </li>
+ </ul>
+
+*/

Doc/Site_dox/MainPage.dox

@@ -38,9 +38,11 @@
  * To download build and install the application, please see \ref
  * install.
  *
- * The \ref quick can help you to understand the architectur of the
+ * The \ref quick can help you to understand the architecture of the
  * library.
  *
+ * The \ref mainexamples page can help you to understand how the test are made.
+ *
  * This software is distributed under a specific License. For more
  * informations, see \ref License.
  *