Updating the restart function

Using restart for "Dipole" simulations was not working: the four geometrical parameters concerning the position and size of the dipole were missing from the settings.hdf file and causing an incorrect initialisation of the charge of the planet.
Deprecated HDF5 functions in Particles3Dcoom.cpp

There were still a few deprecated HDF5 functions in this file.
Deactivation of Parallel HDF5 options

By default the code now compiles using the sequential version of the HDF5 library. To use the parallel version make sure that the Parallel HDF5 version is available in the system and use the following command when configuring the code in the installation directory:

USE_PHDF5=1 cmake <src/dir>

where <src/dir> is the path to the source directory of the code.

NOTE: The same method is used to activate the BATSRUS portions of the code. So if you're planning to use the Parallel HDF5 and BATSRUS you must type:

USE_PHDF5=1 BATSRUS=1 cmake <src/dir>
Bug corrections:

1. Memory leak in EMfields3D.cpp has been patched.
2. Wrong 'if' tests on the constant charge boundary conditions were corrected.
3. B_ext was not applied correctly to the particle mover.
Adding a C post-processing tool. This is an 'old' tool that can be useful if you dont have python in your system.
Modifying the order of the indices when writing the fields in the parallel hdf5 file in order to read it directly in Paraview/Visit with the Xdmf format, wihtout using any postprocessing script.
Changing the Cmake configuration file to make better use of the options. Currently there are two options: parallel HDF5 and coupling with BATS-R-US.

Add -DIPIC_PARALLEL_HDF5=ON to compile the code with parallel HDF5.
Add -DIPIC_BATSRUS=ON to compile with the coupling options.

Alternativelly use 'ccmake' or 'cmake -i', the two options are available in the GUI.
Tool to use HDF5 output files in Paraview

This will allow to use the visualization tools like Paraview and VisIt without having to transform HDF5 into VTK files.
Optional compilation of library as shared

In some systems, depending on the installed libraries configuration, a shared library can not be compiled. In such case the compilation must be done using static libraries. STATIC is now given by default, but shared libraries can be activated with the cmake option -DIPIC_BUILD_SHARED=ON or using the ccmake GUI.
Bug correction: problem with MPI_ALLREDUCE

An incorrect variable type was given to the ALL_REDUCE function. In many systems the unsigned long long and the unsigned long are the same size, but in others they are different causing an out-of-bounds communications leak.
Adding Testing to iPic3D

Using CTest and Cmake we can now perform systematic tests on the code. For the moment the only test available is a comparison of the ConservedQuantities file for the GEM problem. Additional tests can be easely included following the example of the GEM test.
Bug correction: wrong BC treatment

The new test tool showed that a bug was inserted at some point producing an incorrect run of the GEM test.

The error was traced back to commit 01e8f3c15f38f161b90915bec6e77bf1c24bc25f where a constant charge was applied not only to OpenBC conditions, but also to perfect conductor conditions, which caused a bad behavior of the code in the GEM run.
Bug corrections:

1. Changing wrong preprocessor definition to compile using the parallel HDF5 library.
2. Reverting the order of the parallel HDF5 file writing: the output is correct now, but opening the files using the Xmdf format is still swaping the Z and X coordinates. We need to save the output file using the ZYX order, but this requires additional work. For the moment the tool is working fine to have a quick look at the results, and we have other tools for postprocessing.
3. The Xdmf tool writes the necessary file to view the HDF5 results in Paraview and VisIt. I corrected a few bugs and added a 3D extension. WARNING: this format still uses the column-major system swaping the last and first dimensions.
Merge branch 'amaya-library' into merged

Conflicts:
	CMakeLists.txt
	fields/EMfields3D.cpp
	include/EMfields3D.h
	particles/Particles3D.cpp
	particles/Particles3Dcomm.cpp
fixed compile errors from merge