Reworked a bit the Makefile, the Documentation, and pulled in some useful older commits from other branches.

.gitignore

@@ -0,0 +1,32 @@
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+iPic3D
+
+# Local Makefile changes
+Makefile

Documentation/readme.txt

@@ -1,55 +1,74 @@
-How-to install and run iPic3D on your (local) Linux machine.
-Doesn't need sudo or root permissions, everything could be installed locally.
-
-1. Install HDF5 library. The current version working properly with iPIC3D is 1.8.9
-http://www.hdfgroup.org/ftp/HDF5/releases/
-
-$ cd <top HDF5 source code directory>
-$ ./configure --prefix=<location for HDF5 software> 
-$ make 
-$ make check
-$ make install 
-
-
-2. Install the MPICH2 (or OpenMPI) that supports -lmpe library. For example, this one:
-http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.3.2p1/mpich2-1.3.2p1.tar.gz
-During the installation of MPICH follow all the instructions in the README file.
-
-Newer versions of OpenMPI should be fine by default in a linux distro.
-
-3. Set environment variables:
-
-$ PATH=mpich2_install_path/bin/:$PATH
-$ PATH=hdf5_install_path/lib/:$PATH
-$ LD_LIBRARY_PATH=hdf5_install_path/lib/:$LD_LIBRARY_PATH
-
-Note: these paths can also go at the beginning of the makefile.
-
-where mpich2_install_path is the path to the installed MPICH2, and hdf5_install_path is the path to the installed HDF5.
-
-4. Check out the repository:
-
-$ svn co https://svn.esat.kuleuven.be/iPIC/iPic3D/trunk/ iPic3D_folder
-
-where iPic3D_folder is the desired folder for the code.
-
-5. Compiling the code
-
-$ cd iPic3D_folder
-
-$ cp makefiles/makefile.YourSystem makefile
-
-where the makefile.YourSystem is a makefile suitable for your system.
-Set the following paths in the makefile:
-
-INC_HDF5 = -I/hdf5_install_path/include
-LIB_HDF5 = -L/hdf5_install_path/lib
-HDF5LIBS = -L/hdf5_install_path/lib/ -lhdf5 -L/hdf5_install_path/lib/ -lhdf5_hl 
-MPELIB = -L/mpich2_install_path/lib/ -lmpe
-
-Finally, make everything:
-$ make
-
-6. Running iPic3D
-
-$ mpiexec (or mpirun) -n 4 ./iPic3D inputfiles/GEM.inp
+How-to install and run iPic3D on your (local) Linux machine.
+Doesn't need sudo or root permissions, everything could be installed locally.
+
+
+1. Install the MPICH2 (for code development) or OpenMPI (for performance runs).
+
+You may choose to use the official "openmpi" library from your operating system's repository.
+If you do so, you may skip over to step 2.
+
+For example, this version should work:
+http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.3.2p1/mpich2-1.3.2p1.tar.gz
+During the installation of MPICH follow all the instructions in the README file.
+
+Newer versions of OpenMPI should be fine by default in a linux distro.
+
+
+2. Install HDF5 library.
+
+You may choose to use the official "libhdf5-openmpi" package from your operating system's repository.
+Please note that you also need the "libhdf5-openmpi-dev" package for the required include files.
+If you do so, you may skip over to step 3.
+
+The current version working properly with iPIC3D is 1.8.9
+http://www.hdfgroup.org/ftp/HDF5/releases/
+
+$ cd <top HDF5 source code directory>
+$ ./configure --prefix=<location for HDF5 software>
+$ make
+$ make check
+$ make install
+
+
+3. Install H5hut library (optional).
+
+If you want to use also the optional H5hut library, you may follow the same steps as for the HDF5 library as described in step 2.
+You may download this library from:
+https://amas.psi.ch/H5hut/
+Build and installation are linked on this website.
+
+
+4. Set environment variables:
+
+$ PATH=mpich2_install_path/bin/:$PATH
+$ PATH=hdf5_install_path/lib/:$PATH
+$ LD_LIBRARY_PATH=hdf5_install_path/lib/:$LD_LIBRARY_PATH
+
+Note: these paths can also go at the beginning of the makefile.
+
+where mpich2_install_path is the path to the installed MPICH2, and hdf5_install_path is the path to the installed HDF5.
+
+
+5. Download the repository:
+
+$ git clone https://github.com/IWF-Graz/iPic3D.git iPic3D_folder
+
+where "iPic3D_folder" is the desired folder for the code.
+
+
+6. Compiling the code
+
+$ cd iPic3D_folder
+
+Edit the "Makefile" and check the documentation in the "USER-DEFINED SECTION".
+
+Finally, build everything and compile in parallel:
+
+$ make -j
+
+
+7. Running iPic3D
+
+$ mpiexec -n 4 ./iPic3D inputfiles/GEM.inp
+Or for some MPI libraries that do not have "mpiexec":
+$ mpirun -n 4 ./iPic3D inputfiles/GEM.inp

Documentation/units.txt

@@ -1,76 +1,79 @@
-Units in iPic3D
-
----------------------------------------------------------------------------------------------------
-1) The input file.
-
-Everything is normalized to ion plasma parameters.
-So that in the input file Lx, Ly, Lz are in units of ion skin depth:
-
-[L] == d_i.
-
-The time unit is reversed ion plasma frequency:
-
-[t] == 1 / f_{p,i}.
-
-Hence, the light speed is unity:
-
-c == 1 (given in the inputfile).
-
-Charge is normalized to e:
-
-[e] == 1.
-
-Mass:
-
-m_i == 1
-
-Density:
-
-[rho] = 1/4/pi (normalization is done in EMfields Init* method)
-
-Energy:
-
-[Energy] = m_i * c^2
-
----------------------------------------------------------------------------------------------------
-2) Pressures.
-
-If you need to compute, e.g., plasma beta you have to compute the gas and the magnetic pressures:
-
-p_{gas} = u_{th,i}^2 * \rho_i / (4*pi)   +   (m_e/m_i) * u_{th,e}^2 * \rho_e / (4*pi)
-(where the first term in rhs is the ion pressure, and the second term is the electron pressure).
-Note, that you should take the value of a single (x, y, or z) component of the thermal velocity!
-
-p_{mag} = B^2 / (8*pi)
-
-
-For those who forget, I remind that
-
-\{beta} = p_{gas} / p_{mag}.
-
----------------------------------------------------------------------------------------------------
-3) Magnetic permittivity (permeability) of vacuum
-
-\mu_0 = 1. 
-
----------------------------------------------------------------------------------------------------
-4) Alfven speed equals to the B0 in the inputfile
-
-v_A = B_0
----------------------------------------------------------------------------------------------------
-
-5) Currents in iPIC3D (exactly Faraday's law):
-
-j = curl(B)*c/FourPI
----------------------------------------------------------------------------------------------------
-
-6) Velocity distribution
-
-kT/m = vth
-where k is Boltzmann constant, T is temperature, m is particle mass for specie; 
-vth is initial thermal speed for specie (one component!).
-
-So the distribution of the absolute value of velocity (u) should follow the Maxwellian:
-F = 4.*pi * (0.5/pi/uth**2)**(1.5) * u**2 * exp(-0.5*u**2/uth**2) * Ns * du,
-where uth is thermal speed for the specie, Ns=npcelx*npcely*npcelz, du is velocity bin size.
----------------------------------------------------------------------------------------------------
+Units in iPic3D
+
+---------------------------------------------------------------------------------------------------
+1) The input file.
+
+Everything is normalized to ion plasma parameters.
+So that in the input file Lx, Ly, Lz are in units of ion skin depth:
+
+[L] == d_i
+
+The time unit is reversed ion plasma frequency:
+
+[t] == 1 / f_{p,i}
+
+Hence, the light speed is unity:
+
+c == 1 (given in the inputfile).
+
+Charge is normalized to e:
+
+[e] == 1
+
+Mass:
+
+m_i == 1
+
+Density:
+
+[rho] = 1/(4*pi) (normalization is done in EMfields Init* method).
+
+Energy:
+
+[Energy] = m_i * c^2
+
+---------------------------------------------------------------------------------------------------
+2) Pressures.
+
+If you need to compute, e.g., plasma beta you have to compute the gas and the magnetic pressures:
+
+p_{gas} = v_{th,i}^2 * \rho_i / (4*pi)   +   (m_e/m_i) * v_{th,e}^2 * \rho_e / (4*pi)
+(where the first term in rhs is the ion pressure, and the second term is the electron pressure).
+Note, that you should take the value of a single (x, y, or z) component of the thermal velocity v_th!
+
+p_{mag} = B^2 / (8*pi)
+
+
+For those who forget, I remind that
+
+\{beta} = p_{gas} / p_{mag}
+
+---------------------------------------------------------------------------------------------------
+3) Magnetic permittivity (permeability) of vacuum
+
+\mu_0 = 1
+
+---------------------------------------------------------------------------------------------------
+4) Alfven speed equals to the B0 in the inputfile
+
+v_A = B_0
+
+---------------------------------------------------------------------------------------------------
+5) Currents in iPIC3D (exactly Faraday's law):
+
+j = curl(B) * c / (4*pi)
+
+---------------------------------------------------------------------------------------------------
+6) Velocity distribution
+
+k_B * T / m = v_th
+
+where k_B is Boltzmann constant, T is temperature, m is particle mass for specie;
+v_th is initial thermal speed for specie (one component!).
+
+So the distribution of the absolute value of velocity (u) should follow the Maxwellian:
+F = (4*pi) * (1/(2*pi) / v_th^2)^(1.5) * u^2 * exp(-0.5 * (u / v_th)^2) * Ns * du,
+where v_th is thermal speed for the specie, Ns=npcelx*npcely*npcelz, du is velocity bin size.
+
+---------------------------------------------------------------------------------------------------
+

H5hut-io/src/H5hut-io.cpp

@@ -1,4 +1,6 @@
+#ifdef USEH5HUT
 
+#include <mpi.h>
 #include <fstream>
 #include <cmath>
 #include <exception>
@@ -755,3 +757,5 @@ void H5input::ReadPartDataset(hid_t group, std::string dtset, long long nops, lo
   delete [] count;
   delete [] start;
 }
+
+#endif