Output to file is now default and happens in the step() function of the Simulation class. MainBatch streamlined and simplified, initPair is for now the default initial condition for non-graphical simulations. New variables included, namely gridStep and tMax, such that the simulations started from the bash finish after tMax/timeStep iterations. In the following commit I will change the format and content of output files.
Output of particle locations and velocities into "particles_seq.txt" has been implemented. In the next commit grid observables have to be implemented in a different file.
Output of both relativistic and non-relativistic kinetic energy as well as some field observables implemented.
Two-stream instability implemented, output extended such that spectrum files are created after certain periods of time, controlled by a new variable specstep. Eps_0 constant in PoissonSolverFFTPeriodic changed in order to be consistent with the field dynamics.
Merge https://github.com/openpixi/openpixi into upstream

Conflicts:
	pixi/src/test/java/org/openpixi/pixi/parallel/ParallelSimulationTest.java
All files moved to the output/ directory.
ConstantForce added to MainControlApplet in order to enable the use of sliders.
Merge pull request #75 from dgelfand/master

Output extended, two-stream instability implemented.
Fix bug "array index out of bounds"

Index stays within grid size.

Patch by Clemens Müllner.