Add support for openPMD output

[AngelFP]

Since its origin, the only output in Wake-T after tracking a particle distribution through a beamline (or beamline element) has been a simple list of n_out ParticleBunches. To make Wake-T more useful and resemble better what a user typically expects from a plasma simulation code, a proper output to disk should be implemented. This will be done following the openPMD standard by taking advantage of the openPMD-api.

This issue keeps track and compiles all the required and wished features of the diagnostics (as well as bugs/issues which appear during implementation).

Required features:

• Output of particle distributions at each step, as defined by n_out, in:
  • PlasmaStage.
  • PlasmaRamp.
  • PlasmaLens.
  • TMElement.
• Output of all fields used internally (Ez, Wr, rho, CSR wakes...) at each step, as defined by n_out.
  • PlasmaStage.
  • PlasmaRamp.
  • PlasmaLens.
  • TMElement.
• Possibility of specifying name and path of diagnostics directory.
• Write diagnostics of whole Beamline to the same folder (this might include plasma elements, drifts, magnets, etc. which require different attributes and datasets in the output).
• In the plasma elements, output individual components of E and B and not just the combined wakefield W.

Nice to have:

• Option to choose field or particle diagnostics only.
• Or even better, option to specify individual fields and particle quantities to write.
• Option to output plasma particles in quasistatic_2d model.
• Option of writing diagnostics of each element to a separate directory.

Bugs/issues to solve:

• A name parameter should be added to ParticleBunch. Right now all bunches are called electron_bunch in the diagnostics.
• Check that the position field attribute it correctly set (cell centered vs node centered).
• A cleaner way of setting the field dimensions and other parameter could be implemented.
• ED_PIC metadata is currently missing in particle species. Check if/what to add because Wake-T is not a PIC code.
• Same for fields, it is not clear what to write in some ED_PIC metadata.
• No output is currently generated at t=0.
• The attribute iterationFormat is not correct.
• Some fields are transposed in the output and do not agree with the axis order specified in attributes such as axisLabels.
• gridGlobalOffset is not correct. It should add (and not substract) xi_min. Also, it is incorrectly named 'local_offset' in some parts of the code.
• Set iteration encoding to file based.