Plotting
========

Plotting the data produced is all contained in the postprocessing module and specifically the ``--column`` flag or PlotColumns in your input file. When plotting data, a new data file will be written containing all the data that could be plotted. There are three files that can be written; an extended xyz file, a momenta file and an energy file. The program does not read any data from this file, all manipulation of the data is done internally:

To plot two sets of data against each other, for example, time and total energy.

::

  --column time Etotal

The above will only work for a single statistical run. If the calculation was run with more than one statistical run you will need to specify the run you want to plot such as: ::

  --column time "Etotal[0, :]"


This can be extended to plot multiple sets at once. The below example also shows how to split a matrix into a desired shape. The addition of quotes is required to stop bash interfering with the input.

::

  --column time Etotal time "Mtotal[:, 0]"

You can also do basic arithmetic on the data sets such as::

  --column time mag_pot+trans_pot

Possible variables
------------------

Matrix Dimensions Key - ``S = Statistical Runs I = Iterations``, ``N = Number of molecules``, ``C = XYZ Coordinates (3)``

XYZ data - S*I*N*C ::

  position
  magnetisation
  forces
  momentum

Energy data - S*I ::

  Etotal
  mag_pot
  trans_pot
  kinetic

Momenta data - S*I*C ::

  Mtotal
  total_mag
  total_angular
  CoM
  CoM_mom

Other ::

  time - I