Data Processing
===============

After you have run a calculation you can postprocess the data as needed.

To load in the data you need to specify the below options::

  --logs <log file location> --run <run number>

For example if you wanted to access ``~/Logs/n400_298K_1.67e+08gauss_267kHz_10nm/Run10_mol5.1.hdf5``

::

  --logs ~/Logs/n400_298K_1.67e+08gauss_267kHz_10nm/ --run 10

Filetypes
---------

The main file that is created by the program contains all the data from the run.
This can be stored in

* HDF5 (default)
* PKL  (python's pickled format)
* txt

HDF5 files have the added bonus of compressing the data as well as being a highly portable file format. It should also be noted that there is no restart mechanism for raw text files.

Other output files are the result of postprocessing and include an extended xyz file, a momenta file and a energy file.

Postprocessing files
~~~~~~~~~~~~~~~~~~~~

All postprocessing files come in two forms: an averaged file and multiple unaveraged files. The averaging comes from the statistical runs so if there is only one statistic these files will be the same.

Extended XYZ files
``````````````````

The columns in the file are set out as shown::

         |  position | momentum | magnetisation |  forces | 
  n
  <comment data>
  mol0   | x   y   z |  x  y  z |   x   y   z   | x  y  z |
  .
  .
  .
  moln-1 .  .  .


Energy files
````````````

The columns in the file are set out as shown::

  iteration time kinetic_energy translational_potential magnietic_potential Total_Energy

Momenta files
`````````````

The columns in the file are set out as shown::

  iteration time total_momentum(x,y,z) magnetisation_momentum(x,y,z) angular_momoentum(x,y,z)