calculateModeVolume
===================

This script calculates the mode volume based on epsilon and frequency snapshots generated by Bristol FDTD.
This is a short guide. Please refer to the Matlab help for more up to date and detailed documentation::

  help calculateModeVolume

Example usage::

  calculateModeVolume({'epsilon_snaphots.inp','frequency_snapshots.inp'}, 'eps_folder', '../epsilon', 'snap_plane', 'x', 'refractive_index_defect', 1.5);

Using epsilon lookup tables::

  calculateModeVolume({'sim.inp','sim.geo'}, 'epsilon_lookup_table', 'epsilon_1.prn', 'logfile_bool', true, 'logfile', 'MV_epsilon_1.log');

Format of an epsilon lookup table::

  n f(n)
  1 2.1
  2 3
  5 4
  8 5

Arguments
---------

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Required arguments       Description
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inpfile_list             List of input files of the form {'file1.inp','file2.inp',...}
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Optional arguments       Description
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fsnap_folder             folder containing the .prn files for frequency snapshots. Default = '.'
eps_folder               folder containing the .prn files for epsilon snapshots. Default = '.'
snap_plane               direction of the snapshots ('x','y' or 'z'). Default = 'z'
snap_time_number         the number of the snapshot (i.e. 02 in zaaid02.prn for example). Default = biggest number for which snapshots are available.
refractive_index_defect  refractive index used to normalize the mode volume (usually refractive index of the defect/cavity). Default = 1.
is_half_sim              if set to true, the calculated mode volume will be multiplied by 2. Set to 'false' by default.
numID_list               List of numIDs of snapshots to allow selecting specific ones. However the chosen 'snap_plane' direction is still used for filtering, so a snapshot must be in the snap_plane direction and in numID_list to be selected! If not specified or empty, it defaults to a list of all numIDs.
justCheck                If true, the command only lists details about the snapshots that would be used to calculate the mode volume and does nothing else. Default = false.
BFDTD_version            BFDTD version used to create the snapshots. (affects the names of created files) Default = '2013'.
mode_index               Index of the mode for which to calculate the mode volume. Default = 1.
Nmodes                   Total number of modes for which mode volume snapshots are available. Default = 1. (designed for snapshots created as follows: {(z1,f1), (z1,f2), (z2,f1), (z2,f2), (z3,f1), (z3,f2)})
logfile_bool             If true log calculation info to a file in the fsnap_folder, else don't log. Default = false.
incorrectAlgorithm_bool  If true, use the incorrect mode volume calculation used in JQE paper. Only re-implemented for comparison purposes. Should always be left false otherwise! Default = false
logfile                  Specify the name of the file to log to, if logfile_bool is true. If set to an empty string, a default name will be used. Default = ''
integration_sphere       Specify a spherical volume over which to integrate. Format: [xc,yc,zc,radius] where (xc,yc,zc) is the sphere centre and "radius" its radius. If radius<0, the whole volume is used. Default = '[0,0,0,-1]'
epsilon_lookup_table     Specify a file containing a lookup table to use for epsilon values. The file should be in the .prn format with 2 columns.
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