ABM-B and ABM-U (C++ version)

This is a reference implementation of the ABM-B and ABM-U models described in
http://www.npsg.uwaterloo.ca/resources/docs/rse2006.pdf, with modifications
described in http://www.npsg.uwaterloo.ca/resources/docs/ieee07-8.pdf

For detailed information, visit the online pages for:
    - ABM-U: http://www.npsg.uwaterloo.ca/models/ABMU.php
    - ABM-B: http://www.npsg.uwaterloo.ca/models/ABMB.php

The package is licensed under a BSD license, described in LICENSE. 

This was released by the Natural Phenomenon Simulation Group at University of
Waterloo in Waterloo, Ontario, Canada. Please visit http://www.npsg.uwaterloo.ca
for more information.

Usage:
    - Run "make abmu" to make an abmu executible. Run "make abmb" to 
      make an abmb executible. Afterwards,
      run "./abmb samples/lopex_0219-0220.json output.csv" 
      or  "./abmu samples/lopex_0141-0142.json output.csv". You can specify more
      detailed options too, just run "./abmu" to see them all.

Command line flags:
    - -n <int>: Specifies the number of samples to run the monte carlo simulation.
                We recommend 10^5 to get asymptotic convergence

    - -a <float>: Azimuthal angle in degrees to fire rays from.

    - -p <float>: Polar angle in degrees to fire rays from. Values from 0 to 90
                  correspond to the abaxial surface, while values from 90 to 180
                  correspond to the adaxial surface.

    - -s <int>: Wavelength step in nm. Output will occur with every <step> wavelengths

    - -w <int>: Wavelength start in nm. Output will start with this wavelength.

    - -e <int>: Wavelength endin nm. Output will end with this wavelength.

    - -d <path>: Data directory. The data is outlined in the Code Organization section
                 below.

    - -t <int>:  Number of threads. Rule of thumb is double the number of parallel processing
                 units in your computer.

    - -q: Disable sieve and detour effects. This is an in-vivo Vs. in-vitro modelling issue that is
          outlined in the paper here: http://www.npsg.uwaterloo.ca/resources/docs/ieee07-8.pdf

Requirements:
    - The yajl JSON parsing library headers: http://lloyd.github.com/yajl/
      (available in Ubuntu under libyajl-dev)

    - pthreads

Code Organization:
    - 'src/': This folder contains all the code files necessary for ABM-U/ABM-B to run.

    - 'include/': This folder contains all the header files necessary for ABM-U/ABM-B to run.

    - 'data/': This folder contains the data files (e.g., refractive indices) that are needed
               to run ABM-B or ABM-U. All are available here: http://www.npsg.uwaterloo.ca/data/leaves.php
               - 'caro-PAS-400-2500.txt': Specific absorption coefficient of carotenoids (400-2500nm)
               - 'cellulose400-2500.txt': Specific absorption coefficient of cellulose (400-2500nm)
               - 'chloAB-DFA-400-2500.txt': Specific absorption coefficient of chlorophyll a+b (400-2500nm)
               - 'sacwH400-2500.txt': Specific absorption coefficient of water (400-2500nm)
               - 'raH400-2500.txt': Refractive index (real part) of antidermal cell wall (400-2500nm)
               - 'rcH400-2500.txt': Refractive index (real part) of epicuticular wax (400-2500nm)
               - 'rmH400-2500.txt': Refractive index (real part) of wet mesophyll wall (400-2500nm)

    - 'samples/': This folder contains data definitions for samples used for testing of ABM-U/ABM-B.
                  All samples correspond to those mentioned in http://www.npsg.uwaterloo.ca/resources/docs/rse2006.pdf.
                  Samples are specified in a json-like format. 
               - 'lopex_0141_0142.json': Soybean (Soja hispida or Glycine max), a bifacial leaf for ABM-B
               - 'lopex_0219_0220.json': Corn (Zea mays L.), a unifacial leaf for ABM-U

Notes:
    - All concentrations are specified in g/cm^3, and lengths in meters.

    - Data is piecewise-constant interpolated accross 400-2500nm, with data points
      every five nanometers.