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Documentation.md

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+## Description of each FORTRAN files:
+
++ `geom2.f90`  Subroutine computes the new X,Y and Z position of the photon after a scattering event.
++ `global.f90` Subroutine contains all the global variables used in the AOMC model.
++ `interface.f90` Determines the outcome of the photon's interaction with the air-water interface.
++ `light_internal.f90` Subroutine computes the incident angle of the new photon on the water surface.
++ `logbin.f90` Subroutine logs the photon's trajectory.
++ `mc.f90` (main program) This is the main program.
++ `modules.f90` Contains the random number generator function "rand", and the angle summation routine "anglesum".
++ `rand_global.f90` Module is contained in subroutine "modules.f90" and computes the random number "rand".
++ `vsf.f90` Subroutine determines the photon's angle of scatter using the scattering phase function.
++ `water.f90` Subroutine traces the path of a photon from the moment it enters the water to the moment when it lost from the system.
+
+## The input files:
++ `amc.inp`:  Main input file. Defines general environmental parameters such as bottom depth, vertical heterogenaty of water body, and solar zenith angle. Also defines model parameters such as sky model to use, number of photons to run and number of bands to simulate.
++ `conc.inp`: Defines the concentration for each parameters simulated at the different depths (if a vertically heterogenous water body is simulated). This file also allows the user to define the refractive index of each layer.
++ `lamba.inp`
++ `lambs.inp`
++ `lambda.inp`
++ `spf.inp`
+
+## The output files:
+The AOMC model will output 4  " *.out "  files:
++ `aop.out`  A listing by depth and wavelength of all of the apparent optical properties except radiance.
++ `iop.out`   A listing of the inherent optical properties.
++ `rad.out`  A listing by depth and wavelength of radiance at various angles
++ `wave.out` A listing by wavelength of the "just below the surface (0-)" values for several apparent optical properties (this is a subset of the data presented in the aop.out file).