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Model setup

OceanLight.jl simulation reads all required variable from the struct param. The description on how to generate and setup the model is described below in this section.

Input variable

OceanLight.jl accepts and reads the input variables from .yml file. The structure on what variable to includes is shown below.

OceanLight.writeparams — Function
writeparams(data::Dict,fname="light.yml"::String)

Replace the data in the yml file fname to the new dictionary data.

If fname is unspecified, use light.yml as the default file name.

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This function only read the dict format. Hence, we first need to rearrange into dict format, before we can called the function writeparams(). 

# irradiance
nz = 200
dz = 1
nxe = 512
nye = 512
num = 31
ztop = 10
# photon
nphoton = 100000
kr = 10
nxp = 512
kbc = 0
b = 0.006
nyp = 512
a = 0.007
# wave
pey = 0.07853981633974483
nxeta = 512
nyeta = 512
pex = 0.07853981633974483

data=Dict("irradiance"=>Dict("nxe"=>nxe,"nye"=>nye,"nz"=>nz,"dz"=>dz,"ztop"=>ztop,"num"=>num),
            "wave"=>Dict("pex"=>pex,"pey"=>pey,"nxeta"=>nxeta,"nyeta"=>nyeta),
            "photon"=>Dict("nxp"=>nxp,"nyp"=>nyp,"nphoton"=>nphoton,"a"=>a,"b"=>b,"kr"=>kr,"kbc"=>kbc))
Dict{String, Dict{String}} with 3 entries:
  "irradiance" => Dict("nz"=>200, "dz"=>1, "nxe"=>512, "nye"=>512, "num"=>31, "…
  "photon"     => Dict{String, Real}("nphoton"=>100000, "kr"=>10, "nxp"=>512, "…
  "wave"       => Dict{String, Real}("pey"=>0.0785398, "nxeta"=>512, "nyeta"=>5…

Simulation parameters

OceanLight.jl reads all input variables in .yml format through the function readparams(), and store the values in structure Param. Beside our provided value, it will auto-generate some of the parameters that will be used in the simulation. The list and description of all the values can be accessed below.

OceanLight.readparams — Function
readparams(fname="light.yml")

Read parameters from yml file fname.

If fname is unspecified, use light.yml as the default file name.

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OceanLight.Param — Type
struct Param

All the Parameters and their attributes that will be used in the simulation

  • nx::Int64: nx = nxe+1 , nxe is the number of energy grid that we will calculate for the energy in x direction

  • ny::Int64: ny = nye+1 , nye is the number of energy grid that we will calculate for the energy in y direction

  • nxe::Int64: number of energy grid that we will calculate for the energy in x direction

  • nye::Int64: number of energy grid that we will calculate for the energy in y direction

  • num::Int64: constant always set at 31 based on Measurement from Kirk, 1981 (The number of angle measurement in Kirk paper)

  • nz::Int64: number of the layer beneath the sea surface (in z direction) that we will calculate for the irradiance energy

  • x::Vector{Float64}: array of all the x corrdination

  • y::Vector{Float64}: array of all the y cooradination

  • z::Vector{Float64}: array of all the z coordination

  • pex::Float64: pex is being used in function pdfx or the function to calculate the partial derivative of the surface elevation in x direction

  • pey::Float64: pey is being used in function pdfx or the function to calculate the partial derivative of the surface elevation in y direction

  • dx::Float64: the distance between each grid point in x direction

  • dy::Float64: the distance between each grid point in y direction

  • dz::Float64: height difference between each layer that we calculate for the irradiance energy (nz)

  • ztop::Float64: the maximum height above the water surface

  • xmin::Float64: minimum x value (always set to 0)

  • xmax::Float64: maximum x value equal to multiplication between total number of grid point (nxe) and the distance between each grid point (dx) in x direction

  • ymin::Float64: minimum y value (always set to 0)

  • ymax::Float64: maximum y value equal to multiplication between total number of grid point (nye) and the distance between each grid point (dy) in y direction

  • xl::Float64: difference between the maximum and minimum value in x direction

  • yl::Float64: difference between the maximum and minimum value in y direction

  • nxs::Int64: nxs=nxη+1

  • nys::Int64: nys=nyη+1

  • nxη::Int64: same as nxeta value in the light.yml file: the number of wave grid point in x direction

  • nyη::Int64: same as nyeta value in the light.yml file: the number of wave grid point in y direction

  • nxp::Int64: number of grid in x direction that the photon will be emitted

  • nyp::Int64: number of grid in y direction that the photon will be emitted

  • nphoton::Int64: number of photon emitted

  • kbc::Int64: setting the mode of boundary condition: kbc=1 (no interpolation) or periodic BC kbc=0 (interpolation using FFT)

  • a::Float64: absortance coefficient

  • b::Float64: scattering coefficient

  • kr::Float64: the multiple of sphere detector radius to dz (not being used anywhere in the code)

  • ddx::Float64: the distance difference in x direction in which we will emit the photon (total length of physical grid xl devided by total number of photon grid nxp)

  • ddy::Float64: the distance difference in y direction in which we will emit the photon (total length of physical grid yl devided by total number of photon grid nyp)

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