MITgcmTools.jl

Set of tools for running MITgcm, analyzing its results, and preparing model inputs. Examples are provided in test/runtests.jl as well as in examples/run_MITgcm.jl, monitor_run.jl, etc.

Simulated particles from HS94 on cube sphere grid

Index

MITgcm path and run script

The MITgcm_path variable provides the path to the MITgcm folder being used. The MITgcm_compile and MITgcm_run functions can be used to, respectively, compile and run a MITgcm configuration (via the testreport script). An interactive / reactive example can be found in the examples/run_MITgcm.jl Pluto notebook shown below.

Compiling and running MITgcm

Reading MITgcm outputs

MITgcmTools.read_mdsio — Function
read_mdsio(datafile)

Read a MITgcm mdsio file (".data" binary + ".meta" text pair), and return as an Array

p="./hs94.cs-32x32x5/run/"
x=read_mdsio(p*"surfDiag.0000000020.002.001.data")
y=read_mdsio(p*"pickup.ckptA.002.001.data")
z=read_mdsio(p*"T.0000000000.002.001.data")
read_mdsio(pth::String,fil::String)

Read a MITgcm's MDSIO files (".data" binary + ".meta" text pair), combine, and return as an Array

p="./hs94.cs-32x32x5/run/"
x=read_mdsio(p,"surfDiag.0000000020")
y=read_mdsio(p,"pickup.ckptA")
z=read_mdsio(p,"T.0000000000")
MITgcmTools.read_meta — Function
read_meta(metafile)

Read a MITgcm metadata file, parse it, and return as a NamedTuple

p="./hs94.cs-32x32x5/run/"
meta=read_meta(p*"surfDiag.0000000020.002.001.meta")
pairs(meta)
meta.dimList
read_meta(pth::String,fil::String)

Read a MITgcm metadata files, parse them, and return as an array of NamedTuple

p="./hs94.cs-32x32x5/run/"
meta=read_meta(p,"surfDiag.0000000020")
pairs(meta[end])
[meta[i].dimList for i in 1:length(meta)]
MITgcmTools.read_namelist — Function
read_namelist(fil)

Read a MITgcm namelist file, parse it, and return as a NamedTuple

using MITgcmTools
testreport("advect_xy")
fil=joinpath(MITgcm_path,"verification","advect_xy","run","data")
namelist=read_namelist(fil)
MITgcmTools.read_available_diagnostics — Function
read_available_diagnostics(fldname::String; filename="available_diagnostics.log")

Get the information for a particular variable fldname from the available_diagnostics.log text file generated by MITgcm.

MITgcmTools.read_bin — Function
read_bin(fil::String,kt::Union{Int,Missing},kk::Union{Int,Missing},prec::DataType,mygrid::gcmgrid)

Read model output from binary file and convert to MeshArray. Other methods:

read_bin(fil::String,prec::DataType,mygrid::gcmgrid)
read_bin(fil::String,mygrid::gcmgrid)
MITgcmTools.read_flt — Function
read_flt(dirIn::String,prec::DataType)

Read displacements from MITgcm/pkg/flt output file into a DataFrame.

MITgcmTools.read_nctiles — Function
read_nctiles(fileName,fldName,mygrid)

Read model output from NCTiles file and convert to MeshArray instance.

mygrid=GridSpec("LatLonCap")
fileName="nctiles_grid/GRID"
Depth=read_nctiles(fileName,"Depth",mygrid)
hFacC=read_nctiles(fileName,"hFacC",mygrid)
hFacC=read_nctiles(fileName,"hFacC",mygrid,I=(:,:,1))

Format conversions

The impossible MITgcm rendering

MITgcmTools.findtiles — Function
findtiles(ni::Int,nj::Int,mygrid::gcmgrid)
findtiles(ni::Int,nj::Int,grid::String="LatLonCap",GridParentDir="../inputs/GRID_LLC90/")

Return a MeshArray map of tile indices, mytiles["tileNo"], for tile size ni,nj and extract grid variables accordingly.

MITgcmTools.cube2compact — Function
cube2compact(x::Array)

Reshape from e.g. size (192, 32, 5) in cube format to (32, 192, 5) in compact format.

MITgcmTools.compact2cube — Function
compact2cube(x::Array)

Reshape from e.g. size (32, 192, 5) in cube format to (192, 32, 5) in compact format.

Formulae etc

MITgcmTools.SeaWaterDensity — Function

SeaWaterDensity(Θ,Σ,Π,Π0)

Compute potential density (ρP), in situ density (ρI), and density referenced to PREF (Π0 in decibars) from potential temperature (Θ in °C), salinity (Σ in psu) and pressure (Π in decibars) according to the UNESCO / Jackett & McDougall 1994 equation of state.

Credits: code based on a Matlab implementation by B. Ferron Reference: https://www.jodc.go.jp/info/iocdoc/UNESCOtech/059832eb.pdf Check value: ρI = 1041.83267kg/m^3 for Θ=3°Celcius, Σ=35psu, Π=3000dbar

(ρP,ρI,ρR) = SeaWaterDensity(3.,35.5,3000.)
isapprox(ρI,1041.83267, rtol=1e-6)
MITgcmTools.MixedLayerDepth — Function

MixedLayerDepth(Θ,Σ,Δ,mthd)

Compute mixed layer depth from potential temperature (Θ in °C), salinity (Σ in psu) and depth (Δ in method) according to various formulas (mthd == "BM", "Suga", "Kara"). Inputs must be dense vectors without any missing value (or NaN, etc).

D=collect(0.0:1.0:500.0); tmp=(1.0.-tanh.(5*(-1 .+ 2/D[end]*D)));
T=2.0 .+ 8.0*tmp; S=34.0 .+ 0.5*tmp;
(ρP,ρI,ρR) = SeaWaterDensity(T,S,D);

mld=MixedLayerDepth(T,S,D,"BM"); isapprox(mld,134.0)

using Plots
plot(ρP,-D,w=2,label="Potential Density",ylabel="Depth")
plot!(vec([ρP[1] ρP[end]]),-fill(mld,2),label="Mixed Layer Depth",w=2,c="black",s=:dash)