MITgcm File Formats

function monitor(config::MITgcm_config)

Call scan_rundir and show to REPL.

scan_rundir(pth::String)

Scan a MITgcm run directory and then, if found, the standard output text file ("output.txt" or "STDOUT.0000") via scan_stdout.

scan_rundir(config::MITgcm_config)

Scan a MITgcm run directory (joinpath(MC,"run")) and then, if found, the standard output text file ("output.txt" or "STDOUT.0000") via scan_stdout.

scan_stdout(filout::String)

Scan a MITgcm standard output text file ("output.txt" or "STDOUT.0000") and return a NamedTuple of information collected.

• packages : report of packages being compiled and used
• params_time : initial time, model duation, output frequency, etc
• params_grid : type of grid (Curvilinear, Cartesian, ...) and array sizes
• paramsfiles : type of output (usemdsio, use_mnc) and array size (ioSize)
• completed : true / false depending on the end of standard output file (filout)

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.

read_toml(toml_file::String)

Read toml parameter file into an OrderedDict with Symbol keys, consistent with tracked_parameters.toml.

using MITgcm, TOML
pth=joinpath(dirname(pathof(MITgcm)),"..","examples","configurations")
toml_file=joinpath(pth,"tutorial_held_suarez_cs.toml")
params=read_toml(toml_file)

Writing parameters to file is straightforward. For example:

MC=MITgcm_config(configuration="tutorial_held_suarez_cs")
setup(MC)
open(tempname()*".toml", "w") do io
    TOML.print(io, MC.inputs)
end

read_toml(config_name::Symbol)

Read toml parameter file specified by configuration name.

using MITgcm
params=read_toml(:OCCA2)

MITgcm_namelist(groups,params)

Data structure representing a MITgcm namelist file, such as data.pkg, which contains

    groups :: Array{Symbol,1} = Array{Symbol,1}(undef, 0)
    params :: Array{OrderedDict{Symbol,Any},1} = Array{OrderedDict{Symbol,Any},1}(undef, 0)

with model parameters (params) being organized in groups as done in the files.

using MITgcm
fil=joinpath(MITgcm_path[1],"verification","advect_xy","run","data")
nml=read_namelist(fil)
MITgcm_namelist(nml.groups,nml.params)
MITgcm_namelist(groups=nml.groups,params=nml.params)
MITgcm_namelist(groups=nml.groups)

read_namelist(fil)

Read a MITgcm namelist file in native format, parse it, and return as a NamedTuple.

using MITgcm
testreport(MITgcm_config(configuration="advect_xy"))
fil=joinpath(MITgcm_path[1],"verification","advect_xy","run","data")
namelist=read_namelist(fil)

write_namelist(fil)

Save a MITgcm namelist file (native format). In the example below, one is read from file, modified, and then saved to a new file using write_namelist.

using MITgcm
fil=joinpath(MITgcm_path[1],"verification","advect_xy","run","data")
nml=read(fil,MITgcm_namelist())
write(fil*"_new",nml)

or write_namelist(fil*"_new",namelist).

read_all_namelists(input_path)

Read all MITgcm namelist files in input_path, parse them, and return as a NamedTuple of NamedTuples.

using MITgcm; path0=default_path()
input_path=joinpath(path0,"verification","advect_xy","input")
params=read_all_namelists(input_path)

write_all_namelists(params,output_path=tempname())

Write all MITgcm namelist to files in output_path, from corresponding toml file

using MITgcm
params=read_toml(:OCCA2)
write_all_namelists(params)

read_mdsio(fil::String)

Read a single MITgcm MDSIO-type 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(fil::String,rec::Integer)

Read a single variable / record from a single MITgcm MDSIO-type file, and return as an Array.

read_mdsio(fil,1)

read_mdsio(fil::String,nam::Symbol)

Read a single variable / record from a single MITgcm MDSIO-type file, and return as an Array.

read_mdsio(fil,:THETA)

read_mdsio(pth::String,fil::String)

Read a set of MITgcm MDSIO-type files (".data" binary + ".meta" text pair), combine, and return as an Array. Unlike read_mdsio(fil::String) where fil is one complete file name, this method will search within pth for files that start with fil.

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

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)]

read_mnc(pth::String,fil::String,var::String)

Read variable var from a set of MITgcm MNC-type files (netcdf files), combine, and return as an Array. This method will search within pth for files that start with fil.

GridLoad_mdsio(myexp::MITgcm_config)

Load grid variables (XC, YC, Depth, etc) from model run directory (rundir).

GridLoad_mdsio(rundir::String)

Load grid variables (XC, YC, Depth, etc) from model run directory (rundir).

GridLoad_mnc(γ::gcmgrid)

Load grid variabes (XC, YC, Depth) model run directory (joinpath(rundir,"mnc_test_0001")).

GridLoad_mnc(myexp::MITgcm_config)

Load grid variables (XC, YC, Depth) from model run directory (joinpath(rundir,"mnc_test_0001")).

GridLoad_mnc(rundir::String)

Load grid variables (XC, YC, Depth) from model run directory (joinpath(rundir,"mnc_test_0001")).

GridLoad_native(path,files,γ)

Load grid variables from native grid files.

path="GRID_LLC90"
files=["tile001.mitgrid","tile002.mitgrid","tile003.mitgrid","tile004.mitgrid","tile005.mitgrid"]
ioSize=[90 1170]
facesSize=[(90, 270), (90, 270), (90, 90), (270, 90), (270, 90)]

γ=gcmgrid(path,"LatLonCap",5,facesSize, ioSize, Float64, read, write)

Γ=GridLoad_native(path,files,γ)

or using another grid

path="llc_1080"
files=[ "llc_001_1080_3240.bin","llc_002_1080_3240.bin",
        "llc_003_1080_1080.bin","llc_004_3240_1080.bin","llc_005_3240_1080.bin"]
ioSize=[1080 14040]
facesSize=[(1080, 3240), (1080, 3240), (1080, 1080), (3240, 1080), (3240, 1080)]

and for plotting

using GLMakie

#col=log10.(Γ.RAC); rng=(4,8)

#using MAT
#Depth=get_bathy(path,γ)
#col=write(Depth); rng=(-5000,5000)

XC=write(Γ.XC); YC=write(Γ.YC)
ii=findall((XC.>-80).&(XC.<-10).&(YC.>-10).&(YC.<60))
#ii=findall((XC.>-80).&(XC.<-60).&(YC.>15).&(YC.<35))

#ii=1:prod(γ.ioSize)

scatter(XC[ii],YC[ii],color=col[ii],colorrange=rng,markersize=0.1, markerspace = :data)

read_flt(dirIn::String,prec::DataType)

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

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)

read_nctiles(fileName,fldName,mygrid; I, eccoVersion4Release4=false, verbose=false)

Read model output from NCTiles file and convert to MeshArray instance. Setting the keyword argument eccoVersion4Release4=true allows read_nctiles to read in ECCOv4r4 data which has a different file naming convention to previous versions.

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))