Merge branch 'roms-4.1'

Author: Alexander-Barth

.github/workflows/CI.yml

@@ -20,7 +20,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -70,7 +70,7 @@ jobs:
           version: '1'
       - run: |
           sudo apt-get update
-          sudo apt-get install python3-matplotlib
+          sudo apt-get install libnetcdf-dev gfortran make perl netcdf-bin libnetcdff-dev libopenmpi-dev openmpi-bin git python3-pip wget python3-setuptools python3-matplotlib
           git config --global user.name name
           git config --global user.email email
           git config --global github.user username

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GeoDatasets = "ddc7317b-88db-5cb5-a849-8449e5df04f9"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"

docs/make.jl

@@ -5,36 +5,72 @@ using Documenter
 using ROMS
 import Literate
 
-Literate.markdown(
-    joinpath(@__DIR__, "..", "examples", "plots.jl"),
-    joinpath(@__DIR__, "src"),
-    execute = true,
-    documenter = true,
-    # We add the credit to Literate.jl the footer
-    credit = false,
-)
+# Literate.markdown(
+#     joinpath(@__DIR__, "..", "examples", "04_plots.jl"),
+#     joinpath(@__DIR__, "src"),
+#     execute = true,
+#     documenter = true,
+#     # We add the credit to Literate.jl the footer
+#     credit = false,
+# )
 
-Literate.notebook(
-    joinpath(@__DIR__, "..", "examples", "plots.jl"),
-    joinpath(@__DIR__, "src"),
-    execute = false,
-)
+
+files = joinpath.(@__DIR__, "..", "examples", [
+    "01_build_roms.jl",
+    "02_prep_roms.jl",
+    "03_run_roms.jl",
+    "04_plots.jl",
+    "05_plots_makie.jl",
+])
+
+all_notebooks = joinpath(mktempdir(),"all.jl")
+write(all_notebooks, join(read.(files,String),"\n"))
+push!(files,all_notebooks)
+
+for file in files
+    Literate.notebook(
+        file,
+        joinpath(@__DIR__, "src"),
+        execute = false,
+    )
+
+    if !endswith(file,"all.jl")
+        Literate.markdown(
+            file,
+            joinpath(@__DIR__, "src"),
+            execute = true,
+            #execute = false,
+            documenter = true,
+            # We add the credit to Literate.jl the footer
+            credit = false,
+        )
+    end
+end
 
 
 makedocs(
     modules = [ROMS],
     sitename = "ROMS.jl",
     format = Documenter.HTML(
         prettyurls = CI,
-        footer = "Powered by [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl), [Literate.jl](https://github.com/fredrikekre/Literate.jl) and the [Julia Programming Language](https://julialang.org/)"
+        footer = "Powered by [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl), [Literate.jl](https://github.com/fredrikekre/Literate.jl) and the [Julia Programming Language](https://julialang.org/)",
+        #size_threshold = 400_000,
 
     ),
     pages = [
         "Tutorial" => "index.md",
+        "Building ROMS" => "01_build_roms.md",
+        "Preparation" =>  "02_prep_roms.md",
+        "Running ROMS"=> "03_run_roms.md",
+        "Plots" => "04_plots.md",
+        "Plots (Makie)" => "05_plots_makie.md",
+        "Additional information" => "additional_info.md",
         "Reference" => "reference.md",
-        "Plots" => "plots.md",
     ],
 )
 
 deploydocs(repo = "github.com/Alexander-Barth/ROMS.jl.git",
-           target = "build")
+           target = "build",
+           devbranch = "roms-4.1",
+           devurl = "JuliaEO25",
+           )

docs/src/additional_info.md

@@ -0,0 +1,75 @@
+
+## Additional topics
+
+### Nudging towards "climatology"
+
+The nudging towards "climatology" is an optional step to avoid issue (like sharp gradients) near the open sea boundaries.
+A flow relexation zone can be implemented in ROMS by using the followings settings:
+
+```
+LtracerCLM == T T  ! enable processing of CLIM data
+LnudgeTCLM == T T  ! nudge to CLIM data
+TNUDG == 2*10.0d0                    ! days
+```
+
+Make nudging on inflow is stronger than on outflow
+
+```
+OBCFAC == 10.0d0                      ! nondimensional
+```
+
+Set also `NUDNAME` to the file name create by the julia script.
+
+
+### Atmospheric forcing fields
+
+* For the Ligurian Sea, necessary parameters have already been prepared and are available in the file [ROMS-implementation.zip](https://dox.ulg.ac.be/index.php/s/nH8u2DrI1m9mMbC). It containts data download the from
+the ECMWF operational archive (`Atmosphere/ecmwf_operational_archive_2018-12-01T00:00:00_2020-01-01T00:00:00.nc`). This NetCDF file needs to be converted by the julia function `ROMS.prepare_ecmwf`.
+
+* The remaining of this section explained how to download data from the ECMWF operational archive (e.g. for a different domain). These instructions are not needed now.
+* Adapt the file name, longitude/latitude and time range (start one day earlier, and finish one day later) in [`forcing_ecmwf.py`](https://github.com/Alexander-Barth/ROMS.jl/blob/master/examples/forcing_ecmwf.py) and execute the script as follows:
+
+```bash
+python3 forcing_ecmwf.py
+```
+
+List of variables (*: quantities accumulated over the integration period ("step"))
+
+| NetCDF Variable name | Description |
+|----------------------|----------|
+| msl | Mean sea level pressure |
+| u10 | 10 metre U wind component |
+| v10 | 10 metre V wind component |
+| t2m | 2 metre temperature |
+| d2m | 2 metre dewpoint temperature |
+| tcc | Total cloud cover* |
+| sshf | Surface sensible heat flux* |
+| strd | Surface thermal radiation downwards* |
+| ssr | Surface net solar radiation* |
+| str | Surface net thermal radiation* |
+| ewss | Eastward turbulent surface stress* |
+| nsss | Northward turbulent surface stress* |
+| e | Evaporation* |
+| ro | Runoff* |
+| tp | Total precipitation* |
+| sst | Sea surface temperature |
+| par | Photosynthetically active radiation at the surface* |
+
+### Validation
+
+Check out satellite data (e.g. sea surface temperature, sea surface height) at:
+* [CMEMS](https://marine.copernicus.eu/)
+* [PODAAC NASA](https://podaac.jpl.nasa.gov/)
+
+Make some comparison with satellite and the downloaded in situ observation
+
+### Hydrodynamic model troubleshooting
+
+[Hydrodynamic model troubleshooting](https://github.com/gher-ulg/Documentation/wiki/Hydrodynamic-model-troubleshooting)
+
+
+### More information
+
+* [ROMS Wiki](https://www.myroms.org/wiki/)
+* [ROMS Wiki Frequently Asked Questions](https://www.myroms.org/wiki/Frequently_Asked_Questions)
+* K. Hedström. 2016. [Technical Manual for a Coupled Sea-Ice/Ocean Circulation Model (Version 4)](https://github.com/kshedstrom/roms_manual/blob/master/roms_manual.pdf). U.S. Dept. of the Interior, Bureau of Ocean Energy Management, Alaska OCS Region. OCS, Study BOEM 2016-037. 176 pp.