From dfb246820e0c3f6accc3b908cc7c34028698c56a Mon Sep 17 00:00:00 2001
From: Max <maximilian.gelbrecht@posteo.de>
Date: Mon, 4 Dec 2023 09:47:20 +0100
Subject: [PATCH 1/7] period kwarg

---
 src/SpeedyWeather.jl                 |  2 +-
 src/dynamics/prognostic_variables.jl | 13 ++++++++---
 src/output/feedback.jl               |  5 ++--
 src/run_speedy.jl                    | 14 ++++++++----
 test/dates.jl                        | 13 +++++++++++
 test/netcdf_output.jl                | 34 ++++++++++++++--------------
 test/run_speedy.jl                   |  8 +++----
 test/vertical_advection.jl           |  2 +-
 8 files changed, 59 insertions(+), 32 deletions(-)

diff --git a/src/SpeedyWeather.jl b/src/SpeedyWeather.jl
index 3bd0878b4..72b9cf97d 100644
--- a/src/SpeedyWeather.jl
+++ b/src/SpeedyWeather.jl
@@ -18,7 +18,7 @@ import Adapt: Adapt, adapt, adapt_structure
 
 # INPUT OUTPUT
 import TOML
-import Dates: Dates, DateTime, Millisecond, Second, Minute, Hour, Day
+import Dates: Dates, DateTime, Period, Millisecond, Second, Minute, Hour, Day
 import Printf: Printf, @sprintf
 import NCDatasets: NCDatasets, NCDataset, defDim, defVar
 import JLD2: jldopen
diff --git a/src/dynamics/prognostic_variables.jl b/src/dynamics/prognostic_variables.jl
index fd55ccd0a..83c65d6ba 100644
--- a/src/dynamics/prognostic_variables.jl
+++ b/src/dynamics/prognostic_variables.jl
@@ -10,8 +10,8 @@ Base.@kwdef mutable struct Clock
     "current model time"
     time::DateTime = DEFAULT_DATE
     
-    "number of days to integrate for, set in run!(::Simulation)"
-    n_days::Float64 = 0
+    "period to integrate for, set in set_period!(::Clock, ::Dates.Period)"
+    period::Second = Second(0)
 
     "number of time steps to integrate for, set in initialize!(::Clock,::TimeStepper)"
     n_timesteps::Int = 0  
@@ -28,10 +28,17 @@ end
 $(TYPEDSIGNATURES)
 Initialize the clock with the time step `Δt` in the `time_stepping`."""
 function initialize!(clock::Clock,time_stepping::TimeStepper)
-    clock.n_timesteps = ceil(Int,3600*24*clock.n_days/time_stepping.Δt_sec)
+    clock.n_timesteps = ceil(Int,clock.period.value/time_stepping.Δt_sec)
     return clock
 end
 
+"""
+$(TYPEDSIGNATURES)
+Set the `period` of the clock to a new value. Converts any `Dates.Period` input to `Second`."""
+function set_period!(clock::Clock,period::Period)
+    clock.period = Second(period)
+end
+
 """
 $(TYPEDSIGNATURES)
 Create and initialize a clock from `time_stepping`"""
diff --git a/src/output/feedback.jl b/src/output/feedback.jl
index 4486d7566..f3396f6dd 100644
--- a/src/output/feedback.jl
+++ b/src/output/feedback.jl
@@ -86,7 +86,8 @@ function initialize!(feedback::Feedback,clock::Clock,model::ModelSetup)
         (; run_path, id) = feedback
         SG = model.spectral_grid
         L = model.time_stepping
-
+        period = clock.period.value/(3600*24)
+        
         # create progress.txt file in run_????/
         progress_txt = open(joinpath(run_path,"progress.txt"),"w")
         s = "Starting SpeedyWeather.jl run $id on "*
@@ -94,7 +95,7 @@ function initialize!(feedback::Feedback,clock::Clock,model::ModelSetup)
         write(progress_txt,s*"\n")
         write(progress_txt,"Integrating:\n")
         write(progress_txt,"$SG\n")
-        write(progress_txt,"Time: $(clock.n_days) days at Δt = $(L.Δt_sec)s\n")
+        write(progress_txt,"Time: $period days at Δt = $(L.Δt_sec)s\n")
         write(progress_txt,"\nAll data will be stored in $run_path\n")
         feedback.progress_txt = progress_txt
     end
diff --git a/src/run_speedy.jl b/src/run_speedy.jl
index ff5dafcce..8acb02b71 100644
--- a/src/run_speedy.jl
+++ b/src/run_speedy.jl
@@ -2,18 +2,24 @@
 $(TYPEDSIGNATURES)
 Run a SpeedyWeather.jl `simulation`. The `simulation.model` is assumed to be initialized."""
 function run!(  simulation::Simulation;
-                n_days::Real = 10,
-                output::Bool = false)
+                period::Period = Day(10),
+                output::Bool = false, 
+                n_days::Union{Nothing, Real}=nothing)
     
+    if !isnothing(n_days)
+        @warn "run!: n_days keyword is deprecated, use period = Day(n_days) instead."
+        period = Day(n_days) 
+    end 
+
     (;prognostic_variables, diagnostic_variables, model) = simulation
     (;clock) = prognostic_variables
 
     # set the clock's enddate
-    clock.n_days = n_days
+    set_period!(clock,period)
     initialize!(clock,model.time_stepping)
 
     model.output.output = output            # enable/disable output
 
     # run it, yeah!
     time_stepping!(prognostic_variables,diagnostic_variables,model)
-end
\ No newline at end of file
+end
diff --git a/test/dates.jl b/test/dates.jl
index d6e66e96e..e4240719a 100644
--- a/test/dates.jl
+++ b/test/dates.jl
@@ -24,4 +24,17 @@
     L4 = Leapfrog(SG,Δt_at_T31=Minute(60),adjust_with_output=false)
     L5 = Leapfrog(SG,Δt_at_T31=Hour(1),adjust_with_output=false)
     @test L4.Δt == L5.Δt
+
+    # clock tests
+    c1 = SpeedyWeather.Clock()
+    SG2 = SpectralGrid(trunc=31, nlev=1)
+    L6 = Leapfrog(SG2,Δt_at_T31=Hour(1),adjust_with_output=false)
+
+    SpeedyWeather.set_period!(c1, Hour(10))
+    SpeedyWeather.initialize!(c1, L6)
+    @test c1.n_timesteps == 10 
+
+    SpeedyWeather.set_period!(c1, Day(2))
+    SpeedyWeather.initialize!(c1, L6)
+    @test c1.n_timesteps == 48
 end
\ No newline at end of file
diff --git a/test/netcdf_output.jl b/test/netcdf_output.jl
index 031c6ac1b..2c33794b5 100644
--- a/test/netcdf_output.jl
+++ b/test/netcdf_output.jl
@@ -2,14 +2,14 @@ using NCDatasets, Dates
 
 @testset "Output on various grids" begin
     tmp_output_path = mktempdir(pwd(), prefix = "tmp_testruns_")  # Cleaned up when the process exits
-    n_days = 1
+    period = Day(1)
 
     # default grid, Float64, ShallowWater
     spectral_grid = SpectralGrid(;NF=Float64,nlev=1)
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # default grid, Float32, ShallowWater
@@ -17,7 +17,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # FullClenshawGrid, Float32, ShallowWater
@@ -25,7 +25,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # OctahedralClenshawGrid, Float32, ShallowWater
@@ -33,7 +33,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # HEALPixGrid, Float32, ShallowWater
@@ -41,7 +41,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # OctaHEALPixGrid, Float32, ShallowWater
@@ -49,7 +49,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # OctahedralClenshawGrid, as matrix, Float32, ShallowWater
@@ -57,7 +57,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,ShallowWater,path=tmp_output_path,as_matrix=true)
     model = ShallowWaterModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # OctaHEALPixGrid, as matrix, Float32, PrimitiveDry
@@ -65,7 +65,7 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,as_matrix=true)
     model = PrimitiveDryModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 
     # OctaHEALPixGrid, as matrix, Float32, but output Float64 PrimitiveDry
@@ -73,18 +73,18 @@ using NCDatasets, Dates
     output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,as_matrix=true,NF=Float64)
     model = PrimitiveDryModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true;n_days)
+    run!(simulation,output=true;period)
     @test simulation.model.feedback.nars_detected == false
 end
 
 @testset "Restart from output file" begin
     tmp_output_path = mktempdir(pwd(), prefix = "tmp_testruns_")  # Cleaned up when the process exits
-    
+
     spectral_grid = SpectralGrid()
     output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="restart-test")
     model = PrimitiveDryModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true,n_days=1)
+    run!(simulation,output=true;period=Day(1))
 
     initial_conditions = StartFromFile(path=tmp_output_path,id="restart-test")
     model2 = PrimitiveDryModel(;spectral_grid,initial_conditions)
@@ -119,7 +119,7 @@ end
     output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="dense-output-test",output_dt=Hour(0))
     model = PrimitiveDryModel(;spectral_grid,output)
     simulation = initialize!(model)
-    run!(simulation,output=true,n_days=1)
+    run!(simulation,output=true;period=Day(1))
     
     progn = simulation.prognostic_variables
     tmp_read_path = joinpath(model.output.run_path,model.output.filename)
@@ -131,7 +131,7 @@ end
     time_stepping = Leapfrog(spectral_grid, adjust_with_output=true)
     model = PrimitiveDryModel(;spectral_grid,output,time_stepping)
     simulation = initialize!(model)
-    run!(simulation,output=true,n_days=1)
+    run!(simulation,output=true;period)
     t = SpeedyWeather.load_trajectory("time", model)
     @test all(y->y==diff(t)[1], diff(t)) # all elements equal 
     @test diff(t)[1] == Minute(70)
@@ -141,11 +141,11 @@ end
     # at the moment, no error
     # 1kyrs simulation
     spectral_grid = SpectralGrid()
-    time_stepping = Leapfrog(spectral_grid,Δt_at_T31=Minute(60*24*365*10))
-    output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="long-output-test",output_dt=Hour(24*365*10))
+    time_stepping = Leapfrog(spectral_grid,Δt_at_T31=Year(10))
+    output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="long-output-test",output_dt=Year(10))
     model = PrimitiveDryModel(;spectral_grid,output,time_stepping)
     simulation = initialize!(model)
-    run!(simulation,output=true,n_days=365000)
+    run!(simulation,output=true,period=Year(1000))
 
     progn = simulation.prognostic_variables
     tmp_read_path = joinpath(model.output.run_path,model.output.filename)
diff --git a/test/run_speedy.jl b/test/run_speedy.jl
index d263d604f..20072df44 100644
--- a/test/run_speedy.jl
+++ b/test/run_speedy.jl
@@ -3,27 +3,27 @@
     spectral_grid = SpectralGrid(nlev=1)
     model = BarotropicModel(;spectral_grid)
     simulation = initialize!(model)
-    run!(simulation,n_days=10)
+    run!(simulation,period=Day(10))
     @test simulation.model.feedback.nars_detected == false
     
     # ShallowWater
     spectral_grid = SpectralGrid(nlev=1)
     model = ShallowWaterModel(;spectral_grid)
     simulation = initialize!(model)
-    run!(simulation,n_days=10)
+    run!(simulation,period=Day(10))
     @test simulation.model.feedback.nars_detected == false
 
     # PrimitiveDry
     spectral_grid = SpectralGrid()
     model = PrimitiveDryModel(;spectral_grid)
     simulation = initialize!(model)
-    run!(simulation,n_days=10)
+    run!(simulation,period=Day(10))
     @test simulation.model.feedback.nars_detected == false
 
     # PrimitiveWet
     spectral_grid = SpectralGrid()
     model = PrimitiveWetModel(;spectral_grid)
     simulation = initialize!(model)
-    run!(simulation,n_days=10)
+    run!(simulation,period=Day(10))
     @test simulation.model.feedback.nars_detected == false
 end
\ No newline at end of file
diff --git a/test/vertical_advection.jl b/test/vertical_advection.jl
index 52296aaf2..a95efcd68 100644
--- a/test/vertical_advection.jl
+++ b/test/vertical_advection.jl
@@ -10,7 +10,7 @@
                         vertical_advection = VerticalAdvection(spectral_grid),
                         physics=false)
         simulation = initialize!(model)
-        run!(simulation,n_days=10)
+        run!(simulation,period=Day(10))
         @test simulation.model.feedback.nars_detected == false    
     end
 end
\ No newline at end of file

From 2fa8ac9eb2cd9faed76fed0f4b87bf2bee71aaef Mon Sep 17 00:00:00 2001
From: Max <maximilian.gelbrecht@posteo.de>
Date: Mon, 4 Dec 2023 10:00:52 +0100
Subject: [PATCH 2/7] period kwarg docs

---
 README.md                     |  2 +-
 docs/src/how_to_run_speedy.md |  4 ++--
 docs/src/output.md            |  4 ++--
 docs/src/setups.md            | 22 +++++++++++-----------
 docs/src/speedytransforms.md  |  2 +-
 5 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index 67b638bb9..ed1e6e25a 100644
--- a/README.md
+++ b/README.md
@@ -31,7 +31,7 @@ With v0.6 the interface to SpeedyWeather.jl consist of 4 steps: define the grid,
 spectral_grid = SpectralGrid(trunc=31, Grid=OctahedralGaussianGrid, nlev=8)
 model = PrimitiveDryModel(;spectral_grid, orography = EarthOrography(spectral_grid))
 simulation = initialize!(model)
-run!(simulation,n_days=10,output=true)
+run!(simulation,period=Day(10),output=true)
 ```
 and you will see
 
diff --git a/docs/src/how_to_run_speedy.md b/docs/src/how_to_run_speedy.md
index cbf3fe7c1..0c6895d01 100644
--- a/docs/src/how_to_run_speedy.md
+++ b/docs/src/how_to_run_speedy.md
@@ -108,7 +108,7 @@ just ignore those. But the `Leapfrog` time stepper comes with `Δt_at_T31` which
 is the parameter used to scale the time step automatically. This means at a spectral
 resolution of T31 it would use 30min steps, at T63 it would be ~half that, 15min, etc.
 Meaning that if you want to have a shorter or longer time step you can create a new
-`Leapfrog` time stepper. But remember that every model component depends on a
+`Leapfrog` time stepper. All time inputs are supposed to be given with the help of  `Dates` (e.g. `Minute()`, `Hour()`, ...). But remember that every model component depends on a
 `SpectralGrid` as first argument.
 ```@example howto
 spectral_grid = SpectralGrid(trunc=63,nlev=1)
@@ -206,7 +206,7 @@ By default this runs for 10 days without output. These are the options left
 to change, so with
 ```@example howto
 model.output.id = "test" # hide
-run!(simulation,n_days=5,output=true)
+run!(simulation,period=Day(5),output=true)
 ```
 You would continue this simulation (the previous `run!` call already integrated
 10 days!) for another 5 days and storing default [NetCDF output](@ref).
\ No newline at end of file
diff --git a/docs/src/output.md b/docs/src/output.md
index 9cbd9d14e..bc9de3694 100644
--- a/docs/src/output.md
+++ b/docs/src/output.md
@@ -68,7 +68,7 @@ The time axis of the NetCDF output will now look like
 ```@example netcdf
 using NCDatasets
 model.feedback.verbose = false # hide
-run!(simulation,n_days=1,output=true)
+run!(simulation,period=Day(1),output=true)
 id = model.output.id
 ds = NCDataset("run_$id/output.nc")
 ds["time"][:]
@@ -79,7 +79,7 @@ time_stepping = Leapfrog(spectral_grid,adjust_with_output=true)
 output = OutputWriter(spectral_grid, ShallowWater, output_dt=Hour(1))
 model = ShallowWaterModel(;spectral_grid, time_stepping, output)
 simulation = initialize!(model)
-run!(simulation,n_days=1,output=true)
+run!(simulation,period=Day(1),output=true)
 id = model.output.id
 ds = NCDataset("run_$id/output.nc")
 ds["time"][:]
diff --git a/docs/src/setups.md b/docs/src/setups.md
index 67fb83087..c870953ee 100644
--- a/docs/src/setups.md
+++ b/docs/src/setups.md
@@ -14,7 +14,7 @@ complicated setups.
     initial_conditions = StartWithRandomVorticity()
     model = BarotropicModel(;spectral_grid, initial_conditions, planet=still_earth)
     simulation = initialize!(model)
-    run!(simulation,n_days=20)
+    run!(simulation,period=Day(20))
     ```
 
 We want to use the barotropic model to simulate some free-decaying 2D turbulence
@@ -53,11 +53,11 @@ plotted for surface relative vorticity with a unicode plot. The resolution of th
 is not necessarily representative but it lets us have a quick look at the result
 ```@example barotropic_setup
 simulation = initialize!(model)
-run!(simulation,n_days=20)
+run!(simulation,period=Day(20))
 ```
 
 Woohoo! Something is moving! You could pick up where this simulation stopped by simply
-doing `run!(simulation,n_days=50)` again. We didn't store any output, which
+doing `run!(simulation,period=Day(50))` again. We didn't store any output, which
 you can do by `run!(simulation,output=true)`, which will switch on NetCDF output
 with default settings. More options on output in [NetCDF output](@ref).
 
@@ -71,7 +71,7 @@ with default settings. More options on output in [NetCDF output](@ref).
     initial_conditions = ZonalJet()
     model = ShallowWaterModel(;spectral_grid, orography, initial_conditions)
     simulation = initialize!(model)
-    run!(simulation,n_days=6)
+    run!(simulation,period=Day(6))
     ```
 
 As a second example, let's investigate the Galewsky et al.[^G04] test case for the shallow
@@ -97,12 +97,12 @@ Now we construct a model, but this time a `ShallowWaterModel`
 ```@example galewsky_setup
 model = ShallowWaterModel(;spectral_grid, orography, initial_conditions)
 simulation = initialize!(model)
-run!(simulation,n_days=6)
+run!(simulation,period=Day(6))
 ```
 Oh yeah. That looks like the wobbly jet in their paper. Let's run it again for another 6 days
 but this time also store [NetCDF output](@ref).
 ```@example galewsky_setup
-run!(simulation,n_days=6,output=true)
+run!(simulation,period=Day(6),output=true)
 ```
 The progress bar tells us that the simulation run got the identification "0001"
 (which just counts up, so yours might be higher), meaning that
@@ -164,7 +164,7 @@ compare with the last plot
 ```@example galewsky_setup
 model = ShallowWaterModel(;spectral_grid, orography, initial_conditions)
 simulation = initialize!(model)
-run!(simulation,n_days=12,output=true)
+run!(simulation,period=Day(12),output=true)
 ```
 
 This time the run got a new run id, which you see in the progress bar, but can again always check
@@ -207,8 +207,8 @@ output = OutputWriter(spectral_grid,ShallowWater,output_dt=Hour(6),output_vars=[
 model = ShallowWaterModel(;spectral_grid,output,drag,forcing)
 simulation = initialize!(model)
 model.feedback.verbose = false # hide
-run!(simulation,n_days=20)   # discard first 20 days   
-run!(simulation,n_days=20,output=true)
+run!(simulation,period=Day(20))   # discard first 20 days   
+run!(simulation,period=Day(20),output=true)
 nothing # hide
 ```
 
@@ -260,7 +260,7 @@ output = OutputWriter(spectral_grid,ShallowWater,output_dt=Hour(12),output_vars=
 model = ShallowWaterModel(;spectral_grid,orography,output,initial_conditions,implicit,time_stepping)
 simulation = initialize!(model)
 model.feedback.verbose = false # hide
-run!(simulation,n_days=2,output=true)
+run!(simulation,period=Day(2),output=true)
 nothing # hide
 ```
 
@@ -324,7 +324,7 @@ initial_conditions = ZonalWind()
 model = PrimitiveDryModel(;spectral_grid,orography,initial_conditions,physics=false)
 simulation = initialize!(model)
 model.feedback.verbose = false # hide
-run!(simulation,n_days=9,output=true)
+run!(simulation,period=Day(9),output=true)
 nothing # hide
 ```
 
diff --git a/docs/src/speedytransforms.md b/docs/src/speedytransforms.md
index 0afcaba50..5ce1a135e 100644
--- a/docs/src/speedytransforms.md
+++ b/docs/src/speedytransforms.md
@@ -324,7 +324,7 @@ drag = QuadraticDrag(spectral_grid)
 model = ShallowWaterModel(;spectral_grid,forcing,drag)
 model.feedback.verbose = false # hide
 simulation = initialize!(model);
-run!(simulation,n_days=30)
+run!(simulation,period=Day(30))
 nothing # hide
 ```
 

From 1f357cff3995dfd596c167c48ee6d656f92ca752 Mon Sep 17 00:00:00 2001
From: Max <maximilian.gelbrecht@posteo.de>
Date: Mon, 4 Dec 2023 10:05:13 +0100
Subject: [PATCH 3/7] typo in set_period!

---
 src/dynamics/prognostic_variables.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dynamics/prognostic_variables.jl b/src/dynamics/prognostic_variables.jl
index 83c65d6ba..9017ab56d 100644
--- a/src/dynamics/prognostic_variables.jl
+++ b/src/dynamics/prognostic_variables.jl
@@ -34,7 +34,7 @@ end
 
 """
 $(TYPEDSIGNATURES)
-Set the `period` of the clock to a new value. Converts any `Dates.Period` input to `Second`."""
+Set the `period` of the clock to a new value. Converts any `Dates.Period` input `Second`."""
 function set_period!(clock::Clock,period::Period)
     clock.period = Second(period)
 end

From 09ea2f01332091fd7a4cc97aaf09a7ad13188977 Mon Sep 17 00:00:00 2001
From: Max <maximilian.gelbrecht@posteo.de>
Date: Mon, 4 Dec 2023 10:30:32 +0100
Subject: [PATCH 4/7] fix test period kwarg

---
 src/dynamics/prognostic_variables.jl | 2 +-
 test/netcdf_output.jl                | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/dynamics/prognostic_variables.jl b/src/dynamics/prognostic_variables.jl
index 9017ab56d..83c65d6ba 100644
--- a/src/dynamics/prognostic_variables.jl
+++ b/src/dynamics/prognostic_variables.jl
@@ -34,7 +34,7 @@ end
 
 """
 $(TYPEDSIGNATURES)
-Set the `period` of the clock to a new value. Converts any `Dates.Period` input `Second`."""
+Set the `period` of the clock to a new value. Converts any `Dates.Period` input to `Second`."""
 function set_period!(clock::Clock,period::Period)
     clock.period = Second(period)
 end
diff --git a/test/netcdf_output.jl b/test/netcdf_output.jl
index 2c33794b5..3ea7c7833 100644
--- a/test/netcdf_output.jl
+++ b/test/netcdf_output.jl
@@ -131,7 +131,7 @@ end
     time_stepping = Leapfrog(spectral_grid, adjust_with_output=true)
     model = PrimitiveDryModel(;spectral_grid,output,time_stepping)
     simulation = initialize!(model)
-    run!(simulation,output=true;period)
+    run!(simulation,output=true;period=Day(1))
     t = SpeedyWeather.load_trajectory("time", model)
     @test all(y->y==diff(t)[1], diff(t)) # all elements equal 
     @test diff(t)[1] == Minute(70)
@@ -141,11 +141,11 @@ end
     # at the moment, no error
     # 1kyrs simulation
     spectral_grid = SpectralGrid()
-    time_stepping = Leapfrog(spectral_grid,Δt_at_T31=Year(10))
-    output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="long-output-test",output_dt=Year(10))
+    time_stepping = Leapfrog(spectral_grid,Δt_at_T31=Day(3650))
+    output = OutputWriter(spectral_grid,PrimitiveDry,path=tmp_output_path,id="long-output-test",output_dt=Day(3650))
     model = PrimitiveDryModel(;spectral_grid,output,time_stepping)
     simulation = initialize!(model)
-    run!(simulation,output=true,period=Year(1000))
+    run!(simulation,output=true,period=Day(365000))
 
     progn = simulation.prognostic_variables
     tmp_read_path = joinpath(model.output.run_path,model.output.filename)

From 3bacbdea3e64a90b874877f924834c911526f130 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Milan=20Kl=C3=B6wer?= <milankloewer@gmx.de>
Date: Mon, 4 Dec 2023 17:53:14 +0000
Subject: [PATCH 5/7] allow run!(simulation,period=1.23)

---
 src/dynamics/prognostic_variables.jl | 8 ++++++++
 src/output/feedback.jl               | 4 ++--
 src/run_speedy.jl                    | 2 +-
 test/dates.jl                        | 8 ++++++++
 4 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/dynamics/prognostic_variables.jl b/src/dynamics/prognostic_variables.jl
index 83c65d6ba..efe4d4355 100644
--- a/src/dynamics/prognostic_variables.jl
+++ b/src/dynamics/prognostic_variables.jl
@@ -39,6 +39,14 @@ function set_period!(clock::Clock,period::Period)
     clock.period = Second(period)
 end
 
+"""
+$(TYPEDSIGNATURES)
+Set the `period` of the clock to a new value. Converts any `::Real` input to `Day`."""
+function set_period!(clock::Clock,period::Real)
+    @info "Input $x assumed to have units of days. Use Week($x), Hour($x), Minute($x) otherwise."
+    clock.period = Day(period)
+end
+
 """
 $(TYPEDSIGNATURES)
 Create and initialize a clock from `time_stepping`"""
diff --git a/src/output/feedback.jl b/src/output/feedback.jl
index f3396f6dd..3e3a16641 100644
--- a/src/output/feedback.jl
+++ b/src/output/feedback.jl
@@ -86,7 +86,7 @@ function initialize!(feedback::Feedback,clock::Clock,model::ModelSetup)
         (; run_path, id) = feedback
         SG = model.spectral_grid
         L = model.time_stepping
-        period = clock.period.value/(3600*24)
+        days = clock.period.value/(3600*24)
         
         # create progress.txt file in run_????/
         progress_txt = open(joinpath(run_path,"progress.txt"),"w")
@@ -95,7 +95,7 @@ function initialize!(feedback::Feedback,clock::Clock,model::ModelSetup)
         write(progress_txt,s*"\n")
         write(progress_txt,"Integrating:\n")
         write(progress_txt,"$SG\n")
-        write(progress_txt,"Time: $period days at Δt = $(L.Δt_sec)s\n")
+        write(progress_txt,"Time: $days days at Δt = $(L.Δt_sec)s\n")
         write(progress_txt,"\nAll data will be stored in $run_path\n")
         feedback.progress_txt = progress_txt
     end
diff --git a/src/run_speedy.jl b/src/run_speedy.jl
index 8acb02b71..b1ea9919f 100644
--- a/src/run_speedy.jl
+++ b/src/run_speedy.jl
@@ -2,7 +2,7 @@
 $(TYPEDSIGNATURES)
 Run a SpeedyWeather.jl `simulation`. The `simulation.model` is assumed to be initialized."""
 function run!(  simulation::Simulation;
-                period::Period = Day(10),
+                period = Day(10),
                 output::Bool = false, 
                 n_days::Union{Nothing, Real}=nothing)
     
diff --git a/test/dates.jl b/test/dates.jl
index e4240719a..4c040b343 100644
--- a/test/dates.jl
+++ b/test/dates.jl
@@ -34,6 +34,14 @@
     SpeedyWeather.initialize!(c1, L6)
     @test c1.n_timesteps == 10 
 
+    SpeedyWeather.set_period!(c1, 10)
+    SpeedyWeather.initialize!(c1, L6)
+    @test c1.n_timesteps == 10
+
+    SpeedyWeather.set_period!(c1, 10.0)
+    SpeedyWeather.initialize!(c1, L6)
+    @test c1.n_timesteps == 10 
+
     SpeedyWeather.set_period!(c1, Day(2))
     SpeedyWeather.initialize!(c1, L6)
     @test c1.n_timesteps == 48

From d2d34336685125888cce85e99978b8438138681a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Milan=20Kl=C3=B6wer?= <milankloewer@gmx.de>
Date: Mon, 4 Dec 2023 18:05:45 +0000
Subject: [PATCH 6/7] x -> period typo

---
 src/dynamics/prognostic_variables.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/dynamics/prognostic_variables.jl b/src/dynamics/prognostic_variables.jl
index efe4d4355..02f69ad50 100644
--- a/src/dynamics/prognostic_variables.jl
+++ b/src/dynamics/prognostic_variables.jl
@@ -43,7 +43,7 @@ end
 $(TYPEDSIGNATURES)
 Set the `period` of the clock to a new value. Converts any `::Real` input to `Day`."""
 function set_period!(clock::Clock,period::Real)
-    @info "Input $x assumed to have units of days. Use Week($x), Hour($x), Minute($x) otherwise."
+    @info "Input $period assumed to have units of days. Use Week($period), Hour($period), Minute($period) otherwise."
     clock.period = Day(period)
 end
 

From 11ce352c6fcf0511641d58d02cab834bda5e1bfb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Milan=20Kl=C3=B6wer?= <milankloewer@gmx.de>
Date: Mon, 4 Dec 2023 18:19:56 +0000
Subject: [PATCH 7/7] correct dates.jl tests

---
 test/dates.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/dates.jl b/test/dates.jl
index 4c040b343..a92c2122b 100644
--- a/test/dates.jl
+++ b/test/dates.jl
@@ -34,13 +34,13 @@
     SpeedyWeather.initialize!(c1, L6)
     @test c1.n_timesteps == 10 
 
-    SpeedyWeather.set_period!(c1, 10)
+    SpeedyWeather.set_period!(c1, 10)   # assumed to be in days
     SpeedyWeather.initialize!(c1, L6)
-    @test c1.n_timesteps == 10
+    @test c1.n_timesteps == 24*10
 
-    SpeedyWeather.set_period!(c1, 10.0)
+    SpeedyWeather.set_period!(c1, 10.0) # also assumed to be in days
     SpeedyWeather.initialize!(c1, L6)
-    @test c1.n_timesteps == 10 
+    @test c1.n_timesteps == 24*10 
 
     SpeedyWeather.set_period!(c1, Day(2))
     SpeedyWeather.initialize!(c1, L6)