ClimaNeverWorld #17

glwagner · 2023-03-17T01:45:24Z

This PR implements the Neverworld in ClimaOcean.

with @simone-silvestri

Closes #20

navidcy · 2023-03-17T01:46:50Z

YEAH!

I was gonna do it tomorrow but GREAT

glwagner · 2023-03-17T01:49:37Z

Ok, also with @navidcy !

examples/run_neverworld_simulation.jl

codecov · 2023-03-17T14:43:33Z

Codecov Report

Patch coverage has no change and project coverage change: -0.86 ⚠️

Comparison is base (2b02a17) 2.86% compared to head (5d2822c) 2.01%.

Additional details and impacted files

@@           Coverage Diff            @@
##            main     #17      +/-   ##
========================================
- Coverage   2.86%   2.01%   -0.86%     
========================================
  Files          7       9       +2     
  Lines        419     597     +178     
========================================
  Hits          12      12              
- Misses       407     585     +178

Impacted Files	Coverage Δ
src/ClimaOcean.jl	`27.27% <0.00%> (-35.89%)`	⬇️
src/IdealizedSimulations/neverworld_simulation.jl	`0.00% <0.00%> (ø)`
src/NearGlobalSimulations/NearGlobalSimulations.jl	`0.00% <0.00%> (ø)`
...rGlobalSimulations/one_degree_global_simulation.jl	`0.00% <0.00%> (ø)`
...balSimulations/quarter_degree_global_simulation.jl	`0.00% <0.00%> (ø)`
...obalSimulations/twelth_degree_global_simulation.jl	`0.00% <0.00%> (ø)`
src/VerticalGrids.jl	`0.00% <0.00%> (ø)`

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src/LimitedAreaSimulations/neverworld_simulation.jl

navidcy · 2023-03-18T05:48:46Z

src/LimitedAreaSimulations/neverworld_simulation.jl

+    x₁, y₁ = line.p₁.x, line.p₁.y
+    x₂, y₂ = line.p₂.x, line.p₂.y
+
+    # Line segment lengths


these are not any lengths of anything... it's just the differences of the line-segment's coordinates, right?

They are components of a vector that points along the segment?

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

src/IdealizedSimulations/neverworld_simulation.jl

Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

src/IdealizedSimulations/neverworld_simulation.jl

Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

src/IdealizedSimulations/neverworld_simulation.jl

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

Co-authored-by: Gregory L. Wagner <wagner.greg@gmail.com>

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

glwagner · 2023-04-10T06:07:05Z

Can you look this over @navidcy or @simone-silvestri ?

glwagner · 2023-04-10T06:08:05Z

Animation from the last 4 years of a 200 year "CATKE Neverworld" run with a seasonal cycle.

catke_neverworld.mp4

navidcy · 2023-04-10T06:32:56Z

I’ll have a look tomorrow!

simone-silvestri · 2023-04-10T18:13:35Z

examples/gm_one_degree_calibration/distributed_gm_one_degree_model_calibration.jl

-using ParameterEstimocean
-using ParameterEstimocean.Utils: map_gpus_to_ranks!
-using ParameterEstimocean.Observations: FieldTimeSeriesCollector
-using ParameterEstimocean.Parameters: closure_with_parameters


we give up on the 1 degree calibration?

I think so --- do you want to keep maintaining it? I don't think we have plans to return to it so it makes sense to declare now that we are not maintaining it (we can always access this code in git history if we want to). What do you think?

examples/run_neverworld_simulation.jl

src/IdealizedSimulations/neverworld_simulation.jl

Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

navidcy · 2023-04-11T00:08:45Z

examples/analyze_neverworld_simulation.jl

@@ -0,0 +1,43 @@
+using Oceananigans
+using Oceananigans.ImmersedBoundaries: mask_immersed_field!


is mask_immersed_field! used?

navidcy · 2023-04-11T00:09:50Z

examples/animate_neverworld_simulation.jl

+using Statistics
+
+# Some plotting parameters
+ζlim = 6e-5


Suggested change

ζlim = 6e-5

ζlim = 6e-5 # s⁻¹

navidcy · 2023-04-11T00:12:45Z

examples/run_neverworld_simulation.jl

+minimum_turbulent_kinetic_energy = 1e-6
+minimum_convective_buoyancy_flux = 1e-11


Suggested change

minimum_turbulent_kinetic_energy = 1e-6

minimum_convective_buoyancy_flux = 1e-11

minimum_turbulent_kinetic_energy = 1e-6 # m² s⁻²

minimum_convective_buoyancy_flux = 1e-11 # UNITS?

navidcy · 2023-04-11T00:14:28Z

src/ClimaOcean.jl

+        spline = CubicSpline(coordinates, nodes)
+        S = typeof(spline)
+
+        d == :x || d == :y || d == :z || error("Dimension 'd' must be :x or :y or :z")


would that work with a LatitudeLongitude grid with λ/φ coordinates?

yeah, here "x" etc only refers to a positional argument. The only point of using "y" is if you have a two-argument function (such as what we load into GridFittedBottom) and need to call this with (x, y), where the spline only varies in the second argument.

We could also get rid of this concept since I don't think it's needed (yet)

src/IdealizedSimulations/neverworld_simulation.jl

navidcy · 2023-04-11T00:17:09Z

src/IdealizedSimulations/neverworld_simulation.jl

+# Neverworld
+#
+# Ingredients:
+#
+#   * Zonally-periodic domain with continental shelves on all boundaries except Southern Ocean
+#       * longitude = (0, 60)
+#       * 2 configurations in latitude
+#           - Half basin: latitude = (-70, 0)
+#           - Full basin: latitude = (-70, 70)
+#       * z to -4000m
+#       * Southern Ocean channel from -60 to -40 (with a ridge to -2000 m)
+#
+#   * Zonally-homogeneous wind stress with mid-latitude jet and trade winds
+#
+#   * Buoyancy 
+#       * restoring hot at the equator and cold at the poles (parabola, cosine, smooth step function)
+#       * equator-pole buoyancy differential: 0.06 (α * g * 30 ≈ 0.06 with α=2e-4, g=9.81)
+#       * exponential initial vertical stratification with N² = 6e-5 and decay scale h = 1000 m
+#           - eg bᵢ = N² * h * exp(z / h)
+#
+#   * Quadratic bottom drag with drag_coefficient = 1e-3


should these be part of the docstring of neverworld_simulation()?

We can though I'm not a huge fan of massive docstrings, I think they are not user-friendly...

Better to put them in legit documentation which we don't have yet.

OK.

Docstrings could be either user friendly or not, depending on how they are written.

As a user of any repo I feel it's really user-friendly if I do help?> a_method and I get back a useful, meaningful, docstring with some examples that make sense.

Of course I'm in favor of doctstrings, but I don't think we should put anything longer than a page in a docstring...

I think the baseline information most people need is: what are the function arguments. If concise examples can be provided then that is excellent. I'm less sure about docstrings that span multiple pages or contain theoretical background. For example we wouldn't load an entire oceananigans example into a docstring for Simulation. There's a limit beyond which the excess information is hurting not helping

navidcy · 2023-04-11T00:21:13Z

examples/gm_one_degree_calibration/job_script.sh

this might be useful but perhaps we should add it in the repo's wiki or something -- not in the main repo as it was!!

Maybe better to put in Oceananigans wiki since that already has other useful stuff

Neverworld file

b65c321

glwagner added 2 commits March 16, 2023 22:54

Implement neverworld boundary conditions and basic setup

081933a

Couple bug fixes

990730a

navidcy reviewed Mar 17, 2023

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Pretty good bathymetry

963d99d

glwagner and others added 4 commits March 17, 2023 12:27

Updates

8a92fc5

Implement real neverworld bathy

e7eef5c

rename LimitedAreaSimulations -> IdealizedSimulations

4cbc2a8

Merge branch 'main' into ss-glw/clima-ocean-neverworld

d980c3b

navidcy reviewed Mar 18, 2023

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navidcy reviewed Mar 18, 2023

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glwagner added 5 commits March 18, 2023 01:53

Actually add closure to model

06cdafc

Update run script

df37061

Merge branch 'ss-glw/clima-ocean-neverworld' of https://github.com/Cl…

c8c20aa

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

Fix sign error in buoyancy relaxation

2c25634

Fix comment about line segment

698086a

navidcy reviewed Mar 18, 2023

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Update src/IdealizedSimulations/neverworld_simulation.jl

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Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

navidcy reviewed Mar 18, 2023

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Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

navidcy reviewed Mar 19, 2023

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Update src/IdealizedSimulations/neverworld_simulation.jl

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glwagner and others added 6 commits April 9, 2023 18:34

Update src/IdealizedSimulations/neverworld_simulation.jl

391f03c

Add Checkpointer to neverworld simulation

44c6765

Merge branch 'ss-glw/clima-ocean-neverworld' of https://github.com/Cl…

2fc2458

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

Update examples/analyze_neverworld_simulation.jl

c12b052

Co-authored-by: Gregory L. Wagner <wagner.greg@gmail.com>

Animate the neverworld

b01d76f

Merge branch 'ss-glw/clima-ocean-neverworld' of https://github.com/Cl…

b4e508b

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

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glwagner and others added 4 commits April 10, 2023 13:18

Change user interface to specify horizontal resolution

553ca5e

Update src/IdealizedSimulations/neverworld_simulation.jl

014cf8f

Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>

Increase scale height

c3ec6e2

Merge branch 'ss-glw/clima-ocean-neverworld' of https://github.com/Cl…

6169aae

…iMA/ClimaOcean.jl into ss-glw/clima-ocean-neverworld

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glwagner added 2 commits April 10, 2023 20:24

Better interface for vertical stretching

4d242ff

Update climatology script

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glwagner merged commit f19cc1f into main Apr 11, 2023

navidcy deleted the ss-glw/clima-ocean-neverworld branch April 11, 2023 23:51

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ClimaNeverWorld #17

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		@@ -0,0 +1,43 @@
		using Oceananigans
		using Oceananigans.ImmersedBoundaries: mask_immersed_field!

		minimum_turbulent_kinetic_energy = 1e-6
		minimum_convective_buoyancy_flux = 1e-11

ClimaNeverWorld #17

ClimaNeverWorld #17

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