update diagnostic

README.md

@@ -1,10 +1,10 @@
 # WenoNeverworld.jl
 
- <a href="https://mit-license.org">
+ <!-- <a href="https://mit-license.org">
     <img alt="MIT license" src="https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square">
   </a>
  <a href="https://simone-silvestri.github.io/WenoNeverworld.jl/dev">
     <img alt="Documentation" src="https://img.shields.io/badge/documentation-stable%20release-red?style=flat-square">
   </a>
  <a href="https://github.com/SciML/ColPrac">
-    <img alt="ColPrac: Contributor's Guide on Collaborative Practices for Community Packages" src="https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet?style=flat-square">
+    <img alt="ColPrac: Contributor's Guide on Collaborative Practices for Community Packages" src="https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet?style=flat-square"> -->

src/Diagnostics/diagnostic_fields.jl

@@ -16,37 +16,37 @@ import Oceananigans.Models.HydrostaticFreeSurfaceModels: VerticalVorticityField
 
 Returns the three-dimensional vertical vorticity at time index i.
 """
-VerticalVorticity(f::Dict, i) = compute!(Field(VerticalVorticityOperation(f, i)))
+VerticalVorticity(f::Dict, i; indices = (:, :, :)) = compute!(Field(VerticalVorticityOperation(f, i)); indices)
 
 
 """
     KineticEnergy(f::Dict, i)
 
 Returns the three-dimensional kinetic energy at time index i.
 """
-KineticEnergy(f::Dict, i) = compute!(Field(KineticEnergyOperation(f, i)))
+KineticEnergy(f::Dict, i; indices = (:, :, :)) = compute!(Field(KineticEnergyOperation(f, i)); indices)
 
 
 """
     Stratification(f::Dict, i)
 
 Returns the three-dimensional stratification at time index i.
 """
-Stratification(f::Dict, i) = compute!(Field(StratificationOperation(f, i)))
+Stratification(f::Dict, i; indices = (:, :, :)) = compute!(Field(StratificationOperation(f, i)); indices)
 
 """
     PotentialVorticity(f::Dict, i)
 
 Returns the three-dimensional potential vorticity at time index i.
 """
-PotentialVorticity(f::Dict, i) = compute!(Field(PotentialVorticityOperation(f, i))) 
+PotentialVorticity(f::Dict, i; indices = (:, :, :)) = compute!(Field(PotentialVorticityOperation(f, i)); indices) 
 
 """
     DensityField(b::Field; ρ₀ = 1000.0, g = 9.80655)
 
 Returns the three-dimensional density given a buoyancy field b.
 """
-DensityField(b::Field; ρ₀ = 1000.0, g = 9.80655) = compute!(Field(DensityOperation(b; ρₒ, g)))
+DensityField(b::Field; ρ₀ = 1000.0, g = 9.80655, indices = (:, :, :)) = compute!(Field(DensityOperation(b; ρₒ, g); indices))
 
 """
     DeformationRadius(f::Dict, i)