Update name and format

.github/workflows/CI.yml

@@ -55,9 +55,9 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using DepositionMTK
-            DocMeta.setdocmeta!(DepositionMTK, :DocTestSetup, :(using DepositionMTK); recursive=true)
-            doctest(DepositionMTK)'
+            using AtmosphericDeposition
+            DocMeta.setdocmeta!(AtmosphericDeposition, :DocTestSetup, :(using AtmosphericDeposition); recursive=true)
+            doctest(AtmosphericDeposition)'
       - run: julia --project=docs docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Project.toml

@@ -1,4 +1,4 @@
-name = "DepositionMTK"
+name = "AtmosphericDeposition"
 uuid = "1a52f20c-0d16-41d8-a00a-b2996d86a462"
 authors = ["EarthSciML authors and contributors"]
 version = "0.1.0"

README.md

@@ -1,9 +1,9 @@
-# DepositionMTK
+# AtmosphericDeposition
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://earthsciml.github.io/DepositionMTK.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://earthsciml.github.io/DepositionMTK.jl/dev)
-[![Build Status](https://github.com/EarthSciML/DepositionMTK.jl/workflows/CI/badge.svg)](https://github.com/earthsciml/DepositionMTK.jl/actions)
-[![Coverage](https://codecov.io/gh/EarthSciML/DepositionMTK.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/earthsciml/DepositionMTK.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://earthsciml.github.io/AtmosphericDeposition.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://earthsciml.github.io/AtmosphericDeposition.jl/dev)
+[![Build Status](https://github.com/EarthSciML/AtmosphericDeposition.jl/workflows/CI/badge.svg)](https://github.com/earthsciml/AtmosphericDeposition.jl/actions)
+[![Coverage](https://codecov.io/gh/EarthSciML/AtmosphericDeposition.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/earthsciml/AtmosphericDeposition.jl)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 

docs/Project.toml

@@ -1,3 +1,3 @@
 [deps]
-DepositionMTK = "1a52f20c-0d16-41d8-a00a-b2996d86a462"
+AtmosphericDeposition = "1a52f20c-0d16-41d8-a00a-b2996d86a462"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -1,16 +1,16 @@
-using DepositionMTK
+using AtmosphericDeposition
 using Documenter
 
-DocMeta.setdocmeta!(DepositionMTK, :DocTestSetup, :(using DepositionMTK); recursive=true)
+DocMeta.setdocmeta!(AtmosphericDeposition, :DocTestSetup, :(using AtmosphericDeposition); recursive=true)
 
 makedocs(;
-    modules=[DepositionMTK],
-    authors="Chris Tessum <[email protected]> and contributors",
-    repo="https://github.com/ctessum/DepositionMTK.jl/blob/{commit}{path}#{line}",
-    sitename="DepositionMTK.jl",
+    modules=[AtmosphericDeposition],
+    authors="EarthSciML authors and contributors",
+    repo="https://github.com/earthsciml/AtmosphericDeposition.jl/blob/{commit}{path}#{line}",
+    sitename="AtmosphericDeposition.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://ctessum.github.io/DepositionMTK.jl",
+        canonical="https://earthciml.github.io/AtmosphericDeposition.jl",
         assets=String[],
     ),
     pages=[
@@ -19,5 +19,5 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/ctessum/DepositionMTK.jl",
+    repo="github.com/earthsciml/AtmosphericDeposition.jl",
 )

docs/src/index.md

@@ -1,10 +1,10 @@
 ```@meta
-CurrentModule = DepositionMTK
+CurrentModule = AtmosphericDeposition
 ```
 
-# DepositionMTK
+# AtmosphericDeposition
 
-Documentation for [DepositionMTK](https://github.com/EarthSciML/DepositionMTK.jl).
+Documentation for [AtmosphericDeposition](https://github.com/EarthSciML/AtmosphericDeposition.jl).
 
 ```@index
 ```
@@ -40,5 +40,5 @@ and variations of uptake characteristics by individual plant species within the
 
 
 ```@autodocs
-Modules = [DepositionMTK]
+Modules = [AtmosphericDeposition]
 ```

src/dry_deposition.jl

@@ -3,8 +3,8 @@ export defaults, ra, mu, mfp, cc, vs, dParticle, dH2O, sc, stSmooth, stVeg, RbGa
 @constants g = 9.81 [unit = u"m*s^-2", description = "gravitational acceleration"]
 @constants κ = 0.4 # von Karman constant
 @constants k = 1.3806488e-23 [unit = u"m^2*kg*s^-2/K", description = "Boltzmann constant"]
-@constants M_air = 28.97e-3 [unit = u"kg/mol", description = "molecular weight of air"] 
-@constants R = 8.3144621 [unit = u"kg*m^2*s^−2*K^-1*mol^-1", description = "Gas constant"] 
+@constants M_air = 28.97e-3 [unit = u"kg/mol", description = "molecular weight of air"]
+@constants R = 8.3144621 [unit = u"kg*m^2*s^−2*K^-1*mol^-1", description = "Gas constant"]
 
 @constants unit_m = 1 [unit = u"m"]
 """
@@ -14,12 +14,12 @@ Based on Seinfeld and Pandis (2006) [Seinfeld, J.H. and Pandis, S.N. (2006) Atmo
 equation 19.13 & 19.14.
 """
 function ra(z, z₀, u_star, L)
-    ζ = IfElse.ifelse((L/unit_m == 0), 0, z/L)
-    ζ₀ = IfElse.ifelse((L/unit_m == 0), 0, z₀/L)
-    rₐ_1 = IfElse.ifelse((0 < ζ) & (ζ < 1), 1/(κ*u_star)*(log(z/z₀)+4.7*(ζ-ζ₀)), 1/(κ*u_star)*log(z/z₀))
-    η₀=(1-15*ζ₀)^1/4
-    η =(1-15*ζ)^1/4
-    rₐ = IfElse.ifelse((-1 < ζ) & (ζ < 0), 1/(κ*u_star)*[log(z/z₀)+log(((η₀^2+1)*(η₀+1)^2)/((η^2+1)*(η+1)^2))+2*(atan(η)-atan(η₀))][1], rₐ_1)
+    ζ = IfElse.ifelse((L / unit_m == 0), 0, z / L)
+    ζ₀ = IfElse.ifelse((L / unit_m == 0), 0, z₀ / L)
+    rₐ_1 = IfElse.ifelse((0 < ζ) & (ζ < 1), 1 / (κ * u_star) * (log(z / z₀) + 4.7 * (ζ - ζ₀)), 1 / (κ * u_star) * log(z / z₀))
+    η₀ = (1 - 15 * ζ₀)^1 / 4
+    η = (1 - 15 * ζ)^1 / 4
+    rₐ = IfElse.ifelse((-1 < ζ) & (ζ < 0), 1 / (κ * u_star) * [log(z / z₀) + log(((η₀^2 + 1) * (η₀ + 1)^2) / ((η^2 + 1) * (η + 1)^2)) + 2 * (atan(η) - atan(η₀))][1], rₐ_1)
     return rₐ
 end
 
@@ -29,26 +29,26 @@ end
 Function mu calculates the dynamic viscosity of air [kg m-1 s-1] where T is temperature [K].
 """
 function mu(T)
-    return (1.458*10^-6*(T/unit_T)^(3/2)/((T/unit_T)+110.4))*unit_convert_mu
+    return (1.458 * 10^-6 * (T / unit_T)^(3 / 2) / ((T / unit_T) + 110.4)) * unit_convert_mu
 end
 
 """
 Function mfp calculates the mean free path of air [m] 
 where T is temperature [K] P is pressure [Pa], and Mu is dynamic viscosity [kg/(m s)].
 From Seinfeld and Pandis (2006) equation 9.6
 """
-function mfp(T,P,μ)
-    return 2*μ/(P*(8*M_air/(pi*R*T))^0.5)
+function mfp(T, P, μ)
+    return 2 * μ / (P * (8 * M_air / (pi * R * T))^0.5)
 end
 
 """
 Function cc calculates the Cunnningham slip correction factor
 where Dp is particle diameter [m], T is temperature [K], and P is pressure [Pa].
 From Seinfeld and Pandis (2006) equation 9.34.
 """
-function cc(Dₚ,T,P,μ)
-    λ = mfp(T,P,μ)
-    return 1+2*λ/Dₚ*(1.257+0.4*exp(-1.1*Dₚ/(2*λ)))
+function cc(Dₚ, T, P, μ)
+    λ = mfp(T, P, μ)
+    return 1 + 2 * λ / Dₚ * (1.257 + 0.4 * exp(-1.1 * Dₚ / (2 * λ)))
 end
 
 @constants unit_v = 1 [unit = u"m/s"]
@@ -58,7 +58,7 @@ particle where Dp is particle diameter [m], ρₚ is particle density [kg/m3], C
 From equation 9.42 in Seinfeld and Pandis (2006).
 """
 function vs(Dₚ, ρₚ, Cc, μ)
-    IfElse.ifelse((Dₚ > 20.e-6*unit_m), 99999999*unit_v, Dₚ^2*ρₚ*g*Cc/(18*μ))
+    IfElse.ifelse((Dₚ > 20.e-6 * unit_m), 99999999 * unit_v, Dₚ^2 * ρₚ * g * Cc / (18 * μ))
     # Particle diameter Dₚ greater than 20um; Stokes settling no longer applies.
 end
 
@@ -67,26 +67,26 @@ Function dParticle calculates the brownian diffusivity of a particle [m2/s] usin
 (Seinfeld and Pandis eq. 9.73) 
 where T is air temperature [K], P is pressure [Pa], Dp is particle diameter [m], and μ is air dynamic viscosity [kg/(s m)]
 """
-function dParticle(T,P,Dₚ,Cc,μ)
-    return k*T*Cc/(3*pi*μ*Dₚ)
+function dParticle(T, P, Dₚ, Cc, μ)
+    return k * T * Cc / (3 * pi * μ * Dₚ)
 end
 
 @constants T_unitless = 1 [unit = u"K^-1"]
 @constants unit_dH2O = 1 [unit = u"m^2/s"]
 """
 Function dH2O calculates molecular diffusivity of water vapor in air [m2/s] where T is temperature [K]
 using a regression fit to data in Bolz and Tuve (1976) found here: http://www.cambridge.org/us/engineering/author/nellisandklein/downloads/examples/EXAMPLE_9.2-1.pdf
-""" 
+"""
 function dH2O(T)
-    return (-2.775e-6 + 4.479e-8*T*T_unitless + 1.656e-10*(T*T_unitless)^2)*unit_dH2O
+    return (-2.775e-6 + 4.479e-8 * T * T_unitless + 1.656e-10 * (T * T_unitless)^2) * unit_dH2O
 end
 
 """
 Function sc computes the dimensionless Schmidt number,
 where μ is dynamic viscosity of air [kg/(s m)], ρ is air density [kg/m3], and D is the molecular diffusivity of the gas speciesof interest [m2/s]
 """
 function sc(μ, ρ, D)
-    return μ/(ρ*D)
+    return μ / (ρ * D)
 end
 
 """
@@ -95,7 +95,7 @@ where vs is settling velocity [m/s], u_star is friction velocity [m/s], μ is dy
 based on Seinfeld and Pandis (2006) equation 19.23.
 """
 function stSmooth(vₛ, u_star, μ, ρ)
-    return vₛ*u_star^2*ρ/(g*μ)
+    return vₛ * u_star^2 * ρ / (g * μ)
 end
 
 """
@@ -104,7 +104,7 @@ where vs is settling velocity [m/s], u_star is friction velocity [m/s], and A is
 based on Seinfeld and Pandis (2006) equation 19.24.
 """
 function stVeg(vₛ, u_star, A)
-    return vₛ*u_star/(g*A)
+    return vₛ * u_star / (g * A)
 end
 
 """
@@ -113,7 +113,7 @@ where Sc is the dimensionless Schmidt number and u_star is the friction velocity
 From Seinfeld and Pandis (2006) equation 19.17.
 """
 function RbGas(Sc, u_star)
-    return 5*Sc^(2/3)/u_star
+    return 5 * Sc^(2 / 3) / u_star
 end
 
 """
@@ -163,15 +163,15 @@ where Sc is the dimensionless Schmidt number, u_star is the friction velocity [m
 Dp is particle diameter [m], and iSeason and iLandUse are season and land use indexes, respectively.
 From Seinfeld and Pandis (2006) equation 19.27.
 """
-function RbParticle(Sc, u_star, St, Dₚ, iSeason::Int, iLandUse::Int) 
+function RbParticle(Sc, u_star, St, Dₚ, iSeason::Int, iLandUse::Int)
     α = α_table[iLandUse]
     γ = γ_table[iLandUse]
-    A = (A_table[iSeason,iLandUse]*10^(-3))*unit_m
+    A = (A_table[iSeason, iLandUse] * 10^(-3)) * unit_m
     R1 = exp(-St^0.5)
     term_1 = Sc^(-γ)
-    term_2 = (St/(α+St))^2
-    term_3 = 1/2*(Dₚ/A)^2
-    return 1/(3*u_star*(term_1+term_2+term_3)*R1)
+    term_2 = (St / (α + St))^2
+    term_3 = 1 / 2 * (Dₚ / A)^2
+    return 1 / (3 * u_star * (term_1 + term_2 + term_3) * R1)
 end
 
 @constants G_unitless = 1 [unit = u"m^2/W"]
@@ -185,14 +185,14 @@ irradiation [W m-2], Θ is the slope of the local terrain [radians], iSeason and
 dew and rain indicate whether there is dew or rain on the ground, and isSO2 and isO3 indicate whether the gas species of interest is either SO2 or O3, respectively. 
 Based on Seinfeld and Pandis (2006) equation 19.2.
 """
-function DryDepGas(z, z₀, u_star, L, ρA, gasData::GasData, G, Ts, θ, iSeason::Int, iLandUse::Int, rain::Bool, dew::Bool, isSO2::Bool, isO3::Bool) 
+function DryDepGas(z, z₀, u_star, L, ρA, gasData::GasData, G, Ts, θ, iSeason::Int, iLandUse::Int, rain::Bool, dew::Bool, isSO2::Bool, isO3::Bool)
     Ra = ra(z, z₀, u_star, L)
     μ = mu(Ts)
-    Dg = dH2O(Ts)/gasData.Dh2oPerDx # Diffusivity of gas of interest [m2/s]
-    Sc = sc(μ,ρA, Dg)
+    Dg = dH2O(Ts) / gasData.Dh2oPerDx # Diffusivity of gas of interest [m2/s]
+    Sc = sc(μ, ρA, Dg)
     Rb = RbGas(Sc, u_star)
-    Rc = SurfaceResistance(gasData, G*G_unitless, (Ts*T_unitless-273), θ, iSeason::Int, iLandUse::Int, rain::Bool, dew::Bool, isSO2::Bool, isO3::Bool)*Rc_unit
-    return 1/(Ra+Rb+Rc)
+    Rc = SurfaceResistance(gasData, G * G_unitless, (Ts * T_unitless - 273), θ, iSeason::Int, iLandUse::Int, rain::Bool, dew::Bool, isSO2::Bool, isO3::Bool) * Rc_unit
+    return 1 / (Ra + Rb + Rc)
 end
 
 """
@@ -208,14 +208,14 @@ function DryDepParticle(z, z₀, u_star, L, Dp, Ts, P, ρParticle, ρA, iSeason:
     Cc = cc(Dp, Ts, P, μ)
     Vs = vs(Dp, ρParticle, Cc, μ)
     if iLandUse == 4 # dessert
-       St = stSmooth(Vs, u_star, μ, ρA)
+        St = stSmooth(Vs, u_star, μ, ρA)
     else
-       St = stVeg(Vs, u_star, (A_table[iSeason,iLandUse]*10^(-3))*unit_m)
+        St = stVeg(Vs, u_star, (A_table[iSeason, iLandUse] * 10^(-3)) * unit_m)
     end
     D = dParticle(Ts, P, Dp, Cc, μ)
     Sc = sc(μ, ρA, D)
     Rb = RbParticle(Sc, u_star, St, Dp, iSeason, iLandUse)
-    return 1/(Ra+Rb+Ra*Rb*Vs)+Vs
+    return 1 / (Ra + Rb + Ra * Rb * Vs) + Vs
 end
 
 defaults = [g => 9.81, κ => 0.4, k => 1.3806488e-23, M_air => 28.97e-3, R => 8.3144621, unit_T => 1, unit_convert_mu => 1, T_unitless => 1, unit_dH2O => 1, unit_m => 1, G_unitless => 1, Rc_unit => 1, unit_v => 1]
@@ -243,10 +243,10 @@ struct DrydepositionG <: EarthSciMLODESystem
         iLandUse = 10
         rain = false
         dew = false
-		@parameters z = 50 [unit = u"m"]
-		@parameters z₀ = 0.04 [unit = u"m"]
-		@parameters u_star = 0.44 [unit = u"m/s"]
-		@parameters L = 0 [unit = u"m"]
+        @parameters z = 50 [unit = u"m"]
+        @parameters z₀ = 0.04 [unit = u"m"]
+        @parameters u_star = 0.44 [unit = u"m/s"]
+        @parameters L = 0 [unit = u"m"]
         @parameters ρA = 1.2 [unit = u"kg*m^-3"]
         @parameters G = 300 [unit = u"W*m^-2"]
         @parameters T = 298 [unit = u"K"]
@@ -262,7 +262,7 @@ struct DrydepositionG <: EarthSciMLODESystem
         @variables CH2O(t) [unit = u"ppb"]
 
         eqs = [
-            D(SO2) ~  -DryDepGas(z, z₀, u_star, L, ρA, So2Data, G, T, θ, iSeason, iLandUse, rain, dew, true, false) / z * SO2
+            D(SO2) ~ -DryDepGas(z, z₀, u_star, L, ρA, So2Data, G, T, θ, iSeason, iLandUse, rain, dew, true, false) / z * SO2
             D(O3) ~ -DryDepGas(z, z₀, u_star, L, ρA, O3Data, G, T, θ, iSeason, iLandUse, rain, dew, false, true) / z * O3
             D(NO2) ~ -DryDepGas(z, z₀, u_star, L, ρA, No2Data, G, T, θ, iSeason, iLandUse, rain, dew, false, false) / z * NO2
             D(NO) ~ -DryDepGas(z, z₀, u_star, L, ρA, NoData, G, T, θ, iSeason, iLandUse, rain, dew, false, false) / z * NO
@@ -272,5 +272,5 @@ struct DrydepositionG <: EarthSciMLODESystem
 
         new(ODESystem(eqs, t, [SO2, O3, NO2, NO, H2O2, CH2O], [z, z₀, u_star, L, ρA, G, T, θ]; name=:DrydepositionG))
     end
-end 
+end