Merge pull request #263 from brown-ccv/dev-to-master

Dev to master

Project.toml

@@ -1,7 +1,7 @@
 name = "Chamber"
 uuid = "4ddda095-17ec-41dd-95c9-ce16dd2a2f48"
 authors = ["CallieHsu <[email protected]> and contributors"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

README.md

@@ -44,6 +44,7 @@ A `DataFrame` containing the solution with columns:
 - `total_mass`: Total mass of magma chamber (kg).
 - `total_mass_H2O`: Total mass of water in the magma (kg).
 - `total_mass_CO2`: Total mass of CO₂ in the magma (kg).
+- `eps_x`: Crystal volume fraction.
 
 ### Outputs
 A directory named after `output_dirname` or the default value, containing the following files:

scripts/runcode.jl

@@ -32,6 +32,7 @@ A `DataFrame` containing the solution with columns:
 - `total_mass`: Total mass of magma chamber in kg.
 - `total_mass_H2O`: Total mass of water in the magma in kg.
 - `total_mass_CO2`: Total mass of CO₂ in the magma in kg.
+- `eps_x`: Crystal volume fraction.
 
 ## Outputs
 A directory named after `output_dirname` or the default value, containing the following files:
@@ -265,7 +266,7 @@ julia> chamber(composition, end_time, log_volume_km3, InitialConc_H2O, InitialCo
         print_timer_log(io, to)
         close(io)
         df = DataFrame(sol)
-        write_csv(df, erupt_saved, path)
+        write_csv(df, erupt_saved, path, composition)
         if plotfig
             plot_figs(df, path)
         end
@@ -305,6 +306,7 @@ A `DataFrame` containing the solution with columns:
 - `total_mass`: Total mass of magma chamber in kg.
 - `total_mass_H2O`: Total mass of water in the magma in kg.
 - `total_mass_CO2`: Total mass of CO₂ in the magma in kg.
+- `eps_x`: Crystal volume fraction.
 
 ## Outputs
 A directory named after `output_dirname` or the default value, containing the following files:

src/ic_finder.jl

@@ -268,7 +268,7 @@ function IC_Finder(
         end
     end
 
-    if eps_g0 <= 0 || X_co20 < 0
+    if eps_g0 <= 0 || X_co20 < 0 || any(isnan, [X_co20, eps_g0])
         X_co20 = 0.0
         eps_g0 = 0.0
         mco2_diss = m_co2_melt

src/runcode-func.jl

@@ -305,12 +305,9 @@ function affect!(
     erupt_saved::EruptSaved{Float64},
 )
     composition = param.composition
-    storeTime = param_saved_var.storeTime
-    storeTemp = param_saved_var.storeTemp
-    storeTemp = storeTemp[storeTime .< int.t]
-    storeTime = storeTime[storeTime .< int.t]
-    param_saved_var.storeTime = storeTime
-    param_saved_var.storeTemp = storeTemp
+    IsStoreTimeLTt = param_saved_var.storeTime .< int.t
+    param_saved_var.storeTemp = param_saved_var.storeTemp[IsStoreTimeLTt]
+    param_saved_var.storeTime = param_saved_var.storeTime[IsStoreTimeLTt]
 
     if param.dP_lit_dt_0 == 0
         temp_P_lit = 0.0

src/write_csv.jl

@@ -1,4 +1,8 @@
-function write_csv(df::DataFrame, erupt_saved::EruptSaved{Float64}, path::String)::Nothing
+function extend_with_nan(arr::Vector{T}, n::Int64)::Vector{T} where {T<:Float64}
+    return [arr; fill(NaN, n - length(arr))]
+end
+
+function write_csv(df::DataFrame, erupt_saved::EruptSaved{Float64}, path::String, composition::Union{Silicic,Mafic})::Nothing
     number_of_data = size(df, 1)
     println("number_of_data: $number_of_data")
     names = [
@@ -14,13 +18,18 @@ function write_csv(df::DataFrame, erupt_saved::EruptSaved{Float64}, path::String
         "total_mass_CO2",
     ]
     rename!(df, ["timestamp" => "time"])
-    rename!(df, ["value$i" => names[i] for i in 1:10])
+    rename!(df, ["value$i" => name for (i, name) in enumerate(names)])
+    # add eps_x column
+    m_h2o = df[:, "total_mass_H2O"] ./ df[:, "total_mass"]
+    m_co2 = df[:, "total_mass_CO2"] ./ df[:, "total_mass"]
+    df[!, "eps_x"] = crystal_fraction_eps_x.(repeat([composition], number_of_data), df[:, "T"], df[:, "P+dP"], m_h2o, m_co2)
+
+    n = length(erupt_saved.time)
     df_erupt = DataFrame(
-        reduce(
-            hcat,
-            [erupt_saved.time, erupt_saved.duration, erupt_saved.mass, erupt_saved.volume],
-        ),
-        ["time_of_eruption", "duration_of_eruption", "mass_erupted", "volume_erupted"],
+        time_of_eruption = erupt_saved.time,
+        duration_of_eruption = extend_with_nan(erupt_saved.duration, n),
+        mass_erupted = extend_with_nan(erupt_saved.mass, n),
+        volume_erupted = extend_with_nan(erupt_saved.volume, n)
     )
     CSV.write("$path/out.csv", df)
     CSV.write("$path/eruptions.csv", df_erupt)