From 760a530817d885bfdd724492003c1db696f8de3c Mon Sep 17 00:00:00 2001
From: Mark Owkes <mark.owkes@montana.edu>
Date: Wed, 19 Jun 2024 13:51:24 -0600
Subject: [PATCH] Added precompiling - runs case 1

---
 Project.toml      |  1 +
 src/Biofilm.jl    |  2 ++
 src/parameters.jl |  4 +--
 src/precompile.jl | 64 +++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 69 insertions(+), 2 deletions(-)
 create mode 100644 src/precompile.jl

diff --git a/Project.toml b/Project.toml
index 1dfe754..1847140 100644
--- a/Project.toml
+++ b/Project.toml
@@ -13,6 +13,7 @@ Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
diff --git a/src/Biofilm.jl b/src/Biofilm.jl
index af919f4..d10588d 100644
--- a/src/Biofilm.jl
+++ b/src/Biofilm.jl
@@ -11,5 +11,7 @@ include("solver.jl")
 include("parameters.jl")
 include("computes.jl")
 include("postprocess.jl")
+include("precompile.jl")
+
 
 end
\ No newline at end of file
diff --git a/src/parameters.jl b/src/parameters.jl
index 6dc49e3..2acc5e2 100644
--- a/src/parameters.jl
+++ b/src/parameters.jl
@@ -98,8 +98,8 @@ function checkType_setDef(err,d,type,name; default=nothing)
                     @reset d[name] = (d[name], )
                 end
             end
-            # Check type
-            type(d[name])
+            # Enforce type
+            @reset d[name] = type(d[name])
         catch
             err = printError(err,"Parameter $name should be of type $type")
         end
diff --git a/src/precompile.jl b/src/precompile.jl
new file mode 100644
index 0000000..8372c46
--- /dev/null
+++ b/src/precompile.jl
@@ -0,0 +1,64 @@
+using PrecompileTools: @setup_workload, @compile_workload
+@setup_workload begin
+    # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
+    # precompile file and potentially make loading faster.
+    
+    @compile_workload begin
+        # all calls in this block will be precompiled, regardless of whether
+        # they belong to your package or not (on Julia 1.8 and higher)
+        # Input parameters
+        mumax = 20; KM = 3;
+        p = (
+            # --------------------- #
+            # Simulation Parameters #
+            # --------------------- #
+            Title =    "Single Solute and Particulate Case",
+            tFinal =   1.0,   # Simulation time [days]
+            tol =      1e-2,  # Tolerance
+            outPeriod =0.1,   # Time between outputs [days]
+            makePlots = true,
+            savePlots = true,
+
+            # ---------------------- #
+            # Particulate Parameters #
+            # ---------------------- #
+            XNames =["Heterotroph"],    # Particulate names
+            Xto =   [10.0],        # Tank particulate concentration initial condition(s)
+            Pbo =   [0.08],        # Biofilm particulates volume fraction initial condition(s) 
+            rho =   [2.0E4],       # Particulate densities
+            Kdet =  20000.0,       # Particulates detachment coefficient
+            srcX =  [(S,X,Lf,t,z,p) -> 0.0],     # Source of particulates
+            # Growthrates for each particulate
+            mu = [(S,X,Lf,t,z,p) -> (mumax * S[1]) ./ (KM .+ S[1])],
+
+            # ----------------- #
+            # Solute Parameters #
+            # ----------------- #
+            SNames =["Nutrient"],     # Solute names
+            Sin =   [(t) -> 100],   # Solute inflow (can be function of time)
+            Sto =   [10.0],         # Tank solute concentration initial condition(s)
+            Sbo =   [0.0],          # Biofilm solutes concentration initial condition(s)
+            Yxs =   [2.646],        # Biomass yield coefficient on solute
+            Dt =    [4.0E-5],       # Aquious solute diffusion through tank fluid
+            Db =    [6.9E-5],       # Effective solute diffusion through biofilm
+            srcS =  [(S,X,Lf,t,z,p) -> 0.0],     # Source of solutes
+
+            # --------------- #
+            # Tank Parameters #
+            # --------------- #
+            V = 0.1,        # Volume of tank [m³]
+            A =   1,        # Surface area of biofilm [m²]
+            Q =   1,        # Flowrate through tank [m³/d]
+
+            # ------------------ #
+            # Biofilm Parameters #
+            # ------------------ #
+            Nz =  50,       # Number of grid points in biofilm
+            Lfo = 1.0E-5,   # Biofilm initial thickness [m]
+            LL =  1.00E-7,  # Boundary layer thickness [m]
+        )
+
+        t,zm,Xt,St,Pb,Sb,Lf,sol = BiofilmSolver(p) # Run solver
+        biofilm_plot(sol,p) # Plot final results
+    end
+end
\ No newline at end of file