Merge pull request #61 from wenrongcao/main

Add passive tracers documentation

docs/make.jl

@@ -25,6 +25,7 @@ makedocs(;
                                                   ],
         "Run LaMEM" => "runlamem.md",
         "Reading timesteps" => "readtimesteps.md",
+        "Passive tracers" => "readpassivetracers.md",
         "List of functions" => "listfunctions.md",
     ],
     pagesonly=true,

docs/src/Subduction3D.md

@@ -1,5 +1,5 @@
 ```@meta
-EditURL = "../../scripts/Subduction3D.jl"
+EditURL = "../../example_scripts/Subduction3D.jl"
 ```
 
 # 3D Subduction example

docs/src/readpassivetracers.md

@@ -0,0 +1,87 @@
+# Initiate passive tracers and read their information 
+Passive tracers are useful to track the evolutions of the temperature, pressure and their spatial positions of moving materials during the simulation. Passive tracers can be initiated when you start a new model, and they are the Lagrangian points that move with the materials. The initiation and extraction of information from passive tracers can be easily done using the following methods.
+
+### Initiate passive tracers in the model
+Let's use a simple model of a "falling sphere" as the example. We initiate the passive tracers by turning on the flag: `Passive_Tracer=1` and assign a spatial range to populate tracers in the entire simulation box `PassiveTracer_Box=[-1,1,-1,1,-1,1])`. The default tracer density is 100 x 1 x 100 along x, y, z axes. 
+```julia
+using LaMEM, GeophysicalModelGenerator, Plots
+
+model  = Model(Grid(nel=(16,16,16), x=[-1,1], y=[-1,1], z=[-1,1]), PassiveTracers(Passive_Tracer=1, PassiveTracer_Box=[-1,1,-1,1,-1,1]))
+matrix = Phase(ID=0,Name="matrix",eta=1e20,rho=3000)
+sphere = Phase(ID=1,Name="sphere",eta=1e23,rho=3200)
+add_phase!(model, sphere, matrix)
+add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5,))
+
+run_lamem(model,1)
+```
+The model output files should include a file called `output_passive_tracers.pvd` which you can visualize using ParaView. The image below shows the initial state (t=0) of all tracers. Different colors represent  different phases of the tracers: Phase 0 is blue, Phase 1 is red.
+
+![InitialSetupSphere](assets/Passivetracers_pv.png)
+
+### Read passive tracers information back to Julia
+We can check the overall passive tracers information at timestep = 0 using:
+```julia
+data,time = read_LaMEM_timestep(model, 0, passive_tracers=true)
+```
+It returns:
+```julia
+(CartData 
+    size    : (10000,)
+    x       ϵ [ -0.99 : 0.99]
+    y       ϵ [ 0.0 : 0.0]
+    z       ϵ [ -0.99 : 0.99]
+    fields  : (:Phase, :Temperature, :Pressure, :ID)
+, [0.0])
+```
+The `data.x`, `data.y`, and `data.z` are structures that contain spatial information of tracers while parameters such like `data.fields.Phase` contain the phase, temperature, pressure and index (ID) of tracers.
+
+Sometimes we want to select tracers in a smaller region for further investigation. For example, to track the P-T-t evolution of a subducting slab, we can specify a region of interest (e.g., the upper crust portion of the slab) therefore select tracers within that region only.
+
+In the "falling sphere" example, let's find all the "sphere phase" tracers in the 1st quadrant (x>0, and z>0) of the sphere.
+
+```julia
+ID = findall(data.x.val .> 0 .&& data.z.val .> 0 .&& data.fields.Phase .== 1)
+```
+The `ID` parameter records the indices of these tracers. Note we need to do `data.x.val` to get the numerical value of the x-coordinate because `data.x` is a `GeoUnit` structure also containing `unit`, and `isdimensional` information. The dot in front of `>` and `&&`  implies that it is applied to every point the array data.
+
+Once we select the tracers of interest (we now know the ID of these tracers), we can read their information.
+```julia
+passive_tracers = passivetracer_time(ID,model)
+```
+Let's take a look at the `passive_tracers`, and see what information it contains:
+```julia
+# Retrieve the keys from the passive_tracers
+keys_list = keys(passive_tracers)
+
+# Iterate over each key and print the size of the associated data
+for key in keys_list
+    data_size = size(passive_tracers[key])
+    println("Key: $key, Size: $data_size")
+end
+```
+It returns:
+```julia
+Key: x, Size: (489, 4)
+Key: y, Size: (489, 4)
+Key: z, Size: (489, 4)
+Key: Phase, Size: (489, 4)
+Key: Temperature, Size: (489, 4)
+Key: Pressure, Size: (489, 4)
+Key: Time_Myrs, Size: (4,)
+```
+The `passive_tracers` contains spatial coordinates and P, T, Phase properties and also the associated temporal information for all 4 time steps in matrixes. Now let's plot the position of selected tracer at t=0.
+
+```julia
+using Plots
+scatter(passive_tracers.x[:,1], passive_tracers.z[:,1], title="Scatter Plot of Selected Passive Tracers", legend=false, aspect_ratio=:equal)
+```
+![InitialSetupSphere](assets/Passivetracers_plot.png)
+
+We can plot a temporal evolution of P-T of a specific tracer. In the following line, we only select one tracer whose ID==1 among the 489 tracers we selected.
+```julia
+plot( passive_tracers.Temperature[1,:], passive_tracers.Pressure[1,:])
+```
+
+ Since the example "falling sphere" code does not contain much dynamics and it only runs for a few timesteps, the resulted P-T path contain little information. 
+
+It is also doable to plot the the average P, T properties of a small group of tracers of our selection.