From 69565ccae1d2fe012626a51552ad06602c595c80 Mon Sep 17 00:00:00 2001
From: GianlucaFuwa <gianlucafuwa@gmail.com>
Date: Mon, 10 Jun 2024 00:24:35 +0200
Subject: [PATCH] Add dirac operators to docs

---
 docs/make.jl                |  6 ++++--
 docs/src/dirac.md           | 15 +++++++++++++++
 docs/src/fermion_actions.md | 16 ++++++++++++++++
 docs/src/viz.md             | 25 ++++++++++++++++++-------
 4 files changed, 53 insertions(+), 9 deletions(-)
 create mode 100644 docs/src/dirac.md
 create mode 100644 docs/src/fermion_actions.md

diff --git a/docs/make.jl b/docs/make.jl
index ab4ddfd8..b1ab10b0 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -14,10 +14,12 @@ makedocs(
     doctest = false,
     modules = [MetaQCD],
     pages = [
-        "MetaQCD.jl: Metadynamics in Lattice Yang-Mills" => "index.md",
+        "MetaQCD.jl: Metadynamics in Lattice QCD" => "index.md",
         "Usage" => "usage.md",
         "Creating Gaugefields" => "gaugefields.md",
         "Updating a Gaugefield" => "updates.md",
+        "Dirac Operators" => "dirac.md",
+        # "Fermion Actions" => "fermion_actions.md",
         "Biased Sampling Methods" => "biased_sampling.md",
         "Visualization" => "viz.md",
         "Parameters" => "parameters.md",
@@ -29,4 +31,4 @@ makedocs(
     format = Documenter.HTML(),
 )
 
-deploydocs(repo = "github.com/GianlucaFuwa/MetaQCD.jl.git", devbranch="main")
\ No newline at end of file
+deploydocs(repo = "github.com/GianlucaFuwa/MetaQCD.jl.git", devbranch="dirac")
diff --git a/docs/src/dirac.md b/docs/src/dirac.md
new file mode 100644
index 00000000..34d92080
--- /dev/null
+++ b/docs/src/dirac.md
@@ -0,0 +1,15 @@
+# Dirac Operators
+
+To create a Dirac operators, use the constructors below:
+
+```@docs
+WilsonDiracOperator
+```
+
+```@docs
+StaggeredDiracOperator
+```
+
+```@docs
+StaggeredEOPreDiracOperator
+```
diff --git a/docs/src/fermion_actions.md b/docs/src/fermion_actions.md
new file mode 100644
index 00000000..049a41ad
--- /dev/null
+++ b/docs/src/fermion_actions.md
@@ -0,0 +1,16 @@
+<!-- # Fermion Actions -->
+<!---->
+<!-- Instead of explicitly creating the Dirac operator, one can also create the corresponding -->
+<!-- fermion action, with similar syntax: -->
+<!---->
+<!-- ```@docs -->
+<!-- WilsonFermionAction -->
+<!-- ``` -->
+<!---->
+<!-- ```@docs -->
+<!-- StaggeredFermionAction -->
+<!-- ``` -->
+<!---->
+<!-- ```@docs -->
+<!-- StaggeredEOPreFermionAction -->
+<!-- ``` -->
diff --git a/docs/src/viz.md b/docs/src/viz.md
index bdf9bbe4..dc4e26f6 100644
--- a/docs/src/viz.md
+++ b/docs/src/viz.md
@@ -1,18 +1,29 @@
 # Visualization:
-We include the ability to visualize your data. For that, you have to activate and instantiate the visualization project:
+We include the ability to visualize your data. For that, you have pass the the directory
+under "ensembles" that contains your measurements, creating a `MetaMeasuremnts` object
+holding all the measurements in `Dict` where the keys are symbols denoting the observable.
 ```julia
-pkg> activate ./visualize
-pkg> instantiate
+ens = "my_ensemble"
+measurements = MetaMeasurements(ens)
 ```
 
-Now you can create a holder for all measurements in a directory and plot a time series of an observable, specifying its filename (without extenstion) as a symbol:
+Now we can plot a timeseries of any observables measured on the ensemble via the
+`timeseries` method:
 ```julia
-measurements = MetaMeasurements(mydir)
 timeseries(measurements, :myobservable)
 ```
 
-You can also create a holder of a bias potential and plot it. MetaQCD.jl creates the bias files with an extension that gives their type (.metad or .opes), but if you changed the extension you have to provide the bias type as a symbol under the kwarg `which`:
+For hadron correlators there is a special function `hadroncorrelator` that plots the
+mean values of all time slices (without statistical uncertainties). Just specify the hadron
+whose correlator you want to see:
+```julia
+hadroncorrelator(measurements, :pion; logscale=true, calc_meff=false, tf=0.0)
+```
+
+You can also create a holder of a bias potential and plot it. MetaQCD.jl creates the bias
+files with an extension that gives their type (.metad or .opes), but if you changed the
+extension you have to provide the bias type as a symbol under the kwarg `which`:
 ```julia
 bias = MetaBias(myfile, which=:mytype)
 biaspotential(bias)
-```
\ No newline at end of file
+```