From 643baba78eb15a685d959aae718ee3eeade2f806 Mon Sep 17 00:00:00 2001
From: Jaron Kent-Dobias <jaron@kent-dobias.com>
Date: Fri, 19 Oct 2018 01:26:14 -0400
Subject: big library overhual, fixed all examples, added documentation with
 sphinx

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+
+*************************************
+Constructing a System & Running Wolff
+*************************************
+
+The core of the library lies in the :cpp:class:`system` class and its member functions. Here, the state of your model is stored and cluster flip Monte Carlo can be carried out in various ways.
+
+Note that the member objects and functions described here will change when compiled with certain compiler flags active, as described in :ref:`compile`.
+
+.. cpp:class:: template\<class R_t, class X_t> system
+
+Member Objects
+==============
+
+.. cpp:member:: v_t system::nv
+
+   Stores the number of ordinary sites in the model.
+
+.. cpp:member:: v_t system::ne
+
+   Stores the number of ordinary bonds in the model.
+
+.. cpp:member:: graph system::G
+
+   Stores the graph describing the lattice, including the ghost site.
+
+.. cpp:member:: double system::T
+
+   Stores the temperature of the model.
+
+.. cpp:member:: std::vector<X_t> system::s
+
+   The :math:`i\text{th}` component stores the spin state of site :math:`i`.
+
+.. cpp:member:: R_t system::s0
+
+   Stores the state of the ghost site.
+
+.. cpp:member:: std::function <double(const X_t&, const X_t&)> system::Z
+
+   The function that returns the coupling between neighboring sites.
+
+.. cpp:member:: std::function <double(const X_t&)> system::B
+
+   The function that returns the coupling to the field.
+
+Member Functions
+================
+
+.. cpp:function:: system::system(graph G, double T, std::function <double(const X_t&, const X_t&)> Z, std::function <double(const X_t&)> B)
+
+   The constructor for systems. The arguments given are a graph :cpp:any:`G` *without* the ghost spin added, the temperature :cpp:any:`T`, and the coupling functions :cpp:any:`Z` and :cpp:any:`B`. The states of the spins and ghost site are initialized using the default constructors for :cpp:type:`X_t` and :cpp:type:`R_t`, respectively. :cpp:any:`nv` and :cpp:any:`ne` are taken directly from :cpp:any:`G`, after which the ghost site is added to :cpp:any:`G`.
+
+.. cpp:function:: system::flip_cluster(v_t i0, const R_t& r, std::mt19937& rng, measurement<R_t, X_t>& A)
+
+   Performs one Wolff cluster flip to the system. The cluster is seeded at vertex :cpp:any:`i0` and the spins added are transformed by :cpp:any:`r`. A random number generator :cpp:any:`rng` provides required random numbers during, and the relevant measurement hooks defined in the inherited class of :cpp:any:`A` are run during the cluster formation.
+
+.. cpp:function:: system::run_wolff(N_t N, std::function <R_t(std::mt19937&, const system<R_t, X_t>&, v_t)> r_gen, measurement<R_t, X_t>& A, std::mt19937& rng)
+
+   Performs :cpp:any:`N` Wolff cluster flips to the system. One must provide a function :cpp:func:`r_gen` that takes a random number generator, the system state, and the index of the seed site and returns a transformation for each flip. Also required are an object from a class which inherits :cpp:class:`measurement` to run measurements, and a random number generator :cpp:any:`rng`.
+
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