update docs

.github/workflows/cmake.yml

@@ -41,7 +41,7 @@ jobs:
       run: 
         sudo apt-get update 
         && sudo apt-get install sphinx-doc doxygen graphviz libhdf5-dev --yes
-        && pip3 install sphinx-rtd-theme breathe sphinx-sitemap sphinx==7.1 exhale pydata-sphinx-theme
+        && pip3 install sphinx-rtd-theme breathe sphinx-sitemap sphinx==7.1 exhale pydata-sphinx-theme myst-parser
         &&  wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \ | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
         && echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         && sudo apt update

.gitignore

@@ -1,8 +1,10 @@
 *log*
+.vscode/
 *.pdf
 *tempfile*
 .ccls-cache/
 .cache/
 build/
+
 poetry.lock
 compile_commands.json

docs/conf.py

@@ -1,3 +1,7 @@
+""" "
+README.md
+"""
+
 import os
 import sys
 
@@ -19,6 +23,21 @@
     # there may be others here already, e.g. 'sphinx.ext.mathjax'
     "breathe",
     "exhale",
+    # inbuilt extensions
+    # "sphinx.ext.autodoc",
+    # "sphinx.ext.autosectionlabel",
+    # "sphinx.ext.autosummary",
+    # "sphinx.ext.coverage",
+    # "sphinx.ext.extlinks",
+    # "sphinx.ext.graphviz",
+    # "sphinx.ext.imgconverter",
+    # "sphinx.ext.inheritance_diagram",
+    # "sphinx.ext.intersphinx",
+    # "sphinx.ext.linkcode",
+    # "sphinx.ext.napoleon",
+    # "sphinx.ext.todo",
+    # "sphinx.ext.viewcode",
+    "myst_parser",
 ]
 
 # Setup the breathe extension
@@ -67,16 +86,6 @@
 # a list of builtin themes.
 #
 html_theme = "pydata_sphinx_theme"
-# sidebar
-# html_sidebars = {
-#    "**": [
-#        "about.html",
-#        "navigation.html",
-#        "relations.html",
-#        "searchbox.html",
-#        "donate.html",
-#    ]
-# }
 html_theme_options = {
     "header_links_before_dropdown": 4,
     "icon_links": [
@@ -92,7 +101,6 @@
         }
     ],
 }
-html_theme_options = {}
 
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/examples.rst

@@ -0,0 +1,4 @@
+Examples
+========
+
+.. include:: ../examples/**.md

docs/index.rst

@@ -39,11 +39,69 @@ these member vairables:
   * std::vector<std::vector<int>> n_Q
 
 
-Docs
-====
+Example : Single Impurity Anderson Impurity (SIAM)
+---------------------------------------------------
+`(See : examples/rgflowSIAM/main.cpp)`
+
+Define the impurity Model wth onsite energy `eps` and Coulomb energy `U_int`. 
+
+.. code-block:: cpp
+
+  spinhalf impurity(eps, U_int);
+
+The bath for the SIAM is also constructed in the same way. 
+
+.. code-block:: cpp
+
+  spinhalf bathModel(0, 0); // set parameters
+
+Once we have created the bath and the impurity we can 
+construct a `nrgcore` object which will take care of 
+many things that we need to do for the `NRG iterations`.
+This includes calculating static and dynamic quantities
+of the Impurity.
+
+.. code-block:: cpp
+
+  nrgcore<spinhalf, spinhalf> siam(impurity, bathModel);
+  siam.set_parameters(1024);       // set max number of states to be kept
+  siam.add_bath_site({V, V}, 1.0); // V is the coupling og the impurity and first bath site. 
+  siam.update_internal_state();
 
+Next we iteratively add the bath sites in the same way. We 
+also create HDF5 file object to save the Eigenvalues.
 
 
+.. code-block:: cpp
+
+  // file where outputput will be wriiten
+  h5stream::h5stream rfile("resultSIAM.h5");
+  // Iterative add bath sites
+  for (int in = 0; in < nMax; in++) {
+    double rescale = 1.0;
+    if (in > 0) {
+      rescale = std::sqrt(LAMBDA);
+    }
+    siam.add_bath_site({hopping(in, LAMBDA), hopping(in, LAMBDA)}, rescale);
+    // Update System Operators now here if we need to.
+    // This has to be done before updating the systems internal state.
+    siam.update_internal_state();
+    // Save the eigenvalue of the current iteration
+    rfile.write(siam.all_eigenvalue, "Eigenvalues" + std::to_string(in));
+  }
+  rfile.close();
+
+
+Plot the RG flow `(See : examples/rgflowSIAM/plot.py)`.
+
+.. image:: ../docs/image/rgflowSIAM.png
+   :width: 100%
+   :alt: RG flow plot
+
+
+Docs
+====
+
 .. toctree::
   :maxdepth: 2
   :caption: Contents:

nrgcore/include/models/freeModel.hpp

@@ -1,16 +1,11 @@
 #pragma once
 #include "models/fermionBasis.hpp"
 #include "nrgcore/qOperator.hpp"
-#include "nrgcore/qsymmetry.hpp"
 #include "utils/qmatrix.hpp"
-#include <algorithm>
 #include <cmath>
-#include <complex>
 #include <cstddef>
 #include <iostream>
-#include <map>
 #include <optional>
-#include <string>
 #include <vector>
 class freeModel : public fermionBasis {
   /** This is single channel free model class

nrgcore/include/utils/configPerser.hpp

@@ -1,11 +1,9 @@
 #pragma once
-#include <algorithm>
 #include <fstream>
 #include <iostream>
 #include <map>
 #include <regex>
 #include <string>
-#include <vector>
 class configPerser {
   // # start starts with comment
   // spaces are ignored

nrgcore/include/utils/h5stream.hpp

@@ -114,7 +114,7 @@ class dspace {
 };
 // ---- -----------------------------------
 /**
- * @class gspace: Read and write metadata to  a `H5::Group` object.
+ * @class gspace: reading  and write metadata to  a `H5::Group` object.
  * @brief
  *
  */