MWTree and MWNode documentation

docs/conf.py

@@ -18,6 +18,7 @@
 import shutil
 import re
 
+
 # -- Project information -----------------------------------------------------
 
 project = 'MRCPP'
@@ -49,12 +50,9 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-on_rtd = os.environ.get('READTHEDOCS') == 'True'
-if on_rtd:
-    html_theme = 'default'
-else:
-    html_theme = 'sphinx_rtd_theme'
+import sphinx_rtd_theme
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.

docs/index.rst

@@ -28,7 +28,7 @@ The code can be found on `GitHub <https://github.com/MRChemSoft/mrcpp>`_.
    install.rst
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Application Program Interface
 
    mrcpp_api/introduction
@@ -42,6 +42,7 @@ The code can be found on `GitHub <https://github.com/MRChemSoft/mrcpp>`_.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Programmers Manual
+   :caption: Programmer's Manual 
 
-   programmers_manual/clang_tidy
+   programmers_manual/overview
+   programmers_manual/clang_tidy.rst

docs/mrcpp_api/introduction.rst

@@ -98,3 +98,5 @@ the capture list (square brackets), see e.g. `cppreference.com
 <http://en.cppreference.com/w/cpp/language/lambda>`_ for more
 details on lambda functions and how to use the capture list.
 
+
+

docs/mrcpp_api/mwoperators.rst

@@ -11,6 +11,8 @@ program by including:
 
     #include "MRCPP/MWOperators"
 
+.. doxygenclass:: mrcpp::MWOperator
+   :members:
 
 ConvolutionOperator
 -------------------

docs/programmers_manual/MWNode.rst

@@ -0,0 +1,12 @@
+---------------------
+MWNode
+---------------------
+
+This is an introduction to the mwtree class. We write a small overarching summary of the class where we define the 
+algorithm/equation/structure reasoning for having this class or where it fits with the rest of the code.
+
+.. doxygenclass:: mrcpp::MWNode
+   :members:
+   :protected-members:
+   :private-members:
+

docs/programmers_manual/MWTree.rst

@@ -0,0 +1,11 @@
+------------------
+MWTree 
+------------------
+
+This is an introduction to the mwtree class. We write a small overarching summary of the class where we define the 
+algorithm/equation/structure reasoning for having this class or where it fits with the rest of the code.
+
+.. doxygenclass:: mrcpp::MWTree
+   :members:
+   :protected-members:
+   :private-members:

docs/programmers_manual/clang_tidy.rst

@@ -3,10 +3,6 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-==================================
-Programmers manual
-==================================
-
 ----------
 Clang-tidy
 ----------

docs/programmers_manual/overview.rst

@@ -0,0 +1,12 @@
+===============
+Manual overview
+===============
+The following sections show detailed documentation about the classes in MRCPP for programmers.
+
+TODO: maybe add some low level theory/figures/algorithms before showing classes, could help to understand some of the more abstract methods
+
+.. toctree::
+   :maxdepth: 1
+
+   MWTree
+   MWNode

src/operators/IdentityConvolution.cpp

@@ -29,9 +29,10 @@
 
 namespace mrcpp {
 
-/** @returns New IdentityConvolution object
+/** @brief Constructor  of the IdentityConvolution object
+ *  @returns New IdentityConvolution object
  *  @param[in] mra: Which MRA the operator is defined
- *  @param[in] pr: Build precision, closeness to delta function
+ *  @param[in] prec: Build precision, closeness to delta function
  *  @details This will project a kernel of a single gaussian with
  *  exponent sqrt(10/build_prec).
  */
@@ -51,6 +52,19 @@ IdentityConvolution<D>::IdentityConvolution(const MultiResolutionAnalysis<D> &mr
     Printer::setPrintLevel(oldlevel);
 }
 
+/** @brief Constructor of the IdentityConvolution object in case of Periodic Boundary Conditions (PBC)
+ *  @returns New IdentityConvolution object
+ *  @param[in] mra: Which MRA the operator is defined
+ *  @param[in] prec: Build precision, closeness to delta function
+ *  @param[in] root: root scale of operator.
+ *  @param[in] reach: width at root scale (applies to periodic boundary conditions)
+ *  @details This will project a kernel of a single gaussian with
+ *           exponent sqrt(10/build_prec). This version of the constructor
+ *           is used for calculations within periodic boundary conditions (PBC). 
+ *           The \a root parameter is the coarsest negative scale at wich the operator
+ *           is applied. The \a reach parameter is the bandwidth of the operator at
+ *           the root scale. For details see \ref MWOperator
+ */
 template <int D>
 IdentityConvolution<D>::IdentityConvolution(const MultiResolutionAnalysis<D> &mra, double prec, int root, int reach)
         : ConvolutionOperator<D>(mra, root, reach) {
@@ -71,4 +85,4 @@ template class IdentityConvolution<1>;
 template class IdentityConvolution<2>;
 template class IdentityConvolution<3>;
 
-} // namespace mrcpp
+} // namespace mrcpp

src/operators/MWOperator.h

@@ -32,6 +32,13 @@
 
 namespace mrcpp {
 
+/** @class MWOperator
+ *
+ * @brief Fixme
+ *
+ * @details Fixme
+ *
+ */
 template <int D>
 class MWOperator {
 public: