adds crosslinks to doxygen

cpp/full_code/NSE.cpp

@@ -407,7 +407,7 @@ int NSE<rnumber>::Euler_step(void)
 /** \brief Time step with Shu Osher method
  *
  * The Navier Stokes equations are integrated with a
- * third-order Runge-Kutta method \cite shu1988jcp, which  is an explicit
+ * third-order Runge-Kutta method [shu1988jcp]_, which  is an explicit
  * Runge-Kutta method with the Butcher tableau
  *
  *  |   |   |   |   |
@@ -417,23 +417,15 @@ int NSE<rnumber>::Euler_step(void)
  *  | 1/2 | 1/4 | 1/4 | |
  *  | | 1/6 | 1/6 | 2/3 |
  *
- * In addition to the stability properties described in \cite shu1988jcp, this method has the advantage that it is memory-efficient, requiring only two additional field allocations, as can be seen from
+ * In addition to the stability properties described in [shu1988jcp]_, this method has the advantage that it is memory-efficient, requiring only two additional field allocations, as can be seen from
  *     \f{eqnarray*}{
- *         \hat{\bs w}_1(\bs k) &= {\hat{\bs u}}(\bs k, t)e^{-\nu k^2 h} + h \NL[\hat{\bs u}(\bs k, t)]e^{-\nu k^2 h}, \\
- *         \hat{\bs w}_2(\bs k) &= \frac{3}{4}\hat{\bs u}( \bs k, t)e^{-\nu k^2 h/2}
+ *         \hat{\boldsymbol w}_1(\boldsymbol k) &= {\hat{\boldsymbol u}}(\boldsymbol k, t)e^{-\nu k^2 h} + h \textrm{NL}[\hat{\boldsymbol u}(\boldsymbol k, t)]e^{-\nu k^2 h}, \\
+ *         \hat{\boldsymbol w}_2(\boldsymbol k) &= \frac{3}{4}\hat{\boldsymbol u}( \boldsymbol k, t)e^{-\nu k^2 h/2}
  *         +
- *         \frac{1}{4}(\hat{\bs w}_1(\bs k) + h \NL[\hat{\bs w}_1(\bs k)])e^{\nu k^2 h/2}, \\
- *         \hat{\bs u}(\bs k, t+h) &= \frac{1}{3}\hat{\bs u}(\bs k, t)e^{-\nu k^2 h} +
- *         \frac{2}{3}(\hat{\bs w}_2(\bs k) + h \NL[\hat{\bs w}_2(\bs k)])e^{-\nu k^2 h/2},
+ *         \frac{1}{4}(\hat{\boldsymbol w}_1(\boldsymbol k) + h \textrm{NL}[\hat{\boldsymbol w}_1(\boldsymbol k)])e^{\nu k^2 h/2}, \\
+ *         \hat{\boldsymbol u}(\boldsymbol k, t+h) &= \frac{1}{3}\hat{\boldsymbol u}(\boldsymbol k, t)e^{-\nu k^2 h} +
+ *         \frac{2}{3}(\hat{\boldsymbol w}_2(\boldsymbol k) + h \textrm{NL}[\hat{\boldsymbol w}_2(\boldsymbol k)])e^{-\nu k^2 h/2},
  *     \f}
- *
- * .. [shu1988jcp] C.-W. Shu and S. Osher,
- *                 *Efficient implementation of essentially non-oscillatory shock-capturing schemes*.
- *                 J. Comput. Phys.,
- *                 **77**,
- *                 439-471,
- *                 1988
- *                 (doi 10.1016/0021-9991(88)90177-5)
  */
 template <typename rnumber>
 int NSE<rnumber>::ShuOsher(void)

documentation/chapters/cpp_doxygen.rst

------------
-C++ classes
------------
-
+---
+C++
+---
 
 kspace
 ------
 
+`Full doxygen documentation link. <../../doxygen_html/classkspace.html>`_
+
 .. doxygenclass:: kspace
     :project: TurTLE
     :members:
 
 
+
 field
 -----
 
+`Full doxygen documentation link. <../../doxygen_html/classfield.html>`_
+
 .. doxygenclass:: field
     :project: TurTLE
     :members:
@@ -22,6 +26,8 @@ field
 code_base
 ---------
 
+`Full doxygen documentation link. <../../doxygen_html/classcode__base.html>`_
+
 .. doxygenclass:: code_base
     :project: TurTLE
     :members:
@@ -30,15 +36,18 @@ code_base
 direct_numerical_simulation
 ---------------------------
 
+`Full doxygen documentation link. <../../doxygen_html/classdirect__numerical__simulation.html>`_
+
 .. doxygenclass:: direct_numerical_simulation
     :project: TurTLE
     :members:
 
 
-..
 NSE
 ----
 
+`Full doxygen documentation link. <../../doxygen_html/classNSE.html>`_
+
 .. doxygenclass:: NSE
     :project: TurTLE
     :members:
@@ -47,15 +56,51 @@ direct_numerical_simulation
 NSVE
 ----
 
+`Full doxygen documentation link. <../../doxygen_html/classNSVE.html>`_
+
 .. doxygenclass:: NSVE
     :project: TurTLE
     :members:
 
 
-    particle_set
-    ------------
+abstract_particle_set
+---------------------
+
+`Full doxygen documentation link. <../../doxygen_html/classabstract__particle__set.html>`_
+
+  .. doxygenclass:: abstract_particle_set
+      :project: TurTLE
+      :path: ...
+      :members: [...]
+      :protected-members:
+      :private-members:
+      :undoc-members:
+      :outline:
+      :no-link:
+
+
+abstract_particle_rhs
+---------------------
+
+`Full doxygen documentation link. <../../doxygen_html/classabstract__particle__rhs.html>`_
+
+  .. doxygenclass:: abstract_particle_rhs
+      :project: TurTLE
+      :path: ...
+      :members: [...]
+      :protected-members:
+      :private-members:
+      :undoc-members:
+      :outline:
+      :no-link:
+
+
+field_tinterpolator
+-------------------
 
-    .. doxygenclass:: particle_set
+`Full doxygen documentation link. <../../doxygen_html/classfield__tinterpolator.html>`_
+
+  .. doxygenclass:: field_tinterpolator
       :project: TurTLE
       :path: ...
       :members: [...]
@@ -64,3 +109,20 @@ direct_numerical_simulation
       :undoc-members:
       :outline:
       :no-link:
+
+
+particle_solver
+---------------
+
+`Full doxygen documentation link. <../../doxygen_html/classparticle__solver.html>`_
+
+  .. doxygenclass:: particle_solver
+      :project: TurTLE
+      :path: ...
+      :members: [...]
+      :protected-members:
+      :private-members:
+      :undoc-members:
+      :outline:
+      :no-link:
+

documentation/sphinx_static/bibliography.rst

@@ -32,3 +32,8 @@ Bibliography
 .. [drivas2017prf] Drivas, T. D. and Johnson, P. L. and Lalescu, C. C. and Wilczek, M.
     *Large-scale sweeping of small-scale eddies in turbulence: A filtering approach*.
     `Phys Rev Fluids 2 104603 (2017) <https://dx.doi.org/10.1103/PhysRevFluids.2.104603>`_
+
+.. [shu1988jcp] C.-W. Shu and S. Osher,
+    *Efficient implementation of essentially non-oscillatory shock-capturing schemes*.
+    `J. Comput. Phys. 77, 439-471 (1988) <http://dx.doi.org/10.1016/0021-9991(88)90177-5>`_
+