some fixes to the true-SDC documentation (#2587)

Docs/source/FlowChart.rst

@@ -662,12 +662,13 @@ The overall evolution appears as:
 
 #. *Initialization* (``initialize_advance``)
 
-   Here we create the ``MultiFab`` s that store the needed information
+   We first do a ``clean_state`` on the old data (``S_old``).
+
+   We next create the ``MultiFab`` s that store the needed information
    at the different time nodes.  Each of the quantities below is a
    vector of size ``SDC_NODES``, whose components are the ``MultiFab``
    for that time node:
 
-
     * ``k_new`` : the current solution at this time node.
 
       Note that
@@ -700,14 +701,15 @@ SDC Single Iteration Flowchart
 
 .. index:: do_advance_sdc
 
-The update through all time nodes for a single iteration is done by
-``do_advance_sdc``.  The basic update appears as:
-
 Throughout this driver we use the ``State_Type`` ``StateData`` as
 storage for the current node.  In particular, we use the new time slot
 in the ``StateData`` (which we refer to as ``S_new``) to allow us to
 do ``FillPatch`` operations.
 
+The update through all time nodes for a single iteration is done by
+``do_advance_sdc``.  The basic update appears as:
+
+
 #. *Initialize*
 
    We allocate ``Sborder``.  Just like with the Strang CTU driver, we
@@ -756,18 +758,18 @@ do ``FillPatch`` operations.
 
        Then fill all other time nodes as: ``R_old[n]`` = ``R_old[0]``
 
-    * Do the SDC update from node ``m`` to ``m+1``.
+   * Do the SDC update from node ``m`` to ``m+1``.
 
-      We call ``do_sdc_update()`` to do the update in time to the next
-      node.  This solves the nonlinear system (when we have reactions)
-      and stores the solution in ``k_new[m+1]``.
+     We call ``do_sdc_update()`` to do the update in time to the next
+     node.  This solves the nonlinear system (when we have reactions)
+     and stores the solution in ``k_new[m+1]``.
 
 #. Store the advective terms for the next iteration.
 
    Since we are done with this iteration, we do: ``A_old[n]``
    :math:`\leftarrow` ``A_new[n]``.
 
-   We also store ``R_old`` for the next iteration.  We do this by
+#. Store ``R_old`` for the next iteration.  We do this by
    calling the reaction source one last time using the data for each
    time node.
 
@@ -777,6 +779,10 @@ do ``FillPatch`` operations.
 
    ``S_new`` :math:`\leftarrow` ``k_new[SDC_NODES-1]``
 
+#. Store the old and new sources in the State Data.
+
+#. Store the reaction information for the plotfiles.
+
 #. Call ``finalize_do_advance`` to clean up the memory.