More Doc updates. Remove a few member variables that were parsed but …

…never used

Docs/sphinx_documentation/source/Debugging.rst

@@ -18,48 +18,54 @@ In debug mode, many compiler debugging flags are turned on and all
 when a floating point exception occurs. One can then examine those
 files to track down the origin of the issue.
 
-Several other ways to look at the data include:
+Several ways to look at the data include:
 
 1) Writing a :cpp:`MultiFab` to disk with
 
-.. highlight:: c++
+ .. highlight:: c++
 
-::
+ ::
 
- VisMF::Write(const FabArray<FArrayBox>& mf, const std::string& name);
+  VisMF::Write(const FabArray<FArrayBox>& mf, const std::string& name);
 
-and examining it with ``Amrvis`` (section :ref:`sec:amrvis` in the AMReX documentation).
+ and examining it with ``Amrvis`` (section :ref:`sec:amrvis` in the AMReX documentation).
 
 2) You can also use the :cpp:`print_state` routine:
 
-.. highlight:: c++
+ .. highlight:: c++
 
-::
+ ::
 
- void print_state(const MultiFab& mf, const IntVect& cell, const int n=-1);
+  void print_state(const MultiFab& mf, const IntVect& cell, const int n=-1);
 
-which outputs the data for a single cell.
+ which outputs the data for a single cell.
 
 3) If you want to compare old and new plotfiles,
 
-.. highlight:: c++
+ .. highlight:: c++
 
-::
+ ::
 
- fcompare --infile1 plt00000_run1 --infile2 plt00000_run2 --diffvar u_g
+  fcompare --infile1 plt00000_run1 --infile2 plt00000_run2 --diffvar u_g
 
-will print out the maximum absolute and relative differences between the two plotfiles
-for each variable and will also create a new plotfile "diffs" that contains the difference
-in u_g (in this case) between the two plotfiles.
+ will print out the maximum absolute and relative differences between the two plotfiles
+ for each variable and will also create a new plotfile "diffs" that contains the difference
+ in u_g (in this case) between the two plotfiles.
 
-The :cpp:`fcompare` executable can be built in AMReX (go to amrex/Tools/Plotfile and type "make").
+ The :cpp:`fcompare` executable can be built in AMReX (go to amrex/Tools/Plotfile and type "make").
 
-4) Valgrind is another useful debugging tool. Note that for runs using
+Valgrind is another useful debugging tool. Note that for runs using
 more than one MPI process, one can tell valgrind to output to different
 files for different processes. For example,
 
-.. highlight:: console
+ .. highlight:: console
 
-::
+ ::
 
- mpiexec -n 4 valgrind --leak-check=yes --track-origins=yes --log-file=vallog.%p ./incflo.exe ...
+ mpiexec -n 4 valgrind --leak-check=yes --track-origins=yes --log-file=vallog.%p ./incflo.exe ...
+
+
+Also see AMReX's documentation on :ref:`amrex:sec:basics:debugging` for further suggestions. 
+
+If you believe you've encountered a bug or incorrect behavior in incflo, please report the issue
+on incflo's github page `here <https://github.com/AMReX-Codes/incflo/issues>`_ .

Docs/sphinx_documentation/source/InputsInitialization.rst

@@ -17,7 +17,6 @@ The following inputs must be preceded by "incflo" and determine how we initializ
 +----------------------+-----------------------------------------------------------------------+-------------+--------------+
 | | Description | Type | Default |
 +======================+=======================================================================+=============+==============+
-+----------------------+-----------------------------------------------------------------------+-------------+--------------+
 | do_initial_proj | Should we do the initial projection? | Bool | True |
 +----------------------+-----------------------------------------------------------------------+-------------+--------------+
 | initial_iterations | How many pressure iterations before starting the first timestep | Int | 3 |

Docs/sphinx_documentation/source/InputsLoadBalancing.rst

@@ -3,7 +3,9 @@
 Gridding and Load Balancing
 ===========================
 
-The following inputs must be preceded by "amr" and determine how we create the grids and how often we regrid.
+The following inputs must be preceded by "amr" and determine how we create the grids and how often we regrid. The most
+commonly used options are listed here. See the AMReX documentation on :ref:`amrex:Chap:InputsLoadBalancing` for additional
+options.
 
 +----------------------+-----------------------------------------------------------------------+-------------+-----------+
 | | Description | Type | Default |
@@ -30,20 +32,6 @@ The following inputs must be preceded by "fabarray_mfiter" and determine how we
 | | Description | Type | Default |
 +======================+=======================================================================+==========+=============+
 | tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000 |
-| | (3D CPU-only) | | 1024000,8,8 |
+| | | | |
+| | (3D CPU-only) | | 1024000,8,8 |
 +----------------------+-----------------------------------------------------------------------+----------+-------------+
-
-The following inputs must be preceded by "incflo" and determine how we load balance:
-
-+----------------------+-----------------------------------------------------------------------+-------------+--------------+
-| | Description | Type | Default |
-+======================+=======================================================================+=============+==============+
-| load_balance_type | What strategy to use for load balancing | String | KnapSack |
-| | Options are "KnapSack"or "SFC" | | |
-+----------------------+-----------------------------------------------------------------------+-------------+--------------+
-| knapsack_weight_type | What weighting function to use if using Knapsack load balancing | String | RunTimeCosts |
-| | Options are "RunTimeCosts" | | |
-+----------------------+-----------------------------------------------------------------------+-------------+--------------+
-| knapsack_nmax | Maximum number of grids per MPI process if using knapsack algorithm | Int | 128 |
-+----------------------+-----------------------------------------------------------------------+-------------+--------------+
-