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Library set based on dynamicRefineFvMesh and the for OpenFOAM to allow 2D AMR
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Note: This library may require OpenFOAM version 2.3.0 (or greater?). Errors are reported with OF-2.1.1.

Acknowledgements :

Vincent Rivola (vinz @ cfd-online forums) - for sending a 2D damBreak with obstacle case to test.
James Carow - for presenting the same error as VR and alerting me to possible version dependency (Currently unresolved)

Library set based on dynamicRefineFvMesh and the for OpenFOAM to allow 2D AMR

The dynamicMeshDict in <case>/constant should be changed to read:

dynamicFvMesh dynamicRefineFvMeshHexRef4;
    // Standard options here
toggle = 0; // or 1, see toggle_Explanation file


Class based on the dynamicRefineFvMesh. Only a few changes - 
some hardcoded numbers changed from 7 to 3 or 8 to 4, added
new functions refineAtZero() and updateAtZero() to try and
leverage regenerateAlphaClass in the solver. These functions are
also why dynamicFvMesh.H is included locally rather than from
the original OF sources.

Main class. Implements mesh cutting, and is based on hexRef8.
Several new functions, mostly named with a my~ prefix, eg
mySplitSideFaces(). The bulk of the meaningful changes are within
the setRefinement() function.
Initially, the function is similar to the hexRef8 version, and
creates lists of the cells to be refined, splitting faces and 
edges as needed. Unlike for hexRef8, not all faces of cells to
be refined are split - there is a test for orientation of the face
using calcFaceNormalVector() and comparing it with the direction
to not refine. Also changed, the cellMidPoints' points no longer
support a cell.
Only 3 new cells are added in the next section, down from 7.
They are stored in cellAddedCells, just like in hexRef8. After
points have been added, the cellLevel and pointLevels are updated.
This is much earlier than the updates to history_ in hexRef8. The
values of cellLevel and pointLevel are needed to properly match up
face owners and neighbours in the current implementation, but a
copy of the original (pre-refinement) cell levels and point levels
are held in the variables oldCellLevel_ and oldPointLevel_. These
presumably are a waste of space if not used, and so I will probably
remove them once the class is tidier.
The splitting of cells is still done in several sections, as in
hexRef8. Initially, the chosen faces are split (those with
faceMidPoint >= 0). The code for this section is largely the same
as for hexRef8.
The second section holds most of the changes, and is split into two
main parts. In the first part, additional points are added to front
and back (the sides being cut) faces which are not themselves refined.
In the second part, the 'side faces', that is, those which are cut in
one direction, but not along their length, are handled. The handling
of these faces is done by mySplitSideFaces(..).
The third section is (hopefully) never triggered, but is also
unchanged from hexRef8, apart from a diagnostic message at the bottom.
The fourth section adds the internal faces between new cells. This is
done by myCreateInternalFaces(..). myCreateInternalFaces() seems to be
pretty solid, and so I will probably not look at it more until I have
fixed other stuff - especially mySplitSideFaces, which needs some work
for interfaces that become complicated.

Class based on refinementHistory. Few changes, mostly the addition of
some functions. myParentCell(..) is important in numerous places
within hexRef4 during the splitting of cells (in determining owner 
and neighbour). A parentList(..) function is also written, but that is
mostly just to help with diagnostics when things don't work.

This class is new, and not a part of the 2D AMR. Really, it should
probably be in a separate library, but the possibility of linking
it more closely might be something worth looking at later.
The class takes some input parameters (yMid should not be one of them,
but it's currently simpler!) and then recalculates a cosine-based 
perturbation to alpha. This is then remapped and returned to the
solver. The aim is to allow for refinement and remapping of alpha
before the start of the time loop, so that the mesh can be usefully
refined at the start of solving, and since the seed for 'random'ness
is passed by the solver, the alpha perturbation will have the same
shape each time, so long as it is given the same seed. (ie. don't 
generate a new seed each time you initialise an object of 
regenerateAlphaClass type within the solver).

Used to store pointers to each of the many DIAG_XYZ booleans being
held in hexRef4 now, which allow easy customization of the output
to log files of diagnostic/info messages. These can be (currently) 
changed using the format 
*((hexRef4object).diagList.myMap["nameOfVar"]) = true/false;
This is likely to be changed to a function, to make it simpler to 
access and allow some automated checking of the validity of the 
name passed.

Used in hexRef4 to sort and print lists of faces to be refined, along
with a rudimentary description of why faces are set to be refined.
Will be removed when everything works well (at least for dependencies)
Might leave the files in just so that they can be used if wanted.


Test and improve for the damBreak 2D case.
Determine reasoning for errors in pairedFaces for part 3 face
Implement unrefinement.
Check through flux corrections for updateAtZero/refineAtZero. Not all 
fields  exist at that point, so relatively few need correction, but at
least some might (read - alpha).
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