From f67cb834114fadd77a2b6712372c9e486161b72a Mon Sep 17 00:00:00 2001
From: compucell3d <mswat@indiana.edu>
Date: Sun, 8 Jul 2018 00:21:17 -0400
Subject: [PATCH] added lattice type

---
 docs/index.rst        |  1 +
 docs/lattice_type.rst | 66 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)
 create mode 100644 docs/lattice_type.rst

diff --git a/docs/index.rst b/docs/index.rst
index 81eb07c..2b9eedc 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,6 +14,7 @@ You do not have to be an XML guru but you should know how to write simple XML do
 
    introduction
    potts
+   lattice_type
 
 
 Indices and tables
diff --git a/docs/lattice_type.rst b/docs/lattice_type.rst
new file mode 100644
index 0000000..8f5b994
--- /dev/null
+++ b/docs/lattice_type.rst
@@ -0,0 +1,66 @@
+Lattice Type
+~~~~~~~~~~~~
+
+Early versions of CompuCell3D allowed users to use only square lattice.
+Most recent versions allow the simulation to be run on
+hexagonal lattice as well.
+
+.. note::
+
+Full description of hexagonal lattice including detailed
+derivations can be found in “Introduction to Hexagonal Lattices”
+available from `http://www.compucell3d.org/BinDoc/cc3d_binaries/Manuals/HexagonalLattice.pdf <http://www.compucell3d.org/BinDoc/cc3d_binaries/Manuals/HexagonalLattice.pdf>`__
+
+To enable hexagonal lattice you need to put
+.. code-block:: xml
+
+    <LatticeType>Hexagonal</LatticeType>
+
+in the Potts section of the CC3DML configuration file.
+
+There are few things to be aware of when using hexagonal lattice.
+In 2D your pixels are hexagons but in 3D the voxels are rhombic dodecahedrons.
+It is particularly important to realize that surface or perimeter of the pixel
+(depending whether in 2D or 3D) is different than in the case of square
+pixel. The way CompuCell3D hex lattice implementation was done was that
+the volume of the pixel was constrained to be ``1`` regardless of the
+lattice type.
+There is also one to one correspondence between pixels of the square
+lattice and pixels of the hex lattice. Consequently, we can come up with
+transformation equations which give positions of hex pixels as a
+function of square lattice pixel position:
+
+.. math::
+   :nowrap:
+
+   \begin{cases}
+        & \left [ x_{hex}, y_{hex}, z_{hex}  \right ] = \left [ \left ( x_{cart}+\frac{1}{2} \right ) L, \frac{\sqrt[]{3}}{2}y_{cart}L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{ for } y \mod 2 = 0 \text{ and } z \mod 3 = 0 \\
+        & \text{ if } x= \\
+        & \text{ if } x= \\
+        & \text{ if } x= \\
+        & \text{ if } x= \\
+        & \text{ if } x=
+    \end{cases}
+
+
+Based on the above facts one can work out how unit length and unit
+surface transform to the hex lattice. The conversion factors are given
+below:
+
+For the 2D case, assuming that each pixel has unit volume, we get:
+
+where denotes length of the hexagon and denotes a distance between
+centers of the hexagons. Notice that unit surface in 2D is simply a
+length of the hexagon side and surface area of the hexagon with side 'a'
+is:
+
+In 3D we can derive the corresponding unit quantities starting with the
+formulae for Volume and surface of rhombic dodecahedron (12 hedra)
+
+where 'a' denotes length of dodecahedron edge.
+
+Constraining the volume to be one we get
+
+and thus unit surface is given by:
+
+and unit length by: