kreft/iDynoMiCS — pull request #44 by kalden (2013-11-12 16:40:41+00:00)
Title: Declaring Species by Area & Length rather than Number

Changes to initial setup of species such that these can be declared in terms of area rather than as a number of cells. Now the user has the option to specify the number of cells per millimetre cubed. This is then
used to calculate the number of cells that should be introduced to the simulation initially. However the update goes a little further than this - in all the examples, the cell initial setup area is the whole length
of the Y and Z domains, with a height of 1 (to ensure the cells are initially near the substratum). Now the user will have the opportunity of not declaring an initial area at all: if they do this, iDynoMiCS assumes the area to be the length of the Y and Z domains, with a height of 1. This detail has been specified in detail, with examples, in the
new example protocol file that is included in this commit.
Also have clarified that there is a difference between 2D and 3D when specifying cells in this way, so that the code is clear for the future.