Fixed improper matrix-dimension indexing

Traditionally, the y coordinate of a matrix is reversed from the
direction "+y" in cartesian coordinates. Now, the directionToSteps
method takes account of this reversal to give proper neigbors at each
site.
Consolidation of functions, floating point constants
Merge branch 'master' into pipe_flow

Conflicts:
	src/driver.cpp
	src/lattice.cpp
Added pipe boundary conditions