Removed rotationMatrix
The class Defect now has a member named coordinateSystem. All child
classes inherit this so there is no need for a separate rotationmatrix.
Pointers to insert dislocations and dislocation sources
The dislocations and dislocation sources, and other defects in general
are insterted into the same list slipPlane::defects using pointers.
Converting dislocations to defects
Midway through converting all Dislocations to Defects.
Removed function sortDislocations
Replaced by sortDefects.
Removing references to SlipPlane::dislocations
All references to the std::vector<Dislocation> dislocations are replaced
with appropriate references to std::vector<Defect*> defects.
Updating slipPlane to handle a list of defects
Removed references to SlipPlane::rotationMatrix. Replaced by function
calls to SlipPlane::coordinateSystem.calculateRotationMatrix();
Adding functions for updating various vectors
updateDislcoationList function added
Making changes to include the vector<Defect*>. Many compilation errors exist
Added functions for creating and sorting dislocation lists and defect
lists.
Resolved most Defect* related errors and inconsistencies.
Pending: Dislocation::idealTimeIncrement
Added virtual function getVelocity to the Defect class.
Virtual functions for time for Defect.
Return pointers to create lists in simulateSingleSlipPlane functions.
Updated erroneous documentation in dislocation.cpp
Inserted call to SlipPlane::createDefects()
The function createDefects() must be called once all the defects are
read into memory.
Corrected indentation of code in simulateSingleSlipPlane.cpp
Complete definition on slip plane extremities in
SlipPlane::setExtremities through SlipPlane constructor call.
Removed extra * from comment line.
Defined slip plane extremity co-ordinate system within constructor.
Updated order of carrying out operations in readSlipPlane function.
The operations of reading in data are carried out in the following
order:
-Extremities are read in and stored in SlipPlane::extremities.
-Dislocations are read in one by one, and inserted into the std::vector
dislocations.
-Dislocation sources are read in one by one and stored in the
std::vector dislocationSources.
-The two vectors are sorted in ascending order of distance from
SlipPlane::extremity[0].
-The std::vector defects is updated using the function updateDefects:
--The extremities are assigned to the ends of the vector.
--The dislocation list is inserted.
--The dislocationSources list is inserted.
--The defects are all sorted.

Henceforth, care must be taken to call sortDislocations and
sortDislocationSources functions every time a new dislocation or a new
dislocation source is inserted or removed. The updateDefects function
must then be called to update the defects list.
Added vector clear functions to SlipPlane class.