this is the original version used in thehead for supernova
+ now include particle tracer
+ includes explorable image generator

- need to separate into two libraries
- need a better configure file so that there is no hard codes
+ changed Makefile for vidi machine
Merge branch 'master' of dax:/home/yeshi/flowsimulate
+ pull out the options and put into the configure.txt file

Conflicts:
	Makefile
+ able to read hdf5 flow field files
+ able to specify file format to read

- need error checking function to see if file is valid
+ file open error checking
+ removed some unused variables
+ changed Makefile to Makefile.sample so each local version can maintain its own Makefile
+ Changed config file format to json, uses picojson as the parser.
+ added loadConfig() function in Simulator so that main doesn't need to
set so many parameters.
+ changed interface for Simulator

- need to clean up some old interfaces
+ Simulator now takes a config file as input, then each timestep it
needs a vector field.
+ put make path utitlity function to external file
+ Neighbor processe
+ using cmake as the build system
+ separate into 2 libraries: particle tracer and tube generator
Currently the particle advector and the tubing are using two different Particle implementations. This is the initial commit to solve this issue.

+ Added the united Particle class under Utilities.
Changed the particle advector to use the new particle class, next is to change the tubing to use the new particle class
Changed the particle advector to use the new particle class, next is to change the tubing to use the new particle class too
Changed the particle class used in the tubing part.
It's still messy in many ways.
The geometry directory seems to be an overkill, we should be able to simplify it.
Merge branch 'unite_particle'
Done with modifying the two parts to use the same particle class