Testing Branches
Testing Branching, again.
Revert "Testing Branching, again."

This reverts commit 65125c712aaecb5786786dae7d4735fec11317b5.
Revert "Testing Branches"

This reverts commit f969a0d63a776081c2d8697942726a1b31d19189.
Fixed configuration file input from command line argument.
Added a script for run_gpu on the DMC.ASC to take as input. This fixes problems with command line arguments to our simulation.
Simulation should now use statefile path if it is available in the configuration file, and default to using the z-matrix file path otherwise.
Adjusted the linear version to also use statefile or z-matrix input based on which is provided.
Merge pull request #1 from mrhwick/config_file

Config file
modify Makefile to use default rule, can speed up the compile process
generate depend file automatic
remove unused MACROs
Modified: Utilities/src/State_Scan.cpp - fixed state read in. Now getting memory related crash
Merge pull request #2 from mrhwick/David

David
init SimBox class
classes after compile, TODO: modify linearSimulationExample
reconstruction compiled over, so many empty functions
re constructed to object oriented.
first step: make up box and simulator class
TODO: arrange the memory of box inside to make it search quickly.
add random seed to get repeatable results
1.modified data structure to save atom array.
2.modified seed generation method
3.modified the executable file name

Signed-off-by: Zhang Xiao <zhangxiao2000@gmail.com>