Try better neighbor search algorithm

Create a new branch to do some experiments.

Some codes are refactored.
Add friction-induced heat

Also be loyal to the computation procedures of original paper.
Minor changes
Fix bugs
Update README
Refactor codes

Since the codes are at early stage, I have changed many codes~
Add bruce-force searching algorithm and total energy calculation
Try to add codes for initializing

Add TimeManager class for managing time information, and InitData,
InitCond, ShockCase class for initialization.

InitData is an abstract class. Concrete test cases should inherit it.

Compile codes for initLady.cpp.
Check the initialization of density

Add RMSE checking in InitCond.cpp.
Change ShockCase.
Change IdealGas so that the parameters (e.g., cv, gamma) can be changed.