Modularize the code

[KenichiNomura]

To start, use type and module to organize variables and subroutines, make it easier to instantiate the MD context.

[KenichiNomura]

it turns out that passing allocatable array to subroutines require 'interface' of the procedure however writing the interface in the users of the subroutine will make the code messy. Instead, module automatically generates the subroutine interface and use the module is a simpler solution.

There are two ways to share allocatable variable, 1. pass as argument and 2. share through module. Use of module takes care of the two.