Overview of the code structure, user interfaces, and links between the different components. The yellow boxes display the main classes and the inner orange boxes indicate the dependence on the main sub-classes, with class names indicated at the top together with the name of the main file where this is defined. The grey box gives the name of the utility function files. The blue arrows indicate the interfaces with the user. The orange arrows indicate how the different modules are inputs to one another. The grey arrows show how utility functions are used by the classes.