Setting up graphics window

[kasmar00]

Currently, when program starts the graphics window is plain/filled with background (bug?) , then after box is set the atoms appear and simulation automatically starts.
I think, the window should configure itself fully (ie. display box bbox, display buttons, charts etc.) then wait for user input (configuration of simulation through sliders/buttons), generate atoms (this can take a while!), maybe start countdown in seconds and then start simulation.
This probably requires much rework of setting up order in main.