2a: Molecular dynamics

The data from the simulations (provided by Daniel Spngberg) are stored in three files: coordinates.txt contains 3D coordinates of a number of atoms, radii.txt contains the radii of these atoms, and connections.txt defines how the atoms are connected to each other.

One way to visualize the molecules is to represent each atom with a sphere with a radius corresponding to the radius of the atom. Some of the atoms have quite similar radii, so to make it easier to distinguish between these we can color-map the spheres depending on their radius. Finally, the connections between the atoms can be made with cylinders. The image to the right show an example of how the result can look (OBS! this is a solution, not the correct solution).

The files we have available is not in a standard format, so we either have to convert our data into the VTK file format or create our own functions for reading the data. Such functions are provided for you in the Python script ReadPoints.py. If you want, you can also download the file molecules.py that contain some hints on how to read the data. When you have read the data you have a vtkPolyData with points/vertices/cells and it is time to start working.