Function to create molecular geometry from text file.

file_name a string giving the location of the geometry file. It is assumed that geometry is given for each atom on line, e.g.: H 0. 0. 0. H 0. 0. 0.7414

geometry A list of tuples giving the coordinates of each atom. example is [('H', (0, 0, 0)), ('H', (0, 0, 0.7414))]. Distances in angstrom. Use atomic symbols to specify atoms.