Float atomic coordinates

It may also be desirable to store the atomic coordinates read from these files. The purpose of parsing the coordinates from the file and putting them into a separate column is to enable use of the coordinates from within the database. If the column is properly defined as a numeric or float column, this will also ensure that the coordinates are proper numbers. If there is no need for atomic coordinates, it is not necessary to create a column for these. Later sections of this chapter will discuss ways in which these atomic coordinates might be used in SQL functions. 

Basically, two different methods arc commonly used for representing a chemical struchiive in 3D space. Both methods utilize different coordinate systems to describe the spatial arrangement of the atoms of a molecule under con.sidcration. The most common way is to choose a Cartesian coordinate system, i.e., to code the X-, y-, and z-coordinates of each atom, usually as floating point numbers, For each atom the Cartesian coordinates can be listed in a single row. giving consecutively the X-, )> , and z-valnc.s. Figure 2-90 illustrates this method for methane. 

In polar space groups, which have a floating origin (e.g. PI where the origin is entirely arbitrary, or P2i where the origin can be anywhere on the b axis), a shift of the entire atomic model along a polar axis does not violate the space group symmetry. In the presence of a heavy atom in the stmcture, this atom s coordinates can be constrained to certain values (e.g. (0,0,0) for PI or (x, 0, z) for P2i). Alternatively, the sum of the coordinates of all atoms in the stmcture can be constrained to remain constant, which removes one parameter per polar axis. 

However, there is one more feature related to the formation of the heterointerface. Boundary conditions not only require adherence to stoichiometry, since the excessive component interferes with crystal lattice periodicity, but they also require coordination of atomic dipoles on the boimdary (Gleim et al., 2003 Pashley, 1989). All that leads to such effects as "floating" - arrival of not embedded component from the heterointerface to the growing layer surface, sp>atial degradation of the boundary, which is necessary for coordination of dipole moment, etc. Let us consider reception of heterojunction (HJ) GaAs-Ge as an example. 

---