Menus in tetr

Most of the menus have common options:

• Co - (info) show a table with Cartesian and fractional coordinates of all atoms in the unit cell
• S - save the current geometry into an input file (the code format to be chosen next)
• Sy - (info) show (usually, the point) symmetry of the current geometry; in most cases the lattice translations are also included, i.e. two points are thought to be equivalent if they are separated by a lattice translation
• U - undo the last step
• An - (setting) choose the format in which coordinates are to be specified for input in the menus: Angstrom, fractional or atom number (in order of atoms in the system)

A number of options of the main menu allows a user to change the current geometry in various ways. Some options have similar meanings in different menus, although their actual work depends on where they are called from, for example:

• Mv - move one or more atoms in the cell
• Rt - rotate one or more atoms

In many menus when a change in geometry is done, the code allows the user to dump the geometry manually or automatically into a file geom.xyz that is written in the xyz format. If you run any xyz-file previewer (like Xmol), then you can preview the system during the modification process, and this is extremely useful! A number of options (mainly settings) control this:

• XY - (setting) the format of the geom.xyz file (either for Xmol, Ymol or disable); in the latter case the file will not be written after each change of the geometry
• Hs - (setting) either add or not H atoms to the geom.xyz file to preview x,y,z axes (necessary for Xmol as it does not have the axes facility)
• Bb - (setting) breeding box is specified: this option allows you to preview not just the cell, but $N_{1}\times N_{2}\times N_{3}$ extention of it; note, that the actual cell is not changed, this option only affects the atoms written to the geom.xyz file
• W - force writing geom.xyz file for the current geometry

Normally, when choosing a set of atoms, two integers are specified, so that all atoms with numbers between (and including) them are in the list. For instance, choosing 5 and 10 would include atoms 5,6,7,8,9 and 10 into the list. In some cases a non-contagious list is required, e.g. 5, 7-10, 15 and 22. In this case you can ``tag'' atoms (option T) by naming all of them and using a dash if all numbers in between are to be included, e.g. 5 7-10 15 22 for the example above. Note that once atoms are tagged, pressing T again untages them.