Restraints on bond distances are the most commonly used type of restraints implemented in GSAS-II. The notebook tab for them is labeled “Bond” and they operate on atomic coordinates. They are most commonly used for keeping distances between bonded atoms at a target distance, but they can be used on any pair of atoms in a structure, whether bonded or not.
To create a bond distance constraint, you must search for interatomic distances. This is done in a series of steps. Before starting you should have an idea of the bonding environment for each type atom that you wish to constrain and what the current distances range between those atoms. If needed, go to the Phase and use the Atoms tab and the Compute/“Show Distances & Angles” menu command. You may need to change the radius values for atoms. Note that the results are listed on the console window.
Then, select the “Bond” tab, and make note of the “Search range” factor. This will be used to find distances. You will supply a target distance and distances that are up to the length of the Search range” times the “target distance” will be considered as potential restraints. Pairs of atoms with distances longer than that will be ignored. You will then use the “Edit Restr.”/“Add restraint” command and then you will be asked to
Once this is done, distance constraints are placed into the table of constraints shown in the data window. You can edit the target and esd (\(\sigma \)) value directly in the table. Or you can select restraints in the table and change the target or esd values for the selected restraints using “Edit Restr.” menu commands. There is also a menu command that will delete the selected restraints. If no selection has been made in the table before entering any of these the menu commands, then a window will be displayed where restraints can be selected.
As an example for how the origin and target atoms work in searches, consider a structure with Si, O and Al atoms. If the origin is set as the O atoms and the target is set to the Si atoms, then only distances between O and Si atoms will be considered. If both O are Si are selected for both the target and the origin, then O-O, Si-Si, O-Si and Si-O distances will be considered, where the latter two distances are duplicates. There is no problem with including the same pair of atoms twice, but that distance will have double weight compared to one that is only listed once.
The Cambridge Crystallographic Data Center produces a program called Mercury that tabulates distances and angles within a molecule as well as prepares the statistically expected values for those distances from the structures in the Cambridge Crystallographic Database using the CSD-Core/Mogul Geometry Check. This is primarily of use for organic moieties in structures. See the GSAS-II Help page on Restraints for more information on this command. When used from the Distance tab, constraints will be created for distances from this file.