Diamond Version 5 User Manual: Building up structural parts

Filter

Exclude unwanted atom positions or symmetry operations from being used in most of the building operations

This article in brief:
- Excluding Atoms or Symmetry Operations
- Effects of the Filter

Previous article: About atoms, atom groups, bonds, and bond groups
Next article: Connectivity, part 1: Bonding spheres

Diamond offers a special function that can exclude selected atoms of the parameter list, selected symmetry matrices, or selected Bravais translations from being used during all functions that build up structural parts. By default this filter is not active, which means that all atoms, symmetry matrices, and Bravais translations will be considered.

Depending on your intention, it might be useful to exclude particular elements from the generation procedure. This can be done with the Filter dialog. See "Excluding Atoms or Symmetry Operations" how to do this.

This filter takes effect on almost every function that builds up a structural part. See "Effects of the Filter" how these functions are affected.

Excluding Atoms or Symmetry Operations

The exclusion of atoms, symmetry operations, or Bravais translations is managed with the Filter dialog.

To open the Filter dialog, choose the Filter command from the Build menu.

In the list Atom groups you find all atom groups of the current compound. In the list Atom sites from parameter list all atoms from the atomic parameter list are mentioned separately. Therefore some atom groups may be mentioned more than once. By defaut (the filter is not active), all atom groups and all atom sites have a checkmark set. If you clear the checkmark for an atom group, the checkmarks of all corresponding atom sites are unchecked automatically. On the other hand, setting the checkmark for an an atom group results in setting all checkmarks for the corresponding atom. To select all atoms belonging to an atom group except those of one particular site, first select the atom group, and then reset the selection of the desired atom site.

Each atom of the parameter list represents a particular number of symmetry equivalent atoms. These atoms arise from the application of the symmetry operators and Bravais translations, which are defined by the space group. Symmetry operators and Bravais translations of the current structure can be found in the corresponding lists Symmetry operations and Bravais translations.

By choosing only one single atom, one symmetry operation, and one Bravais translation, only one atom can be generated. But note that you have to select at least one atom, operator, and translation, because otherwise no atoms can be generated.

The selection of atoms has an effect on all following operations, which generate atoms. If the status of the current selection is overlooked, this can lead to misunderstandings. Therefore DIAMOND shows a warning symbol at the lower left corner of the structure window, whenever an atom or operator is excluded:

This is no error message, but it should remember you, that some atoms could not be generated, though you might expect this.

To reset the exclusion of atoms, symmetry operations, or Bravais translations (that means to switch off the filter), use the Select all button in the Filter dialog, and then press OK.

The warning symbol will disappear after the filter has been switched off.

Effects of the Filter

The exclusion of atoms, symmetry operations, and Bravais translations takes effect on the following building operations:

1. Generation of atoms within distinct ranges of the crystal structure lattice (unit cell, enclosure boxes around a selected atom, etc.). See "Filling cell ranges".

2. Filling of fixed spheres as well as of coordination spheres. See "Filling spheres".

3. Generation of molecules and completion of molecular fragments. See "Generating molecules" and following articles.

The filter also takes effect on the construction of coordination polyhedra, since atoms within the coordination spheres may be generated if necessary. See "Creating Coordination Polyhedra".

The filter does not take effect on the direct generation of atoms using the Add Atoms command or the Add All Atoms and Connections command from the Build menu. See "Generating atoms directly".

Previous article: About atoms, atom groups, bonds, and bond groups
Next article: Connectivity, part 1: Bonding spheres