Bilbao Crystallographic Server Structure Data Converter & Editor |
The Structure Data Converter & Editor program is written to quickly convert or manipulate structure data submitted in various different file formats, as well as constructing one from scratch.
A structure is basically defined by the lattice parameters of its unit cells along with the information on the atomic sites such as the atomic species, positions and occupancies. If the structure contains some kind of symmetry, then it can be further represented by including the symmetry information through the corresponding space group which summarizes the symmetry operations that are compatible with the structure (i.e., those that leave the structure unchanged). This way, by specifying the symmetry information, only the information on the atomic sites in the asymmetric unit is sufficient.
For a 3-dimensional crystal system, there exist a total of 230 different sets of symmetry operations, named as space groups. Each of the space groups is uniquely identified with respect to the symmetry operations it contains and the list of these operators can be accessed using the GENPOS tool.
Since the above mentioned space groups only act on the atomic positions, they do not have the necessary means to handle magnetic information. In order to achieve this, the time-reversal operator (-1'|0,0,0) is implemented into the 230 non-magnetic space groups (also known as crystallographic or Federov space groups) to produce a set of 1651 magnetic space groups (also known as Shubnikov space groups). Depending on the procedure of introducing the time-reversal to the source Federov space group, a magnetic space group can belong to one of the 4 types. To list the symmetry operators of the magnetic space groups, the MGENPOS tool can be used.
A space group is identified by its unique sequential number. For the crystallographic space groups, this index is a number in the range of [1,230]. For the magnetic space groups, depending on the notation (BNS or OG) it can consist of two numbers (in the case of BNS) or three numbers (OG). Structure Data Converter & Editor program uses the BNS notation ("###.###" format - the first index being the corresponding Federov space group index; the second being the overall index, i.e. [1,1651]) to identify the magnetic space groups.
The Structure Data Converter & Editor program accepts input data in one of the following file formats:
Apart from these file formats, a new structure can be constructed from scratch using the start with a "blank" structure option in the main page of the program.
Once a structure is imported (and optionally edited) the program can export it in the file formats discussed above. Since magnetic space groups & magnetic moments are not supported in VESTA, in order to export to VESTA file format, the structure is first taken to P1 space group (i.e. its symmetry information is removed) and then "arrows" are assigned to each magnetic site to represent the magnetic moments. Thus, even though the program accepts VESTA files with higher symmetries, the VESTA files it will produce will only include structures defined in P1. For the CIF and mCIF formats, the actual symmetries are preserved.
Space Group Information: It is given in the BNS notation ###.###, with the first index corresponding to the crystallographic (Federov) space group and the second index being the overall index (a number in the range of [1,1651]).
If the space group index is entered as a single number ("###"), then it will be assumed as the Federov space group number (magnetic space group of type I) and the index will be restored to that of the corresponding in the BNS notation (e.g. "42" will become "42.219" for the Fmm2 magnetic space group of type I).
If the space group index is given in the OG notation's format ("###.###.###"), it will be re-written as its corresponding space group in the BNS format (e.g. "42.4.312" will become "42.222" for the Fm'm'2 magnetic space group of type III). Although the BNS and OG space group settings for the type I (Federov), II (gray), III (translationgleiche) magnetic space groups coincide, since for the type IV (klassengleiche) magnetic space groups they differ, it is highly recommended that the usage of the OG notation in the program should be refrained.
It should be noted that: A change in the space group information updates the symmetry operations information (in standard settings) from the database.
Symmetry Operations: If the symmetry operations are listed in the input file, then by default, they will be used. Otherwise, or by clicking on the "Populate with operators from database" button located at the end of the expanded list of the operators, this information will be filled with the operators of the corresponding space group in the standard setting, read from the database.
One can also define the symmetry operations manually. The program recognizes the operators in one of the following formats:
(Note that all the operators must be presented in the same format.)
Specification of all the symmetry operations is not required: by entering the generators, the other operations can be derived automatically.
Sites Menu: This menu can be used to manipulate atomic information. Note that, the corresponding button should be clicked (as opposed to hitting enter) in order to activate the desired effect.
Structure Menu: The buttons here acts on the structure, exporting its data in one of the supported file format, as well as removing a relevant information, re-ordering the sites or visualizing the structure.
Miscellaneous:
Bilbao Crystallographic Server (http://www.cryst.ehu.es) |
For comments, please mail to cryst@wm.lc.ehu.es |