Bilbao Crystallographic Server Structure Data Converter & Editor

Help Page

• Introduction
• Structural Data
• Space Groups
• File Types
• Input
• Output

• Space Group Information
• Symmetry Operations
• Sites Menu
• Add # atoms more
• Remove selected atoms
• Change the selected atoms' symbol to #
• Select the atoms with the symbol: #
• Structure Menu
• Export to VESTA/CIF/mCIF Format
• Remove the symmetries
• Remove the magnetic information
• Re-order the sites
• Visualize
• Miscellaneous
• Discovering symmetres via FINDSYM

Background Information

Introduction

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.

Structural Data

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.

Space Groups

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.

File types

The Structure Data Converter & Editor program accepts input data in one of the following file formats:

• BCS: The Bilbao Crystallographic Server (BCS) file format is the standard format used throughout the server's tools. It contains the space-group, lattice and sites information (for the asymmetric unit shell) assumed to be given in standard setting (one can use our SETSTRU tool to convert to other settings). As of the moment, the occupational and magnetic information are not supported.


• CIF: The Crystallographic Information File format is developed by the International Union of Crystallography and is a widely used, standard-assumed file format. Although it has many supported tags for defining additional structural information, unfortunately a consensus on the representation of magnetic information hasn't been reached yet.


• mCIF: As the ISOCIF program, developed by Harold T. Stokes and Branton J. Campbell started supporting magnetic space groups and magnetic moment information, Stokes and Campbell extended the CIF dictionaries by adding magnetic related tags such as "_magnetic_space_group_BNS_number", "_magnetic_space_group_symop_operation_timereversal", "_magnetic_atom_site_moment_crystalaxis_mx", etc.. To discern this extended CIF file, they also relabeled the existing tags like "_magnetic_cell_length_a", "_magnetic_space_group_symop_operation_xyz" and thus the mCIF format came into being. Although one can store all magnetic related information to a mCIF file, its -for the moment- incompatibility with most of the crystallographic software makes it difficult to import the magnetic data contained within.


• VESTA: Developed by Koichi Momma, VESTA is a highly advanced, yet simple to use 3D visualization program for structural data. Even though it has no direct support for magnetic space groups / magnetic moments, nevertheless they can be represented by assigning vectors to atomic sites.


• VASP: The Vienna Ab initio Simulation Package, developed by Jürgen Hafner, Georg Kresse, Doris Vogtenhuber & Martijn Marsman, is mainly an ab-initio calculation software, accepting its structure input data in P1. Currently our Structure Data Converter & Editor tool only supports the POSCAR/CONTCAR files with "Direct/Fractional" atomic coordinates.

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.

Information on the program usage

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:

• x,y,z,+1
• 1. x,y,z mx,my,mz +1
• x,y,z

(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.

• Add # atoms more: Adds the desired number of "X" atoms to the structure.
• Remove selected atoms: Removes the atoms with their boxes checked from the structure.
• Change the selected atoms' symbol to #: A batch renaming utility to quickly assign a different symbol to the selected atoms.
• Select the atoms with the symbol: #: Marks the atoms with the given symbol(s) as checked. More than 1 symbol can be specified using space or comma as seperator (e.g. "Ba, Ti O").

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.

• Export to VESTA/CIF/mCIF Format: Prepares a file containing the structure's data in the requested format. The prepared file contents are presented in a text box for eye-balling / copy & paste purposes, as well as the file being ready for download via the link above the text box.
  
  When exporting the structure data to CIF format, the magnetic information is discarded -- likewise, exportation to VESTA format causes the structure to be represented in P1 setting. However, this operations happen in the background, not affecting the actual structure's information in a reduction of symmetry/magnetism.


• Remove the symmetries: Takes the structure down to P1, removing all the symmetries, hence explicitly presenting the elements of each atomic orbit. (Note that the elements of the atomic orbits can be listed in the "Structure Summary" pane, without actually removing the symmetries by simply clicking once on the "Export to VESTA format" button.)


• Remove the magnetic information: Sets all the atomic sites' magnetic moments to (0,0,0), thereby removing the magnetic data (doesn't affect the symmetry operations, though).


• Re-order the sites: The atomic sites are re-grouped with respect their symbols and their labels are re-assigned using the symbol and the index.


• Visualize: Prepares a Jmol script for the visualization of the structure. After clicking this button, the "Please follow this link to visualize the structure using Jmol." link that appears following the menu should be opened to view the structure in a new window/tab.

Miscellaneous:

• Discovering symmetries via FINDSYM: When a structure is presented in a triclinic space group (P1, P-1), the "Find Symmetry" button is revealed at the end of the menu, with a "Tolerance" specification. Activating this button runs the FINDSYM program, developed by H. Stokes and D.M. Hatch of the Brigham Young University (more information is available through their website: http://stokes.byu.edu/iso/findsymhelp.html), in the background and updates the structure with the found high-symmetry structure, reporting the relating transformation matrix, as well. For structures that posses monoclinic or higher symmetries, we recommend using our server's PSEUDO tool.