Bilbao Crystallographic Server

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Bilbao Crystallography Server
Bilbao crystallographic server logo.png
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Bilbao Crystallographic Server main page
Type of site
Scientific Tools (Crystallography & Solid State Physics)
Available in English
Owner University of the Basque Country
Created byMois I. Aroyo, J. Manuel Perez-Mato, Gotzon Madariaga
URL www.cryst.ehu.es
Launched1997
Current statusOnline

Bilbao Crystallographic Server is an open access website offering online crystallographic database and programs aimed at analyzing, calculating and visualizing problems of structural and mathematical crystallography, solid state physics and structural chemistry. Initiated in 1997 by the Materials Laboratory of the Department of Condensed Matter Physics at the University of the Basque Country, Bilbao, Spain, the Bilbao Crystallographic Server is developed and maintained by academics. [1]

Contents

Information on contents and an overview of tools hosted

Focusing on crystallographic data and applications of the group theory in solid state physics, the server is built on a core of databases and contains different shells.

Space Groups Retrieval Tools

The set of databases includes data from International Tables of Crystallography, Vol. A: Space-Group Symmetry, [2] and the data of maximal subgroups of space groups as listed in International Tables of Crystallography, Vol. A1: Symmetry relations between space groups. [3] A k-vector database with Brillouin zone figures and classification tables of the k-vectors for space groups is also available via the KVEC tool.

Magnetic Space Groups

In 2011, the Magnetic Space Groups data compiled from H.T. Stokes & B.J. Campbell's [4] and D. Litvin's [5] 's works general positions/symmetry operations and Wyckoff positions for different settings, along with systematic absence rules have also been incorporated into the server and a new shell has been dedicated to the related tools (MGENPOS, MWYCKPOS, MAGNEXT).

Group-Subgroup Relations of Space Groups

This shell contains applications which are essential for problems involving group-subgroup relations between space groups. Given the space group types of G and H and their index, the program SUBGROUPGRAPH provides graphs of maximal subgroups for a group-subgroup pair G > H, all the different subgroups H and their distribution into conjugacy classes. The Wyckoff position splitting rules for a group-subgroup pair are calculated by the program WYCKSPLIT.

Representation Theory Applications

The fourth shell includes programs on representation theory of space and point groups. REPRES constructs little group and full group irreducible representations for a given space group and a k-vector; CORREL deals with the correlations between the irreducible representations of group-subgroup related space groups. The program POINT lists character tables of crystallographic point groups, Kronecker multiplication tables of their irreducible representations and further useful symmetry information.

Solid State Theory Applications

This shell is related to solid state physics and structural chemistry. The program PSEUDO performs an evaluation of the pseudosymmetry of a given structure with respect to supergroups of its space group. AMPLIMODES performs the symmetry-mode analysis of any distorted structure of displacive type. The analysis consists in decomposing the symmetry-breaking distortion present in the distorted structure into contributions from different symmetry-adapted modes. Given the high and low symmetry structures, the program calculates the amplitudes and polarization vectors of the distortion modes of different symmetry frozen in the structure. The program SAM calculates symmetry-adapted modes for the centre of the Brillouin zone and classifies them according to their infrared and Raman activity. NEUTRON computes the phonon extinction rules in inelastic neutron scattering. Its results are also relevant for diffuse-scattering experiments.

Structure Utilities

A set of structure utilities has been included for various applications such as: the transformation of unit cells (CELLTRAN) or complete structures (TRANSTRU); strain tensor calculation (STRAIN); assignment of Wyckoff Positions (WPASSIGN); equivalent descriptions of a given structure (EQUIVSTRU); comparison of different structures with support for the affine normalizers of monoclinic space groups. STRUCTURE RELATIONS calculates the possible transformation matrices for a given pair of group-subgroup related structures.

Incommensurate Crystal Structures Database

The Bilbao Crystallographic Server also hosts the B-IncStrDB: Bilbao Incommensurate Crystal Structures Database, a database for incommensurately modulated and composite structures.

Scientific Research

In addition to receiving citations from scientific articles [6] [7] and theses, [8] [9] the Bilbao Crystallographic Server also actively publishes research reports in internationally reviewed articles, [10] as well as hosting/participating in international workshops, summer schools and conferences. [11] A list of these publications and events are accessible from the server's web page..

Development History and People

The Bilbao Crystallographic Server came to life in 1997 as a scientific project by the Departments of Condensed Matter Physics and Applied Physics II of the University of the Basque Country (EHU) under the supervision of J. Manuel Perez-Mato (EHU) and Mois I. Aroyo (EHU), in coordination with Gotzon Madariaga (EHU) and Hans Wondratschek (Karlsruhe Institute of Technology, Germany) with funding from the Basque government and several ministries of the Spanish government. The initial code was written by then Ph.D. students Eli Kroumova (EHU) and Svet Ivantchev (EHU) and the very first shells related to retrieval tools, group-subgroup relations and space group representations have soon appeared online. [12] [13] [14] [15]

Afterwards, in collaboration with Harold T. Stokes and Dorian M. Hatch from Brigham Young University, USA, the server extended its services to include symmetry modes analysis. Asen K. Kirov, a Ph.D. student from Sofia University, Bulgaria contributed to the server, working on programs dedicated to irreducible representations and extinction rules.

In 2001, Ph.D. student Cesar Capillas began his research on the server and became the main developer and system administrator focusing on structure relations, such as pseudosymmetry and phase transitions. Danel Orobengoa, also a Ph.D. student, joined the developer team in 2005 and worked mainly on symmetry modes, k-vector classification tables and non-characteristic orbits (in collaboration with Massimo Nespolo of the Nancy-Université, France), writing his Ph.D. thesis on the applications of the server for ferroic materials.

In 2009, Ph.D. student Gemma de la Flor and post-doc Emre S. Tasci were recruited for the development team: de la Flor working mainly on the identification and interpretation of symmetry operations, structure comparison and Tasci becoming the new system administrator and main developer, focusing in the structure relations concerning phase transitions. The Bilbao Crystallographic Server team took its current (2012) line-up in 2010 with the addition of Ph.D. student Samuel Vidal Gallego, his main research field being the magnetic space groups. [16]

Related Research Articles

<span class="mw-page-title-main">Crystallography</span> Scientific study of crystal structures

Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics. The word crystallography is derived from the Ancient Greek word κρύσταλλος, and γράφειν. In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.

<span class="mw-page-title-main">Crystal system</span> Classification of crystalline materials by their three-dimensional structural geometry

In crystallography, a crystal system is a set of point groups. A lattice system is a set of Bravais lattices. Space groups are classified into crystal systems according to their point groups, and into lattice systems according to their Bravais lattices. Crystal systems that have space groups assigned to a common lattice system are combined into a crystal family.

<span class="mw-page-title-main">Space group</span> Symmetry group of a configuration in space

In mathematics, physics and chemistry, a space group is the symmetry group of a repeating pattern in space, usually in three dimensions. The elements of a space group are the rigid transformations of the pattern that leave it unchanged. In three dimensions, space groups are classified into 219 distinct types, or 230 types if chiral copies are considered distinct. Space groups are discrete cocompact groups of isometries of an oriented Euclidean space in any number of dimensions. In dimensions other than 3, they are sometimes called Bieberbach groups.

<span class="mw-page-title-main">Bravais lattice</span> Geometry and crystallography point array

In geometry and crystallography, a Bravais lattice, named after Auguste Bravais, is an infinite array of discrete points generated by a set of discrete translation operations described in three dimensional space by

In crystallography, a crystallographic point group is a three dimensional point group whose symmetry operations are compatible with a three dimensional crystallographic lattice. According to the crystallographic restriction it may only contain one-, two-, three-, four- and sixfold rotations or rotoinversions. This reduces the number of crystallographic point groups to 32. These 32 groups are one-and-the-same as the 32 types of morphological (external) crystalline symmetries derived in 1830 by Johann Friedrich Christian Hessel from a consideration of observed crystal forms.

<span class="mw-page-title-main">Fiber diffraction</span> Subarea of scattering, an area in which molecular structure is determined from scattering data

Fiber diffraction is a subarea of scattering, an area in which molecular structure is determined from scattering data. In fiber diffraction the scattering pattern does not change, as the sample is rotated about a unique axis. Such uniaxial symmetry is frequent with filaments or fibers consisting of biological or man-made macromolecules. In crystallography fiber symmetry is an aggravation regarding the determination of crystal structure, because reflections are smeared and may overlap in the fiber diffraction pattern. Materials science considers fiber symmetry a simplification, because almost the complete obtainable structure information is in a single two-dimensional (2D) diffraction pattern exposed on photographic film or on a 2D detector. 2 instead of 3 co-ordinate directions suffice to describe fiber diffraction.

In crystallography, a Wyckoff position is any point in a set of points whose site symmetry groups are all conjugate subgroups one of another. Crystallography tables give the Wyckoff positions for different space groups.

Ralph Walter Graystone Wyckoff, Sr. was an American scientist and pioneer of X-ray crystallography. He was elected member of the National Academy of Sciences in 1949 and Foreign member of the Royal Society, on April 19, 1951.

The International Union of Crystallography (IUCr) is an organisation devoted to the international promotion and coordination of the science of crystallography. The IUCr is a member of the International Council for Science (ICSU).

<span class="mw-page-title-main">Molecular symmetry</span> Symmetry of molecules of chemical compounds

In chemistry, molecular symmetry describes the symmetry present in molecules and the classification of these molecules according to their symmetry. Molecular symmetry is a fundamental concept in chemistry, as it can be used to predict or explain many of a molecule's chemical properties, such as whether or not it has a dipole moment, as well as its allowed spectroscopic transitions. To do this it is necessary to use group theory. This involves classifying the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule. Symmetry is useful in the study of molecular orbitals, with applications to the Hückel method, to ligand field theory, and to the Woodward-Hoffmann rules. Many university level textbooks on physical chemistry, quantum chemistry, spectroscopy and inorganic chemistry discuss symmetry. Another framework on a larger scale is the use of crystal systems to describe crystallographic symmetry in bulk materials.

<span class="mw-page-title-main">Crystallographic image processing</span>

Crystallographic image processing (CIP) is traditionally understood as being a set of key steps in the determination of the atomic structure of crystalline matter from high-resolution electron microscopy (HREM) images obtained in a transmission electron microscope (TEM) that is run in the parallel illumination mode. The term was created in the research group of Sven Hovmöller at Stockholm University during the early 1980s and became rapidly a label for the "3D crystal structure from 2D transmission/projection images" approach. Since the late 1990s, analogous and complementary image processing techniques that are directed towards the achieving of goals with are either complementary or entirely beyond the scope of the original inception of CIP have been developed independently by members of the computational symmetry/geometry, scanning transmission electron microscopy, scanning probe microscopy communities, and applied crystallography communities.

A Euclidean graph is periodic if there exists a basis of that Euclidean space whose corresponding translations induce symmetries of that graph. Equivalently, a periodic Euclidean graph is a periodic realization of an abelian covering graph over a finite graph. A Euclidean graph is uniformly discrete if there is a minimal distance between any two vertices. Periodic graphs are closely related to tessellations of space and the geometry of their symmetry groups, hence to geometric group theory, as well as to discrete geometry and the theory of polytopes, and similar areas.

In mathematics, a rod group is a three-dimensional line group whose point group is one of the axial crystallographic point groups. This constraint means that the point group must be the symmetry of some three-dimensional lattice.

In mathematics, a layer group is a three-dimensional extension of a wallpaper group, with reflections in the third dimension. It is a space group with a two-dimensional lattice, meaning that it is symmetric over repeats in the two lattice directions. The symmetry group at each lattice point is an axial crystallographic point group with the main axis being perpendicular to the lattice plane.

In solid state physics, the magnetic space groups, or Shubnikov groups, are the symmetry groups which classify the symmetries of a crystal both in space, and in a two-valued property such as electron spin. To represent such a property, each lattice point is colored black or white, and in addition to the usual three-dimensional symmetry operations, there is a so-called "antisymmetry" operation which turns all black lattice points white and all white lattice points black. Thus, the magnetic space groups serve as an extension to the crystallographic space groups which describe spatial symmetry alone.

<span class="mw-page-title-main">Ted Janssen</span>

Theo Willem Jan Marie Janssen, better known as Ted Janssen, was a Dutch physicist and Full Professor of Theoretical Physics at the Radboud University Nijmegen. Together with Pim de Wolff and Aloysio Janner, he was one of the founding fathers of N-dimensional superspace approach in crystal structure analysis for the description of quasi periodic crystals and modulated structures. For this work he received the Aminoff Prize of the Royal Swedish Academy of Sciences in 1988 and the Ewald Prize of the International Union of Crystallography in 2014. These achievements were merit of his unique talent, combining a deep knowledge of physics with a rigorous mathematical approach. Their theoretical description of the structure and symmetry of incommensurate crystals using higher dimensional superspace groups also included the quasicrystals that were discovered in 1982 by Dan Schechtman, who received the Nobel Prize in Chemistry in 2011. The Swedish Academy of Sciences explicitly mentioned their work at this occasion.

This is a timeline of crystallography.

<span class="mw-page-title-main">CrystalExplorer</span> Crystal structure analysis software

CrystalExplorer (CE) is a freeware designed to analysis the crystal structure with *.cif file format.

<span class="mw-page-title-main">Dichromatic symmetry</span> Two-colour symmetry (examples, history and dimensional counts)

Dichromatic symmetry, also referred to as antisymmetry, black-and-white symmetry, magnetic symmetry, counterchange symmetry or dichroic symmetry, is a symmetry operation which reverses an object to its opposite. A more precise definition is "operations of antisymmetry transform objects possessing two possible values of a given property from one value to the other." Dichromatic symmetry refers specifically to two-coloured symmetry; this can be extended to three or more colours in which case it is termed polychromatic symmetry. A general term for dichromatic and polychromatic symmetry is simply colour symmetry. Dichromatic symmetry is used to describe magnetic crystals and in other areas of physics, such as time reversal, which require two-valued symmetry operations.

<span class="mw-page-title-main">Polychromatic symmetry</span> Symmetry with three or more colours

Polychromatic symmetry is a colour symmetry which interchanges three or more colours in a symmetrical pattern. It is a natural extension of dichromatic symmetry. The coloured symmetry groups are derived by adding to the position coordinates (x and y in two dimensions, x, y and z in three dimensions) an extra coordinate, k, which takes three or more possible values (colours).

References

  1. http://www.cryst.ehu.es/html/doc/bcs_about.html About the Bilbao Crystallographic Server and its authors.
  2. Wondratchek, Hans (2010). International Tables for Crystallography, Vol. A1: Symmetry Relations Between Space Groups. John Wiley & Sons. ISBN   978-0-470-68908-0.
  3. Hahn, Theo (2010). International Tables for Crystallography, Vol. A: Space-Group Symmetry. John Wiley & Sons. ISBN   978-0-470-66079-9.
  4. http://stokes.byu.edu/magneticspacegroups.html Table of Magnetic Space Groups.
  5. http://www.bk.psu.edu/faculty/litvin/Download.html Archived 2011-11-19 at the Wayback Machine Magnetic Groups.
  6. Web of Science data of articles citing: Aroyo MI; Perez-Mato JM; Capillas C; et al. (2006). "Bilbao crystallographic server: I. Databases and crystallographic computing programs". Zeitschrift für Kristallographie. 221 (1): 15–27. doi:10.1524/zkri.2006.221.1.15.
  7. Web of Science data of articles citing: Aroyo MI; Kirov A; Capillas C; et al. (2006). "Bilbao crystallographic server. II. Representations of crystallographic point groups and space groups". Acta Crystallographica A. 62 (2): 115–128. CiteSeerX   10.1.1.433.5991 . doi:10.1107/S0108767305040286. PMID   16489249.
  8. A list of theses mentioning the Bilbao Crystallographic Server.
  9. A list of theses based directly on the applications hosted by the Bilbao Crystallographic Server.
  10. A list of Bilbao Crystallographic Server related articles.
  11. A selected list of conferences in which, work from Bilbao Crystallographic Server has been represented .
  12. Kroumova E, Perez-Mato JM, Aroyo MI (1998). "WYCKSPLIT: a computer program for determination of the relations of Wyckoff positions for a group-subgroup pair". J. Appl. Crystallogr. 31 (4): 646. doi:10.1107/S0021889898005524.
  13. Ivantchev S, Kroumova E, Madariaga G, Perez-Mato JM, Aroyo MI (2000). "SUBGROUPGRAPH - a computer program for analysis of group-subgroup relations between space groups". J. Appl. Crystallogr. 33 (4): 1190–1191. doi:10.1107/S0021889800007135.
  14. Kroumova E, Aroyo MI, Perez-Mato JM, Ivantchev S, Igartua JM, Wondratschek H (2001). "PSEUDO: a program for a pseudosymmetry search". J. Appl. Crystallogr. 34 (6): 783–784. doi:10.1107/S0021889801011852.
  15. Ivantchev S, Kroumova E, Aroyo MI, Perez-Mato JM, Igartua JM, Madariaga G, Wondratschek H (2002). "SUPERGROUPS: a computer program for the determination of the supergroups of the space groups". J. Appl. Crystallogr. 35 (4): 511–512. doi:10.1107/S002188980200732X.
  16. "About the Bilbao Crystallographic Server", Bilbao Crystallographic Server's official wiki entry.