Symmetry and Crystallographic web tools. Practical session.

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May 14, 2013

Symmetry and Crystallographic web tools. Practical session.



May 14, 2013


  1. Zaragoza, May 2013 Symmetry and Crystallographic web tools. Practical session.

    Miriam Marqués Arias MALTA-Consolider Team and Dpto. de Química Física Universidad de Oviedo
  2. Zaragoza, May 2013 Where to look for crystal structures? •

    ICSD (Inorganic Crystal Structure Database) http://www.fiz-; NAVY • Crystallography Open Database How to visualize them? • VESTA (Visualization for Electronic and Structural Analysis) • XCrysDen (X-window CRYstalline Structures an DENsities) Some useful crystallographic webs
  3. Zaragoza, May 2013 Where to find crystallographic and solid state

    programs and utilities free of charge? • Bilbao Crystallographic Server • ISOTROPY Bilbao Crystallographic Server Database from International Tables for Crystallography (Volumes A, A1,E)+ database on incommensurate structures, and a k-vector database with Brillouin-zone figures and classification tables of the wave vectors. Some useful crystallographic webs
  4. Zaragoza, May 2013 Bilbao Crystallographic Server

  5. Zaragoza, May 2013 Tools gathered into shells with a common

    application field related to group theory, crystallography and solid-state physics applications. Interface tabulated data. Standard and default settings. Input: space group number. GENPOS: generators and general positions in different settings. Bilbao Crystallographic Server
  6. Zaragoza, May 2013 WYCKPOS: lists the Wyckoff positions with Wyckoff

    letters, multiplicities and symbols of the site-symmetry groups. HKLCOND: gives access to general and special reflection conditions. MAXSUB: gives access to the maximal subgroups of a given SG, characterized by the index and transformation matrix- column pair (P, p) that relates the standard bases of group and subgroup. KVEC: wave-vector database and Brillouin zone figures. (CDML: primitive reciprocal vectors, ITA: conventional reciprocal vectors). Different lattice parameters relations can lead to different Brillouin-zone figures. Time for exercises 1, 2 and 3. Bilbao Crystallographic Server

    all, read the basics on subgroup-group relationships... SUBGROUPGRAPH: retrieves all possible group-subgroup chains of intermediate maximal subgroups that relate the group G and the subgroup H and a graphical representation. Example: group-subgroup relations between G=P622 No. 177, and H=C2, No. 5. a) without index: table with the possible intermediate space groups and the indices. b) with index: the matrix transformations are also given. WYCKSPLIT: lists the splittings of the Wyckoff positions from G to H. You need to know the matrix transformation. Bilbao Crystallographic Server
  8. Zaragoza, May 2013 CELLSUB: determines and clasifies all subgroups H

    compatible with a specific multiple of the unit cell of G (ik index). COMMONSUBS: searches for common subgroups H between two space groups G1 and G2 without group- subgroup relation. Input: G1,G2,Z1,Z2 and index (the number of formula units in H is the same for both structures). Go to exercise 4 APPLICATION: STUDY OF PHASE TRANSITIONS Based on symmetry aspects: 1) Group-subgroup related: structures related by small atomic displacements (displacive in Buerger’s notation). Bilbao Crystallographic Server
  9. Zaragoza, May 2013 An order parameter η measures the distance

    of the low symmetry to the high-symmetry (η=0) structure. The low-symmetry phase approaches the transition to higher symmetry continuously. T-driven transition: usually the symmetry of the l.t. phase is a subgroup of that of the h.t. phase. p-driven transition: not known. Bilbao Crystallographic Server
  10. Zaragoza, May 2013 2) No group-subgroup related: the transition is

    quite abrupt (reconstructive) (no order parameter). One phase transits in a continuous way to the other following a transition path (atomic displacements + lattice strains). Transition involves an intermediate structure whose space group is subgroup of the two end phases. Order parameter or reaction coordinate: a degree of freedom of the intermediate structure. Symmetry restrictions: 1) The number of formula units of the intermediate structure can not change along the path. 2) Atoms must remain in the same types of Wyckoff positions along the path. Bilbao Crystallographic Server
  11. Zaragoza, May 2013 Structural conditions: Transformations with smaller atomic displacements

    and lattice strains are in general favoured (read the notes on structural analysis of a transition). Energetics: A symmetry analysis cannot predict the energetically most favourable transition path. It requires to explore the energy landscape and, in particular, the energy barrier that separates both phases. 1) A crude approximation: interpolation of the structural parameters (defined in the intermediate structure) of the limit phases and calculation of the Gibbs free energy along the path. Bilbao Crystallographic Server
  12. Zaragoza, May 2013 2) Choice of a parameter of order

    (atomic coordinate, lattice parameters ratio...). Example: B3/B1 phase transition in Zn0, ZnS and SiC under p. B3: zinclende (F4-3m) Z=4; M ¼ ¼ ¼ (4c) X 0,0,0 (4a) aI B1: rocksalt (Fm-3m) Z=4; M ½ ½ ½ (4b) X 0,0,0 (4a) aII Intermediate state: R3m Z=1 M x,x,x (3a) X 0,0,0 (3a) Order parameter x(M) (¼ -- ½) B3: aR =aI /2 αR = 60º B1: aR =aII /2 αR = 60º Go to exercises 5, 6 and 7. Bilbao Crystallographic Server
  13. Zaragoza, May 2013 TRANPATH: finds common subgroups H between two

    space groups G1 and G2 without group-subgroup relation. (COMMONSUBS). Every path is checked for compatibility of the Wyckoff position splittings (WYCKSPLIT). The WP’s occupied by a given atom in G1 and G2 must give rise to the same WP por that atom in H. The lattice strain (STRAIN) and atomic shifts are compared to threshold values. INPUT: Z1,Z2, description of the G1 and G2 structures (space group, lattice parameters, number, type and coordinates of atomic positions, maximum strain and atomic shifts allowed and maximum cell multiplication. Go to exercise 8 and 9. Bilbao Crystallographic Server
  14. Zaragoza, May 2013 APLICATION: Γ-POINT VIBRATIONAL MODES SAM: access to

    irreducible representations of the Γ-point vibrational modes. In a crystal, 3n phonons (n= number of atoms in the primitive cell), 3 acoustic ones. site species for atomic displacements (Tx,Ty,Tz) in site group Bilbao Crystallographic Server site species for lattice vibrations in the crystal Γcrys= Γeq. set 1 + Γeq. set 2 + ….. Γvib = Γcrys - Γacous INPUT: space group (factor group) and occupied WPs. CORRELATION TABLES
  15. Zaragoza, May 2013 Example: Vibrational modes for C3 N4 (spinel).

    Fd-3m, N, Ct and Co at 32e, 8a and 16d sites, respectively. Point group Raman act. Species IR active Bilbao Crystallographic Server
  16. Zaragoza, May 2013 A 3D visualization package for electronic &

    structural analysis. Developers: Koichi Momma & Fujio Izumi. Runs on Windows, Mac OS X and Linux. Input files: 42 formats: CIF, ICSD, PDB...Output in *.VESTA format. Exports graphic-data files. To run just type VESTA in the folder containing the executable. It opens the MAIN WINDOW consisting of: Menu bar: “File”, “Edit”, “View”, “Objects”, “Utilitites”, “Help”. Horizontal bar: tools for viewing along axis, rot+trans Vertical bar: tools for selecting atoms, distances, angles... Graphical area: the structures are displayed. Text area: information on the structures. VESTA
  17. Zaragoza, May 2013 Giving phase data: “File” menu New structure

    (to create a new structure) or Open (to edit a given structure). A dialog box appears with several tabs. Unit cell tab: lattice parameters & symmetry. Clicking the Option button a transformation matrix can be selected. Structure parameters tab: symbols, labels, charges, x,y,z, occupancies of atoms. To search for bonds: Edit Bonds. To add a new bond specification, click the New botton, select atoms to bond and minimun and maximum lenghts. Several searches modes Lattice planes: Edit Lattice planes. VESTA
  18. Zaragoza, May 2013 To create coordination polyhedra: The “Search A2

    bonded to A1” or “Search atoms bonded to A1” should be selected. A1: central atom. Objects tab: Structural models: ball-stick, space filling polyhedra..... Properties: General (unit cell, axis...), atoms (resolution, atom style, radius, color), bonds(resolution, style), polyhedra (types), isosurfaces (isosurface level). “File” menu and: Save (.VESTA) format, export images (raster, vector). Go to exercises 9 and 10. VESTA
  19. Zaragoza, May 2013 CP localization and basin integrations are applicable

    to • Molecular crystals • Ionic compounds • Metals • Covalent solids ELF: Implementation in solids
  20. Zaragoza, May 2013 Well differentiated chemical ELF objects: the molecules.

    Lewis picture:  Carbon core, K-shell  Double bond, B(C=O). Multiplicity determined by the number of basins, not the charge  Oxygen core, K(O)  Oxygen lone pairs, LP(O). O-C=O↔O=C=O 53% 47% - + Implementation in solids
  21. Zaragoza, May 2013 Topology of ELF in ions enables to

    define Ionic properties (superbasins) →similar to QTAIM Absence of bond basins Only closed-shell basins, spherical and complete charge transfer :  K(Na) (≈2 ē),L(Na) (≈8 ē)  K(F) (≈2 ē),L(F) (≈8 ē) Implementation in solids
  22. Zaragoza, May 2013 Implementation in solids 3D network of bonded

    atoms Metallic bond is shared interaction: • Flat ELF profile • Low population, multicentric