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First Time User Guide to Crystal Viewer Tool on nanoHUB.org

First Time User Guide to Crystal Viewer Tool on nanoHUB.org. Abhijeet Paul Sebastian Steiger Ben Haley Gerhard Klimeck NCN @ Purdue University West Lafayette, IN 47906, USA. Topics Discussed. What are crystals ? How are they represented ? Basics of crystallography :

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First Time User Guide to Crystal Viewer Tool on nanoHUB.org

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  1. First Time User Guide toCrystal Viewer Toolon nanoHUB.org Abhijeet Paul Sebastian Steiger Ben Haley Gerhard Klimeck NCN @ Purdue University West Lafayette, IN 47906, USA

  2. Topics Discussed • What are crystals ? • How are they represented ? • Basics of crystallography : • Lattice vectors, primitive cells, unit cells • Bravais lattices, Miller indices and planes • What is Crystal Viewer? • Features • Capabilities • A first look at the tool • Screenshots • What happens when you just hit SIMULATE? visualize Silicon crystal • Example for triclinic lattice simulation • References • Tool History • Appendix: Bravais lattices and Miller planes

  3. Crystals

  4. What Are Crystals? • Crystalsare • Periodic arrangement of atoms in space • 1D, 2D or 3D arrangements • Simplest periodic block can be a single atom • Eg: Copper, Gold, Silver, Iron, etc. ∞ ∞ 2D Lattice 1D Lattice 3D Lattice

  5. Representation of Crystals • Crystal is represented by • Lattice: Points in space repeated periodically • Basis :Group of atoms repeated at each lattice point. LATTICE CRYSTAL BASIS here: GRAPHENE

  6. Steps to Construct a Crystal • Basis& Lattice together form the crystal. • A basis can have one or more atoms • In the last slide the basis had 2 atoms. • Translate the basis in the space (at lattice points) to obtain the crystal structure. • T = La1+ Ma2 + Na3T= Translational vector, L,M,N => integers • a1,a2 & a3 are called Latticevectors orBravaisvectors. • LatticeVectors are not unique: Three different lattice vectors produce the same lattice structure. a1 a1 a2 a2 a2 a1

  7. Crystallography : About the Basis… • Basis:Can be as simple as one atom, or a complex many atom system. • The volume belonging to a single copy of a basis is also called a unit cell or simply a cell. • The unit cell with minimum volume is the primitive cell, and the corresponding basis has a minimal number of atoms: primitive basis. • Atoms are linked together using bonds. 2 atom basis (e.g. Graphene) 1 atom basis 4 atom basis (e.g. Wurtzite) bond

  8. Miller Planes and Indices • Miller indices are method to describe planes and directions in crystals. • They are three integers l, m, n which together give a (real-space) lattice vector: T= la1+ ma2+ na3 • Negative integers are represented by with a bar on top of the number. • (lmn) represents a Miller planeperpendicular to T. • [lmn] denotes a directionparallel to T. • <lmn> denotes the family of directions which are crystallographically equivalent to [lmn]. • {lmn} denotes the family of planes which are crystallographically equivalent to (lmn). [110] [111] Images obtained from Crystal Viewer tool on nanoHUB.org

  9. Crystal Viewer the nanoHUB.org tool

  10. What is Crystal Viewer? • Visualize: • 3D crystals of different materials • Miller planes of crystals • All 14 possible Bravais lattices in 3D • Carbon-based 2D (graphene), 1D (nanotubes) and 0D (buckyballs) materials • Download the crystal structure in PDB file format • Get information on lattice vectors, atomic positions etc.

  11. Crystal Viewer Tool : First look • Two types of simulations: • Visualize crystal of a specific material • Visualize one of 14 Bravais lattices These options depend on what is chosen on the top Press “Simulate” when done with the options

  12. Output: Unit cell Miller plane visualized in a periodically repeated unit cell Crystal information (text) Crystals of Materials Materials are grouped w.r.t their lattice structure Turn Miller plane visualization on/off By default, the visualized unit cell will also contain atoms from neighboring unit cells which lie at the boundary. Check to exclude these atoms.

  13. Output: Carbon structure Crystal information (text) Crystals of Materials: Carbon Meshes 2D-periodic graphene (1 sheet) or graphite (>1 sheets) C60 molecules (buckyballs) (nonperiodic) 1D-periodic carbon nanotubes

  14. Output: Unit cell Unit cell repeated in all directions Miller plane visualized in a periodically repeated unit cell Crystal information (text) Bravais lattices 14 Bravais lattices are grouped into 7 lattice systems Set size of Bravais vectors (choice depends on what lattice is selected) Turn output (2) on/off Turn output (3) on/off

  15. What happens when you just hit “SIMULATE”? Default Output: Default Input: Images from Crystal Vieweron nanoHUB.org • Simulate the Silicon crystal • Show [100] Miller plane useful for bug reports and reproduction of results

  16. Bravais lattice simulation : Input to Output INPUT OUTPUT Triclinic unit cell Side lengths Angles between Bravais vectors # repetitions of unit cell in every direction Larger grid size Note: the diagonal bonds should not be there. Images obtained from Crystal Vieweron nanoHUB.org

  17. References • Link to the tool: • http://nanohub.org/tools/crystal_viewer • Homeworkassignment using the tool: • https://nanohub.org/resources/4200  Use the tool to learn about crystals.  Feel free to post about: • bugs • new features you want  Contact the developers in case you want to collaborate for some work using this tool.

  18. History of the Tool Crystal Vieweris an ongoing outreach effort by the Klimeck group @Purdue: • Developers up to version 1.23 (based on MATLAB®):Abhijeet Paul, Victoria Savikhin • Starting with v2.0: NEMO5 simulation engine by Sebastian Steiger, Michael Povolotskyi, TillmannKubisand Hong-Hyun Park. Material database by Ben Hailey.Special credits go to Michael for the general lattice construction and the input parser, and Sebastian for the implementation of all necessary crystal structures, PDB output and testing the new tool. • The tool was hooked up with NEMO5 by Sun Xingshu under the supervision of Sebastian. • General supervision: Gerhard Klimeck. • Last update of this document: May 2011

  19. Additional Material

  20. References • URLs on crystal information, miller indices & Bravaislattices: • http://cst-www.nrl.navy.mil/lattice/ • http://en.wikipedia.org/wiki/Bravais_lattice • http://serc.carleton.edu/research_education/crystallography/xldatabases.html • http://webmineral.com/ • http://en.wikipedia.org/wiki/Miller_index • Book about crystals (and solid-state physics): • Kittel, Charles (1996) [1953]:Introduction to Solid State Physics (Seventh Edition ed.). New York: John Wiley & Sons. pp. 10. ISBN 0-471-11181-3. http://www.wiley.com/

  21. Appendix A : Bravais lattices S: simple B: body centered F: face centered E: end face centered

  22. Appendix B: Miller Planes & Directions Some Important Miller directions Some Important Miller planes Images from http://en.wikipedia.org/wiki/Miller_index Author: Christophe Dang Ngoc Chan

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