1.1 Introduction to Crystal Structures

Understanding Crystal Structures

http://engineering.unt.edu/materials/sites/default/files/scharf/MTSE%203010/Class8_handout%20MTSE%203010%202013.pdf

Tri-clinic simulation boxes

http://lammps.sandia.gov/doc/Section_howto.html#howto_12

Lattice Transformations

Hexagonal to Orthohexagonal

Sometimes it is more convenient to reprepresent a hexgaonal crystal structure in a projection normal to the c axis. A good way to do this is to transform an orthohexagonal cell.

a'=a+b

b'=-a+b

c'=c

Therefore, the transformation matrices are

hexagonal to orthohexagonal
- T=(0.5 -0.5 0.0 / 0.5 0.5 0 / 0 0 1)
- For CrystalMaker, use (1 -1 0/ 1 1 0/0 0 1)
S=(1,1,0/-1 1 0/0 0 1)

Searching for Ideal Bulk Crystal Structures (no defects)

The starting point for creating most structure files is identifying crystal structures without defects. I've found that getting reliable structure files can be somewhat problematic.

Crystallography Open Database

Originally setup by Professor Armel Le bail, and now with an international board of editors, this database contains over 48,000 entries, which can be freely downloaded in the CIF format.

Link to COD

MSA Crystal Structure Database

This site is an interface to a crystal structure database that includes every structure published in the American Mineralogists, The Canadian Mineralogists, European Journal of Minerology and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The database is maintained under the case of the Mineralogical Society of America and the Mineralogical Association of Canada, and financed by the National Science Foundation.Make sure to choose the .cif datafile

Link to AMC Crystal Structure Database

MatNavi

Link to MatNavi

Developing Crystal Structures

Vesta

I use Vesta quite a bit because it generates POSCAR files from .cif files. Otherwise, it is somewhat limited.

Link to Vesta

Crystal Maker

http://www.crystalmaker.com/

Grain Boundary Studio

http://staff.aist.go.jp/h.ogawa/GBstudio/indexE.html

Understanding Crystal Structures

http://ocw.mit.edu/courses/earth-atmospheric-and-planetary-sciences/12-108-structure-of-earth-materials-fall-2004/lecture-notes/lec7.pdf

Structure Conversion Files

This is a pretty sharp tool for converting a .cif file into a lammps file.

http://physics.bu.edu/~erikl/research/tools/crystals/read_cif.py

Making POSCAR files

To make POSCAR files for VASP, I usually export a .cif file in Crystal Maker then convert that file into a POSCAR file in VESTA.

Making LAMMPS Files

Viewing Structures

Atomeye

If you are using Windows, you an XWindows clients such as Xming

Potentials

http://www.ucl.ac.uk/klmc/Potentials/

Stacking Faults

In crystallography, a stacking fault is a type of defect which characterizes the disordering of crystallographic planes. They are local regions of incorrect stacking of crystal planes associated with the presence of partial dislocations.

A stacking fault produced by vacancy agglomeration as an intrinsic stacking fault.

A stacking fault produced by interstitial agglomeration as an extrinsic stacking fault.

Unstable stacking fault

[1] LAMMPS stacking fault energy.

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