Crystal Data Entry Example

Example 1: Crystal Data File Creation

On this page we explain how to generate a crystal structure input file using the command line program EMmkxtal. This can also be done via the EMsoftWorkbench GUI.

Gathering all the necessary parameters

Before you can generate a crystal structure input file, you need to find the following pieces of information from the literature:

• Chemical Formula: this will be useful to generate the filename.
• Crystal system: cubic, tetragonal, hexagonal, orthorhombic, rhombohedral, monoclinic or anorthic (triclinic).
• Lattice Parameters: depending on the crystal system, you may only need one parameter, or all six.
• Space group number: a number between 1 and 230; EMsoft uses the International Tables for Crystallography, Volume A, for all crystallographic conventions. Only standard settings are available for the space groups, but some space groups may have two origin settings.
• Atom coordinates: these are fractional coordinates, and you will need one triplet for each atom in the asymmetric unit.
• Site occupation parameters: in the range [0..1], these parameters describe the occupation of each lattice site. Generally, those numbers are set to 1.0.
• Debye-Waller factors: for each atom in the asymmetric unit, we also need the value of the isotropic Debye-Waller factor in units of nm^2. If this factor is not known for your material, then you will need to set a reasonable value; experience has shown that a value in the range [0.004,0.006] is almost always resonable.

For this example, we will use the structure of Nickel, which has a lattice parameter of 0.35236 nm and belongs to space group 225 (Fm-3m). The asymmetric unit consists of only one atom, Ni, with atomic number 28, at position (0.0,0.0,0.0), full site occupation of 1, and a Debye-Waller factor of 0.0035 nm^2 at room temperature. [For a listing of DW factors for elemental crystals, a good reference is: L.-M. Peng, G. Ren, S.L. Dudarev, and M.J. Whelan. Debye–Waller Factors and Absorptive Scattering Factors of Elemental Crystals. Acta Crystall. A, 52:456–470, 1996]

Entering the data using coordinate triplets

From the command line, start the EMmkxtal program. The program will print out a few messages and then asks for the crystal system:

 Select the crystal system :
  1. Cubic
  2. Tetragonal
  3. Orthorhombic
  4. Hexagonal
  5. Trigonal
  6. Monoclinic
  7. Triclinic

 Note about the trigonal system:
 -------------------------------
 Primitive trigonal crystals are defined with respect to a HEXAGONAL
 reference frame.  Rhombohedral crystals can be referenced with
 respect to a HEXAGONAL basis (first setting), or with respect to
 a RHOMBOHEDRAL basis (second setting).  The default setting for
 trigonal symmetry is the hexagonal setting.  When you select
 crystal system 5 above, you will be prompted for the setting.


  crystal system ---> 

In this case, we have a cubic crystal structure, so enter the value 1. Then the program will ask for the necessary lattice parameter(s), in this case only one:

Enter lattice parameters
     a [nm] = 

Enter the value 0.35236; then the program will list all the cubic space groups along with their sequential numbers for the cubic crystal system:

 195: P 2 3      196: F 2 3      197: I 2 3      198: P 21 3    
 199: I 21 3     200: P m 3      201: P n 3      202: F m 3     
 203: F d 3      204: I m 3      205: P a 3      206: I a 3     
 207: P 4 3 2    208: P 42 3 2   209: F 4 3 2    210: F 41 3 2  
 211: I 4 3 2    212: P 43 3 2   213: P 41 3 2   214: I 41 3 2  
 215: P -4 3 m   216: F -4 3 m   217: I -4 3 m   218: P -4 3 n  
 219: F -4 3 c   220: I -4 3 d   221: P m 3 m    222: P n 3 n   
 223: P m 3 n    224: P n 3 m    225: F m 3 m    226: F m 3 c   
 227: F d 3 m    228: F d 3 c    229: I m 3 m    230: I a 3 d   
 --------------------------
  Enter space group number : 

Enter the value 225. If the selected space group has two origin settings, then this is the point where you would be asked to select setting 1 or 2. Then you will see a periodic table with the atomic numbers and chemical symbols. For each atom in the asymmetric unit, you will first be asked for the atomic number:

 Enter atoms in asymmetric unit

 ------------------------------------ Periodic Table of the Elements --------------------------------------

1:H                                                                                                    2:He
3:Li  4:Be                                                               5:B   6:C   7:N   8:O   9:F  10:Ne
11:Na 12:Mg                                                             13:Al 14:Si 15:P  16:S  17:Cl 18:Ar
19:K  20:Ca 21:Sc 22:Ti 23:V  24:Cr 25:Mn 26:Fe 27:Co 28:Ni 29:Cu 30:Zn 31:Ga 32:Ge 33:As 34:Se 35:Br 36:Kr
37:Rb 38:Sr 39:Y  40:Zr 41:Nb 42:Mo 43:Tc 44:Ru 45:Rh 46:Pd 47:Ag 48:Cd 49:In 50:Sn 51:Sb 52:Te 53: I 54:Xe
55:Cs 56:Ba ----- 72:Hf 73:Ta 74:W  75:Re 76:Os 77:Ir 78:Pt 79:Au 80:Hg 81:Tl 82:Pb 83:Bi 84:Po 85:At 86:Rn
87:Fr 88:Ra -----
57:La 58:Ce 59:Pr 60:Nd 61:Pm 62:Sm 63:Eu 64:Gd 65:Tb 66:Dy 67:Ho 68:Er 69:Tm 70:Yb 71:Lu
89:Ac 90:Th 91:Pa 92:U
 ----------------------------------------------------------------------------------------------------------
  ->  Atomic number : 

Enter 28 for Nickel. Then you will see:

 ->  Fractional coordinates, site occupation, and Debye-Waller Factor [nm^2] : 

Enter the five (floating point) numbers, separated by commas: 0.0,0.0,0.0,1.0,0.0035. The program then asks if you want to add another atom to the asymmetric unit:

  ->  Another atom ? (y/n) 

For fcc Nickel, there are no additional atoms, so enter n; if there were additional atoms, the program will prompt you for the next atomic number, then the coordinates, and so on until all atoms have been entered. Then you will see the following prompt:

Enter output file name (*.xtal)

Enter Ni.xtal; for more complex structures you should pick a file name that describes the chemical formula and perhaps the structure name. For instance, for TiO2 in the rutile form, you could select TiO2-rutile.xtal as the filename. Note that all the structure files are placed in a single location set by the EMsoftXtalFolderName configuration variable.

Entering the data using Wyckoff positions

From the command line, start the EMmkxtal program with the option -w; this will tell the program to use the Wyckoff special positions to enter atom coordinates. [Note that this option is not yet available through the EMsoftWorkbench GUI] Instead of asking for the atom coordinates, the program will list the available Wyckoff positions and ask you to pick one; for the space group 225, the program would list (after the Periodic Table):

Wyckoff positions for space group 225
-------------------------------------
4a ( 0, 0, 0 )
4b ( 1/2, 1/2, 1/2 )
8c ( 1/4, 1/4, 1/4 )
24d ( 0, 1/4, 1/4 )
24e ( x, 0, 0 )
32f ( x, x, x )
48g ( x, 1/4, 1/4 )
48h ( 0, y, y )
48i ( 1/2, y, y )
96j ( 0, y, z )
96k ( x, x, z )
192l ( x, y, z )
 WPstring : DaaaDbbbFcccKaccKxaaLxxxNxccNayyNbyyPayzPxxzQ
  ->  Atomic number, site occupation, Debye-Waller factor : 

Enter the values 28, 1.0, 0.0035; then you will see the prompt:

->  Wyckoff position : 

and you should enter 4a for Nickel. In this case, no coordinate values need to be entered, but in other cases, the program will prompt for any necessary fractional coordinates. Note that the WPstring listed above is just informational; this is how all the Wyckoff positions are encoded in the program (one such string for each space group). The remainder of the program execution is similar to the description in the previous section. This concludes the example.