3. Building the first crystal

There are several perfect crystal structures text files (.txt) that comes with jems. It is conceivable that the user will not find in this small library of structures the one he is looking for. When he is interested in crystal defects, jems does not, for sure, contain it. The user must then describe the unit cell parameters, the space-group or symmetry elements and the atoms position within an orbit. This description must be unambiguous in order to get useful results out of jems. A little knowledge of crystallography is assumed in what  follows. These pages describes the steps required to setup a new crystal structure. 3-D models using are drawn using the java3D API.

3.1 Perfect unit cell

Clicking on the jems icon, should start the application and open the following window (figure 3.1). The toolbox contains menus short cuts to open a crystal file,, print the crystal file, , save a crystal file,, define an atom,, the RPS Code,,  the space-group,, to draw a diffraction pattern,, a perspective view,, a stereogram,, a transfer function,, open the microscope dialogue,, the specimen dialogue, and the copyright,! Not all tools are available when there is no crystal defined.

Figure 3.1

The file menu that is used to load a crystal file  is activated using the mouse or Alt+F or using the small folder icon. Each icon comes with a little tip text that explains briefly its use. The tip text appears when the mouse is left a few seconds on the icon. In order to create a new crystal file atoms must be placed in a unit cell, the cell lattice parameters and the Regular Point System code or the space-group must be defined. The RPS code defines the orbit of an atom placed at position (x, y, z). The range of the atom coordinates is [0.0, 1.0[. 

For example to define the GaAs unit cell, one clicks on the atom icon in order to activate the Atom definition dialog that holds the list of the unit cell atoms (one per orbit). Figure 3.2 shows this dialog.

     

Figure 3.2

The dialog contains an empty list of atoms , a status line, 4 little buttons used to add one atom, suppress a selected atom, suppress all atoms of the list and modify a selected atom. The Add, Replace and Cancel buttons are used to add the atoms of the list to the unit cell, replace the atoms of the unit cell by those of the or to cancel the atom definition respectively.

Clicking on the "+" button will activate the "Atom editor dialog" (figure 3.3):

Figure 3.3

This dialog allows to specify the atom kind, Wicknoff notation, x, y, z coordinates, Debye-Waller temperature factor, site occupancy and an absorption factor. For GaAs two atoms must be defined:

The As atom is easily defined indeed, and added to the list of the Atom definition dialog. A status message is displayed in a text input field that can also be used to directly enter the atom parameters.

Figure 3.4

The fractional coordinates of the As atom can be directly entered in the x, y and z text input field (do not forget to press the Enter key after each coordinate). Pressing the Done button will quit this dialog and just defined atoms in the list of the Atom definition dialog.

Figure 3.5

Pressing the Add button will close this dialog and will make the just defined list of atoms appears on the main jems window as a list and a 3-D drawing (figure 3.6):

Figure 3.6

It is now time to define the unit cell parameters and the space-group. For GaAs the unit cell is cubic with a=0.569 nm and the space-group is F-43m. The Space-group selection dialog is shown on figure 3.7:

Figure 3.7

Selecting "Cubic", the list of the cubic space-group is displayed (figure 3.8):

Figure 3.8

Centric space-groups are grouped in the first box, non-centric in the second box. The F-43m space-group is selected and a defined. Pressing the "OK" button will terminate the description of GaAs. As a result the list of all the atoms in the unit cell as well as a 3-D drawing appear on the main jems window (figure 3.9):

Figure 3.9

Now all the menus items and icons are active. It is time to save the newly created crystal file. These files are plain-text files that can be edited and/or modified using a text editor.

file|C:\JavaCW\jData\Cubic\GaAs.txt
system|cubic
HMSymbol|216|24|0|0| F -4 3 m 
rps|0| x , y , z 
rps|1| x , -y , -z 
rps|2| -x , y , -z 
rps|3| -x , -y , z 
rps|4| y , z , x 
rps|5| -y , -z , x 
rps|6| y , -z , -x 
rps|7| -y , z , -x 
rps|8| z , x , y 
rps|9| -z , x , -y 
rps|10| -z , -x , y 
rps|11| z , -x , -y 
rps|12| y , x , z 
rps|13| -y , x , -z 
rps|14| y , -x , -z 
rps|15| -y , -x , z 
rps|16| z , y , x 
rps|17| -z , -y , x 
rps|18| -z , y , -x 
rps|19| z , -y , -x 
rps|20| x , z , y 
rps|21| x , -z , -y 
rps|22| -x , -z , y 
rps|23| -x , z , -y 
lattice|0|0.5690
lattice|1|0.5690
lattice|2|0.5690
lattice|3|90.0000
lattice|4|90.0000
lattice|5|90.0000
atom|0|Ga,a,0.0000,0.0000,0.0000,0.0050,1.0000,0.0520
atom|1|As,a,0.2500,0.2500,0.2500,0.0050,1.0000,0.0540
aff|0|Ga|2.321,65.602,2.486,15.458,1.688,2.581,0.599,0.351|Doyle - Turner Acta Cryst. A24 (1968),390
aff|1|As|2.399,45.718,2.79,12.817,1.529,2.28,0.594,0.328|Doyle - Turner Acta Cryst. A24 (1968),390

The following tags are recognized:

file filename of the crystal file.
system crystal system (triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic)
HMSymbol Hermann-Mauguin symbol of the space-group
rps regular point system (orbit)
lattice lattice parameters (0 : a, 1 : b, 2 : c, 3 : a, 4 : b, 5 : g) (a, b, c in nm)
atom atom symbol, Wickhoff notation, x, y, z, Debye-Waller, occupancy, absorption
aff atomic form factor

The line starting with the HMSymbol tag contains the space-group number, the number of RPS code, a flag (0 for non-centric unit cells, 1 for centric), a second flag for alternate setting and the Hermann-Mauguin symbol. A vertical bar separates the various fields of the line.

In the particular case of GaAs, the regular point system code is not really necessary for the F centered unit cell is the only absolutely required information. The same crystallographic information could have been obtained by directly entering the RPS code (figure 3.10):

Figure 3.10

Using this dialog, the RPS code can be reduced to just "x ; y ; z" using the "C" button (figure 3.11):

Figure 3.11

The crystal file is then simply:

file|C:\JavaCW\jData\Cubic\GaAs.txt
system|cubic
HMSymbol|0|1|0|2| F centered
rps|0| x , y , z 
lattice|0|0.5690
lattice|1|0.5690
lattice|2|0.5690
lattice|3|90.0000
lattice|4|90.0000
lattice|5|90.0000
atom|0|Ga,a,0.0000,0.0000,0.0000,0.0050,1.0000,0.0520
atom|1|As,a,0.2500,0.2500,0.2500,0.0050,1.0000,0.0540
aff|0|Ga|2.321,65.602,2.486,15.458,1.688,2.581,0.599,0.351|Doyle - Turner Acta Cryst. A24 (1968),390
aff|1|As|2.399,45.718,2.79,12.817,1.529,2.28,0.594,0.328|Doyle - Turner Acta Cryst. A24 (1968),390

Now the space-group number is 0, there is one RPS code, non centric space-group, space-group defined using RPS code (2) and finally the Bravais lattice.

 

3.2 Defects

At present, there is no tool to help create crystalline defects. Nevertheless, the same crystal file structure can be used to enter crystal defects. The S5 <310> grain boundary in Au is defined as:

file|G:\JavaCW\jData\AuSigma53.txt
system|triclinic
HMSymbol|1|1|0|0| P 1 
rps|0| x , y , z 
lattice|0|1.6610
lattice|1|0.6430
lattice|2|0.4070
lattice|3|90.0000
lattice|4|90.0000
lattice|5|90.0000
atom|0|Au,a,0.0000,0.0000,0.0000,0.0049,1.0000,0.0340
atom|1|Au,a,0.0000,0.0000,0.0000,0.0049,1.0000,0.0340
atom|2|Au,a,0.4010,0.0110,0.0000,0.0049,1.0000,0.0340
atom|3|Au,a,0.1550,0.1890,0.0000,0.0049,1.0000,0.0340
atom|4|Au,a,0.8400,0.1890,0.0000,0.0049,1.0000,0.0340
atom|5|Au,a,0.3150,0.4110,0.0000,0.0049,1.0000,0.0340
atom|6|Au,a,0.6810,0.3890,0.0000,0.0049,1.0000,0.0340
atom|7|Au,a,0.5000,0.5440,0.0000,0.0049,1.0000,0.0340
atom|8|Au,a,0.0780,0.6000,0.0000,0.0049,1.0000,0.0340
atom|9|Au,a,0.9180,0.6000,0.0000,0.0049,1.0000,0.0340
atom|10|Au,a,0.2370,0.8000,0.0000,0.0049,1.0000,0.0340
atom|11|Au,a,0.7590,0.7890,0.0000,0.0049,1.0000,0.0340
atom|12|Au,a,0.5990,0.9890,0.0000,0.0049,1.0000,0.0340
atom|13|Au,a,0.2720,0.0890,0.5000,0.0049,1.0000,0.0340
atom|14|Au,a,0.7180,0.0430,0.5000,0.0049,1.0000,0.0340
atom|15|Au,a,0.0390,0.2890,0.5000,0.0049,1.0000,0.0340
atom|16|Au,a,0.4220,0.2890,0.5000,0.0049,1.0000,0.0340
atom|17|Au,a,0.5730,0.3000,0.5000,0.0049,1.0000,0.0340
atom|18|Au,a,0.9530,0.3000,0.5000,0.0049,1.0000,0.0340
atom|19|Au,a,0.1930,0.4890,0.5000,0.0049,1.0000,0.0340
atom|20|Au,a,0.8020,0.5000,0.5000,0.0049,1.0000,0.0340
atom|21|Au,a,0.3530,0.6780,0.5000,0.0049,1.0000,0.0340
atom|22|Au,a,0.6380,0.7000,0.5000,0.0049,1.0000,0.0340
atom|23|Au,a,0.1160,0.8670,0.5000,0.0049,1.0000,0.0340
atom|24|Au,a,0.4960,0.8890,0.5000,0.0049,1.0000,0.0340
atom|25|Au,a,0.8790,0.9000,0.5000,0.0049,1.0000,0.0340
aff|0|Au|2.388,42.866,4.226,9.743,2.689,2.264,1.255,0.307|Doyle - Turner Acta Cryst. A24 (1968),390

In most cases defining crystal defects  is a matter of writing a dedicated program. jems uses these files the very same way it uses crystal files (figure 3.12):

Figure 3.12 Au S5[310] grain boundary model.

3.3 Crystal models using java 3D

3-D crystal models are activated using the Java3D check box of the Parameters (menu) Preferences (menu-item) Imaging (tab). Models are drawn either in projection (fig. 3.13) or in perspective (fig. 3.14). Models are saved as .jpg files.

Figure 3.13 GaN [1,1,0] 3-D model (projection).

Figure 3.14 GaN [1,1,0] 3-D model (perspective).

The 3-D dialogue is shown in fig.3.15. It allows to rotate (mouse-left), zoom (mouse-left + Alt), translate (mouse-right) , add bonds, draw a frame, duplicate the unit cell or cut it by a plane.

Figure 3.15 The 3-D dialogue.