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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: As at (0,0,0) Ga at (1/4,1/4,1/4) 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 system filename of the crystal file. crystal system (triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic) regular point system (orbit) lattice parameters (0 : a, 1 : b, 2 : c, 3 : a, 4 : b, 5 : g) (a, b, c in nm) atom symbol, Wickhoff notation, x, y, z, Debye-Waller, occupancy, absorption 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):
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 3.14 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.