How We Did Crystal Structures
The C++ program, written by Andrew Schultz, used to create the .xyz crystal
structure files is available here.
chem.h and vector.h are also
available.
Setup
The program reads the coordinates for the unit cell from a file and reproduces it.
The unit cell must be rectangular and must have one corner at the origin. The other
corner is defined by the user. Atoms with coordinates equal to 0 must be omitted as
these are duplicated elsewhere in the cell. The program compensates for this. The
user is asked for the coordinates opposite the origin, the expansion ratio (if needed.
see this for more information), and the number of
duplications in each direction.
The program calculates the number of atoms that will be in the final structure
compensating for those atoms omitted from the original unit cell. If x, y and z
are the coordinates of an atom, and cx, cy and cz are the coordinates of the unit
cell corner opposite the origin, then the coordinates X, Y and Z of a position it
occupies in the structure would be calculated using the formulas:
X=x+i*cx
Y=y+j*cy
Z=z+k*cy
where i, j and k can range from -1 to the number of duplications in the x, y or z
direction. -1 is included so that atoms with coordinates of 0, which are omitted
from the unit cell are included in the final structure. This also produces some
atoms whose coordinates in the structure are negative. These are not included in
final crystal structure.
HTML
This sections assumes a basic knowledge of HTML.
The atoms we used in the unit cells are of varying elements for two reasons. First,
the different elements are displayed as different colors. Second, it is possible to
cause certain elements to disappear at the push of a button. The following code is
used in our page to display the crystal structure:
<embed src="rcry.xyz" width=500 height=500 script="set boundbox on
restrict elemno=1
spacefill 125" align=left
display3D=spacefill name="crystal">
- set boundbox on draws the box around the atoms.
- restrict elemno=1 causes only the hydrogens (simple cubic) to be displayed
- name="crystal" gives this structure a name which can be referenced in other parts
of the page.
This code is used in the same page to cause the face centered cubic structure to
appear:
<embed align=absmiddle type="application/x-spt" width=25 height=25
button=push target="crystal" script="
restrict not (elemno=3 or elemno=7)
spacefill 125">
- type="application/x-spt" is necessary to alert Chime that this is a script
- button=push specifies how the object will appear on the web page
- restrict not (elemno=3 or elemno=7) specifies that everything but the elements in
the body centered and tetrahedral positions should appear. This leaves the hydrogens
at the corners and the yellow sulfurs at the face centered positions.
- spacefill 125 specifies how to display the newly selected atoms.
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