Jmol users/developers
The 10.x prototype
(http://www.stolaf.edu/people/hansonr/jmol/test/proto) now supports a
wide range of functionality in relation to fractional coordinates. These
are specified as one might expect:
{1/2, 0, 1/2}
as simple fractions. Braces here,{}, are necessary. It is the "/" sign
itself that indicates we are working with fractional coordinates. Thus,
{0.5, 0, 0.5}
refers to the actual point x=0.5, y=0, z=0.5, while
{0.5/1, 0/1, 0.5/1}
refers to fractions of the unit cell -- x = a./2 , y = 0, z = c/2.
The denominator "1" is optional here, and since all coordinates must be
fractional if any one is, one can write:
{0.5, 0, 0.5/}
for a simpler, more easily read indication of fractional coordinates
when decimal numbers are used instead of simple fractions.
Examples of use include
center {1/2, 0, 0}
#centering on a given point in the unit cell
spin {0,0,0/} {1,1,1/} 10
rotate {0,1/2,0} {0,3/2,0} -20
#spinning and rotating about internal axes defined in relation to the
unit cell
draw line1 150 {1/2, 0, 0} {1/2, 1,0}
draw line2 150 PERP {1/2, 0, 0} {1/2, 1,0}
draw plane1 PERP PLANE {1/2, 0, 0} {1/2, 1,0}
draw plane2 {0, 0, 0/} {0, 1,0/} {0, 1, 1/} {0, 0, 1/}
#drawing points, lines, and planes based on fractional coordinates.
Note that the two endpoints of any line define an internal spin axes
when clicked on by the user.
dipole {0, 0, 0/} {0,1/,0}
#defining dipole vectors based on crystallographic coordinates
In addition, I've added three new atom label format codes, %X, %Y, and
%Z, which display the
fractional coordinates. These can be formatted to, say, deliver only two
decimal digits:
%.2X %.2Y %.2Z
Note that lower case:
%x %y %z
still gives the standard cartesian coordinates.
--Bob Hanson
When and apply to the unit cell system, when appropriate.
A 1 in the denominator is optional, so
{0.5/, 0, 0.5/}
also refers to the crystallographic fractional coordinate system.
Note that only one "/" is necessary:
{0.5/, 0, 0.5}
is still fractional coordinates.
So, we have:
center {1/2, 0, 1/2}
#center on the ac face
draw axis1 150 {0/,0,0} {1/,1,1}
#draw an axis through {0,0,0} to {1,1,1}, centered between those
points and 150% of their distance long.
draw plane1 {0/,0,0} {1/,0,0}, {1/,1,1}
#draw a plane through these points
draw plane1 {0,0,0/} {1,0,0/}, {1,1,0/}, {0,1,0/}
#draw a plane through these points
etc.
Bob Hanson
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