At this stage in the refinement we have a good fit for the experimental
parameters, but need to improve the crystallographic model.
To reduce the number of parameters needed in the initial stages of this
part of the process, we will define a constraint that requires a
single overall Uiso value for all atoms.
GSAS/EXPGUI Alumina tutorial (part 10)
Group Uiso parameters &
Refine coordinates and Overall Uiso.
Note that at this stage in the refinement, the peak shape agrees well, but
there are significant differences between the observed and computed
intensities. This implies that the crystallographic model is in some
To group atoms so that they share a single atomic displacement parameter
(displacement parameter is the preferred name for "temperature factor"),
the parameters need to be constrained together.
The Constraints panel allows constraints to be defined to link parameters
together. At present EXPGUI allows constraints to be created for
atomic parameters and for profile terms. GSAS implements many other types
of constraints, but they must be accessed via the GSAS EXPEDT program.
Press the "New Constraint"
button at the bottom of the window to create a new constraint on
While it is not needed in this case, in many projects it is best to
refine an overall displacement parameter in the initial refinements for
this parameter. In many refinements, there simply are not sufficient
data to allow every atom to have an independently refined displacement
parameter, in these circumstances, it is useful to group atoms together
so that chemically similar atoms are constrained to have the same displacement
It should be noted that these constraints do not actually require that
the parameters have the same value. In fact, the constraints require that
the shifts that applied in future refinement cycles have their ratios
defined by the constraint values. Thus, for parameters to be contrained to
be equal, the parameters must start at the same value as well as have
the constraint ratio set to 1.
After pressing the "New Constraint" button, the window to the right
is created. From top to bottom, the phase is selected as phase 1 (there is
no other choice in this example), both atoms are selected
(to select a range of atoms use a mouse "drag" or hold the control key while clicking the [left] mouse button; selecting all atoms can also be done by
press the right mouse button. Finally select UISO for the parameter, leave
the multiplier as 1 and press "Save"
The Constraints panel now shows the constraint created in the previous
step, as seen below.
Now we are ready to set the refinement flags for the atoms on the Phase panel.
Select both atoms in the list using the mouse. Select the X flag
(near the bottom of the panel), this means refine x, y and z, as allowed by
symmetry. Since the Al atom is on a special position, (0,0,z), only the
z coordinate will be changed. Likewise the O atom is at a (x,0,1/4) position
and only the x coordinate will be changed. Also select the U flag to refine
the displacement (temperature) parameter for the two atoms. The previously
defined constraint will be applied automatically.
Refinement of these three atomic parameters
has a enormous impact on the quality of the fit,
as seen by the improvement in the agreement seen in the GENLES run below.
The LIVEPLOT output shows a tremendous improvement in the agreement as well.
Initial Fitting of Profile Parameters