CMPR is a multipurpose program for powder diffraction data
that provides the following features:
The following sections of this web page describe the various
modes within the program. Most sections have links to screen dumps of the GUI
with a link marked
"View panel" or something similar.
The most recent additions are noted with the "new"
image, while
other changes that have been
added in the previous few versions are flagged with this
image: 
.
There are a number of shortcuts implemented by pressing
keyboard keys. A list of them follows, either upper or lower case may be used.
Some of these case will function only in certain sections of CMPR.
CMPR consists of a number of program sections (panels) that are
selected using the "notebook tabs" directly below the menu bar.
This panel is used to read diffraction data in a number of
formats.
To read a file into a buffer, select the format on the
right and then select a file
on either the window that pops up (Windows) or on the central pane (UNIX).
Note that files can be read either by double-clicking (with the left button)
on them or by pressing the Open (or Read) button.
After a file has been read, it appears in the plot window and
if the legend is active (see the Display options panel) the name
appears in the legend. Also see the
buffer selection section to see how one or more
buffers can be plotted.
It is quite easy to extend CMPR to support additional formats as well.
(No compiler is needed). For information on creating a new routine for
reading data, see the Customizing section, below.
This causes the selected buffer(s) to be written.
The box at the top shows the directory where files will be written.
Note that forward slash characters (/) are used, even for Win-95 and -NT.
It is quite easy to extend CMPR to support writing additional
formats as well.
(No compiler is needed). For information on creating a new routine for
writing data, see the Customizing section, below.
The plot panel is used to display one or more buffers.
To select a single buffer, click on the buffer name.
A range of buffers can be selected by dragging with the mouse.
Individual buffers can be selected or deselected by holding the control
key and clicking on the buffer name.
The plot is updated when the "Update Plot" button is pressed or
with a mouse double-click.
The "Postscript out" button causes a postscript copy of the plot window
to be created. Settings on the
Display options panel determine where the file is created
or how it is printed.
Plots can be exported to
grace, a publication-quality graphics package
where the displayed plot can be enchanced and annotated. This works
very nicely.
Alternately, the information on the plot
can be exported as a .CSV (comma separated variable) file
that can be read by lots of graphic programs, but it will be up
to you to designate the formatting.
This panel is also used to change the way a file is displayed.
This is done by selecting the file(s) to be changed and then
using the appropriate checkboxes to select the color, line type,
symbol type and size.
The changes will be made when the "Apply Changes" button is pressed.
This panel is used to modify the stored values in one or more buffers. One can
specify constants to multiply the x and y values and constants to add to
the x and y values (addition is done after multiplication).
It is also possible to transform the x and y scales.
The x-axis can be transformed between Q, d-space and 2-theta units
for an arbitrary wavelength.
Intensities (y values) can be transformed to square roots
[Sqrt(I)], base 10 logarithms [Log(I)]. The I/sig(I) divides each
intensity by its estimated error, providing an estimate of the
signal-to-noise
and the
I2/sig(I)2 mode scales each intensity value so that
that estimated error is the square-root of the intensity, thus
showing raw counts prior to scaling (or the equivalent).
Conversion is done before constants are added or multiplied.
Changes are applied when the "Rescale" button is pressed.
If more than one scaling or transformation is applied, the
operation is applied to the results from the previous operation.
However, if the "Reset previously applied scaling" checkbox is selected,
the x and y values are reset to the values that were read in,
before any scaling or transformation is done.
The Combine panel is used to create a new buffer set by adding or
subtracting up to five other buffers. The buffers must have the same
number of data points. No attempt is made to offset buffers, so they must
all start (and end) with the same x value.
This panel generates a list of the allowed reflections for a given
set of unit cell constants and extinction conditions. It is possible
to specify symmetry by space group or by selecting individual
translational symmetry operations.
Space groups should be entered as specified in GSAS:
Enter the centering condition or cell type (P, R, A, B, C, I or F)
and then the symmetry along each appropriate axis, with spaces between
each axis. Append a final "R" for rhombohedral settings. Some examples
are: "P 1 21/c 1" or "P 21/c" for P21/c and
"R 3 m" and "R 3 m R" for the hexagonal and rhombohedral settings
of R3m, respectively. If an incorrect space group is entered,
no error message is generated, but no extinctions are generated.
Unit cells may be input with either
direct or reciprocal cell parameters.
The reflections are generated and placed in a separate window
when the "Compute" button is pressed.
This table can be saved to a disk file by entering a file name
and pressing the "Save as" button.
This panel generates a stick-figure plot of the allowed reflections
for a given set of unit cell constants. Reflections can be omitted or
highlighted if extinct due to symmetry.
Unit cells may be input with either
direct or reciprocal cell parameters. Use of
reciprocal cell parameters has proven valuable for indexing powder diffraction
data with low symmetry unit cells where some reciprocal unit cell vectors
are known from electron diffraction.
Symmetry can be specifed by space group or by selecting individual
translational symmetry operations. Space groups
are entered as used in GSAS. Enter the centering condition and then the
symmetry along each appropriate axis, with spaces between each axis. Append
a final "R" for rhombohedral settings. Some examples are: "P 1 21/c 1"
or "P 21/c" for P 21/c and "R 3 m" for and "R 3 m R"
for the hexagonal and rhombohedral settings of R 3 m, respectively.
If an incorrect space group is entered, no error message is generated,
but no extinctions are generated.
After the unit cell parameters have
been entered
and the "Compute" button is pressed, reflections are generated
and displayed as a stick figure.
At this point list of buffers is then displayed.
If symmetry information was entered before
the compute button was pressed, the extinct reflections are not included in
the reflection list. If symmetry information is entered after the compute
button is pressed, the extinct reflections are highlighted in yellow.
To superimpose the stick figure on
one or more buffers, select the buffers and press "Update Plot" button.
The plot will respond to changes in the unit cell parameters or zero
correction made either by typing value(s) into the entry boxes or by sliding
the bars to the left of each number. The zero correction is added to two-theta
values.
Unit cell symmetry can be raised by selecting a higher symmetry cell
from the list in the middle. To lower the symmetry, a new peaklist must
be created.
To redisplay a previously generated set of reflections, select the
appropriate buffer using the "Select peaklist" button in the upper
left of the panel. Note that this recenters the unit cell sliders and recomputes
the reflections
within the requested angular range
(see Options).
Individual reflections can be
labeled by holding the Shift key and clicking on the reflection position
with the left mouse button (shift-left-click). All reflections can be labeled
by holding Shift key and double-clicking anywhere in the plot with the
left mouse button (shift-left-doubleclick). Individual reflection labels
will be typically be erased automatically after a given number of seconds,
set in the Options panel;
an erase time of 0 means that reflections labels
are not automatically erased.
Holding the Shift key and clicking anywhere with the right mouse
button (shift-right-click) clears labels for all reflections
(Mac: Command+shift+mouse).
The size of reflection labels can be changed on the Options panel.
(see Options).
Note that the size for the reflection markers, with respect to the Y
axis, is determined by the "Maximum and Minimum Y values" on the right
side of the screen.
In the example images,
(View panel
or plot), the reflection list was generated
using space group R -3 but then space extinctions for
R -3c are labeled. Thus,
the reflections made extinct by the
c-glide are shown in yellow. Reflections extinct in R -3
are not shown.
Fit is used for profile fitting of selected regions of a
pattern. Peaks are fit with a pseudo-Voigt where eta is the "mixing term."
A value of 0.0 for eta selects a completely Gaussian peak shape and a value of
1.0 selects a completely Lorenztian peak shape.
To fit peaks:
- A buffer to fit is selected using the "Select Dataset" button in the upper
left. If only one appropriate dataset is present, it is selected automatically.
- A buffer to record the peak positions is selected. The first
peak list (if any) is the default, but it is also possible select "new"
which will add peaks to an empty list.
- Select a data range to be fit.
The range must contain less than 1000 data points.
The range can be set using the mouse to zoom and the
S/Z/F/B/E keyboard shortcuts
or use the "Set range to fit" submenu.
This creates a dialog box (view)
to set the data range with three options:
-
use the mouse to zoom in on a region and press the "Set from zoom" button, or
-
type an upper and lower two-theta value in the "Fit Range" boxes, or
- shift the range using an increment and "Add increment to limits" button.
When a range of data is selected, any peaks found in the peakfile in that
data range are displayed on the plot and are added to the peak list menu
to the right.
-
There are two methods for adding new peaks to the menu:
- by pressing the "P" key (P for Peak) while positioning the mouse
to the location of the peak maximum (shift+double-left-click also works)
- by pressing the "set" button in any row of the peak table and then
pressing the "P" key, after moving the desired peak maximum. This "set"
button can also be used to redefine peaks in the table.
-
Select parameters to refine:
Once at least one peak has been entered, and a suitable range has been
selected, a "Run GPLSFT" button appears. Select the parameters to be refined
by clicking on the appropriate boxes to the right of the parameters
-
Optimize parameters by pressing the "Run GPLSFT" button.
The least-squares algorithm in the program is far from robust.
It is wise to first refine the peak
areas and FWHM terms and then add background and eta and peak positions
after reasonable fits are obtained. If the fit blows uo, refine fewer
parameters at a time or decrease the damping value.
Once a refinement has been done, the
peak positions in the peak list buffer are updated also
a "Undo last cycle" button is shown. Pressing this button resets
the values in the various boxes to their values from before the refinement (it
does not change the values in the peak list buffer).
If you want to save the fitted curve, the "Store Fit" button
creates a buffer with the current fit result.
The GPLSFT program can use the Finger-Cox-Jephcoat correction for peak
asymmetry. For this correction, three terms must be known: the diffractometer
radius, the half-height (or half-width) of the sample and of the detector.
Values may be specified in any consistent units. (NIST would prefer that
you use metric units, of course.) While these values can be refined, do
so with care: do not refine too many variables at the same time, use a
small number of cycles and set the damping factor to a small number.
By default fit results are shown superimposed on the plot of the fit,
but the results can be placed in a separate window by deselecting
the "Report fit results in plot window" checkbox on
the Options panel.
I would like to find a Windows program that accepts ASCII input
and control files that can be used to generate publication-quality
graphics, so that I can generate input files in that format as well.
