High Score and High Score

HIGHSCORE & HIGHSCORE PLUS
Quick Start Guide

HighScore &
HighScore Plus
Quick Start Guide
EDITION NOTICE: 4022 339 14082, August 2013

This is the original publication of Edition 2 of this document, to be used with
HighScore & HighScore Plus version 4.0 or higher.
HighScore & HighScore Plus Quick Start Guide
ACKNOWLEDGMENTS
All registered and unregistered trademarks, domain names and copyrights herein
are the property of their respective owners.
DISCLAIMER
The information provided herein is supplied under a non-exclusive license
authorizing its use solely for and in conjunction with PANalytical's products.
Although diligent care has been used to ensure that the information is accurate,
nothing contained herein can be construed to imply any representation or warranty
as to the accuracy, currency or completeness of this information.
COPYRIGHT NOTICE
2013, PANalytical B.V., Almelo, The Netherlands
PANalytical B.V.
Lelyweg 1
7602 EA, Almelo
The Netherlands
Tel: +31 546 534444
Fax: +31 546 534598
Internet www.PANalytical.com
Page GP - ii
General Pages
Contents
Chapter 1 Introduction
Chapter 2 Starting HighScore and Enabling the Examples Database
Chapter 3 Loading and Displaying Data
Chapter 4 Pattern Treatments
Chapter 5 Automatic Profile Fitting
Chapter 6 Performing Search - Match - Identify
Chapter 7 Changing the Scores
Chapter 8 Running a User Batch
Chapter 9 Phase Identification Strategy and Troubleshooting
Chapter 10 Searching and Refining a Unit Cell (HighScore Plus)
Chapter 11 Automatic Rietveld Refinement (HighScore Plus)
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Page GP - iv
Chapter 1
Introduction
1.1 INTRODUCTION............................................................ 1 - 3
1.2 HIGHSCORE PLUS......................................................... 1 - 3
1.3 CONVENTIONS USED................................................... 1 - 3
Page 1 - 1
Page 1 - 2
Chapter 1. Introduction
1.1 INTRODUCTION
This document is intended to help you to use the described software quickly and
efficiently. The examples are arranged in a certain order. We advise you to follow
this order by starting with Chapter 2 and then proceeding through the rest of the
chapters. Feel free to experiment with alternatives and different views.
We will use the measurement Mixture3.xrdml for many examples in the Quick
Start Guide. The sample used for this measurement is an artificial mixture of three
minerals. The PANalytical Example Database, delivered with HighScore and
HighScore Plus, fits this measurement.
This document is not designed to show in detail or explain all the various
possibilities of the software. For most of the examples in this document, only one
route to perform a task is shown. To explore other methods, you can experiment
with the system and learn the other possibilities yourself.
1.2 HIGHSCORE PLUS

The software packages HighScore and HighScore Plus are similar in most respects.
The Plus package includes more additional functionality, such as Rietveld,
Pawley, and LeBail refinements and crystallographic analyses.
1.3 CONVENTIONS USED

An instruction is preceded by a bullet .
Menu items, keys and buttons on a window are shown in bold text, for
example: File > Open.
If there is a difference between the information given in this document and
what you see on your screen, follow what you see on your screen.
Page 1 - 3
Page 1 - 4
Chapter 2
Starting HighScore and Enabling the

Examples Database
2.1 INTRODUCTION............................................................ 2 - 3
2.2 STARTING HIGHSCORE ................................................ 2 - 3
2.3 CUSTOMIZING THE INTERFACE................................... 2 - 4
2.4 ENABLING THE EXAMPLES DATABASE ...................... 2 - 6
Page 2 - 1
Page 2 - 2
Chapter 2. Starting HighScore and Enabling the Examples Database
2.1 INTRODUCTION
This chapter shows you how to start up HighScore or HighScore Plus, how to set up
the desktop, and finally how to select the examples database delivered with the
system.
2.2 STARTING HIGHSCORE
Double-click the HighScore icon or the HighScore Plus icon
.
The HighScore or HighScore Plus window is displayed, see Figure 2.1.
Figure 2.1 HighScore Plus Initial Window
Page 2 - 3
2.3 CUSTOMIZING THE INTERFACE

Before working through the examples in this Quick Start Guide, we advise you to
reset the user interface to its initial state.
NOTE: After completing the examples, you can restore the interface to your
personal preferences.
Select View > Toolbars > Customize.

The Customize window is displayed.
Select the tab Options.
Clear the check boxes Show full menus after a short delay and Menus
show recently used commands first, see Figure 2.2.
Click Close.
Figure 2.2 Customize Window
Page 2 - 4
Select Customize > Program Settings. In the lower left corner, click
Reset All to Default and then click Yes and OK to confirm it.
Select Customize > Defaults. In the lower left corner, click Restore
Factory Defaults and then click OK.
Select File > New to open a new empty document.
Select View > Reset all Toolbars and click Yes to confirm it.
Select View > Panes Default Setting.
Select the View menu and ensure that the option Lock Pane Positions is
checked. If not, check this option.
On the Desktop toolbar at the bottom right of the window, select the
desktop layout Phase-ID. Your window should now look as in Figure 2.3.
Figure 2.3 Empty Document With Phase-ID Desktop
Page 2 - 5
You can completely customize the desktop to your own requirements, but the most
usual working layout (to start with) is with the Main Graphics pane at about the
same relative size as shown in this example. If a particular toolbar is not present on
the desktop as default, you can always enable it with the menu View > Toolbars. In
the same way, the various panes can be hidden or displayed.
For these examples, we advise you to make your desktop look like this example by
selecting the desktop Phase-ID on the bottom right toolbar. Try other
pre-programmed desktop settings and observe the changes in the graphical user
interface at any time.
To preserve your changes to the desktop appearance, you must save the changed
desktop under its existing name or a new name, using View > Desktop > Save
Desktop. Another possibility is to use no desktops at all (select the desktop
<None>). This selection will save your changed settings automatically when you
close the last open document in the software.
You can adjust the relative size of the different panes by moving the horizontal and
vertical splitter bars in exactly the same way as in Windows. When two monitors are
used, you can even distribute the different panes of the HighScore application
between them, and then save this setup as a desktop.
NOTE: To distribute the panes in this way, first clear the option View >
Lock Pane Positions.
2.4 ENABLING THE EXAMPLES DATABASE

For demonstration purposes only, a very small examples database is delivered with
the software. We will use this database for the examples in the Quick Start Guide.
Enable pattern retrieval from this example database as follows:
Select Customize > Manage Databases from the menu. The Manage
Databases window is displayed, see Figure 2.4.
Page 2 - 6
Figure 2.4 Manage Databases Window
Navigate to the PANalytical Example Database folder in location

C:\Documents and Settings\user.name\My Documents\PANalytical\
X'Pert HighScore Plus\ExampleDb\ (Windows XP), or
C:\Users\user.name\Documents\PANalytical\X'Pert HighScore Plus\
ExampleDb\ (Windows 7).
Make sure that the check box Use is checked. In the bottom of the
window, you should see a pie chart with the total number of patterns (16)
in the database. This small database is ready for use now, it does not need
conversion.
Click the database Properties button. If properties are displayed, you can
be sure that the selected database is available for use.
Page 2 - 7
NOTES: a. The PANalytical Example Database is not suitable for performing

phase analysis on unknown samples. It is also not suitable for
testing or demonstrating the phase identification capabilities of
HighScore.
You need an ICDD (or another) reference database or a large
number of user reference patterns in order to explore the
capabilities of the software and to perform identification examples.
b. The PANalytical Example Database is also not suitable for adding
your own user reference patterns to the patterns that are already
present. How to create a new, empty reference database is described
in the HighScore Help.
Click File > Close or click to close the document.
Page 2 - 8
Chapter 3
Loading and Displaying Data
3.1 INTRODUCTION............................................................ 3 - 3
3.2 LOADING A SCAN ........................................................ 3 - 3
3.3 DISPLAYING A SCAN ................................................... 3 - 5
3.3.1 Display Panes .................................................................................... 3 - 5
3.3.2 Viewing Exercises ............................................................................. 3 - 7
3.4 RETRIEVING A REFERENCE PATTERN .......................... 3 - 7
3.5 DISPLAYING A REFERENCE PATTERN ....................... 3 - 10
Page 3 - 1
Page 3 - 2
Chapter 3. Loading and Displaying Data
3.1 INTRODUCTION
Loading and then displaying data are the most common tasks when you are using
HighScore. There are many ways to display data and the different views allow
even more combinations. In this chapter, we will perform some simple examples.
3.2 LOADING A SCAN

If HighScore is not already running, double-click the icon on the desktop
to start it.
Select File > Open. The Open window is displayed, see Figure 3.1.
Figure 3.1 Open Window
Page 3 - 3
Navigate to the folder Tutorial in location

X'Pert HighScore Plus\ (Windows XP), or
(Windows 7).
In the field Set Files of type, select All files (*.*) to display all files (of
different data formats) in the folder.
Select Mixture3.xrdml and click Open to open this file.
A copy of the selected file is loaded into a new HighScore document.
Because this is the first scan of the document it automatically becomes the
anchor scan.
Figure 3.2 HighScore Document Window
Page 3 - 4
3.3 DISPLAYING A SCAN
3.3.1 Display Panes

The Main Graphics pane shows the complete anchor scan in Analyze View.
Figure 3.3 Main Graphics Pane
Page 3 - 5
The Additional Graphics pane displays the zoom overview. Because you have not
yet zoomed in, the complete scan range is displayed in reverse colors.
Figure 3.4 Additional Graphics Pane
The first time that this program is used, the Pattern List tab is on top. In general,
the last-used tab will be on top.
Figure 3.5 Pattern List Tab
Page 3 - 6
3.3.2 Viewing Exercises

Zoom in by dragging in the Main Graphics pane. Zoom out by
double-clicking in the Main Graphics pane. Do this a few times to see how
it works. Observe the Additional Graphics pane. Try to display only a part
of a peak.
Click the Zoom Intensity button ( ) on the Tool Palette on the
left-hand side of the HighScore window to enable or disable zooming in
on the Y-axis direction. Observe the Additional Graphics pane. Try to
display only a part of a peak.
Click the Set Y-axis Scale button ( ) to toggle the Y-axis.
You can also use the small arrow button next to the Set Y-axis Scale
button to select the scale directly (Linear Y-Axis, Square Root Y-Axis or
Logarithmic Y-Axis).
3.4 RETRIEVING A REFERENCE PATTERN

Select Reference Patterns > Retrieve Pattern by > Restrictions.
Select the tab Strings.
In the Mineral Name field, enter calcite and click Load.
Figure 3.6 Retrieving a Reference Pattern by Restrictions

Page 3 - 7
Click Close.
Several changes take place in your diffraction document, see in Figure 3.7:
a. The Main Graphics pane displays the lines (often called sticks) of the
reference pattern in Analyze View.
b. The Additional Graphics pane also displays the sticks of the pattern in
most views.
c. The Pattern List tab displays a summary of the retrieved reference
pattern.
Figure 3.7 Reference Pattern Lines Displayed in Analyze View
In the Main Graphics pane, select the Pattern View at the bottom to
display the reference pattern lines without the scan data, see Figure 3.8.
Page 3 - 8
Figure 3.8 Reference Pattern Displayed in Pattern View
NOTE: Because the peak list is empty, no peaks are displayed in the upper part
of the Pattern View.
Page 3 - 9
3.5 DISPLAYING A REFERENCE PATTERN

Select the Pattern List tab and right-click in the list of accepted reference
patterns to open the shortcut menu.
Figure 3.9 Pattern List Shortcut Menu
Select Show Pattern to display details of the reference pattern.

Alternatively, double-click the reference pattern in the Pattern List tab.
Details of the reference pattern are displayed, see Figure 3.10.
Page 3 - 10
Figure 3.10 Reference Pattern Details
Close the Reference Pattern window.

Select the Analyze View again, either by selecting View > Main
Graphics > Analyze View, or by selecting the Analyze View tab on the
bottom of the Main Graphics pane.
Click (Show Reference Patterns) to toggle the display of the
reference pattern lines in the Main Graphics pane.
NOTE: The high intensity areas of the scan marked in gray are those features
of the scan explained by the loaded reference pattern. The (first 20)
reference patterns are automatically matched and scored against the
anchor pattern.
To save the document, click File > Save Document, accept the proposed
name Mixture3.hpf and then click Save.
Click File > Close or click to close the document.
Page 3 - 11
Page 3 - 12
Chapter 4
Pattern Treatments
4.1 INTRODUCTION............................................................ 4 - 3
4.2 BACKGROUND DETERMINATION ............................... 4 - 3
4.3 PEAK SEARCH .............................................................. 4 - 6
Page 4 - 1
Page 4 - 2
Chapter 4. Pattern Treatments
4.1 INTRODUCTION
Pattern treatment allows you to modify existing data and to generate additional
derived data. Pattern treatment is used to prepare the data for phase analysis,
crystallographic analysis and sometimes for a structure refinement.
The two most important treatments are background determination and peak search.
A proper background determination is very important for phase analysis using the
measured net profile data. Peak search is required when you want to include peak
data in the search-match-identification process or when you need to perform profile
fitting or indexing.
4.2 BACKGROUND DETERMINATION

to start it.
Select File > Open.
(Windows 7).
NOTE: Do not open the document Mixture3.hpf that you saved in the
previous example.
A copy of the selected file is loaded into a new HighScore document.
Because this is the first scan of the document it automatically becomes the
anchor scan.
Select Treatment > Determine Background.
A window opens and the background is automatically determined. The
background is displayed as a green line in the Main Graphics pane, see
Figure 4.1.
Page 4 - 3
Figure 4.1 Anchor Scan with Background Preview
Look at the title bar of the Determine Background window to confirm

that you are using the Identify1 parameter set, see Figure 4.2.
Figure 4.2 Determine Background Window
Page 4 - 4
NOTES: a. If you have another title than Identify1, click More to expand the
window, then select the parameter set Identify1 from the list.
b. In general, you start a function in HighScore by clicking a button
labeled with the desired action in a window before any processing
of the data is done. The automatic determination of the background
is an exception to this; it automatically starts when Determine
Background is selected from the Treatment menu.
Change the Bending factor by moving the slider on the Automatic tab of
the Determine Background window.
You can watch the corresponding changes in the background as they
change (simultaneously) in the Main Graphics pane. Zoom in so that you
can also see small changes.
Click the up and down arrows of the Granularity field and watch the
changes of the background again. This parameter changes the number of
intervals used for background determination. The default value of 20 fits
most ordinary scans.
By moving the slider and clicking the up and down arrows you have
actually changed the way that the background is determined.
Look at the title bar of the Determine Background window again. It has
changed into Determine Background - [Untitled], indicating that the
new (changed) parameter set has not yet been saved under a specific name.
Restore the Bending factor and Granularity fields to their original
setting and click Accept to accept the background. The Determine
Background window is closed and the accepted background is displayed
in its color in the graphics.
Select the Anchor Scan Data tab to display a list with the data. The Iback
column displays the numerical background data that you just generated.
Page 4 - 5
Figure 4.3 Numerical Background Data
4.3 PEAK SEARCH

Select Treatment > Search Peaks. The Search Peaks window opens
with the Identify peak search parameter set.
NOTE: If you have another title than Identify, click More to expand the
window, then select the parameter set Identify from the list.
Page 4 - 6
Figure 4.4 Peak Search Window
Click Search Peaks. Detected peaks are displayed inside and above the
Main Graphics pane by solid (K1 and Kmixed peaks) or dashed (K2
peaks) orange lines.
Peaks that are not explained by a reference pattern, have a little V mark
when they are displayed above the Main Graphics pane. A calculated
profile in preview color (based on the actual peaks) is also displayed, see
Figure 4.5.
NOTES: a. This is only a preview of the result. If you close the window now,
no peaks are written into the diffraction document. You can check
the quality of the peak search by the peak sticks and the profile
before accepting any result. Zoom in for more details.
This is the normal behavior of HighScore. This in contrast with
the special behavior of Treatment > Determine Background as
described in Note b. on Page 4-5.
b. The peak search window becomes semi-transparent when it loses
the focus. Clicking it puts the focus back on the window.
Click Accept to add the detected peaks to the document and close the
window.
Page 4 - 7
Figure 4.5 Anchor Scan Including Peak and Background Data
Click (Set Display of Peaks) to toggle the display of peaks. You can
also use the small arrow button next to the Set Display of Peaks button to
select one of the options directly. Explore all four display options.
Figure 4.6 Set Display of Peaks Options
Select the Peak List tab. The tab displays the numerical details on every
detected peak.
Page 4 - 8
Peaks derived from the K2 wavelength are indicated by a different (gray)

background color in the peak list, see Figure 4.7.
Figure 4.7 Peak List
To save the complete document (including background data and the peak
list), click File > Save Document, accept the proposed name
Mixture3.hpf and then click Save. Confirm overwriting the document.
We will use this document again in Chapter 5 - Pattern Treatments and in
Chapter 6 - Performing Search - Match - Identify.
Page 4 - 9
Page 4 - 10
Chapter 5
Automatic Profile Fitting
5.1 INTRODUCTION............................................................ 5 - 3
5.2 PREPARATION .............................................................. 5 - 3
5.3 EXERCISES .................................................................... 5 - 4
Page 5 - 1
Page 5 - 2
Chapter 5. Automatic Profile Fitting
5.1 INTRODUCTION
This chapter gives you an example how to fit a profile using an automatic fit
parameter set. This is called single peaks profile fit or non-phase peak fitting.
Non-phase peak fitting means putting a calculated profile around each peak in such
a way, that it follows the original measured scan data as close as possible.This
mathematical description of the profile describes the peak parameters much better
than a simple peak search can do. This better peak description is used for peak
deconvolution, unit cell refinements, line profile analysis, or structure solution. It is
generally not required for phase identification.
5.2 PREPARATION
to start it.
Open the document Mixture3.hpf that you saved in the previous
example. It contains peak data and background data. Profile data is also
present, but this profile is calculated from the peak data and not fitted
(= refined) in any way yet.
In the Additional Graphics pane, right-click to open the shortcut menu and
select Show Graphics > Difference Plot. The Additional Graphics pane
now displays the difference between measured scan data and profile data.
Make sure that the calculated sum profile is displayed in the Analyze
View of the Main Graphics pane. If not, select View > Display Mode >
Show Calculated Profile to enable the profile display.
A fast alternative is to click (Show Calculated Profile) in the
Display Mode toolbar of the Main Graphics pane.
desktop layout Profile Fitting.
Verify that the existing background is used and not refined during profile
fit as follows:
In the Refinement Control tab, select Background. Then, in the Object
Inspector tab, select Method > Use available background, see
Figure 5.1. Press Enter to confirm.
Page 5 - 3
Figure 5.1 Selecting Use available background
Finally check if the fitting mode is set to automatic as follows:

Select Analysis > Fitting. Check that the field Fitting Mode is set to
Automatic.
An alternative is to select Automatic in the Fitting toolbar.
5.3 EXERCISES
Start an automatic profile fit as follows:
Select Analysis > Fitting > Start Fit and then select <Profile fit> Default
Profile Fit.
An alternative is to click (Fit Profile) in the Fitting toolbar and then
select the parameter set from here.
Make sure that you have zoomed out completely. Profile fitting is only
executed on that part of the scan that is currently displayed.
NOTE: The actual fitting range depends not only on the zoom range, but also
on the option to ignore the actual zoom range for fitting. To set this
option via Analysis > Fitting > Ignore Zoom Range or via the Fitting
toolbar.
View the small window displaying the R-value graphic, and notice the
overall quality of the fit as fitting progresses, see Figure 5.2.
Page 5 - 4
Figure 5.2 R-Value Graphic Window
Figure 5.3 Anchor Scan and Profile After First Profile Fit
Page 5 - 5
The profile is fitted to the existing peaks. The existing background is used
and left unchanged. The background currently used is (deliberately) a bit
too high, cutting into the peak feet. This is desirable for phase
identification, but is not optimal for a profile fit.
NOTE: In the Refinement Control tab, double-click Global Variables to open
the Object Inspector pane. Select Global Settings > Agreement
Indices to view the values of the R-values and Goodness of Fit, see
Figure 5.4.
Figure 5.4 Agreement Indices, Initial Fit
Determine the background again with the field Bending factor set to 0,
the field Granularity set to 30 and the Use smoothed input data check
box cleared, see Figure 5.5. Click Accept to accept the new values.
Page 5 - 6
Figure 5.5 More Suitable Background Settings
In the Refinement Control tab, double-click Global Variables to open

the Object Inspector pane. Select Global Settings > Unassigned Peaks
Fitting > Common Peak Fit Settings.
Select Asymmetry Type > Split Width, which better describes the slight
asymmetry of the peaks at low angles, see Figure 5.6. Press Enter to
confirm.
Page 5 - 7
Figure 5.6 Asymmetry Type - Split Width
Perform the profile fit in the same way as before, using the predefined
parameter set <Profile fit> Default Profile Fit.
the Object Inspector pane. Select Global Settings > Agreement Indices.
Page 5 - 8
Now the fit looks better. You should obtain an Weighted R profile value
of about 6.80 and a Goodness of Fit value of about 1.44, see Figure 5.7
and Figure 5.8.
Figure 5.7 Agreement Indices, Improved Fit
Figure 5.8 Anchor Scan and Profile After Improved Fit
Page 5 - 9
Click File > Close or click to close the document. Do NOT save (click
No to the question Do you want to save the changes?).
Page 5 - 10
Chapter 6
Performing Search - Match - Identify
6.1 INTRODUCTION............................................................ 6 - 3
6.2 SEARCH AND MATCH.................................................. 6 - 3
6.3 IDENTIFICATION........................................................... 6 - 5
Page 6 - 1
Page 6 - 2
Chapter 6. Performing Search - Match - Identify
6.1 INTRODUCTION
In this chapter we will search and match possible candidates and then manually
identify the phases of the example file. Because we will use the small PANalytical
Example Database delivered with the software, this is not a real situation, but it
gives you a good example of what to do.
NOTE: The PANalytical Example Database is not suited in any way to
demonstrate the phase identification capabilities of HighScore. You
need a large reference database with 100.000 patterns or more to
compare this software with other packages on the market. Possible
choices are an ICDD product, the PAN-ICSD or the free COD database
for instance.
6.2 SEARCH AND MATCH

to start it.
example. It contains peak data and background data, which were
assembled in Chapter 4 - Pattern Treatments.
desktop layout Phase-ID.
Select Analysis > Search & Match > Execute Search & Match.
The Search & Match window appears with a certain parameter set, see
Figure 6.1.
Page 6 - 3
Figure 6.1 Search & Match Window
Make sure that the program uses the correct parameter set (Default) for
the search and match procedure that you are going to perform. If
necessary, click More and then select Default from the list. The name of
the selected parameter set name is shown in the title bar of the window.
Click Search.
After a while, a preview of the Candidates list is displayed on the lower
half of the Pattern List tab. Simultaneously, the Additional Graphics pane
shows the scan in Compare Mode view.
Click OK to accept the result.
The Candidates list shows 11 entries ordered by scores from high to low.
Page 6 - 4
Figure 6.2 Candidates List
If necessary, click the column header Score to sort the candidates as

shown in Figure 6.2.
6.3 IDENTIFICATION
The next step is to manually accept candidates that have a high score and that match
the peaks and features of the measurement. Several views in the Additional
Graphics pane support the visual comparison between reference pattern sticks and
the measurement.
Select View > Additional Graphics > Compare Mode (or right-click in
the Additional Graphics pane).
Select View > Display Mode > Peaks in Main Graphics > Show Peaks
Outside to display only peaks outside the scan.
To get a better view on the measured scan, clear option View > Display
Mode > Show Calculated Profile.
Drag the first candidate pattern (00-038-1479, chromium oxide) from the
Candidates list to the Accepted Ref. Patterns list in the upper half of the
Pattern List tab to accept it.
Page 6 - 5
When you select this pattern, it is highlighted and its lines are displayed
(for comparison) in the Additional Graphics pane.
Observe the following changes (you can use Edit > Undo and Edit >
Redo to see the changes several times):
a. Some peaks in the Main Graphics pane have lost the V mark. These
peaks have been explained by the accepted reference pattern. Peaks
still marked with a V are not yet explained.
b. High intensity areas in the Main Graphics pane are indicated in gray.
These scan features are explained by the accepted reference pattern.
If no scan features are marked in gray, click (Show Explained
Features) in the Display Mode toolbar. If necessary, zoom in to view
the features more clearly.
c. The Candidates list now has candidate 00-005-0586, calcium
carbonate on top. The score of this pattern has changed slightly with
respect to the previous situation.
Accept the next two patterns (one after the other) from the top of the
Candidates list. When you accept the third reference pattern, observe the
dramatically changing scores of the remaining candidates.
Check if the accepted patterns are indeed minerals and comply with the
sample description as follows:
Right-click a specific reference pattern in the Accepted Ref. Patterns list
and select Show Pattern to view the subfile information of that pattern,
see Figure 6.3. Alternatively, you can also look at the Subfiles column of
the Accepted Ref. Patterns list.
Page 6 - 6
Figure 6.3 Show Reference Pattern Details
NOTE: Move the mouse pointer over a clipped (= partially visible) cell to
display a tooltip with the complete information in that cell for a few
seconds, see Figure 6.4.
Page 6 - 7
Figure 6.4 Tooltip Displaying the Contents of a Clipped Cell
Look for any unexplained peaks or features in the Main Graphics pane.
Click (Show Reference Patterns) in the Display Mode toolbar to

display the reference pattern lines in the Main Graphics pane. One small
peak around 42 2Theta is not explained, but it is doubtful whether this is a
real peak or just some noise.
A second unexplained peak around 79.3 2Theta is actually a K2 peak
wrongly assigned as a K1 peak, see Figure 6.5. You can easily check this
with the spectral lines tool, accessible via Tools > Spectral Lines.
Page 6 - 8
Figure 6.5 Scan Showing Unexplained Peak
To save the complete document (including the candidate list and the
accepted reference patterns), click File > Save Document, accept the
proposed name Mixture3.hpf and then click Save. Confirm overwriting
the document.
Page 6 - 9
Page 6 - 10
Chapter 7
Changing the Scores
7.1 INTRODUCTION............................................................ 7 - 3
7.2 CHANGING THE SCORES ............................................. 7 - 3
Page 7 - 1
Page 7 - 2
Chapter 7. Changing the Scores
7.1 INTRODUCTION
This chapter gives you an example how to change the scores of the search and match
results in the Candidates list.
The scores, displayed in the Candidates list and in the Accepted Ref. Patterns list,
depend on the parameter set used for the search and match procedure. These scores
can also be changed at any time after the search and match step. In a real situation,
changing the scores can bring other candidates to the top of the list and help you to
identify more phases.
7.2 CHANGING THE SCORES

to start it.
example. It contains peak data and background data, reference patterns
and a candidate list, which were assembled in Chapter 6 - Performing
Search - Match - Identify.
Remove the reference pattern 00-035-0816, calcium fluoride, by
dragging it from the Accepted Ref. Patterns list into the Candidates list
below.
Make sure that the Pattern toolbar is displayed at the bottom right of the
window. If not, select View > Toolbars > Pattern Toolbar to enable it.
Click the Select Data Source button on the Pattern toolbar a few times to
toggle the data used for scoring. Watch the score of the Fluorite reference
pattern.
You can also use the small arrow button next to the Select Data Source
button to select the source directly.
NOTE: The appearance of the button represents the selected data source:
(Profile), (Peak List) or (Both).
Click (Match Intensity) to include or exclude the quality of
matching relative intensity in the score. Watch the changing scores.
Page 7 - 3
The buttons Select Data Source and Match Intensity are often used to
change the scores of a Candidates list.
Click the Select Scoring Scheme button on the Pattern toolbar to toggle
between phase scores: (Single Phase) and (Multiple Phase).
Click (Allow Pattern Shift) a few times. Watch the scores and scale
factors changing.
The buttons Select Scoring Scheme (normally set to Multiple Phase) and
Allow Pattern Shift (normally disabled) are seldom used to influence the
scores.
Click File > Close or click to close the document. Do NOT save (click
No to the question Do you want to save the changes?).
Page 7 - 4
Chapter 8
Running a User Batch
8.1 INTRODUCTION............................................................ 8 - 3
8.2 RUNNING USER BATCHES ........................................... 8 - 3
Page 8 - 1
Page 8 - 2
Chapter 8. Running a User Batch
8.1 INTRODUCTION
All actions that you performed in Chapter 4 - Pattern Treatments and Chapter 6 -
Performing Search - Match - Identify can be done automatically in a
pre-programmed way. User batches allow you to perform a complete analysis by
just a click of a button. The HighScore software comes with default user batches
using pre-programmed pattern restrictions.
Using all your knowledge about the sample is the most powerful tool for phase
identification that you have. In the Restrictions tab of the Search & Match
window, you can enable certain reference patterns to fulfill one or more conditions
that will be used for search and match.
In this example, we will not use any restrictions, but search through the complete
(but very small) PANalytical Example Database.
8.2 RUNNING USER BATCHES

to start it.
Select File > Open.
Select Tools > IdeAll.
Alternatively, click IdeAll on the Batches toolbar at the bottom of the
window.
The pre-programmed batch IdeAll is executed. It performs the following
steps:
a. Background determination.
b. Peak search.
c. Divergence slit conversion from automatic to fixed divergence slit
intensities (this step is actually not executed, because the measurement
Mixture3.xrdml was performed using a fixed divergence slit, see
Figure 8.1 and Figure 8.2).
d. Search and match on the complete PANalytical Example Database
(= no restrictions).
e. Automatic identification of high-scoring candidates.
Page 8 - 3
Look for any unexplained peaks or features in the Main Graphics pane.
Double-click on the first accepted pattern 00-035-0816, calcium fluoride
to display its complete information. Check if it belongs to the minerals
subfile, then close the Reference Pattern window.
Select File > Save As to save the document including the correctly
identified phases as MixtureBatch.hpf.
Figure 8.1 Warning While Running a User Batch
Select File > Properties and then select tab Process log to view the details
of the batch.
Figure 8.2 Process Log Showing Batch Step Not Executed
Page 8 - 4
Chapter 9
Phase Identification Strategy and

Troubleshooting
9.1 INTRODUCTION............................................................ 9 - 3
9.2 PATTERN TREATMENT SEQUENCE.............................. 9 - 5
9.2.1 Determine the Background................................................................ 9 - 5
9.2.2 Search Peaks with a High Significance ............................................. 9 - 6
9.2.3 Convert Intensity ............................................................................... 9 - 6
9.2.4 Strip K2 ........................................................................................... 9 - 6
9.3 IDENTIFICATION........................................................... 9 - 6
9.4 TROUBLESHOOTING .................................................... 9 - 8
Page 9 - 1
Page 9 - 2
Chapter 9. Phase Identification Strategy and Troubleshooting
9.1 INTRODUCTION
There is no general recipe for phase identification. Figure 9.1 shows the major steps
to identify an unknown sample in HighScore in a simplified and schematic way. See
Section 9.2 and Section 9.3 for more information about pattern treatment and
identification.
Figure 9.1 Phase Identification Strategy
Page 9 - 3
The steps shown in Figure 9.1 are:
Start Load a measurement.
Pattern This usually comprises:

Treatments 1. Determine the background. This is helpful before
searching peaks and it is crucial when using profile data
for identification.
2. Search peaks with a high significance. (Do not try to use
very small peaks; also use profile data for input.)
3. Convert intensities to fixed slit intensities when an
automatic (-compensating) divergence slit was used.
This step is optional, but it will result in measured
intensities matching the reference data better.
4. Strip K2. This step is also optional; many people prefer
to look at the original data. When not done on purpose,
this step is performed in a hidden way by the search and
match algorithm.
Search and Match Start search and match to build a new Candidates list.
Identification Accept candidates based on score and scale factor values.

Visually check the graphics.
Check the lists for more textual information.
Ide... Batch The steps above are performed automatically in the user batch
Programs programs beginning with Ide in the name.
Change Range/ Concentrate on the unexplained features and/or peaks by using the
Peaks Included Track Graphics Range function,
or exclude already explained peaks and start a new search and
match step to build a new Candidates list.
Change Either the previous restrictions were too tight, excluding some of
Restrictions the phases present in the sample, or they were too wide, including
many isotypical patterns and completely filling the Candidates list.
Page 9 - 4
Change scores, Put other patterns to the top of the Candidates list (to your
group candidates attention) by changing the scoring parameters,
or group together similar patterns by clustering the candidates.
The idea is to identify as many phases as possible from the existing
candidate list before starting search and match again.
Select standard Select one identified pattern with simple, fixed chemistry as an
internal standard.
All Correctly Check all the patterns that were identified automatically.
Explained? There is no guarantee that an automatic identification is correct.
End Save your result as a diffraction document in hpf format.
It is always good to include all information about the sample that you have. Use the
subfiles defined by ICDD or build dedicated restrictions tailored to the samples and
analytical problems you encounter.
NOTE: The identification examples always start by searching the full reference
database (no restrictions). This is done to demonstrate the capabilities
of HighScore in a worst case scenario, but it is not necessarily the best
approach to all phase identification problems.
9.2 PATTERN TREATMENT SEQUENCE
9.2.1 Determine the Background

Background determination should be done before the peak search. When no
background data is present, peak search automatically generates its own background
data.
When profile data is used for identification, a proper background determination is
crucial. If you have any doubt, it is generally better to determine the background too
high rather than too low for phase identification.
Page 9 - 5
9.2.2 Search Peaks with a High Significance

Do not try to locate all small peaks. When you select profile data for phase
identification, all intensity above the background is taken into account including
very small peaks that are difficult to locate.
9.2.3 Convert Intensity

Convert intensity to fixed slit intensity in case an automatic (-compensating)
divergence slit was used.
This is optional. The converted intensity will match the reference data better, which
results in better scores when the function Match Intensity ( ) is used.
9.2.4 Strip K2
If not performed explicitly with the function Strip K Alpha2 ( ), K2 stripping
is performed silently when it is relevant. Most users prefer silent K2 stripping
because they want to see the original measured data in the graphics.
9.3 IDENTIFICATION
Several tools are available to control the match of a candidate or accepted pattern:
Explained scan regions (graphically)
Matched peaks (graphically, textually)
Matched peaks by reference codes (textually)
Matched reference pattern lines (textually)
Number of matched lines, number of new matched lines (textually)
Page 9 - 6
When you cannot identify all phases from the Candidates list of the initial search
and match, perform the following steps:
1. Change the scores to find more candidates from the existing Candidates
list.
a. First change the data source with the buttons (Profile),
(Peak List) or (Both).
b. Now match the parameter with the button (Match Intensity).
c. When you are looking for minor phases, disable the function Demote
Unmatched Strong ( ).
d. Do not enable the function Allow Pattern Shift ( ), unless you
have strong solid-solution effects or an incorrect sample height. In case
of the usual small pattern shifts, this parameter often favors patterns
that do not fit very well to the measurement.
e. You can also experiment with the Select Scoring Scheme functions
(Single Phase) and (Multiple Phase) and with the Auto
Residue function ( ).
2. The next step is to repeat search and match with new, different restrictions
(and/or different parameters).
a. It is possible that the correct pattern was excluded because the
restrictions in the initial search and match were too tight, preventing
the correct pattern from showing up in the Candidates list.
b. It is also possible that the initial restrictions were too wide, allowing
many isotypical pattern to be included and completely fill the
Candidates list, leaving no space for other candidates.
c. If necessary, repeat step 1 with the new Candidates list. Many
identification problems can be solved this way.
3. This step is optional. When you have already identified one or several
phases, but you cannot identify more components in a mixture, this could
be caused by a sample height or an alignment problem. In this case, it
helps to select an already identified pattern with a well defined, stable
chemistry and use it as an internal standard.
a. Right-click in the Accepted Ref. Pattern list and select Correct Scan
with Pattern. The measurement with peaks and background is now
Page 9 - 7
shifted in a way to fit optimally to the standard selected pattern.

NOTE: Use this option with care. Selecting a pattern with variable chemistry
(= solid solutions possible) as internal standard can disrupt the correct
identification of more phases.
Do not use the function Allow Pattern Shift (step 1d) together with
selecting an internal standard (optional step 3).
4. If you still have no success, enable the function Track Graphics Range
( ). Now zoom in on the low-angle region containing unexplained
peaks and features and check the Candidates list. Only the peaks and
features in the visible (zoomed-in) region are now taken into account. If
there are no new matches found in the top of the Candidates list, you
could also start a new search and match using only the zoomed-in range as
input.
a. As an alternative, you can exclude all already matched peaks and
perform a search and match again using only the remaining peak data
as input.
b. If necessary, repeat steps 1 and 2 with the new Candidates list.
9.4 TROUBLESHOOTING
If you have no success or very strange results:
First look at the background. A background level that was determined too
low results in every reference pattern matching your measurement.
Check the document wavelength, which is usually derived from the anchor
scan. If missing in the anchor data, it is supplied by the default instrument
settings and could not match the actual scan data.
Check which databases are used for search and match. Make sure there is a
reference pattern in these databases appropriate to your measurement.
NOTE: All patterns present in the pattern list are treated as knowns when you
start search and match. This means that they are kept in the pattern list
and the first 20 are scored. With the auto-residue function enabled, these
first 20 patterns also influence the scores of all candidates.
Page 9 - 8
Chapter 10
Searching and Refining a Unit Cell

(HighScore Plus)
10.1 INTRODUCTION.......................................................... 10 - 3
10.2 LOADING A MEASUREMENT..................................... 10 - 3
10.3 SEARCHING FOR PEAKS ............................................ 10 - 4
10.4 SEARCHING AND REFINING A UNIT CELL ................. 10 - 6
10.5 SAVING THE RESULTS.............................................. 10 - 10
Page 10 - 1
Page 10 - 2
Chapter 10. Searching and Refining a Unit Cell (HighScore Plus)
10.1 INTRODUCTION
This chapter describes how to load a measurement and set the actual wavelength.
(The rlf file format cannot store information about the used wavelength used). It
continues with a search for diffraction peaks. The first eight peaks (reflections) are
used to start a unit cell search (also called indexing) using the TREOR and DICVOL
indexing routines. A good cell candidate is then refined taking all diffraction peaks
into account. Finally, the result is stored.
To prepare for this example, select the desktop layout Structures. The
corresponding arrangement of the panes and lists is best for the following
examples.
10.2 LOADING A MEASUREMENT

(Windows 7).
Select TaSSe.rfl and click Open to open this file.
Select the Scan List tab and double-click in the scan to open the Object
Inspector pane. Select Instrument Settings and make sure that check box
Incident Beam Monochromator is checked. This sets the wavelength for
the current data set to Copper K1 only, see Figure 10.1.
Page 10 - 3
Figure 10.1 Selecting Incident Beam Monochromator
Select File > Save As. In the field Save as type, select PHILIPS binary
scan (*.rd). This format stores the proper wavelength together with the
scan data. You have now corrected important instrument information and
converted a scan from rfl file format to rd file format.
10.3 SEARCHING FOR PEAKS

Select Treatment > Search Peaks. Click More and select the Default
parameter set. The name of the actual parameter set shown in the title bar
of the Search Peaks window. Click Search Peaks to start the function
and click Accept to accept the results, see Figure 10.2.
Page 10 - 4
Figure 10.2 Search Peaks Window
The Main Graphics pane shows the peaks and a theoretical profile. Zoom
in around 60 to 65 2Theta as shown in Figure 10.3. You can see that the
peak search algorithm has incorrectly identified a peak at about
61 2Theta. Move the cursor over the peak to see detailed information.
Page 10 - 5
Figure 10.3 Peak Incorrectly Identified
Open the Peak List tab and locate the only peak that is not properly at its
place (peak no. 17). This peak was already selected when you moved the
cursor over it. To delete the peak, pressing Delete or right-click and then
select Delete.
10.4 SEARCHING AND REFINING A UNIT CELL

Select Analysis > Crystallography > Search Unit Cell.
Select General > Indexing Method (bottom part of the window) and
select Treor.
Page 10 - 6
Figure 10.4 Search Unit Cell Window
Click Execute Cell Search in the middle of the Search Unit Cell
window. The Cell Candidates window is displayed showing some cell
candidates. Click Cancel to close the window.
Change Indexing Method to Dicvol. Click Execute Cell Search again
and view the Cell Candidates window with all cell candidates.
Figure 10.5 Cell Candidates Window
Select one of the cell candidates (all are nearly the same, which is a strong
indication for a possible unit cell) and click Refine Cell.
The Refine Unit Cell window is displayed, see Figure 10.6. Make sure
that the Default parameter set is used for a cell refinement.
Page 10 - 7
Figure 10.6 Refine Unit Cell Window
Click Start Refinement and select tab Calculated and Observed Peaks,
see Figure 10.7. The window shows (in text and as a graphic) the
calculated and indexed peaks and their deviation from the theoretical
values. The tab Unindexed Peaks should be empty.
Page 10 - 8
Figure 10.7 Cell Refine Results
Click OK to accept the results and close the window. Open the
Refinement Control tab. A phase Search Unit Cell Result 1 is displayed.
The parameter Unit Cell shows the actual refined unit cell parameters.
The Object Inspector pane displays derived data, like the cell volume and
the estimated cell volume error. It also displays the error of the unit cell
axis or angle selected in the refinement control.
When the phase color is accidentally red, double-click the phase to open
the Object Inspector pane. Change the color of the phase (parameter
Display Color) and watch the peaks displayed in the Main Graphics pane.
All peaks are assigned to the phase and therefore have the phase color, see
Figure 10.8. No non-phase peaks should remain in this example.
Page 10 - 9
Figure 10.8 Object Inspector - Phase Display Color Selection
10.5 SAVING THE RESULTS

To save the complete document (including scan data, background data
peaks, phase data, list of cell candidates and history of the analysis steps),
click File > Save Document, accept the proposed name TaSSe.hpf and
then click Save. Confirm overwriting the document.
Page 10 - 10
Chapter 11
Automatic Rietveld Refinement

(HighScore Plus)
11.1 INTRODUCTION.......................................................... 11 - 3
11.2 LOADING THE DATA.................................................. 11 - 3
11.3 AUTOMATIC REFINEMENT ........................................ 11 - 4
11.4 A BETTER REFINEMENT ............................................. 11 - 8
Page 11 - 1
Page 11 - 2
Chapter 11. Automatic Rietveld Refinement (HighScore Plus)
11.1 INTRODUCTION
This chapter describes the Rietveld refinement of an artificial mixture of two
minerals. The goal of this example is quantitative phase analysis. This is an easy
example using predefined refinement steps. An automatic fitting parameter set for
phase fits rules this Rietveld refinement.
11.2 LOADING THE DATA

(Windows 7) and open the file 25-75.rd.
A few crystal structures are delivered with HighScore Plus. The
Structures folder is found next to the Tutorial folder.
Select File > Insert to insert the file Example.cry, containing the
missing crystal structure data. Now select the crystal structures of Fluorite
(2) and Corundum (4) and click OK to insert them into the current
diffraction document, see Figure 11.1.
Figure 11.1 Insert Fluorite and Corundum Structures
Page 11 - 3
11.3 AUTOMATIC REFINEMENT

Select the desktop layout Rietveld Analysis on the Desktop toolbar.
Select Analysis > Fitting. Check that the option Fitting Mode (third
option in the shortcut menu) is set to Automatic. Correct if necessary.
Select Analysis > Fitting > Start Fit > and then select <Phase fit>
Default Rietveld to start the refinement with the default Rietveld
parameter set. Wait until the refinement is finished.
Figure 11.2 Rietveld Menu Structure
Page 11 - 4
Figure 11.3 Rietveld Refinement Progress
Display the peaks and the calculated profile in the Main Graphics pane.
Set the Additional Graphics pane to display the difference plot. To enlarge
minor differences, you can disable the dynamic difference scale in the
Additional Graphics pane (right-click menu).
Page 11 - 5
Figure 11.4 Rietveld Fit
Zoom in and observe different parts of the profile and of the difference
plot. In the Refinement Control tab, double-click Global Variables to
open the Object Inspector pane. Select Global Settings > Agreement
Indices to view the values of Goodness of Fit and Weighted R profile.
Figure 11.5 Agreement Indices
Page 11 - 6
The phase amounts are usually displayed together with the phase legend in
the Main Graphics pane, see Figure 11.4. Alternatively, you can open the
Quantification pane and view the pie chart, see Figure 11.6. The result is
78.3 % Corundum and 21.7 % Fluorite, which is rather close to the true
weight percentages (75 % and 25 %).
Figure 11.6 Quantification Pane
Page 11 - 7
11.4 A BETTER REFINEMENT

Select Analysis > Fitting. Change the option Fitting Mode (third option
in the shortcut menu) to Manual. In this mode, you can enable and disable
refinable items at will and automatic fitting parameters are no longer used.
Select the Refinement Control tab again and right-click to open the
shortcut menu. Select Refine All > V's. Repeat the previous steps and
select Refine All > U's. Start the refinement again with Analysis > Fitting
> Start Fit and wait until it is finished.
A fast alternative is to click (Start Rietveld Refinement) on the
Fitting toolbar to start a refinement.
Page 11 - 8
Figure 11.7 Refinement Control Shortcut Menu
Select the Refinement Control tab again and right-click to open the
shortcut menu. Now select Refine All > Peak Shape Parameter 1's. Start
the refinement again with Analysis > Fitting > Start Fit and wait until it
is finished.
Page 11 - 9

the Object Inspector pane again. Select Global Settings > General Fit
Properties and change the value of Peak Base Width for Fit from 20 to
30 (FWHMs). Press Enter to finish your input and then start the
refinement again.
Figure 11.8 Setting Profile Base Width
We have now achieved a better calculated profile with smaller differences to the
measurement. This is proven by the agreement indices Goodness of Fit
(GOF) = 2.70 and the Weighted R profile (Rwp) < 11.34.
The phase amounts have changed a little (23.1 % for Fluorite and 76.9 % for
Corundum) and are closer to the given values. The phase quantification is within
2 % of the true values, which is a good result for a standardless phase analysis.
NOTE: A good fit and low R-values do not guarantee a proper quantitative
phase analysis.
Page 11 - 10
Figure 11.9 Agreement Indices
Page 11 - 11
Page 11 - 12

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HIGHSCORE & HIGHSCORE PLUS

Quick Start Guide

Quick Start Guide

EDITION NOTICE: 4022 339 14082, August 2013

1.2 HIGHSCORE PLUS

1.3 CONVENTIONS USED

Starting HighScore and Enabling the

2.2 STARTING HIGHSCORE

Double-click the HighScore icon or the HighScore Plus icon

Figure 2.1 HighScore Plus Initial Window

2.3 CUSTOMIZING THE INTERFACE

Select View > Toolbars > Customize.

Figure 2.2 Customize Window

Figure 2.3 Empty Document With Phase-ID Desktop

2.4 ENABLING THE EXAMPLES DATABASE

Figure 2.4 Manage Databases Window

Navigate to the PANalytical Example Database folder in location

NOTES: a. The PANalytical Example Database is not suitable for performing

Loading and Displaying Data

3.2 LOADING A SCAN

Figure 3.1 Open Window

Navigate to the folder Tutorial in location

Figure 3.2 HighScore Document Window

3.3 DISPLAYING A SCAN

3.3.1 Display Panes

Figure 3.3 Main Graphics Pane

Figure 3.4 Additional Graphics Pane

Figure 3.5 Pattern List Tab

3.3.2 Viewing Exercises

3.4 RETRIEVING A REFERENCE PATTERN

Figure 3.6 Retrieving a Reference Pattern by Restrictions

Figure 3.7 Reference Pattern Lines Displayed in Analyze View

Figure 3.8 Reference Pattern Displayed in Pattern View

3.5 DISPLAYING A REFERENCE PATTERN

Figure 3.9 Pattern List Shortcut Menu

Select Show Pattern to display details of the reference pattern.

Figure 3.10 Reference Pattern Details

Close the Reference Pattern window.

4.2 BACKGROUND DETERMINATION

Figure 4.1 Anchor Scan with Background Preview

Look at the title bar of the Determine Background window to confirm

Figure 4.2 Determine Background Window

Figure 4.3 Numerical Background Data

4.3 PEAK SEARCH

Figure 4.4 Peak Search Window

Figure 4.5 Anchor Scan Including Peak and Background Data

Figure 4.6 Set Display of Peaks Options

Peaks derived from the K2 wavelength are indicated by a different (gray)

Figure 4.7 Peak List

Automatic Profile Fitting

Figure 5.1 Selecting Use available background

Finally check if the fitting mode is set to automatic as follows:

Figure 5.2 R-Value Graphic Window

Figure 5.4 Agreement Indices, Initial Fit

Figure 5.5 More Suitable Background Settings

In the Refinement Control tab, double-click Global Variables to open

Figure 5.6 Asymmetry Type - Split Width

Figure 5.7 Agreement Indices, Improved Fit

Figure 5.8 Anchor Scan and Profile After Improved Fit

Performing Search - Match - Identify

6.2 SEARCH AND MATCH

Figure 6.1 Search & Match Window

Figure 6.2 Candidates List

If necessary, click the column header Score to sort the candidates as