Guide to Basic X-Ray Powder Diffraction Data Analysis using - MIT

By Earl Matthews,2014-04-02 04:39
8 views 0
Guide to Basic X-Ray Powder Diffraction Data Analysis using - MIT

    Introduction to PANalytical X’Pert HighScore Plus v3.0

    Scott A Speakman, Ph.D.

    MIT Center for Materials Science and Engineering

    This document will introduce you to some of the basic functionality of PANalytical X’Pert HighScore Plus, v3.0. There is much more that can be done with the program. Some of the

    instructions in this document will allude to things that you can do in HighScore Plus without

    telling you how to do them. In such cases, this is because a quick reading of the relevant help

    section in HighScore Plus will clearly tell you how to accomplish the task.

The last page of this document gives you some keywords you might search one in the help to

    learn about more advanced tools.

    I. Selecting a User Interface and Program Settings

    a. Desktops pg 2

    b. Restoring Defaults pg 2

    c. Panes pg 3

II. Displaying Data and Basic Manipulation

    a. Opening Data pg 4

    b. Zooming In/Out pg 4

    c. Comparing Multiple Scans pg 5

III. Opening a PDF Reference Pattern

    a. Retrieving a Card by Reference Code pg 6

    b. Searching for a Reference Pattern pg 6-9

    i. Using Chemistry as search parameters pg 7

    ii. Using Quality Marks as search parameters pg 7-8

    iii. Using Subfiles as search parameters pg 9

    c. Manipulating Reference Patterns pg 9

    d. Testing for K-beta peaks pg 10

IV. Search-Match

    a. Fit Background pg 10

    b. Find Peaks pg 11

    i. Change the display of peaks pg 12

    c. Optional Steps: Convert Slits and Strip Kα2 pg 12

    d. Search-Match pg 13-14

    V. Calculating Penetration Depth of X-Rays pg 15

    VI. List of Other Features in HighScore Plus pg 15 Appendix A. Overview of the GUI pg 16-19

    Revised 27 March 2012 Page 1



    “Desktops” are predefined arrangements of windows and toolbars in HighScore Plus. You can create your own or use one of the default desktops provided with the HighScore Plus program.

    Default Desktops are designed to be optimal for specific tasks, such as Phase ID or Profile Fitting. If you start using HighScore Plus and the desktop is arranged in a way that you are unfamiliar with, you can change the desktop to one that is more useful.

To select a desktop, go to the menu View > Desktop

     Select a Desktop from the menu list, not from the Dropdown menu.

     Useful desktops are: Phase-ID, Line Profile Analysis, and Structures.

     You can also change the desktop layout to your preference and save it as a new desktop

    (see Customizing the Application in the help).

Restoring Defaults

    If you begin using HighScore Plus and it is behaving in an unusual way, you may want to restore the program behavior to its factory defaults. In order to do this:

Go the menu Customize > Program Settings

     Click on the button Reset All to Default o

    o Click on the OK button to close the window

    o You can also explore Program Settings to modify the look, feel, and performance of

    the program such as options for display behavior, automatic backing up of analysis

    files, behavior during pattern simulation or Rietveld refinement, and data treatments

    applied automatically when you open a file

Go to the menu Customize > Document Settings

    o Click on the button Reset All to Default

    o Click on the OK button to close the window

    o Note: this menu is only available after you have opened a file

    o You can also explore the Document Settings to change options for the graphic display,

    the analyze view, and labeling for legends and peak markers


    By default, the menus only show the most recently used commands. To turn off this feature, so that you can see all commands in the menus:

     Select the menu View > Toolbars > Customize

     Select the tab Options

     Uncheck the box next to “Menus show recently used commands first”

     Click Close

Revised 27 March 2012 Page 2


    There are different work areas in HighScore Plus, called “Panes”. There are up to four different

    Panes. Each Pane is a window that contains a certain element of the document. The Panes are:

     Main Graphics shows the primary plot of your data for analysis and manipulation

     Additional Graphics shows modified plots of your data to assist in analysis

     Lists Pane contains tables of information that provide an overview of your data and

    summarizes the results of your analysis

     Object Inspector is a dynamic list that provides detailed information about any item that

    you select in HighScore plus. In some desktops, it is a separate pane; in some desktops, it

    is part of the Lists pane.

     To resize the panes, drag your mouse to the border between two panes until the cursor

    changes to , then left-click and drag to resize the pane.

    Main Graphics

    Lists Pane &

    Object Inspector

    Additional Graphics

This image shows the basic layout of the “Phase-ID” desktop

    Appendix A provides more detailed information about the panes and toolbars commonly used in HighScore Plus.

Revised 27 March 2012 Page 3


Opening Data

    To Open a data set, go to File>Open

    ; If you select multiple files, each one will open in its own document.

Zooming in Main Graphics

     Zoom in by left-click and dragging in the Main Graphics pane. Zoom out by double-clicking in the Main Graphics pane.

     When zoomed in, you can use the scroll bar at the bottom of the Main Graphics pane to move

    the zoom view left and right

     When zoomed in, hold down the Alt key and left-click and drag the mouse:

    o If you drag the mouse left-right, you will scroll left or right

    o If you drag the mouse up-down, you will

    zoom in or zoom out x (y autoscales to the

    maximum intensity in the zoomed view)

     Use the Automatic Scale button of the Tool

    Palette toolbar to switch autoscaling of intensity on

    or off

     Use the Zoom Intensity button of the Tool

    Palette toolbar to switch zooming in Y-axis direction

    on or off.

You change the Y-axis scale by toggling with the

    "Set Y-axis Scale" button from the Tool Palette


    o To switch directly to a "Linear Y-Axis",

    "Square Root Y-Axis" or "Logarithmic Y-

    Axis" scale use the small button next to it.

    You can use the additional graphics pane to manipulate your zoom view by enabling the Zoom Overview.

     Right-click in the Additional Graphics pane

     Select the menu Show Graphics > Zoom Overview

    o The Additional Graphics pane will show you your entire scan, with a black box

    highlighting the zoomed region

    o To move the zoom region, left-click and drag the black highlight box

    o To resize the zoom region, left-click and drag the white dot at the side of the black

    highlight box.

Right-clicking in the Main Graphics pane will give you a menu with shortcuts to several options,

    including analyses (determine background, strip K-Alpha2, etc) and cursors (show spectral lines,

    insert peaks, etc).

    Revised 27 March 2012 Page 4

Comparing Multiple Scans

To compare multiple data sets

    ; Open the first data file using the menu File > Open.

    ? This will be the “Anchor Scan”

    ; Use the menu File > Insert to add additional scans to the document.

    ? Select all of the additional data files that you want to add and click OK

    ? You can select multiple files to insert by using shift+click or ctrl+click ; In the Main Graphics Pane, go to the Compare or 2D tabs to view all of the scans

To adjust scan properties such as line color

     Go to the Scan List tab in the Lists pane to see a list of all of the scans.

     In the Scan List, select the scan that you want to modify

     Go to the Object Inspector

     You can adjust properties of the scans, such as line color or name, in the Object Inspector.

To scale scans so that their intensities are similar:

     Go to the menu Treatment > Adjust to Anchor

     In the “Adjust” drop-down menu, select the scan that you want to adjust

     Select the Scale Factor, Vertical Shift, or Both tab

    o Scale Factor adjusts the net intensity of the pattern, multiplying every data point by the

    scale factor. This is useful if two patterns were collected with a different scan rate or the

    samples had different packing densities, producing different overall intensities.

    o Vertical Shift will move the entire pattern up or down by a set amount. This is often done

    to match the background without scaling the intensity.

    o Both will both scale the pattern intensity (to match the peak maximum) and to shift the

    pattern up/down to match background

     In Method, select Fit Maximum, Fit Background, or User Defined

     The program will fit based on the part of the pattern visible in the Main graphics. o

     Click the Adjust button

    o The program will show you a preview of the result.

    o You can change the adjustment (for example, the user defined value) and then click

    Adjust again to preview the new result.

     Click the Accept button

     In the Main Graphics pane, go to the Compare tab to view the multiple scans.

Note: Treatment and Analysis tools only work on the Anchor scan

    Revised 27 March 2012 Page 5

III. Opening a PDF Reference Pattern

    The Powder Diffraction File (PDF) is a database of X-ray powder diffraction patterns maintained by the International Center for Diffraction Data (ICDD). You can find more information about the PDF, including tutorials and references, at

Data in the PDF comes from:

     publications, journals, scientific periodicals and theses

     ICDD grants for new materials

     Data collections donated by companies or individuals

     Data from other database organizations that are licenses by the ICDD

To Retrieve PDF Patterns using the PDF Reference Number

    1) Go to the menu Reference Patterns > Retrieve Pattern By > Reference Code

    2) In the dialog box, type in the Reference Code(s) for the PDF card(s) that you want to open 3) Click Load

    4) The cards will be loaded into the Pattern List in the Lists Pane

    In older literature, you may see reference to JCPDS cards. The JCPDS database was the predecessor to the PDF. You can use the original JCPDS reference number to retrieve that entry in the PDF database.

To search the PDF Database for References

    If you do not know the reference code for the PDF card for the material that you are interested in, you can search the PDF database for the relevant entries.

1) Go to the menu Reference Patterns > Retrieve Pattern By > Restrictions

    2) In the Restrictions dialogue window that opens, you define parameters to restrict which

    patterns will be retrieved from the database. If you defined no parameters at all, then all

    patterns in the database would be retrieved.

    a) Each tab in the Restrictions window allows you to control a different subset of search

    parameters. In each of the tabs, you can set the parameters for searching the PDF

    database for reference patterns.

    ) b) The options available in the tabs are described on the next page (pg 7

    c) Each tab that is being used to constrain the search will be highlighted with a red flag

    d) The information bar at the bottom of the window tells you how many patterns will be

    retrieved with the current set of restrictions. This number should be less than 10; anything

    more is difficult to manage. If you cannot make this number less than 10, then you

    should use Search & Match (pg 11) instead.

    3) Once you have set up your search parameters, using as many or as few Restrictions as you

    like, then you click Load to perform the search and find the reference patterns.

    a) The reference patterns will be added to the Pattern List pane.

    b) If you have other reference patterns already loaded, the Combine Patterns dialogue will

    ask you to specify how you want to combine the new patterns with the previous. Make

    your choice and click OK.

    c) The Restrictions window will remain open, allowing you to retrieve more references

    i) If you are done finding reference patterns, then click Close.

    Revised 27 March 2012 Page 6

    The tabs that you can use to constrain you search of the PDF database are:


    This is the most common restriction that you will use.

    ; You have three fields to specify what compositions you want to find in the database: ; “All of:” all of these elements together must be present in each reference pattern ; “At least one of:” one or more of these elements must be present in each reference pattern ; “None of:” none of these elements must be present in each reference pattern

    ? If you click on the button Add Rest to None Of, then every element not listed in “All of:”

    or “At least one of:” fields is added to the “None of:” field

; The Min and Max Number of Elements controls how many unrestricted elements are

    allowed in the retrieved reference patterns


     In this example, 2146 patterns will be

    retrieved. These patterns would include

    FePO4, LiPO4, and LiFePO4; but would

    also include any material that contains P

    and O, Li or Fe, and any other element

    for example, Fe2AsP3O12 or RbFeP2O7.

In this example, only 181 patterns will be

    retrieved. All elements except Li, Fe, P,

    and O were added to the “None of:” field

    by clicking the Add Rest to None Of

    button. Patterns loaded would include

    FePO4, LiPO4, and LiFePO4.


    This is another very useful restriction to use.

    ; It is highly recommended that you check the entry “Skip marked as deleted by ICDD”

    ? Entries are deleted from the database if they are replaced with better references or they

    are found to be wrong.

    ? These entries are kept in the electronic database in case you need access to them (perhaps

    an old paper references a now obsolete PDF card), but you normally do not want these

    entries to be included in your search results.

    ; You can use the other settings to restrict what type of reference cards you search. The quality

    marking system of the ICDD is explained on the next page (pg 11)

    ; You can also use this tab to exclude data that was not collected at standard pressure and

    temperature (“Skip non-ambient temperature” and “Skip non-ambient pressure”)

Revised 27 March 2012 Page 7

    PDF cards have quality marks assigned by the ICDD to indicate how reliable the data is.

    Star (S, +). Indicates the pattern represents high-quality diffractometer or Guinier data. The chemical composition has been well characterized.

     The intensities have been measured objectively-- no visual estimation is allowed. Good range and an even spread of intensity.

     Completeness of a pattern is sensible

     Each reflection with d-value less than or equal to 2.500 Angstroms has at least three

    significant figures after the decimal point. Reflections with d-value less than or equal to

    1.2000 Angstroms have at least four significant figures after the decimal point. No serious systematic errors exist.

     The |Δ2Θ| of a qualifying reflection is less than or equal to 0.05 degrees. In the case of

    multiply-indexed reflections, only the minimum absolute Δ2Θ is considered.

     The average |Δ2Θ| value is less than 0.03 deg. for qualifying reflections.

     No un-indexed, space group extinct or impurity reflections are present.

Indexed (I). Indicates the pattern has been indexed.

     There is a reasonable range and even spread in intensities.

     Completeness of the pattern is sensible.

     Reflections with d-value less than or equal to 2.000 Angstroms have at least three significant

    figures after the decimal point.

     No serious systematic errors exist.

     No qualifying reflection has an absolute Δ2Θ greater than or equal to 0.20 degrees.

     The average absolute Δ2Θ value should be less than or equal to 0.06 deg.

     The maximum number of un-indexed, space group extinct or impurity reflections is two, but

    none of these reflections is among the strongest eight lines.

    Blank (B). Indicates the pattern does not meet the Star, Indexed, or Low-Precision criteria.

    Low Precision (O, ?). Indicates the diffraction data have been taken on poorly characterized material, a sample with known (or suspected) problems such as preferred orientation, or that the data are known (or suspected) to be of low precision.

     Data from a multi-phase mixture.

     Data from a phase poorly-characterized chemically.

     The "O" quality mark is commonly assigned to patterns for which no unit cell is reported Usually, the editor has inserted a comment to explain why the "O" was assigned. The number of un-indexed, space group extinct or impurity reflections is three or more. One of the three strongest reflections is un-indexed.

    Prototyping (P). Indicates the structural data that was assigned to a particular entry from the Linus Pauling File. Prototype structure is an editorial action to assign a space group and coordinates for entries that have not recovered this information from the primary literature. Rietveld (R). Indicates the d-values are directly the result of Rietveld refinement of the data. Hypothetical (H). Indicates the structure is calculated theoretically from the atomic positions and thermal parameters of an isostructural compound

    Revised 27 March 2012 Page 8


    This tab is used to restrict the search to certain

    subfiles of the PDF. Data in the PDF comes

    from several different sources. The data is

    organized into subsets depending on the

    source and subfiles depending on

    characteristics of the material. In HSP, you

    can search for entries from a single

    subset/subfile, a combination of subsets and

    subfiles, or from all subsets.


    This restriction tab can be used to specify parameters of the crystal structure for all retrieved entries, such as the Crystal System (cubic, hexagonal, …), Density (theoretical density based on

    crystal structure), or lattice parameters. This restriction is not used that often.


    This restriction is used to search for text in the PDF reference, such as a specific Mineral Name

    (hematite, etc) or Compound Name (polyethylene, etc). This restriction is not used that often.


    Once you have searched the database and added reference cards, you can view them in the Main

    Graphics pane and manipulate them in the Lists Pane and Object Inspector

In the Lists Pane, go to the Pattern List tab. You can:

    ; Make the pattern Visible or Hidden by checking/unchecking the Visible column

    ; Change the pattern color by using the drop-down menu in the Display Color column

    ; Open the reference card by double-clicking on an entry

    ? The entry will contain information such as formula, unit cell information, the reference

    that the entry came from, and a list of peak positions and intensities.

    ? You can use the peak list in the reference card to decide where you want to scan. A card

    might list several peaks at low angles (below 20deg 2theta) that are very informative.

    After 55.74deg 2theta, all of the diffraction peaks are weak. Therefore, a good scan range

    would be from 5deg to 56deg 2theta.

In the Object Inspector, you can manipulate the display of the Reference Pattern (color, scaling)

    ; Click on an entry in the Pattern List

    ; go to the Object Inspector

    ? Settings in the Display section of the Object Inspector will let you change the visual

    display of the reference pattern in the Main Graphics

    ? Other sections display information about the reference card

    If you want to compare your data to the reference card for a specific phase, it is easier to use the search-match procedure, explained on the next page.

Revised 27 March 2012 Page 9

To Test for K-Beta Peaks

    1) Select the menu Tools >Spectral Lines

    a) You now control a cursor that indicates the position of the K-alpha1 peak 2) Position the cursor over a major K-alpha1 diffraction peak

    a) The solid blue line shows the position of the corresponding K-beta peak

    b) The dotted lube line shows the position of the corresponding W L-alpha peak

    c) The dotted red line shows the position of the corresponding K-alpha2 peak 3) You only need to check the one or two strongest peaks of the pattern for the presence of K-

    beta peaks. The intensity of a K-beta peak is proportional to the intensity of the

    corresponding K-alpha1 peak.


    There are several steps involved when you want to determine the identity of unknown phases in your diffraction pattern.

1) Fit the background.

    a) Select the menu Treatment > Determine Background

    b) Use a small bending factor (0-2) and a granularity between 15 to 30

    c) When the background is good, Accept the background (do not Subtract).

     The granularity parameter changes the number of intervals used for background


     The bending factor slider adjusts the curvature of the background Revised 27 March 2012 Page 10

Report this document

For any questions or suggestions please email