05 HighScore Plus

1

Phase identification and quantification

Phase ID and ‘simple’quantification

X-ray Powder Diffraction (XRPD)

This presentation describes PANalytical’s solutions for phase identification and simple quantification (based on calibration or Reference Intensity Ratio) in crystalline material.

2

2Phase identification and quantification

X-ray powder diffraction technique

20 30 40 50 60 70 802Theta (°)

0

10000

40000

90000

160000

Inte

nsity

(cou

nts)

Angular positions

Relative intensities

100 % intensity

X-ray diffraction data is collected as a scan with intensity as a function of scattering angle (2Theta)The angular positions of the diffraction peaks give information about which crystalline phases are present in the sample.The relative intensities of the peaks are used to calculate the quantity of the phases.

3


Phase mixture

Quartz (SiO2)

+

Salt (NaCl)

SiO2 + NaCl

Characteristic diffractograms

Superposition of the peaks

In a phase mixture the individual diffraction patterns are superimposed.

In a quantitative analysis the relative amounts of the phases are determined.

4


Phase identification

Collect the diffraction pattern for the unknown sample

Comparison with a database of known diffraction patterns

• ICDD – Int. Centre for Diffraction data

• PAN-ICSD, or free alternatives

100.000 – 500.000 possible patterns

Determination of peak positions and intensities

SiO2NaClPhase

identification:

Phase = crystalline material with a typical 3D atomic arrangement

Position [°2Theta] (Copper (Cu))

50 55 60 65 70 75

Counts

0

5000

10000

SiO2 + NaCl

The phases are identified by comparison of the measured diffractogram with a database, such as the ICDD database

5


Reference Databases

• A reference database with known diffraction patterns of pure phases is mandatory for phase identification.

• There are several commercial or free possibilities:

1. Commercial ICDD reference databases

2. Commercial PAN-ICSD ref. database

3. The free COD reference database

4. Special, user-made reference databases

Since phase identification is basically a comparison between the unknown measurement and known (reference) diffraction patterns, a reference database is mandatory for phase identification.

There are several commercial and non-commercial alternatives available, which are discussed on the following pages.

HighScore can use several reference databases at the same time, but all possible combinations are not supported due to our contracts with the database suppliers.

6


ICDD Reference Databases

ICDD = International Centre for Diffraction Data

• Offers time-restricted licenses for several database products without (PDF2) or with (PDF4) crystal structure data, for single or multiple PC’s.

• Best data quality, good coverage of old and new phases, high price, yearly license

• Inorganic, organic and mineral databases available

• Link: http://www.icdd.com/

The ICDD was formerly called the JCPDS.

Their licensing changed with the introduction of a true database format. Use of the database(s) is restricted to one PC per license,licenses run either for one year or for five years.

The databases are usually updated once a year, new entries are critically reviewed to ensure a high database quality.

For a fast access with HighScore the ICDD databases should be converted into HighScore’s own database format.The converted database does check the original license from the ICDD and cannot be copied.

7


PAN-ICSD Reference DatabaseICSD = Inorganic Crystal Structure Database

• The PAN-ICSD is a PANalytical reference database derived from the ICSD.

• It contains reference patterns and crystal structures from inorganic (and some mineral) phases.

• Licensing is the same as for PANalytical analysis software:

Up to 10 PC’s at one adress, no time limit (!)• Original link: http://www.fiz-karlsruhe.de/icsd.html

The PAN-ICSD is the PANalytical version of the ICSD crystal structure database. It contains crystal structure data and, in contrast to the original product, calculated reference data as well and can be used for search-match.

The licensing is similar to PANalytical software products and different from the original product.There is no time-limit, but there no updates available, you can only buy a complete new PAN-ICSD.A new version is issued once a year usually. There is no need to convert this database for use with HighScore.

The data quality is good, the coverage is good as well, the price is moderate. The ICSD contains less ordinary, practical phases or minerals and is more inclined towards inorganic chemical synthesis.

8


COD = Crystallography Open Database

• Contains crystal structures from literature (inorganic, organic, minerals)

• PANalytical has calculated a reference database for search-match from this data, including crystal structure data.

• This database is available free-of-charge! No limits on the number of PC’s or usage time!

Download adress:

www.crystallography.net/archives/2010/PANalytical/

The COD is a free crystal structure database built from scientific publications by volunteers. This initiative was started by Prof. Armel Le Bail.

PANalytical has converted this database into a search-match database ready for use (just download and unzip, no conversion needed).This database is usually updated a couple of times per year, versions are in the \archives\year\subfolder of the COD website.

The coverage is reasonable, the same is true for the quality (automatic checks by software). The COD is rapidly growing.

(Since we cannot be sure about the ownership of every entry in the COD, for legal reasons PANalytical has decided NOT to distribute the COD directly,but to support the COD website and to offer downloads from this website.)

9


Possibilities and limitations

• It is often possible to identify up to 10 phases in a phase mixture

• Typical detection limits are in the order of 0.1 to 1 % per phase

Other parameters can also be determined:

• Degree of crystallinity

• Crystallite size

It is possible to analyse 10 or more phases in a phase mixture with a detection limit of 0.1 to 1 % depending on the sample type.

The degree of crystallinity can be determined in samples which also have an amorphous (non-.crystalline part). In such a case the non crystalline part does not contribute to the diffraction peaks – one can only observe a broad “hump” at lower angles.

The crystallite size influences the width of the individual diffraction peaks. A phase with a very small crystallite size will give broader diffraction peaks.

10


Typical samples

Powder specimen from

• Cement

• Pharmaceuticals

• Minerals

• New materials

• …

Typical samples that are analyzed are all kinds of crystalline materials. Care should be taken when preparing the sample so that preferred orientation is avoided.

If the material is sensitive to air it can be put inside a glass capillary.

If other temperatures are requested the instrument should be equipped with a non-ambient chamber. It is also possible to measure under a protective atmosphere or under a controlled humidity in some of these chambers.

11


Typical configuration

• Pre-aligned optics• Measurement in

transmission or reflection

• Sample in glass capillary if sensitive to air

• Option for non-ambient conditions

Here the instrument is configured in the so-called Bragg-Brentano geometryas commonly used to perform X-ray diffraction experiments in a reflection mode.

Thanks to its modular concept the instrument can quickly be reconfigured for other type of measurements,such as thin film analysis, residual stress or texture determination.

For materials with low X-ray absorption, such as organic materials, the measurement can preferably be done in transmission mode.

Option for non-ambient conditions (low or high temperature, controlled humidity)

12


Software used for data collection

• X’Pert Data Collector

• X’Pert Quantify

• X’Pert Industry

A data collection software is needed to run the measurement. Depending on the main type of application this can be either the Data Collector, Industry or Quantify. The SW saves the data file in a common format, the so called XRDML format. This file is then used in the evaluation step.

13


Software used for analysis

• X’Pert Highscore for phase identification– Database is also needed: ICDD, ICSD, …

• X’Pert Quantify for quantification using a calibration model, selected from 10 available calibration models

• X’Pert Industry for quantification using calibrations in a more flexible way

For the phase identification HighScore (or HighScorePlus) is needed together a database such as the ICDD database.It is also possible to build up your own database by saving experimental data. These patterns can either be used as a separate database or added to an existing database.

In HighScore phases are identified by comparing the experimental peak positions and relative intensities with those of the reference database. A high score (probable match) is found when (almost) all the observed peaks are matched with those of the diffraction pattern. Additional information about the sample can be used to make the analysis quicker and avoid situations with many candidates with approximately the same score.

In a ‘simple’ quantitative analysis one or more reflections (peaks) from each phase are calibrated to give a calibration line with observed intensity (height or area) as a function of concentration of that phase. The calibration is set up by using standards (samples with known amount of that phase). Depending on the type of sample there are many different models available in the Quantify software to set up the calibration.

It is also possible to use the Industry software to set up the calibration. This is the most flexible software where you set up and program your model for the analysis.

14


Typical analysis in Highscore

The result of the phase identification is presented in both graphical and tabular form.

The upper left window (main graphics) shows the experimental data (diffractogram) together with the identified peaks using different colors for the different phases.There is a semi-quantitative result based on the Reference Intensity Ratio method (RIR method) which can be displayed as a pie chart.

The lower left window (additional graphics) shows the peak list (experimental data) and the individual peaks of the different phases found (from the database)

The right-hand side shows the information about the identified phases in a table.

The windows and buttons can be set up to suit the needs of the individual user.

15


Calibration method for quantitative analysis

A set of known standards is measured. The net intensity (height or area) of (at least) one peak per phase is used to set up the calibration line (observed intensity vsconcentration). This calibration is then be used to quantify the calibrated phase in samples similar to the standards.

16


Automated measurement and analysis

• A measurement is followed by analysis using user batches in Highscore

• APP is used to link the measurement with the analytical method

• Scripts are used to trigger evaluation with specific settings

Automatic sample changer

The optional automatic sample changer is used to automate the measurements. In this way, a whole batch of samples can be measured without any user intervention.

The analysis can also be automated by setting up user batches in Highscore. These can be fine tuned to the user’s needs by using scripts.

The Automatic Processing Program (APP) is the link between measurement and analysis. A specific type of sample/measurement kick starts the analysis software which produces the final result in the form of a user-defined report.

17


Analysis report from Highscore

Position [°2Theta] (Copper (Cu))

20 30 40 50 60 70

Counts

0

5000

10000

15000

Mixture3

Visible Ref.Code Score Compound Displ.[°2Th] Scale Fac. Chem. Formula Name* 01-082-1484 74 Chromium Oxide 0.000 0.178 Cr2 O3

* 01-086-2334 72 Calcite 0.000 0.390 Ca ( C O3 )

* 01-075-0097 60 Fluorite 0.000 0.975 Ca F2

Result summarized in an analysis report

Reports can be configured using a template

At the end of the data analysis an analysis report with all relevant details is created. There are some basic report templates that comes with the software. These can be edited and saved under different names, allowing anything from a simple one-page report to a more thorough report including all steps in the analysis.

18


Supporting material

• Quick Start Guides for Data collector, Industry, Quantify and Highscore

• On-line help in the software (F1)

• Tutorials in HighScore

• Basic XRD course

Example measurement files for doing exercises in data analysis are included when software is installed. These are used in the Quick Start Guide and with examples in the on-line help.

1

09-08-2006

A Major Update of X’Pert HighScore Plus

Denver X-Ray Conference Dr. Thomas DegenPANalytical B.V.Almelo, The Netherlands

2

09-08-2006

Overview

1) What’s new in version 3.0

2) Demo of some new features

•Candidate clustering

•Profile fit and LPA analysis

•Charge flipping

In the first part of my talk I’ll give you a short overview about the most important new features added to version 2.5.In the second part I will shortly demo some of those new features.

What’s new in version 3.0• Search-Match and pattern retrieval functions

Option to use multiple databases simultaneously

The first feature block is about new database related features. This part of the software was completely redesigned from scratch to allow for multiple database access. This is getting more and more important because more and bigger databases are available each year. What you see on the current slide is that we are using 4 databases in parallel: A PDF4 Plus, a PDF4 Organics, the PAN example database plus a user database. You can see that in this case the pattern count can easily exceed 700.000 patterns.

3

What’s new in version 3.0Use crystallographic properties and strings like color, formula, compound name as restrictions and get a live preview of matches passing the applied filters.

If you are using such a huge quantity of patterns, it is increasingly important to have powerful restrictions tooling available in order to decrease the amount of patterns for further analysis. We added the option to use strings like color, formula compound name etc and also crystallographic properties as restrictions. What is even more useful is, that whatever restriction you choose, you get a live preview of how many hits are passing the current set of filters. Another nice feature is the “Fuzzy” string search were you can enter parts of strings and in a dialog you get to see all possible matches and their count.

4

What’s new in version 3.0Added candidate list clustering to drastically reduce complexity and to remove silly duplicates

Search-Match is an analysis that in one respect profits from big database (it is more likely to find your special pattern), but in another respect is suffering from it. The reason for suffering is that you get more and more doublets that are actually spoiling /flooding the candidate list. HS+ has one feature on board that can deal with such situations: Cluster Analysis. And that is what you can do now, you can simply cluster the whole candidate list and all similar patterns will fall into distinct groups. The advantage is that you get a very clean and short list that just contains patterns that are really different. All similar pattern are hidden behind the plus node sign and can be made visible on demand.

5

What’s new in version 3.0• More additions:Support for measured reference profiles (as available from ICDD release 2008 on)Graphical thumbnail hints for reference patternsSupport for mass conversion of CIF files from a folder to a reference databaseCompletely redesigned Edit/Copy/Create user pattern dialog

But there are much more new features concerning database and Search-Match/Pattern Retrieval. We now support measured profiles in databases as for example present since PDF4 Plus release 2008. Retrieval as well as storage inside the database is supported. User databases are now completely separated from commercial databases. Another advanced feature is the possibility to create user databases based on CIF files. The files can stem for example from own single crystal structure determinations or from the Internet. The user just selects a folder and HS+ converts all found CIF’s into a database containing all meta information, structure data (for Rietveld analysis) and peak sticks for Search-Match. Also the reference pattern editing facilities are completely renewed. Users now can edit all reference data as well as structure data that is present in the reference database. Candidate patterns can be visualized by sizable semi-transparent graphical thumbnail hints.

6

What’s new in version 3.0• Cluster Analysis

Much faster than before, speed up by a factor 5 -10 depending on data type and scoring settings

Clustering now includes more scoring methods like Spearmans Rho or Pearsons R for easy comparison of non-XRPD like data sets (Raman, IR, NMR…)

The next part of the software that is renewed is the Cluster Analysis. <short explanation what it is…>The most prominent new feature here is the speed up by a factor of 5 to 10 depending on the data type and scoring settings. To achieve better out of the box support for non-XRPD data like NMR, IR or Raman we added more scoring methods like: Spearmans Rho and Pearsons R

7

What’s new in version 3.0Cluster confidence intervals can be represented by semi-transparent spheres

Clusters can be removed from the 3D PCA score plot (on demand):

To better visualize the relations of clusters in the 3D PCA score plot we added the display of confidence intervals of clusters by semi-transparent spheres. Furthermore complete clusters can now be hidden in the score plot on demand to get a clearer picture in complex cases.

8

What’s new in version 3.0• Profile Fitting

The Profile fitting is completely reprogrammed using a new boundconstraint parameter estimation (BCPE), non-linear least-squares algorithm

Available profile functions are PearsonVII, pseudo-Voigt and Voigt function in non-, single-split and double split mode. Another available asymmetry description is the FCJ algorithm for the pseudo-Voigt function

Peaks can be grouped arbitrarily and different groups can be refined using different profile functions.

Another part that is completely rewritten from scratch is the Profile Fitting engine. It is now based on a bound constrained parameter estimation algorithm.This algorithm makes the fitting both fast and stable. Available profile functions arePearsonVII, pseudo Voigt and Voigt in non-, single- and double split mode. The FCJ (Finger, Cox & Jephcoat) algorithm is available too for the pseudo Voigt function.Peaks can be grouped arbitrarily and different groups can be refined using different profile functions.

9

What’s new in version 3.0Profile fitting is executed in automatic or manual (expert) mode

Automatic mode:(Controlled by parameter sets)

Manual mode:(All refine flags are set manually)

Profile fitting can be used in automatic, parameter set controlled, mode or in a manual “expert” mode where all refinement flags can be set manually.In automatic mode this task is executed automatically based on the selected parameter set. A parameter turn-on sequence is often not necessary, all parameters are refined simultaneously.In manual mode the user can select one or multiple peaks and in the Object Inspector he can checkmark refine flags like refine- position, FWHM, area or shape.

10

What’s new in version 3.0Individual peak profiles are shown as lines, or hatched or solid (with blending)areas.All peak parameters can be changed graphically, all corresponding views are updated in real-time.

In complicated cases it can be very hard to decide on the quality or meaningfulness of a fit. To support the user in this task we added advanced drawing and editing capabilities. Individual profiles can now be either shown as lines, hatched or solid (with blending). Furthermore peak features like height, position and FWHM can be changed graphically by using the drag rectangles or the peak line. While doing this, all lists and the rest of the graphics are updated in real time.

11

What’s new in version 3.0• Line Profile Analysis

Williamson-Hall Plot

Sin(Theta)0.950.90.850.80.750.70.650.60.550.50.450.40.350.30.250.2

Stru

ct. B

* C

os(T

heta

)

1.05

1

0.95

0.9

0.85

0.8

0.75

0.7

0.65

0.6

0.55

0.5

0.45

0.4

Struct. B * Cos(Th) = 0.25(8) + 0.8(1) * Sin(Th)Chi square: 0.0644416

Size [Å]: 349.33(8)Strain [%]: 0.20(3)

Single line method for individual peak analysis, after:T.H. de Keijser, J.L. Langford, E.J. Mittemeijer and A.B.P. Vogels, J. Appl. Cryst. (1982), 15, 308 - 314

Williamson-Hall plot with live update during fitting and peak manipulation for the analysis of multiple peaks

In addition to the new profile fit features we also added Line Profile Analysis to HS+. The LPA analysis is based on the universal shape concept where theLorentzian and Gaussian broadening is calculated from basic peak features like FWHM and shape. This makes the analysis independent of the used profile function. The analysis is possible for single peaks as well as for a whole scan. A nice feature is that all related plots like for example the Williamson-Hall fit/plot are updated in real time during profile fitting or when peak parameters are changed manually.

12

What’s new in version 3.0Additional features: Instrument resolution function plot, FWHM/Beta plot and size/strain calculations using the universal shape parameter with support of single line method

To further support the LPA analysis more plots were added like: A plot that shows the instrumental profiles (Gauss and Lorentz broadening)A broadening plot that shows both Lorentzian and Gaussian part of the total broadening.Fits through these curves are made by a Caglioti types curves or by a 2nd order polynomial.The Universal Shape plot shows the calculated universal shape for all fitted peaks

13

What’s new in version 3.0

• Charge Flipping / Fourier Analysis

Integration of the “Superflip” package by Lukas Palatinus from the EPFL. This charge flipping software package can simply be started by a mouse click after a LeBail or Pawley fit

As a new features for the plus part of HighScore we added a Charge flipping option as well as enhanced Fourier analysis. For Charge Flipping we integrated theSuperflip package of Lukas Palatinus from the EPFL (École polytechnique fédérale de Lausanne). Superflip can simply be started with a mouse click after a LeBail orPawley fit.

14

What’s new in version 3.0The progress of the structure solution can be followed graphically in a new OpenGL electron density/structure viewer that supports 2D/3D meshes, point clouds and surfaces

The electron density map peaks can be shown as a full list or reduced to symmetry dependent positions, hiding equivalent positions behind plus signs.

The currently focused peak in the list is marked too in the 3D plot

The progress of the structure solution can be followed graphically in a new 3D OpenGL electron density/structure viewer that supports display of 2D/3D meshes, point clouds and surfaces. The electron density map peaks can either be shown as a full list or reduced to symmetry dependant positions hiding equivalent positions under nodes. Selecting one peak in the list shows the selected position in the 3D graphics

15

What’s new in version 3.0The viewer can also be used to overlay the solved (or a model) structure, to show electron density surfaces and to visualize (difference) Fourier maps

As you can see here the viewer can be used too to overlay either the solved structure or a different model structure. Further the same viewer can be used to visualize difference Fourier maps and to pick atoms from these maps.

16

What’s new in version 3.0

• Completely revised scripting supportVisual debugger for user scripts Tooltip evaluation of variables

Option to set break points

Visualization of the script content(Code Explorer)

Another part of the package where we massively added new features is the scripting component. In the old version it was quite hard to use because you have just an script/text editor and when the script eventually fails it is almost impossible to find out what's going wrong. The new version however contains a full blown visual debugger that allows step by step execution of scripts as well as tool tip evaluation of variables, an option to set break points and a code explorer that shows, which variables and procedures are actually recognized by the compiler. The objects for scripting are documented in the help system. Armed with these tools and examples cripts supplied, even an inexperienced programmer can write small but powerful scripts on his own.

17

18

Summary • To see more features of HighScore Plus V 3.0,

please come to our booth for an extended demonstration.

•DEMO

HS+ has of course much more features that I am not able to show in such a short 15 minutes presentation. So please come to our booth to get an extended demo.Thank you very much for your attention!

05 HighScore Plus

Documents

Transcript of 05 HighScore Plus