WinXPOW_3.05

WinXPOW Software Manual Version 3.05 (c) STOE & Cie GmbH 2011

STOE & CIE GmbH, Hilpertstraße 10, D-64295 Darmstadt Phone (+49) 6151 / 9887- 0 Fax (+49) 6151 / 988788 E-mail: [email protected] Homepage: www.stoe.com

Contents 1 General

1-1

1.1 1.1.1 1.1.2

Introduction GeneralRemarks InputElemen ts

1-1 1-1 1-1

1.2

Install ation

1-3

1.3

TheMainMenu

1-6

1.4

User

1-7

2 Instrument Parameters

2-1

2.1

Introduction

2-1

2.2

Configurati on

2-2

2.3

PSDsettings

2.4

Defaults

3 Diffractometer Control

2-6 2-10

3-1

3.1

Introduction

3-1

3.2 3.2.1 3.2.2 3.2.3 3.2.4 3.2.5 3.2.6 3.2.7 3.2.8 3.2.9

File New Open Save SaveAs Print PrintPreview PrintSetup Most RecentFileList Exit

3-2 3-2 3-2 3-2 3-2 3-3 3-3 3-3 3-3 3-3

3.3 3.3.1 3.3.2 3.3.3 3.3.4 3.3.5

Setup Detector Generator Sample Changer Title / Comment Options

3-4 3-4 3-4 3-5 3-5 3-5

3.4 3.4.1 3.4.2

Diffractom eter Open Shutter CloseShutter

3-7 3-7 3-7

WinXPOW Software Manual

0-2

3.4.3 3.4.4 3.4.5 3.4.6 3.4.7

DriveCircles Set Slit Width Sample Changer(NextSample) Sample Position EraseIP-PSD

3-7 3-8 3-9 3-10 3-11

3.5 3.5.1 3.5.2 3.5.3

Ranges ScanMode ScanRange(s) ScanUsage

3-12 3-12 3-13 3-15

3.6

Measure

3-19

3.6.1 3.6.2 3.6.3 3.6.4 3.6.5 3.6.6 3.6.6.1 3.6.6.2 3.6.6.3 3.6.6.4

Data Collection StepScan Count BeamOptimizat ion Sample Position Measureme nt PSDCalibr ation General PSD Calibration– File PSD Calibrat ion – Measure PSD Calibrat ion – Evaluati on

3-19 3-20 3-21 3-21 3-23 3-24 3-24 3-24 3-25 3-27

4 High-Temperature Data Collection

4-1

4.1

Introduction

4-1

4.2

Configurati on

4-1

4.3 4.4 4.4.1 4.4.2 4.4.3 4.4.4 4.4.5

Creationof the RawDataFile HighTemperatureDataCollect ion File HTCParam eterFile Setup Inputof a Temperatur e Program Preferencess HTC Measureme nt, RunandControl

4-3 4-4 4-4 4-5 4-6 4-8 4-9

5 Graphics

5-1

5.1

Introduction

5-1

5.2

Files

5-2

5.3

View

5-4

5.4

Options

5-6

5.5

Window

5-11

6 3D-Graphics

6-1

6.1

Introduction

6-1

6.2

Files

6-2

6.3

View

6-3


0-3

6.4 6.4.1 6.4.2 6.4.3 6.4.4 6.4.5

Options Colour Font Labels Scaling Title

7 Raw Data Handling

6-5 6-5 6-6 6-6 6-7 6-7

7-1

7.1

Introduction

7-1

7.1.1 7.1..2 7.1.3 7.1.4 7.1.5

Menu-,Caption-,Status-andToolbars LayerPanel HistoryPanel RangeViewWindow Report Panel

7-2 7-2 7-3 7-3 7-4

7.2 7.2.1 7.2..2 7.2.3

File DifferentWorking Modes Export Files Preferences

7-5 7-6 7-7 7-8

7.3

View

7-10

7.4

Param eter

7-10

7.5

Ranges

7-11

7.6

Operations

7-13

8 Pattern Fitting

8-1

8.1

Introduction

8-1

8.2

File

8-1

8.3

Param eters

8-4

8.4

Operations

8-10

8.5

View

8-14

8.6

Options

8-16

9 Peak Calibration

9-1

9.1

Introduction

9-1

9.2 9.3

Files MatchPeaks

9-1 9-2

9.4 9.4.1 9.4.2

Calculat e Calculatepolyno mials Calculate spline

9-4 9-4 9-4

9.5

Calibratepeakfile

9-6

9.6

Auto calibrate

9-6

9.7

Write IP calibrati on

9-6


0-4

10 Index & Refine

10-1

10.1

Introduction

10-1

10.2

File

10-2

10.3

View

10-3

10.4 10.4.1 10.4.2 10.4.3

Index IndexingParam etersfor Werner’ s algorithm (TREOR) IndexingParam etersfor Visser’salgorithm (ITO) IndexingParam etersfor Louër’salgorithm(DICVO L)

10-4 10-4 10-6 10-7

10.4.4 10.5

Outputfrom the indexi ng routines Refine

11 Theoretical Pattern

10-10 10-11

11-1

11.1

Introduction

11-1

11.2 11.2.1 11.2.2

File Exam ple CIFfile TINfile forma t

11-2 11-3 11-5

11.3 11.3.1 11.3.2 11.3.3 11.3.4

Setup CrystalParam eters AtomList Patter n Param eters Loadfrom ICDD

11-7 11-8 11-10 11-12 11-14

11.4

View

11-15

12 Crystallinity

12-1

12.1

Introduction

12-1

12.2

File

12-3

13 Size / Strain

13-1

13.1

Introduction

13-1

13.2

File

13-3

13.3

View

13-4

13.4

Options

13-4

13.5

Output

13-5

14 System-Evaluation

14-1

14.1

Introduction

14.2

Themenu- andtool-bar

14-2

14.3

TheCaption-Bar

14-5


14-1

0-5

14.4

TheOperation Bar

14.5

TheDisplayWindow

14-10

14.6

TheReport Bar

14-12

14.7

Exam ple for Processing Data

14-14

14.8

Preference Dialog

14-15


14-5

0-6

1. General

1.1 Introduction

1.1.1 General Remarks The WinXPOW Program Package is a true 32 bit Windows application with all the benefits of the graphical user interface of Microsoft Windows 2000, Windows XP and Windows 7. This manual cannot explain how to use Windows, so the user should be familiar with its basic operations.

1.1.2 Input Elements When the program is started, the main menu bar is presented to the user. The menus can be selected by a mouse click on the menu text, or by pressing ALT followed by the underlined letter (hotkey) on the keyboard. In most cases a drop-down menu with more selections will be opened. When a shortcut key exists for a menu item, this is indicated. The menu items can behave in different ways : • • •

Selections that can be turned on and off. When turned on, a check mark is displayed. Items take effect as soon as selected. Items requiring further information, which is usually obtained dialogthrough boxes . This is indicated by an ellipsis ( ... ) following the menu item text.

The WinXPOW programs use three different kinds of dialog boxes : 1. Common dialog boxes supplied by Windows ( Open File, Save File as ... ) which are used in almost all Windows applications with the same design and input elements ( selection of drive, directory and file names ). Because they are supplied by the user’s version of Windows, their input elements will be named in the language used by Windows. WinXPOW uses only English names, so it is possible that two different languages are used in the same dialog boxas ! For operations, makes usefiles. of the convention that the default directory for output files is the same the file directory of theWinXPOW corresponding input 2. Dialog boxes where parameters can be entered. Here the user is confronted with the full variety of input elements available under Windows : Edit fields Radiobuttons Checkboxes Listboxes Pushbuttons

• • • • •

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Fieldscontaining textor numericalvalueswithfull editingfunctionalit y Representa single choicein a set of mutually exclusi ve choices Optionswhichcanbe turnedon or off Displaychoicesor results Buttonswhich initiatean action

3.05 Software Manual - General

1-1

Many of the list boxes allow selection of more than one entry. To select multiple entries, use the mouse together with the SHIFT or CTRL keys, as for example in the Windows file manager. TheEnter key is used differently as compared with other Windows applications. When Enter is pressed after modification of a parameter value, other fields depending on that parameter will be updated. Sometimes it is also used to start an action. As will be seen later, this behaviour simplifies program handling. These boxes provide two buttons for Okay exit andCancel ( ), another possibility isESC thekey orClose from the top right corner of the box; both are equivalent Cancel . to

Only when the Okay button is pressed, the new set of parameters will be stored,Cancel whereas button the causes all changes to be ignored. 3. Dialog boxes which also provide diffractometer operations in addition to the previous type. Common to all is the following set of buttons.

TheStart button will start the operation ( Scan, Data collection ), all other buttons except Stop will then be disabled until it is finished. With Stopthe button the current operation will be stopped immediately. Exit Finally closes the dialog box and returns to the previous menu or dialog box. When parameters related to the procedure have been modified, they will be updated as Start soon is selected. as

For convenient viewing and printing of text files which have been created by WinXPOW, the utilitiy ‘Textview‘ is supplied.

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1.2 Installation POW package comes with an installer application. The installer should be used toPOW The WinX install the WinX package or perform an upgrade of an existing installation. You Ad ministrat must have or ' privileges ' for running the installer application. It is strongly recommended to close all other programs during the installation process. Especially any running program from an older WinXPOW version must be closed, otherwise the upgrade may fail!

WinXPOW_3.00_Setup.exe Start the installer application by double clicking on the icon. The installer wil open and Next shows a welcome screen. Press the>’‘ button to proceed.

The installer will present the software license. To proceed with the installation you must accept the license agreement. Press Next the ‘ >’ button to proceed.

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On the next screen the installer will show you the location where the software will be installed. Usually you should >’ button accept the default location and never change it.Next Press the ‘ to proceed.

Now the installer will copy all files onto the computer and perform all necessary setup steps.

If no error occurred during installation the installer will present a last page.Finish By pressing ’ buttonthe you ‘ leave the installer.

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stadip.lic If you have installed WinXPOW for the first time on the computer the license ’file must ‘ be manually copied to the WinXPOW setup folder ( as described on the last installer page ) before using the software.

When performing an update the installer will not change any existing setup- , instrument- and user files. Nevertheless it will save all previous WinXPOW programs into a new folder called ‘programs_before_x.xx’ ( with x.xx equal to the installed version ).

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1.3 The Main Menu The available items of the main menu are shortly described here. Each item consists of a group of related functions and will be discussed in detail in the following chapters.

• •

•

•

•

•

•

‘User ’ is used to select the user‘s parameter file. ‘Diffract1 ’ and Diffract2 ‘ ’ comprise routines for setting up an instrument parameter file, collecting raw data, controlling a diffractometer, and calibrating PSDs for up to two separate diffractometers controlled from one computer. ‘Raw Data ’ is used for handling and displaying of raw data, format conversion, peak picking, profile fitting and evaluation of internal standards. ‘Cell’ contains a collection of routines that index powder patterns, refine lattice constants, or generate patterns from user input. ‘Phase Analysis ’ comprises the (optional) phase identification routine, which is also conveniently used for browsing through the ICDD data base, and a module to calculate crystallinity indices of partly crystalline samples. 'Extras ' contains a viewing tool for ASCII files, a particle-size analysis routine and an (optional) reflectometry evaluation program. ‘Help’ provides information about the program and on-line help texts.

Exit is not a menu item on its own, but is available through the User menu item, as in most Windows applications. A shortcut keystroke for exit is ALT + F4. The third possibility to exit Close is to select command the from the Control Menu ( in the top left corner of the window ). The‚Change Directory‘ button is used to change the default directory for file input/output operations.

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1.4 User The user parameter files can be handled in ‘User’ the option . It is good practice to assign every user working on a given computer his own user file where default values, file names etc. are continuously updated. The user files may, alternatively, also be associated with certain projects or sample types.

‘Select User’ opens a dialog box with the names of all user files in the system. The eight most recently used user files can also be selected from the ‚recent file list‘. ‘New User’ is used to create new user file entries. ‘Login’ , ‘Logout’ , ‘User Management’ are functions used by thePOW WinX GMP-package and are described in a separate manual. ‘Exit’ terminates the WinXPOW program package. This is possible after all WinXPOW programes had been closed.

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2 Instrument Parameters

2.1

Introduction

‘Instrument Parameters’ defines the diffractometer system in terms of available options, hardware settings, serial line and USB definitions and all other relevant information. The type of diffractometer used is displayed in the title bar.

‚File ‘ contains the options ‚New‘ ( which is only enabled if no existing instrument parameter file has been found ) and ‚Exit‘. ‚Configuration ‘ is used to input parameter settings via six property sheets, ‚Configuration‘, ‚Hardware‘, ,Ranges‘, ‚Generator‘, ‚SPC‘ (sample position control), and ‚HTC‘ (high temperature control). ‚PSD settings ‘ change the parameters of position sensitive detectors (PSDs) and their counting electronics via the property sheets ‚Interface‘, ‚Linear PSD‘, ‚Curved PSD‘, in case of an image plate detector ,IP-PSD‘ and in case of the Mythen 1k detector ‘Mythen 1k’. ‚Defaults ‘ allows the user to define default data collection parameters.

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WinX 3.05 Software Manual – Instrument Parameters

2-1

2.2

Configuration

The Configuration property sheet offers combo boxes and check boxes to define all available parts of the diffractometer system. The syntax of all s erial port definit ions must b e COMx : baudrate, data bits, parity. The baudrate shou ld always b e left at 960 0 as all ST OE int erfaces have thi s baud rate set ex fact ory. Data bits are 8 for all generator and diffractometer types and 7 for the high-temperature and sample position control lers. P arity is N for all generators and diffractometers, E for the high temperature controller and O for all types of sample position -, slit sys tem - or monochromator angle - controllers. The property sheet defines the basic setup of the diffractometer (e.g. radiation type used) as well as available options like high-temperature stage or sample changer which might be mounted on the system. As far as detectors are concerned, the principal availability of PSDs or scintillation counter is input here, not the current setup. Temperature attachments, sample position control and sample changer exclude each other from being used. These options have therefore to be input according to the current diffractometer setup.

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In theHardware property sheet the installation parameters of the respective hardware setup of the system are defined. Only fields referring to options defined as part of the system in Configuration the ‚ ‘ property sheet are enabled. ‚Dead tim e of Sci.Counter ’ refers to the dead time correction of the Scintillation Counter. If a non zero value is provide the measured intensities will be corrected as : I’ = I / ( 1 – I * c). ( with I’ = estimated intensity, I = measured intensity, c = correction factor ).the position ‘Sample changer posi tion ’ defines of the sample holder, and therefore the position of the omega circle, when changing a sample with the transmission sample changer. Thedistance values describes the geometry of the diffractometers beam path.

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TheRanges property sheet offers edit fields to define the maximum permissible angular positions, the positions of the reference marks and the check box for the reflection mode. Again only fields referring to options defined as part of the system in the ‚Configuration‘ property sheet are enabled.

TheGenerator property sheet is used to define the tube ratings and – if a PC-controlled generator like the Seifert ID 3003 is available – the serial line definition. In the example below, the COM settings are not accessible as a generator with manual control has been selected in the Configuration sheet. The maximum tubes values should be carefully edited according to the installed x-ray tube and generator. Improper values will destroy the x-ray tube and/or the generator! For appropriate values please refer to operation manuals of the tube and generator!

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The SPC property sheet defines the resolution, moving speed and serial line definition of sample holders with additional PC-driven translational, rotational or tilting movement. Usually, no changing of the stepping resolution or stepping speed will be necessary as the default values correspond to the hardware settings of the various attachments. Incorrect setting of the ‚Steps‘ parameter will lead to wildly incorrect positioning of the motors while incorrect ‚Speed‘ settings will result in loss of reproducibility.

TheHTC property sheet defines the controller type, serial line definition, PID parameters, thermocouple type, and the maximum permissible temperature and ramp rate of a high temperature attachment. Care should be taken when changing any of these parameters because an incorrect setting will invalidate all software precautions against inappropriate user input and might result in damage to the high temperature chamber. In case of nonlinear characteristics of the temperature the run of the temperature curve can be corrected by a ‚Calibration file‘ (see chapter 4.2. HTC – Configuration). In the exam ple below, the PID values are good standard values for the thermocouple S. If a thermocouple K (NiCr/Ni) is installed, 300 / 8 / 1 for Proportional band / Integral Time / Derivative Time are a better choice.

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2.3

PSD settings

The ‚PSD settings‘ comprise the definition of the interface type between controlling computer and counting electronics and the parameters for the PSDs defined as part of the system in the ‚Configuration‘ sheet. If a wire PSD (curved or linear) is installed, Interface thesheet is used to define the type of connection between PSD counting electronics and computer.

The interface type ‚PDT-ISA‘ has to be selected for all compact PSD supply units delivered after November 1994 bearing the STOE logo on its front panel, which are connected to the controlling computer by a thick black cable conduit containing two small cables with green and orange plugs and a ribbon cable. Compact PSD supply units delivered after April 2004 normally contain additional USB inserts which establish the connection between the PSD electronics and the computer by an USB cable. Compact ETH supply units delivered after July 2010 are connected via Ethernet cable. The (hexadecimal) base address for the parallel board and the (decimal) USB Identifier must correspond to the dip switch settings in the hardware, respectively (see the PSD hardware manual for the dip switch coding). Default values for PDT-ISA interfaces are 0x310. In case of USB interfaces the respective identifier number of the insert in the PSD electronics has to be chosen. In case of the ETH interfaces the switch settings (Switch 1 and 2) must be chosen to match the position of the switches 1 and 2 in the interface. Using these switches the user can choose between 4 different IP addresses for the interface: 10.0.2.128 (switch 1 and 2 are both off, standard case), 10.0.2.129 (switch 1 is on, switch 2 is off), 192.168.2.128 (switch 1 is off, switch 2 is on), 192.168.2.129 (switch 1 and 2 are both on).

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ThePSD sheet contains the ‚Calibration settings‘ which show the date of the last PSD calibration evaluated and written to the instrument parameter file. The calibration file name of the currently active calibration is also given. The radio buttons beneath are used to switch off and on the use of the calibration curve during data collection and should always be set to ‚Yes‘ and ‚Address‘, respectively. Changing these settings should only be done for good reasons as correct peak positions and intensities can only be obtained when both correctionsView are…active. ’ button The ‘ opens a diagram showing the calibration curves stored in the instrument parameter file.

‚First Channel‘ and ‚Last Channel‘ define the actual address range which is used when collecting data with the PSD and, therefore, the active angular range of the PSD. The PSD Stepsize is θthe between increment two in adjacent 2 channels (defaults : 0.005 for the linear PSD and 0.015 for the curved PSD). θ / channel Angular range ( °2θ ) = ( Last Channel – First Channel ) * PSD stepsize ( °2)

Running the PSD calibration routine and updating the instrument parameter file will update the values for the first and last channel used according to the values selected in the PSD calibration routine (see chapter ‚PSD Calibration‘). TAC, Delay, TDC Resol. , andHV refer to electronic settings of the PDT counting electronics. These values are a characteristic of every PSD / counting electronics pair and should not be changed from their factory settings without a very good reason. PSD calibration has to bePSD performed when any of5200 theseforvalues been changed. The default values In forany the case, PSD a high voltage HV ) is( for = an linear 4800, respectively PSDshas delivered after Nov. 2009, and 4300 for a curved PSD. The TAC range is usually between 3200 and 3800 for the linear PSD, and between 2300 and 2700 for the curved PSD. When using a ETH counting electronic the TAC must be set to 173. The delay value is in the range 110-150 for the linear PSD and 150-200 for the curved TDCPSD. Resol.The setting is only relevant for an ETH counting electronic. When operating a linear PSD with a ETH counting electronic the TAC value is 173 and it should not be changed or used to calibrate the PSD. Instead the TDC Resolution value has to be adjusted. Normal values are 10300 to 10900 for 230 mm sample-detector distances, or 7400 to 7700 for 330 mm. When operating an ETH interface and beginning with versionPOW 3.04 , theof user WinXmust also provide the Firmware Version and the Module number of the ETH interface.

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If an image plate PSD is installed, the ‚IP-PSD‘ sheet contains the ‚Calibration settings‘, some electrical hardware settings, and the type of IP-PSD. the

For a 140° IP-PSD ‘IP-PSD large’ has to be chosen, (ver. ‘1)’ refers to detectors with tooth belt ( manufacted before March 2004 ), while ‘(ver. 2)‘ refers to newer detectors with flat belt. When operating an IP-PSD 80° IP-PSD small‘ ‘ has to be chosen. Theactivati on of theInverse ‘ Scan ’ option is only necessary when operating certain STADI-MP setups. If a calibration has been performed the ‚Calibration settings‘ show the date of the last calibration evaluated and written to the instrument parameter file. The calibration file name of the currently active calibration is also given. The check box ‚2Theta correction‘ is used to switch off and on the use of the calibration during data collection and should always be marked when an up-to-date calibration file is given. Samplingrate , Triggerposition , andScanrange refer to electronic settings of the IP-PSD. These values are a characteristic of every IP-PSD / counting electronics pair and should not be changed from their factory settings without a very good reason. When a IP-PSD calibration is used, it has to be performed in any case when any of these values has been changed. The default values for the Samplingrate are between 970 and 990. The value for the Triggerposition is usually between 30 and 40 for the small IP-PSD, and between 60 and 70 for the large IP-PSD (given in degrees 2theta). Samplingrate and Triggerposition are normally valid for every 2theta position of the detector. In contrast, when measuring on different positions, a separate calibration file should be recorded for every position of the IP-PSD thus avoiding small deviations in 2theta. θ ) internal The Scanrange is the maximum angular range ( detector which is°2simultaneously detected by the IPPSD.

If a Mythen detector is installed, Mythen the1k property tab containsCalibration the setting s, options and hardware settings for this detector.Calibration The settings are identical to those already described for wire linear PSD: the user should read the corresponding documentation. It should only be mentioned here, View that…by ’ pressing the ‘ button a diagram appears showing the calibration curves stored in the instrument parameter file and the MIP of the

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Mythen detector used to measure the calibrations. If the MIP shown are all zero (uninitialized), the calibrations were measured with a version ofPOW WinX earlier than 3.04.

‚First Channel ‘ and Last ‚ Channel ‘ define the actual address range which is used when collecting data with the Mythen 1K detector and, therefore, the active angular range of thePSD detector. Stepsize The is the increment in 2theta between two adjacent channels (defaults : 0.01). θ / channel Angular range ( °2θ ) = ( Last Channel – First Channel ) * PSD stepsize ( °2)

Performing a Mythen 1K calibration and updating the instrument parameter file will update the values for the first and last channel used according the values selected the calibration (seeatchapter Calibration‘). The Address’ ‘ setting tells theto measuring programsduring PSDCal and PowDat which ‚PSD address should the Mythen detector be contacted: this is normally Address set to0 unless Mythen has been predefined Addrwith ess 1. Theactivati on of theInverse ‘ Scan ’ option is only necessary when operating certain STADI-MP setups. The Use ‘ defa ult keV threshold ’ option is normally activated and corresponds to threshold value about half of the energy of the anode radiation (the exact value depends on the internal calibration of the detector): photons having energies less than this threshold are not counted. To suppress fluorescence, the user might deactivate this options and specify a new value for the threshold in keV up to a maximum of 65.5 keV accordingly to his special needs. WinX Starting with version 3.04 of POW, the user must also provide Firmware Version andModule number of the specific Mythen system he wants to connect to using Change the button Mythen1K Identification Parameters. If the Mythen system has Firmware Version lower than M2.0.0 (like M1.3.0) DCS-MAC also Ad dress the of the Detector Controlling System must be given. Values for DCS-MAC and Module must benumber taken from theSystem “ Information Sheet ” which is delivered with all Mythen systems: the DCS-MAC isred highlighted and the Module in number in blue. During start-up PSDCal and PowDat check that the Mythen Identification Parameters given in input by the user correspond to those queried from the Mythen Hardware and refuse to activate the detector if they differ. Changes of the Mythen Identification Parameters or Mythen Settings cause entries to be written in GMP Log file.

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2.4

Defaults

This dialog box is intended for the setup of a standard data collection procedure which will be used for the creation of the raw data file if no raw data file is opened by the user after starting the ‚Diffractometer Control‘ module.

The edit and list boxes contain a short version of the ‚Scan Mode‘ and ‚Edit Ranges‘ parameter input tools of the ‚Diffractometer Control‘ program. Please refer to the Diffractometer Control manual, chapter ‚Edit Ranges‘ for a detailed description of these input windows.

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3 Diffractometer Control / PSD Calibration

3.1

Introduction

The Diffractometer Control module is used for all diffractometer operations like data collection, PSD calibration, alignment etc. with the exception of high-temperature data collection which is a separate program. The PSD calibration program is an individual program started directly from the MainMenu. POW MainMenu allows communication with two different diffractometer systems from one computer at the The WinX same time. If more than one diffractometer is active in the menu bar, select the one you Diffract.1’ wish or to use – ‘ ‘Diffract.2’ – and start Diffractomete ‚ r Control ‘.

The program then checks the necessary communication lines to the diffractometer and detectors and displays an error message if communication could not be established. In this case, the user should check whether the appropriate system components are switched on and if the communication cables are connected properly to the computer and system interfaces.

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WinX 3.05 Software Manual – Diffractometer Control

3-1

When the initial check has been completed, the program displays the current instrument parameters in the lower splitter window. A raw data file should always be created if data collection is to be performed, otherwise collected data may be lost if all warnings are ignored by the user. For low-level-diffractometer commands like driving the circles or doing a step scan, a raw data file name need not to be given.

3.2

File

3.2.1 New To create a new raw data file the New option ‘ is ‚ used. This file will be created in the folder determined by the user directory and receive default scan mode and range settings. The user may then alter the file settings according to his wishes, and rename it after that by theSave option As...‚‘.

3.2.2 Open To load an existing raw data file, Open option ‘ is‚ used. This is indicated when data collection parameters for a new measurement shall be copied from an existing raw data file. For that purpose, this existing raw data file should be opened and then written to the new file name using Save the option as... ‘. Raw ‚ data subsequently collected will then be stored in the new file. When an existing raw data file actually contains measured data a warning will be displayed in case the user tries to overwrite these data by initializing data collection again. After the raw data file has been created with the option ‚New ‘ or loaded with the option Open ‘,‚ the main window displays the fundamental settings of this file like diffractometer type, radiation and detector used. If the file has been created on quite another instrument, with another wavelength, or with other fundamental parameters differing from the current setup, the error message ‚This file cannot be used with the current instrument configuration‘ is displayed and a new raw data file should be created or the system configuration changed accordingly.

3.2.3 Save During data collection, data are saved automatically to the raw data file. However, if some scan ranges have been changed in a file and no data collection started yet, it may be useful to store the changes done so far to the raw data file. This can be done using the Save option ‘. ‚

3.2.4 Save As The Save ‚ As… ‘ option is useful for copying all relevant file information including scan range parameters to another file, either new or old. Data collection settings can thus be used for several files without the need of typing them in every time a new file is created. If the currently loaded file contains collected data, these data are not copied to the new file.

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3.2.5 Print This option prints the most recently collected powder diagram displayed in the upper splitter window, after the user has defined the print options in the standard Windows Print box.

3.2.6 Print Preview opens a Windows standard WYSIWYG window of the printout.

3.2.7 Print Setup opens a Windows standard printer setup window.

3.2.8 Most Recent File List contains the names of the eight most recently used file names.

3.2.9 Exit POW main menu. If parameters have been edited by the user, but not stored yet, the user is returns to the WinX prompted whether he wants to update the current file or not.

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3.3

Setup

3.3.1 Detector If more than one kind of detector is defined in the instrument parameter file, the user may switch from one detector to the other using this option after replacing the detector on the diffractometer’s 2Theta arm. Only those detectors are accessible for selection which have been defined in the ‚Instrument Parameters‘ Configuration sheet. If two kinds of PSD are connected to a PDT type of PSD interface, all changes relating to electronic and HV settings are executed automatically. When the user attempts to switch to a Mythen 1K detector, the Mythen Identification Parameters (MIP) given in Instpar withChange the Mythen1K Identification Parameters button are compared with the values queried directly from the Mythen hardware and the detector switch is going to fail if they differ (the detector is therefore not available for usage). After a successful detector initialization, the program also compares the MIP in the calibration (see “PSD Calibration”) with the MIP queried from the Mythen Hardware. Under GMP, the Mythen detector is made available for usage only if the two MIP sets are identical (therefore the calibration was measured with the same system presently connected). In non-GMP environments other situations are also allowed: the program warns the user that a mismatch between MIP was detected and expects the user to explicitly allow or forbid the activation of the detector.

3.3.2 Generator

The dialog box which is opened after selecting this option serves a twofold purpose : The first is to document the generator settings in the raw data file for comparison reasons. The second requires a generator with an interface to the computer so that the generator settings entered can be transferred to the generator and set accordingly. The edit boxes ‚kV‘ and ‚mA‘ and the ‚Exit‘ button are always accessible, even if a manual type of generator is part of the system. In case of a computer-controlled generator, additional buttons and an additional check box are activated : ‚Set kV, m A ‘ sets the generator to thengs ratigivenin the ‚kV‘ and ‚mA ‘ boxes. ‚Shutdown ‘ switches the high voltage to0 2kVandthe current to mA 5 as thelower pow er limit for tube ng. idli If the ‚Shutdown at the end of data collection‘ box is checked, the generator is automatically set to minimum power (20 kV, 5 mA) every time a data collection has been completed. This feature is useful for runs overnight or over weekends, if data collection stops sometime in the middle of the night and there is no need to run the tube at full power until its settings are decreased by the user. POW


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3.3.3 Sample Changer This option is only activated when a sample changer has been defined as part of the system in the ‚Instrument Parameters‘ Configuration sheet. When ‚Enabled‘ is selected, all requests for a new sample issued by the program will be sent to the sample changer. This is the normal operation mode. For testing purposes the sample changer may be ‚Disabled‘ and the user will be prompted to insert a new sample manually every time the program requires one.

3.3.4 Title / Comment This option opens an input window for the definition of a file title and additional comments. This information may also be input just before the data collection is started (see chapter 3.6.1)

3.3.5 Options A dialog is opened with several property sheets where some several aspects of the program could be edited. The Common ‘ ’ property sheet contains two options : if ‘the ‘network ’ option is enabled and the file that will contain the measured data is located on a network drive, the measured data will be stored first on a local drive and copied after the successfully completed measurement to the designated file location. This option could be used to prevent a break of the data collection resulting from instable or slow networks. ‘local path ’ holds the path on the local computer where the measured data should be stored temporarily. The optionerasing ‘ IP-PSD’ could be used when accomplishing HTC measurements using very long time spans for temperature stabilisation or tempering steps. The long time spans between two measurements, and therefore erasure cycles, may result in an increase of the detectors background. When editing a non zero value the IP-PSD detector will be erased before a new measurement if it wasn’t erased before in the given time span.

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The After ‘ Measurem ent’ sheet contains actions to be done after a measurement was successfully finished. If the optionprint ‘ diagram after measure ment’ is activated the measured data will be print out on the local default printer. The execute ‘ script ’ option allows executing an external script (i.e. batch file, Visual Basic script) or external program after each measured file. ‘Script parameters ’ holds, if needed, the parameters for the script. The user can either provide literal parameters as well as certain macros. While the literal parameters will be left unchanged when calling the script, the macros will be substitute with the current values from the running measurement. The macros $FILEPATH and $FILENAME will be substitute with the file path and file name of the currently measured data file, while $USERNAME will be substitute with the name of the current user. For example, if the path of the currently measured file is “D:\Data\D356.raw”, the parameter /U line $FILEPATH “ ” will be translated /U to “D:\Data\D356.raw”. Analogous “/U $FILENAME” will result in /U“ D356.raw” By activating the option wait for ‘ script termination ’ the next measurement will not be executed until the script has terminated. It should be avoided that the script asks for user input, since this will block further measurements if the whole measurement is running unattended. The Tasklist ‘ Setup ’ sheet is described in in chapter 3.5.3 ‘Scan Usage’.

output filewith hea‘ der The‘Printing Setup ’ sheet is used to define somediagram aspect of printing. When choosing ’ the will be printed together allinfo data collection parameters at the bottom. frame With Pen ‘ Width ’ the user can control the thickness of the frame surrounding the data and header info. With ‘ format ’ the Date‘ format ’ andTime user can control the output of the current date and time which will be printed – if not suppressed by choosing ‘no output’ - in the upper right area of the surrounding frame. By clicking the ‘Defaults’ button the options will be reset to default values .

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3.4

Diffractometer

3.4.1 Open Shutter While the shutter is always automatically opened when data are collected, this option is used to open the shutter for alignment purposes. The shutter status window in the program’s lower splitter window is changed accordingly. Note is on no the feedback from thethe diffractometer’s safety circuit the computer. It may well or bethe thatlike. the shutter is shown: There as open monitor while safety circuit has closed thetoshutter due to open panels

3.4.2 Close Shutter Selecting this option closes the shutter. When a data collection run has been finished or when the users exits the program, the shutter is closed automatically.

3.4.3 Drive Circles All commands relating to circle movement (without data collection) are accessible from the dialog box which is opened when this option is selected. ‚DriveMode‘

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definesthe relation between2Thetaand Omega positions : When ‚Coupled‘is selected,only one value for 2Theta needs to be entered in the ‚Move to‘ edit box, Omega will be set to half this value. When ‚Independent‘ is selected, values for 2Theta and Omega need to be entered; if only one value is given, Omega will remain at its current position.


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‚Requested Pos.‘ is displayed in the edit box here w the ngular a positi ons for 2T heta andOmega may beentered. ‚Current Po sition‘ is displayed belowthe reques ted position and shows thecurrent positions ofthbo circles. ‚Synchronize‘

is an important procedurewhen the diffractometer interfacehas beenswitchedoff. Afterswitching on again, position information is lost and all circles are reset to 0. The ‚Synchronize‘ command drives both the 2Theta and Omega circles to mechanical reference marks defined by micro switches and encoder marks and assigns values stored in the instrument parameter file (Instrument Parameters : Ranges sheet : 2Th, Omg (Ref) ) to these positions. Note : The program requests the user to drive both circles manually to positions physically above the reference marks as both circles begin to move in negative direction until the appropriate microswitch is depressed; if one of the circles is positioned below this position, the circle will move into the low-angle limit switch and the program will stall.

‚CheckPositions‘ performs m ovement similarto the ‚Synchronize‘ comm and but also compares the expected (=stored) reference position to the actual position. If they are not identical, the stored reference position is assigned to the current position and a warning message appears. ‚Defineas‘

allowsthe userto correctzeroposition errorsinducedby small changesof the primarybeam. The positions entered in the ‚Requested Position‘ edit box will be assigned to the current positions thus changing the zero position of the circles. Usually a standard peak of known position is scanned at regular intervals (e.g. every week using the ‚Step Scan‘ option) and the peak maximum determined in this way is then re-defined to its theoretical value. The program also automatically updates the current detector’s reference marks so that the next ‚Synchronize‘ command executed will locate the correct circle positions.

‚Moveto‘

executesthe command to move 2Thetaand Omega to the positions definedin the ‚Moveto‘ edit box. The same effect can be achieved when the enter key is hit in the ‚Requested Position‘ edit box.

‚ViewingPosition‘ easy drivesaccess the 2Theta to a positi on wh ich aligning allows thepurposes. user to moun t the microscope and to haveon the kind to the arm sample stage for The viewing position depends of detector currently in use. ‚Stop‘

interruptsthe movement of circles at once.Thebuttonis onlyactivewhilecircles are moving.

‚Exit‘

closesthe dialogbox.

3.4.4 Set Slit Width opens a dialog box with edit boxes for the width of the automated divergence and receiving slits. If no automated slit system is defined in the instrument parameter file, this option is disabled. ‚Receiving Slit‘

is the widthof the slit in front ofthe detectorin mm. The edit box is usedto inputthe requested setting, the greyed box labelled ‚Current‘ shows the current opening.

‚Divergence Slit‘

is the width ofthe slit betwee n tube an d sample in mm. The edit boxis used to input the requested setting, the greyed box labelled ‚Current‘ shows the current opening. The permissible range for both slits is 0 to 2 mm. There is a mutual influence between the setting of this parameter and the next three parameters. Every time any of these four parameters is changed and the enter key pressed, the other edit boxes are updated accordingly.

‚Divergence Angle‘ allows the input of a certai n opening angle fromhich w the width inmmis calculat ed by the program. ‚Sample Area‘

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is the widthof the primarybeamintercepti ng the sample in mm and thus the irradiatedwidthof the sample. For a given slit width (and divergence angle) it depends on the angle between sample surface and primary beam, Omega.


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‚at Omega‘

is the incidenceangle for whichthe sample area is calculatedfrom the slit setting (or vice versa).

‚SetSlit‘

starts the movement of bothslit system s to theirrespective requestedpositions.

‚Home‘

finds the referencemarks of both slit systems and is useful to restartthe slit co ntroller ifslit limit switches have been activated.

‚Defineas‘

allows the use r to re-define the currentslit widths asthe reque sted w idths. This will alsochangethe values of the slits’ home positions accordingly.

‚Stop‘

interruptsslit movement immediately.

‚Exit‘


3.4.5 Sample Changer (Next Sample) This option opens a dialog with commands for operating the sample changer. If no sample changer is defined in the instrument parameter file, this option is disabled.

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‚next sa mple‘

will rem ove the currently loaded sample fromthe measuringposition andinsert thenextsample.

‚Reset‘

will resetthe internalcounterto the firstsample.

‚Goto‘

is disabledfor a transmission sample holderas it is shown in the example above.For othersample changers, this button is used to move a definite sample directly to its measuring position.

‚Calibr ate‘

opensa dialogbox wherethe useris allowed to re-define the positions of the sample change r. This is an option a transmission sample holder cannot execute and is therefore also disabled in the example above. When calibrating a ‚High Throughput‘ sample stage, the user is allowed to change its position either using relative values for the moving distances, or absolute values defining the absolute position (the corresponding box has to be checked for that purpose). All buttons are the same as described in the following chapter 3.4.6.

‚Stop‘

interruptssample changermovement.

‚Done‘


3.4.6 Sample Position This option opens a dialog box with edit boxes for the positions of an automated sample holder. If no sample position control is defined in the instrument parameter file, this option is disabled. The layout of the dialog box depends on the type of the automated sample holder defined in the ‚Instrument Parameters‘. The example below is for a ‚High Throughput‘ sample stage with two independent movements, translation x and translation y. The edit boxes arevalues. used to input the requested positions of both motors, the greyed boxes beneath show their respective current

‚Moveto‘

startsthe movement of the sample stageto the requestedposition in x and y.

‚(search)Home‘ is used to find the reference arks mw hich locate a defined position even fter switching a off the controller of the ‚High Throughput‘ sample stage. ‚Spin‘

is an optionthe ‚HighThroughp ut‘ sample stagecannotexecute.For othersample holders,it is used to start continuous rotation about a movable axis.

‚DefineAs‘

allowsthe userto re-define the currentpositions as the requestedones.This will alsochangethe values of the home positions of the translational movements accordingly.

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‚Stop‘

interruptsmotormovement immediatel y.

‚Exit(Done)‘


3.4.7 Erase IP-PSD Selecting this option erases the IP-PSD when installed. This is normally not necessary to execute manually because after a data collection run recorded with an IP-PSD has been finished the detector is erased automatically.

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3.5

Ranges

3.5.1 Scan Mode The number of accessible input elements in the Scan Mode dialog box is strongly influenced by the diffractometer and detector type in use. Seen below is an example for a transmission diffractometer with linear PSD.

‚ScanMode‘

relates to the type of sample holderwhichis used.It influencesthe movement of the circles during measurement in the following way : ‚Transmission‘ and ‚Reflection‘ mode usually keep a constant 2:1 ratio between 2Theta and Omega position (the exact relation is however defined with the ‚Scan Type‘ edit box described below); ‚Debye-Scherrer‘ keeps Omega constant at 0° for every 2Theta. If the ‚Reflection‘ mode is set on a transmission diffractometer, a constant offset of 90° is added to Omega to account for the different orientations of sample surface relative to the primary beam in transmission and reflection geometry. Note : The 90° offset for ‚Re flection‘ scans is taken into a ccount for all commands in the ‚Measure‘ pull-down menu, but not for the ‚Drive‘ commands which refer to the ‚true‘ physical circle positions. Likewise, the angle display in the status window always shows the physical position of the circles !

With Bragg-Brentano- and Theta-Theta-diffractometers, the only possible scan mode is ‚Reflection‘. ‚ScanType‘

Thislist box is only activatedif ‚ScanMode‘ is not set to ‚Debye-Sc herrer‘ . Its setting overrides the default scan modes for ‚Transmission‘ and ‚Reflection‘ explained above. ‚2Theta‘ defines a scan with moving counter, but Omega kept constant at a user-defined value. ‚Omega‘ is a scan with fixed detector position and moving Omega ( rocking curve ) which may only be selected if a scintillation counter is used. Oscillating the well plate of a ‚High Throughput‘ sample stage during the measurement can be performed by checking the box ‚Oscillate Wells‘.

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‚2Theta : Omega‘ invokes the normal 2:1 coupling between 2Theta and Omega positions during the scan. ‚Independent‘ lets the user define 2Theta and Omega movements independently from each other; e.g. a certain Omega-offset and/or a 1:1 ratio between 2Theta and Omega step width may be entered in the ‚Edit Ranges‘ dialog box. ‚PSDMode‘

can only be change d between‚Stationary‘and ‚Moving‘if a linear PSD is the currentdetector. ‚Stationary‘ are all scans which require less than four PSD positions to scan the selected 2Theta range. ‚Moving‘ is the usual PSD mode for the linear PSD if a complete powder diagram is to be collected.

‚OmegaMode‘

is only activatedif a PSD is selectedas current etector. d ‚Fixed‘eans m that foreveryPSD position Omega will be driven to 2Theta divided by 2 and will remain there for all the measuring time of this PSD step. ‚Moving‘ Omega means that the Omega circle is continuously moved during data collection which usually requires longer step times and thus should only be used if additional particle randomization is required. ‚Gandolfi‘ is only used when the corresponding sample holder is mounted and ‚Debye-Scherrer‘ is chosen for the ‚Scan Mode‘.

‚Oscill ate Wells‘

can only be activated hen w a ‚HighThroughp ut‘ sam ple stageis mountedand a continuously movement of the well plate during the measurement is requested. By checking this box, the well plate performs a moving in the Omega range between –5 and+5° (‚Omega Mode‘ has to be switched to ‚Moving‘).

‚Pointsto be added‘ is only acti vated for a PSD as current detector. This options i useful ot gain intensit y at the expense of data resolution. When two addresses of the PSD ADC (analog-digital-converter) are summed up to one data point in the raw data file, the nominal step width of data points is doubled and the intensity per data point is approximately doubled, too. For very badly diffracting samples this value may be increased up to a point where the nominal data step width is about a third of the expected peak halfwidths. ‚Correcti ons‘

displays kind ofthe raw data be applied to the scan. on ‚Instrument how to the change kind correction of raw which data will correction please refer For to information the chapter Parameters‘. If a scintillation counter is the current detector, the only possible correction is ‚Dead time‘ which will only affect intensities, not positions. If ‚Dead time‘ in the Instrument Parameters‘ Hardware sheet is set to 0, no correction at all will be applied. For PSDs, position and intensity corrections may be applied. For details, see the ‚PSD calibration‘ part and the chapter ‚Peak Calibration‘ of this manual.

3.5.2 Scan Range(s) This option is used to define scan ranges after the fundamental scan properties have been defined in ‚Scan Mode‘. The upper part of the dialog box which is opened after selection of the ‚Scan Range(s)‘ option shows the detailed scan mode and detector as setup in the ‚Scan Mode‘ dialog box. The list box shows the scan ranges currently defined. Every raw data file may contain a maximum of 8 scan ranges, regardless whether they are identical or differ in certain parameters and regardless of the order in which they are to be measured. Note that the fundamental parameters defined in ‚Scan Mode‘ are identical for all ranges. With a range highlighted, one of the three first buttons below the list box may be pressed : ‚+‘

will copythe currentl y highlightedscanrangeafterthe last scanrange.Theusermay then alter the settings of the new scan range according to his wishes. When no range is present at the beginning, a new scan range is created receiving default scan range settings.

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‚-‘

deletesthe highlightedscanrangefromthe list.

‚OK‘

storesthe change s beforeleavingthe dialogbox.

‚Cancel‘

discardsall changesandleavesthe settings as theywerebeforeopeningthe dialogbox.

By double an on range a dialog box will open to edit the settings. range parameters. layout of for the aEdit dialog boxclicking depends theentry system configuration and allowing the ‚Scan Mode‘ Below is The an example transmission diffractometer with linear PSD in ‚Moving‘ PSD- and 2Theta:Omega scan mode.

For systems without automated slits or with a PSD, the edit boxes in the last row are disabled and the user may only input the 2Theta range, stepwidth and dwell time per step. If a scintillation counter is used for data collection, a dwell time of 0 may be input. In this case, a continuous scan with hardware-fixed speed will be performed.

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When automated slits are used on a Theta-Theta-diffractometer, the user may input the (fixed) receiving slit width in mm in the edit box ‚Rec. Slit‘. The width of the divergence slit may be input in either of two ways : When the divergence slit width is input in the ‚Div.Slit‘ edit box, the width remains constant during the scan. Due to the variation of the angle between sample surface and primary beam the sample area irradiated by a beam of fixed width decreases with increasing Omega. On the other hand, the penetration depth of the beam increases with increasing Omega thus leading to a ‚constant volume‘ irradiation of the sample over the whole scan range (at least as long as the projected beam size does not exceed the sample area). When the divergence slit width is input in the ‚Sample Area‘ edit box, the slit width is automatically varied ω

over scan‚Sample range inArea‘ suchisa not way)the (~sin thatarea the itself, irradiated area remains throughout thearea scan.(inThe input the in the but sample the required width of constant the sample irradiation mm). The irradiated area is of course also influenced by the height of the beam which is defined by the choice of vertical divergence slits and does not change with Omega.

3.5.3 Scan Usage For all st andard tasks ‚Scan Usage‘ is setot ‚Single Sam ple‘ and nee d not be chang ed. If any other scan usage is selected, data will not be written to the ‚master, file‘ but to a set of files named filename.raw filename.001, filename.002 etc. Theextension of the first ile m f ay be selected by entering it in thest‚Fir File num ber‘ edit box. The master file should however be kept after data collection has been completed as it provides a fast way of accessing the whole set of adhering files in the 3DGraphics - routine.

One feature which is useful for monitoring changes in samples with time is the possibility to select ‚Repetition‘ as scan usage. The program will then repeat all scan ranges defined in ‚Edit Ranges‘ as many times as input with a userdefined waiting time between repetitions. When appropriate accessories for the diffractometer are defined as part of the system in the instrument parameter file, scan usage may also be set to ‚High-temp.‘, ‘Sample-pos.‘ or the like. In the case of ‚Multi-sample‘ runs using an automated sample changer, the box ‚Individual Parameters‘ may be checked by the user which enables the ‚Ranges, Files, ...‘ button. By pressing the ‚Ranges, Files, ...‘ button an input window is opened which allows the change of the default file titles, comments, file names and scan ranges that the different samples will receive.

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‚Sample‘ may be any valid sample num ber ( 1, 2, 3 …or A1, G5, H1 2 when using the gh-t hi hroughput samplechanger). ‚Range‘ is only activated if more than scan 1 ran ge has been created in the ‚Edit Ranges‘indow w sa described in chapter 3.5.2. It provides the possibility to have different samples measured with different scan parameters, i. e. in different scan ranges and with different scan times. The total number of possible different scans is limited to the usual maximum number of ranges in a file, eight. In this case, setting up requested scan ranges in the ‚Edit Ranges‘ box does not necessarily mean that all samples will be collected in all these scan ranges. By selecting one of these ranges for an individual sample the assignment of the scan range to be measured to the sample is achieved. If all ranges defined shall be measured for a sample, a rangeber num of 0 must be enter ed. may be any valid filename ( the extension.rawwill beaddedby the program). A double-check for already existing files with the filenames input (which would be overwritten) will be done when pressing the ‚OK‘ button.

‚File‘

‚Title‘

By default, everyfile will rec eivethe title givenfor themasterfile plusthe identificati on ‚sample x‘ (xis the sample number). This standard title may be changed by the user. If ‚&‘ is the first character in the title given, the input string will be appended to the title defined for the master file (if necessary, suitably truncated).

‚Comment‘ The ed ited text w ill be insert into the com ment field of the e masuredfile. If ‚&‘ is the first charact er in the comment given, the input string will be appended to the comment defined for the master file (if necessary, suitablyrunca t ted). ‘Reset’ will a ssignthe program ’s defaultvaluesto all samples. ‘Reassign’ will change the sam ple numbe r of every entry,so that the sample num bers start ing with 1 and are consecutive. This command may be usefull after editing a sample list for the transmission- or reflection samplechanger, which could not change sample randomly. ‘OK’

will ex it fromthe windowafter ch eckingthe currentdirectory for existing files withfilenames as change d by the user.

‘Cancel’ will discard allanges ch andreturn to the ‘ScanUsage’ window. All values may be changed by double-clicking on the corresponding entry and confirming with the key. Additionally, measurements of single samples may be deleted by highlighting the corresponding line and pressing the minus-button.

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Another way to edit the data is to import them from a spreadsheet program with the Drag&Drop mechanism. The user prepares a spreadsheet having as many rows as with “Number of Samples” specified and at least 4 columns containing the sample’s index number, the range, the name of the RAW file and its title. The columns can be arranged in any order and they can also be non-sequentially arranged. To inform the program which column of the spreadsheet contains which information, the “Setup / Options … / Tasklist setup” property sheet is used.

By default the dialog box searches the sample index number in column A, the range in column B, the file name in column C and the title in column D. But the user can also use a spreadsheet containing more columns and then change the letters in the dialog box correspondingly. The user can specify up to 4 columns as title by entering in the “Tasklist setup / Title” more than one character labelling each column and separating them with commas (,) so that the entire title of the measurement is obtained by joining the individual contents of the specified columns. The following table for example contains an extra column (column C) that the program must ignore because it contains only a comment and no data relevant for the measurement: A

B 1 2 3 4 5 6

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1 2 3 1 2 3


C Comment1 Comment2 Comment3 Comment4 Comment5 Comment6

D File.001 File.002 File.003 File.004 File.005 File.006

E Title1 Title2 Title3 Title4 Title5 Title6

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This table can be processed using the following settings in the “Tasklist setup” dialog box: Samplenumber Range Filename Title

A B D E, C

When the table is ready, the user simply selects all rows and columns of interest in the spreadsheet, copies them and then right-clicks on the white area of the “Individual Ranges / Files / Titles” dialog box: a context menu appears containing the command “Paste” that can be executed. The content of the spreadsheet table will be transferred into the dialog box.

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3.6

Measure

3.6.1 Data Collection starts data collection after scan mode and scan ranges have been defined using the appropriate options in the ‚Ranges‘ menu item’s pull-down menu. In the dialog box a title and a longer user text describing details of the sample or the data collection may be entered. By checking the ‚Print data when finished‘ box an automatic printout of the diagram on the standard system printer may be invoked.

By pressing the ‚OK‘ button data collection is started which displays the ongoing measurement in the main window. If the raw data file already contains measured data, the user will be prompted whether he really wants to overwrite these. Measuring with a linear PSD, the raw data file is automatically updated with counts after a certain time has elapsed. Data which have already been saved to the file are displayed in blue, unsaved data in red. The ‚Stop‘ button of the small info window may be used to interrupt data collection at any time. Red datapoints will in this case be lost, blue datapoints will be kept in the raw data file. When a IP-PSD is used for the measurement, data are shown at the end of the data collection due to the different PSD technique using an image plate which is only read out completely after exposition.

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3.6.2 Step Scan This option is used for the alignment of the diffractometer and a quick check of peak positions. The collected data are not stored in a raw data file, but only displayed on the screen. The ‚Scan Centre‘ edit box is used to define the middle of the step scan to be undertaken. The first value corresponds to 2Theta, the second to Omega. When ‚Drive Mode‘ in the ‚Drive Circles‘ dialog box is set to ‚Coupled‘, Omega need not be given; it is automatically set to 2Theta / 2. ‚Time‘ defines the measuring time per detector step. For the scintillation counter, the total count time is therefore the product of ‚Time‘ and ‚Nsteps‘, for a PSD (which remains stationary during the scan) the total count time is equal to the count time per step. Depending on the detector in use, the ‚Step Size‘ edit box is either disabled (for PSDs) or enabled (for a scintillation counter). The ‚NSteps‘ edit box is used to define the number of steps the scintillation counter takes around the requested peak position or to define the number of data points that are shown on the screen for a PSD.

After completion of the scan, the peak’s centre of gravity, integral intensity and integral breadth are displayed and the detector to angle the position of the detected centre of gravity. thebutton. scanned peak was a standard peak of known position, is themoved 2Theta may now be corrected using the ‚DefineIfas‘ The ‚Start‘ button starts the step scan after the scan parameters have been defined in the edit boxes. ‚Stop‘ immediately interrupts the scan and is only activated while the scan is in progress. ‚Exit‘ closes the dialog box.

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3.6.3 Count This option is only enabled when a scintillation counter is selected as detector. When clicking on this option, the shutter is opened with both circles at their current positions and the monitored count rate is displayed numerically and graphically on the screen. Data are not stored to the raw data file.

3.6.4 Beam Optimization This option is enabled if a motorized primary monochromator has been defined as part of the system in the ‚Instrument Parameters‘ routine. It performs the same measurement as the ‚Step Scan‘ option but moves the monochromator in small steps during the beam optimization repeating the step scan with the monochromator angle slightly changed. Thus, monitoring the peak intensity (proportional to the primary beam intensity with all other parameters constant) changing with the monochromator position lets the program drive the monochromator to the optimum angle leading to a maximum of beam intensity. Depending on the step time selected, this procedure may take between 2 and 10 minutes.

The input boxes are the same as for the ‚Step Scan‘ option described in chapter 3.6.2 with the addition of the ‚Check Alpha1‘ checkbox. If this is checked, the program will not only look for the local intensity maximum, but will scan a larger range of the monochromator angle with a coarser resolution making sure that α1 radiation the beamand is K not the closely spaced α2. K When theαK 1 maximum has been identified by the program, the variation of peak intensity with monochromator angle is displayed.

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After that it automatically performs the optimization of the monochromator setting at this monochromator position with the smaller normal monochromator step width.

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3.6.5 Sample Position Measurement The option ‚Sample Position Measurement‘ is a special scan mode for texture and crystal orientation problems. It only works with a computer-controlled sample positioning device in combination with a scintillation counter, which is moved to a user-defined 2theta position and remains at this position counting intensities while the sample is moved through the primary beam. The Omega position is also kept at a fixed angle (independent of 2Theta) during the scan.

If several degrees of freedom are available from the sample stage used, the sequence of their movement is selected from the 'Sequence' list box. The uppermost movement is executed in the innermost loop and is taken as the x-axis for the on-line display during data collection. The range for sample movement is given in mm for translations and in degrees for rotations. The 'Scan Mode' used for the measurement is taken as entered in the appropriate dialog box (see 3.5.1). The output file is an ASCII file with default extension *.spm containing a header describing important parameters of the experiment and a table of the count rates at different sample positions : ! STOE SPM File : C:\winxpow\DATA\sijustiertx.spm ! created at 30-Oct-98 07:53 by WinXPOW Wavelength : 1.54060 Cu 2Theta,Omega : 28.440 14.220 Time/Step : 1.0 Sample Pos.1 : -10.00 10.00 0.10 201 Translation X Sample Pos.2 : 0.00 0.00 0.00 1 Translation Y Sample Pos.3 : 0.00 0.00 0.00 1 Rotation (Phi) DataPoints : 3 201 -10.00 0.00 0.00 4.0 -9.90 0.00 0.00 5.0 -9.80 0.00 0.00 3.0 -9.70 0.00 0.00 43.0 -9.60 0.00 0.00 188.0 -9.50 0.00 0.00 384.1 -9.40 0.00 0.00 460.2 -9.30 0.00 0.00 668.4 -9.20 0.00 0.00 954.9 -9.10 0.00 0.00 988.0 etc.

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3.6.6 PSD Calibration 3.6.6.1 General This option is not intended for data collection, but starts a necessary calibration procedure for wire PSDs and the Mythen 1K detector. This procedure needs to be performed every few months and should only be done by qualified personnel. To account for even the smallest deviations of the electronic address scale from the true 2Theta scale and to determine the response function of each individual PSD, two standard samples – NBS silicon and amorphous metal foil of high iron content - are provided with every PSD which are used in this procedure. PSD calibration comprises two procedures :

•

Calibration Curve : A sample of known lattice constants is placed in the sample holder and one of the peaks

(with precisely known peak position) is measured at different PSD positions so that the peak maximum is measured at different electronic addresses. The difference between theoretical and observed peak position is tabulated (together with the peak’s integral intensity and halfwidth) for every address at which the peak maximum was detected. •

Address-Check : A sample giving no Bragg peaks but only high uniform background ( for Cu radiation,

amorphous iron foil) is measured with the PSD at a fixed 2Theta position. When the counting statistics are good enough ( > 10000 counts in every address), the measured intensities in the usable address range should all be equal within 1% statistical error. Deviations from the mean intensity value are thus due to electronic bias or PSD-specific sensitivity differences over the length of the counting wire. Dividing the mean intensity by each individual intensity thus provides an efficient address-wise intensity calibration by multiplying every measured intensity in this address by this address-specific factor. When selecting the option ‚PSD Calibration‘, a program window opens up which offers several options in pull-down menus. M any of them are well known from the diffractometer control window(see chapters 3.1 – 3.5).

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3.6.6.2 PSD Calibration – File Parameters and results of the PSD calibration are stored in two files, one binary with the extension ‚.cal‘ for calculations, and one in ASCII format of the same name but with the extension ‚.lcl‘ for later inspection and documentation. It is good practise to give a new name to each calibration run and not to overwrite old files so that the ‚history‘ of the PSD can be documented if necessary. To create a new calibration file, New option ‘ is ‚used. The default file name is ‚noname.cal‘ which is supplied by the program. If a Mythen detector is selected as current detector, the Mythen Identification Parameters (MIP) described under “Instrument Parameters” are copied also in the ‚.cal‘ file and printed in the ‘lcl’ file. They are also displayed on the main window of the program as “Firmware version”, “mod” (Module number both in decimal and hexadecimal number format) and “DCS-MAC”. ‚Open ‘ opens an existing calibration file. If the opened ‚.cal‘ file was generated with a Mythen 1K detector system, the program shows on the main window the Mythen Identification Parameters of the system used to measure the ‚.cal‘ POW of file. If the ‚.cal‘ file was generated with a version earlier WinXthan 3.04, the MIP are zero, that is, uninitialized. If a Mythen 1K detector is connected, the MIP contained in the ‚.cal‘ file are compared with those of the presently connected Mythen 1K detector and, if they differ, the program might prevent the user from performing operations like changing or adding calibrations (see 3.6.6.3) or writing the calibration to the IPR file for later use in PowDat (see 3.6.6.4). ‚Save ‘ can be used to store the calibration parameters and calibration curves. These are, however, also stored automatically after calibration data have been measured. ‚Save As ‘ lets the user rename the calibration file. This should be done after a new calibration file is created and before any changes to the parameters etc. are made or a calibration measurement is started. ‚Graphics Export ‘ is only activated when a calibration curve or an address check diagram has been evaluated. With this option the user is allowed to save the displayed data in a graphic format. ‚Exit ‘ is intended to exit the PSD calibration routine.

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3.6.6.3 PSD Calibration – Measure When both types of wire PSDs are installed, the user may select the one to calibrate with the option ‚Detector‘. ‚Parameters‘ opens a dialog box which allows the user to define the parameters for the calibration measurements:

‚CalibrationPeak‘

is the theoreti cal 2Thetavalueof the standardpeakwhichshall e b usedfor position calibrat ion ( e. g. 28.443° for the Si(111) reflection using α1 radiation). CuK

‚First PSDAddress‘ and ‚Last P SD Address ‘ define the(electr onic) add ress rang e whichshall bescannedduring ca libration. Thesevalues can easily be obtained using the ‚Measure‘ - ‚Address Check‘ and ‚Evaluate‘ - ‚Address Check‘ commands ( see chapters 6.4.4 and 6.4.5 ). ‚Measu ringTime‘

is the dwell time of the PSD at eachposition.

‚2ThetaInterval ‘

is the step widthby whichthe PSD is moved over the standardreflection. 0.1° is usuallya good choice for the linear PSD, 0.5° for the curved PSD.

‚Addr.Check Position‘is the posit ion at which the PS D will collect data stati onary (either usi ng the am orphous sample for intensity calibration or any sample for determining the first and last address for the calibration measurement). For the linear PSD, every value between approx. 15 and 45° is acceptable, the curved PSD should be positioned at 30° as the fluorescence background of the iron sample is slightly angular dependent and is only constant in the aforementioned 2Theta range. ‚OmegaPosition‘

is the fixed position of the sample duringdata collecti on (either usingthe amorphoussample for intensity calibration or the sample for the calibration measurement). Using e. g.the Si(111) reflection with CuK α1 radiation, the value should be 14.221°.

The options Calibration ‚ Curve ‘ andAddress ‚ Check ‘ in the menu ‚PSD Calibration – Measure‘ allow the user to start the corresponding routine for the calibration of the PSD. If a Mythen 1K is selected as current detector, the user can replace, measure again or add missing calibrations only to a if‚.cal‘ the MIP file in ‚.cal‘ file exactly match the MIP of the Mythen 1K system presently connected.

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When Calibration ‚ Curve ‘ is chosen, a dialog box is opened, and the user is prompted to press the ‚Start‘ button. After doing so, the program starts the calibration run displaying one measured peak after the other and listing the observed peak positions, addresses of the peak centre, deviations from the expected position, intensities and halfwidths. All these data are also automatically written to the calibration files (*.cal and *.lcl). By clicking on a list box item, the profile of this particular measurement can be recalled to the screen. With the ‚Stop (Measurement)‘ button, the run of the measurements may be terminated. ‚Exit‘ brings the user back to the PSD calibration menu (disabled duringmeasurem ent).

WhenAd ‚ dress Check ‘ is selected from the menu, the program will display the accumulated count rates in the main window and continue collecting data until the user clicks on the ‚Stop‘ button.

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3.6.6.4 PSD Calibration – Evaluation From this menu item either the ‚Calibration Curve‘ routine or the ‚Address Check‘ procedure can be evaluated. ‚Calibration curve ‘ will display the outcome of the calibration curve routine in two diagrams : the upper one showing the variation of position offset with PSD address number, the lower one showing the variation of the standard peak’s integrated intensity. The user may select the useable address range either by clicking on one of the two red lines and moving them to the desired position or by entering an address in one of the edit boxes of the ‚Calibration‘ dialog box. The useable address range thus defined should show no spikes or drop-outs in either of the diagrams, but only a smoothly varying curve. A smoothed cubic spline is fitted to the data points in the selected address range; the degree of smoothing is again set by the user by moving the sliders to a position where the interpolated curve fits the observed data well enough without showing too many sharp turns. In general, the smoothing for the position data in the upper diagram will be smaller than for the intensity data which may be effected by poor counting statistics. No point of the spline should be further than 0.005° (for the linear PSD) away from a data point.

Only the smoothed splines will be written to the instrument parameter file (see 6.4.6) and will thus be available for all consecutive data collections, so the choice of address range and smoothing should be made with care.

‚Addr ess Check ‘ will display the accumulated counts over the PSD addresses which have been collected with the ‚Measure‘ Check‘ Again user may the useable address range either by moving the red cursor lines- ‚Address or by entering theoption. first and last the address in theselect appropriate edit boxes.

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At the end of the calibration procedure it is important to activate the stored files so that the corrections will be applied to every measurement. This is done by selecting ‚ ‘. Thus, the instrument parameter file will be updated Write IPR file with the evaluated PSD calibration. If a calibration for the currently active PSD is already stored in the instrument parameter file, a warning is given. Under GMP if one has chosen Mythen as current Measure detector / Detector (/ system, ‘ is ‚ Mythen 1K is checked) and has opened an old ‚.cal‘ file also created by a Mythen Write IPR file the allowed only if the two systems have identical MIP (therefore they are the same system). In non-GMP environment the program warns the user that a mismatch was detected and expects the user to decide Write IPR whether fil e ‘ the ‚ operation should be completed or not.

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4 High-Temperature Data Collection

4.1 Introduction The‚HTC Data Collectio n’ module is a separate program and controls the low- and high-temperature data collection. It provides the set-up of the temperature program and data collection parameters and calls the normal data collection module when executed. The module is, among others, capable of controlling STOE’s high temperature 0.65 ovens and Oxford Cryosystem’s Cryostream coolers. The application is accessible from the ‘Diffract.1’ respectively ‘Diffract. 2’ pull-downPOW menu mainofmenu. the WinX

4.2 Configuration POWWinX The‚HTC Data Collection‘ module is only active under the main menu when a high- / low-temperature device is chosen in‚Instrument the Parameter‘ menu. To activate one of the optional devices ‚Instrument open Parameter‘ from the W inXPOW main menu and select the mounted high- / low-temperature device ‚Config‘ from the sheet.

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For the co nfiguration of the temp erature dev ice set-up select the ‚HTC‘ sheet from this ‚Instrument Configuration ‘ page.

Choose the actual ‚Controller Type‘ and‚Thermocouple‘ . The‚Maximum Temperature‘ is automatically selected dependent on the thermocouple and corresponds to the maximum temperature pre-set in the HTC controller. The ‚COM Settings‘ , as there are baud rate, data bits and parity should not be changed, only the COM port number should be changed according to the hardware setting of the PC. The ‚Maximum inputRamprate‘ of the is shown on the left side of the COM setting and is 100°/ min by default and should not be above ‚PID Parameters‘ this rate. The are used to control the temperature handling, the given default values are very well tested with respect to the controller type and should not be changed. To achieve the minimum possible error in the temperature reading, a correction curve for the thermocouple reading may be set up by defining a temperature calibration file and activating the “Use calibration” button. Such a correction curve must be defined in an ASCII file with the following format : ! TEMPERATURE CALIBRATION FILE 1.01 # Soll 10

Ist 10

125

130

573

593

1064

1112

The first line must contain the file ID exactly as shown above; lines starting with “#” character will be treated as comments and ignored. The first value in every line refers to the true sample temperature (in °C), the second to the thermocouple reading (in °C). A linear interpolation will be done for temperatures between given calibration pairs; for temperatures outside the lowest or highest temperature in the calibration file, the offset for the last entry will be used

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without extrapolation. (E.g., for the file given above a requested temperature of 300° will correspond to a thermocouple reading of 310.9° and a requested temperature of 1200° will equal 1248° thermocouple reading.) Using the temperature calibration will result in a systematic discrepancy between the temperature shown on the controller display and the PC monitor, the size of the offset being equal to the temperature difference calculated from the calibration curve. The temperature calibration file is read in every time the HTC module is started; it must therefore not be deleted while in use. Changing the contents of the temperature calibration file will affect every HTC run after (re-)starting “HTC data collection” from the main menu. By leaving the ‚Instrument Parameter‘ menu, the instrument parameter file will be updated automatically.

4.3 Creation of the Raw Data File Before starting the HTC data collection module a raw data file must have neem created file which contains the required measuring parameters ‚Detector‘ as ‚Scan Mode‘ ‚Angle Ranges‘ etc. (see Chapter 3 for additional information), but does not contain any measured data. In addition to the usual raw data file creation, in HTC data collection one has to‚Scan select Usage‘ the option in the ‚Ranges‘ pulldown menuandselect the opti onTemperature‘ ‚ in the‚Scan Usage‘ window.

The option ‚First File Number‘ will be the extension of the first raw data file in a series of HTC measurements, e.g. ‚*.001‘. Therefore it is possible to continue a previous HTC measurement under the same raw data file name at a specified temperature and completing the data collection by the insertion of a consecutive file number.

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4.4 High Temperature Data Collection Select‚HTC Data Collection‘ from the main menu. If more than one diffractometer is active in the menu bar, select the one where the high- /low-temperature device is mounted, either – Diffract.1 or Diffract.2 ‚HTC Data– and start Collection‘ .

The program first calls the data collection module which checks the necessary communication lines to the diffractometer and detector and displays an error message if communication could not be established. After these checks the HTC data collection main menu is called automatically.

4.4.1

File

Before a measurement can be performed a HTC parameter file must be loaded or created newly. With the option New’ ‘ a new, empty file is created, while Filewith / Open ‘ ’ a previously created file could be loaded into the application. With Save’ ‘ an disk. edited file could be stored on disk. Before a measurement is performed the HTC parameter file must be stored on With Save ‘ as ’ a loaded file could be stored under a different name. ‘Print ’, ‘Print Preview ’ andPrint ‘ Setup ’ are commands to print out the contents of the application main window and select and configure the used printer. ‘Graphic export ’ provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the combo box ‘Save as type’. The available formats are Enhanced Metafile ( which will be the most adequate format when importing the display into other applications ), TIFF- and Windows Bitmap file. With deactivated option ‘only Diagram’ the output will be identical to the printed

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version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page, regardless of the current aspect ratio of the display. To maintain the current aspect ratio the ‘keep aspect ratio’ option should be activated.

‘Exit’ will terminate the application, this is only possible if no measurement is running.

4.4.2

Parameter File Setup

To change parameters or to check the default values, ‚Parameters‘ selectfrom the ‚Setup‘ pull-down menu. In the displayed dialog two sheets are present Raw Data : ‘ File ’ to select araw da ta file to be sed u for m easureme nt (see above or Chapter 4.3) Default and ‘ Parameters ’ for editing the pre-set default parameter‚Temperature values. Step‘ etc. are shown.

‘Temperature Step ’ is the default temperature step for each ramp toRamp execute. Rate ’ ‘andRamp ‘ Time ’ is the rate a ramp should be performed respectively the time span a ramp should last. In the later case the resulting rate should not exceed the controllers Hold limits. time‘ ’ is the time span the application will wait before performing a measurement. Only if ‚Measuring During Hold‘ is marked, the data collection module will be activated and data will be collected according to the chosen raw data file.

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Also, like in the normal data collection, a raw data file name has to be given, otherwise an error message is displayed while executing the HTC data collection. The selected values in ‚Set-up the Parameters‘ menu will be used as defaults‚Temperature in the Program‘ .

4.4.3

Input of a Temperature Program

To set up a temperature program select ‚Temperature option Program‘ from theSetup‘ ‚ menu. The figure below shows the beginning of a temperature program input using the defaults described above.

The easiest way to set up a temperature program is to define proper defaults and to add the desired steps. ‘Add Ramp’ and Add ‘ Hold’ will insert a ramp respectively hold step with the corresponding default values at the marked position in the list. ‘Add Step’ will insert a single temperature step consisting of a ramp and hold step, as well with the corresponding default values. Add‘ St eps’ will add an arbitrary amount of temperature steps, only limited by the allowed temperature range of the controller. New steps will be insert at the marked list position. ‘Delete’ will delete the marked steps from the list ‘Parameters ’ gives the user a quick access to the Setup Parameter dialog to change the default values. ‘Load List ’ gives the possibility to load directly an already edited list from another HTC parameter file, the loaded list will replace a potentially edited list. This could also be done by just drag‘n drop a HTC parameter file onto the temperature list. This is a very versatile method to work with template curves. However a temperature list was created it is possible to change every step by just double-clicking on the desired step. A dialog will open giving the opportunity to change every step parameter. When editing a ramp, the editable parameters are the temperature and the ramp rate respectively the duration of the ramp. When changing the

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temperature the application will adjust the temperatures of the subsequent steps accordingly. When editing a hold the user can change the hold time ( see above ), can switch on or off the data collection module and if this is activated which range(s) of the raw data file should be measured. A range could be selected by typing the range number. If more than one range should be measured the numbers must be separated by commas ( i.e ‘1,3’ will select range 1 and 3). Consecutive ranges could be selected by typing the first and the last number separated by a hyphen ( i.e. ‘1 – 3’ will select range 1, 2 and 3). The next two figures illustrate the investigation of the quartz transformation at 573 °C which is often used for temperature calibration purposes. The first window displays the input of the ramp/hold interval, temperature, measurement stages, the approximate duration of the experiment etc.

After leaving this menu by pressing ‚OK‘ the main window displays a graphical presentation of the above temperature program. The programmed ramp steps and hold stages are displayed.

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4.4.4

Preferences

The Preference dialog comprise options controlling the graphics layout and the logging options of the application.

The ‘Look’ sheet gives the user the facility to change the temperature unit and colour of the displayed temperature curves. The user can change the temperature unit at any time between ‘Celsius’ ( mostly in case of high temperature measurement ) and ‘Kelvin’ (common for low temperature measurements).

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The‘Logging’ sheet gives access to the applications logging ‘System options. logging’ will control the creation of a normal’ system logging file: ‘ andverbose ‘ ’ will activated the creating of such a file. In generally this file is only needed for diagnostic reasons ( ie. in case of hardware or communication problems ). The file contains all executed temperature steps, error messages and none’‘ will inhibit the creation. other diagnostic infos. Caution: when settingverbose to ‘ ’ the application will keep a complete log of the communication between application and temperature controller resulting in a rapidly growing log file. This option should only be used temporarily to debug communication or controller related issues and should be deactivated during regular measurements! ‘Temperature logging ’: if enabled the application will write a second log file with temperature readings. The file contains the current time, the runtime, the target and actual temperature, the temperature error and the controller status in csv-format. This file is suitable for further processing with, for example, a spreadsheet.

4.4.5

HTC Measurement, Run and Control

To start the programmed HTC measurement ‚Execute‘ press theoption in the above menu or clickExecute on the’ ‘ button in the lower part of the main window. Start the HTC measurement‚OK‘ with . The HTC controller is initialised and ramping to the first temperature starts. The window shows the status of the HTC data collection, theRamp actual or Hold step), ‚Temperature‘ ( , the ‚Power‘ used, the current ‚Error‘ , meaning the difference between the actual temperature and the setpoint chosen by the temperature controller. ‚Step Time‘ is counted down and indicates het rem aining measuring/r amp time and m ight show negative values if a step takes longer then expected. ‚Hold‘ The time stepfor is the a sum of the waiting time and the measuring time. ‚Total Time‘ shows how long the program will still be running. During the experiment the shown diagram is constantly updated, the measured temperature will be displayed in red, following the temperature program, displayed in blue. These default colours could be changed with the Preference dialog ( 4.4.3 ) to any desired colour.

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As soon as the first measuring hold has been reached and the temperature is stabilised (for 10 sec the error must be less than a software - calculated Delta T) within an appropriate time (10 min), (otherwise the controller is shut down and a warning message is displayed), the data collection menu is called and starts the data collection with respect to the selected range(s) automatically.

As in the normal data collection, the raw data file is automatically updated with counts after a certain time has elapsed. Data which have already been saved to the file are displayed in blue, unsaved ‚Stop‘ data button in red. The

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of the small info window may be used to interrupt data collection at any time. Red datapoints will in this case be lost, blue datapoints will be kept in the raw data file. The HTC program can always be stopped during the various steps ‚Shutdown‘ by pressing button the in the lower part of the HTC data collection main menu. The application will After the end of the experiment the ‚HTC data coll ection’ menu shows how well the temperature has followed the programmed temperature diagram. The data collection menu will display the diagram collected during the last hold / measurement state

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5 Graphics

5.1

Introduction

The Graphics program is accessible from the ‚Raw Data‘ pull-down menu of the WinXPOW main menu.

It can display raw data and peak lists and perform peak search, background correction and raw data smoothing. Intensity scaling can be chosen from linear, square root or logarithmic axes displaying total counts, counts per second 2 ( 1/d or relative intensities; x-axis scaling can be 2theta, == or Q ). 1/d The number of windows is nearly unlimited as is the number of diagrams in a window. The graphics program is a multi-document application; the windows standards are the same as in applications like Word, Excel etc.. The most important windows properties are described in chapter 5.5.7.

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5.2

Files

The menu item ‘File’ offers the standard Windows utilities to read and write files, to re-open recently used files and to print the graphics. The file formats that the program can handle are : •

the standard STOE peak files in ASCII format with default extension *.pks or *.pth.

•

the standard STOE binary raw data files with default extension *.raw or *.rth.

•

STOE graphic files (default extension *.grs) containing the complete information about the state of the graphics program. These files can be used for storing the current graphics and recalling the exact look of the graphics at a latter time.

Immediately after the start of the program, only the ‘Open’ and ‘Recent files’ options are available from the pull-down menu.

The Open’ ‘ command loads the contents of an existing file - either a raw data or peak file - into the program and displays the file contents in a new window. The Load ‘ Graphic ’ andSave ‘ Graphi c' commands lets the user write and read graphic files (*.grs). With theLoad ‘ and Print Graphic ” command the user could load a previously saved graphics file (*.grs) and immedeatly print it out. With theSetup ‘ ‘ command the user could access a dialog in which certain aspects of the program could be edited. The Printing ‘ ’ sheet is used to define some aspect of printing. When choosing ‘output file header info’ theatdiagram will be printed together with all data collection parameters the bottom. With ‘Frame pen width’ the user can control the thickness of the frame surrounding the data and header info. With ‘Data format’ and ‘Time format’ the user can control the output of the current date and time which will be printed – if not suppressed by choosing ‘no output’ - in the upper right area of the surrounding frame. By clicking the ‘Defaults’ button the options will be reset to default values.

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The Colour ‘ Setup ’ sheet is used to define the various colours associated with the loaded data, labels, background etc. The colour selection may either be done via the RGB formalism (if a button is clicked, the edit windows or spinner buttons of the basic colours red, green and blue may be used to change the current colour settings) or by the ‚Choose Colors‘ button which opens the standard Windows colour dialog. If more than 16 curves are loaded in a window, the colour coding is repeated starting from the colour associated with curve 1.

‘Export Graphic ’ provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the Save combo as typebox ’. The “ available formats are Enhanced Metafile (which will be the most adequate format when importing the display into other TIFF-, applications), JPG- andWindows Bitmap file. With deactivated option ‘only Diagram(s) ’ the output will be identical to the printed version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page, regardless of the current aspect ratio of the display. To maintain the current screen keepaspect ratio the ‘ aspect ratio ’ option should be activated. The Print ‘ ’, ‘Print Preview ’ andPrint ‘ Setup ’ commands control and format the output of the program’s main window to the system printer. The Exit ‘ ’ command terminates the application and returns control to the WinXPOW main menu.

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5.3

View

This menu comprises several options controlling the graphics layout. Activated options will be marked with an leading checkmark.

‘Whole Diagram ’ resets a former zoom command by displaying both axes starting from the minimum value of all loaded diagrams to their respective maximum value. The tool button remains depressed as long as the complete diagram is displayed. By clicking on the ‚Whole‘ button again, the zoomed-in state may be recalled. ‘Position Info ’ switch on or off the display of the current cursor position (position and intensity) in the left part of the main window’s status bar. ‘Crosswire ’ Changes the cursor to a crosshair extending over the whole active window. This representation is useful for comparing peak positions of diagrams loaded into the same window. ‘Grid Lines ’ adds or removes a rectangular pattern to and from the window. If the option Rescale ‘ on Load ’ is activated.the program will automaticly rescale the axes to fit the new data. If deactivated the axis will be left unchanged, even if the new data won’t fit into the actually axes. The options File‘ Names ’ switch on or off whether the file names will be displayed in the upper left corner of the diagram. The File ‘‘ Titles ’ switch, ‘Titles on orinoff whether the ‘and file titles will beNumber displayed in thethe upper of the diagram. The options options Title Left Aligned’ Reverse Order Show ‘ Range ’ control wayleft thecorner titles are actually displayed. The default behaviour of displaying the title right align could be changed Title Left with the option ‘ Aligned ’. The file titles are displayed from top to bottom in the order the curves are loaded, the activated option ‘Titles in Reverse Order ’ will invert this order. The option ‘Show Range Number’ switch on and off the display of range numbers. ‘Toolbar ’ removes / brings back the toolbar with shortcut buttons above the main window. ‘Status bar ’ removes / brings back the status bar beneath the main window.

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The ‚Position Info‘, ‚Whole Diagram‘, and ‚Grid Lines‘ commands are also available from these toolbar buttons:

When the cursor is not n the i ‚Posit ion Inf o‘ mode , it may beused to define a zoom -in window bymoving ti to any point in the diagram, pressing the left mouse button and holding it depressed while moving the opposite corner of the rubber box to the requested position. Releasing the left mouse button will change the display to an enlarged representation of that diagram part which was contained in the rubber box. Scroll bars will be added to the diagram enabling the user to move the diagram horizontally and vertically, if necessary.

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5.4

Options

This menu item comprises commands which changes the appearance of the graphics windows as well as tools for editing and manipulating peak and raw data.

‘Scaling Axes ’ allows the user to input exact values for the viewport and to choose from several scaling modes for the intensity and angle axis. The data limits in the bottom right part of the dialog box are given for comparison. Wherea s ‚2Theta‘(or ‚Om ega‘ in the case foa rocking curveithwthe de tector kept at aixed f pos ition) is he t most popular scaling for the x-axis of ractogram a diff , the 1/d or 1/d**2- scaling is useful or fcom paring da ta sets collected with different wavelengths. The x-axis will be automatically reset to the maximum viewport necessary for the curves currently loaded if the type of scaling is changed. The intensity scaling will usually be done on a linear scale. Square root scaling gives a better representation of the background and leads to error bars of identical absolute size for every data point. Logarithmic scaling is used for high-resolution diffractograms or reflectograms from thin films, wafers etc.. Absolute intensity scaling will label the intensity axis with the counts accumulated over the respective count time of the data collection. Cou nts / sec norm alizes these cou nts to a cou nt rate per sec nad is thus use ful for com paring diagrams collected with different measuring times. Relative intensity scaling sets the strongest intensity in every diagram to 100%. The Y offset may be used to shift diagrams displayed in one window vertically by a certain amount. This mode increases the visibility, but should be switched off if correct intensity information is to be taken from the display as the offset is not taken into account when the ‚Position info‘ is invoked.

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The Absolute / Relative / Linear / Square Root / Logarithmic scaling options are also available from these tool bar buttons :

The Fonts ‘ ’ option is used to select the lettering type and size used for the title axes labels, notes. ‘Labels ’ Is used to add d-spacing - , index - or other labels to the diagram. The option needs at least one peak file loaded from which the data for labelling can be taken. hkl-labelling can only be done if a peak file containing peak indices has been loaded. 2Theta - and d-value labelling can be chosen independently from the x-axis scaling, whereas 'same as axis' automatically writes the peak positions in 2theta, 1/d or 1/d**2 depending on the setting for the x-axis. The Find ‘ Peaks ’ tool opens a dialog box from which a peak search in the loaded raw data can be started. It is disabled if no or more than one raw data file is loaded in the active window or if a peak list is loaded together with the raw data.

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Estimated Ha lfwidth : An approximate value for the peak halfwidth must be given. This parameter can be used to discern between sharp and broad peaks. When both kinds of peaks are present in a diagram, it is usually impossible to identify both classes of peaks in one run of the peak search. For data collected with the linear PSD or IP-PSD 0.15°, for data collected with the Mythen1K detector 0.08° will be usually a good value. Significance Level : The significance level sets a lower limit to the peak heights; it is defined as the ratio of the maximum peak intensity to background. Peaks which are found by the slope criterion, but have a peak height below the given significance limit, will be discarded. Intensity Limit : The intensity limit is an additional criterion applied to a peak identified in the peak search algorithm. All peaks having an absolute height less than the input value will be discarded. Setting it to 0 will accept all peaks matching the significance criterion, values above 0 will increasingly reduce the number of peaks Remove Alpha2 Peaks : Checking this box will scan the peak list for pairs of Alpha1/Alpha2 peaks and discard the Alpha2 reflection. To match the Alpha1/Alpha2 criterion, the peak position of the second peak must be within 0.02° of the theoretical Alpha2-reflection as calculated from the Alpha1-position and its intensity must be between 45 and 55 % of the corresponding Alpha1 peak. Remove Spikes : When this box is checked, a search for peaks of abnormal halfwidth will be performed in the peak list which passed the other criteria. Peaks of a halfwidth less than 25% of the estimated halfwidth defined above will be discarded as spikes. The ‚Defaults‘ button loads approximately correct parameters for most problems in case the user has completely lost track of the parameter setting‘s meaning and effects. By press ing the ‚OK‘ button the peakrch sea is st arted. When it si finished, the num ber of oun f d peaks is displ ayed in a message box and the menu bar layout changes. In this mode, the user may add peaks at any position by pointing the cursor to the desired peak position and clicking on the left mouse button. Accordingly, peaks may be removed by moving the cursor onto the bar of a peak and clicking on the right mouse button. Peaks may also be moved in the drag-and-drop way : When the cursor changes to a cross ( whenever the cursor is close enough to a peak in x and within the peak height in y ), a peak may be ‚picked up‘ by left-clicking and moving it to the required position and intensity and placing it there by releasing the mouse-button. In order to invoke the standard zoom-in option, it is advisable to keep the cursor above peaks in the diagram or below the x scale, so that peaks are not inadvertedly shifted instead of zooming in.

‚Exit‘ brings the user back to the normal graphics mode.

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The menu bar item ‚Write Peakfile‘ saves the peak list to file. ‚Restart‘ brings the dialog box ‚Peak Search Parameters‘ back on the screen so that the user may restart the peak search with a different set of parameters. ‚Next Range‘ and‚Prev. Range‘ are enabled only if the raw data file contains more than one scan range and are used to switch to the next / previous scan range for peak identification.

The Edit ‘ Peaks ’ option opens the same edit window as the ‚Find Peaks‘ command does after the peak identification with the same possibilities to add or remove peaks by mouse-clicks. The Smooth ‘ Raw Data ’ is option opens a dialog box which asks for the number of data points which are to be averaged. It is only enabled if one raw data file is loaded in the current window. The smoothing is done after an algorithm described by Allmann (see below). This value may either be input as the average peak halfwidth (in degrees 2theta) from which the program calculates the number of points by dividing it by the data step width or directly as the number of data points to be used. After pressing the ‚OK‘ button, the smoothed curve is displayed together with the srcinal raw data.

R.Allmann, Smoothing by digital filters and a new peak search routine. EPDIC 2, Mat.Sci.Forum 133-136, 323 (1993) R. Allmann, Röntgenpulverdiffraktometrie, Clausthaler Tektonische Hefte 29, Verlag Sven von Loga, Köln 1994

The Background ‘ ’ tool starts an automatic background-removal routine which may as well be altered by the user. The option is only available if only a single raw data file is loaded in the current window. If the option is selected, the menu layout is changed and the program displays a background-spline function calculated from a number of automatically selected background points. There are three options for the user to change the background generated by the program : By left-clicking on one of these points, they may be moved to any position in the diagram and - by releasing the mouse button again – may be placed at a different location. The spline function will be automatically re-calculated. The very first and very last point of the diagram may not be shifted in their position, but may only be altered in their height. By double-clicking anywhere in the diagram, an additional background point is inserted and the background - spline re-calculated. By either clicking on the ‚Inc.Smo.‘ / ‚Dec.Smo.‘ menu items or by hitting the ‚+‘ / ‚-‘ keys on the numeric keypad, the degree of smoothing of the spline function is changed. By increasing the smoothing further and further, a straight background in the form of a linear regression will be obtained. By decreasing the smoothing factor further and further, the background will follow exactly through all background points, sometimes tending to overshoot between the points.

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When the background line has been defined, the ‚Subtract BG‘ option may be used to create a raw data file with the backg round-co rrected data. The default extension for backgroun d-subtracted data s *.rmb i . When the ‚Exit‘ option is selected, the background selected so far is written to the srcinal raw data file (without changing menu the srcinal and may e.g. be used in the fitting routine (see chapter 8). Subsequently, the normal graphics bar is data) restored. The Sign ‘ file ’ command allows to “sign” a GMP raw data file. An entry “File signed” will be appended to the file’s Audit Data, including name of the user who signed the file and the date he signed. Only users that have the “Sign” privilege are allowed to sign a file: this privilege can be given or removed using the “User Management” functionality in MainMenu. After choosing this command, the user is asked to enter his username and password. This functionality is disabled if WinXPOW is not running in an GMP controlled environment, or the data where not measured under GMP. A file can only be signed once.

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5.5

Window

comprises commands concerning either a particular window of the graphics display (‚Add Raw Data‘, ‚Add Peak Data‘, ‚Add ICDD data‘, ‚Delete Curve‘, ‚Split‘) and commands regarding the order and shape of all currently opened graphics windows (‚Cascade‘, ‚Tile Horizontally‘, ‚Tile Vertically‘, current window list).

Whereas da ta loaded ith w ‚File‘-‚Open‘ are alwaysispl d ayed in awindowof thei r own, the Add‚ Raw Data‘ command displays a newly loaded file in the currently active window together with all other already loaded curves. The default extension for files shown in the standard windows ‚Open‘ menu is *.r*. If a window has been split (see chapter 5.5.5), the diagram will be displayed in the currently selected upper or lower part of the window. ‘Add Peak Data’ has the same functions as ‚Add Raw Data‘ for the opening of peak files. The default extension for files shown in the standard windows ‚Open‘ menu is *.p*. The Add ‘ ICDD Data’ tool loads peak lists from the ICDD data base into the current graphics. The dialog will asked the user for the requested PDF card number (Product ID). The format of this card number was changed and dependes on the installed database. However the program recognizes which version of the ICDD data base is installed and asks the user to input the card number using either the older 6-digit [nn-nnnn] or the newer 9-digit [nn-nnn-nnnn] format. For both formats only digits, hyphens (as separator) and blanks (ignored) are acceptable characters: the PDF card „[01-082-0505]“ should be therefore entered as „01-082-0505“

The Edit ‘ Curve ’ option opens a list box showing all curves in the currently selected part of the window. By clicking on one line and then pressing the ‚Delete‘ button, the corresponding diagram is flagged for removal from the display. When the window is closed using the ‚OK‘ button, the flagged curves will be removed (and the colours newly assigned to the remaining diagrams). By pressing the ‚Cancel‘ button, the changes will not become active. By

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selecting one entry with a left-mouse-click and moving the mouse up- or downwards, still pressing the left mouse button, the order of the curves, and with it the order they are drawn, can be altered.

The scale factor and title of each curve may be changed by double-left-clicking on the corresponding line. A dialog box is opened which shows an edit box with the current title for the selected curve and a checkbox for curve scaling. By default, the check mark 'scaling' is not checked and the corresponding intensity set to 100, which means that the intensities are displayed as read from the respective files. If the user checks this mark, the maximum intensity of the curve may be scaled to any required value (the intensity input in the edit box must always be in ABSOLUTE count rate regardless of the y-scaling currently selected).

Using theSplit ‘ ’ option, every window may be split into two parts separated horizontally. By using the toolbar buttons shown below that part of the window, which is to receive all keyboard and mouse input, may be selected. The border line between the two window parts may be moved when the cursor is close to it and changes to a double-arrow.

‘Cascade ’ aligns all windows which are currently not minimized one on top of the other with only the title bar being visible above the other diagrams. ‘Tile Horizontal ’ aligns all windows which are currently not minimized one above the other in landscape format, while ‘Tile Vertically’ aligns all windows which are currently not minimized one beside the other in portrait format. ‘Current window list ’ lists all graphic windows which are open at the moment either minimized, maximized or in any other state. Clicking on its name makes it the active window.

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5.5.1 Window handling Every graphics window has a title bar of its own with a document icon in its top left corner. By clicking on this icon, a pull-down menu is opened which contains the Windows standard windows control commands. As this menu is provided by the operating system, it will be in the language defined in the appropriate System Setup routine. When the window is maximized so that it fills the whole main window, the document icon is moved to the leftmost position of the main window’s menu bar. By right-clicking on the mouse anywhere in the window area a formatting window may be opened which allows a short-cut to functions like ‚Add ... Data‘ , ‚Split‘ , ‚Edit Curve‘, ‘Insert Note…’ and ‚Scaling Axes‘ which have been explained above in the context of their respective pull-down-menus. The 'Insert Note' option, however, is not available from the pull-down-menus as the cursor position at which the right mouse-click is executed is taken as the top left corner of the position of the text to be entered. The corresponding dialog box and the handling of userdefined notes are explained in the next chapter.

5.5.2 Editing user notes When the 'Insert note' option has been invoked from the above window, a dialog box is opened which allows the input of any text which will be positioned in the diagram in such a way that the top left corner of the note will be at the cursor position at which the formatting window was opened by right-clicking. The colour of the notes text could be controlled by clicking in the coloured rectangle. Existing notes may be moved by left-clicking on the text and dragging- and dropping to their new positions. They may also be edited by double-left-clicking on the text in which case the above dialog window opens again. The text and the color may then be altered or the 'Delete' button pressed to remove the whole note from the diagram. To copy text to another position, the clipboard function may be used: The existing text in the above window is selected with the cursor and Ctrl-C pressed. On opening the window at another position, the standard text is again selected and Ctrl-V pressed. This will overwrite the standard text with the one selected before. To save the text inserted into the diagram, the 'Save Graphic' option described in chapter 5.2 can be used.

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6 3D-Graphics

6.1

Introduction

The 3D-Graphics program is accessible from the ‚Raw Data‘ pull-down menu of the WinXPOW main menu. It can display sets of raw data from high-temperature runs, time-resolved experiments or any other combination of powder data on linear, square root or logarithmic scale in a user-defined perspective. The program also offers the option of a ‚Pseudo-Guinier-film‘ representation where peak intensities are colour-coded.

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6.2

Files

The menu item ‘File’ offers the standard Windows utilities to read and write files, to re-open recently used files and to print the current 3D graphics. The program can handle STOE raw data files and 3DGrafix files.

‘Open’ reads the contents of existing raw data files into the program and displays their contents. As long as no data have been loaded, a dummy picture is displayed. There are two ways to load a set of raw data into the program : One is to load a single raw data file which has been used as a master file for a multi-file data collection e.g. with a hightemperature attachment, sample changer or sample position control (see chapter 3.5.3 ). This master file is accompanied by a set of corresponding data files (usually with the same name but extensions ranging from *.001 to .nnn) which are automatically read into the program once the master file is opened. The second possibility is to open several raw data files which are then ‚single-sample‘ files and contain raw data. All these data are then read in and displayed. Ifhey t contain ‚z information‘ (see chap ter 7) hey t may subsequently be aligned in the orde r of z. By pressing the right mousebutton while the cursor is inside the main window, the z order may be reversed. ‚Save Meta fil e‘ lets the user write the current graphics to an *.emf file ready for import into other programs. 'Load Graphic' reads an existing 3DGraphics file restoring the display saved in this file. 'Save Graphic' stores all information about the current display status to a file with default extension *.g3s. This file may be read in at a latter stage to restore the graphics in the way they were when saved. The raw data are NOT stored in the 3DGraphics file and may therefore not be deleted even if the display has been saved. ‘Print’ - ‘Print Preview’ - ‘Print Setup’ printer.

control and format the output of the program’s main window to the system

The‚Recent file list‘ contains the last eight files which have been opened. ‘Exit’ terminates the 3D graphics routine and returns control to the STOE main menu.

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6.3

View

allows the user to change the graphics layout.

‚Toolbar‘ removes / brings back the toolbar with shortcut buttons above the main window. ‚Status bar‘ removes / brings back the status bar beneath the main window. ‚Centre‘ moves the cube in its current orientation to the centre of the window and, if necessary, re-sizes it to fill the window . This command is also available from the toolbar button .

‚Default Cube‘ resets the perspective to a standard view and is useful if the cube has been manually twisted beyond repair. ‚Cube Mode‘ switches to a representation of a flexible cube which defines the perspective of the drawing. When the user presses the left mouse-button on one of the squares in the middle of the cube edges, the corresponding edge changes its colour and may be moved until the mouse-button is released again. The front and back face of the cube may also be shifted as one block when the cursor is moved to the centre of the crosshair and the left button is pressed.

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To move the cube around within the window, click on the arrow-crosshair in the middle of the cube. When it changes its colour, the cube may be shifted within the window until the left mouse-button is released again. The ‚Centre‘ command described above is also available in this display mode. To go back to t he normal 3D re presentation, re move the check mark fr om this menu item or us e the toolbar button described below. The same procedure has to be followed by scaling the x,y and z-axis. Check the correspondin g button , scale the x, y, z-axis or the cub e and uncheck the button again. Note : It is possible to make two cube edges exactly coinciding. The singularity thus produced may only be resolved by using the ‚Default Cube‘ command. ‚CubeMode‘and‚TopView‘may be invokedandswitchedoff by the toolbar buttons

, respecti vely.

‚Top View‘ switches to a two-dimensional representation of the data in the form of a moving Guinier-film experiment.

The size and position of the rectangle correspond to the size and position of the cubes’s front face in the ‚cube mode‘ representation. Intensities are colour-coded as defined in the ‚Colour Setup‘ dialog box. The scaling mode currently selected (linear, square root or logarithmic) is maintained. The intensities of the lines are indicated above the Top View‘ window.

‚Recolour‘ applies the colour definition as set up in the ‚Options‘ –‚Colour‘ dialog box to the currently selected range of raw data. ‚Start colour‘ will be assigned to the first diagram in the display, ‚end colour‘ to the last diagram displayed and the diagram colours in between will be interpolated taken into account the ‚middle colour‘ definition. This option need only be selected if the z-Range of the display has been changed by the ‚Scale - Z-Range‘ option. This option is also accessiblefrom the toolbarbutton .

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6.4

Options

This menu item comprises commands which change the appearance of the graphics without changing the perspective of the drawing : ‚Colour‘, ‚Font‘ , ‚Labels‘ , ‚Scaling‘ , and ‚Title‘.

6.4.1 Colour

The scheme is defined three colours which arecolour assigned to the first, and last diagram in the data colour set. For every diagram in by thethe graphics, the appropriate is calculated by middle linear interpolation between theraw colours defined. All colours including those for background, text and grid lines are defined by their RGB values which may either be entered in the edit box via the keyboard or by using the attached spin buttons.

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The check boxes ‚Draw filled diagrams‘ and ‚Use Border pen for diagram‘ define the look of the graphics. If ‚Draw filled diagrams‘ is not checked, every diagram will be displayed as a polygon built from all count rates; otherwise the area between the zero-level and the count rate will be filled with the appropriate colour. If the ‚Border pen‘ is not checked, the polygon will be drawn in the appropriate diagram colour, otherwise in the colour used for text and border (usually black).

6.4.2 Font This option opens the standard Windows dialog box from which the user may select the type and size of the label lettering. The language used in this box depends on the user’s systems settings.

6.4.3 Labels This option allows the user to define the layout of the outer part of the cube.

By using the spin buttons ‚Label Position X‘, ‚Label Position Y‘ and ‚Label Position Z‘ the cube edge which will receive the labelli ng of the axis ma y be selected . The edge currently select ed is highlighted he in tdraw ing in he t right-handside of the dialog box. When no edge is highlighted, labelling for the corresponding axis will be omitted. The radio buttons ‚Z axis mode‘ allow the user to define the aligning criterion used to order the diagrams along the z axis. ‚N‘ will stack the diagrams starting with the file having the smallest number as extension and ending with the largest. ‚Time‘ will start with the oldest file and end with the most recently measured one and so displays the duration

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of the experiments. The labelling of the second button depends on the kind of measurement performed. It may e.g. be ‚Temperature‘, ‚Sample position‘ or the like. The check box ‚Draw grid lines‘ switches the display of grid lines on and off. If ‚Draw Box‘ is not checked, all of the outer part of the cube including labels and grid lines will be omitted from the display. The 'Axis' edit windows may be used to change all axis titles and to define the labelling of the z-axis.

6.4.4 Scaling This option sets the viewport limits for all three axes and the scaling mode for the intensity ( = Y ) axis.

The edit boxes ‚X-Range‘, ‚Y-Range‘ and ‚Z-Range‘ are used to define the actually displayed part of the raw data set. The X-Range values are given in degrees, the Y-Range is the intensity axis and the meaning of the Z-Range values depends on the se tting of the ‚Z-axis mod e‘ described in the previou s chap ter. If a file contain ‚z informa tion‘ (see chapter 7) theyay m subseq uently bealignedin the order of z. By pressing the right mouse button while the cu rsor si inside the main window, the z order may be reversed. Thetruncation of the visible portionsmay alsobe perform ed withthe toolbarbuttons . Using these buttonsa represe ntation of aexible fl cube appears, similar to het one in the ‚cubeode m ‘ . Thedifferent axis may be scaled according to the needs. In the case of the x-axis the adjusted section then can be moved through the cube by pressing the left mouse button on the centre of the crosshair. They offer graphical support for the selection of the viewport in the same way as the ‚cube mode‘ does. Clicking on the button labelled with the arrow-crosshair resets the display to the full range of the data set. The radio buttons ‚Scaling‘ allow the selection of a function for the intensity axis. The same may be done from the toolbarusingthe buttons .

If the che ck boxis‚Individual‘ chec i k%. ed, all diagram s are sho wn on a relative sca le, .i e. the maximum intensity of every diagram scaled tos 100

6.4.5 Title opens a dialog box allowing the user to enter a title describing the displayed experiment which is shown in the bottom left corner of the window.

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7 Raw Data Handling

7.1 Introduction The Raw Data Handling routine provides tools for the modification and conversion of the binary STOE raw data files *.raw like absorption correction or conversion of the raw data for Rietveld analysis. After selection of the ‘Raw Data Handling‘ from the pull down menu item ‘Raw Data‘ the following window is displayed. Title Bar

Menu Bar

Tool Bar

Caption Bar Range View Windo w Layer Panel

Report Panel

History Panel Status Bar

The program window is split into five separate areas. In the upper Menu , Tool area andCaption the Bar are positioned. All basic operations can be started with these Caption panels.Bar Thewill show important messages (such as position info of the mouse pointer or operating mode of the program etc.). Most important area of the window for working with raw data Range filesView is the Window (centre / right of the program window). The changes to the raw data loaded will be displayed in this window.

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On the left hand side of the program window Layer Panel the and theHistory Panel are located. The Layer Panel enables a quick and comfortable way to edit separate ranges and their display properties. TheHistory Panel will list all operations done by the user. basic In working the mode all of these operations can be reversed and macros can be applied or edited. On the bottom of the program window Report the Panel is placed. All info from the source file or the working copy and program errors are displayed here.

7.1.1 Menu-, Caption-, Status- and Toolbars

File Toolbar

Range View Toolbar

Operations Toolbar

TheMenu Bar will be explained in detail in chapter 7.2. basic In working the mode three toolbars (see above) are displayed. The File Toolbar contains the buttons ‘New File‘, ‘Open File‘, ‘Multiple Open‘, ‘Import File‘, ‘Export File‘, ‘Merge Files‘, ‘Page Setup‘, ‘Print Preview‘, ‘Print‘ and ‘Info‘. All functions of the buttons are identical to the same named functions in theMenu Bar (see below). The Range View Toolbar contains the buttons ‘Position Info‘, ‘Crosshair‘, ‘Grid‘, ‘Show All‘, ‘Move‘, ‘Separate View‘ and ‘Axes Scale‘. Again the functions of the buttons are identical to theMenu functions Bar . in the The Operations Toolbar contains the buttons ‘Absorption Correction‘, ‘Angle Correction‘, ‘Alpha 2 Stripping‘, ‘Dead time Correction‘, ‘Fold Diagram‘, ‘Background‘ and ‘Smooth‘. All functions are explained below in detail. All Toolbars can be moved from its position. To align them in their original position select ‘Restore Original Layout‘ from the View drop down menu from Menu theBar TheCaption Bar and the Status Bar will show important information during the work with the Caption program. The Bar will display mostly the current working mode or the position info of the mouse Statuspointer. Bar is used The to show a progress bar during applying operations masterinorthe batch- working mode.

7.1.2 Layer Panel The Layer Panel consists ofLayer a Panel Toolbar (functions of this toolbar are equal to the ones which can be selected from the Menu Bar see chapter 7.5 for more info) and a tree figure of all the ranges loaded. The basic entry of the tree is the loaded raw data file. The two separate range arrays Source and Working Copy correspond to the srcinal loaded, unedited data and the current edited data. With the check boxes at the left side of the ranges the ranges can be hidden or shown in the Range View Window . A right click on a range will open a context menu to edit properties of the range. With a right click on a source range the range display properties (line width and colour) can be edited and the range can be selected. If a range is selected all the data points in the raw data file will be shown as black dots in the Range View Window. Ranges can be selected through the context menu or by clicking the number of the range on the keyboard. A right click on a working copy will open a context menu where, besides the options of the context menu of the source files, all range operations can be selected. A double click on one of the ranges will open the properties dialog directly and displaying parameters can be set. With a double click on the Working Copy or Source entry of the tree all viewing properties of the ranges which belongs to the entry can be altered altogether. POW


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7.1.3 History Panel TheHistory Panel consists ofHistory a Panel Toolbar and a list of operations done to the loaded raw data file. The toolbar contains the three buttons ‘Save History’, ‘Play Macro File’ and ‘Edit Macro’. When a raw data file is loaded by the program a temporary history file will be created. In this history file all operations will be logged. If a file is closed (due to the exit of the program or loading another file etc.) the temporary history file will be deleted. With the button ‘Save History’ the current history file can be saved to a user selected location. The default extension of a history file is *.hst. A macro can be applied to the loaded raw data file. The macro must be saved as a macro file first. A macro file has to be created with Macro the Edito r . TheMacro Editor can be started be the ‘Edit Macro’ button History in the Panel Toolbar . The list of applied operations History in the Panel can be used to reverse operations. To reverse the operations just click twice on an entry of the list, to reverse to the state of the data right after the operation connected to this entry was applied. To receive further information to the applied operation move the mouse pointer over the entry and read the displayed tooltip. If an operation of a macro file could not been carried out, it will be shown in red in the history list. Errors occurred during the playing of the macro will be listed in an error report which will be Report displayed Panelin. the Operations which caused an error cannot be reversed.

7.1.3.1

The Macro Editor

TheMacro Edito r will hold a list with the previous applied operations (file operations like save and load and extract to file are removed from this list because of their incompatibility with the macro function). With the ‘New Macro’, ‘Open Macro’ and ‘Save Macro’ button on the upper right side of the Macro Editor the handling of the macro file can be accomplished. The default extension of a macro file is *.hmc. The list of operations on the left side of the editor can be altered by drag and drop of the list entries to change the sequence of the operations, by double click to change important parameters of the operations and by adding operations by clicking the symbols of them on the right side of the dialog. After entering a new operation from the toolbar the parameters of this option will be asked for. After the editing of the list the macro file should be saved and can be applied to raw data files by pushing the ‘Play Macro File’ button.

7.1.4 Range View Window TheRange View Window displays the current data. The user is able to zoom into the diagrams, display a crosshair and/or a grid, give out the position info of the mouse pointer, pan, show all, separate the source and the working data etc. All of these operations can be selectedMenu fromBar theor through the Range View Toolbar . If the diagram is zoomed a double click will display the whole diagram. With a right mouse click a context will be shown, which contains the most important operations for the displaying of the data. If a range is selected from this context menu all other ranges will be hidden and only the srcinal source range and the edited working range will be shown. Both ranges will be ‘selected’ (see chapter 7.1.2 for more info).

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7.1.5 Report Panel The Report Panel contains a toolbar and the report of the loaded data. In the report all important settings of the raw data file loaded and edited are summarized. With the toolbar important file, print, search, copy and format operations can be selected. With Save ‘ as ’ the report can be saved as an ASCII text file (*.txt) or in the rich text format (*.rtf). If the text is saved to an ASCII text file, all format settings will get lost. To keep the font settings the report must be saved in the rich text format. The Print ‘ Preview ’ button will open a preview of the text as it will be set on a print out. In ‘Page Setup ’ important settings for the margin of the print page can be set. The properties sett here, are independent of the page setup done from the File Toolbar or from the Menu Bar . If a different printer should be chosen, it must be done in this Page Setup dialog. ‘Print ’ will print out the report without showing the usual printer dialog. All important settings must be done from the Page Setup dialog. With Font ‘ ’, ‘Font Size ’, ‘Bold ’ andItalic ‘ ’ the font used in this report and its properties can be altered. The Report ‘ Form ’ can be chosen on the upper right side of the panel. The short report contains only the information of the settings of the given ranges but not the data of the ranges themselves. This data will only been shown if the full report is selected. If an error occurred during the work (mostly batchin or themaster working mode) an error report will be created, if desired and set in the preferences (see chapter 7.2.3. for more details). An operation which could not been carried out while playing a macro file, will write the error as well to the error report. To show the Errorerror report the ‘ Report ’ can bee selected fromReport the ‘Form ’ menu. While working with protected files (GMP mode) Audit Data’ the ‘of the file can be displayed in the full or short report. The user can select if the working data of the raw data file or the loaded unedited data from the file should be shown. To select the source of the report the menu Fromitems Working ‘ ’ or From ‘ Source ’ can be chosen.

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7.2

File

The menu item ‘File’ offers the standard Windows utilities to reset to a new document, to read and write files, to reopen recently used files, to import or export files, to merge ranges of different raw data files and to print and export graphics shown inRange the View Windo w. ‘New…’ resets the program to the clean state as if the program was started. The list of operation done, stored inHistory the Panel and theReport Panel will be cleaned and the raw data file will be removed from memory. ‘Open…’ reads the contents of an existing raw data file, with the default extension *.raw, smoothed raw data files (*.rsm), background subtracted raw data files (*.rmb), calculated raw data (*.rtf) and other files in the raw data file format (like repetition files etc.). By opening a raw data file containing more than one measured range, all these ranges will be loaded into the current raw data handling procedure. If a file is opened which is currently being measured, a warning message is displayed. It is not possible to assess and alter the data during measurement. To check data and work with currently measured ranges anyway, a working copy of the file must be created. The warning dialog displaying will ask you if such a file should be created. The copy, if created, will be loaded afterwards. After opening a raw data file, its name is displayed in the Title Bar of the raw data handling main menu,Range the View Window and theLayer Panel will display the different ranges, the History Panel will show that a file was loaded Report an the Panel will report measurement parameters, background points as well as further information about hetexperim ent. ‘Multiple Open’ will open a list of files in a batch operating mode (see chapter 7.2.1 for more information). ‘Save‘ and ‘Save As…’ are onlyactivated if a parameter file has been loaded from which the file name can be taken. The program lets the user write the modified raw data file to a file of the same or a different name, still in the STOE binary format. ‘Import…‘ formats and loads files with a different but specific raw data file format. ‘Export…‘ provides the user with the possibility to convert the raw to an ASCII, GSAS, Fullprof, XFIT, CSD; UDF, ICDD PDF3, and MSI format compatible with other crystallographic software, especially Rietveld-Programs (see chapter 7.2.2 for more info). ‘Merge…‘ writes two different raw data files into one file as consecutive ranges. Of course, files which are to be merged must have the same wavelength, detector and diffractometer type used. ‘Print…’ will print out the graphic currently shown Range in the Vie w Windo w. ‘Print Preview’ will show a preview of the graphic which will be printed. ‘Page Setup…’ enables the user to set individual settings for the print out of graphics. ’Export Graphic…’ will export the graphic into the following formats: Windows Enhanced Metafile (*.emf), TIFF file (*.tif); Windows Bitmap (*.bmp) and JPG image (*.jpg). Additionally it can be decided if only the diagram should be exported and if the aspect ratio should be kept. When the JPG image format was chosen, the compression quality can be set. ‘Preferences…’ let the user set individual preferences of the program layout, and behaviour Fehler! (see chapter Verweisquelle konnte nich t gefunden werden. for more info). The‘Most Recent File List‘

contains the names and directories of the files most recently opened.

‘Exit‘ terminates the raw data handling routine and returns control to the STOE main menu. If the raw data file has been modified by the user, but not stored yet, the user is prompted whether he wants to update the current file or not.

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7.2.1

Different Working Modes

-

If a single raw data fil e (which wa s notsavedundersecured MP G protect ion) is loaded the programwill work in thebasic working mode. An srcinal unchanged raw data diagram and a diagram which shows the result of the chosen operation on these raw data will be displayed. All ranges can be edited separately and correction operations will affect all ranges. The history of operations done to the srcinal file is reversible. A defined macro file can be used to perform defined operations automatically. Only saving the file will finalize all the done processes. After saving the file and opening it again, the operation done to the srcinal file are irreversible.

-

If a ma ster file (in whichlladata of temp erature or repe tition measurements w ill be stored) is loade d, the prog ram will switch to the master working mode. NOTE: In this mode the operations done to the files are irreversible. All corrections and adaption of the separate ranges will be stored directly in the files which are selected. It is therefore highly recommended to make a backup copy of all the files of the serial measurement.

The program will perform this for the user, if the user selects the option that the program should work with a backup copy of the serial measurement. After loading the files, a different toolbar will be shown.

File select

Stop

Accumulate Ranges

Master Combine

In the first (left) part of the toolbar a specific file (with a selected index) can be chosen for displaying from the serial measurement. The Stop button will terminate operations currently performed. Accu mu lat The e Ran ges button and the Master Combine button will perform special operation only valid master in the working mode. The other button will perform operations as described below to all the files of the serial measurement. Both operations will create new raw data files. Accu mu late Ranges will accumulate all the intensities of the ranges in the selected files. For instance: The intensities of the range 1 from file 1 will be added to the intensities of the range 1 from file 2; range 2 from file 1 will be added to range 2 of file 2 and so on. The resulting summated intensities will be saved to a selected file. Master Combin e will do the equal operation Accu asmulat e Ranges. Instead of the addition of the intensities the combine algorithm will be used as described below. NOTE: The usage of Accumulate Ranges and Master Combine is mostly reasonable for repetition measurements.

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-

If more than one ‘single’ file is loadedMultiple by the Open’ ‘ option from theFile menu the program will switch batch to the working mode. The files loaded to this mode can be chosen in the batch select file dialog. In this dialog a list of the file to load are stored. This list can be extended with new files (Add Files) and can be cleaned (Clear List). In the file dialog, opened after pushing the Add Files button more than one file can be selected. Thebatch working mode is identically to master the working mode in most parts. The history is as well irreversible and all changes will be saved to the individual files directly. Different master to the working mode, inand thebatch working combine mode ranges could not accumulated a master procedure canbenot be performed. This program mode should be used as a quick and easy way to perform corrections to a list of files.

7.2.2

Export Files

Files loaded can be converted into different file formats. If ‚Export…‘ is chosen form File the menu, an export file dialog with further parameters is opened. The output file which will contain the converted data will have the same name as the basic raw data file with a different extension corresponding to the output format. The directory in which the output file will be stored can be chosen in the upper field of the export dialog. In the editable drop down list field the output format can be selected. The settings for the different formats are selected in the Settings field in of the dialog. The first three options are identical for all output formats. -

If ‘avoid negative intensities’ is selected, all the data of the srcinal file is increased automatically till all intensities are greater than zero.

-

If ‘convert intensities to counts/seconds’ is selected, all the measured intensities will be divided by the measuring time in seconds needed to measure these intensities.

-

If ‘overwrite files without asking’ is selected newly created export files will overwrite existing files if present in the selected output directory.

Individual Format Settings: -

Format of the X/Y files: output file can remain X and Y values or only Y values.

-

Format of GSAS files: the instrument parameter information in the *.gda file will be set to STADIP.PRM or different selected values.

-

Format of Fullprof files: two different formats can be selected (Id=0 and Id=10). For more information about these formats please refer to the Fullprof manual.

Exporting Files can as well be performed in the different working modes.

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7.2.3

Preferences

In the Edit Preferences Dialog the general behaviour, the graphical layout of the diagram and printing preferences can be changed. The general program settings define the behaviour of the error handling, warning management and other prompt messages given out by the program. The drop down list after ‘Old File Format Handling’ describes the interaction with old raw data files. The possible options are ‘Do not care’ to open old files without warning prompt, ‘Prompt warning’ to give out a warning on loading the old format, and ‘Do not process old files’. If the check for unsaved data is disabled, the program will not check if any raw data file is edited but not saved before closing the file. In the next drop down field the behaviour of creating backup copies in the master working mode can be defined. The possible choices are ‘Always ask’ to show a message prompt after opening a master file, ‘Create Backup without asking’ for the creation of the backup files without a message prompt, or ‘Never create Backup’. With the next drop down list the error handling in the master working mode can be altered. It can be chosen between ‘Write to Error Report’ to give out every error to a report which will be displayed in the report panel, ‘Show Error Prompt’ to give out an error warning without stopping the process, ‘Break’ to get an error warning and stop the process afterwards, and ‘Do not care’ to work without any prompt or report. If ‘Ask to open Masterfile…’ is enabled, the program will recognise if the file to be opened is part of a series and will send a n messageto ask the user he if t master ile f should bepened o instead. The enabling of the “Apply calculations always to all files” will disable the dialog to select special files to apply operations to, when working in the master mode. The properties of the batch working mode can be changed with the last two check boxes ‘Do not prompt errors’ and ‘Overwrite files…”. When the first is checked, the error prompt which will be displayed if incompatible files are added to the batch file list will be suppressed. The second check box suppresses the warning messages in the batch working mode. The diagram appearance defines output of diagrams on the screen and in print outs. In the box ‘drawing settings’ the basic colours, the line width of the diagram and the showing of a zero line can be altered. In the next drop down list the position of the filename can be aligned and the title of the top diagram (which shows the srcinal raw data file before alteration) and the below diagram (which shows the current altered raw data file) can be edited. The locations of the diagrams correspond here to the ‘split’ view.

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The printer settings can be used to alter the appearance of the graphic print out.

Date and Time of the Print Out

STOE-Frame

On every printed diagram the STOE-Frame will be shown. This STOE-Frame consists of a box around the diagram and a title field at the top of the page. If the date or the time is enabled in the preference dialog, on the right side of the title the date and/or the time of the print out is given. The field in the middle of the title shows an editable text, which can be defined in the WinXPOW MainMenu. The orientation, the margin of the frame and the settings for the ‘Bundsteg’ (with possible ‘Lochermarke’) can be set in the Page-Setup-Dialog which is assessable through the toolbar button or the File-menu see above. All settings can be reset to the default values by clicking the Reset butt on.

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7.3

View

The pull down menu ‘View‘ changes the display of the file contents on the screen. If ‘Position Info’ is checked,θ− theand 2 the intensity position of the mouse pointer will be displayed in the caption bar. ‘Crosshair’ will connect the mouse pointer with the diagram frame, forming a crosshair. If ‘Show Grid’ is enabled a grid will be displayed over the diagram. With ‘Zoom all’ and ‘Pan’ a zoomed diagram can be handled. With ‘Split’ the two files (srcinal loaded before the editing and the current working file) can be viewed in a split or in an overlay mode. In the split view the diagrams of the source and of the working file will be separated. The top diagram displays corresponds to the source file and the lower button diagram shows the edited ranges. To enable the split view, both files must be displayed with at least one range. If all ranges of one file are hidden, only the other file will be displayed in the overlaid mode. With ‘X-Axis Scale’ and ‘Y-Axis Scale’ the scale of the axes can be altered. The 2. The Y-Axis can be scaled to relative and absolute values. X-Axis can be scaledθ,to1/D 2 and 1/D In the last three menu entries the layout of the whole program can be altered. With ‘Restore Original Layout‘ the layout of the program before the alteration can be restored.

7.4

Parameter

This option activates the pull down menu shown on the right side. -

‘Title‘ allows the user to change the raw data file title.

-

‘Wavelength‘ allows to change the wavelength used for the data collection to a different standard wavelength or to user defined one. NOTE: Obviously, this needs only to be done if the data has been accidentally collected with an incorrect instrument parameter file setting. Input of an incorrect wavelength will lead to disastrous results when observed θ2- values are converted to d-spacing by any of the evaluation programs!

-

‘Generator‘ allows to change the generator-settings stored in the raw data file.

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7.5 Ranges The menu item ‘Ranges‘ activates the pull down menu shown on the right, with the options to com bine, delete etc. ranges f collected o pow der pa tterns as w ell as ot add, subtract or divide ranges from an other file. All of this operations can be chosen as well from the toolbar in the Layer Panel or in the context menu if a range Layer in thePanel is clicked by a right click on a range. NOTE: If a range operation is selected in the Ranges menu or in the Layer Panel toolbar a range must be chosen first to proceed. To choose the operation in the context menu requires no selection of specific ranges.

When working in master working mode or batch working mode the operation selected will be applied to all selected files (which can be selected in the file select dialog in the master working mode which is only displayed if it is enabled in the preferences of the program). In master or batch mode all icons shown in the pull down menu Σ-symbol got a at the upper left corner.

‘Add Ranges‘ performs the requested operation between a scan range of the current raw data file and a scan range of another range or ranges of the same raw data file. One or more ranges can be activated by a mouse click and using the CTRL-key. These ranges will be added by pressing ‘OK‘ to the range specified in the ‘Select Range to add to‘ drop down list in the upper right corner of the displayed window. All ranges could be added to the selected range by pushing the ‘All Ranges‘ button in the lower left corner of the dialog.

The tool ‘Combine Ranges‘ creates a single range from two ranges with θdifferent ranges.2The option requires two ranges collected with the same scan mode; otherwise an error message is given. If the scan ranges overlap, the intensities in the overlapping region will be added with weights linearly proportional to their angular position:

I()x (=) I1 x ⋅ I(x) : I1(x) : I2(x) : x1 : x2 :

x1

−x

x1

− x2

() + I 2

x

⋅

x

− x2

x1

− x2

newintensityat x intensit y at x in the first range intensit y at x in the second range endof first range startof secon d range

If the two scan ranges do not overlap, a warning message will be displayed and a zero line will be inserted in the region between the end of the first range and the start of the second range. If the number of points for the new range exceeds the maximum permitted number per range, i.e. 16384, the new range will be truncated at this point and a warning message will be displayed. ‘Delete Ranges‘ removes a range from the current raw data file.

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The option ‘Truncate Ranges‘ reduces the angular range for a selected scan range in order to eliminate useless data points (i.e. shadowing effects from sample holders etc.).

‘Adapt Intensities’ is used to either multiply all intensities in a range by a user-defined factor, to set the maximum intensity in a range to a certain value with all the other intensities being changed accordingly maintaining the relative intensity relations, the smallest intensities a minimum or to slide the range(s) to to a cut defined value. This option to may be usefulvalue for comparison reasons, or to avoid negative intensity values, but invalidates the counting statistics. NOTE: Data manipulated in this way should therefore

never be used for quantitative work.

‘Add Points ‘ is useful to gain intensity at the expense of data resolution. When two points are added up to one data point in the raw data file, the nominal step width of data points is doubled and the intensity per data point is approximately doubled, too. For very badly diffracting samples this value may be increased up to a point where the nominal data step width is about a third of the expected peak half widths. Otherwise this option may be used to reduce the amount of collected data points in order to save disk space or load this modified file after conversion into older shareware programs.

One or more ranges out of a multi range – raw data file may be extracted to another‘Extract file using the option Ranges‘ . ‘Add File‘, performs the requested operation between a scan range of the current raw data file and a scan range of another or the same raw data file. The scan parameters of the two ranges have to be identical otherwise a warning message is displayed and the operation is aborted. When the second file has been accepted by the software the relative intensity of the first range with respect to the second range and vice versa can be influenced by the multiplication factors (m1 for the first and m2 for the second range). These ranges will then be added in the specified ratio by pressing ‘OK‘. ‘Subtract File‘ performs the same operation between a scan range of the current raw data file and a scan range of another or the same raw data file only in the reverse case. The second range will be subtracted from the first range according to the chosen ratio. ‘Divide File‘ performs the division of a scan range of the current raw data file by scan range of another or the same raw data file after choosing a specific factor ratio.

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7.6

Operations

The menu item ‘Operations‘ activates the pull down menu shown on the right, with options like ‘Absorption Correction‘ , ‘Angle Correction‘ etc. These operations can be performed to all the files of serial measurement or to files selected in the batch file list. When the operation menu item are displayed in thebatch working mode or in the master working mode the icons will display a smallΣ-symbol in the upper left corner. All the menu items can be selected directly from the operations tool bar or the batch/master toolbar and will affect all ranges of the opened files.

The option ‘Absorption Correction‘ calculates the effect of the transmission factor input for the data collection geometry (Transm ission,Reflectionor Debye-S cherrer). The applied formulas are: I(corr) = I(obs) . xp e (µ.t / cos )θ

for transm ission

I(corr) = I(obs) / [ -1 exp( -µ2. .t / sinθ ) ] for reflection For the Debye-Scherrer geometry, the tables of Weber (K. Weber, 23, 720 Acta(1967)) Cryst. are used. A cubic spline is used twice for the interpolation between the tabulated q-values and between the tabulated µ×R-values. Note: The absolute intensities will be strongly affected by the absorption correction. The usual Poisson counting statistics are no longer valid for the corrected raw data.

If the raw data collection has been done in Transmission-mode, where the transmission coefficient can be determined experimentally, the parameter expected by the program is I/I of the attenuated primary beam intensity by 0, the ratio the sample to the not attenuated intensity of the primary beam.

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To obtain I and I user has to execute the following procedure: 0 the 1. The settings of the current (mA) and voltage (kV) have to be reduced to 20 mA and 40 kV before or after the norma l measureme nt. 2. The small plate in front of the PSD with the 6° aperture has to be exchanged against the one with the brass filter by unscrewing the plastic screws and introducing the attenuator instead. 3. The primary beam stop has to be removed. θ =at0,2 3. The sample in the flat sample holder s tohabemeasured for at least 60 c. se with the PS D stationary the obtained count rate is I. 4. The same measurem ent with anmp e ty sample ho lder and the fixi ng ring of sam e diam eter as the one used for the sample has to be repeated for the same period of time. The count rate is then I 0. If the data collection was done in reflection or Debye-Scherrer-mode, the value expected by the program is µ×R, which has to be calculated from attenuation coefficients µ (one can get this value easily by using the Program ‚Theoretical pattern’), sample density (which has to be assumed between 0.5 and 0.7, depending on how easily the sample could be inserted into the capillary) and sample thickness (which is R, half the diameter of the capillary). µ×R is then calculated by µ * sample density * R. ‘Angle Correction‘ provides a possibility to correct the angular scale of the raw data a posterior. If the user file contains a correction polynomial created and chosen by the ‘Peak Calibration‘ routine, this polynomial will be applied to the RAW data file. ‘Alpha2-stripping‘ performs the Rachinger correction for data which have not been collected with monochromatic Kα1-radiation. This correction removes α2-peaks all K from the diagram. The option is not activated if the data have been collected using a primary monochromator. ‘Deadtime cor rection‘ provides a possibility to apply a dead time correction to the data. This is normally done by the data collecting software a scintillation has been used for data collection. If such a correction has already been applied the when program will give ancounter error message. The applied formula is: I (corr ) =⋅

I (obs)

1 − τ I (obs )

‘Fold diagram‘ provides a possibility to fold the data, collected with an IP-PSD in symmetrical setting, around zero. In such a wa y a scan rangeithw an an gular ange r o f -55 to +60 degree 2theta result ing a scan rangeithwan an gular range of0 to 55 degree 2theta and doubled intensit y. This opti on is on ly accessibl e if data coll ected w ith an IP-PSD have been loaded.

‘Edit Background‘ starts an automatic background-removal routine which may as well be altered by the user. If the option is selected, the menu layout is changed Layer - (the , theReport - and the History panel will be hidden) and the program displays a background editing toolbar (see below) and a background-spline function calculated from a number of automatically selected background points. Increase/Decrease Smoothing Factor

Subtract Background

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Range Selection Tools


7-14

With the first button on the toolbar a modified background file will be saved. With the next two buttons the smoothing of the background spline can be altered. The Range to be edited can be chosen with the next buttons. The ‘Ok’ button on the right side of the toolbar will end the editing of the background. If the background was edited, the user is asked if the changes should be kept. There are three options for the user to change the background generated by the program: By left-clicking on one of these points, they may be moved to any position in the diagram and - by releasing the mouse button again – may be placed at a different location. The spline function will be automatically re-calculated. The very first and very last point of the diagram may not be shifted in their position, but may only be altered in their height. By double-clicking anywhere in the diagram, an additional background point is inserted and the background - spline re-calculated. By either clicking on the toolbar buttons or by hitting the ‚+‘ / ‚-‘ keys on the numeric keypad, the degree of smoothing of the spline function is changed. By increasing the smoothing further and further, a straight background in the form of a linear regression will be obtained. By decreasing the smoothing factor further and further, the background will follow exactly through all background points, sometimes tending to overshoot between the points.

When the background line has been defined, the ‚Subtract Background‘ button may be used to create a raw data file with the background-corrected data. The default extension for background-subtracted data is *.rmb. When the ‚Stop‘ button is pushed, the background selected so far is stored in the srcinal raw data (without changing the srcinal data). Subsequently, the normal graphics menu bar is restored. Note: The .background points will be lost after applying other operations. To store the background points for using them in other programs like Fit, the file has to be saved directly after calculation and editing the background points.

If background editing is selectedbatchin the or master working mode only a dialog will appear (shown on the right) where a Background Smooth Factor can be defined and it can be selected if the background correction should be applied directly to the file (a background spline will be calculated and subtracted from the data of the file and the file will be saved afterwards) or if only background points will be calculated and saved in the file (to edit the background afterwards with programs like Fit).

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If the option ‘Smooth Diagram‘ is selected, the menu layout is changed Layer (the , theReport and theHistory panel will be hidden), the program displays a smooth editing toolbar (see below) and a preview of the range data after applying the smooth function. Editing Tools for Parameters

Apply Smooth Function

Stop Button

Range Selection Tools

The smoothing is done according to an algorithm described by Allmann (see below). The parameter for this algorithm may either be input as the average peak half width θ (in ) from degrees which 2 the program calculates the number of points by dividing it by the data step width or directly as the number of data points to be used. With the ‘Apply Smooth Function’ button the algorithm will be applied to the data and the newly created data will be saved. The default extension for a smoothed raw data file is *.rsm. When the ‘Stop‘ button is pushed the program will end the preview mode for smoothing.

If ‘Smooth’ is selected inbatchthe or master working mode only a dialog will appear (shown on the right), where the two factors can be defined. After pressing the ‘OK‘ button the smooth algorithm will be applied to all selected files.

R. Allmann, Smoothing by digital filters and a new peak search routine. EPDIC 133-136, 2, Mat.Sci.Forum 323 (1993) R. Allmann, Röntgenpulverdiffraktometrie, Clausthaler Tektonische Hefte 29, Verlag Sven von Loga, Köln 1994

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8 Pattern Fitting

8.1

Introduction

The Pattern Fitting routine is used to determine profile parameters and integrated intensities from observed powder patterns. A variety of constraints makes it possible to achieve meaningful results even for complicated patterns. The program is started from the ‚Raw Data‘ pull-down menu of the WinXPOW main menu.

The menu items of the Pattern Fitting routine comprise ‚File‘, ‚Parameters‘, ‚Operations‘, ‚View‘, ‚Options‘, and ‚Help‘. The left-hand side of the status bar usually displays the cursor position, the right-hand side the statistical descriptors of the most recently run least-squares-fitting.

8.2

File

The ‘File’-menu item offers the standard Windows utilities to read and write files, to re-open recently used files and to print the results.

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WinX 3.05 Software Manual – Pattern Fitting

8-1

8.2.1 New‘ Deletes all loaded data from memory but keeps parameter settings like ‚Overall Parameters‘ or view parameters.

8.2.2 Open Reads the contents of an existing file - either a peak or raw data file - into the program. After opening a file, its name is displayed in the title bar of the main program window. To perform a pattern fitting, at least a raw data file must have been opened. If no peak file is read, a peak list can be generated with the ‚Find Peaks‘ option described in chapter 8.4.1.

8.2.3 Read ICDD Data Importing a peak list from an installed ICDD database. This item is activated only if an ICDD database is installed.

8.2.4 Save As Lets the user write the current peak list to a file. This may either be an existing or new *.pks file or a file having the STOE peak file format but the extension *.pft denoting that the contents of this file have been generated by the pattern fitting routine. Also, the calculated step intensities may be written to a raw data file with extension *.rft.

8.2.5 Update Raw File Can be used to store the background line defined with the option described in chapter 8.4.3. to the raw data file currently loaded. This item is disabled if a raw data file which was measured under GMP was opened in an not GMP controlled envirom ent.

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8.2.6 Print / Print Preview / Print Setup Control and format the output of the current graphic display to the system printer.

8.2.7 Export Graphics Provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the combo Save as box type‘ ’. The available formatsEnhanced are Metafile (which will be the most adequate format when importing the display into other TIFFapplications), andWindows Bitmap file. With deactivated option ‘only Diagram(s) ’ the output will be identical to the printed version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page, regardless of the current aspect ratio of the display. To maintain the current aspect keep aspect ratioratio the ’‘ option should be activated.

8.2.8 Recent File List The most recent file list contains the names of the eight most recently used file names for quick re-loading.

8.2.9 Exit Terminates the Profile Fitting – routine and returns control to the WinXPOW main menu.

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8.3

Parameters

provides input facilities for all parameters concerning the fit of modelled data to observed data.

8.3.1 Overall Parameters This dialog box is used to define the kind of background function, the kind of wavelength used to collect the diagram nd the 2theta-dependent asym metry function of the peakprofiles.

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Thebackgro und function of the diagram may be defined either as a series of Tschebyschev polynomials or as a conventional power series, which may be selected by radio buttons. The Tschebyschew polynomials are usually more robust and mathematically better behaved than a power series representation. Themaximum order for both kinds of function is proposed by the program as the 2theta-range of the diagram divided by 20, but not exceeding 6. It may be changed by the user and should, if in doubt, rather be given too small than too large. For short 2theta regions ( 5-10° ), the maximum order should be set to 1 (= linear background) to avoid artefacts of the background function. For a strictly horizontal background line varying only in height but not in inclination, max. order is set to 0. Usually, there will be no need to change background the coefficients and their fixation. In the beginning, all coefficients should be allowed to vary. If a convincing background representation has been found, but the refinement is not quite stable, all coefficients may be fixed with the ‚Fix all‘ button leading to a background line not varying with the peak parameters. Individual terms of the background representation may be fixed as well using the corresponding check boxes. The empirical background as defined with the ‚Operations‘ – ‚Background‘ option (see chapter 8.4.3) may be taken into account during refinement orAdd not.emp If ‚iric al backg roun d‘ is checked, this user-defined background line will be added to all calculated intensities thus preserving correct counting statistics and weights. The user-defined background line will never be refined. If the user-defined background alone shall be used to account for the background line, the (refineable) polynomial representation may be switched off by setting its maximum order (see above) to -1. The monochrom atisation of the primary beam may be select ed with the Add ‚ Alph a2 peaks‘ checkbox. For diagrams collected with a primary monochromator and thus pure Kalpha1-radiation, it must not be checked. If it is checked, the intensity ratio alpha2/alpha1 may be entered (usually 0.5) and may be either fixed or refined. Having the intensity ratio refined usually leads to a smaller R-value, but is only advisable if a large portion of a diagram is fitted simultaneously. If the fitting region contains only a few peaks, closely spaced peaks may be missed and ascribed to an incorrect intensity ratio. Peak asymmetry is described by a modification of the method of Finger et al. (Finger, J.Appl.Cryst., 31, 111, (1998) and Finger,Cox & Jephcoat, J.Appl.Cryst. 27, 892 (1994)). Finger's srcinal approach uses two (physically significant) parameters H/L and S/L to describe the 2theta-dependent asymmetry of all peaks. For data collected on the STOE diffractometers, one parameter defined as the average of the two srcinal terms was found to describe the asymmetry equally well: the value of this parameter must be between 0 and 1. Values outside this range written in the user file will be reset to 0 on the successive start of the application. As the algorithm involves convolution of profiles, it is quite time-consuming. Therefore,number the of steps used for the numerical integration of every data point of a peak profile may be varied. Usually, values around 50 work both reasonably accurate and reasonably fast. In the early stages of refinement, the asymmetry parameter should either not be used or be fixed to a known value specific for the measuring parameters.

8.3.2 Peaks The dialog box ‚Edit Peaks‘ is used for the definition of profile parameters for individual peaks or a set of peaks defined as a group. A group has identical profile shape and other relevant group-properties described in 8.3.3. Every peak belongs to exactly one group; a group number of –1 assigned to a peak will exclude this peak from all calculations during the refinement. The main list box in the centre of the dialog box displays all peak data for the current refinement problem. The refinement flags are indicated by ‚V‘ (for ‚variable‘) or ‚F‘ (for ‚fixed‘) after the parameters. By left-clicking on one of the lines it becomes highlighted and the peak data from that line are transferred to the four edit boxes and three corresponding check boxes at the top of the dialog box. In these boxes, the parameters and their refinement flags (fixed or not) may be changed. When the changes are done, Replace pressing ‘ button the ‚ moves the new parame ters back into the ain m list box. Pressing the Delete‘ ‚ button while one of the peaks is highlighted removes it from the peak list. Clicking on Insert the‘ ‚button adds the peak data currently in the edit boxes to the peak list. Caution : Having two identical peaks in the peak list will result in a singular least-squares matrix.

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The refinement flags m ay also bechangeden-suit e: While a peak( or several peakslect seed byShift- or Strgleftclicking ) is highlighted,Free thePeak‘ ‚ button will set all three individual refinement flags for position, intensity and width to variable, whereas Fix the Peak‚‘ button will fix all three parameters. Fix The all ‘ and ‚ Free ‚ all ‘ buttons refer to the parameter in the column beneath which they are positioned; pressing the first ‚Fix all‘ button will e.g. set the position of all peaks in the list to ‚fixed‘; whereas pressing the last ‚Free all‘ button will set all FWHMs to ‚variable‘.

The Delete ‚ -‘ button is used to remove all peaks having a group number of –1 (and therefore excluded from calculations) permanently from the list. Reset The -‘ button ‚ changes all group numbers from –1 to 1 thus including these peaks into calculations again. ‚Edit Group ‘ provides a shortcut to the ’Edit Group‘ dialog box described in 8.3.3. ‚Set Group ‘ is useful to assign a group number to several peaks simultaneously: After selecting the peaks by Shift- or Strg-leftclicking, a group number may be entered into the group number edit box which will be transferred to all currently highlighted peaks when pressing the ‚Set Group‘ button. The Go ‚ To ‘ button is only active if the graphic display has been zoomed and does not show the whole diagram. By clicking on the ‚GoTo‘ button the graphics display will be scrolled so that the currently highlighted peak in the list box is within the visible part of the diagram. The'Close' button closes the dialog box. It may, however, be left open during refinement. The peak data are then autom aticall y updated during cycles.

8.3.3 Groups The ‚Edit Groups‘ dialog box is used to define group properties which are common to all peaks within this group. The profile function may be selected from the radio-buttons either as Pearson or Pseudo-Voigt. The simpler Lorentzian, squared Lorentzian and Gaussian functions may be chosen by selecting a Pearson type profile with a fixed profile parameter of 1, 2 or above 10, respectively. For the mathematical definitions of these functions see chapter 11.3.3.

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The edit boxes and check boxes are used to enter parameters and refinement flags. These settings are transferred to the currently selected and highlighted group by pressing Replace ‘the button. ‚ Pressing the Insert‚ ‘ buttonwill adda new group to the list with the properties defined in the edit and check Delete‘ boxes. removes ‚ the highlighted group(s) only if the group number is currently not assigned to any peaks. The Fix ‚ Group ‘ and Free ‚ Group ‘ buttons are used to change all refinement flags of the group simultaneously. In contrast to the change of individual refinement flags using the check boxes, these changes are automatically tranferred to the group list box and need not be activated by ‚Replace‘. TheProfile Parameter is eit her the Pe arson expon ent (which ust m exceed0.5) or the G auss m ixing parameter (between 0 and 1) depending on the choice of the profile function (see chapter 10.3.3 for the respective formulas). The profile shape is always the same for all peaks in a group and may be either be set to ‚Fixed‘ or varied during refinement. TheIntensity factor , Zeroshift andHalfwidth of a group are only refined if peak intensities, positions and halfwidth of all peaks in this group have been respectively fixed in the ‚Edit Peaks‘ dialog box – regardless of the setting of their group refinement flags. These three parameters are used together with the individual peak parameters, i.e. the integrated intensity of a peak is the individual peak intensity multiplied by the group intensity factor; its position is the individual position plus the group zeroshift; and its FWHM is the sum of the individual halfwidth and the group halfwidth. The interplay between individual peak parameters and group parameters allows e.g. the fixation of an intensity ratio of two peaks by assigning only these peaks to one group, entering their intensities manually, fixing the intensities in the ‚Edit Peaks‘ dialog box and then refining the intensity factor for the corresponding group.

The Normalize ‚ ‘ buttons allow the transfer of the group parameters to the individual peak parameters of all peaks belonging to the selected group; i.e. normalizing the intensity factor will multiply all individual peak intensity by the factor and reset it to 1; normalizing the zeroshift (halfwidth) will add the zeroshift (group halfwidth) to all peak positions (peak halfwidths) and reset it to 0. The only exception from this rule is described below. The peak halfwidths of all peaks in a given group may also be refined as a function of 2Theta using the Cagliotti formula ifHalfwidth ‚ as function ‘ is checked. In this case, the individual halfwidths of peaks belonging to the group are totally ignored. When normalizing the halfwidths, the individual halfwidths are therefore discarded and replaced by the halfwidths calculated from the formula. The three parameters, which may also be individually fixed or varied, correspond to U, V, and W in the formula

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FWHM2 = U . tan2 θ + V . tanθ + W

8.3.4 Regression This dialog box defines some optional properties of the non-linear refinement. Termination of the refinement is controlledConvergence by the ‚ limit ‘ and theMaximum ‚ number of cycles ‘. The convergence limit is the maximum relative difference χ2 - values of of two subsequent cycles so that the refinement is considered converged and terminated. If ‚Linear regression before nonl inear ‘ is checked, one linear cycle is calculated every time a non-linear refinement is started. This option helps to keep refinements stable. ‚Draw diagram after each cy cle ‘ may beused to sw itch onand off the on-line display of calculated curves after each refinement cycle. ‚Add empir ical backg round‘ is used to include background previously defined using the ‚View‘-‚Background‘ option. This check box is the same as in the ‚Overall Parameters‘ dialog box and is explained there (chapter 8.3.1). The Weighting ‚ scheme ‘ can be chosen from unit weights, √I and1/ 1/I. The usual weighting scheme arising from the Poisson counting statistics is√1/ I. The Stepwidth ‚ for simulated pattern ‘ affects only theimulation S –operation, i.e. he t calculation of a raw data diagram from given peak and overall parameters without taking into account observed raw data. The edit and check boxes belonging Check to the abnormal ‚ FWHM ‘ field are used to set up an automatic exclusion of those peaks from further calculations, which have been distorted during the refinement. All peaks having a halfwidth less than ‚Min.(%)‘ of the average halfwidth or exceeding ‚Max.(%)‘ of the average FWHM are assigned a group num ber of –1, if ‚Exclude ab norma l peaks‘si checked.The group num ber of –1 indicat es a peak which is not to be used in further calculations (see 8.3.2). The same happens to peaks below a certain integral intensity level, Exclude if the peaks boxwith ‚ intensity < checked. The required minimum intensity is entered in the corresponding edit box.

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‘ is

8.3.5 Regions The default fit region is the whole measured pattern. If however, only portions of the diagram shall be fitted, the Regions dialog box is used to define them. The list box contains the currently defined regions, which may be selected using the left mouse button. The region input into the edit box at the top may be moved into the list box by three possible actions:

‚Insert‘

adds the new region to the others taking into account possible overlap and combining two overlapping regions into one larger region.

‚Replace‘ discards thecurrently highlighted region and replaces it with the new region again testing for overlap with other regions. ‚Exclude‘ cuts the regionin theedit b ox fromthe appropriate region(s) in the list box creating – if necessary – two regions out of one. ‚Delete‘

removesthe highlighted regionsfromthe list.

‚DeleteAll‘ removesall region s. The ‚2theta‘ and ‚D-space‘ buttons are used to define the units in which the regions are defined and displayed.

8.3.6 Load / Save Parameters The Save ‘ Parameters ’ could be used to store a set of parameters ( peaks, regions, background, groups ) for later use. The parameters are stored in files having the extension *.par. A previous stored parameter set could be reload with theLoad ‘ Parameters ’ option, overwriting all current parameters.

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8.4

Operations

The ‚Operations‘ pull-down menu comprises all commands starting calculations with peak or raw data.

Most of these commands are also available from the following toolbar buttons : ‚Si‘ = Simulation = EditPeaks ‚S‘ = Scaling ‚L‘ = LinearRegression = EditBackground ‚N‘ = Nonlinear Regression ‚N1‘ = one cycle of nonlinear regression

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8.4.1 Find Peaks ‚Find Peaks‘ opens a dialog box from which a peak search in the loaded raw data can be started. Peaks previously loaded are discarded. Estimated Halfwidth : An approximate value for the peak halfwidth must be given. This parameter can be used to discern between sharp and broad peaks. When both kinds of peaks are present in a diagram, it is usually impossible to identify both classes of peaks in one run of the peak search. goodfor value data collected with the lineardetector PSD oraIPPSD is 0.15°,Awhile dataforcollected with the Mythen1k good value is 0.08°. Significance Level : The significance level sets a lower limit to the peak heights; it is defined as the ratio of the maximum peak intensity to background. Peaks which are found by the slope criterion, but have a peak height below the given significance limit, will be discarded. Intensity Limit : The intensity limit is an additional criterion applied to a peak identified in the peak search algorithm. All peaks having an absolute height less than the input value will be discarded. Setting it to 0 will accept all peaks matching the significance criterion, values above 0 will increasingly reduce the number of peaks found. Remove Alpha2 Peaks : Checking this box will scan the peak list for pairs of Alpha1/Alpha2 peaks and discard the Alpha2 reflection. To match the Alpha1/Alpha2 criterion, the peak position of the second peak must be within 0.02° of the theoretical Alpha2-reflection as calculated from the Alpha1-position and its intensity must be between 45 and 55 % of the corresponding Alpha1 peak. Remove Spikes : When this box is checked, a search for peaks of abnormal halfwidth will be performed in the peak list which passed the other criteria. Peaks of a halfwidth less than 25% of the estimated halfwidth defined above will be discarded as spikes. The Defaults ‚ ‘ button loads reasonable values for the above edit boxes. By pressing the ‚OK‘ button the pea k search is started. When it isfinished , the peaks foundare displayed in the graphics window and are written to the peak list accessible from the ‚Parameter‘ - ‚Peaks‘ option.

8.4.2 Edit Peaks If the ‚Edit Peaks‘ option is activated (visible either by the depressed tool button or the check mark in front of the pulldown menu option) interactive changes to the peak list may be made by mouse-clicks on the diagram. The relevant conventions are as follows : Double-clicking anywhere in the diagram while the cursor is the usual arrow inserts a new peak with the according 2theta - position and intensity and the average FWHM of all peaks in the region into the peak list. Moving the cursor in the vicinity of an existing peak changes it to a cross. As long as the cursor is in this shape, the peak may either be moved by drag-and-drop to change peak position and/or intensity or can be deleted from the peak list by right-clicking. Caution : When trying to zoom in while this option is active may lead to accidental movement of peaks when the fact that the cursor changes his shape to a cross is ignored.

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8.4.3 Edit Background This option is used to define a background line independent from the polynomial representations used for refinement. This empirical background line may then either be used in addition to the refineable background or instead of it (see Overall Parameters, chapter 8.3.1). If the Background option is applied for the first time during a session, the program proposes reasonable background points. The number of these points differs between 2 and 16 depending on the number of pattern data points. The maximum number of background points is 64. If the raw data file already contains background information from a previous background run ( either in Graphics or Profile Fitting ), the stored background points will be loaded and displayed. If there are at least 3 background points a background curve is shown which is computed by a smoothing cubic spline interpolation routine. The number, positions and intensities of the background points may be changed by mouse-click. The two points at the left and right border of a pattern are not deletable, but they can be moved vertically. Double-clicking anywhere in the diagram while the cursor is the usual arrow inserts a background point at the cursor position and recalculates the spline function. Moving the cursor in the vicinity of an existing background point changes the cursor to a cross. As long as the cursor is in this shape, the background point may either be moved by drag-and-drop to change its position or may be deleted by right-clicking. The background function will again be recalculated.

Pressing the – key of the numeric keypad reduces the smoothing of the background curve. The smallest possible smoothing causes the background curve to match the background points exactly. Pressing the + key of the numeric keypad increases the smoothing of the background curve. The largest possible smoothing causes the background curve to be a straight line which need not match the background points. When the background has been described in a satisfying way, it is possible to store the background function in the raw data file using the ‚Update Raw File‘ command from the ‚File‘ pull-down menu.

8.4.4 Clear Background removes the information set up in the 'Edit Background' option; i.e. zeroes the observed background line.

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8.4.5 Simulation This option calculates a diagram using the overall, peak, and group parameters as currently defined and displays it. No changes to the parameters are done. The option is useful if the type of peak profile or background line are totally unknown. Trying different settings out helps in getting reasonable starting values before starting the refinement cycles.

8.4.6 Scaling This option refines only the background line but takes into account overall, peak, and group parameters as currently defined. The option can be used at the beginning of a refinement to provide the program with a reasonable background estimate. The background parameters must of course have been allowed to vary in the ‚Overall Parameters‘ dialog box.

8.4.7 Linear Regression This option refines only peak intensities and background but leaves peak positions, halfwidths and profile parameters fixed. This kind of refinement should be run between the scaling and the nonlinear routine thus eliminating the danger of oscillations during the early stages of refinement.

8.4.8 Nonlinear Regression This option starts the complete refinement of all parameters which have not be fixed explicitly or which are fixed by group considerations ( see 8.3.3 ). Depending on the settings in the ‚Regression‘ dialog box explained in 8.3.4 additional actions will be taken, e.g. eliminating peaks of a too narrow or too large halfwidth from consideration. During calculation, the statistical descriptors of the refinement will be updated in the right-hand side status bar. To interrupt calculation, click on the red traffic light button in the tool bar.

8.4.9 Integrate regions This option opens a dialog window similar to the ‚Regions‘ window described in 8.3.5. The regions selected so far are displayedin a list together ith w theintegratedeak p intensit y in this region which is calculated as the sum of all intensity values in the region minus a linear background calculated from the n leftmost and rightmost points of the region. The parameter n may be entered in the edit box below the list box. The default value for n is 10. After changing the number of background points, the integral intensities are re-evaluated if the ‚Calculate‘ button is pressed. ‘Save Result’ lets the user save the integration results in a text file. This option is useful, if peak shapes are quite irregular and cannot be simulated by any of the analytical peak shape functions.

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8.5

View

In the pull-down menu ‚View‘ commands affecting the layout of the window are combined.

8.5.1 Clear removes all calculated lines from the display leaving only the observed raw and peak data.

8.5.2 Regions must be checked if a bar beneath the x-axis shall display the regions defined as explained in 8.3.5. If this mode is active, it is also possible to re-define the regions by moving the cursor to the region bar. When the cursor is positioned on the beginning or end of a region, it turns into a bidirectional arrow and moving it by drag-and-drop extends or truncates the region accordingly. If the cursor is positioned inside a region, it turns into a cross and similar drag-and-drop action will remove the defined parts from the region.

8.5.3 Difference must be checked so that a splitter window beneath the diagram shows the difference plot.

8.5.4 Position Info must be checked in order to have the cursor position continuously updated in the left pane of the status bar. This optionis alsoaccessiblethroughthe toolbarbutton .

8.5.5 Grid Lines switchesan underlying grid for thediagramon andoff. This op tion is alsoacces sible throug h the too lbar bu tton

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.

8.5.6 Whole Diagram resets a zoomed image to the display of the complete pattern. As long as the button is depressed, it is possible to go back to the zoomed state by releasing the button by clicking on it. This option is also accessible through the toolbar button .

8.5.7 Toolbar switches the toolbar on and off.

8.5.8 Status Bar switches the status bar on and off.

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8.6

Options

The ‚Options‘ menu comprises commands affecting the display of the main window as well as tools for recalling parameters from previous fit runs and storing parameters temporarily.

8.6.1 Edit File Title allows the user to change the diagram title which is displayed and printed. The File Title will be also used as title for the.rft file. If the checkbox Copy“ File Title to RAW file ” is checked ( file the next time the user performs Update an Raw “ File ”.

), the titlewill be copied also in the.raw

8.6.2 Set fit. as obs. Pks replaces the ‚observed‘ peak list with the refined peak list. The ‚observed‘ peak list are the starting values provided either by reading a peak file or by executing the ‚PeakSearch‘ option. This list is not accessible to the user after refinements, but may be displayed in the graphics depending on the ‚Window‘ – settings shown below. It is only kept for comparison reasons of the type before / after refinement.

8.6.3 Save FitParam produces a copy of the current parameter list in the memory which may later be re-loaded. This is useful to recover parameters which have become unreasonable during a refinement run.

8.6.4 Reset FitPara_X The X in the command may be one of the characters ‘P’, ’S’, ‘L’, ‘N’ or ‘1’ referring to the resetting of parameters before a simulation, scaling, linear, non-linear or 1 cycle of non-linear run.

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8.6.5 Graphics opens a dialog box where the layout of the program window can be set up. The display of all curve types may be switched off and on and the size and viewport of the splitter windows defined. .

8.6.6 Colours opensa dialog boxhere w the colours associat ed with the diff erent observed and calcul ated curves m ay beedited. The functionality is the same as in the ‚Colours‘ option of the graphics program described in 5.4.2.

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9 Peak Calibration

9.1

Introduction

The module ‚Calibrate Peaks‘ allows the user to calculate correction terms for the 2theta scale of data collected with an internal standard or otherwise known peak positions. While the program deals only with peakfiles, it can however store a correction term in the userfile which may be used to correct raw data files with the Raw data handling module, which is accessible from the ‚Raw Data‘ - pull -down - menu of the WinXPOW main menu. The 2theta errors and the correction curves are shown in a diagram. The program can use polynomals up to order four or splines to calculate correction terms.

9.2

Files

comprises options to load peak files into the program, to save corrected peak lists and to print out data from the program. ‚Open‘ is used to load the two required peak-sets into the program: One peak file containing the observed peak data and one set containing the standard peak-set ( or the whole sample in case the correction polynomial is to be used as an external standard ). By choosing ‘Peak file’ the standard peak-set is read from a peak file, while choosing ‘ICDD Database’ this set could be loaded from an ICDD database. The ‚…‘ browse-buttons provide the standard Windows function for file selection.

‚Save‘ and ‚Save As ‘ lets the user write the calibrated peak list either to the very peak file from which the observed data have been read or to a peak file of another name. Both items are only activated if the observed peak list has been changed either by the automatic calibration routine or the ‚Calibrate Peakfile‘ command. ‘Print’ - ‘Print Preview’ - ‘Print Setup’ printer.

control and format the output of the current graphic display to the system

‘Export Graphics ’ provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the combo box ‘Save as type ’. The available formats are Enhanced Metafile (which will be the most adequate format when importing the display into other applications), TIFFand Windows Bitmap file. With deactivated option ‘only Diagram(s) ’ the output will be identical to the printed version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page,

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regardless of the current aspect ratio of the display. To maintain the current aspect ratio the ‘ keep aspect ratio ’ option should be activated. The ‚most recent file list‘

contains the names of the six most recently used file names for quick re-loading.

‘Exit’ terminates the peak calibration routine and returns control to the STOE main menu.

9.3

Match Peaks

This command scans the two peak lists – calibration peaks and observed peaks - for peak pairs which lie within a given 2Θ window. A dialog box allows the input of two parameters :

The Intensity limit is a cutoff-value below which the program will ignore all peaks from both the calibration and the observed peak files. The 2Θ window is the 2Θ range around a calibration peak which the program will search for matching observed peaks. If more than one observed peak is within the 2theta window, the peak closest to the calibration peak will be assigned to it. Clicking the OK Button will start the matching routine.

When the program has assigned pairs of calibration / observed peaks, the results are displayed in the main window and may be altered manually by the user ignoring the parameters described above. In addition, the resulting peak pairs and their deviations are shown in a child text window :

The ‚File’ menu of this text window contains the standard Windows ‘Print,’ ‘Print Preview’ and ‘Print Setup’ printing commands.

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In the upper part of the main program window the matching peaks from the measured peakfile will be shown in red while the rest of the observed peaks will be drawn in gray. The calibration peaks will all be drawn in blue. Around the calibration peaks the 2Θ window is shown as a light gray rectangle. Zooming can be performed by leftclicking and dragging the appearing rectangle to the required size, then releasing the left mouse button. The toolbar buttons with the arrow and crosshairs provide the possibility to switch on position information output in the left status pane and to go back to the display of the full 2 Θ /intensity range from a zoomed-in state, respectively. The peak pairs thus displayed may be edited in a very easy way by pointing the cursor at them and clicking on the left or right mousebutton : If you wish to connect a measured peak to a calibration peak, first select the calibration peak by pointing at it with the cursor and pressing the left mouse button. The cursor shape will be altered indicating that you are now editing a peak pair. In addition, the text in the status bar will tell you so. Now select the measured peak to which you want to attach the calibration peak by pointing at it and pressing the left mouse button again. This operation may as well be used for peaks already in use as for peaks which are yet unassigned. In the former case, the new manual assignment will override the old one. CAUTION: you are not limited in your assignments by the parameters you entered for the peak matching routine! To delete a connection between a calibration and a measured peak point at the calibration peak und press the right mouse button. If peak pairs have been edited, the calibration polynomials have to be re-calculated as described in the next chapter.

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9.4

Calculate

9.4.1 Calculate polynomials This command calculates the 2Θ-offset defined as the position of a calibration peak minus the position of the matching observed peak for all peak pairs and performs a least - squares fit to the 2Θ-offset against 2Θ with correction polynomials up to order 4. If there are less than 3 pairs of peaks the program will refuse to calculate any polynomals and issue an error message.

In this case, after clicking the OK-Button, another ‚Match Peaks‘ run with a different set of parameters may be started or more peak pairs may be added manually. After calculation of the correction polynomials, the results are shown in the lower part of the main window. The 2theta offsets for all peak pairs are shown as black squares and the calculated correction polynomials as curves of different colours. The data should be checked for consistency; e.g. the example below might require checking of the two peak pairs around 2Θ = 50° as they look like outliers on the polynomial curves.

9.4.2 Calculate spline This command calculates the 2Θ - offset defined as the position of a calibration peak minus the position of the matching observed peak for all peak pairs and performs a least - squares fit to the 2 Θ-offset against 2Θ with a spline. This method is used to calculate a 2theta correction for a IP-PSD detector.

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After calculation of the correction spline, the results are shown in the lower part of the main window. The 2theta offsets for all peak pairs are shown as black squares and the calculated correction splines as a blue curve. The spline smoothing factor could be adjusted with a floating dialog. The factor could be changed by moving the arrow or by typing a factor into the dialog an pressing the C-button.

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9.5

Calibrate peakfile This command applies the correction polynomial selected by the user to all peaks in the loaded range of the observed peak file. The polynomial showing the smallest χ2 value ( i.e. the best fit with the smallest number of parameters ) is highlighted as the default in the edit list. The user may, however, choose any polynomial from the list to be applied. By clicking on the ‚OK‘-button, the 2Θ - and d-values of all peaks in the selected range will be shifted by the amount calculated from the selected polynomial. The modified peak list will not be written directly to the file, but must be saved using the ‚Files‘ suboption ‚Save‘ or ‚Save As‘.

In addition, the selected polynomial is automatically written to the user file and may be used in the ‚Raw Data Handling‘ module to correct the raw data file ( from which the observed peak data have been taken ) as well by selecting the ‚2Theta correction‘ option. If the polynomial is to be used as an external standard, it may also be applied to other raw data files.

9.6

Auto calibrate

This option performs all three steps described above automatically. No user input is allowed / required. The calibration polynomial used to re-calculate the observed is also automatically written χto2 the useroffile for subsequent 2Θ-correction of the corresponding rawpeak datalist) (iswhich the one showing the smallest value all calculated polynomials. The user file is updated with the polynomial with minimum χ2, too, but the peak file will not be updated automatically and requires saving using the ‚Files‘ suboption ‚Save‘ or ‚Save As‘.

9.7

Write IP calibration

This option is only available if a spline had be used to calculate a calibration curve. With this option the calculated spline could be stored into the Instrument Parameter file (IPR-file) to be used as a IP-PSD calibration. This command only stores the spline into the Instrument Parameter file but did not activate the use of the calibration. This is be done with the program Instrument Parameters .

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10 Index & Refine

10.1

Introduction

The Index & Refine module comprises three indexing routines and a lattice parameter refinement option. The implemented indexing algorithms are based on •

Werner’s TREOR program (see e.g. P.-E.Werner, L.Eriksson, M.Westdahl, Journal of Applied Crystallography 18, 367 (1985) )

•

Visser’s ITO routine (see e.g. J.W.Visser, Journal of Applied Crystallography 2,89 (1969) )

•

Louër’s DICVOL program (see e.g. A.Boultif, Journal D.Louër, of Applied Crystallography 37, 724 (2004) ).

‘File‘ contains the standard Windows options for opening, saving and printing files and. ‚View‘ is used to control the layout of the main window. ‚Index‘ contains a property page for the setting of the indexing parameters and the starting commands for

the indexing routines. ‚Refine‘ opens a dialog box for the definition of the lattice constants refinement parameters and starts the

refinement routine.

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10.2 10.2.1

File Open

reads the contents of an existing peak file (default extension *.pks or *.pth) into the program. When a peak file has been opened, its name is displayed in the title bar of the program’s main window.

10.2.2

Save As

stores the outcome of the lattest indexing / refining to a peak file and a list file. The peak file name may be the same as the one used for reading the observed peaks. The list file contains all results as displayed in the child text window and has the same file name as the peak file and an extension signifying the type of routine used to produce the output : Output from Werner’s routine is called *.lwr, output from Visser’s routine *.lvs, output from Louër’s routine *.llr, output from lattice constants refinement *.lrf. In the case of Werner indexing or lattice parameter refinement the peak file is updated by the symmetry and spacegroup information, the calculated lattice constants and the peak indices.

10.2.3

Print List File

sends the current contents of the text child window to the default printer.

10.2.4

Most Recent File List

10.2.5

Exit

the Most Recent File List contains the names of the files most recently opened.

terminates the application and returns control to the WinXPOW main menu.

POW


10-2

10.3

View

The View ‚ ’ menu contains options controlling the layout of the application.

10.3.1

List File

is used to open and close the child text window containing the results from the indexing or refining routines.

10.3.2

Graphics Update‘

when not activated, Werner’s algorithm will not update the lower window with the currently checked solution during the indexing. This will speed up the search a little.

10.3.3

Toolbar

is used to switch off and on the display of the window’s toolbar.

10.3.4

Status Bar

is used to switch off and on the display of the window’s status bar.

POW


10-3

10.4

Index

‚Parameters‘ opens a property page for the input of the control parameters for the three indexing routines.

‚Run Werner‘ , ‚Run Visser‘

and‚Run Louër‘ start the selected indexing routine. These commands are also available from the toolbar buttons ‚W‘,‘V‘ and ‚L‘.

10.4.1

POW

Indexing Parameters for Werner’s algorithm (TREOR)


10-4

The control parameters defining Werner’s algorithm are : Max.celledge

defines the maximumlengthof a,b or c (in Angstrom) which a possiblesolution may have.

Max.cellvolume

3) which a possible solution may have. definesthe maximumvolume(in Angstrom Together with the ‚Max. cell edge‘ this parameter strongly influences the number of possible solutions and thus the execution time of the routine.

Max. # of peaks

allows the user tolimit the number of peaks usedfor the tri al indexing to thefirst n peaks with the smallest 2Theta-values in the peak list. As peak positions at higher angles may be incorrect due to peak overlap, it may be advisable to use a smaller number of peaks. Independent of the number of used lines, the algorithm uses only the first 20 lines to find a possible solution. After refinement of a possible solution against these 20 lines the observed and calculated peak positions are compared again, this time using ALL lines in use. Then the number of unindexed lines (calculated from ALL used peaks) and the figure-of-merit used peaks are checked against the requested input values. Only if the number of unindexed lines is smaller and the figure-of-merit larger than requested, the solution is displayed.

2Theta window

definesa matchingpair of observedand calculat ed peaks. If theabsolutedifference between an observed peak position and a calculated peak position is less than the 2Theta window (in degrees), the observed peak will be considered indexed. This parameter strongly influences the number of possible solutions and thus the calculation time. 0.05 is usually a good value.

Uninde xedlines

is the pe rmissibl e number n of pea ks which donot match a ny calculat ed peak belonging to a certain solution. If more than n observed peaks are unindexed, the solution will not be displayed. The value should not exceed 5 and should be set to 2 for standard data.

Peak intensity limiteliminates all peakswith arelative inten sity less than the Peak intensity mit li fromthe calculations regardless of their 2theta position. This option is useful for obtaining at least a sub-cell of a superstructure by eliminating the weak reflections or to index a sample with a suspected high number of spurious lines. The reason for eliminating peaks must of course be a good one and the outcome of the indexing treated as a possible approximation of the correct solution ! This parameter is the only one which is automatically transferred to the property sheets of the other indexing algorithms as it is more a function of the quality of the input list as of the algorithm. Required FOM

is the minimum figure-ofmerit as defined by de Wolff (Journalof Applied Crystallography 1 (1968) 108) which a solution must have in order to be displayed on the screen. Thee dWolff - FOM is calculated by 20 M = Q20 / ( ε2** N20 ) where 2) - value of the twentieth observed Q20 is the Q (=1/d line,average deviation ε the between observed and calculated Q-value of the first 20 lines and N20 the number of calculated lines up to the twentieth observed line. Due to the lattest parameter, the FOM is inversely proportional to the cell volume. Therefore, very large cells like zeolites will seldomhaveFOMs larger than or 1 2 reg ardless ofthe data uali q ty. In these cases, the required FOM must be lowered to 1, whereas in ‚normal‘ cases 5 is a good choice for this parameter.

POW


10-5

Crystalsystem

is the crystal ystem s in whicha solution is initially sough t. If no solution matching the criteria is found in this system, the next one will be searched in the order cubichexagonal-tetragonal-orthorhombic.

10.4.2

Indexing Parameters for Visser’s algorithm (ITO)

The control parameters defining Visser’s algorithm are : Max. # of peaks

allowsthe userto limit the number of peaksused to the first npeakswiththe smallest 2Theta-values in the peak list. As peak positions at higher angles may be incorrect due to peak overlap, it may be advisable to use a smaller number of peaks. Visser’s algorithm treats only the first 40 lines of the input as observed data. All lines exceeding this limit will be ignored. On the other hand, Visser’s routine needs a MINIMUM of 20 observed lines and will yield an error message when tried to be run with an input of less than 20 lines.

2Theta window

definesa matching pair ofpeak observed and calculat peaks . If the absolute difference between an observed position and aedcalculated peak position is less than the 2Theta window (in degrees), the observed peak will be considered indexed. This parameter strongly influences the number of possible solutions and thus the calculation time. 0.05 is usually a good value.

Uninde xedlines

is the pe rmissibl e number n of pea ks which donot match a ny calculat ed peak belonging to a certain solution. If more than n observed peaks are unindexed, the solution will not be displayed. The alue v shou ld norma lly bein the rang e from 1to 5.

POW


10-6

Peak intensity limiteliminates all peakswith arelative inten sity less than the Peak intensity mit li fromthe calculations regardless of their 2theta position. This option is useful for obtaining at least a sub-cell of a superstructure by eliminating the weak reflections or to index a sample with a suspected high number of spurious lines. The reason for eliminating peaks must of course be a good one and the outcome of the indexing treated as a possible approximation of the correct solution ! Bear in mind that at least 20 input peaks are necessary for Visser’s algorithm. This parameter is automatically transferred to the property sheets of the other indexing algorithms as it is more a function of the quality of the input list as of the algorithm. Required FOM

is the minimum figure-ofmerit as defined by de Wolff (Journalof Applied Crystallography 1 (1968) 108) which a solution must have in order to be displayed on the screen. Thee dWolff - FOM is calculated by 20 M = Q20 / ( ε2** N20 ) where 2) - value of the twentieth observed Q20 is the Q (=1/d line,average deviation ε the between observed and calculated Q-value of the first 20 lines and N20 the number of calculated lines up to the twentieth observed line. Due to the lattest parameter, the FOM is inversely proportional to the cell volume. Therefore, very large cells like zeolites will seldomhaveFOMs larger than or 1 2 reg ardless ofthe data uali q ty. In these cases, the required FOM must be lowered to 1, whereas in ‚normal‘ cases 5 is a good choice for this parameter.

Formula weight and Observed density are optional input. If the formula weight is given, the program calculates the number of formula units per unit cell Z for each solution and writes it to the extended output file named visser.out which is not automatically displayed on the screen but written every time the routine is run. These parameters transferred between Louër propertytwo sheet as they are areautomatically characteristics of the sample andthe notVisser of theand indexing algorithm. 2Theta zeroerror

allows the input of aknown systema tic zero-off set of theobserved p eak positions. Even if such a shift is present, this value need usually not be given as the program refines the 2Theta zero-point automatically and is quite robust against zero-offsets of up to some hundredths of a degree.

10.4.3

Indexing Parameters for Louër’s algorithm (DICVOL)

The control parameters defining Louër’s algorithm are quite extensive but do not allow for any unindexed lines. All used lines ( = lines in the peak file with a relative intensity above the peak intensity limit and among the first n peaks where n is the user-defined maximum number of peaks ) must therefore belong to one phase so that this algorithm can succeed.

POW


10-7

Max.cell edge 1 2 3 define he t maximu m length in Angstrom for hree the t celledges respecti vely which a possible solution may have. Min.cell volume

3) which a possible solution may have. If no definesthe minimumvolume(in Angstrom clues to the approximate volume are available, it should be set to 0.

Max.cellvolume

3) which a possible solution may have. definesthe maximumvolume(in Angstrom Together with the ‚Max. cell edge‘ this parameter strongly influences the number of possible solutions and thus the execution time of the routine.

Min. mono. angle and Max. mono. angle define the range for the monoclinic angle. A range between 90 and 125 will usually be sufficient if no clues are available. Max. # of peaks

allows the user tolimit the number of peaksusedfor indexing to thefirst npeakswith the smallest 2Theta-values in the peak list. As peak positions at higher angles may be incorrect due to peak overlap, it may be advisable to use a smaller number of peaks. In the case of low-symmetry patterns, this parameter is closely related to the 2Theta window. As more and more peaks are input increasing the 2theta value of the last peak, the program will require the 2Theta window to become smaller and smaller. If the error message ‚Experimental error too large!‘ is issued from the algorithm after the list of input lines or the output list contains no solutions at all the user may either reduce the 2theta window or the number of lines used.

POW


10-8

2Theta window

definesa matchingpair of observed and calculat ed peaks . If theabsolutedifference between an observed peak position and a calculated peak position is less than the 2Theta window (in degrees), the observed peak will be considered indexed. This parameter strongly influences the number of possible solutions and thus the calculation time. As Louër’s algorithm usually needs higher-precision data than the other two routines, 0.03 is the standard value.

Peak intensity limiteliminates all peakswith arelative inten sity less than the Peak intensity mit li fromthe calculations regardless of their 2theta position. This option is useful for obtaining at least a sub-cell of a superstructure by eliminating the weak reflections or to index a sample with a suspected high number of spurious lines. The reason for eliminating peaks must of course be a good one and the outcome of the indexing treated as a possible approximation of the correct solution ! This parameter is automatically transferred to the property sheets of the other indexing algorithms as it is more a function of the quality of the input list as of the algorithm. Required FOM

is the minimum figure-ofmerit as defined by de Wolff (Journalof Applied Crystallography 1 (1968) 108) which a solution must have in order to be displayed on the screen. Louë r’s version of the deolf W f - FOM is calculated by nM= Qn / (ε 2* * Nn ) where Qn is the Q 2)(=1/d - value of the last observed εline, the average deviation between observed and calculated Q-value of all lines and Nn the number of calculated lines up to the last observed line. Due to the fact that this FOM takes into account ALL used lines whereas Werner and Visser only make use of the twenty innermost lines, Louër’s FOM usually differs significantly from the other FOMs; however, the FOM is not an important criterion for Louër’s routine and may be set to 0.

Formula weight and optional influence input. In contrast to Visser’s algorithm,calculates these values bothObserved are givendensity - have are a dominant on the output : the program the – if expected volume for one formula unit and discards all solutions which are not within a certain error limit from a multiple of this volume ! Thus, these input values have to be correct or should not be entered at all. If only one of these values is given, it is ignored and the possible solutions are not narrowed down by Z considerations. These two parameters are automat ically transferred between the Visser and Louër property sheet as they are characteristics of the sample and not of the indexing algorithm. Max impurit y lines this is themax. nu mber of lines thelgori a thm will accep ted asimpurit y or spurious lines. The algorithm will remove this lines and recalculate a solution. Search for zero-point error check this parameter to let the algorithm check for an zero point error in the input data Refinezeropoint

checktis param eter toperforma least-squarerefinement of the zero-point error

Do extended search check this parameter to perform an extended (exhausted) search in volume domains (this option will increase the CPU time needed) Search crystal systems : These check boxes are used to select the crystal system for which a solution to the indexing problem is sought. Multiple choices are possible, but lead to rather long computation times if more than one of the selected systems is lower than orthorhombic.

POW


10-9

10.4.4

Output from the indexing routines

Due to different implementations of the three indexing algorithms, their output handling is slightly different : When Visser‘s and Louër’s routines have finished, they open a child window displaying their output. Werner’s algorithm may be interrupted anytime by clicking the toolbar button with the red traffic light. The possible solutions of all three routines are written into the main window and – after completing the search - the user may double-click on any of them to open a child window showing the indexing of the data with the currently selected cell (highlighted in red in the main window). The relevant data contained in this window like Cell parameters and Crystal System can be directly transferred into the applications Theoretical pattern (Theo) “Setup Crystal Parameters” dialog box through a Copy&Paste or a Drag&Drop operation. This operation is described at paragraph 11.3.1 of this manual.

POW


10-10

10.5

Refine

The parameter input for the Lattice constants refinement tool looks like this :

Symmetry information may either be entered as ‚Crystal system‘ plus ‚Bravais type‘ or as the phase’s space group (either in abbreviated Herman-Mauguin notation or as the space group number as defined in the International Tables). In the ‚Space group‘ edit box blanks must be used to separate symmetry elements (e.g. ‚F 21 21 21‘). The monoclinic crystal system requires the unique axis being b. Rhombohedral axes are not supported and must be transformed to hexagonal ones and the Bravais type ‚R-Centred‘ . From the ‚Lattice parameters‘ edit fields only those necessary for the given crystal system are accessible. Lattice constants have to be given in Angstroms. The ‚2Theta window‘ defines a matching pair of observed and calculated peaks. If the absolute difference between an observed peak position and a calculated peak position is less than the 2Theta window (in degrees), the observed peak will be considered indexed. During refinement, the program will try to reduce the window as much as is possible without observed peaks becoming unindexed. ‚2Theta zero‘ allows the input of a constant 2theta-error introduced by poor 2Theta-calibration of the diffractometer. The check box ‚Refine 2Theta zero‘ is used to enable or disable refinement of this value together with the cell parameters. If ‚Use peak file indices‘ is chec ked, the starting values for refi nement are o nt taken from the ‚Lattice parameter‘ edit fields but are generated from all peaks in the peak file which are single-indexed (i.e. which havean index tri ple in the ne li after their FWH M and do not havean ‚M‘ (=multiple) flag followingthese indices). Pressing the ‚OK‘ button starts the refinement. The results will be displayed in an automatically opened child window. To produce a list file with the same name as the peak input file and the extension .lrf, select the ‚Save‘ option of the ‚File‘ pull-down menu.

POW


10-11

The refined Cell Parameters, the Symmetry information (Spacegroup if given or Crystal System and Lattice Type) and other relevant data can be transferred through Copy&Paste or Drag&Drop to the “Setup Crystal Parameters” dialog box of Theo. This operation is described at paragraph 11.3.1 of this manual.

POW


10-12

11 Theoretical Pattern

11.1

Introduction

The Theoretical Pattern program can calculate peak positions and Miller indices from lattice constants and symmetry information (either crystal system, Laue group or space group) as well as the full pattern from cell metrics and atomic coordinates. To generate a full pattern, the atomic structure may be entered via the program’s editing options as well as loaded from a file. The program is started from the pull-down menu of the main menu item ‚Cell‘

POW

WinX 3.05 Software Manual – Theoretical Pattern

11-1

11.2

File

The menu item ‘File’ offers the standard Windows commands to read and write files, to re-open recently used files and to print data or graphics. The file formats that the program can read are • standard STOE parameter files for THEO with default extension *.tin (see chapter 11.2.2) • standard STOE single crystal parameter files with default extension *.crs (a slightly modified version of the TIN format containing no atomic parameters but spacegroup and cell metrics produced by the STOE Stadi4 and IPDS

controlprogram s) • Shelx instruction files with default extension *.ins (please refer to the srcinal Shelx manuals for a description of the format) are fully supported (e.g. FVAR, long form of SFAC (12 coefficients), riding hydrogens with negative U). The spacegroup symbol is recognized from the CELL information and SYMM The CELL instructions. constants must therefore conform to the crystal system (e.g. orthorhombic phases require all angles equal to 90.00 and tetragonal systems require a being identical to b). • CIF files *.cif as defined by the IUCr. For an example, see chapter If the file11.2.1. contains multiple data blocks, that is, multiple “data_ datablockname” keywords, only the crystal structure contained in the last data block is used as input f or the calculation. Multiple data blocks can be found occasionally in CIF files exported by the CCDC databank. File formats written by the program are • STOE binary raw data with extension r aw*.rth data( from th eoretical calculation) • STOE peak files with extension peak *.pthdata ( from th eoretical calculation). This file contains only the peaks whose relative intensity is larger than 0.01 • plain ASCII text files containing all relevant information about peak intensities, indices, Lorentz-, polarisation-, and absorption corrections with extension listing *.lthfrom ( theoretical calculation) • standard STOE parameter files for THEO with default extension *.tin.

POW


11-2

‘Open’ reads the contents of an existing parameter file - either a *.tin, *.ins, *.crs or *.cif file - into the program. After opening a parameter file, its name is displayed in the title bar of the main program window. ‚Save‘ is onlyactivated if a parameter file has been loaded from which the file name can be taken. The program will write / update the following files after the theoretical pattern generation has been performed: • • • •

the *.tin parameter file an ASCII list file of the same name as the *.tin file and extension *.lth a peak file of the same name as the *.tin file having the extension *.pth if a full patter was generated, a raw data file of the same name as the *.tin file having the extension *.rth.

‚Save As‘ lets the user write the current parameters and generated peaks (and raw data) to files of a different name. ’Export ’ lets the user generate a NBS*AIDS32 file (*.nbs) from the calculated intensities. This file can be added as a User Card to a PDF2 database ( please refer to the Search/Match manual for more details about PDF2 databases and UserCards). In the opening dialog the user can choose the cards file and subfile attribute. It’s possible to choose more than one file or subfile. When choosing ‘Mineral’ a ‘Mineral nam e’ must begiven.

‘Print Graphics’ - ‘Print system printer.

Preview’ - ‘Print Setup’

control and format the output of the program’s main window to the

'Print List File' sends the current contents of the text child window to the default printer. 'Export Graphics' provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the Save combo as typebox ’. The “ available formats are Enhanced Metafile (which will be the most adequate format when importing the display into other TIFF- applications), andWindows Bitmap file. With deactivated option ‘only Diagram(s) ’ the output will be identical to the printed version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page, regardless of the current aspect ratio of the display. To maintain the current keep aspect aspect ratio ratiothe’ ‘ option should be activated. TheMost Rece nt File Lis t contains the names of the files most recently opened. POW ‘Exit’ terminates the pattern generation routine and returns control tomain the WinX menu.

POW


11-3

11.2.1

Example CIF file

The following CIF file was generated by the ICSD Retrieve software and shows some typical features of the CIF structure:

data_75107-ICSD

Note: if more than one datablock (keyword data_datablockname) is present in the CIF file, only the information present in the last one is used by Theo

_audit_creation_date _audit_creation_method

98-12-03 'generated by RETRIEVE 2.0'

_database_code_ICSD _chemical_name_systematic _chemical_formula_structural _chemical_formula_sum

75107 'Dicalcium chromium tantalum oxide' 'Ca2 (Cr Ta) O6' 'Ca2 Cr O6 Ta'

_publ_section_title ; Competition of covalency between Cr^III^-O and Ta^V^-O bonds inthe perovskites Ca~2~CrTaO~6~ and Sr~2~CrTaO~6~ ; loop_ _publ_author_name 'Choy, J - H' 'Park, J - H' 'Hong, S - T' 'Kim, D - K' _journal_name_full 'Journal of Solid State Chemistry' _journal_coden_ASTM JSSCBI _journal_volume 111 _journal_year 1994 _journal_page_first 370 _journal_page_last 379 _cell_length_a _cell_length_b _cell_length_c _cell_angle_alpha _cell_angle_beta _cell_angle_gamma _cell_volume _cell_formula_units_Z _symmetry_space_group_name_H-M _symmetry_Int_Tables_number _symmetry_cell_setting

5.4199(1) 5.4936(1) 7.7108(2) 90 90.02(1) 90 229.6 2 'P 1 21/n 1' 14 monoclinic

loop_ _symmetry_equiv_pos_as_xyz 'x,y,z' '1/2+x,1/2-y,1/2+z' '-x,-y,-z' '1/2-x,1/2+y,1/2-z' loop_ _atom_type_symbol _atom_type_oxidation_number Ca2+ 2.000 Cr3+ 3.000 Ta5+ 5.000 O2-2.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol

POW


11-4

_atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_attached_hydrogens _atom_site_calc_flag Ca1 Ca2+ 4 e 0.007(2) 0.0390(4) 0.7504(8) 1. 0 d Cr1 Cr3+ 2 c 0. 0.5 0. 0.726(3) 0 d Cr2 Cr3+ 2 d 0.5 0. 0. 0.274(3) 0 d Ta1 Ta5+ 2 c 0. 0.5 0. 0.274(3) 0 d Ta2 Ta5+ 2 d 0.5 0. 0. 0.726(3) 0 d O1 O24 e 0.278(2) 0.301(3) 0.958(3) 1. 0 d O2 O24 e 0.299(3) 0.279 0.540(3) 1. 0 d O3 O24 e 0.919(2) 0.477(1) 0.739(2) 1. 0 d _refine_ls_R_factor_all

11.2.2

0.038

TIN file format

The most convenient way to set up a .tin parameter file is to use the Setup options of the program and to store these data to file. In this case, the user need not know the exact file structure. If, however, the file shall be prepared by external program s or editors,the AS CII file format is described in thister. chap The input file useful to perform a full pattern generation with THEO is an ASCII file of a similar INS' file format as the '*. in the SHELX system (exception: keyword SYMM - see below). The first four characters in each line are regarded either as a keyword or as the name of an atom in the structure. Valid keywords are: TITL

followedby a blankandanystring containi ng up to 75 characters

αf1iK WAVE followedby ablank anda chemical symbol (eit her Ag ,Mo,Cu,Co,Cr Fe) or andthe str ing 'a1' is to be α2Kis to be used. Alternatively, any wavelength may be given in Angstrom units. used or 'a2' if

CELL

followed by thelattice con stants in the order ,ab,c,alpha,beta,ga mma. All six latt ice con stants m ust begiven even for high-symmetry-lattices. Cell edges must be given in Angstrom units. The default setting for the monoclinic crystal system is the unique axis being b. Rhombohedral axes may be entered if the letter ‚R‘ ( not case sensitive ) is appended to the space group symbol. ‚R –3 m‘ expects hexagonal axes and ‚R –3 m r‘ rhombohedral atti l ce constants.

SPGR followed yb a blank anda valid space-group bol sym(Herma n-Maug uin short for m symbols as used in the International Tables). Alternatively, the number of the spacegroup corresponding to the International Tables may be given. The program supports all possible Bravais settings. For details of srcin selection etc. see chapter 11.3.1. For compatibility with the Visual XPOW package, the keyword SYMM may be used synonymously. SFAC

followed by a blan k anda list of up to ten ch emical symb ols identif ying the kindf oatoms resent p in the structure.

UNIT

followedby as manynumbers asthere aresymbo ls in the FAC S line identifying the total num ber ofatomsof each type within the unit cell (in the same sequence as in line SFAC ).

ZERR

followed by an integer identifying the number of formula units in the unit cell.

END

will instruct the programto ignoreanylinesfollowing this ke yword.

-XYZ

Anyline beginning ith w character s which arenot akeywordwill be assum ed to bean input ne li for oneatom in the structure. Following the atom identifier (1 to 4 characters) 6 values are required in the order listed below: n(sfac) is the po sition number of the atomtype in the SFAC list. xyz are the fractional coordinates of the atom.

POW


11-5

SOF

U

is thesite occu pationfactor (m ultiplicity ofthe atom's site ivi d ded by the m ultiplicity ofthe general position in the given space group). Statistical occupancy of sites may be multiplied by the SOF to be taken into account, too. π2.8 is the isotropictemperaturefactor. oTconve rt fromB to U, divideB by

Keywords may be omitted fromTIN' thefile '*. and the corresponding parameters entered via the ‚Crystal parameter‘ and‚Atomlist‘ dialog oxes b .

Examples for valid '*.TIN' files : 1)

TITL SYMM WAVE CELL SFAC SI1 END

Silicon F d 3 m z Cu A1 5.4309 5.4309 5.4309 90 90 90 Si 1 .125 .125 .125 .041667 .015

2)

SFAC Ca1 W(1) O(1)

Ca W O 1 0 .25 .625 2 0 .25 .125 3 0.150 0.009 0.211

Missing SOF and displacement parameters will be set to the sit e multipl icit y and a default value of 0. 01, respectively.

Examples for invalid '*.TIN' files : 1)

TITL Silicon SYMM F d 3 m s WAVE Cu A1

Keyword SFAC missing

CELL 5.4309 90 90 .015 90 SI1 5.4309 1 .000 5.4309 .000 .000 .041667 END 2)

TITL SYMM WAVE CELL SI1 SFAC END

POW

Silicon F d 3 m z Cu A1 5.4309 5.4309 5.4309 90 90 90 .125 .125 .125 .041667 .015 Si


No atom typ e (referring t o the SFAC list) given – atom will be omitted

11-6

11.3

Setup

From the menu item ‚Setup‘ all information required for the pattern calculation may be entered. ‚Crystal Parameters ‘ opens a dialog box for the input of the basic cell parameters. ‚Atom List‘ opens a dialog box with editing options for atom types, atomic positions, displacement parameters and occupancy factors. ‚Pattern Parameters‘ allows the definition of diffractometer geometry and peak shape.

POW


11-7

11.3.1

Crystal Parameters

Crystal Parameters : using this dialog box the user can input cell parameters, cell contents and other basic parameters.

The edit box ‚Title‘ is used to input a string describing the project. ‚Formula‘ is the sum formula of he t sub stance;ons i like Fe3+ (OT N Fe+3! ) may be input as well. In the case of ions, the stoichiometric factor must be separated by a blank from the charge number. From the formula string, element (or ion) symbols are extracted and available as ‚atom types‘ in the ‚Atom Thislist‘ means dialog that all box. atom types for which atomic positions are to be entered must be given in the formula. If the parameters are read from a *.tin file, the formula is calculated by dividing the ‚UNIT‘ numbers for every atom type by the ‚ZERR‘ number (see ch apter 10.2.1).If structure inf ormation has be en readfrom an*.ins file containing theold' ' SFAC format with full scattering factor information, the 'Formula' edit box is disabled as any elemental input in this window would replace the loaded scattering factors with their 'built-in' standard values. The edit box ‚Mol.Wt.‘ displays the molecular mass of the substance when a formula is present. If the formula is changed, the mol.weight window is updated. The user may however override the calculated value by entering a figure in this edit box (note that a user-defined mol. weight will be overridden again by choosing a different wavelength as the elemental information is updated in this case). ‚Z‘ is the number of formula units per unit cell. From this figure, the molecular mass, the cell constants and the formulathe de nsity andattenuation factor are lculated. ca ‚Laue Symmetry‘ is a list box containing the 12 Laue groups (plus 2 groups ‚Trigonal R -3‘ and ‚Trigonal R –3 m' defining rhombohedral groups on rhombohedral axes and 'Monoclinic 2/m C' allowing the choice of c as the unique axis). ‚Lattice type‘ is a list box containing all permissible lattice centrings for the selected Laue symmetry. The‚Space group‘ edit box accepts Herman-Mauguin short form symbols as well as the space group numbers according to the International tables. Blanks may be input, but are are not considered by the verification routine.

POW


11-8

Neither is the input case- sensitive. The symmetry information is taken from a table containing all space groups in all possible settings except monoclinic cells with unique axis a and multiple cells like C4. The monoclinic crystal system defaults the unique axis to b. To select c as the unique axis, it is either sufficient to put in a space group like P21/b from which the selected setting is evident or a 'c' has to be appended to the space group symbol (e.g. P 21 c). The same effect may be achieved by entering the full symbol P 1 1 21. Spacegroups with two possible choices of srcin like P m m n require an additional character 's' or 'z' following the name of the space group : 'Z' denotes the srcin on the center of symmetry, 'S' the srcin selected off-center. If such a spacegroup is entered by its spacegroup number without further information, 's' will be used as the default setting. The spacegroup number may also be followed by one of the characters '1' or '2' to force the program to use the settings 'S' or 'Z', respectively (according to the numbering in the International Tables). Rhombohedral axes may be entered if the letter ‚R‘ is appended to the space group symbol. ‚R –3 m‘ expects hexagonal axes and ‚R –3 m r‘ rhombohedral lattice constants (in the case of rhombohedral axes, the lattice centring will also be changed from R to primitive). Only those edit boxes of‚Cell theParameters‘ edit field are enabled which are necessary for the given crystal system and setting. Lattice constants have to be given in Angstroms. The list box ‚Radiation‘ is used to define the wavelength for which the diagram is to be calculated. ‚Generate F ull Pattern‘ is a check box which is only enabled if atoms have been input in the ‚Atom List‘ dialog box. ‚2Theta (Min, Max)‘ describes the begin and end of the 2theta range for which peak positions will be calculated. The data necessary to fill this dialog box can also be “dropped” or “pasted” from the main window of Index or from the “Results From Lattice Parameter Refinement ” window of Index onto the “Setup Crystal Parameters” dialog box. To performDrag&Drop a from the Index main window to Theo a) The user starts Index, loads a .pks or .pth file (manual at paragraph 10.2) and performs an indexing using one of the algorithms available (paragraph 10.4). A set of solutions is displayed on the main window of the Index application b) The user left-clicks on a solution to highlight it (see picture below) and, keeping the mouse left button pressed, “drags the solution” over the “Setup Crystal Parameters” dialog box. When the cursor is on the dialog box, the user “drops the solution” by releasing the mouse left button To performCopy&Paste a from Index main window to Theo: a) The user starts Index, loads a .pks or .pth file and performs an indexing b) The user right-clicks on selected a solution. A context menu appears with a single Copy command “ unrefined cell params to Theo ”. The user performs the “Copy” operation. He then right-clicks on the “Setup Crystal Parameters” dialog box. Another context menu appears with a single Paste cell command params “ from Index ”. The user performs the “Paste” operation. To perform the P aste ope ration correctly, it is important not to right-click on any of the edit boxes or controls but on a region of the dialog b ox where there a re no contr ols, for example, on the title bar where the window title “ Setup Crystal Parame ters” appea rs When transferring data from Index main window to Theo, unrefined only Cell the Parameters, the Crystal System, the Wavelength and the .pks .or .pth file Title are going to be transferred. The Laue symmetry is set to the lowest Laue symmetry compatible with that Crystal System and the lattice type is set to Primitive.

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11-9

Drag&Drop or Copy&Paste operations can be performed also from Results theFrom Index Lattice “ Parameter Refinement ” window as shown in the figure above: this window appears after the successful completion of a refinement. In this caserefined the cell parameters are transferred to Theo with the number of significant figures compatible with the standard deviation obtained at the end of the refinement. Also, if the refinement was run using a specific Crystal System / Lattice Type combination or a specific Spacegroup, this information is also transferred to Theo.

11.3.2

Atom List

The Atom ‚ List‘ option in the pull-down menu is only enabled if a formula has been defined in the ‚Crystal Parameters‘ dialog box. When defining atom positions in spacegroups with ambiguous setting of the srcin, it is important to have the para meters in accordance with the choice of srcin d efined by the space group identification.

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11-10

To input a new atom, first press the ‚New Atom‘ button, then select an atom type from the list box, press ‚Set Type‘ and proceed with defining the atom name, positions etc. To change an atomic parameter of an existing atom, click on the atom in the atom list box which will transfer all atom data to the edit boxes above. These may then be changed. By pressing the enter key in any of these edit boxes the parameters will be transferred back to the atom list box. To delete an atom, click on the appropriate line in the atom list box and then the ‚Delete‘ button. ‚Name‘ is a unique identifier for every atom in the structure. ‚Type‘ can either be selected from the atom types list box and written to this edit box by pressing the ‚Set type‘ button or typed into the edit box. Only atom types shown in the atom type list box which are part of the formula are accepted as input. ‚x/a, y/b, z/c‘ are the fractional coordinates of the atom. The site multiplicity for the atom's position is calculated automatically. For atoms on special positions like 1/3 or 2/3, it is important to input at least 5 significant digits (0.33333 and 0.66667) so that the program recognizes the correct multiplicity. ‚Occupancy‘ is by default set to 1 for every new atom and needs only to be changed if the site is occupied statistically, either sharing the position with another atom type or with a lattice vacancy. ‚Occupancy‘ multiplied by the ‘Multiplicity‘ of the site gives the site occupation factor SOF used in the .tin files. ‚U11,U22,U33‘ and ‚U12,U13,U23‘ are the components of the anisotropic temperature factor. When a number is entered in any of these edit boxes other than U11 the atom is automatically labelled anisotropically. The change from isotropic to anisotropic temperature factors may also be done by pressing the ‚Anis/Iso‘ button which will change the 2

corresponding flag of the currently highlighted atom in the atom list box. To convert from πB.to U, divide B by 8

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11-11

11.3.3

Pattern Parameters

This dialog box can only be opened if the ‚Generate Full Pattern‘ box of the ‚Crystal Parameter‘ dialog box has been checked as the parameters set in this box are only important for the calculation of raw data. The‚Geometry‘ radio buttons are used to select the sample type and beam path for the experiment. This parameter especially influences the absorption correction if a Mu*T other than zero is entered, otherwise the effect on relative peak intensities is only significant at high angles. If absorption is not taken into account, the intensities for a DebyeScherrer (=capillary) sample and a reflection sample measured with fixed slits (‚Constant Sample Area‘ not checked) are identical as the irradiated volume remains constant over 2Theta, whereas high-angle peaks measured in transmission geometry (2:1 coupling between 2Theta and omega) have a higher relative intensity due to the increase of irradiated volume with θ1/cos . The‚Monochromator‘ buttons are used to define the kind of primary monochromator used. The knowledge of the dspacing of the monochromator’s reflecting plane is necessary for the polarization correction factor. For Germanium, the (111) plane is assumed to be the monochromator surface, for quartz the (101) reflection.

The ‚Profile Function‘ used for calculation of the raw data curve from the integrated intensities may be chosen from five alternatives :

Lorentz(= Cauch y):

. Y=Y x) / h 2) ]-1 L1 ( (x - o o. [ 1 + C

Squared Lorentz:

. Y=Y x) / h 2) ]-2 L2 ( (x - o o. [ 1 + C

Gauss:

. Y = Yo . exp[ -C x) / h 2)] GS ( (x - o

PearsonVII: Pseudo -Voigt :

2 -m . . PS ( (x - o) Y=Y o [1+C x / h )] . Y = Yo . ( 1 - n .)[ 1 + C x) / h 2) ]-1 L1 ( (x - o

+ Yo . n . CLG .exp [ - G CS . ( (x - ox) / h 2) ] xo: Yo: h:

POW

Peak position Maximumcountingrate (at o x) Fullwidthat halfmaximum(FWH M)


11-12

m: n: Cx:

Pearsonexponen t of the PearsonVII function Gauss componentof Pseudo -Voigtprofile Constantcoeffici entsspecificto eachprofile

For the Pearson VII and Pseudo-Voigt functions, the variable profile parameter may be input in the edit box beneath the ‚Profile Function‘ buttons either ‚Pearson labelled Exponent‘ or ‚Gauss Component‘ depending on the profile type selected. Using the ‚Peak asymmetry‘ radio buttons and edit boxes the user can simulate the peak asymmetry observed in diffraction patterns when detector and sample heights are not small compared with the detector-to-sample separation. Following the srcinal method of Finger et al (van Laar, J. Appl.Yelon Crys. (1984),17, 47; Finger, Cox, Jephcoat J. Appl. Crys. (1994),27, 892 and Finger J. Appl. Crys. (1998),31, 111), the peak asymmetry that arises from axial divergence can be described in terms of two physically relevant H/L parameters andS/L, whereH is the detector half-height, S is the sample half-heightL and is the sample-to-detector distance. A modification of this approach here used, implemented also in the pattern fittingFit program (see paragraph 8.3.1), uses a single parameter equal to the average of the H/L andS/L parameters, that (H/L+S/L)/2. is, TheAppr ox. in tegrat ion po in ts per deg ree box determines the approximate number of integration points and therefore the accuracy in the evaluation of the peak asymmetry (see Finger 1994): large values might slow down the calculation of the theoretical pattern. The standard value of 100 points per degree is acceptable. The checkbox Abort integ ratio n if accuracy can no t be maintain ed is a sort of safeguard against meaningless input (H/L+S/L)/2 in the parameter which might lead to long and not correct calculations: if the program can not perform the integration with the same number of points per degree for all peaks, the calculation is aborted. This is normally an indication that the value of the asymmetry parameter is not reasonable or that too many integration points per degree were chosen. This checkbox should always be left checked (as in the picture). •

Only the .rth file is corrected for peak asymmetry: the .pth file, the theo.log file and the .lth file contain the uncorrected peak positions and intensities. Also the peak positions shown at the bottom of the pattern as short magenta lines correspond to the uncorrected peak positions (see paragraph 11.4). If the user wishes to create a peak file which contains the shifted position of the peaks caused by the introduction of asymmetry, he must load the asymmetry corrected .rth Graphic file using or Fit, perform a peak search and save the resulting peak file.

•

When calculating the peak integrated intensity in presence of asymmetry, the conventional Lorentz factor for powder diffraction measurements is used.

The edit box ‚2Theta ( Min,Max,Step)‘ is used to define the 2theta range in which the raw data are to be collected and the step width defining the angular distance between adjacent data points. ‚Mu*T‘ allows the input of the sample’s attenuation factor for the calculation of the absorption correction (transparencycorrection in the case of reflection geo metry). The intensit ies calculated from the structure I(uncorr) are multipied by the absorption factor appropriate for the geometry selected : Transm ission:

. exp ( µ I(abs)= I(uncorr) - t / cosθ )

Reflection:

. [ 1 - exp( - µ2 t / sinθ ) ] I(abs)= I(uncorr)

Debye-S cherrer:

The cylinderabsorption tables ( Internati onal Tables and referencestherein ) are interpolated twice by a cubic spline between the tabulated q-values and between the tabulated µ×R-values.

θ)( = x1 + x2 * tan θ. ‚Halfwidth‘ defines the variat ion of peak halfwidth n (i degrees) with 2thet a as FWHM ‚Max.Intensity‘ is the count rate which will be assigned to the data point of the highest intensity in the diagram.

If ‚Generate Alpha2 Peaks‘ is checked, every generated reflection will be calculated for the selected alpha1 radiation as well as for the corresponding alpha2 wavelength. The intensity ratio is taken as 2:1. ‚Constant Sample Area‘ is only significant if ‚Reflection‘ geometry is selected. It multiplies all intensities by a factor sinθ to simulate data collection with a variable divergence slit which keeps the irradiated sample area but not the sample volume constant.

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11.3.4

Load from ICDD

‘Load from ICDD’ allows the user to copy crystallographic data like cell parameters, chemical formula and spacegroupfrom a PDF2card direct ly into theapplication. Please note, that PDF2 cards don ’t cont ain atomsite infos at all and that not all cards contains all required datas.

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11.4

View

‚Whole Diagram‘ resets a former zoom command by displaying both axes starting from the minimum value of the calculated diagram to its maximum value. ‚Position Info‘ changes the cursor to a crosshair and displays the current crosshair position in the left part of the main window’s status bar. 'Labels' is used to select the labelling of the generated peaks in the main window. The peaks may either be identified by their 2theta-position, their d-spacing or their Miller indices. ‚Grid Lines‘ adds o r removes a rectangular pat tern to andfrom the window. 'List File' opens and closes the child text window containing the list of calculated peaks. ‚Toolbar‘ removes / brings back the toolbar with shortcut buttons above the main window. ‚Status bar‘ removes / brings back the status bar beneath the main window. The ‚Position Info‘, ‚Whole Diagram‘, and ‚Grid Lines‘ commands are also available from these toolbar buttons:

When the cursor is not n the i ‚Posit ion Inf o‘ mode , it may beused to define a zoom -in window bymoving ti to any point in box the diagram, pressing the left mouse buttonthe andleft holding it depressed moving opposite of the rubber to the requested position. Releasing mouse button willwhile change the the display to ancorner enlarged representation of that diagram part which was contained in the rubber box. Scroll bars will be added to the diagram enabling the user to move the diagram horizontally.

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12 Crystallinity

12.1

Introduction

The module ‚Crystallinity‘ is used to determine the crystallinity index of an unknown sample, either by comparing the diagram obtained from it with diagrams obtained from two other samples of known crystallinity or by first-principles calculation. The application is started from the pull-down menu of the WinXPOW main menu item ‘Crystallinity’

Standa rds m ethod :

Ideally, the two standards should have a crystallinity of 100% (crystalline standard) and 0% (amorphous standard), respectively. As such samples are not always available, the program provides the possibility to use standards of another (but in any case well-known) crystallinity indexes. It requires four measurements to be performed with exactly the same data collection setup and parameters including the generator settings : the two standard samples, the unknown sample and a blind run for air scatter correction.

POW

3.05 WinX Software Manual – Crystallinity

12-1

The program calculates a least-squares fit for all data points in the three diagrams ( which have been corrected for airscatter ) according to the equations : I(2θ) = m. ( xc . Ic(2θ) + (1xc) . Ia(2θ) ) m .......

sample mass

xc .......

crystallinity index ( 0...1)

I(2θ)....

count ratefor the unknown sample at a given θ2

Ic(2θ)...

count ratefor the 100%crystall ine standa rd at the sameθ2

Ia(2θ)...

countrate for the 100%amorphousstandardat the sameθ 2

In the case non-ideal ‘standards’ their ( known ) crystallinity index may be taken into account : I(2θ) = m. ( x’ . Ic(2θ) + (1x’) . Ia(2θ) ) m .......

and

xc = a +x’ . ( b - a )

sample mass

xc .......

crystallinity index ( 0...1)

x’ .......

apparent crysta llinityindex

I(2θ)....

count ratefor the unknown sample at a given θ2

Ic(2θ)...

θ 2 count ratefor the standardhavingcx= b at the same

Ia(2θ)...

count ratefor the standardhavingcx= a at the same θ 2

Single- sample method :

The single-sample-method requires the user to define the portions of the diagram due to air scatter and inelastic scattering, amorphous scattering and Bragg scatter. If aI(2 I θ) are known for the whole diagram, the c(2θ) and crystallinity index is calculated from xc = Σ Ic(2θ) / ( LP * F * T/ )Σ { Ic(2θ) / T+ aI(2θ) } / ( LP * F )

summing over θ2 .

The Lorentz-Polarization factor LP, the average formfactor F, and the temperatureθ-dependent factor T are all 2 functions : θ) ) / ( sin**2θ LP(2θ) = ( 1 + cos**2(2 ( ) * cos (θ) )

F(2θ)

= Σ f (n,2θ)

T(2θ)

= exp( - 2* B sin**2 θ() / λ**2 )

summingoverall atomsn in the formula unit

The sample’s overall formula and average temperature factor have to be known and to be entered into the program in order to be able to apply the single-sample method.

Note:

Sample abso rption is always neglected, the program thus only orks w w ell c (within x +/- 3 % of the true crystallinity ) for transmission data of organic samples or reflection data.

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12.2

File

comprises options load data files into the application and to print out the graphical representation of the calculations.

‚Open‘ is used to select the desired algorithm and load the required raw data files for the selected algorithm into the application

By choosing the Standards ‘ ’ method the four required raw data files are loaded: The ‚Raw data file‘ of the unknown sample, both crystalline standard files and the air scatter file. For the two standard files, their respective crystallinity indices must be entered. For ideal standards, the parameter ‚Crystallinity (%)‘ is 100 for the crystalline standard and 0 for the totally amorphous standard.. Editing the values 2Theta(min) and 2Theta(max) gives theoption to excludeparts of thediagramfrom calculation. By default the application calculate the crystallinity from the total overlapping range of all files. On pressing the ‚OK‘ button, the fit described above is performed. The result is displayed in an info box and written to a text file having the same name as the raw data file and extension *.lcr. In addition, a raw data file is created with the same name but extension *.rcr which contains the intensities calculated from the intensities in both standard files multiplied by their respec tive contributions to the pattern of the unknown sample. This diagram is also displayed in the main window together with the srcinal unknown raw data.

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12-3

In the case the ‚ Single-sample‘ algorithm is to be used, only two input boxes remain active after checking the appropriate radio button. Both files must have been created before starting the crystallinity analysis module using the ‚Background‘ option in the Graphics program. The background-corrected raw data file is generated from the srcinal raw data by fitting a rather straight line to the background (thus eliminating air scatter and inelastic scattering) and saving the remaining diagram to file. This file is then background-corrected for a second time, now fitting the background to the amorphous hump. After subtracting this hump, the remaining ‚Bragg-only‘ diagram is stored to another file name, which is subsequently loaded as the crystalline scatter file.

On pressing the ‚OK‘ button, another dialog box is opened which prompts the user for the formula unit and the average temperature factor B of the sample. For organics, B is usually around 4; for inorganics values between 1 and 2 are usually correct. The exact formula has usually little influence on the result, whereas the temperature factor can affect the crystallinity to within some percent. The result is displayed in an info box and written to a text file having the same name as the raw data file and extension *.lcr.

,Export Graphic ’ provide an opportunity to create files in different formats for importing the display into other applications. The user can choose the desired format with the Save combo as typebox ’. The “ available formats are Enhanced Metafile (which will be the most adequate format when importing the display into other TIFF- applications), andWindows Bitmap file. With deactivated option ‘only Diagram(s) ’ the output will be identical to the printed version, otherwise only the diagram itself will be exported. The default behaviour is to rescale the display to a DIN-A4 page, regardless of the current aspect ratio of the display. To maintain the current keep aspect aspect ratio ratiothe’ ‘ option should be activated. ‘Print’ - ‘Print Preview’ - ‘Print Setup’ The‚most recent file list‘

control and format the output of the current graphic display to printer.

contains the names of the most recently used file names for quick re-loading. POW

‘Exit’ terminates the application and returns control to the main WinX menu.

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13 Size / Strain

13.1

Introduction

The module ‚Size / Strain‘ allows the user to calculate crystallite size and microstrain from peak widths. The application is started from the pull-down menu of the WinXPOW main menu item ‘Size / Strain’.

The algorithms provided range from the simple and robust Scherrer- and Wilson-formulas to Williamson-Hall-plots and profile decomposition into Lorentz- and Gauß-portions using the procedure of de Keijser, Langford, Mittemeijer et al.. All algorithms are based on the variation of the integral breadth over 2theta. The two fundamental equations are : K⋅ λ L ⋅ cosθ

(1) Particle-si ze-broad ening :Scherrer-equation

β=

Microstr ain-broad ening: Wilson-eq uation(1)

β = 4 ⋅ e⋅ tanθ

POW

WinX 3.05 Software Manual – Size / Strain

13-1

with

β= K= λ = L= e=

integralpeak bread th sizefactor wavelength volume-average particle size( = D) 'upper-li mit' meanstrain

(2) usually gives a good indication of the extend of If both broad eningeffects are pre sent, the W illiamson-H all plot these effects:

β ⋅ cosθ =

K⋅ λ L

2

+ 16 ⋅ e⋅

sin

θ

β ⋅ cos θ

The size factor K which differs with particle shape (spheres, cubes, octahedral or the like) is set to unity in this program. For all three formulas, β is the integral breadth of the pure specimen broadened profile function F(x). This is the measured (observed) profile H(x) corrected for the instrumental resolution G(x). As the observed profile H(x) is the result of a convolution of F(x) with G(x), this correction is not easily performed. The effect that the convolution of F(x) with G(x) has on the halfwidths of H(x) depends on the profile functions (Gauß, Lorentz or any intermediate) for F(x) and G(x). The instrumental resolution function G(x) varies smoothly with 2theta. Hence this function can be obtained by measuring a suitable standard with lines as sharp as possible like Si, LaB6 or Scheelite. In the case that the profiles can be described by a Voigt- or pseudo-Voigt shape, a practical way of solving this (3,4). Within this method, the integral breadths of the Lorentzproblem was developed by de Keijser and co-workers and Gauß- components of the measured H(x) and G(x) profiles are extracted using the ratio of integral breadth (=beta) to full-width-at-half-maximum (=gamma) and accurate polynomial approximation formulas. The calculation of the F(x) profile is then done for the Gauß- and Lorentz-part of the Voigt-function separately :

β F,Lorentz= β H,Lorentz- β G,Lorentz

and

β F,Gauß2 = β H,Gauß2 - β G,Gauß2 .

As particle-size-broadening leads to a Lorentzian shape of F(x) and strain-broadening to a Gaussian profile for F(x) (5), the deconvolved Lorentzian breadth of F(x) can subsequently be used in the Scherrer-equation to determine the particle size and the Gaussian breadth of F(x) may be inserted into the Wilson-formula to calculate the microstrain. The literature cites at least three parameters describing the amount of microstrain : the 'apparent 'upper strain' η, the 2> which may be related to each other by limit' strain e and the root-mean-square √
η = 4 . e = 2 √. (2π) . √

andthus e= 1.25√. .

The program lists both e√ and .

Peak data input into this program must have been fitted by the 'Profile Fitting' module using Pseudo-Voigt functions and individual peak widths not represented by the Caglioti formula !

(1)

H.P.Klug, L.E.Alexander, X-Ray Diffraction Procedures, John Wiley & Sons, New York 1974, 655ff.

(2)

G.K.Williamson, W.H.Hall, Acta Met. (1953) 1, 22

(3)

Th.H.de Keijser, J.I.Langford, E.J.Mittemeijer, A.B.P.Vogels, J.Appl.Cryst. (1982) 15, 308

(4)

Th.H.de Keijser, E.J.Mittemeijer, H.C.F.Rozendaal, J.Appl.Cryst. (1983) 16, 309

(5)

R.A.Young, The Rietveld method, Oxford University Press 1993, 163ff.

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13.2

File

comprises options to load peak files into the program, to save a list file and to print out data from the program. ‚Open ‘ is used to load the two required kinds of peak files into the program : One peak file containing (fitted) peak data from a standard sample reflecting the instrumental G profile and one containing the observed = broadened peak data, the H profile. These peak files are generated using the 'Profile Fitting' module. The ‚Browse‘ buttons provide the standard Windows function for file selection.

When both files have been read, the program displays the list of observed peaks with all of these peaks selected. The user may either accept all peaks or discard those peaks from the list by clicking on them which shall not be used for the size / strain evaluation. Pressing the 'OK'-button will continue the program by opening the 'Options' dialog box. If the 'Cancel'-button is pressed, no peaks are loaded and the user has to supply new peak data by using the 'File'-'Open' option again. ‚Save Report ‘ lets the user write the program output to a text file which receives a default file name identical to the observed peak file but with extension *.lsz. The item is only activated if data have been loaded and evaluated. ‘Print’ - ‘Print Preview’ - ‘Print Setup’ control and format the output of the current graphic display to the system printer.

The‚most recent file list‘ contains the names of the six most recently used file names for quick re-loading. ‘Exit’ terminates the routine and returns control to the WinXPOW main menu.

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13.3

View

This menu comprises commands affecting the layout of the main window and the visibility of the text child window.

'Toolbar' removes / brings back the toolbar with shortcut buttons above the main window. 'Status bar' removes / brings back the status bar beneath the main window. 'Split' invokes the cursor used to shift the limits of the main window's three splitter windows. 'ListFile' switches off and on the display of a child window listing the results.

13.4

Options

This dialog box allows the user to select the algorithm for the size / strain evaluation. The 'Calculation' radio buttons allow the user to choose between two different evaluations of the 2theta-dependance of the peak broadening effect. 'Use functions' will perform a leastsquares-fit according to the Scherrer- and Wilson-formula to the F breadths (using the breadth parameter selected with the next two input options). 'Use mean value' will apply the two formulas independently for every peak, calculate a size- resp. strain-parameter for each line and take the average of these parameters. The difference between the results obtained with the two methods is usually small (typically 1-10% of the calculated value depending on the number of peaks evaluated); if the difference exceeds about 20%, this is an indication that the data do not follow the theoretical prediction at all. The setting of these radio buttons do not influence the Williamson-Hall-Plot. The check box 'Use D econvolutio n' is usually checked as the profile decomposition procedure described in 13.1. is the most accurate way of separating the size and strain broadening effects. However, the raw data must be of very good quality and the fitting performed as accurately as possible; especially the background must be defined unambiguously and the peak counting statistics have to be excellent. If these prerequisites cannot be met for some reason, it is preferable to retreat to a

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13-4

simpler size / strain estimation (i.e. use the Scherrer-, Wilson- and Williamson-Hall-formulas with the total breadths of the H profile minus the total breadths of the G profile) rather than expect correct results from an advanced algorithm fed with insufficient data. Therefore, this box should not be checked for poor data. The'Breadth' radio buttons are only enabled if the 'Use deconvolution' check box is not checked; i.e. if no separation of the peak profiles in Lorentz- and Gauß-components is to be performed. This crude particle size estimation is usually done when the data are noisy, peaks are overlapping or the background is ill-defined. In these cases, the FWHM of peaks is less prone to errors than the integral breadth and should be used in the Scherrer- and Wilsonequations instead of the integral breadths. The'2Theta window for deconvoluti on' controls the assignment of observed peaks to standard peaks. As the peak width as well as the peak shape usually change with 2theta for F-, G- and H-profiles, the standard peak used to correct the H profile for instrument broadening must be in the same 2theta region as the broadened peak. Ideally, the standard is the same substance as the broadened sample but showing no peak broadening effects. In this case, every broadened peak may be corrected with its unbroadened analogon in the standard. Peak positions would vary very little and a small 2Theta window can be used. The use of the very same substance as a standard is, however, not always feasible and laboratory standards like Si or LaB6 must be used. In these cases, the permissible width of the 2theta window depends on the size of the broadening effect and may be the larger the larger the broadening is; i.e. the less important the G contribution becomes. If the instrumental FWHM is e.g. in the range of 0.1° and the broadened peaks are more than 2° wide, the 2theta window may be up to 10° without introducing a significant error (of course presuming a 'normal' variation of peak width and peak shape with 2theta for the instrumental profile). Pressing the 'OK' button will start the calculation and display the results on the screen. 'Cancel' will discard all changes which have been entered and return to the main menu.

13.5

Output

The result of the calculations is displayed graphically in the three splitter windows of the main window. The top left display shows the results of the particle-size evaluation, the top right window the results of the strain calculation, and the lower window the Williamson-Hall-plot. Depending on the setting of the 'Calculation' option, the top left window either shows the variation of the breadth measure with λ/cosθ ( if 'use functions' has been selected) or the variation of the calculated particle size D with 2θ ( if 'use mean value' has been selected). Accordingly, the top right window either shows θ -the breadth / tan variation or the strain e over 2ectively. θ, resp For a perfect fit to the Scherrer- or Wilson-equation, D resp. e should be the same for all peaks, θ, i.e. constant with 2 if the calculation mode 'use mean value' is selected. The parameter calculated for the particle size is the volume-averaged particle size D; the strain parameters output are the strain e and the r.m.s. strain (for definitions, see 13.1 and the literature cited therein). A child text window displays all information relevant for the task performed. This output may be written to file using the 'Save epo R rt' option in the 'Fil e' pull-down menu.

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14 System-Evaluation

14.1

Introduction

The System-Evaluation module is a graphic interface to observe powder pattern and calculate their refining lattice parameters. For a better description it has been (sub-)divided to the following parts: 1. graphic interface to display powder pattern, define background points and allocate peaks, 2. pattern fitting, using the Fit-module of the WinXPOW software suite, 1, ITO 2 and DICVOL 3 and the refining routine (see index & refine 3. indexing via the programs TREOR module of the WinXPOW software suite), 4). 4. space group determination of crystallographic powder data (ExtSym

The module provides an easy way for data processing and preparing data for further analyses. Menu and Tool Bar Ca ti on Ba r

D i s l a W i n d ow

O er at ion Ba r

Re or t Bar

1

J.W.Visser, Journal of Applied Crystallography 2,89 (1969) P.-E.Werner, L.Eriksson, M.Westdahl, Journal of Applied Crystallography 18, 367 (1985) J.W.Visser, Journal of Applied Crystallography 2,89 (1969) 4 A.J.Markvardsen, K.Shankland, W.I.F.David, J.C.Johnston, R.M.Ibberson, M.Tucker, H.Nowell, T.Griffin, Journal of Applied Crystallography. 41, 1177(2008) 2 3

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WinX 3.05 Software Manual – System Evaluation

14-1

The program main window is split into five parts: -

The menu- and tool-bar

-

The operations-bar

-

The caption-bar

-

The display window

-

The report bar.

These five parts should be described in the following chapters.

14.2 14.2.1

The menu- and tool-bar File

The File’-menu ‘ item offers the standard Windows utilities to read and write files, to re-open recently used files and to print the results. For further information please consult the RawDat chapter 7.2.

14.2.2

View

The View’-menu ‘ item provides the utilities for the control of the display. Their closer description has been documented in the chapter 7.3 of the RawDat documentation.

14.2.3

Operations

The Operations ‘ ’-menu item contains two basic editing functions. The first function is the editing of the background points and the manipulation of the background curve, the second is a smoothing operation which can be performed to the data points. Both operations are described in the RawDat manual section (see chapter 7.6).

14.2.4

Peaks

The Peaks’-menu ‘ item lists the operations for peaks, phases and regions alignment. ‘Search Peaks ’ starts the peak search algorithm, scanning the raw data for significant peaks. For this operation the current search parameters will be used. After loading a powder-diffraction file (Stoe RAW-file), these parameters will be set to default values, depending on the measurement conditions. Following peak searches will add the found peaks to the existing peak list. This can lead to double entries. The peaks found by the algorithm will be grouped in the phase called ‘PeakSearch’. To prevent double entries, it is highly recommended to clear the current peak list before searching. ‘Clear Peak Li st ’ deletes all current peaks, not concerning their properties like phase or if indexed. ‘Edit Peaks ’ starts the peak editing mode as described below.

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‘Edit Peaks Dialog ’ displays the peak list dialog (see below). Range Selector

Lock Columns

Edit Buttons

In Stoe RAW-files more than one measurement range can be stored. On top of the dialog one of these ranges can be chosen. Changes in this selection will display the corresponding peaks to this range. The header line of the peak list table can be clicked for sorting or to switch on/off all values below the values in the corresponding column below. An ‘unlocked/locked’-icon indicates if the value before the icon will be free or fixed for refinement in the next fit cycle. 2Theta, Half-width, Intensity and Phase values can be edited manually. Negative or zero values are not allowed in the ‘phase’ fields. Gabs in the phase list must be prevented. New peaks can be entered through clicking the ‘New Peak’ button at the bottom of the dialog or through the context menu (right mouse button). Peaks can be selected through the usual mouse clicks. Holding down the shift-key will select all peaks between the first and the last click. Every left click will select one single peak, while unselect the last selected one. Holding down the ctrl-key while clicking, enables the users to select more than one entry. Selected peaks can be deleted through the ‘Delete Peak’-button or through the context menu. ‘Edit Region ’ starts the region editing mode as described below. ‘Edit Regions Dialog ’ displays the regions dialog.

This dialog can be handled similar to the ‘Edit Peaks Dialog’ above. New entries can be made by a click on the corresponding button or from within the context menu, displayed after clicking the right mouse button. Selected entries can be deleted by the button or context menu. Values in the ‘Begin’ column must be smaller than values in the ‘End’ column. Overlaps of regions should be prevented. A warning will indicate an overlap which will be truncated or deleted after closing the dialog by clicking the OK button.

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‘Edit Phases ’ starts the region editing mode as described below. ‘Edit Phases Dialog ’ displays the phases-dialog.

Color Selector Field Use/Refuse Phase Show/Hide Phase Name of the Phase Selected Phase

The handling of this dialog is similar to the regions dialog described above. The columns ‘Index’ and ‘NPeaks’ displays only information and can not be edited. By pressing the corresponding ‘Sel.’ field, a ‘working’ phase can be defined. This selected phase will be used to proceed with further processes. A name for the specific phases can be set. This names will be displayed in the phase editing modus, see below for further information. To show or hide phases in the display can be chosen by clicking the corresponding field in this dialog. If phases are refused for further process, the peaks belonging to this phases within the defined regions will be removed before the next pattern fitting cycle. In the last column the color of the peaks belonging to this phase can be edited. Throughwill thebecontext menu the right mouse phases merged to the(pressing first selected phase in thisbutton) list. selected phases can be merged. All selected After a pattern fitting cycle peaks with abnormal parameters will be sorted out into ‘refused’-phases, indicating that these peaks could not be well fitted. It is recommended not to use this peaks for further process.

14.2.5

Help

The ‘Help’-menu item list displays information about the program.

14.2.6

Tool-Bar

Most of the commands described above can be called directly by clicking the corresponding button in the toolbar.

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14.3

The Caption-Bar

The caption bar displays current information and the state of the Position program. Info ’ is If been ‘ enabled in the menu- or in the tool-bar, the position (intensity and 2Theta) of the mouse pointer will be shown in the caption bar.

14.4

The Operation Bar

Three operation tabs add up to the operation bar. -

the Guided ‘ Mode ’-tab,

-

the Advanced ‘ Mod e’-tab,

-

the Display ‘ ’-tab.

With the help of the commands- and entry fields in the first two tabs the program can be controlled. Displaying options can be set in the third tab.

14.4.1

The ‘Guided Mode’-tab

In this tab the basic operations and settings are combined. Tab Header Command Button Current state with state icon

Selector Section Separator

Help Bar

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In the list on the left side the buttons are stored. Pressing these buttons will execute external programs or internal routines or change the editing modus. On the right side of the list the current states of the buttons or a selection list are shown. On the very right side an icon will display the success of the performed operations. All of the command- and input- buttons are sorted into six sections. In the global section loading of the file and basic operations are stored. The fit section consists of the button to start the external fit program. The selection and execute button for the index routine has been put to the index section. In the GenHKL section the execute button for the HKL file generating data fit is stored. Buttons for executing the external program ExtSym and selecting the most probable extinction symbol, are placed in the ExtSym section. In the final section RefineSG the button to refine the chosen space group with a final fit is placed. The buttons will further be explained in detail. ‘Load File ’-button opens a file dialog. If this button is pressed and the warning for unsaved data is not prevented in the preferences, the user will be asked to save the current unsaved data, which will be lost otherwise. If a file has been loaded, the name of this file is shown in the information field on the right side of the button. Only displayed if more than one range is presented in the Select Raw-file Range the’-button ‘ will open a dialog where a working range can be chosen. The Background ‘ ’-button starts or ends the background editing mode. The Regions ‘ ’-button starts or ends the regions editing mode. The Peaks‘-button ‘ starts or ends the peak editing mode. ‘Run Fit ’ will execute the pattern fitting module. For more information to the fit program please read the chapter 8 of this software manual. If more than one phase is defined, Select thePhase ‘ ’ entry will be displayed. By a mouse-click on the entry the phase list dialog will be opened. The Run ‘ Routine ’ entry in the list will execute the on the right side of the entry selected external program. To choose the external program, pressing the the ‘switch’-icon on the far right side of the entry. If a cell suggestion has been selected and refined pressing Generate the HKL ‘ File ’ button will fit the generated theoretical peaks corresponding to the selected suggestion. After the fit an HKL file will be generated and if not deactivated in the preferences, the user will be asked where to save this file. ‘Run ExtSym ’ executes the external program ExtSym. With the help of the Extinction ‘ Symbol ’-selector a possible extinction symbol can be selected. With a click on the left side of Refine the SpaceG ‘ rou p’-button a final fit can be performed. After this fit a final HKL-file will be created. During the work with the ‘Guide Mode’-tab small information of the process is displayed at the right side of the command buttons. At the right side of the section buttons an ‘emotional icon’ will indicate the quality of the results. NOTE: The check for the quality of the results bases on distinct absolute values. The result itself depends on many environment variables like the quality of the data set. A ‘bad’ indication must therefore not indicate that something went wrong during the operation.

On the bottom of the bar a ‘Help Bar’ will display an assisting text.

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14.4.2

The ‘Advanced Mode’-tab

The ‘Advanced Mode’-tab contains below the command buttons fields to edit important preferences for the external and internal algorithms. With the help of the tool bar the sections can be switched. On the bottom of the bar a ‘Help Bar’ will display assisting information depending on the chosen field. Tab Header Tool-Bar Command Buttons

Property Entries

Help Bar

The ‘Command Buttons’ are similar to the buttons of the ‘Guide Mode’-tab. Indicators on the right side of the entries show the process and the quality of the analyses. Below the command buttons ‘Property Entries’ for individual editing of settings are presented. In theGlobal ‘ Prefs ‘-section the min and max values of the regions can be edited. Additionally to the above described guide buttons Save a ‘PeakFile ’ entry is placed in this section. A click on this entry will write a Stoe-PeakFile.

In theFit ‘ Prefs ’-section basic preferences for the external program Fit can be edited. Additionally to the above described guide button a ‘Reset Settings’-button is placed in this section. This button will reset all individual settings done in this section and will reset all former received fit results. The ‘lock’-icon on the right side of a value indicates whether the value is free for refinement. A click on this icon will change the free/fixed behavior during refinement. For more information about the values, which can be edited in this section, please refer to chapter 8 of this manual. If Fit is executed for the first time the 2Theta values of the peaks will be fixed for refinement and only the intensities and the half-width of the peaks will be free for refinement. In a second cycle the 2Theta values of the peaks will be freed for refinement.

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In the Index ‘ Prefs ’-section basic preferences for the external indexing programs can be edited. Additionally to the above described guide buttons a ‘Reset Settings’-button is placed in this section. This button will reset all individual settings done in this section and will reset all former received refine results. With the top routine selecting button the below properties will be changed depending on the routine chosen. All values are similar to the values described in chapter 10 of this manual. If an external indexing program is started by pressing the “Run Routine”-button a status dialog will open which monitors the external process and gives out a text which will be written by execu ted process. This dialog is closed if the ‘OK’ button on this dialog (only enabled if the external process has finished) or the ‘Fixed’-button on the upper right side of the dialog has been set to ‘Release’ and the process has been finished.

In the Cell ‘ Setup ’ section the refinement parameter and the cell settings can be altered. The first two values Zero‘ Shift ’ and 2Theta ‘ Ref.Window ’ are crucial for the internal refinement algorithm. An inaccurate zeroshift will lead to false indexed peaks. During the refinement the 2Theta window is minimized. The finally reduced 2Theta window is saved for the next refinement cycle. This window corresponds to the correlation between symmetry based calculated peaks and the observed peaks from the peak search or manual allocation. If this window is too small it can lead to a higher number of peaks which could not be indexed.

NOTE: If the number of peaks which can not be indexed during refinement is getting higher, please check the values for the ‘Zero Shift’ and ‘2Theta Ref.Window’. If the zero-shift is too big or the 2Theta window too small, the values should be set back to default values (0.0° for zero-shift and 0.08° for the 2Theta window) and refinement should be repeated. POW


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In theGenHKL ‘ Prefs ’ section the settings for the fit of the symmetry based calculated peaks can be altered. With a reset button all the settings can be set back to default values. Due to the theoretical calculations peaks are generated which are located very near to each other, and can not be resolved with the fit algorithm. To prevent faulty results these peaks will be filtered and removed before fit and added back to the peak list afterwards (by overwriting their parameters with fitted parameters from overlapping peaks). The finally created HKL-file will contain all the theoretical calculated peaks. The filterResolution ‘ Window ’ can be defined in this section. If this window is too big interactions between peaks can not bee detected. With the choice of a too small window the fit of the peaks can lead to typical artifacts. These artifacts lead to peaks which are excessively huge, whereas the interacting peaks right next to this peak will be negative. The other parameters are well defined in chapter 8 of this manual. If ‘Generate HKL File ’ is executed at the first fit cycle only the intensities and if set in the peak dialog, the half-widths of the peaks are free for refinement. In a second fit cycle the cell data will be free for refinement. In a third optional cycle the profile parameters ‘u’, ‘v’ and ‘w’ will be free for refinement (if fixed before). The ExtSym ‘ Prefs ’ section displays the settings which will be send to the external program ExtSym. For more information about these values please see the manual of ExtSym. The additional entries Reset‘ Settings ’ and Save ‘ Generated ’ enables the user to reset to default values and to save the generated peaks to a Stoe peak file.

The RefSG ‘ Prefs ’ section corresponds to a final fit with a selected space group. Again all settings can be set back to default values by click onReset the Setting “ s” entry. A description of the displayed parameters is given in chapter 8 of this manual.

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14.4.3

The ‘Display’-tab Tab Header Tool Bar

Show/Hide-Checkboxes

The Display ‘ ’-tab can be handled similar to the Layer Panel in RawDat specified in chapter 7.1.2 of this manual. In difference to the Layer Panel show/hide buttons for special HKL values are shown in the tool bar of the ‘Display’-tab. With the help of these buttons calculated peaks which fulfill discrete reflection conditions can be displayed or hidden. The icon of the button corresponds to the special reflection condition.

14.5

The Display Window

This window is a tool for displaying the basic raw data, for manual editing of data points and for monitoring the progress.

In the basic raw data displaying mode the raw data curve, the resulting curves of the fit, the observed peaks and the calculated reflections are shown. The curve offers valuable information about the quality of the divergence fit last performed (see chapter 8 for further information). Tools for working with this window are specified in chapter 7 of this manual. An additional tool for working with this display is the ‘Zoom Diagram’.

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The Zoom ‘ Diagram ’ contains two slider controls and a small version of the whole diagram. With the help of the slider controls at the bottom and on the right side of the window a zoom area can be adjusted. A small rectangle represents the chosen zoom area. This box can also be dragged around with the mouse pointer. Moving the mouse pointer over the box and clicking into it with the left mouse button, holding this button and moving the mouse will shift the box in the diagram. During the movement the main display window will show the chosen region.

14.5.1

Region Editing Modus

In this modus the regions can be defined. To edit these regions the mouse pointer has to be placed near the end or the start of a region. If editing can be performed the mouse pointer will change into a bar with arrows at both sides pointing to the opposite directions. If the left mouse button is clicked and hold down, the region can be adjusted. If the mouse pointer will be moved directly over the region bar at the bottom of the diagram and is placed over the blue region representing a defined region the mouse pointer will change into a pointing hand. Clicking this region with the left mouse button, holding down the button and moving the mouse will shift the region. If a region collides with another region both regions will be combined. A right pressed button on a region will delete the selected region. All regions but one can be deleted. If the end or the start of the region is outside the zoomed area, a white arrow will be shown (see diagram). A double click on the blue region bar will open a dialog to edit this region by an input of discrete values.

14.5.2

Peak Editing Modus

In this modus peaks can be edited. A peak editing tool bar will be displayed above the diagram. Buttons of this tool bar are explained below. ‘Seach Peaks ’ will start the peak search algorithm (chapter 14.2.4). Clear ‘ Peak Lis t’ will delete all current peaks not concerning their properties like phase or if indexed. The next five entries of the tool bar are well documented in chapter 8.4.1 of this manual and should not be explained here further. The than Consider ‘ Background ’ button will delete observed peaks which are not significant bigger the background. If the Au ‘ tomatic Mode’ button is checked, an algorithm will try to find best values for the parameters above, to perform the best possible peak search. A ‘Reset’ button will set some of the parameters back to default values.

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Peaks can also be allocated manually. For adding a peak-marker into the diagram double click the location, were the peak should appear. After the double click the maximum in the raw data curve at this position will be searched and the peak will be shifted to this maximized position. The automatic search for the best position of a peak can be disabled by pressing Sticky the Add ‘Peaks ’ button in the Basic ‘ Operations ’ tool bar displayed in the upper right side of the program. If the left mouse button kept pressed near an existing peak-marker, this peak-marker can be shifted to a new position. A right click on an existing peak-marker will delete it. Blue lines at the bottom of the diagram display the defined regions. If presented, the resulting cumulative curve of a fit will be shown as well.

14.5.3

Background- and Smooth-editing Modes

These two modes have been specified in chapter 7.6 of this manual.

14.6

The Report Bar

The ‘Report Bar’ contains two different panels, the ‘Report’-panel and the ‘Index Result’-panel.

14.6.1

The Report Panel

The report panel is similar to the report panel in RawDat (see chapter 7.1.5). Moreover this report panel contains additi onal reports.

The Overview ‘ ’-report will display all the important results received during the processing of the Stoe RAWfile. It contains the following eight sections:

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-

Current Info : most important results for indication of the quality of the results,

-

File Info : header information of the loaded Stoe RAW-file,

-

Selected Range Info : information about the selected range of the Stoe RAW-file loaded,

-

Fitting Info : results from the first fit of the allocated peaks process,

-

Index Info : results of the executed external or internal indexing routines,

-

Selected Solution : information about the refined (and therefore selected) cell suggestion,

-

HKL File Generation : results from the fit of the calculated peaks,

-

ExtSym Overview : results form the external program ExtSym,


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-

SpaceGroup depending HKL File Generation : result of a final fit.

The RawDat’-report ‘ is described in chapter 7.1.5 in this manual, as well as the possible Audit-selection of ‘ Trail ’ andFull ‘ Report ’. In thePeak-File ‘ ’ report the current allocated peaks will be listed as saved to a common Stoe peak-file. The Fit ‘ Report ’ contains all information of the last performed fit. All errors during the operations will be stored in the ‘Error Report’. The next two reports Index‘ Report’ as output of the indexing program Sel.and Solution ‘ ’ as overview over the refinement of a selected cell suggestion, are the common output of the indexing programs (see chapter 10 for further information). The Generated ‘ Peaks ’-report contains a list of all current generated peaks, calculated based on the cell metric or the space group depending on the process of the work. The ExtSym ‘ Report ’ contains the output of the ExtSym program and a peak list. NOTE: The list of peaks which has been calculated in the ‘ExtSym Report’ contains only the current displayed peaks. The list can therefore be altered by choosing the HKL conditions which must be fulfilled by enabling/disabling this conditions in the ‘Display’-tab tool bar (see above).

14.6.2

The ‘Index Result’-panel

In the Index ‘ Result ’-panel the cell suggestion for the peaks allocated in the loaded Stoe RAW-file are displayed.

The tool bar on top of this panel can be used to reset to values and to sort the below listed suggestions. A click on the “Reset” button will reset all suggestions to the values calculated by the indexing routine. All refined results will be lost. To sort the suggestions in this list, first the display has to be changed to alphabetical, by pressing the corresponding button in the tool bar. After that, the suggestions can be listed depending on their occurrence in the output of the indexing routine, on their FOM values, or on their cell volume. Clicking one of the buttons more than once will change from ascending to descending order and back. A mouse click with the left mouse button will refine the selected suggestion. Depending on if the zero-shift should be fixed or free for refinement, one or a series of refinement cycle(s) will be performed. A context menu, available by clicking an entry with the right mouse button, enables the user to delete or set back the selected suggestion.

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14.7

Example for Processing Data

1. After the start of the program a Stoe RAW-file has to be loaded. The SymEval program can not process master files or a series of files. 1.1.To choose a range to proceed will only be necessary if more than one range is presented in the Stoe RAW-file. 2. If background points are not provided by the Stoe RAW-file a new background has to be allocated. To proceed, the background working mode has to be started. During this start a theoretical background will be set. Background points can be altered or added or deleted afterwards to correct the calculated background. 3. It is highly recommended to define the working region for further data procession. Beam-Stop areas or high-angle areas without noticeable peaks should be cut off, to improve further results. 4. Most important to proceed is the allocation of peaks in the loaded curve. The first change to the peak edit mode will perform an automatic search for peaks in which all search parameters will be automatically adjusted to receive the best search results. To check this search by zooming in the diagram and by allocating, deleting or adding peaks is highly recommended. 5. The next step in the processing of the data is a fit of the allocated peaks. 5.1.If the results of the fit indicates that peaks are missing or should be deleted, these peaks should be edited by re-entering the peak edit mode. Peaks with abnormal shifts, half-width or intensities will be rejected, set back to values before the fit and sorted out to additional phases. These phases can be edited or deleted through the phase edit mode or the phase list dialog. 6. Next an indexing routine has to be started. If the indexing program does not deliver any cell following tried out: -suggestions, Change thethe max numberpoints and should the maxbenumber of possible un-indexed peaks in the advanced mode - Change the indexing algorithm. Choices are: - Werner algorithm (extern with TREOR program or use of the internal process) - Louer algorithm (extern with DICVOL program) - Visser algorithm (extern with ITO program) 7. Select and refine a suggestion by clicking on a list entry in the index result panel. The un-indexed peaks will be flagged with a red ‘UNINDEXED’-label (if ‘Peak Labels / X-Lables / HKL’ is enabled). Please mind that too many un-indexed peaks may indicate a wrong symmetry, especially if comparative strong peaks are un-indexed. Other explanation for un-indexed peaks may be fault values for refinement (see chapter 14.4.2 for further information) or impurities in the sample. 8. Next a fit of the theoretical generated peaks and a generation of a HKL file should be proceeded. In a first fit-cycle the 2Theta values are fixed and only the intensity of the peaks is free for the structure refinement. The half width will be calculated as function during the refinement. A second cycle will fit thecycle peaks freeing cell parameters structure recommended willwhile calculate thethe parameters ‘u’ and for ‘v’ the of the profile refinement. function (if A notthird freed before). 9. The generation of a HKL file should be followed by the execution of the program ExtSym. This program will calculate the probability of extinction symbols describing the fitted peaks. These symbols will be presented in a list box and can be chosen by the user. 10. After choosing an extinction symbol from the list and a corresponding space group, the new settings can be used to generate peaks which can be fitted against the srcinal data curve.

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14.8

Preference Dialog

The preference dialog can be displayed by pressing the corresponding button in the tool bar or selecting the menu entry in the menu bar. Five sections of preferences can be altered. The General ‘ ’-section contains the more global settings for the program behavior. All Stoe RAW-files can be loaded with this program. Files created with obsolete software suites can have a different internal structure. This so called ‘old format’ can be imported into the SystEval program but not written back to disk. All Files saved by SystEval will be written in the newest Stoe RAW-file format. The handling of files in an old RAW-file format can be altered in the corresponding field of the preferences. New generated or edited background data for ranges will be saved to the loaded files. If edited data should be kept, a warning message will appear after changing background points. This can be prevented by disabling the box in the preference dialog. The program behavior during export and the display of warning dialogs during the fit process can be changed in the corresponding fields of the preferences dialog. In the Diagram ‘ ’-section, the colors and appearance of the diagram presented in the program can be set. Entries in this preference section are self explaining and similar to the preferences described in the RawDat section of this manual. In theDisplay ‘ ’-section the settings for the display of peaks can be edited. In the first list box the srcin of the peak data can be set. The peak data can be loaded from file or created with the usual peak search algorithm. Choices are as followed: -

‘Do nothing’ will only load the Stoe RAW-file.

-

‘Ask for existing peak file’ will display a file dialog for loading a peak file manually.

-

‘Search for existing peak file’ will load a peak file with the same name as the Stoe RAW-file loaded in the same directory or will display the file dialog if no peak file with the same name has been found.

-

‘Automatic mode’ will search for an existing file and if no file has search. been found or selected it will automatically perform a peak

-

‘Search for peaks automatically’ will perform a peak search with automatic adjusted settings every time a Stoe RAWfile is loaded.

Every theoretical peak will be calculated without a zero-shift depending on the used diffraction system. To apply the zero-shift in the display to the generated peak, enable the corresponding checkbox in this dialog. POW


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If peak labels should not be overwritten only the first label of a peak will be displayed if two labels are too near each other and would overlap in the display. The cumulative curve presented from a fit can be scaled on the total region or on the zoomed region displayed on screen. This scaling behavior can be set in the corresponding field of this dialog. In the Printing ‘ ’-section a few self explaining parameters for the printout can be set. In the Saving ‘ ’-section of the preference dialog the automatic saving behavior of the program can be edited. If the program is closed, while data were not saved, a warning will be displayed. To avoid this warning, the corresponding checkbox must be disabled. In the edit field a project directory can be set up. In this project directory all important data processed will be saved, without asking the user. Opening of a Stoe RAW-file will save this file into the project directory. All fit-result files (*.rtf), all peak files (*.pks), all HKL-files (*.hkl), and all project file (*.exres) will be saved automatically to this directory. After the creation of an HKL-file and the execution of the Fitprogram the user is asked for a place and the name of the file to be saved. To save the HKL- and Fit-files without asking (giving them the same filenames as the loaded RAW-file in the same directory), the corresponding checkboxes must be enabled/disabled. If the project file should be saved without a warning, every time a file is closed a project file (*exres) will be written to the location of the file loaded or in the project directory if defined.

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WinXPOW_3.05

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