WinNormos2

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12.08.2008 WinNormos-for-Igor® 1

Wissenschaftliche Elektronik GmbH

WinNormos-for-Igor®

Version 2.30 (March 2008)

Version for Microsoft Windows or Apple MACRuns with Igor version 6 and above

Sold by Wissel GmbH

Introduction:

Here at last is WinNormos, the Windows-version of Normos. This is WinNormos-for-

Igor®, which is a version which works from within the Igor® graphics and numerical

treatment program. Igor® is produced by Wave Metrics®, and can be easily obtained at

their web site: www.wavemetrics.com where a demo version can be easily down-loaded.

Contents of the CD:

1. File “WinNormos2.doc”: A short introduction to installing & using WinNormos-for-

Igor.

2. Files “SetupIgor6.exe” (Microsoft Windows) and “Igor6.dmg” (Apple MAC): files

for installing the current version of Igor®. With this, you can test WinNormos-for-

Igor®, either a demo version or a full production version.

3. Check the site www.wavemetrics.com and download a newer version if one is available.

4. Directory “Spectra”, containing some demonstration spectra.

5.

File “WinManual.pdf”: file containing complete documentation for WinNormos-for-Igor.

6. File “WinNormos.xop” in one of the WinNormos_PC directories (Microsoft

Windows) and directory “WinNormos.xop” in one of the WinNormos_MAC

directories: compiled library of WinNormos routines which Igor® links to on loading.

7. Directory “WinNormos-for-Igor.uxt Template”, containing the following directory

and file:

1. Directory “WinNormos-for-Igor.uxt Folder”, directory containing the Igor®

script files involved in WinNormos.

2. File “WinNormos-for-Igor.uxt”: text file which, together with the directory

“WinNormos-for-Igor.uxt Folder”, forms an Igor® template for a WinNormos

experiment.

7. Several files with ending .pxp: these are different example files.

To install WinNormos-for-Igor® you just need to do the following:

1. Install Igor® from CD by starting SetupIgor6.exe or Igor6.dmg (this will run for a

certain time in full mode. If you have a licence, it will continue in full mode, else it

switches to demo mode).

2. Copy the file/diectory WinNormos_XOP.xop from CD into the WaveMetrics

subdirectory “Igor Extensions”. (C:\programs\Wave Metrics\Igor Pro Folder\IgorExtensions)


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3. Copy the subdirectory “WinNormos-for-Igor® Template” from CD to the

subdirectory “Igor Pro Folder”. (“C:\programs\Wave Metrics\Igor Pro (Demo)

Folder”)

4. Installation is finished

5. Start Igor®.

6.

Within Igor®, open the Template file “WinNormos-for-Igor.uxt” using Menu File ->Open. (“C:\programs\Wave Metrics\Igor® Pro (Demo) Folder\WinNormos -for-

Igor®\WinNormos -for-Igor.uxt”) This should start-up showing the WinNormos

graphics panel, and a short Notebook documentation (which can be printed out).

7. A note on the difference between Igor® “Templates” (.uxt, .pxt) and “Experiments”

(.uxp, pxp). Both can be stored using a packed (.pxt, .pxp) or unpacked (.uxt, .uxp)

format. By storing your work as an “Experiment”, only the data for relevant to the

treated spectra are stored, not the script files which are in the template directory. The

script files (which are invisible to the user) defining what the buttons do etc. are taken

from the original Template directory. Thus this should not be subsequently moved.

Also, changes (corrections) and additions will be automatically used the next time

you open your previous experiments! 8. Now you can look at the demonstration spectra included in the template, or load up

other ones. These can be fitted in any way you like.

9. You can load different spectra and fit them using either “Site” or “Dist”, or both.

10. If you have a production version of Igor® (not the demo-version), you can then save

the whole collection of fits in an Igor® “Experiment” file. This can be re-started later

and includes all fits and data. Or you can re-start the Template file and start a new

experiment. (Note that saving is not possible with the included Igor® demo version,

but will work with the full production version.)

11. In the Demo version of WinNormos, Site can fit one subspectrum with up to 3 free

fitting variables (including the background, which is always fitted). Dist can fit one

block with up to 3 fitting variables.12. Setting up for your screen resolution is no longer necessary (script files since

August 2006).

13. There are now short help windows for each tab card, accessed by clicking on the

“Help” button.

WinNormos

WinNormos-for Igor® is a group of two fitting programs used to evaluate Mössbauer

spectra. They are combined into one Igor® "Experiment" including spectrum folding.This Introduction and the user's guide have been written to introduce these programs with

the help of some simple examples. To set-up WinNormos-for-Igor®, first install Igor® as

per Igor® manual. Then add the file WinNormos.xop to the correct Igor® folder (or

create a link to it, as explained in the Igor® manual). Then start Igor® and load the

Normos-for-Igor® unpacked experiment template WinNormos-for-Igor.uxt.

When finished treating one or more spectra, there are two different methods to save your

results for later. You store all the data folders (spectra and fits) as a new “Experiment”

under a different name, including all data and calculations, for example the unpacked

experiment MyExperiment.uxp. You can then re-start this experiment later. Note that

storing as an experiment, and not as a template, has the following advantage. In case youreplace your template and template directory with an improved one, then when you


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restart your experiment you will be automatically using the new template files! There

is no need to go back and reload the template anew. The same is true if you replace the

XOP file. This is schematically illustrated below.

Setting up for your screen resolution and default isotope: Procedure Window.

NEW: The second method to treat several spectra is to use the Save and Load buttons on

the first tab card to save and later reload one spectrum plus fits. Thus you could treat

several spectra, saving each separately, and then when you wanted to create a graphic

containing one or more of them, load the appropriate ones into WinNormos and create the

plot.

The file “Procedure” (no extension!) contains commands which are executed at start-up.These include one command for screen resolution and one for the default isotope. This

file can be edited before entering Igor® to conform to your wishes. The command

screenSetup(1400,1050) sets up the screen for a resolution of 1400 x 1050. This should

be no longer necessary to change as the program will detect your resolution automatically.

SetDefaultIsotope("57Fe") will set up for 57Fe as default.

Save Experimentas

Load & Fitour s ectra

WinNormos-for-Igor®

Some files in Template or

XOP file replaced.

Save again

YourExperiment.u

Load & Fit

other s ectra.

Restart Igor®

and


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The Experiment contains a graphical panel with a series of "tab cards". The first tab card

"Spectrum" seen above is for reading-in spectra and folding (as necessary) as well as

defining the velocity scale. The panel shows a demonstration file loaded into Igor®. The

raw spectrum is shown on the lower left. Any number of different spectra (with different

names) can be read-in using the "Read-in New Spectrum" tab, and selected using the pull-

down menu at the top of the left side of the panel. The "Read-in New Spectrum" tab

creates the following panel:Note in Format box, choice of number of text lines, VMAX listed on first text line, ignore

leading column of numbers. The last should be checked if the first column contains

channel numbers (older multichannel format). If you store the correct VMAX as the

leading number on the first line of text, then check the correct box and this will be used

automatically. The last option is for an Ortec binary file. If checked, the above choices

will be hidden.

The first line of buttons is: Get File, Replot File, and Accept, Reject and Edit. To choose a


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file, press “Get File”. The usual file dialog appears where you can select a file. The file

will be plotted and the panel looks like that to the left.

Note that the spectrum is plotted vs. channels after skipping the number of assumed text

lines in the box. The text lines are shown in the text box to the right. If this is not correct,

then change in “# Lines Text:” Set Velocity scale, maximum velocity, isotope andbackground, then if everything is correct, press “Accept”. Pressing “Reject” will exit with

no new spectrum. Pressing “Edit” will start an edit dialog where fallen channels can be

corrected. When finished, then quit, saving results. Spectrum format can be selected by

the pull-down box. Check the Help button for more information.

Now we go back to the original spectrum display card.

After reading in the spectrum, you can set the maximum velocity, the possible folding

point ("PFP") & fold the spectrum. If the check-box "Linearize" is checked, the velocity

scale will be linearized after folding.

On the right side, final values of the folding point (PFP), as well as estimated geometryeffect, background and resonant area are shown. These two latter values will be used later

in setting up the fit. In the graph below, the raw as well as the folded spectrum is shown.

The latter includes the assumed velocity profile.

WinNormos-Site:

The program for treating a discrete set of subspectra, each representing different values of

the hyperfine constants, is accessed through the 2nd and 3rd tab cards. The 2nd tab (Site-

Data) card sets up the general fitting conditions and selects fitting parameters which refer

to the whole spectrum. (Users of the DOS version will find the structure familiar. This is

intended.)


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Constant parameters are on the left side of the panel, and possibly variable parameters on

the right side. On the left side there are also fields showing the convergence. The names

of the parameters are the same as used before in the DOS version, making a transition

easier. In the list of variables, checking the check-box will select that as to be varied. If

the check-box is grey, the corresponding parameter cannot be varied, but perhaps changed

before the fit. If the check box is grey and the arrows to the right of the numeric fieldabsent, the field indicates a constant value which cannot be changed by the user. If there

is no name to the left of the check-box, then the field is not used at all. Fitting is started by

clicking the "Do Fit" button with "Fit" selected from the pull-down menu. Otherwise, a

zero-fit trial can also be done. The "Do Report" button will construct an Igor® Notebook

window including the graphics and numerical results. This can be printed out and/or

stored separately in "RTF"-format (readable in Word, for example). In addition, a table of

results and a separate graphical window will be generated. The graphical window can be

edited via all Igor® commands, and stored in any convenient format. The table can be

copied to the clip board and put into any program with arrays of numbers for plotting

independent of WinNormos or Igor® (for example, in Excel or Origin...).

The next tab panel defines the different subspectra. Note that both the total number of

subspectra (NSUB), and the currently displayed subspectrum (currentSub) can be chosen

independently (1


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On the left side of the above panel there are two check boxes: one is for setting the value

of VMAX after fitting a calibration spectrum (see below), and the second is for setting up

a fit. By clicking this second one, you get the following panel. First click the "start"

button once. (This becomes the "Finish" button for exiting.) Then the hook-cursor

function is activated. Click at the maximum (minimum here) of a spectral line, holdingthe left mouse taste down. Then "pull-out" a Lorenzian line which approximates the

experiment.

The green line is the trial line. Then click one of the appropriate line numbers at the top: 1

to 6. In the above case its 1! This will add the trial line to the fit, recalculate the theorysum and difference. The above procedure can be repeated for the lines belonging to one

"site" (singlet, doublet, sextet). After each line is chosen, the hyperfine constants are

recalculated. NaN indicates that no number is possible yet (too few line choices).

When enough lines have been selected, you may adjust the hyperfine constants if you


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like. Pushing the select button will make a subspectrum from the constants, add it to the

theory spectrum and recalculate the error differences. Then a new panel appears below.

By pressing "Accept", this trial subspectrum will be added to the list of fitting subspectra,

and all fields will be reset to NaN, so you may continue to select lines. When you are

done, press "Finish" and the above panels will disappear. Now you see the added

subspectrum (here, sextet line), and resulting difference plot. Note that in the Site-Para

panel, this subspectrum has been added, and NSUB and currentSub incremented.

In this way, you can build a model spectrum consisting of several subspectra. For each

subspectrum, select variables using first the "currentSub" to move through the subspectra,

and checking the appropriate subspectra.

The other push-button for calibration is useful after fitting a room temperature iron

spectrum. The value of VMAX will be adjusted to obtain Bhf = 33.1 T. A further fit

might refine this value a bit. Please note that the isomer shift (assuming a 57Co source in

Rhodium) should be about -0.106 mm/s. If it is positive, then change the sign of VMAX

in the first panel and re-fit.

By pressing the Plot button the following type of window is generated:


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This can be modified using the Igor® commands, and stored in many different formats.

The report button generates the above graph as well, and puts it onto a Notebook window,

as well as all the relevant numerical results. In addition, the following type of table is

generated. The columns include the velocity, the experimental spectrum, the theoretical fit

and all subspectra. (For distribution spectra, one subspectrum per block.) These can then

be stored, the report in "Rich Text Format", .rtf, and the tables are stored as data files.Names are given to all suggested files including the name of the spectrum, and the type of

fit used (here, Site).

Fitting series of similar spectra:

Note that on the Site-Para card, there are two buttons, for storing and loading models.

These functions store and retrieve the model you have generated (number of subspectra,

type, etc.). Thus if you fit a series of similar spectra, then store one of your models and

you can retrieve it for starting a fit with a new spectrum. Or you can use it to store and

retrieve several models.

WinNormos-Dist:

The Dist-Data, Dist-Block and Dist-Xls panels are for using the Distribution program.

This program is intended to treat problems including a distribution of hyperfine

parameters (and thus the name) mainly useful for metallic glasses, etc. The distribution

can be either in hyperfine magnetic field Bhf, quadrupole splitting EQ, or isomer shift.

The possible applications of this program range from very simple to very complex and

specialized. The main possibilities are:

• 1/2-3/2 Mössbauer transitions (57Fe, 119Sn, 197Au standard).

• Distributions in Bhf, EQ or ISO. Any combination is acceptable.

• Including separate sub-spectra for crystallized components usefulFor partially crystallized amorphous or nano-crystalline materials.

• Including different correlation effects between hyperfine parameters

such as hyperfine field Bhf and isomer shift , or hyperfine field

and quadrupole effect EQ .

• Different types of distribution profiles and line forms including

Gaussian and Voigt form distributions.

• Polarized source experiments with spin-texture evaluation.

The main Dist-Data panel sets the constants applying to the whole spectrum:


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The Block tab is used to define one or a series

of distribution

blocks. For each block, set number of subspectra, width, lambda, beta1 and beta2 as well

as the type of distribution and the type of the subspectra. The starting value of the

histogram (example BHF) and step value (for example DTB) are on the right side of the

panel. Note that for a histogram fit, these two cannot be set as variable, but their values

can be changed.

The last panel shows the crystalline subspectra:


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StackPlot:

The stack plot tab yields this window:

Spectra to be plotted can be selected clicking “Add” and deleted by clicking “Delete”.

The “Site”-fit or the “Dist”-fit can be selected by clicking on the words to right in the list.

The momentary plot is shown on the lower part.

By clicking on “Plot List”, the following can be generated:

If you want to make changes (scale, etc.) you can use all the Igor® graphical commands.

For instance click on the numbers of the velocity scale, and you will get the Igor®

window to change the scale of this axis. The distribution is plotted to the right in a

separate subwindow. Here as well any Igor® commands can be used to change the plot.

The plot can be saved by clicking on “Save Plot”.


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ResPlot:

The (new) card ResPlot is for plotting hyperfine results for a series of identical fits with

respect to temperature, field or pressure as given on the “Spectrum” card.

Variables can be selected by clicking on them. Shift-click selects several. The plot will

change dynamically. The x-axis is selected on the centre panel. Data can also begenerated in an Origin®-friendly format by using the button or by clicking on a column.

WinNormos2

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Transcript of WinNormos2