winnormos-for-igor®physics-astronomy-manuals.wwu.edu › winnormos3.pdf · igor®, which is a...

14.05.09 WinNormos-for-Igor® 1

Wissenschaftliche Elektronik GmbH

WinNormos-for-Igor® Version 3.00 (May 2009)

Version for Microsoft Windows or Apple MAC Runs 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. Notes on version 3:

1. There is a new graphical user interface. Overall the GUI runs more quietly. 2. An error in calculating quadrupole doublet areas was corrected. 3. Many new plotting options available.

Contents of the CD:

1. File “WinNormos3.pdf”: 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 “WinNormos3-Manual.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\Igor Extensions)

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 you replace your template and template directory with an improved one, then when you 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 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:

Save Experiment as YourExperiment.uxp

Load & Fit your spectra in Igor®.

WinNormos-for-Igor® Template

Some files in Template or XOP file replaced.

Save again YourExperiment.uxp.

Load & Fit other spectra.

Restart Igor® and YourExperiment.uxp



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 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 and background, 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 geometry effect, 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.)



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 field absent, 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 <= currentSub <= NSUB). The subspectrum type can also be chosen from a list. On the right side, there is a list of the relevant subspectrum variables, which are fixed (no check) or variable (checked). The grey positions are not used for the current subspectrum type. The starting values in the first column can be changed. Results and error bars are shown in columns 2 and 3 respectively. The fit is shown below, including the deviations between theory and experiment.



The constants are set on the left hand side (number of subspectra, which kind, and which one is the current subspectrum). The variable parameters are set on the right hand side. If there is more than one subspectrum, then parameters can be coupled by clicking on the blank field at the right hand side. 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, holding the 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 theory sum 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 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:

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 useful For 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: 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:



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”.

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 be generated in an Origin®-friendly format by using the button or by clicking on a column.

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