Visual EPR
Visual EPR
Content
Preface
7
7
11
15
20
21
23
29
29
32
36
37
Section C:
43
Algebraic operations
44
References
46
Contents
Page 1
Preface
The Visual EPR package consists of several complementary programs devoted to help
researchers and students to treat experimental spectra of Electron Paramagnetic Resonance, EPR
or Electron Spin Resonance, ESR, to simulate observed spectra and their angular dependences, to
obtain spectroscopic characteristics, and to prepare representative figures for publication.
At present, the Visual EPR package includes following programs designed to facilitate various
aspects of EPR spectra treatment:
Fields.exe to calculate energy levels and resonance magnetic fields, simulate spectra,
and compare experimental and calculated angular dependencies,
Params.exe to determine spin-Hamiltonian parameters by fitting experimental data,
View_spc.exe to view and compare measured spectra, treat them (filtering, baseline
correction, peak-picking) and collect angular dependence of resonance line positions,
intensities and widths in a file,
FAIW.exe to represent on one plot four-dimensional table of angular dependences of
resonance magnetic field, line intensities and widths (Fields-Angles-Intensities-Widths
dependencies), to compare observed and calculated dependencies, and to prepare the
picture for publication,
Cos_Eul.exe to find principal values and directions of principal axes of general
Cartesian and irreducible tensors of second rank.
These everyday programs can accelerate experimental data treatment, enhance trustworthiness of
obtained results, improve accuracy of determined characteristics, and increase efficiency of
conducted research in laboratories, which need in characterization of magnetic properties.
Because of visual representation of calculation results, they can also be used for educational
purposes.
Valentin Grachev (Valentyn Grachov)
Visual EPR
a, b, c*
x, y, z
1, 2, 3
X, Y, Z
B, Bp; p = x, y, z
B1, B1p; p = x, y, z
bkq, ckq;
k=2, 4, 6; q=-k,, k
ekq, fkq;
k=2, 4, 6; q=-k,, k
gpq
ggpq
Symmetrical gg or g2 tensor
gn
Nuclear g-factor
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Visual EPR
I, Ip; p = x, y, z
J, Jpq; p, q = x, y, z
Okq; q=0,, k
kq; q=1,, k
Qpq; p, q = x, y, z
S, Sp; p = x, y, z
Tkq; q=-k,, k
Greek symbols
, ,
, ,
Xi, Eta, Zeta - Euler angles for the description of crystal misalignment
(German definition)
Bohr magneton
Nuclear magneton
Other terms
ns1, ns2
Ms
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Visual EPR
.gep
Input file for Fields.exe and Params.exe program. It contains all required
information about paramagnetic center symmetry, spin-Hamiltonian
characteristics, instrumentation parameters etc. The file can be created using the
spreadsheet in Fields.exe.
.gfm
.grm
.grt
.jdx
Spectrum file in the format recommended by the Joint Committee on Atomic and
Molecular Physical Data Exchange (JCAMP-DX) for electron magnetic
resonance. Can be viewed and treated with the help of View_spw.exe.
.fls
Spectrum file often used in computerized EPR spectrometers. Can be viewed and
treated with the help of View_spw.exe.
.dsc, .dta
Bruker description and spectrum data files (BEST format). Input file for
View_spw.exe.
.par, .spc
Bruker parameters and spectrum data files (binary format). Input file for
View_spw.exe.
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Visual EPR
Synopsis
View_spw.exe is developed to view and treat experimental spectra. This includes filtering (using
convolution with Gram polynoms, Gaussian and Lorentzian, as well as fast Fourier
transformation and moving average), baseline correction, peak-picking, decomposition to
separate Gaussian or Lorentzian lines, and algebraic operation with the spectra. The program
allows to estimate positions, intensities and widths of constituent lines, to compare observed and
calculated spectra, and to prepare a high quality picture for publication. It has built-in possibility
for the pipeline processing of many spectra in one folder or 3D-spectra. The program allows also
to create four-dimensional tables of angular dependences of resonance magnetic field, line
In the first section we explain main possibilities offered for viewing and comparing spectra.
In the second section we consider details of spectrum treatment: first and second integrals,
derivative, filtering, decomposition, and resolution enhancement.
Third section is devoted to algebraic operation with discrete spectra.
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Visual EPR
Scale of
angles
Status bar
Graphic
panel
Comment string
Fig. A1
In the case of EPR spectra the x-axis on the Graphic panel has values of the swept
magnetic field at the bottom and y-axis has values of signal intensity on the right part
of the Graphic panel. For convenience, a Scale of effective g-factors can be also
drawn on the top of the Graphic panels (Fig. A1 and A2).The button with the glyph
on the right is now down on the Horizontal toolbar that means that single
spectrum view mode is selected.
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Visual EPR
Click on the B-button on the File buttons bar (indicated by green arrow on Fig.
A1). Choose another *.spc file with calculated or measured spectrum in the Open
dialog, for instance, 12oc_39.spc. The spectrum is loaded in the B-layer of the
graph. Load the third spectrum 12oc_59.spc into C-layer of the graph by clicking on
C-button. Now you can overlay these three layers and compare these spectra using
tools of the Horizontal toolbar or Menu/View.
Set down the button indicated by red arrow on the Horizontal toolbar on the Fig
A2. This switches the view to Overlay with original intensities. All layers are now
drawn with one scale for intensities, namely, using intensity scale of active layer (the
button of the active layer is highlighted). Since every layer has own Scale of
magnetic fields and Scale of intensities, the result Graphic panel can have different
view, if different layers are active. The view allows comparing absolute intensities of
spectral lines. This is convenient if some measurement conditions were changed (for
instance, the direction of magnetic field with respect to crystal axes in this example).
Scale of
effective
g-factors
Scale of
magnetic
fields
Fig. A2
In the view mode Overlay with normalized intensities the intensities of all
spectra are normalized in such a way that minimal and maximal values exactly fit the
Graphic panel (Fig. A3). This mode is convenient for comparison of spectra with
completely different intensities, for instance, an experimental spectrum with the
intensity scale about 104 a.u. and calculated spectrum with absolute intensity about 1.
Other examples are comparison of spectra measured at different temperatures,
microwave frequencies etc.
Viewer for spectra
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Visual EPR
Fig. A3
Cascade of spectra - all spectra are now drawn with their original intensities, but
the intensity scale of the graph is calculated as a sum of their absolute intensities, and
every next spectrum is placed below previous one without overlapping of their lines
(Fig. A4). This allows easily follow a tendency of spectra changes.
Fig. A4
Waterfall of spectra (Fig. A5) - all spectra are now drawn with their original
intensities, but one by one with an equal offset. In this case some lines can overlap.
Viewing and comparison of spectra
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Horizontal
toolbar
Vertical
toolbar
Fig. A5
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Show/Hide a grid
Copy page
Spectrum
decomposition
Overlay with
original
intensities
Create *.grt-file
Show single/all spectra
Overlay with
normalized
intensities
Cascade of
spectra
Waterfall
of spectra
Fig. A6. Speed buttons of the horizontal toolbar.
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Visual EPR
Load a spectrum for A-layer opens standard File dialog to locate and load a file
with a spectrum for A-layer. To load a file to another layer you can simply hit
corresponding File button (B, C, D, E, F, G, H or I) with the Left mouse button.
Hitting a File button with the Left mouse button you can also activate (or move to
the top) any layer with already loaded data, i.e. with the name of the file on the button.
To delete contents of a layer hit the File button with the Right mouse button. This
makes empty the Graphic Panel, and the name of the file on the File button disappears
(of course, this does not delete any data from a hard disk). You need two clicks to
reload a file to any layer: Right mouse button to make the layer free, and then Left
mouse button to open File dialog.
Open thumbnail viewer (see 5.Tumbnail viewer in this Section).
Set Single layer view mode for the active layer.
Overlay layers with original intensities, Overlay Layers with normalized
intensities, Cascade of spectra, and Waterfall of spectra redraws the Graphic
panel with data for all layers. Lines or symbols of the active layer are drawn in the last
turn (top layer). Scales for x and y axes are installed using parameters of the active
layer. Therefore, if you activate another layer with different range for x and y axes, the
picture changes: it will be drawn with other scales and with data of the active layer on
the top. Examples of the overlay view are shown on Figs. A2-A5.
Show ge, n for active spectrum displays 10 labels of effective g-factor for EPR
spectra or Larmor frequencies of several nuclei for ENDOR spectra. No action in the
case of other spectra.
Adjust picture size on the Graphic panel - change the size of the picture. It can be
used to prepare the picture on the Graphic panel for saving, printing or copying. It
allows you to fit the picture to the maximal size of the panel or to build it with the ratio
of sides 16:9, 4:3, 1:1, 3:4, and 9:16.
Change thickness of all lines can be used to prepare the picture on the Graphic
panel for saving, printing or copying. It changes thickness of all graphic lines: axes,
angular dependences etc.
Save graphic panel open a Save Picture dialog to save a high resolution picture of
calculated energy levels, spectrum or dependencies in a graphic format like png, jpg,
tif etc.
Show/Hide a grid can be used for estimations of angles and resonance fields. When
it is On the 1010 grid appears on the Graphic panel.
Copy page copies the picture on the Graphic panel to the clipboard.
Viewer for spectra
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Fig. A7
It is supposed that all spectra in the folder with the active spectrum were filtered and
their peaks were saved in corresponding *.pks files before using the dialog. By click
on Build and Save you call a procedure, which collects positions, intensities and
widths of the peaks from all *.pks files into one *.grt file.
Viewing and comparison of spectra
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Fig. A8
Fig. A9
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Scale dialog for active spectrum allows you to change scales for magnetic field
(X-axis), and intensities (Y-axis).
Fig. A10
Every axis has input strings for a Name or Title, its Units, start, end and shift values: From, To,
and Shift. The From and To values have also prompt strings with actual ranges of fields and
intensities taken from the input file. If the New box is checked, the input strings become
accessible, and you can input required start and end values. You can select also the number of
Labels on the x- and y-axes, and positions and kind labels for y-axis (green arrows on Fig. A8).
X-axis has values of magnetic field on the bottom, and effective g-factor on the top of the graph.
X-axis has two different scales: linear on magnetic field, and reciprocal (effective g-factor). The
last is convenient for comparison of EPR spectra measured with different microwave frequencies
(for instance, in X-band and Q-band).
The check box Hide near the Comment string (red arrow on Fig. A10) allows you to hide or
show the Comment string.
Estimation of line width after click on this button the mouse cursor becomes
Split cursor. Move mouse to the left wing of any line (maximal value of line
intensity in the case of derivative absorption signal) and press Left mouse button
down. A vertical line appears on the graph its x-position determines an initial point
for the line width estimation. Move mouse without the button release to the right
wing of the spectral line the second vertical line follows the mouse cursor
movement. Release the left mouse button at the minimal value of line intensity in the
case of derivative absorption signal - the x-position of this point determines final
point for the estimation. The estimated value of the line width appears on the Status
bar.
Viewer for spectra
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Estimation of line intensity move mouse to the left wing of any line (maximal
value of line intensity in the case of derivative absorption signal) and press Left
mouse button down. A curve represented Gaussian/Lorentzian line appears on the
graph x- and y-positions of this point determine left wing for the
Gaussian/Lorentzian line. Move mouse without the button release to the right wing of
the spectral line the intensity and width of the Gaussian/Lorentzian follows the
mouse cursor movement. Release the left mouse button at the minimal value of line
intensity in the case of derivative absorption signal - the x- and y-position of this
point determines final point for the estimation. The estimated value of the line
position (center of the line) and width, as well as line intensity (as an absolute value
and a per cent of the y-scale) appears on the Status bar.
The Right mouse button click on this button calls a dialog,
which allows you can change the Gaussian/Lorentzian line
representation See Figure on the right).
Fig. A11
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Fig. A12
Fig. A9
Fig. A13
Fig. A10
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Fig. A14
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Fig. A16
Close the active spectrum close data file of the active layer, and de-activate the
layer button.
4. Status bar
Status bar has three panels.
Status Bar
First panel
Second panel
Third panel
The first panel of the Status bar allows you quickly estimate resonance magnetic field and
intensity for every data point on the Graphic panel. When mouse cursor moves over the
Graphic panel, the X and Y positions of the cursor are transformed into current values of
magnetic field and intensity, as well as into effective g-factor (Geff), which is calculated using
current magnetic field and microwave frequency shown on the second panel.
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Visual EPR
The second panel of the Status bar shows also microwave frequency for active input file and
temperature if it present the description.
The third panel is used for prompts and some other information. For instance, this panel shows
the number of peaks of open data file or viewing directory.
5.
Thumbnail viewer
Often a folder with measured spectra has hundreds of spectra (sometimes even both
EPR and ENDOR spectra), and it is rather difficult to find required spectrum using
file names only. The thumbnail viewer helps you to solve the task (Fig. A17).
Depending on selected thumbnail size and screen resolution the view shows 20-100
pictures with basic information about the spectra. EPR spectra have blue line,
ENDOR spectra green line, other spectra or spectra without description file red
line.
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Fig. A18
Fig. A19
Viewer for spectra
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6.
Menu
All important actions in the FAIW.exe can be made with the help of speed buttons. Some of
them (opening dialogs, rearranging windows) you can make using traditional menu.
File
Items in the Menu/File allow opening
corresponding dialogs.
Open A, Open B, Open C, Open D opens
a standard Open dialog to find required file,
load data from the existing file and place its
contents into corresponding layer. Most
popular formats of spectral files are
supported: dta, spc, fls, asc, jdx, dat, and txt.
Close active closes current active layer
opened during the FAIW.exe execution
making it free for loading new data.
Close all closes all layers opened during the View_spw.exe execution.
Save spectrum opens a dialog, which allows you to select what should be calculated and what
is the preferable format for the saved file. The last allows you to convert the active spectrum
from original format to another required format.
Save Picture as opens a dialog to save the picture on the Graphic panel in a file of one of
graphic formats: TIFF image (*.tif) recommended by journals of American Institute of
Physics, Bit Map image (*.bmp), Portable Network Graphic (*.png), JPEG image (*.jpg), GIF
image (*.gif), or Windows HD Photo (*.hdp).
Printer setup opens standard MS Windows dialog.
Print opens a dialog to print the image on the Graphic panel. By default the names and titles of
all opened files are also printed below the picture. If necessary, you can change this option as
well as indents in the corresponding dialog - Menu/Format/Indents (see below).
Exit closes all layers and exit program. It is supposed that you have saved yourself the file(s),
which you need.
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Edit
Fig. A19
Restore last deleted points restore the points erased between cursors at the last selection.
Another way to restore erroneously erased points is to reload the input file.
Viewer for spectra
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Edit parameters in par-file opens a dialog, which allows you to modify the description file in
the pair of spectrum files *.spc and *.par. Here you can add some information, which for some
reason was missing in the file.
Fig. A20
Format
The items of the Menu/Format open dialogs allowing to modify data representation on the
Graphic panel.
The Axes (Scale dialog for active spectrum, Fig. A10), Colors (Change symbol color, Fig.
A14), and Symbols (Dialog for symbol selection, Fig. A13) were described above.
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Fig. A21
Fig. A22
Fig. A23
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Peak-Picking attributes opens a dialog below, which allows to modify information used for
peak-picking procedure described in the Section B. Treatment of spectra.
Fig. A24
Treatment
The items of the Menu/Treatment group call procedures, which operates with data of open
active spectrum. All but two lasts are identical to procedures called by the buttons of the Vertical
toolbar. They are described in the Section B. Treatment of spectra.
Algebra
The items of the Menu/Algebra group call procedures, which operates with data of two or more
open spectra. They are described in the Section C: Algebra.
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Visual EPR
Manipulations
The items of the Menu/Manipulations group call procedures, which operates with data files
without opening the spectra.
Peak-picking all applies current or default filter setting for peak-picking all spectral files in
the directory selected by Open dialog. It can be used before a creation of <*.grt>file if the
spectra were not treated earlier.
Create <*.grt> file the procedure is described in details in the Section B: Treatment of
spectra.
Separate spectra in 3D-file splits one Bruker 3D-file consisted of N-spectra into N pairs
<*.spc> and <*par> files; each of them has one spectrum only. The procedure is useful, for
instance, if different filters or baseline corrections must be applied for peak-picking of different
spectra, or if a part of the spectra should be extracted for further treatment, comparison and
publication.
Help
About shows the author, Copyright and version number of the program.
Content shows a link to the latest version of the Visual EPR documentation.
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Fig. B1
Second integral of the spectrum - the procedure calculates the second integral of the
active spectrum, estimates its minimal and maximal values (red arrow on Fig B2)
normalize it to adjust the double integrated spectrum to the Graphic panel.
Fig. B2
Treatment of spectra
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If required, you can change scales of the first and second integral in
a dialog (Fig. B3). The dialog appears if you click Right mouse
button on the integral button. Deactivate the check box
Normalize, and click on Up/Down buttons to set up desirable gain
(the scale of Y-axis) for the integrated spectrum. You can use this
dialog also to save the integrated spectrum and to carry out pipeline
treatment of all spectra in the folder of the active spectrum by
checking the box Treat all spectra.
Fig. B3
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Fig. B5. Original (blue line) and derivative (pink line) spectra. No convolution
applied.
Fig. B6. Original (blue line) and derivative (pink line) spectra. The derivative
spectrum obtained with convolution (m=2).
Treatment of spectra
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If small satellite lines are located on the left wing of strong dominant line, their peak to peak
intensity can be negative the peak of the left wing is lower than the peak of the right wing. You
have a choice to take into account such lines or to ignore them by checking or unchecking the
box Skip Int_1 < 0 (blue arrow in Fig.B7).
Real spectrum of a sample with several paramagnetic defects can have
both broad and narrow lines. View_spw.exe has a possibility to use two
filters with different widths for treatment of complicated spectra. Check
the box One/two [x] filters in the red rectangle, and track bars for the
second Filter width and Lowest Peak Int. appears in the dialog (Fig. B8).
It is supposed that the width of the first filter is larger than the width of the
second one. Three new check boxes Merge lines 2, Skip Int_2 <0, and
Skip allied peaks give you significant power and flexibility for the
visual peak picking.
There are three built-in procedures for base line correction: Smoothed
line, Fourier cut and Manual polynom.
Warning. You should switch the Show filtered selector to Baseline in
order to see it.
Smoothed line the spectrum baseline is chosen as a smooth curve. Its
position and curvature can be adjusted by the number of Smooth
repetitions (a slider of the track bar in the green rectangle).
Fourier cut - the spectrum baseline is chosen as a smooth
curve obtained by Fourier transformation of the spectrum
with very broad filter width.
The baseline can be adjusted by proper choice of the
baseline width (a slider of the track bar in the magenta
rectangle).
If Manual polynom for the baseline correction is selected
an additional dialog (Fig. B9) appears on the top of the
screen, and you can select by clicking Left mouse button
Fig. B8
the points on the active spectrum, which can be used as
reference points in order to build a polynom representing
the baseline. You can choose the polynom order (blue
arrow on Fig. B9). The number of spectral points must be
larger (preferably significantly larger) than the polynom
order. Fig. B10 shows an example of spectral point
selection (pink diamond symbols) and calculated baseline.
Fig. B9
Treatment of spectra
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Dialog for peak-picking attributes it is supposed that the treated spectra are
derivative of absorption signal with normal phase (left wing of lines has positive
intensities, right wing negative ones). If you have other kind of spectra, this dialog
allows you to change the default setting, as well as the size of symbols for peaks.
Fig. B11
Mark line center and/or line wings this button cyclically change a show for the
peaks: 0 show no peaks on the spectrum, 1- show marks corresponding to line
centers, 2- show marks corresponding to the left and right wings of lines, 3- show
three marks for every line on the left and right wings and on the line center.
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Fig. B12. An example of filtering and peak picking of EPR spectrum. Original
spectrum is represented by green line, filtered spectrum by pink line, positions of
line centers by red squares. Although the filtered spectrum is used for peak-picking,
symbols corresponding to line center and wings are drawn on the original spectrum.
Fig. B13. An example of base line correction and peak-picking. Original spectrum is
represented by blue line, baseline by pink line, positions of line centers by red
squares, positions of left and right wings by brown corners..
Treatment of spectra
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Fig. B14. An example of resolution enhancement: original (green line) and enhanced
(pink line) spectra.
Menu/Treatment/Simulate spectrum using peaks if positions and widths of a
spectrum are determined using filtering and peak picking procedure described above,
it is possible to simulate the spectrum in a supposition that all lines have the same
shape (Gaussian or Lorentzian). The dialog has only a selector for the choice of the
common line shape, and a check box for line intensities.
The simulation is not always precise, since different lines can have different shape
(Fig. B15).
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Fig. B15. An example of simulation of original spectrum (blue line) by the sum of Lorentzians
(pink line) with positions and widths determined by peak picking procedure.
Decomposition to separate lines
Decomposition of overlapped lines to separate Gaussian or Lorentzian
components the procedure uses the following dialog.
Fig. B16
Closed lines
Bevel
Switch to next or
previous ten lines
Show/save parameters
Load peaks from *.pks file
Edited values
Up/Down buttons
Number of active line
Treatment of spectra
Dialog for
multiplicity
choice
Visual EPR
Change shapes
of all lines
if checked
Change forms
of all lines
if checked
Fig. B17
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more than 10 lines is required to simulate the spectrum click the Left/Right Switch
to next/previous ten lines (Fig. B18).
There are two drop down lists and two dialogs, which allow changing shape form and
multiplicity of every line.
Right away you can select between built-n Gaussian, Lorentzian, and triangle
shapes. If the box all is checked any changes of the line shape are applied to all open
lines. You can select one of two different choices for normalization for Gaussian and
Lorentzian in the Norm dialog (Fig. B18, green rectangle on the Figs. B16-B17).
Fig. B18
The View_spw.exe grants you also a possibility to use also two user defined shapes
(for, instance, specific powder spectrum). Such lines must be loaded before using (the
buttons for Open file dialog are indicated on Figs. B16-B17). The file with the user
defined line in the form of derivative should be simple ASCII file with two columns
for X and Y data. Number of X and Y values should be less than 1024 this is
sufficient for simulation; larger number simply increases simulation time. Original
forms of the user lines are easily calculated by integration.
There are two forms for lines: original (line shape with positive phase) and
derivative. If the box all is checked any changes of the line form are applied to all
open lines.
If several lines are open two spectra are calculated: the first spectrum consists of sum
of the separate lines (Sum), and the second one is the difference between the treated
spectrum and calculated Sum spectrum (Difference). The check boxes Show sum
and Show difference (Fig. B17) help you to choose what you want to see on the
Graphic panel one of the spectra, both or nothing. The Y-position of the Difference
line is determined by the spin-edit in the Norm dialog (blue arrow on Fig.18).
Treatment of spectra
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After rough set up of lines to required position you can adjust the experimental
spectra using fitting procedures. The Decompose to separate lines procedure gives
you maximal flexibility for that. Every line has a set of check boxes, which allows
fixing or varying any characteristic of any line. For instance, if the box with label X
of a line is checked the line position is fixed, if the boxes with labels I or W are
unchecked the line intensity and width will vary when you click on the Fit selected
button in the green rectangle on Figs. B16-B17. However, you can vary positions of
all lines independently on checked/unchecked boxes if you hit the Fit X button, or
vary intensities of all lines only (Fit I) or widths of all line only (Fit W).
The number of iterations after one click on any Fit buttons is determine by the
corresponding spin-edit in the Norm dialog (green arrow on Fig.18).
Fig. 19 shows an example of decomposition to separate lines of a spectrum with
overlapping lines. To obtain such a picture check the box Keep (in order to keep the
lines after closing the Decomposition dialog) and the box Fill before closing the
Decomposition dialog. If the box Keep is unchecked all lines disappear after the
dialog is closed.
Fig. 19. Experimental spectrum (blue line) is fitted with three Gaussian lines (light
blue, green and pink lines with filling) with mean square deviation about 1%. Light
blue spectrum at the bottom of the Graphic panel is the Difference spectrum.
After fitting you can see and save the list of result characteristics of all lines by hitting
the Show/Save parameters button (Fig B16). This opens the dialog
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Fig. B20
The dialog proposes you to save the result list of characteristics (including line
shapes, forms, multiplicities, and splittings) in a file with a special format (blue arrow
on the Fig. B20). The file will have the same name as the treated spectrum, but the
new extension .gsd. Another possibility is to save all peaks only without information
about line shapes, form etc. (green arrow on the Fig B20). Such a file with peaks only
is used for the creation of angular dependencies. It also has the name of the treated
spectrum, but its extension is .pks.
Checking others boxes in the dialog you can save also spectra for sum of all
contributed lines, difference between experimental spectrum and the sum, as well as
every components in separate spectral files or all components in one multicolumn
files. These files can be viewed independently by View_spw.exe. The chosen .jdx
format for the files is convenient, since its content is a simple text, which can be
easily imported to other programs (like Origin or Excel).
If one or both these files exist you can load the saved data during a subsequent
treatment by click on the buttons Load parameters from *.gsd file or Load peaks
from *.pks file
Treatment of spectra
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In the Decompose to separate lines procedure you can also turn a line into a
multiplet. After you hit the button below Multiplicity label the following dialog
appears on the screen.
Fig. B21
Here you can choose the number of lines in the multiplet (Multiplicity), relative
intensity its components (equal intensities, combinatoric or Pascal intensities or
arbitrary intensities from the edit string), relative widths (all equal or proportional to
numbers in the edit string), and relative splittings (all equal or proportional to
numbers in the edit string).
After you close the Multiplet characteristics dialog the caption of the button below
the Multiplicity label changes reflecting the choice that you made, and additional
Edit string for the characterization of relative splitting
appears in the bevel on the right of the Multiplicity button.
The Close all button allows you to close all line except the first one and begin a new
line separation and fitting.
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Fig. C1
Here you can choose the coefficient k for partial contributions of the B, C, D,, I spectra in the
A-spectrum, possible shifts of the spectra along x- and y-axes. To change parameters for any
spectrum check the New box, and the edit strings becomes accessible.
The radio group Show what (blue arrow on Fig. C1) allows you to choose what should be
calculated and show: Average of BCD, Sum of BCD, A - Average(BCD), or
A - Sum(BCD). The calculation result can be saved in a file if you check the box Save result.
The Deviation A-B procedure simply calculates mean square deviation of all points of the
A-spectrum from the points of the B-spectrum. The calculation result appears on the Status bar.
The deviation is zero for identical spectra and can be very large for different spectra.
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The Decomposition A => BCD procedure allows you to estimate partial contribution of the
BCDI spectra to the A-spectrum. The estimation result appears on the Status bar.
For instance, if A-spectrum is complicated spectrum with contribution of Cr3+ and Fe3+, B is the
spectrum of Cr3+, and C is the spectrum of Fe3+, the procedure can be applied for estimation of
relative contribution of Cr3+ and Fe3+ in the A-spectrum.
Before starting the Create <*.grt> procedure, you should create *.pks files with
positions of peaks , intensities and widths for all files in a folder using Filter or Peak
Picking All procedures. Otherwise the <*.grt> will be empty.
The Create <*.grt> procedure opens a dialog that allows you to determine a content
of the file (Fig. D1). For instance, if you create a file with angular dependence of EPR
spectra for FAIW.exe, Fields.Exe, and Params.exe programs, you should set up or
select:
The name of the output file (the Edit string on the top of the dialog),
The kind of resonance (blue arrow on Fig. D1),
The parameter characterized the dependency (green arrow on Fig. D1). The
orientation of external magnetic field B is characterized by polar and
azimuthal angles, and , or Theta and Phi. If magnetic field rotates in zx
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plane, Theta is variable parameter, but Phi is equal to 0o. If magnetic field
rotates in zy plane, Theta is variable parameter, but Phi is equal to 90o. If
magnetic field rotates in xy plane, Phi is variable parameter, but Theta is equal
to 90o. The choice of variable angle must be made by the radio button
indicated by green arrow; the value of the second constant value must be
introduced in the Edit string indicated by yellow arrow on Fig. D1.
The location of information about the variable parameter. In the case of
angular dependencies it can be: strings with labels Theta and Phi in *.par files,
strings with goniometer angle (GAN) in *.dsc files, or the value of the angle
in the name of the file.
Fig. D1
After hitting the Build and Save button the file is created and number of string in the file appears
on the Status bar.
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References
1. A.Savitzky, M.J.E.Golay, Smoothing and differentiation of data with simplified
least squares procedures, Anal. Chem., 36, 16271639 (1964).
2. B.C.H.Turton, A novel variant of the SavitzkyGolay filter for spectroscopic
applications, Meas. Sci. Technol., 3, 858863 (1992).
3. P.A.Gorry. General Least-Squares Smoothing and Differentiation by
theConvolution (Savitzky-Golay) Method. Anal. Chem., 62, 570-573 (1990).
4. P.A.Gorry, General least-squares smoothing and differentiation of
nonuniformly spaced data by the convolution method. Anal. Chem., 63, 534
536 (1991).
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