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NAME
Artemis - interactive EXAFS data analysis
DESCRIPTION
Artemis is a program for analyzing EXAFS data using theoretical standards from Feff. Artemis includes
interfaces to Atoms and Feff as well as forms for defining parameters and applying those parameters to
the paths from the Feff calculation. Artemis uses chi(k) as it's input. It does not handle any data
processing chores, such as converting raw data to mu(E) or doing background removal. Artemis's sister
program Athena is the data processing program.
SYNOPSIS
Artemis is a graphical and interactive program written in the perl programming language, using the Tk
display engine, the Ifeffit EXAFS library, and the PGPLOT plotting library. (See below for a list of
relevant URLs.)
Artemis helps you organize all aspects of a fitting project, including running the Feff calculation,
settings parameters for the Fourier transform and fitting of the data, parameterizing the paths from the
Feff calculation, running the fit, and plotting the results. The Artemis window is divided into three
panels. The largest panel is the space where most of the work happens. Its content is model and depends
on the state of the Data and Paths List. This list is in the center, skinny panel. The other skinny
panel contains the controls the are used to specify how plots are made.
At the top of the window are the menubar and the project bar. The project bar displays the name of the
current project file. It also contains an indicator that tells you if the project has been modified
since the last time it was saved. Clicking on the modified indicator will save the project (just like
C-s or the "Save project" item in the File menu). At the bottom of the screen is the echo area, where
Artemis writes all sorts of helpful messages as you use the program.
The Data and Paths list contains a tree-like list of all of the objects that can be manipulated as you
use Artemis. When the program starts, two such items are displayed. As you run Feff calculations,
import Feff paths and other data sets, and run fits, more items are added to this list. In total, there
are five kinds of entries in this list, each of which controls a diffferent aspect of Artemis. These
five kinds of list entries are: (1) fitting parameters, (2) data, (3) fits, (4) Feff calculation, or (5)
Feff path. When you click on an item in the Data and Paths List, that item will be "selected" and
"anchored". A selected item is highlighted in orange. An anchored item is outlined with a dashed line.
Only one item can be anchored. 0, 1, or more items can be selected.
The anchored item determines the mode of the large panel. For instance, when the "Guess, Def, Set" item
is anchored, the main panel will display a page used for setting the fitting parameters. When a data
item is anchored, the main panel will display a page for setting Fourier tranform parameters, the fitting
range, and other parameters associated with the data. Many functions in Artemis depend upon the mode of
the main panel. Some features are available only in certain modes. Each of the modes is described in
its own document section. See "SECTIONS OF THE DOCUMENT".
Plots in Artemis are always made using the selected items. To plot, for example, data, a fit, and
several individual paths, it is necessary to select each of those items. Many other functions in Artemis
also work on the set of selected items.
Anchoring and setting paths is usually done by using the mouse in the Data and Paths List, although there
are several other ways of changing the anchor and selection using the mouse or the keyboard. Here is a
list of mouse events useful in the Data and Paths List:
Left mouse button
Clicking the left mouse button will clear all selections then select and anchor the item clicked.
The main panel will display the page apporpriate to the anchored item.
Center mouse button
Clicking the center mouse button will anchor the item clicked without changing the selection. The
main panel will display the page apporpriate to the anchored item.
Right mouse button
Clicking the right mouse button will anchor the item clicked without changing the selection. It will
also post a menu of functions appopriate to the item clicked. These menus are the same as the menus
in the menubar at the top of the window. The main panel will display the page appopriate to the
anchored item.
Control key + left mouse button
Clicking the left mouse button while holding down the control key will add the item clicked to the
group of selected items. The anchor is not changed.
Shift key + left mouse button
Clicking the left mouse button while holding down the shift key will select all items between the
anchor and the item clicked, inclusively. The anchor is not changed.
Left mouse button + mouse drag
Clicking the left mouse button then dragging the mouse while holding down the button will select all
items that you drag the cursor over. The item initially clicked will be anchored and the main panel
will display the page appopriate to the anchored item.
Control-k, Control-j
Hitting the k or j keys while holdong the control key will move the anchor to the previous or next
item in the list without changing the selection. The main panel will display the page appopriate to
the anchored item. These two key sequences, behave differently when the Guess, Def, Set item is
anchored. See The Guess, Def, Set page for details
Control-l
Hitting the l key while holding down the control key will put focus on the Data and Path List. This
allows you to navigate the list using the arrow keys.
The color and font of the text in the Data and Paths List indicates the status of each item. Any item
written in black, upright text is an item that can be plotted. When a data set or Feff path is excluded
from the fit, it will be written in brown text. The Guess, Def, Set item and the Feff calculation items
are written in italic text. The italic text indicates items that cannot be plotted. Although these non-
plotable items can be selected, they will be ignored when a plot is made.
ARTEMIS: The Data Page
ARTEMIS - The data page
The data page is displayed in Artemis's main panel when a data item is anchored in the Data and Paths
List. See the main document section for an explanation of anchoring and selecting items in the Data and
Paths List.
The data page is divided into five sections. At the top is a box containing the title lines associated
with these data. These are read from the input data file, but can be edited at any time by the user.
When the data are written to output files, the contents of this box are written as headers. Below the
titles box is the name of the data file that was imported. Below that are four boxes containing groups
of related controls.
Data toggles
This box contains three toggles that control certain aspects of the fit. The first two are only relevant
in a multiple data set fit. When setting up a project containing a multiple data set fit, it is
sometimes useful to exclude an entire data set from the fit without deleting it from the project. This
can be done with the first toggle. When a data set is excluded, it and all items beneath it are shown in
brown text in the Data and Paths List to indicate that they have been excluded from the fit.
After the fit is complete, Artemis wants to show off her handiwork and display a plot of the data and the
just-finished fit. In the case of a multiple data set fit, you might have a preference about which data
set gets plotting. Click this toggle on for your prefered data set.
The third toggle tells Artemis to do a corefinement of the background spline when it performs the fit.
This corefinement is, effectively, the same operation that was performed by Athena to remove the
background from the data. The "rmin" parameter serves the same purpose as Athena's "rbkg" parameter.
When the fit is performed with the background corefinement, a spline is used to fit the Fourier
components of the data below "rmin" and the Feff paths are used to fit the Fourier components between
"rmin" and "rmax". The number of parameters used to determine the spline is the number of independent
points in that portion of the data: "2*delta_k*delta_R/pi", where "delta_k" is the range of the Fourier
transform and "delta_R" is the range between 0 and "rmin". The advantage of doing the background
corefinement, other than the possibility of making the fit look nicer at low R, is that correlations
between the background parameters and the fitting parameters can be measured.
Fourier transform and fitting parameters
This box contains the controls used to set the ranges of the forward Fourier transform and of the fit.
The fit range is also used as the backward Fourier transform range when a plot is q space is made. See
"Pluck buttons" for a discussion of the little quare buttons marked with a blue x.
Other controls are used to set the functional forms of the Fourier transform window used in k and R. The
widths of the sills of those functions are set usng the entry boxes labeled "dk" and "dr".
k-weight parameters
The controls in this box are used to set the values of k-weight to be used in the fits. There are togles
for turning on k-weight of 1, 2, or 3. There is also a toggle for specifying an arbitrary value of
k-weight.
These are the k-weight values used in the fit but not the k-weight used to plot the data. These two
purposes of k-weight are handled independently by Artemis. See Plotting in Artemis for a discussion of
the plotting k-weight controls.
People sometimes get confused by the concept of multipl k-weights for fitting. The prupose of choosing a
low or high value for k-weight is to attempt to emphasize either the low- or high-k end of the data.
Because different regions of the data are sensitive to different kinds of parameters, one might choose a
low or high value to increase the precision of measurement of certain parameters. Doing multiple
k-weight fits is a sort of compromise -- a way of emphasizing both ends of the data in the fit.
The fit is determined by minimizing a quantity called chi-square. Chi-square is evaluated by summing the
squares of the difference between the data and the theory. Since the FT is complex, there is a real part
and an imaginary part. So chi-square is proporitional to:
/ \
sum < Re[ data(R) - th(R) ]^2 + Im[ data(R) - th(R)]^2 >
R \ /
In a multiple k-weight fit, there are simply more terms in the sum. Let's take a kw=1&3 fit as an
example. This summation is made for the kw=1 data and theory. And the summation is made for the kw=3
data and theory. The summations are added together and the full sum is used to evaluate chi-square.
At the end of the day, there is only one set of guess parameters that have been optimized by the fit.
These guess parameters along with the set parameters are used to evaluate the def parameters and the path
parameters. The path parameters are used to evaluate the exafs equation for each path. The exafs
equations for the paths are summed up to make the best-fit theoretical chi(k). You have a data chi(k)
and a best-fit chi(k). Those can then be plotted however you like -- even using a k-weight that was not
used in determining the fit.
Other parameters
The last box contains several controls that did not fit into theother boxes. There is a menu for
selecting the fitting space. You can choose to fit the data in any of k, R, or q space. The default is
to fit in R.
Epsilon is the uncertainty used to evaluate chi-square. Normally it is fine to let Artemis use the
default value (which is determined from the RMS value of the data between 15 and 25 angstroms in
R-space). In some situations, you may find it useful to explicitly set a value for epsilon.
After the fit, Artemis writes a log file documenting the fit. Among the information in that log file are
the correlations between all the fitting parameters. You can set the level below which Artemis will
exclude a correlation from this report.
Finally, there is a menu for selecting the path to use for phase corrected plots. This menu contains the
first five paths from each Feff calculation used with the data set. When a path is selected for phase
corrected plots, the full phase shift of that path -- both the central atom and scattering atom portions
-- will be subtracted from anything that is Fourier transformed before it is plotted. If a path is
selected for phase correction and you make a plot of, say, the data, the fit, and several paths, the
selected phase shift will be subtracted from each item before it is plotted. Phase correction is for
plotting only. Fits are always done on non-phase-corrected data.
Pluck buttons
Several of the controls on this page a have a small button with a blue x next to them. These are called
pluck buttons and are used for grabbing values from the plot window. When you click on one of these
buttons, a prompt will be written to echo area asking you to click on a pointin the plot. When you do
so, the value that you clicked on will be inserted into the entry box adjacent to the pluck button.
Artemis is careful not to let you pluck a k-value from a plot in R, or vice versa.
Context menus
As you pass the mouse over labels on the data page, the text under the mouse will change color. This
color change is an indication that mouse clicks will do something. A left mouse click on one of these
labels will cause a brief description of that parameter to be displayed in the echo area. Many of these
descriptions also suggest reasonable values for the parameter.
Clicking the right mouse button on one of the labels will post a context menu of useful function. One
such function is restore that parameter to its default value. If you have a muliple data set fit, the
other menu options allow you to constrain the parameter between data sets.
The labels at the top of the boxes are all sensitive to the left mouse button. The labels atop the
Fourier transform and fit range box and the k-weights box are also sensitive to the right mouse click.
ARTEMIS: Guess, Set, Def Parameters
ARTEMIS - Guess, set, def parameters
This page is used to define the parameters of the fitting model. In Artemis there are six kinds of
parameters:
Guess
Guess parameters are the ones that are optimize during the course of the fit to best-fit the theory
to the data.
Def Def parameters are typically expressed as math expressions which may be functionally dependant upon
other parameters. These math expressions are updated throughout the course of the fit. As the guess
parameters are update, so are the def parameters.
Set Set parameters are evaluated at the beginning of the fit and not updated throughout the fit. This is
the main difference between def and set parameters. Set parameters can be numbers or math
expressions.
Restraint
Restraints are math expressions which, like def parameters, are updated throughout the course of the
fit, but which take on a special role in the fit. A restraint is evaluated and added in quadrature
to the evaluation of the chi-square parameter. A restraint, therefore, can be used to incorporate a
a bias in the fitting result towards a piece of prior knowledge about the physical system. See the
Ifeffit for a complete discussion of restraints.
Skip
Skip parameters are maintained in the project but are not used in any capacity in the fit. The point
of a skip parameter is to maintain but not use a complicated parameter with a complicated math
expression.
After
An after is similar to a def parameter in that it may be a math expression dependent upon other
parameters. An after is not, however, a part of the fitting model. Instead it is a parameter that
will be evaluated upon completion of the fit using the best fit values. The list of after parameters
will be reported in the log file. Using an after parameter anywhere in your fitting model will
result in Artemis reporting an error in the model. Afters can depend upon other afters, but you
should take care in with the order that the afters appear in the list. The after parameters will be
evaulated only once after the fit, thus circular or out-of-order dependencies will not be resolved.
The Guess, Def, Set page is divided into two sections. At the top is a listbox containing the list of
all defined parameters. At the bottom is the edit area which contains the controls used to establish the
parameters.
The parameter listbox
This area contains a four-column list of all the parameters defined in a project. The left-most column
counts the parameters. The second column contains a tag identifying the type of the parameter. The
third column contains the parameter name. The right-most column contains the parameter's math
expression.
Parameters are coded by color and by the tag in the second column. Guess parameters are written in
purple text and have the "g:" tag. Def parameters are written in green text and have the "d:" tag. Set
parameters are written in black text and have the "s:" tag. Restraints are written in pink text and have
the "r:" tag. Skip parameters are written in grey text and have no tag. After parameters are written in
blue-grey text and have the "a:" tag.
There are a large number of mouse clicks and key sequences that serve a purpose in the listbox:
1. A left mouse click selects a parameter and displays it in the edit area.
2. A double click of the left mouse button selects a parameter, displays it in the edit area, and
prompts you for the parameter annotation. See "Parameter annotations".
3. A right mouse click selects a parameter, displays it in the edit area, and posts a contextual menu
about that parameter. The menu has several items in it. The "Move" submenu is sued to reposition
the current parameter in the list. The "Make" submenu serves to change the type of the parameter.
The "Copy" item will replicate the anchored parameter, appending a few characters to the end of its
name. The "Build restraint" item is discussed below. The "Annotate" menu item prompts for the
parameter annotation. The "Find" menu item will search through all parameter and path parameter math
expressions and show you how that parameter is used in the project. The "Grab" menu item is only
enabled for guess parameters and will insert the best-fit value from a fit as the value for that
parameter. Finally the "Discard" menu item will remove that parameter from the list after prompting
for confirmation.
4. Control-d will define the parameter in the edit area.
5. Control-g will grab the current parameters best-fit value from a fit.
6. Control-e will show the editing area if it is hidden.
7. Control-k and control-j will move the selection up and down in the list. Note that these two key-
sequences serve to move the anchor up and down in the Data and Path List when the Guess, Def, Set
page is not showing.
8. Control-n will clear the selection and focus on the parameter name entry box so that you can create a
new parameter.
9. Control-y will prompt you to then hit any of the g, d, s, r, k or e keys to set the type of the
parameter. This is only way of setting the parameter type that does not involve the mouse.
Extended selection
Multiple items in the list of parameters can be selected using the control-click, shift-click, and click-
drag sequences described for the Data and Paths List and for the log viewer. Only the anchored list item
(i.e. the one surreounded by a dashed line and displayed in the edit area) can have its name and math
expression edited.
The advantage of extended selection is that certain of the context menu options discussed above in item
#3 can operate on many parameters at once. By doing extended selection then clicking the right mouse
button somewhere in the selected region, the context menu will be posted with options for the group of
selected parameters. Currently, groups of parameters can have their types set and can be discarded in
this manner.
If you right-click outside the selected region, the extended selection will be cleared and the parameter
clicked on will be anchored and selected.
The edit area
There are three rows of controls in the edit area. The top row has two entry boxes. The smaller one on
the left is for entering the name of the parameter. The larger one on the right is for entering the
parameter's math expression.
Below the entry boxes are a set of five radiobuttons for selecting the type of parameter being edited.
At the bottom of the edit area are five buttons for acting upon the parameter being edited. The "Undo
edit" button clears the entry boxes and discards whatever changes were just made. The "New" button is
used to define a brand new parameter. It clears the entry boxes, unselects parameters in the listbox,
and gives focus to entry box for entering the parameter name. The "Grab" button becomes enabled after a
fit is run. It inserts the best-fit value for a guess parameter. The "Discard" button deletes a
parameter from the list. A dialog pops up confirming deletion. Finally, the "Hide" button removes the
edit area from view to allow more parameters to be visible in the listbox. When the edit area is hidden,
it is replaced by a button for restoring the edit area.
Here are the details of the behavior of these controls:
1. Hitting return in the parameter name entry box defines the parameter, inserts or updates it in the
listbox, and puts focus on the math expression entry box. If a math expression has not yet been
defined, the parameter will be defined as 0.
2. Hitting return in the math expression entry box defines the parameter, inserts or updates it in the
listbox, and leaves focus on the math expression entry box.
3. Clicking on any of the radiobuttons defines the the parameter, inserts or updates it in the listbox,
and leaves the focus unchanged.
Parameter annotations
An annotation is a short text string that is associated with the parameter. This string is written to
the echo area whenever the parameter is selected in the listbox on the Guess, Def, Set page. The purpose
of he annotation is to write a little hint about the role played by the parameter in the fiting model.
If a guess parameters has no annotation when a fit is run, its annotation will be generated
automatically. The automatic annotation for a guess parameter is its best fit value +/- its error bar.
The automatic annotation for a def, after, or restrain parameter is its evaluated value after the fit.
Building restraints
One of the items in the context menu displayed when right-clicking on a parameter is for building
restraints based on guess or def parameters. This tool provides a dialog for constructing one particular
type of restraint -- the type that coerces a parameter to stay within a boundries for its value. The
dialog prompts for a minimum and maximum value and for a term called the "amplifier". The math
expression constructed is this one:
restrain param_res = penalty(param, min, max) * amp
The penalty function evaluates to 0 when "param" is between "min" and "max", to "abs(min-param)" when
"param" is less than "min", and to "abs(param-max)" when "param" is greater than "max". This is added in
quadrature to reduced chi-square as the fit is evaluated.
The amplifier term determines the magnitude of the penalty. A large value for "amp" will force the
fitted value of "param" not to stray too far outside its bounds. A small value will allow the fit more
freedom to let "param" deviate from your initial guess.
See the Ifeffit FAQ, question 8.1 for more discussion of restraints, including discussion of other ways
to set restraints that do not involve the "penalty()" function.
A cautionary note: restraints are not always appropriate. As an example, if a fit is returning a
negative value for sigma^2, it may not be appropriate to apply a stiff restraint as a way of forcing that
sigma^2 to be a value that you expect. Often, a negative sigma^2 is indicative of some other problem in
the fitting model such as excessive structural disorder, a coordination number that is forced to be too
small, the incorrect atomic species for a backscatterer, or some such. Using a restraint on sigma^2 in a
case like this would not fix the problem. Quite the opposite, it might foster a false sense of
accomplishment by "fixing" the sigma^2 "problem" without actually addressing the actual problem in the
fitting model.
Highlighting
There is an option in the GDS menu for highlighting parameters. This prompts you for a text string. Any
parameter names or math expressions that match that string will be marked with a green background. This
is particularly useful for large parameter lists. The text string is interpreted as a perl regular
expression and so any valid perl metacharacters can be used. (This includes regular expressions using
"(?{ code })" and other similar constructions, a practice the author of Artemis does not recommend, but
does not prevent.)
Importing and exporting text files
For large, complex fitting models, it may be convenient to edit the parameter list with a text editor or
even to write a program which generates the parameters and writes them to a text file. In that case, it
is convenient to be able to import and export a textual respresentation of the parameter list. These
files are of a simple format. Any line like these:
guess a 5
set b 6
def c a+b
can imported to and exported from the Guess, Def, Set page via the GDS menu. In an imported file, any
line beginning with any of "guess", "def", "set", "restrain", "after", or "skip" will be imported as a
parameter. The second word on the line will be taken as the parameter name and the remaining words on
the line will be concatinated to form the math expression. On export lines will follow this format:
type name = math_expression
Very little error checking is performed upon import to verify that the parameter is defined sensibly, so
use this feature with caution.
ARTEMIS: ATOMS, The Crystallographic Front End to FEFF
ARTEMIS - ATOMS, The Crystallographic Front End to FEFF
The purpose of Atoms is to generate a "feff.inp" file from crystallographic data. The hard part of
making a "feff.inp" file is creating the long list of atomic coordinates. Atoms thus makes the hard part
of running Feff easy, at least for crystalline matrials.
This page can be used to create input data for Atoms from scratch. It will also be used to display
crystallography data imported from an "atoms.inp" file or a CIF file. To import an "atoms.inp" file or
CIF file, use the normal file import dialog.
The title box
At the top is a text box for entering title lines identifying the crystallographic data. These lines
will be written to the "feff.inp" file and to the top of the Feff interpretation page. This is a good
place to cite the literature reference or to provide other important information about the crystal.
Crystal parameters
To the left side of the page are entry boxes for entering space group, lattice constants, and lattice
angles of the crystal. A space group must always be provided. Atoms is very flexible about how the
space group symbol is entered. You can use the Hermann-Maguin or Scheonflies symbols or the index of the
space group from the International Tables. The algorithm that interprets the symbol is insensitive to
white space and capitalization -- "P m -3 m" and "PM-3M" are interpreted the same. For complete details
about how the symbols are interpreted, see the Atoms docuemntation on Bruce's web site.
Lattice constants are entered in units of Angstroms, angles are entered as decimal numbers in degrees
(and not in arc minutes -- i.e. 89 and a half degrees is entered as 89.5 rather than 89'30"). Many space
groups have symmetries that make some lattice angles and constants the same. In those situations, it is
only necesary to fill in the essential values. For instance, a cubic space group only requires a value
for the "a" constant. Atoms will know to set the other lattice constants the same and to set the angles
to 90 degrees. For lower symmetry groups, you must provide all the necessary information.
Below the lattice constants are entry boxes for "Rmax" and the shift vector and a menu for selecting the
absorption edge of the Feff calculation. "Rmax" is the radial extent of the cluster that will be written
to the "feff.inp" file. Some space groups are given in the International Tables with two different
origins -- i.e. the origin is placed at sites with two different point symmetries. The fractional
coordinates of the sites are different for the two different settings of the crystal. In those cases,
Atoms requires that you use a particular one of the two choices. If your input data has used the other
origin choice, it should be fairly obvious. In that case, coordination numbers and distances to the
coordination shells will usually be obviously wrong. When you use one of the space groups for which two
origin choices exist, Artemis will issue a warning. If you suspect that the wrong origin choice has been
used, insert the values for the shift vector that were reported in the warning message.
On occassion, crystals are reported in the literature using origins other than the standard one used in
the International Tables. A famous example is germanium oxide. Here is the crystal data for GeO2:
title GeO2 (hexagonal)
space p 32 2 1
a=4.98502 c=5.64800
rmax=6.0 core=Ge
shift 0 0 0.66667
atoms
Ge 0.4513 0.0 0.0
O 0.3969 0.3021 0.0909
For some reason, the crystallography reference for this material uses an origin that is shifted by 2/3 in
the z direction relative to the origin used in the International Tables. To get Atoms to compute this
structure correctly, the shift vector given above must be used.
The atoms list
To the right side of the page is the list of unique crystallographic sites. As new sites are created,
they are inserted into the list. The sites are not edited directly, instead the editing area at the
bottom of the screen is used and the list of all sites is displayed here. This works much the same as
the Guess, Def, Set page.
To edit a site, left-click on its entry in the list. It's element symbols, coordinates, and site tag
will be displayed in the edit area. A right click on a site in the list will post a context menu with
several functions that can be perfromed on that site. You can re-order the list using the "Move" menu
item. A site can be copied and the copy added to the list using the "Copy" menu item. The "Discard"
menu item completely removes the site from the list. The list supports extended selection. When many
sites are selected (i.e. highlighted in yellow), the "Discard" menu item will work on all the selected
sites.
Sites can also be reordered using the keyboard. "Alt-k" and "Alt-j" can be used to move the selected
site up or down in the list.
The edit area
At the bottom of the page is the collection of widgets used to actually create and edit unique
crystallographic sites. The element box is used to insert the two-letter element symbol for the site.
The site will not be created if this is not a valid symbol. The tag can be any 10-letter string used to
identify the site. The tag is used to differentiate sites that contain the same element.
The boxes for the "x", "y", and "z" coordinates can be filled with floating point numbers or simple
fractions. That is, 0.5 and "1/2" are both acceptable. These coordinates are fractional positions in
the unit cell and are not Cartesian coordinates.
Once you have created all sites in your crystal, click the "Run Atoms" button. This will process the
crystallographic data, create the "feff.inp" file, display the "feff.inp" page.
Atoms template files
The "feff.inp" data that is generated when the "Run Atoms" button is pressed is determined by the
contents of a special template file. Artemis is distributed with a number of template files serving
different purposes. The structure of the "feff.inp" data is set by the value of the "atoms->template"
preference. The default value is "feff", which tells Artemis to use the template file suitable for
running Feff6.
If you want to run some other version of Feff, you should set the "atoms->template" preference variable
to the appropriate value. Templates are provided with Artemis for writing Feff7 and Feff8 input files.
Feff8 input files can be written which are suitable for XANES or non-self-consistent EXAFS calculations.
Sometimes, it is useful to modify template files for writing out specialized "feff.inp" data. If these
modified template files are placed in "~/.horae/atp/" (unix) or "C:Program Files\Ifeffit\horae\atp"
(windows), Artemis will be able to find them.
Final note
A full explanation of how the Atoms algorithms works is beyond the scope of this document page.
ARTEMIS: The FEFF Input File
ARTEMIS - The FEFF input file
This page displays the Feff input data, which includes some control parameters and a long list of atomic
coordinates. This page is no more sophisticated than a text box which serves as a primitive editor and a
button at the bottom for running Feff. Explaining Feff is beyond the scope of this document.
When feff is finished, you will presented with a dialog asking how many paths to import. The choices are
none, the first path, the first 10 paths, and all paths. The number in the third option is configurable
in the preferences dialog. Should you ever need to rerun Feff after starting a project, "none" is
usually the right answer. The other options may result in one or more paths being defined twice in the
project -- a confusing situation.
If Feff fails to run to completion, Artemis will try to recognize the problem and post a suggestion for
how to solve the problem. If Artemis does not recognize your problem, explain it Bruce so he can add
that problem to Artemis's database of troubleshooting solutions.
ARTEMIS: Interpretation of the FEFF Calculation
ARTEMIS - Interpretation of the FEFF calculation
This page provides a concise overview of the Feff calculation. At the top of the page is a summary of
some of the statistics of the calculation. Below that is a chart showing the details of each path from
the calculation. For each path, the degeneracy, the half path length and the amplitude factor are shown.
The last column shows a tokenized summary of the scattering path -- this allows you to see at a glance
which atoms were involved in the path.
The information and context menus available on this page allow you organize, understand, and manipulate
the paths in this Feff calculation. Pretty much all functions involving the paths except writing math
expressions for the path parameters are available on this page.
The interpretation chart
The colors and fonts used in the chart convey information:
Bold, black font
These are paths that have been imported into the project and are included in the fit.
Bold, brown font
These are paths that have been imported into the project but are excluded in the fit.
Normal, black text
These are paths that have not been imported into the project but which are available to be imported.
Normal, grey text
These are paths that are unavailable for importation into the project. These can be made available
by re-running the Feff calculation. After the Feff run, it is best to choose the "import no paths"
to avoid reimporting paths already in the project. After that, these paths will be written in
normal, black text, indicating that they are available for import.
Light brown background
The light brown background is used to indicate single scattering paths.
Light blue background
The light blue background is used to indicate collinear or nearly collinear multiple scattering
paths.
Context menus
There are interesting and useful context menus on every part of this page. These menus are available by
right clicking.
Right clicking anywhere in the text box at the top of the page will pop up a menu with options for
viewing files from the Feff calculation.
Right clicking in the interpretation chart will post a menu of options relevant to the path on the line
on which you clicked. Each of the four kinds of paths given by the four fonts described above has its
own menu.
For paths that are imported in the fit, the menu offers options for plotting the path, displaying that
path's page, including or excluding the path in the fit, selecting or deselecting that path for plotting,
making that path the default for evaluation of def parameters after a fit, displaying the text of the
file containing the path, or discarding the path. The choices for including or excluding and for
selecting or deselecting depend on the state of that path in the Data and Paths List. Also some options
might be greyed out depending on the state of that path.
For paths that have not been imported into the project, the context menu allows you to import the path
with the option of displaying its page or leaving the display on the Feff interpretation. For paths that
are unavailable for import, a message saying so is posted when one of those lines is right-clicked.
The interpretation chart allows for extended selection of lines in the chart. You can select additional
paths by holding the control key while clicking with the left mouse button. Holding the shift key while
left clicking selects all line between the anchor (the one outlined with a dashed line) and the one you
click on. You can also click and drag to select all the lines you drag over. When more than one line is
selected, the content of the context menu change to reflect functionality that makes sense for many
paths. Extended selection in the interpretation chart is therefore a good way of including/excluding,
selecting/deselecting, or plotting a large number of paths.
The context menu that pops up when many lines are selected may be a little surprising. Its contents
depend upon the state of the anchored line, which in this case is the one that you right-click on to post
the menu. The options in the context menu will be suitable to the state of the anchored selection
regardless of the states of the other selected lines. If you choose a menu item that does not make sense
for some of the selected lines, those lines will be ignored.
Here is a concrete example. Suppose that you select a number of lines, some of which are included in the
fit and some of which have not been imported in the fit. If you then right click on one of the included
paths, you will get options appropriate to included paths. If you then ask to plot the selected paths
along with the data, the included paths will be plotted and the imported paths will be ignored. If,
instead, you click on one of the paths that has not been imported yet, the context menu will give you the
option of importing the selected paths. In that case, the paths that have already been imported will be
ignored.
Trouble shooting
On occassion you might see that lines in the Feff interpretation do not properly report on the contents
of the path. When this happens, site tags are replaced by this string: "<?>". There are a couple common
reasons you might see the "<?>" tags:
1. You have done some advanced voodoo with Feff, editing the "files.dat" or "paths.dat" files then
rerunning the last module to produce specialized output.
2. You have discovered a bug in the algorithm Artemis uses to harvest information from the Feff
calculation. IN that case, you should send the "feff.inp" file or the Artemis project file to Bruce
so he can fix the problem.
Note that the appearance of the "<?>" tags is probably not an indication that Feff has misbehaved. The
Feff calculation has to run to completion and generate its normal output before this problem can manifest
itself. The Feff calculation is almost certainly usable to analyze the data. The Feff interpretation
page is Artemis's attempt to organize information about the Feff calculation in some user-friendly
format. That this organizational effort failed is not necessarily an indication that Feff failed.
ARTEMIS: The Path Page
ARTEMIS - The path page
The path page is displayed whenever a Feff path is selected from the Data and Paths List. This page is
used to establish the math expressions of the path parameters for this path.
At the top of the page is a line identifying which Feff calculation this path is from. Below that are
three toggles. One is used to include of inlcude or exclude the path from use in the fit. There are
many other ways in Artemis to include and exclude paths other than to use this toggle. See The Feff
interpretation page and "artemis_menubar" for more discussion of this. Also Control-t is the same as
clicking this toggle.
The second toggle is used to specify paths that you would like plotted after a fit (or sum of paths) is
finished. By default, the data and the fit (or sum) is plotted after the fit (or sum) and no paths are
plotted. Any paths selected for plotting will be added to the plot after the fit (or sum) is finished.
The third toggle is used to set which path is the default path for evaluation of Def parameters after the
fit. It is possible to write math expressions which evaluate differently for different paths. An
example might be a math expression using the "reff" parameter. For any such Def parameters, it is
necessary to tell Artemis which path should be used for the reporting of those parameters in the log
file. The default is to use the first path listed in the Data and Paths List.
Below that is a box which summarizes the path. This gives some statistics about the path as well as
displaying a color-coded "map" of the scattering path. The central atom is always displayed in red text.
Other atoms are in black text. The grey text shows the length and scattering angle of each leg of the
path. In the case of a high-order multiple scattering path which has legs which have a non-zero Eulerian
eta angle between them, the eta angle will be displayed as well. If that last sentence was gibberish, it
suffices to know that paths of that sort are almost never observable in real EXAFS data.
At the bottom of the page is the list of path parameters. This is the most important section of the page
because it is here that the details of the fitting model are realized. There is an entry box for each of
the various types of path parameters. The math expression approporiate for each parameter should be
entered in the entry box.
When a Feff calculation is imported into Artemis, a set of automatic parameters are generated, entered
into the list on the Guess, Def, Set page, and entered into the path parameetr boxes for each path
imported. The default behavior of Artemis is to generate a set of parameters appropriate for a simple,
single scattering, first shell fit. While it might be OK to immediately click the big green button, most
fitting models will require substantial editing.
The right mouse button serves many important purposes on the path page. Clicking the right mouse button
anywhere in one of the entry boxes will highlight the word underneath the cursor and post a menu. The
entries in the menu are for for defining the word as a parameter on the Guess, Def, Set page. For each
parameter type there is the option of jumping or staying. In either case, the parameter is defined and
added to the list on the GDS page. For jumping, the GDS page is then displayed. For staying, the
current path page remains displayed.
Right clicking on one of the path parameter labels will post a menu of functions related to defining path
parameter math expressions. The "Edit" option will pop up a dialog used for entering a math expression
and then optionally exporting its value to other paths. The "Clear" option doies just that.
The various "Export" options are ways of constraining path parameters to be the same for other paths.
The "Grab" options make the current path parameter the same as the path parameter in the previous or
following path.
The "sigma^2" label has some additional options. These insert the syntactically correct text appropriate
to using either the Correlated Debye or single frequency Einstein models for the sigma^2 of the path.
To enable the display of spaces for the "dphase", "k_array", "amp_array", or "phase_array" path
parameters, you must click on the "Extended path parameters" button in the Paths menu.
ARTEMIS: The Log Viewer
ARTEMIS - The log viewer
When a fit is anchored in the Data and Paths list, the log file viewer is displayed in the main panel.
The purpose of this page is to examine log files from the most recent fit or from previous fits. These
log files can be read individually or reports can be generated based on their contents.
When this page is displayed, each fit is entered into the list box on the left side of the page. Double
clicking the left mouse button on a fit in the listbox will display that fit's raw log file. Right
clicking on a fit will post a menu with choices for displaying that fit's log file in raw, quick, or
columnar form or for performing some other tasks related to that fit.
Much more interesting than displaying the log files, though, is to generate reports on the log files.
Near the top of the page is a combo box for selecting among the parameters on the Guess, Def, Set page.
Choosing one, then clicking on the "Write report" button will find extract that parameters best-fit value
and uncertainty from each log file. This feature allows you to track the evolution of individual fitting
parameters as you develop your fitting model.
The combo box containing the names of the fitting parameters is filled using the contents of the Guess,
Def, Set page. Sometimes it may be useful instead to fill the combo box with the parameter names
extracted from a log file. This would be useful, for instance, for examining a parameter that is was
used at one point, but is no longer on the GDS page or has been made into a skip parameter (and so is not
included in the combo box by default). To do this, right click on a fit and select the "Get parameter
list" item.
Some modifications can be made to the reports generated by the log viewer. Clicking on the "Compute the
average value" button tells Artemis to compute the arithmetic mean and standard deviation of the
parameter from the values extracted from the various log files. These will be displayed in the header of
the report.
Clicking on the "Fit Einstein temperature" button will tell Artemis to fit sigma^2 data to a model
consisting of a single frequency oscillator plus a constant offset. The report header will then contain
the best fit values and uncertainties for the characteristic temperature and constant offset. This
calculation will only happen is the figures of merit for the selected log files are temperatures and the
best fit values for the chosen parameter are reasonable sigma^2 values. This function makes a series of
checks on the figures of merit and best fit values to determine if they seem to be data appropriate for
this calculation. These heuristics can be tuned by setting parameters in the logview section of the
preferences dialog.
The final item in the context menu that is displayed when right clicking on an item in the log files list
is an option to restore that fitting model. Among the information that is saved every time a fit is made
is a complete description of the fitting model, including which data file is being fit, the complete list
of Feff path used, and all fitting, data, and path parameters. This feature allow you to revert Artemis
to the state it was in when a past fit was made. When you do this reversion, Artemis will clear out the
contents of the Data and Paths List and then recreate the project in the form of the selected fitting
model. This is more that just a change of parameter values. Artemis keeps track of all data and Feff
paths used throughout the course of the project and can restore even fits that are significantly
different from the current fit.
Importing Athena project data || Output files || Artemis project files ||
ARTEMIS: Plotting Data
ARTEMIS - Plotting data
Plots in Artemis are made using the selected items in the Data and Paths List, which are the ones
highlighted in orange. See the main document section for an explanation of how to selected items for
plotting.
At the top of the plot panel are three big, red buttons. One is for making a plot in k-space, one is for
R-space, and the third is for q-space (i.e. back-transformed k-space).
k-Weighting
Below the plot buttons are a set of radiobuttons for setting the k-weight to use in the plots. The
k-weight chosen will be used to weight a plot in k-space or to weight data for Fourier transforming. The
same k-weight is used for each selected item. The button marked "kw" needs some explanation. When this
button is chosen, the k-weight to use in the plot will be determined from the data being plotted. If the
arbitrary k-weight enabled for the data set,the value for the arbitrary k-weight will be used, other wise
the smallest k-weight value enabled will be used. There are two reason to use the "kw" button. One is
to plot using your arbitrary weight. The other is to make a plot of two or more data sets using a
different k-weight for each data set.
Note that these k-weight controls are unrelated to the controls which set the k-weight used in the fit.
K-weighting for fitting and plotting are controlled independently.
Selecting What Gets Plotted
Below the k-weight radiobuttons are menus for choosing which part of the complex functions chi(R) or
chi(q) to plot. Plots involving multiple parts of the complex functions (e.g. real+envelope) are not
currently possible.
Below these menus are three checkbuttons used for plotting the Fourier transform window, the background
function, and the residual. If the window button is pressed, the appropriate window function will be
plotted in any plot. The background and residual functions are only plotted if one of the selected items
is a fit. The background will only be plotted if a background corefinement was made for that fit. If a
fit is not among the selected items, the background and residual will not be plotted. Note that a plot
with more than one selected fit may be quite confusing if the background or residual buttons are
depressed since the background and residual will be plotted for each fit.
The ranges over which the plot will be made in the three spaces are controlled by the three sets of entry
boxes.
Extra Plotting Features
The two additional tabs in the plotting panel contain the controls for the following utilities:
Indicators
Indicators are vertical bars that can be placed at user-chosen locations in k-, R-, or q-space. These
indicators will get displayed every time a plot is made. The idea is that indicators are a guide to the
eye, drawing attention to a place of interest as the data being plotted changes.
Indicators selected in either k- or q-space will be plotted in both k- and q-space, but not in R-space.
Likewise, indicators selected in R-space will not be plotted in k- or q-space.
Several characteristics of the indicators, including the number, the linetype, and the color, can be set
in the Plot section of the preferences dialog.
The indicators play well with each of the plotting options described below.
Stacking
Stacking refers to a vertical displacement the various traces. This is most useful for plotting the
various path contributions in k-space, but is sometimes useful in other kinds of plots as well. Stacking
requires three parameters which are set in the stacking notecard. The first control is series of radio
buttons for choosing whether stacking happens in k-space, always, or never. If the k-space option is
chosen, then q-space plots of the real or imaginary parts will also be stacked. (Basically, the
"k-space" choice refers to any wiggly function of wavenumber.) The other two controls set the initial
offset value and the increment between staces.
Inverting
Inverting is a useful tool for displaying the path contributions in "|chi(R)|" plots. When this is
selected, the "|chi(R)|" from any paths included in the plot will be multiplied by -1 so that they stick
down below the zero-axis. Hopefully this kind of plot help reduce clutter while still helping to show
which paths contribut where. The radiobuttons on this notecard allow you choose between never inverting,
inverting "|chi(R)|", or inverting both "|chi(R)|" and "|chi(q)|". The real and imaginary parts in R- or
q-space are never inverted. chi(k) is also never inverted. Inverting is turned off whenever stacking is
selected and would effect the current plot (i.e. you cannot stack and invert at the same time).
Data set offsets
This feat ure is useful for multiple data set plots. This is similar to stacking in that the parameter
denotes a vertical offset for use i the plot. Each trace associated with a particular data set is
plotted at the same lavel, but the data sets will be offset by the amount specified by this control.
This provides a way of simultaneously visualizing all parts of a multiple data set fit. Negative values
are recommended, with a negative offset, the traces will be plotted in the same order from top to bottom
as in the plot legend.
Stacking is disabled when data set offsets are used. Inverting is used with data set offsets, although I
think this results in confusing plots.
Palettes || Using the Data and Paths List || =head1 ARTEMIS: Editing Math Expressions
ARTEMIS - Editing math expressions
The math expression editing dialog is a way of setting path parameter math expressions for many paths at
once. It works on a given path parameter, e.g. it sets e0 or sigma^2 for many paths but does not touch
other path parameters. This dialog is available in two different context menus. If you right click on a
path parameter label on the path page and selection "Edit for many paths", then the dialog will pop up
for editing that parameter. If you right click on an entry on the Feff interpretation page and select
the "Edit path parameters" cascade, then select a path parameter, the dialog will pop up for editing that
parameter.
Operation of the dialog
The dialog is fairly simple. At the top is a text entry box for typing in your math expression. Below
that are various radiobuttons for specifying how to apply the math expression to the various paths in
your project. The options are:
1. Add the math expression to every path in the current Feff calculation.
2. Add the math expression to every path in the each Feff calculation.
3. Add the math expression to every path in the each Feff calculation associated with the current data
set.
4. Add the math expression to selected paths (i.e. the ones highlighted in orange in the Data and Paths
list).
Tokens
You can write your math expressions using token. Tokens are short character strings which will be
replaced by path-specific information as the math expression is applied to each path. The tokens are:
%i The path index from the Feff calculation. This is actually computed from the name of the
`feffNNNN.dat' file from the Feff calculation. For instance, if the file is `feff0029.dat', then %i
will expand to 29.
%I The path index from the Feff calculation, padded to fill four characters. For instance, if the file
is `feff0029.dat', then %I will expand to 0029.
%r The effective path length (or "reff") from the Feff calculation for the path.
%d The degeneracy of the path.
%D A template for the Debye function. This always expands to the string "debye(temp,thetad)" and may
need be edited after the fact to use the correct variable names. This is offered because the author
finds it hard to remember the order of the arguments to the Debye function.
%E A template for the Einstein function. This always expands to the string "eins(temp,thetae)" and may
need be edited after the fact to use the correct variable names. This is offered because the author
finds it hard to remember the order of the arguments to the Einstein function.
ARTEMIS: Automated First Shell Theory
ARTEMIS - Automated first shell theory
Sometimes thinking about a fitting model is more than a problem merits. You just want a quick 'n' dirty
stab at the first shell -- perhaps to measure the centroid of the distribution, perhaps to tell if a
sample is 4- or 6-coordinated. Whatever.
Artemis is not extremely well suited to rapid-fire, first shell analysis. By design, Artemis tends to
force the user to slow down and think hard about every step. Artemis is powerful, but she ain't simple.
The quick first shell (QFS) theory tool is an attempt at addressing this shortcoming. It works like
this:
1. Import some data. Set the Fourier transform and fitting parameters to suitable values.
Specifically, be sure to set the fitting range such that it encloses the first peak of the data.
2. Select "Quick first shell theory" from the Theory menu. This will display the QFS dialog.
3. The QFS dialog provides spaces for selecting the parameters for a simple first shell theory. These
include the atomic species of the absorber and the scatterer, the absorption edge of the experiment,
the approximate distance between the absorber and scatterer, and the coordination geometry to use in
the Feff calculation.
Currently the following coordination geomatries are available:
• 4-coordinate crystal
• 6-coordinate crystal
• octahedral molecule
• tetrahedral molecule
• square-planar molecule
The QFS theory is probably not highly sensitive to the choice of coordination geometry. Since the
unknown sample is probably not well described by any of these geometries, they are all merely
approximations for use in a quick 'n' dirty fit.
4. Once you have set up the parameters for the QFS theory, click the "Do it!" button. This will step
through the following without pausing:
a. Build an input file for the Feff calculation
b. Run Feff
c. Import the first path from the Feff calculation
d. Create a set of guess parameters for the amplitude, the sigma^2, the e0, and the delta R. Also
created are set parameters for the third and fourth cumulants, but they are set to zero. These
higher cumulant set parameters are created to make it easy to consider higher cumulants in
subsequent fits merely by changing them from set to guess.
If you have a mixed first shell, you might choose to repeat steps 2 through 4 two or more times.
At the end of this sequence, you are left with Artemis in its normal state. You may need to adjust the
parameters used in the fit. The QFS dialog is really just a tool for initially setting up the project.
It in no way changes the normal operation of Artemis.
If you import data from an Athena project file, the species of the absorber and the edge will be set
correctly when you start the dialog.
The Menubar || The preferences dialog ||
REFERENCES
Here are the relevant URLs:
IFEFFIT
http://cars.uchicago.edu/ifeffit
PGPLOT
http://www.astro.caltech.edu/~tjp/pgplot/
Perl
http://www.perl.com
perl/Tk
http://www.lehigh.edu/~sol0/ptk/
MISSING FEATURES
You betcha!
WHAT'S IN A NAME?
Artemis was the goddess of the hunt, an apt metaphor doing EXAFS analysis. ARTemis is also a pun on the
nature of EXAFS analysis that works in English and in the romance languages.
AUTHOR
Bruce Ravel <bravel@anl.gov> (c) 2001 - 2006 http://cars.uchicago.edu/~ravel/software/ Ifeffit is copyright (c) 1992 - 2006 Matt Newville newville@cars.uchicago.edu http://cars.uchicago.edu/ifeffit/