6. The GDS window

The Big Trick in Artemis

The parameters of the EXAFS equation are not the parameters of the fit. The parameters of the EXAFS equation are written in terms of the parameters of the fit.

As a consequence, path parameter values (see Fig. 5.5) are math expressions. These math expressions are functions of the actual fitting parameters.

Some of these math expressions are quite simple. For example, in the gold metal example in the previous chapter, the math expressions for S²₀ and E₀ were simple functions, each of a single parameter. The math expression for ΔR, however, was a function of alpha and reff, while the σ² math expression used the debye function and two parameters.

All of these parameters must be defined in the GDS window. This window contains a grid with a series of buttons down the right side. It is displayed and hidden using the GDS button on the left side of the Main window. Here are the contents of the GDS window from the gold metal example. The four variable parameters in the fit along with the fixed sample temperature needed by the debye function are shown. A new variable parameter is being defined in line 6.

The second, third, and fourth columns in the grid are filled by simple text boxes. The first column contains a drop down menu from which the parameter types can be chosen.

Fig. 6.1 The GDS window.

6.1. Parameter types

Every parameter of any type used in any math expression must be defined on the GDS widow. Any variable parameter defined on the GDS window must be used in a math expression.

There are 9 types of parameters in ARTEMIS. They are color coded in the grid to give you a visual indication of each parameter's type.

guess

This is a parameter of the fit. Its value will be adjusted to find the best fit of the model to your data. Its initial value is usually a number, but can be a math expression. In that case, the initial value will be the initial evaluation of the math expression.

def

This is a parameter that is defined as a math expression dependent upon other guess, def, or set parameters. Its value is updated throughout the fit. As discussed elsewhere in this manual, sophisticated use of def parameters is key to successful model building and effective use of ARTEMIS.

set

A set parameter is one that is evaluated at the beginning of the fit, but not evaluated subsequently. Although a set parameter can take a math expression as its value, it is more typically used to represent a constant (i.e. a number) used elsewhere in the fitting model.

lguess

An lguess parameter is a tool used to simplify model creation for a multiple data set fit. It can be used in math expressions for two or more data sets. When the fit is started, an actual guess parameter will be created for each data set in which the lguess is used. As an example, suppose your multiple data set fit includes data on a series of binary alloys. If x is a mixing parameter between the two alloys and is different for each sample, you might then use math expressions containing x and (1-x) for S²₀ parameters of paths representing the two metallic species in each fit. With x an lguess parameter, independent mixing parameters will be floated for each data set. The point, then, of an lguess is to facilitate the chore of editing path parameter math expressions using ARTEMIS' tools for pushing path parameter values across paths. This is discussed in more detail in the discussion of the characteristic value.

skip

A skip parameter is one that is not used in any capacity in the fit, but which you do not want to discard from your fitting project. Changing a parameter to skip is rather like “commenting it out”.

restrain

A restraint is a math expression that is evaluated and added in quadrature to χ² to evaluate the fit. That is, the fit is optimized in the presence of the restraint. The point of this is to add prior knowledge to a fit. Restraints will be discussed in more detail later in this document.

after

An after parameter is very similar to a def parameter in that it takes a math expression that depends on other parameters. It is not, however, used in any way in the fit. Instead, it is evaluated at the end of the fit and reported to the log file. This is used to make interesting calculations based on other parameters as part of the record of the fit. An after parameter should never be used in the math expression for a path parameter. Here's an example.

penalty

This takes a math expression representing a user defined penalty to the happiness calculation. This feature has not yet been implemented in ARTEMIS.

merge

A merge parameter is a parameter which has been multiply defined under the same name as part of combining fitting projects or importing structural units. A fit cannot proceed with any parameters in this state. This feature has not yet been implemented in ARTEMIS.

Todo

Penalty and merge parameters have not been implemented.

6.2. User interaction

Todo

Explain drag and drop

6.2.1. Button bar

The stack of buttons on the right side of the GDS window contains many of the main functions of the GDS window.

Use best fit

This button makes the most recent best fit value into the initial guess for every guess parameter in the grid.

Reset all

This button tells IFEFFIT or LARCH to reset all parameters to their initial values.

Highlight

This button prompts you for a string. All parameters with names or math expressions matching the string provided will be highlighted with a yellow background. This feature is particularly useful in large fitting models with many parameters. In the image above, you can see that all parameters matching brc1 have been highlighted. The string to match can actually be any valid Perl regular expression.

Evaluate

Clicking this button will evaluate all parameters and insert their evaluations into the fourth column of the grid. This is used to “spell-check” your math expressions for def and other parameters. In the image above, this button has been clicked and the evaluations have been inserted into the fourth column.

Import GDS, Export GDS

The next two buttons are used to import or export a simple text file with the names and definitions of all the parameters.

Discard all

This button does just that, after prompting to be sure that is what you want to do.

Add a site

This button appends a blank row to the end of the grid.

6.2.2. Keyboard shortcuts

When one or more rows are selected, you can use the following keyboard shortcuts to change the parameter type of that set of parameters.

• Alt-g: convert to guess
• Alt-d: convert to def
• Alt-s: convert to set
• Alt-l: convert to lguess
• Alt-k: convert to skip
• Alt-r: convert to restrain
• Alt-a: convert to after
• Alt-p: convert to penalty

6.2.3. Context menu

Clicking on a line in the grid selects the entire line. Control- clicking of a line adds that line to the selection. Shift- clicking adds all lines between the selected and clicked upon lines.

Fig. 6.2 Right clicking on any line in the grid, including the label containing the line number, will post this menu.

Copy, cut, paste

These three options copy, cut, and paste lines from or to the GDS grid. The cut function is one way of discarding a parameter. Another is to simply delete the name in the second column.

Insert blank lines

The insertion options complement the Add a site button by adding blank rows to the middle of the grid.

Change selected to

This sub-menu provides yet another way of changing the parameter type of the selected lines of the grid. If you have more than one line selected, they will all get changed to the option you choose from the submenu.

Grab best fit

This changes the initial guess of the selected lines to the most recent best fit value(s).

Build restraint

Fig. 6.3 This posts a dialog that helps you name and define a restraint based upon the value of the parameter in the line clicked upon.

This will use IFEFFIT's penalty function with the lower and upper bounds as its arguments and multiplied by the scaling factor. The example shown will make this restraint:

restrain res_enot = 1000 * penalty(enot, -5, 5)

and add it to the end of the grid. The penalty function will evaluate to 0 when enot stays between -5 and 5. As the value of enot strays outside that range, the restraint will evaluate to a value of 100 times the distance outside the range. This, then, is added in quadrature to χ² when the fit is minimized. You can read more about this, including how to choose the value of the scaling parameter, in the discussion of restraints.

Annotate

This prompts you for a text string to describe the parameter in the line clicked upon. The intent is to allow you document the role of the parameter in your fitting model. This annotation is displayed in the GDS window's status bar when that line is selected.

Find parameter

This posts a small window with a text box reporting all GDS parameters and path parameters which have math expressions containing this parameter.

Rename parameter globally

This allows you to rename a parameter and have its new name inserted every place in the fit where that parameter is used. All instances in other parameters on the GDS page and in the math expressions for parameters of all paths will be changed. Essentially, this is a global search and replace for parameter names.

Explain

Finally, the items in this submenu write a short text to the status bar explaining the various parameter types.

6.2.4. Creating parameters from math expressions on the path page

Parameters can be created from the path page. When you right click on a word in a math expression for the one of the path parameters, a menu pops up which allows you to set the word you clicked upon as GDS parameter.

Fig. 6.4 Creating GDS parameters by right clicking on a math expression on the Path page.

If you have not yet defined the word you right click on, then the GDS window will appear on screen, and the parameter will be inserted into the GDS table as the type of parameter selected from the menu.

If the word has already been defined, then its type will be changed to the type you select from the menu.

If the word is something that is not allowed in IFEFFIT as a parameter name (things like dr1 and cos are reserved words and cannot be used as parameter names) then the menu will not be posted. Likewise, the menu will not be posted if you right click on a number.

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