Cerius2 Modeling Environment

10       Working with Graphs

Graphical output is generated by a wide variety of Cerius² application modules. This information is automatically formatted and displayed as a graph. The controls in the Graphs module allow you to save and reload graphs and also give you great freedom to manipulate the appearance of the graphs. For example, you can scale and annotate graphs, as well as change the color ranges used, to highlight important areas for presentation.

This section explains

This section contains information on:

Creating graphs

Displaying and editing graphs

Managing graphs

You should already know...

The basics of starting Cerius² and using its interface are demonstrated in Introducing Cerius2 and described in The Cerius2 Interface.

Graphs in Cerius² are produced as output from calculations in various other application modules. How to set up and run the appropriate calculations are discussed in the documentation for the relevant application modules.

Accessing the tools

The tools for handling graphs are accessed from one of the decks of cards in the main Visualizer control panel. To access the Graphs module, click the deck selector (see also Access to application modules) and choose TABLES & GRAPHS from the list that appears. Then click the title of the GRAPHS card to bring it to the front. The deck of cards menu area should now look like this

Additional information

Please see the on-screen help for details on the functioning of each control on the GRAPHS card.

Creating graphs

Ordinarily, graphs are created and displayed automatically as the result of some calculation in a Cerius² application module. If you are dealing with such graphs, you do not need to read this section.

However, you may want to create a graph from a blank "user graph" and selected data. Or you may want to import and graph data from a file output by an Insight II module.

Finding information

This section includes information on:

Starting a new, empty graph

Specifying the type of graph

Selecting data to plot

Loading graphs

Related information

Controlling which one(s) of several plots (which are held in computer memory during a Cerius² session) are displayed in the Cerius2 Graphs window is discussed under Selecting and displaying graphs.

You should already know...

How to access the Graphs module is described under Accessing the tools.

Starting a new, empty graph

Select the Gallery/Manager menu item from the GRAPHS card to access the Gallery Manager control panel.

Creating a new graph

To create a new graph, check a check box in the Display column, to the left of the blank line below the last name, if any, in the list of graph names in the Gallery Manager control panel.

Check the Edit check box to the right of the name (User Graph v#) of the new graph. Make sure all other Edit check boxes are unchecked.

Additional information

Please see the on-screen help for details on the functioning of each control in the Gallery Manager control panel.

Specifying the type of graph

Concepts

An x-y data set is an ordered series of independent coordinates in a plane. The data points in a set may be connected by lines or displayed in styles such as histogram, points, or delta lines.

A 2D Cartesian data set is a regular grid of points in a plane, sometimes with symmetry properties. Each point is associated with a real value, such as an intensity or an energy. Different real values are usually color-coded to differentiate them.

A 2D polar data set is similar to a 2D Cartesian data set, except that it is mapped in polar coordinates.

A special type of 2D data set is used to display LEED/RHEED reflections and single-fiber diffraction patterns. These are called x-y-z plots, where circles whose radii represent the value of the z coordinate are drawn in the xy plane. This is different from a 2D contour plot in the delta style. The latter draws circles on a regular grid, whereas the x-y-z plot places circles only as prescribed by the x,y coordinates.

Accessing the tools

If you already have the Gallery Manager control panel open (Accessing the tools), click the Graph Manager... pushbutton in the Gallery Manager control panel to access the Graph Manager control panel.

Alternatively, select the Graph/Manager menu item from the GRAPHS card to access the Graph Manager control panel.

Specifying the type of graph

Set the Type popup to the desired graph type.

Additional information

Please see the on-screen help for details on the functioning of each control in the Graph Manager control panel.

Selecting data to plot

Related information

Loading graphs containing data sets is discussed in Loading graphs. Generating data for graphs is discussed in the documentation for the relevant application modules.

Accessing the tools

If you already have the Gallery Manager control panel open (Accessing the tools), click the Graph Manager... pushbutton in the Gallery Manager control panel to access the Graph Manager control panel.

Alternatively, select the Graph/Manager menu item from the GRAPHS card to access the Graph Manager control panel.

Selecting the data

To add a data set to the new graph, check the Display check box(es) next to the names of the data sets that you want to display in the currently editable graph. (The name of this graph appears near the top of the Graph Manager control panel.) You can only select data sets that are of the appropriate type (Specifying the type of graph).

Additional information

Please see the on-screen help for details on the functioning of each control in the Graph Manager control panel.

Tip

Loading graphs

Once a graph file has been loaded, each graph and its data sets can be manipulated in exactly the same way as those newly created by Cerius² (see, for example, Displaying and editing graphs). Old and new graphs can be displayed side by side in the Cerius2 Graphs window, or old and new data sets can be displayed together in a single graph. However, Insight and Cerius² data cannot be mixed in one graph.

Accessing the tools

To load graphs saved from Cerius², select the File/Load Graphs menu item from the GRAPHS card to access the Load Graphs control panel.

To load graphs saved from Insight II, select the File/Import Insight TBL menu item from the GRAPHS card to access the Import TBL File control panel.

Finding and loading graph files

Using the file browser in the control panel to navigate the directory structure is fairly intuitive. The procedure is described under Loading model structure files.

If the name of the file you want to load does not end in .grf (Cerius²) or .tbl (Insight), change the name in the filename text entry box as desired (see File formats).

For Cerius² graphs, loading the graph also loads its included data sets.

However, since Insight graphs contain multiple data sets, you need to first select the graph and then choose the desired types of data to be plotted. Then click the PLOT pushbutton to load the graph and the desired data sets.

Additional information

Please see the on-screen help for details on the functioning of each control in the Load Graphs and Import TBL File control panels.

File formats

Because all Cerius² graphs are saved in the .grf format, most graphs loaded in are also in this format. However, the Cerius² graph system recognizes and correctly loads graphs in the .xy and .con formats used by CERIUS prior to version 3.1.

Cerius² can also read in graphs that were saved in the Insight II program's .tbl format. (Cerius² .tbl files are not the same format as Insight .tbl files.)

Cerius² recognizes graph files according to their format, so it is not strictly necessary to save them with the standard filename extensions. However, it is generally less confusing and more convenient to do so.

For detailed information about Cerius² file formats, please see File Formats. Insight files are described in separate file formats documentation.

Displaying and editing graphs

When a graph is output by an application, it automatically appears in a separate Cerius2 Graphs window (sometimes called a gallery). You may want to change such things as:

• How many graphs are currently displayed in the window.

• The range of data points that are visible.

• The text that accompanies a graph.

This section includes information on:

Selecting and displaying graphs

Selecting which data sets to display and edit

Labeling and annotating graphs

Changing graph axes and scale

Changing plotting style and color

Related information

How to print the contents of the Cerius2 Graphs window is explained under Printing models and graphs.

You should already know...

How to access the Graphs module is described under Accessing the tools. How to load graphs from files is described under Loading graphs.

Selecting and displaying graphs

Accessing the tools

Select the Gallery/Manager menu item from the GRAPHS card to access the Gallery Manager control panel. (The graph window is also referred to as the gallery.)

Selecting graphs to display

To display or hide particular graphs, check or uncheck the appropriate check boxes in the Display column to the left of the list of graph names in the Gallery Manager control panel.

For changes in the graphs displayed to occur immediately, make sure the Auto check box is checked. If the Auto check box is unchecked, you need to click the SHOW pushbutton to update the graph window. Turning off automatic updating can be faster if you are dealing with graphs containing many data points, which may therefore be slow to update.

Accommodating graphs within the graph window

You can allow Cerius² to set the graph window width and height automatically by setting both the Gallery Width and Gallery Height popups to AUTO.

If you prefer some other width and/or height, set the Gallery Width and Gallery Height to the desired numbers of columns and rows (respectively) of graphs to display.

Tip

Selecting graphs for editing

To enable graphs to be edited, check or uncheck the appropriate check boxes in the Edit column to the right of the list of graph names in the Gallery Manager control panel.

Only graphs of the same type (Specifying the type of graph) can be edited simultaneously.

Additional information

Please see the on-screen help for details on the functioning of each control in the Gallery Manager control panel.

Selecting which data sets to display and edit

Related information

How to select a graph for display and editing is discussed under Selecting and displaying graphs.

Accessing the tools

If you already have the Gallery Manager control panel open (Accessing the tools), click the Graph Manager... pushbutton in the Gallery Manager control panel to access the Graph Manager control panel.

Alternatively, select the Graph/Manager menu item from the GRAPHS card to access the Graph Manager control panel.

Selecting a data set

To display or hide particular data sets, check or uncheck the appropriate check boxes in the Display column to the left of the list of data set names in the Graph Manager control panel.

To enable the display style (etc.) of data sets to be edited, check or uncheck the appropriate check boxes in the Edit column to the right of the list of data set names in the Graph Manager control panel.

Additional information

Please see the on-screen help for details on the functioning of each control in the Graph Manager control panel.

Labeling and annotating graphs

Related information

Selecting graphs (Selecting and displaying graphs) and data sets (Selecting which data sets to display and edit) for editing are discussed above. Specifying immediate or delayed updates of the graph display is presented under Selecting graphs to display.

Accessing the tools

To change the text of data-set keys, select the Data/Plotting Attributes menu item from the GRAPHS card to access the Plotting Attributes control panel. Alternatively, click the Plotting Attributes... pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel.

The controls that are included in this control panel depend on what type of graph is being edited.

To perform any other function listed under Labeling and annotating graphs, select the Graph/Annotation menu item from the GRAPHS card to access the Graph Annotation control panel. Alternatively, click the Graph Annotation... pushbutton in the Graph Manager control panel to access the Graph Annotation control card.

Changing text annotations

To change the text of the x- or y -axis label, enter the text in the x Axis Label or y Axis Label entry boxes in the Graph Annotation control panel.

To change the text of the graph's title, enter the text in the Graph Title entry boxes in the Graph Annotation control panel. Several entry boxes are available, so you can use multi-line titles.

To change the text of data-set color-code keys, select one (only) data set and enter the text in the Label entry box in the Plotting Attributes control panel.

To display or hide hkl labels next to data circles on x-y-z graphs, check or uncheck the Include hkl Labels check box in the Plotting Attributes control panel.

Displaying annotations

To display or hide axes, axis labels, the title, all the data-set keys, or cell indications, set the appropriate Annotation Options popups in the Graph Annotation control panel. (A --> popup label means that several graphs are selected for editing and that the annotation options differ for those graphs, or that no graph is selected.)

Additional information

Please see the on-screen help for details on the functioning of each control in the Graph Annotation and Plotting Attributes control panels.

Changing graph axes and scale

Related information

Selecting graphs (Selecting and displaying graphs) and data sets (Selecting which data sets to display and edit) for editing are discussed above. Specifying immediate or delayed updates of the graph display is presented under Selecting graphs to display.

Accessing the tools

To shift only selected data set(s) along the y axis, select the Data/Plotting Attributes menu item from the GRAPHS card to access the Plotting Attributes control panel. Alternatively, click the Plotting Attributes... pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel.

To change the proportions of the graph window, select the Gallery/Manager menu item from the GRAPHS card to access the Gallery Manager control panel.

For all other scaling or axis-shifting tasks, select the Graph/Scaling menu item from the GRAPHS card to access the Graph Scaling control panel. Alternatively, click the Graph Scaling... pushbutton in the Graph Manager control panel to access the Graph Scaling control panel. The controls available in this control panel depend on the type of graph you have selected for editing. (The name of this graph appears near the top of the Graph Scaling control panel.)

Changing x and y axes

The x- and y-axis ranges can be changed for x-y and 2D Cartesian graphs. The angle between the axes can be changed for 2D Cartesian graphs.

To explicitly set the range of values covered by the x and y axes, enter values in the Min x, Max x, Min y, and Max y entry boxes of the Graph Scaling control panel. For 2D Cartesian graphs, you can also set the range values relative to the width of the data set.

For x-y graphs, you can also choose among several options for automatic axis scaling, by choosing from the Axis Scaling popup in the Graph Scaling control panel.

To force the axes in a 2D Cartesian graph to be drawn perpendicularly, check the Force Rectangular Axes check box in the Graph Scaling control panel. For example, check this box when viewing HRTEM output for nonorthogonal periodic cells, to view the graph as a rectangle rather than a parallelogram.

Changing angles in polar graphs

To set the minimum and maximum displayed angles in 2D polar graphs, use the Min Angle and Max Angle entry boxes in the Graph Scaling control panel. The angles are defined clockwise (in degrees) from north (up).

To set the displayed radius in 2D polar graphs, use the Max Radius entry box in the Graph Scaling control panel.

Shifting a data set along the y axis

To shift a curve or other representation of a data set up or down the y axis of an x-y graph, enter a value in the Y Offset entry box of the Plotting Attributes control panel. This does not change the actual data points.

Scrolling a graph

X-y graphs can be scrolled along either axis.

To scroll the graph along the x or y axis, use the arrow tools in the Scroll controls of the Graph Scaling control panel.

To return the view to its original position (that is, centered on the same area as before you began scrolling), click the reset button (in the center of the arrow tools) or press <Home> on the keyboard.

You can also scroll graphs interactively, by placing the cursor within a graph, depressing the middle mouse button, and dragging the mouse in any direction within the xy plane.

Changing size or proportions of a graph display

The proportions (rectangular or square) of all types graphs can be changed. In addition, the x and y axes of x-y graphs can be expanded or contracted (zoomed, see Expanding or shrinking an axis).

To change the proportions of the Cerius2 Graphs window and any graph(s) it contains, grab a corner of the window with the cursor and drag it. Changing the graph window's width and height (Accommodating graphs within the graph window) also affects the proportions of the displayed graphs.

Alternatively, you can set the window proportions by entering a number in the Aspect ratio entry box in the Gallery Manager control panel.

Expanding or shrinking an axis

To zoom in on a specific part of the displayed graph, hold down <Alt> and the middle mouse button and drag out a rectangle over the desired part of the graph.

To expand the graph along the x or y axis, use the tools in the Zoom controls of the Graph Scaling control panel.

To contract the graph along the x or y axis, use the tools in the Zoom controls of the Graph Scaling control panel.

To return the view to its original position (that is, to the same magnification as before you began zooming), click the reset button (in the center of the Zoom tools) or press <Home> on the keyboard.

You can also zoom graphs interactively, by placing the cursor within a graph and:

• Holding down the middle and right mouse buttons and dragging the cursor in the model window.

or:

• Holding down <Shift> plus the middle mouse button and dragging the cursor in the model window.

Additional information

Please see the on-screen help for details on the functioning of each control in the control panels mentioned in this section. Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions.

Changing plotting style and color

Related information

Selecting graphs (Selecting and displaying graphs) and data sets (Selecting which data sets to display and edit) for editing are discussed above. Specifying immediate or delayed updates of the graph display is presented under Selecting graphs to display.

You can also edit the color ranges (see Color ranges) that are used to color-code values shown in graphs.

Accessing the tools

Select the Data/Plotting Attributes menu item from the GRAPHS card to access the Plotting Attributes control panel. Alternatively, click the Plotting Attributes... pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel. The controls available in this control panel depend on the type of graph you have selected for editing.

Changing line style and color in x-y graphs

To change the plot style used for selected data sets in x-y graphs, set the Style popup.

To change the line style (when the plot style is line, histogram, or delta) used to plot selected data sets in x-y graphs, set the Lines popup. Styles other than SOLID work best when data points are spaced relatively far apart.

To change the color used for selected data sets in x-y graphs, select a color from the Color popup.

Changing the style of 2D graphs

To change the style (contour lines, continuous shading, or delta) used to differentiate ranges of values in 2D Cartesian and 2D polar graphs, set the Style popup.

Specifying color use in 2D graphs

For 2D Cartesian and 2D polar graphs, as well as x-y-z graphs, you can specify:

• The color range (Color ranges) that is used.

• The direction in which the color range is used for the contour and continuous styles of 2D graphs (that is, which color represents a high value and which low).

• Whether the color scale is applied in a linear or log way.

• The number of contours used in contour-style 2D graphs (fewer contours means faster redrawing when you make changes).

• How smooth is the color shading for continuous-style 2D graphs.

• The range of values that are mapped to colors.

• The exposure, brightness, and contrast of the displayed colors.

Please see the on-screen help for details on the functioning of each control in the Plotting Attributes control panel.

Managing graphs

You may be running an application that produces many graphs. However, you can, for example, control how new graphs are added to the graphing system and remove graphs from the gallery manager.

Finding information

This section includes information on:

Controlling default display format

Preventing replacement of old graphs

Removing graphs and data from a Cerius2 session

Saving graphs

Related information

Controlling which one(s) of several plots (which are held in computer memory during a Cerius² session) are displayed in the Cerius2 Graphs window is discussed under Selecting and displaying graphs.

Saving preferences is discussed under Using saved sessions as preferences settings.

You should already know...

How to access the Graphs module is described under Accessing the tools.

Controlling default display format

Controlling formats in generated graphs...

For example, in doing a series of Rietveld refinements, you may be most interested in a particular data range. After the graph from the first refinement appears, you can zoom in on the desired data range and then set these graph axes as your preferences. When graphs that are output from subsequent refinement are sent to the graph window, the graph axes remain in your region of interest and do not revert to showing the entire data set.

... and in graphs loaded from files

By default, when a graph file is loaded, it uses the same axis scales, types of annotations, and other settings that were in effect when the file was saved. However, you can override some of these settings before loading the graph file.

Accessing the tools

Select the Gallery/Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel. Alternatively, click the Expert Functions... pushbutton in the Gallery Manager control panel to access the Graphs Expert Functions control panel.

Resetting the default graph format

To retain current graph format settings in future graphs (in the current Cerius² session), after the first graph is output from an application module, format it as desired (see Displaying and editing graphs). For example, display only the "interesting" data points by scrolling along the x and/or y axes (Scrolling a graph) and/or by expanding or contracting one or both axes (Expanding or shrinking an axis), then make sure that the Axis Scaling popup in the Graph Scaling control panel is set to FIXED.

In the Graphs Expert Functions control panel, check the desired Keep Same check boxes to apply features of the current graph's format to future graphs:

• Gallery Content--To regenerate only graphs having the same name(s) as currently displayed graphs.

• Graph Axes--To retain the same axis scale (Expanding or shrinking an axis) and labels (Changing text annotations).

• Graph Content--To display only data sets having the same name(s) and to maintain the same plotting order.

• Plot Attributes--To use the same style and color (Changing line style and color in x-y graphs), y-axis offset (Shifting a data set along the y axis), and key (Changing text annotations) for data sets (having the same names) as in the previous graph.

Additional information

Please see the on-screen help for details on the functioning of each control in the Graphs Expert Functions control panel.

Preventing replacement of old graphs

Controlling graph replacement when many graphs are generated...

For example, a graph of energy vs. minimization step can be produced by the Minimizer module each time a minimization is run; and in the Rietveld module, each refinement produces a new diffraction data set. The graph and data set(s) from the preceding run are lost when this happens.

The default is to overwrite any old version of these graphs with the newest one. This prevents many versions of obsolete graphs from accumulating in the graph window and in computer memory. However, if you want to retain old versions of graphs along with the new ones, you can:

• Place the new graph in the graph window next to the old graph.

or:

• Place the new data set in the same graph along with the old data set.

As another example, when a graph file is loaded, the graphs in the file usually replace those currently shown in the graph window (although the previous graphs and their data sets are still present in memory). However, you can load a graph file without displaying its graph(s) immediately.

Accessing the tools

Select the Gallery/Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel. Alternatively, click the Expert Functions... pushbutton in the Gallery Manager control panel to access the Graphs Expert Functions control panel.

Preventing old graphs from being overwritten

After the first graph is output from an application module, set the Data Placement popup in the Graphs Expert Functions control panel to ADDITIONAL GRAPH.

When a new graph is generated by your application module, both it and the older graph are displayed in the graph window.

Adding new data to an existing graph

After the first graph is output from an application module, set the Data Placement popup in the Graphs Expert Functions control panel to COMBINE WITH EXISTING.

When a new graph is generated by your application module, the new data set is displayed in the older graph that is already displayed in the graph window.

Additional information

Please see the on-screen help for details on the functioning of each control in the Graphs Expert Functions control panel.

Removing graphs and data from a Cerius2 session

Related information

You can completely reinitialize Cerius² by starting a new session (Starting a new session).

Selecting graphs (Selecting and displaying graphs) and data sets (Selecting which data sets to display and edit) for display are discussed above.

Accessing the tools

Select the Gallery/Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel. Alternatively, click the Expert Functions... pushbutton in the Gallery Manager control panel to access the Graphs Expert Functions control panel.

Deleting all invisible graphs and data sets

First make sure that all graphs (Selecting and displaying graphs) and data sets (Selecting which data sets to display and edit) that you want to keep are currently displayed in the Cerius2 Graphs window.

To remove all undisplayed graphs and data sets, click the CLEAN pushbutton in the Graphs Expert Functions control panel.

Deleting all graphs and data sets

To delete all graphs and their data sets from both display and memory, click the Reset menu item on the GRAPHS card.

Additional information

Please see the on-screen help for details on the functioning of each control in the Graphs Expert Functions control panel.

Saving graphs

A saved graph file contains all graphs and data sets just as they appear in the current graph window.

Important

Related information

Creating your own directories or subdirectories is described under Making custom directories.

Accessing the tools

To save graphs from the current Cerius² session, select the File/Save Graphs menu item from the GRAPHS card to access the Save Graphs control panel.

Saving graphs to a file

Once you have located the directory in which you want to store your graph, click the SAVE pushbutton. (Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Finding model file(s).)

Additional information

Please see the on-screen help for details on the functioning of each control in the Save Graphs control panel.

File formats

Cerius² saves graphs in .grf format and automatically adds .grf to the filename if you have not specified some other extension.