Thermochemistry Viewer Panel

Thermochemistry Viewer Panel Features

• Load Data for Selected Entries button
• X-Axis option menu
• Y-Axis option menu
• Base units options
• Additional data section
  • Temperature text boxes
  • Pressure text boxes
  • Compute button
• Pressures list or Temperatures list
• Free energy loss (%) list
• Entries list
• Plot buttons
• Update axes ranges option
• Legend option
• Plot area
• Status bar

Load Data for Selected Entries button

Load thermochemical data from the entries that are selected in the Project Table. The entry titles are listed in the Entries list. The entries must have associated thermochemical data properties, such as for Jaguar thermochemistry calculations (see Thermochemical Properties from Jaguar Calculations, Frequency-Related Keywords in the Jaguar Input File), and adsorption energy calculations (see Adsorption Energy Calculations Panel).

X-Axis option menu

Choose the property to plot on the X axis, from Temperature and Pressure. The variation in the other property can be displayed as plot series. Temperature is displayed on a linear scale, pressure is displayed on a logarithmic scale.

Y-Axis option menu

Choose the thermodynamic property to display on the Y axis. The list includes Free energy, Enthalpy, Entropy, Adsorption free energy, and Desorption free energy.

Base units options

Choose the base energy units for the properties: energies are shown in kcal/mol or kJ/mol, for example.

Additional data section

Add temperature/pressure data points to the plot, computed from Jaguar frequency data. Points that duplicate those in the input are not recomputed. This means you can specify ranges that cover the input points and extend their range, and only the new points are computed: for example, the original set has temperatures from 300 to 500 K and pressures from 1 to 100 atm, and you want to extend the ranges to 300 – 700 K and 1 to 1000 atm, with the same increment.

Temperature text boxes

Specify the starting temperature in K, the number of temperature steps, and the increment in the temperature for each step.

Pressure text boxes

Specify the starting pressure in atm, the number of pressure steps, and the factor by which the previous pressure is multiplied at each step.

Compute button

Calculate the enthalpy, entropy, and free energy at the specified data points and append the energy properties to the input structures.

Pressures list or Temperatures list

List of pressures (P) or temperatures (T) used to calculate thermochemical properties. Which it is depends on the choice made for the X axis (it's the other one). You can select multiple values to show plots for each value.

Free energy loss (%) list

List of percentage free energy loss (dG) for molecule adsorption. Only present if Adsorption free energy or Desorption free energy is selected as the Y-Axis. You can select multiple values to show plots for each value. Include None in your selection to show plots for entries without free energy loss data.

Entries list

List of entries for which thermochemical data can be plotted. You can select a single entry or multiple entries to plot the thermochemical data. It may be useful to show plots for multiple entries to see how the differences in structure affect the thermochemistry.

Plot buttons

Use these buttons to configure the plot.

• Zoom In—Zoom in on the plot. Each click zooms in by a predefined factor, enlarging the view of the current center of the plot. You can also zoom in on a particular area by dragging out a rectangle.
• Zoom Out—Zoom out by a predefined factor. Each click zooms out by a predefined factor, to show more of the plot.
• Axes—Set the range and labeling options for the axes. Opens the Axes Parameters Dialog Box.
• Reset View—Reset the view of the plot to the original zoom and pan values.
• Series—Set up the appearance of the plot series, such as color, symbol, lines. Opens the Series Parameters Dialog Box.
• Copy—copy an image of the plot to the clipboard, for use in other applications.

Update axes ranges option

Update the ranges of the axes automatically when the plotted data changes. When this option is not selected, the axis range does not change with changes in the plotted data (choices from the list. Deselecting this option is useful when you set the axis range in the Axes Parameters Dialog Box. This option is reselected when structures are loaded, a different property is plotted or the units change.

Legend option

Display a legend in the plot.

Plot area

The chosen thermodynamic property is plotted against the pressure or temperature in this area. Plots for all selected values of pressure or temperature and entries are shown together in this area.

You can zoom in to an area by dragging out a rectangle.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.