Spectrum Plot Panel

In this panel you can plot IR/Raman, UV/visible, VCD, ECD, and NMR spectra from data generated by Jaguar and phonon spectra generated by Quantum ESPRESSO. You can plot multiple spectra in stacked or overlaid format, and plot weighted averages of multiple spectra.

To open this panel: click the Tasks button and browse to Quantum Mechanics → Plot Spectra. This panel can also be opened from a number of other places in the Task Tool.

  • Using
  • Features
  • Additional Resources

Using the Spectrum Plot Panel

The Spectrum Plot panel plots spectra from several sources.

  • Jaguar produces transition frequencies and transition probabilities that can be used to plot spectra, but does not provide any information on line widths. Default values of the widths are provided and can be changed. Multiple spectra can be displayed on separate plots, stacked vertically, or on a single plot, either overlaid or as a weighted average.
  • Spectra in which the band shape is calculated are generated with the Calculate Band Shape Panel. These spectra can be shown as convolution spectra, in which the line shapes are determined as part of the calculation, or the raw spectra can be plotted by applying settings in this panel. When you choose to plot these spectra you are given a choice of which one you want to plot. If you choose to plot convolution spectra, you cannot import raw spectra at the same time, but you can import experimental spectra.
  • Phonon spectra from Quantum Espresso can be plotted.
  • Experimental spectra can also be imported.

To generate spectral data for plotting:

  • For UV/Vis spectra, run calculations from the Jaguar Spectroscopy Panel.

    You can also run a TDDFT calculation with Excited State selected in the Theory tab of the Jaguar panel.

  • For UV/Vis spectra including vibrational transitions, run a Band Shape calculation (see Calculate Band Shape Panel).

  • For IR/Raman spectra, run a frequency calculation (select Vibrational frequencies in the Properties tab of the Jaguar panel, Raman spectroscopy if needed).

    IR spectra can also be generated from the Jaguar Spectroscopy Panel.

  • For VCD and ECD spectra, run calculations from the Jaguar Spectroscopy Panel.

    You can also use the Jaguar panel and select the appropriate property in the Properties tab of the Jaguar panel, with the appropriate calculation type (DFT for VCD, TDDFT singlet in TDA for ECD).

  • For NMR chemical shifts of hydrogen, boron, carbon, nitrogen, fluorine, and phosphorus atoms, run calculations from the Jaguar Spectroscopy Panel.

  • For phonon spectra, run a QE calculation with Phonons selected in the Property section (see Quantum ESPRESSO Calculations Panel).

To display spectra in the Spectrum Plot panel:

  1. Select the entries in the Project Table for which you want to plot spectra.

    These entries must have been incorporated (or imported) from a Jaguar job that generated spectral data.

  2. Choose Applications → Jaguar → Spectrum Plot.

  3. Choose the spectrum type from the Type option menu.

  4. Optional: Choose the line shape and units, if available.

  5. If plotting multiple spectra, choose the plot format from the Multiple spectra option menu.

    If you chose Average weighted by property, click Choose Property to select an entry property to use for the weights. Suitable properties might be concentrations or Boltzmann weights. If you do not choose a property, equal weights are used.

  6. Click Plot Spectra for Selected Entries.

    The spectra are plotted. If the spectrum file can't be found, a file selector opens so you can locate and open the spectrum file.

Once you have displayed the spectra, you can make various changes.

  • To change the color, line style, or line width for a spectrum, choose it from the Spectrum option menu, then click the Options toolbar button and make the changes in the Figure options dialog box.

  • To change the frequency or wavelength scale or the half-bandwidth for all spectra, select Share scale factors and bandwidths, then make settings in the Scale factor and Half-bandwidth text boxes (or with the sliders).

    To change the frequency or wavelength scale or the half-bandwidth for each spectrum independently, firs deselect Share scale factors and bandwidths, then choose the spectrum from the Spectrum option menu and make settings in the Scale factor and Half-bandwidth text boxes (or with the sliders). For a stick spectrum, set the half-bandwidth to 0.

  • To label peaks in the spectrum with the frequency and intensity, select the lines in the table, then click Label Selected Frequencies.

  • To display a legend that shows the color, style, and width of the lines used for each spectrum, select Legend.

If you have multiple spectra, you can switch between overlaid, stacked, and averaged by selecting from the Multiple spectra option menu. You can change the weighting property also.

To save an image of the spectrum click the Save image button on the toolbar.

You can then select an image format, navigate to a location and save the image file.

If you choose a different spectrum type from the Type option menu, you must click Plot Spectra for Selected Entries again to load spectrum files for the new type and plot them.

Spectrum Plot Panel Features

Type option menu

Choose the type of spectrum that you want to display. The selection of the type sets the filter for the spectrum files, so that only those of the appropriate type are read or listed.

If you change the spectrum type between UV/Vis or ECD and either VCD or IR/Raman, the current spectra are cleared, and you must click Plot Spectra for Selected Entries to import the spectrum files for the new spectrum type. VCD, IR, and Raman spectra can be displayed at the same time.

Plot option menu and Browse/Load buttons

Choose the source of the spectra to be plotted.

  • Spectra for Selected Entries (N)—Read the spectrum files (.spm) of the chosen spectrum type for the N entries that are selected in the Project Table and plot the spectra. A Load button is displayed to the right of the menu to load the spectra for plotting.

    If any spectrum files cannot be found, a file selector opens for each missing file, so that you can select the correct spectrum file. The file selector title includes the entry title and entry ID. Once all the spectrum files have been opened, the spectra are plotted according to the settings made in the panel. Colors and line styles are assigned automatically, but you can change them if you want.

    If the spectrum is from a band shape calculation, you can choose to show the molar absorptivity spectrum instead of the raw intensity spectrum. Choosing the molar absorptivity spectrum disables the controls for the line shape and band width, as this spectrum is a convolution spectrum in which the shape and width are already included. While the convolution spectrum is displayed, you cannot add raw intensity spectra, for which the shape and width must be specified; but you can import experimental spectra.

  • Spectra for Workspace Entries (N—plot spectra for the N entries that are included in the Workspace. A Load button is displayed to the right of the menu to load the spectra for plotting. If a spectrum is not present in the project, a file selector opens so you can locate it. This operates in the same way as for Spectra for Selected Entries, above.

  • Other Theoretical Spectrum—Read a theoretical (predicted) spectrum from a .spm file. A Browse button is displayed to the right of the menu. A Browse button is displayed to the right of the menu. Any Boltzmann properties in the Project Table of the loaded spectra is used for Boltzmann averaging. If no Boltzmann properties exist as entries in the Project Table, the -out.mae file in the directory is read to fetch these properties.

  • Other Experimental Spectrum—Read an experimental spectrum from a file. A Browse button is displayed to the right of the menu. The file can use the extensions .txt, .csv, and .prn, and the data can be separated by spaces, tabs, or commas.

    An experimental spectrum must consist of pairs of frequency and intensity values, one per line, with the values separated by a delimiter. The experimental spectra are always displayed, and are not included in any averaging. Experimental spectra have no data on the positions or intensities of lines, so the Frequency table is empty, and controls for the line shape or scaling factor are not available.

Align to Experimental button

Align a theoretical VCD, IR, or Raman spectrum to an experimental spectrum. Opens the Align to Experimental dialog box, in which you can choose the experimental and theoretical spectra from the spectra imported into the Spectrum Plot Panel, and set options for the alignment in the Align to Experimental Options Pane. When you click Align & Plot, the spectra are aligned, the dialog box closes, and the aligned theoretical spectrum is plotted.

Export button

Export the spectra to a tab-delimited file. The file contains two columns for each spectrum, with the x (frequency) and y (intensity) data. They are labeled with the spectrum name as name-X and name-Y. The data exported include the line broadening. This feature should be useful for importing spectra into other plotting programs.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

This area displays the spectra. You can use the toolbar to change the overall positioning and zoom level of the spectra. The plot title lists the plot type, theory, solvent, and whether the plot is an average of multiple conformers. If conformation search was not performed, Averaged is not shown in the title.

Line shape option menu

Choose the line shape used for the spectrum. The available shapes are Lorentzian and Gaussian. Disabled for convolution spectra.

Units option menu

Choose the units for the display of the energy, from nm or wavenumbers. Only available for UV/Vis spectra.

Normalize option

Scale the intensities so that the maximum absolute value of the displayed intensity is 1. The maximum value of the input intensity is reported in the legend.

Show as transmission option

Display transmission intensity instead of absorption intensity on the y-axis. Only present for VCD or IR/Raman spectra.

Legend option

Select this option to display a legend for the spectra in the top right corner of the plot area. The legend displays the line type, the entry title and entry ID. You can drag the legend anywhere in the plot area.

Bin band shape spectral lines using a width of N cm-1 text box and Update button

Consolidate vibrational lines from a UV/Vis band shape spectrum that are close together into a single line, by a binning technique. This procedure speeds up the generation of the spectrum. Each bin of lines is replaced by a single line at the intensity-weighted centroid of the lines, with intensity equal to the sum of the intensities of the lines. Choosing the bin width is a balance between speed and accuracy. Larger bins will produce spectra faster, but if the bins are comparable in size to the line broadening (half-bandwidth), you may see artifacts of the binning in the spectrum.

After changing the bin width, click Update to recalculate the spectrum.

Multiple spectra option menu

Choose how to display multiple spectra.

  • Overlaid—The spectra are plotted on top of each other on the same plot. There is only one Y axis.
  • Stacked—Each spectrum is plotted separately (with its own Y axis), in a vertical stack. Zooming and panning works on all spectra simultaneously.
Share scale factors and bandwidths option

This option links the scale factors and band widths for all the spectra. Deselect it if you want to make changes to individual spectra.

Add averaged spectrum option menu and Select button

Add an average of all the calculated spectra to the plot. Choose how the spectrum should be averaged, then press Select to open a dialog box. Choose which spectra to average, name the averaged spectrum with the New spectrum prefix text box, and select Add to add the averaged spectrum to the plot.

If Arithmetic is selected, you can apply weights to the spectrum by adding a “spectrum weight” property to the Project Table, and selecting the Add Weights option in the dialog box.

If Boltzmann averaging is selected, actual Boltzmann averaging is performed. Boltzmann averaging can only be applied to spectra with a Boltzmann property (r_j_Boltzmann_weight, r_j_Total_Free_Energy_(au)_298.15K_1.00E+00atm, r_j_Final_energy) in the Project Table.

Spectrum option menu

Choose the spectrum for which you want to change the parameters.

Scale factor text box and slider

Scale the frequencies of the spectral lines by the specified factor. Disabled for convolution spectra.

Half-bandwidth text box and slider

Specify the half-bandwidth (related to full width at half maximum) for the spectral lines. Disabled for convolution spectra.

Spectrum toolbar

The toolbar has tools for manipulating the spectrum selected from the Spectrum option menu:

Info
Display information on the selected spectrum.
Invert
Invert the y-values of the selected plot. Click the button again to reverse the invert. Only present for VCD and ECD spectra.
Hide/Show
Hide the selected spectrum from the plot. To show the spectrum, click the button again.
Delete
Remove the selected spectrum from the plot.
CIEx and CIEy text boxes

These noneditable text boxes display the x and y values in the CIE xyY color space, obtained by fitting the spectrum to the standard CIE XYZ color matching functions. See CIE 1931 color space for more information. These boxes are only present if the spectrum type is UV/Vis.

Spectral line table

This table lists the frequency, intensity, and symmetry of the spectral lines in the spectrum that is selected from the Spectrum option menu. A fourth column, Offset, allows you to shift individual lines, by editing the value in this column. The spectrum is recalculated after changing the offset. You can select multiple table rows with shift-click and control-click.

Label Selected button

Label the lines that are selected in the table with both the value and the intensity.

Shift only option

Label peaks with the value only, without the intensity.

Show split tree option

Display split tree-diagram annotations to see how the spin's signal is split through spin-spin coupling. These annotations are an approximation and may not always align perfectly with the spectrum.

Clear Labels button

Remove the labels from the spectrum.

Offset Selected By button and text box

Offset the selected lines in the table by the amount given in the text box. This allows you to quickly apply an offset to multiple lines. The spectrum is recalculated when the offset is applied.

Clear All Offsets button

Set all offset values to zero.

Vibrational Normal Mode Analysis button

Analyze the vibrational modes that contribute in a defined region of a band shape spectrum and animate the modes in the Workspace using the Vibrations panel. When you click this button, the Vibrational Normal Mode Analysis Dialog Box opens, and two vertical green lines are drawn on the spectrum. These lines mark the range of the spectrum that is to be analyzed, and can be dragged to the left or right to change the range.

This button is only available if you are plotting a band shape spectrum , and you have selected the Print information for intense transitions option in the Calculate Band Shape Panel when you generated the spectrum.

Tutorials

Related Topics