Procedures <Prev Next>

Line Position Fitting

This is the preferred method of determining constants from an experimental spectrum, and can be used when lines are reasonably well resolved. Where this is not the case it may be possible to do contour fitting, but note that this may not give good results.

The procedure described here works best using a mouse; it is possible with a trackpad or other pointing device, but a little fiddly. Where right click is required, mac users will probably want to use Ctrl+Normal Click which is equivalent to right click for a single button mouse or trackpad.
  1. Overlay the experimental spectrum over the PGOPHER simulation. Note that for the process described here, peaks in the experimental spectrum should be pointing upwards, rather than downwards as is sometimes used for absorption spectra. If the experimental spectrum is plotted separately you can right click on the experimental spectrum and select invert or otherwise select Overlays, Invert from the main menu. 
  2. Drag the simulation and/or manually adjust the constants so that you can match at least some peaks between the two spectra. The assignment process works best if you start with low J transitions near the band origin. To adjust constants open the constants window which allows typing in values or adjusting them with the mouse.
  3. Right click on a peak that can be assigned to a peak in the experimental spectrum. A Line List Window will appear:

    You will normally want to arrange the windows so that the simulation and the line list do not overlap. Selecting View, Arrange Windows from the main menu may help.
  4. All the lines close to the mouse (within a few pixels on the screen) will be shown selected, which will often catch more than one rotational transition as above. The intensity of the individual transitions (shown under Strength) is normally enough to indicate if you have a sensible selection of lines. The next step will ignore the weaker lines, or you can adjust the selected lines with the mouse. (You can delete the unwanted transitions by selecting the required rows with the mouse and pressing the delete button . Note you can adjust that the settings controlling the number of peak displayed and assigned from the Line List Options Window.)
  5. Measure the corresponding peak in the experimental spectrum by dragging the across the peak with the right mouse button. (Press with the right mouse button to the left of the peak, drag the mouse to the right of the peak, and release). The peak position will be determined from the spectrum and a marker indicating the determined position will be displayed. Note:
  6. Provided Auto is selected in the line list window, the "Position" column in the line window of the selected rows will change to that of the experimental peak and the “Std Dev” will be set to 1 to indicate a measured, rather than a calculated frequency. (If Auto is off press the Assign button to do this manually.)
  7. Repeat steps 3 to 6 to assign a few more peaks.
  8. To check that you have the correct assignments, press the "Test" button. The program will read and plot your assignments:
  9. It is easy to misassign peaks, and wrongly assigned peaks can distort the fit quite badly. To correct an assignment, select the corresponding rows(s) with the mouse and either:
  10. Given a reasonable number of assigned peaks you can perform a fit. Select the parameters you want to float by going to the constants window (View, Constants) and set "Float" to "yes" by each of the parameters you want to float. Notes:
  11. Click Fit in the line list window.
  12. If the results look reasonable, then press "Fit" repeatedly until the error converges. Note that the residuals and calculated positions displayed are the values before the fit, rather than after.
  13. If the fit does not look good, the Undo Fit button in the log window will step constants back one fit cycle for each press
  14. Complete the fit by repeating from step 3, adding more peaks to the line list and floating more parameters.
  15. A complete report on the fit can be obtained from the Log window:
    1. Clear the log window with the clear button
    2. Press the "fit" button in the line list window
    3. In the log window the copy button: will copy the report to the clipboard, or alternatively use the save as button to save the log to a file.
  16. The contents of the line list window are normally saved to, and loaded from, the .pgo file, though it is more flexible to save the assignments to a separate file. See the next section for how to do this.

Common Problems

Line lists in separate files

It is normally more flexible to work with assigned lines in an external file for larger fits as only limited editing is possible in the line list window. External files are text files, normally with a .lin or .obs extension, and will accept a wide variety of directives and formats in addition to the line list as displayed in the line window. Directives allow more control over the fit; for example, a "stop" directive will cause the rest of the file to be ignored, allowing fits to part of the data, and a "Units" directive allows the units to be set for the following lines allowing, say, data from microwave and infra-red spectra to be combined. For more details see Combined and Multi-State Fits and the Line List Input File Format. A custom text editor, the Tabslave Editor, is distributed with PGOPHER which has been specially designed for editing these files. See Fitting example - the A-X transition in C3 for a worked example in line position fitting involving two overlapping transitions, which demonstrates the process, and why it might be useful. The procedure below describes how to generate a basic version of the file from the line list window.

To set the file:
  1. Press More Button and select "Save to File" to save the current line list to a file. Any of the formats presented will work in simple cases; see the discussion in Multiple State Fitting example - the A-X transition in C3 for more information on the possibilities. Use "Branch" or "Simple" format for straightforward applications.
or (to set a previously generated file):
    1. Go to the log window(View, Log).
    2. Press the button and browse to the file (or where you would like the file to be created). This will put the file name in the observations file name window. (The file name should typically end in .lin or .obs).
    3. Press the Edit Button . If the file does not exist you will be asked if you want to create it. If the Slave Editor is set up correctly, this should start.
To add observations to the file:
  1. Use "More, Copy Branch Table", "More, Copy Simple Format" or the copy button( in the line list window)to put your assignments onto the clipboard. These produce different text formats, and one of the first two is likely to be easier to work with.
  2. Paste the assignments into your observations (.lin) file, and save it.
To use this file, rather than lines in the line position window:
  1. Use the Fit Button in the log window, rather than the line list window. If the Slave Editor is in use, then the contents of all slave editors are saved before starting the fit. Note that if a slave editor is unable to save a file that has been modified then the fit will not start and the slave window will come to the front or flash.
  2. Assignments are best added to the external file by copying and pasting from the line list window.