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Older Method for Automatic Assignment and Fitting - The ν11 band of cis-1,2 Dichloroethene

Note: This page has been superseded for this particular spectrum by a method including the nearest lines window - see Automatic Fitting of the nu5 band of cis 1,2-Dichloroethene. It has been left in the documentation because it is a legitimate way of working where the aim is to match small sections of a spectrum.

This page provides a detailed walk through to accompany "Automatic Assignment and Fitting of Spectra with PGOPHER". C. M. Western and B. E. Billinghurst, Physical Chemistry Chemical Physics, 19, 10222 - 10226 (2017), doi:10.1039/c7cp00266a. It describes the process of assigning and fitting a high resolution (0.001 cm−1) spectrum of the ν11 band of cis-1,2-dichloroethene at 570 cm−1, taken at the Canadian Light Source. It assumes some familiarity with the basic operation of PGOPHER, as in Walk-through of Simulating and Fitting a Simple Spectrum.   The raw initial spectrum is provided as nu11raw.ovr; this essentially as saved by the spectrometer, but with the only region around the ν11 band saved.

A. Converting to a line list

The first step is to convert the spectrum to a list of line positions and intensities. This can be done with an external tool if required, but the internal tool is described here.

  1. Load original spectrum, nu11raw.ovr.
  2. Right click on the overlay and select "Baseline...". This brings up a window allowing a baseline algorithm to be chosen, and then an automatic peak finder to be run. Tools for zooming and panning are available at the top of the window, and work in the same way as those on the main window.
  3. Press the "Baseline" button to calculate a baseline. The orange line shows the calculated baseline, and the green line indicates the upper limit of the points used in calculating the baseline. This spectrum clearly has a ripple in it; setting "Window" non-zero turns on a algorithm involving a moving average over the specified window to identify the baseline. It works by attempting to identify points on the baseline (within the "Noise Multiplier"); for this spectrum turning on the "Dense" option in the drop down menu, found by clicking on the small down arrow by the "Baseline" button helps. Try 100 for the "Window" and  0.5 for the "Noise Multiplier". Pressing "Baseline" should yield a display like this:

    The baseline around the band heads is not right, but these are too dense for simple assignment anyway.
  4. If you want to save the spectrum with the baseline subtracted, select "Apply to New" from the drop down menu to generate an overlay as shown in the upper trace, though this is not necessary in this case.
  5. To try the line finding algorithm, zoom in on a small region so that individual lines are clearly visible. Turning on "Live update" from the drop down menu (next to the "Baseline" button) will show the lines found in the upper window in blue automatically as the parameters are changed. (Note this can be slow if the selected region is large.) Adjust the "Noise Multiplier" to give a sensible set of peaks indicated in the top trace. It is not necessarily the same as used for the baseline calculation - in this case a "Noise Multiplier" of 2 is promising, giving a display something like this:
  6. From the drop down menu, select "Make Linelist". This will generate a line list that shows in the main window.
  7. The resulting line list is saved as nu11line.ovr. To save space the raw spectrum has been deleted, though for the later steps it can be helpful to have both spectra available, and peaks missed by the automatic peak finder can be measured manually if needed. (To load two overlays at once drag and drop both files onto the main window, or use "File, Load Overlay..." followed by "File, Add Overlay...".

B. C2H235Cl2

1. Rough Alignment.

The obvious starting point is with the most abundant species. An initial simulation is provided in cisC2H235Cl2initial.pgo. This is a standard asymmetric top simulation set up as follows:

  1. Constants for both states were initially set to those determined by a microwave spectrum of the ground state (Leal et al, 1994).
  2. As this is a near prolate top, the upper state parameters were converted to use Bbar = ½(B+C) and δ = B−C, as the spectrum is relatively insensitive to the latter.
  3. Some manual adjustments to the Origin, and Bbar were made to obtain a spectrum that was roughly right by comparing to a low resolution spectrum from the PNNL database (Sharpe et al, 2004).
  4. The simulation suggests the region around the 35Cl2 band head, excluding the 35Cl37Cl band head is likely to be dominated by the 35Cl2 species, so this is used as the starting point for the fit:

2. Initial search for Ka = 6 lines

Looking for Ka = 6 lines is a good starting point as higher K values typically behave very close to a symmetric top, so the spectrum is unlikely to be sensitive to δ. In addition the lines will all have much the same contribution from A, so only two parameters, Bbar and the Origin, will be needed to fit this set of lines.

  1. For an initial search for Ka = 6 lines open the transitions window (View, Transitions) and select:
    1. "Change" as "<>", which hides the Q branch transitions. The Q branch is unlikely to make a good search target because almost all of the lines are blends.
    2. Upper state Ka as 6.
    3. Upper state symmetry as O+. This selects one of the pair of near degenerate Ka = 6 lines, which are not resolved here. (Which of the two is chosen is not important.)
    4. Make sure "Filter" is checked and then select:
  2. The resulting plot confirms the regular pattern, much like the classic P and R branch combination of a linear molecule, which will therefore be described by two effective parameters:
  3. When you are happy with the selection displayed click "Add". This will add entries to the line list window for all the transitions selected by the transitions window.
  4. In the line list window, make sure "More, Advanced" is selected to make the advanced settings visible. Set "Accept" to the maximum error you expect for the "check" transitions - in this case try 0.001, approximately the line width.
  5. Bring up the auto fit window with "Overlays", "Autofit..."
  6. Set "Window" to the search window for the initial fits, i.e. how far each side of the initial line positions you want to search. This should reflect how far out you think the lines might be - try 0.3 cm−1 here, which is approximately the distance between the selected lines.
  7. Select the upper state parameters to float in the constants window. - in this case Bbar and Origin.
  8. Select the lines for the trial assignment in the line list window - these should be lines that you are reasonably confident will be clear in the spectrum. In this case two lines are enough, and the P branch region looks clearest. Some separation in J is likely to give the best determination of constants, so try P(11) and P(14) (These appear with their full labels, qP6,6(11) and qP6,9(14) respectively). To select these two lines, click on (say) the P(11) line and use the up (or down) arrow buttons at the top of the line list window to move it next to the P(14) line. Then click and drag over the P(11) and P(14) rows so that both are selected.
  9. The file at this stage is saved as cisC2H235Cl2_A.pgo.
  10. Press "Search" in the Auto Fit window. There will be a short delay as the search is done.
  11. When the search is complete, the best fits will be presented in the auto fit window, which lists:
    • nOK - the number of "check" transitions within the "Accept" window
    • Residual - the RMS observed - calculated for these "check" transitions.
    • SumI - the sum of observed intensity for these "check" transitions.
    • The values of the constants obtained for each fit.
    • Trial - The number of the trial. (This is typically only useful for debugging purposes.)
    • nDiff - the number of transitions different to the selected fit. This is only displayed if one of the fits is selected.
    Some additional information is shown in the log window.
  12. To try out an individual fit, double click on that row. This will update the line list window with all the assignments made by that fit, and display the residuals window with the obs-calc plotted for the assignments made. The standard PGOPHER fit process can then be used to refine the fit. If you don't like the result, the "Reset" button will discard the new assignments and reset the parameters.
  13. In this case none of the fits look promising, though each fit has a low residual. Inspection of the results indicates a wide variation in the origin values, but the location of the origin is pretty clear in the experimental spectrum. To limit the possible range for parameter values, set the maximum permitted change (+ or −) in the "Std Dev" column in the constants window for the required constant. This will speed up the search process, as trials can be discarded more quickly. In this case try a value of 0.1 for the Origin, and try again from step 9 above. (Make sure you have pressed "Reset" so that all assignments are removed.)
  14. Now fit number 3 looks promising, especially looking at the region around 568.7 cm−1:
    This shows the K sub bands with approximately the right spacing, though the detail is wrong.
  15. Once you have found an initial fit that looks good, press fit in the line list window a couple of times. This will fit all the assigned lines in the normal way, and produce revised constants. The residuals window can be very helpful here; for the worked example here it clearly indicates one transition as much a much worse fit than the others, so should be checked:
    To do this, right click on the point in the observations window and try one of the following:
    1. Select "Show and Edit". This will highlight the relevant observation in the line list window, and centre the plot on the transition. (This is most useful if the "Expand range" button () is pressed a few times so the window only shows a small plot range.) Setting the "Std Dev" for this line to blank in the line list window will remove it from the fit.
    2. The quick fix (... to sweep it under the carpet) is simply to select "Remove Point(s)". This will set "Std Dev" to 0 for this transition, excluding it from the fit.
  16. After a refit, the resulting file is saved as cisC2H235Cl2_B.pgo.

3. Initial fit of the Ka structure of the P(13) lines

While the K sub-bands are now in approximately the right place, the structure within them is not right. The obvious constant to fit next is A, as this determines the structure within the sub-band. δ = B−C is also important,but the range of Ka can be chosen to be insensitive to this. (Note the selection rule for this band is ΔKa = 0, so selection can be in the upper or lower state.) To see the Ka dependence, set up the plot as follows:

  1. Turn on the Fortrat plot (Plot, Fortrat, Show). This adds an extra window, where the vertical axis is a selected quantum number. For the current case two changes need to be made to make the plot usable:
    1. Low intensity lines need to be ignored for the purposes of plotting; in the constants window, select the "Simulation" object and set "MinI" to 0.1
    2. The quantum number plotted defaults to J, but Ka is more useful. In the same "Simulation" object, set "FortranQno" to A.
  2. Pressing the simulate button now gives a plot showing the higher Ka lines are close together, and show a regular pattern, but the pattern of the lower Ka lines is much less obvious. The plot below shows the P(13) region, which looks reasonably clear:
  3. Given the lines are all close together, it is not obvious that the current assignments of Ka = 6 lines are correct, so it is probably best to remove all the assignments. Press Clear In the line list window to do this.
  4. The plot above suggests Ka ≥ 5 lines form a regular pattern, and do not show any asymmetry splitting at this resolution. As the lower Ka lines are stronger, this suggests a search in A using Ka = 5 and 6 as fit transitions, with higher Ka lines as check transitions. To set this up, open the transitions window and, clear any Ka and symmetry values set, and set lower J = 13. "Change" should strictly be "P", though makes no difference in this case.
  5. Hit Add to add these transitions to the line list window. To exclude the Ka < 5 lines from the fit, delete them from the line list window. Individual lines can be deleted by clicking on the line, and then the delete button (the cross ) in the top row. In this case sorting the lines first ("More, Sort On, Branch" in the linelist window) can speed things up, as multiple lines can be selected by clicking and dragging before deleting.
  6. To set the search up, select one P5 and one P6 line, using the up and down arrow buttons if necessary to move them next to each other, and then clicking and dragging to select the two rows.
  7. Some adjustments are also required in the auto fit window; the search range can be reduced - try "Window" = 0.03 cm−1. "Max Blends" needs altering also; this sets the maximum number of assignments that can be assigned to any one observed line, and the as the sub-band looks as though is has a band head blends are likely - try 3 for this, rather than the default of 0.
  8. The parameters to float should now be A and Origin; BBar should be fixed as the lines selected will not determine this. Floating the Origin gives a way for the relative position of the sub-band to be varied. Note that this will have StdDev set, which will limit the search range; I suggest clearing this, or at least increasing the value to avoid unreasonably restricting the search range.
  9. The file at this stage is available as cisC2H235Cl2_C.pgo.
  10. Press Search; this is now a very quick search, and the first fit looks very promising:
  11. Press fit a couple of times. The residuals window might not indicate any problems at first glance, but changing the horizontal axis to Ka reveals a systematic trend. This is selected by setting "X" to "A", which gives:
  12. Right clicking on the Ka =11 mark in this window, selecting "Show and Edit", and zooming the display a couple of times indicates a possible reason - perhaps the assignment should have been made to the weaker peak to higher frequency, rather than the stronger peak to lower frequency:
  13. Approaches to fixing this include manually making the alternative assignment; right clicking and dragging on the observed transition will replace the assignment with the newly measured peak, as the transition will be selected in the line window. The measurement can be on the original spectrum (for peaks that were not found in the original line list generation) on in the line list, where the assignment has failed. Note that you may have to do this twice, as most lines are doubled because of the unresolved asymmetry splitting.
  14. Alternatively, simply exclude this (pair of) lines from the fit - right click on the point in the residuals window, and select Remove Points. Fitting now gives a much smaller residual (by a factor of 4) and no obvious trend:
  15. To recalculate the positions of the unassigned lines in the line list window, click on "All" in the line list window (to select all the lines) and then "Update", which will replace the "Position" column with values calculated with the current set of constants for transitions that have not been assigned (i.e. where "Std Dev" is blank or zero).
  16. With this updated calculated line list, the "Nearest" button in the linelist window will assign any unassigned lines to the nearest line in the line list, provided it is within the acceptance window. In this case it assigns the Ka = 11 lines to the alternative peak:
  17. After a pressing Fit a couple of times, the resulting file is saved as cisC2H235Cl2_D.pgo.

4. Complete fit of the Ka structure of the P(13) lines

The next step is to add the Ka < 5 lines back into the line window, and determine δ = B−C. To do this:

  1. Bring up the transitions window - this should still have lower J = 13 as above, unless you have changed something. Hitting "Add" will add the low Ka transitions back to the line list window. Provided "Discard Duplicates" is selected, only lines not already present in the line list window will be added. For all the Ka values to be included, you will have to ensure the plot range is sufficient - if you have zoomed in following the instructions above zoom out.
  2. To set the search up select a single low Ka, say Ka = 0, and float Origin, A and BDelta. To avoid limiting the search range, clear the "Std Dev" column for these parameters. Note that, as the other assigned lines will be included in the trial fit, only a single selected line is needed, even though three parameters are to be determined.
  3. Given the large spread of the low Ka transitions, a slightly larger search window might be required - try "Window" = 0.1. (The search will in any case be fast, as only a single line is assigned.)
  4. The file at this stage is saved as cisC2H235Cl2_E.pgo.
  5. Pressing "Search" is again very quick, and the first two fits  are quite promising. Note that the simulated spectra for the two fits are very similar, and a useful indicator for this is the nDiff column, which indicates that these two transitions only have two transitions with different assignments:
  6. Given the similarity, either fit could be used; the differences are likely to be resolved at a later stage. Taking the first fit (as it has the lowest residual) and pressing fit a couple of times gives a good fit with an average error much less then the linewidth. The residuals window suggest a couple of lines have slightly larger errors, and investigation indicates these are blended lines:
  7. Removing these for the time being and fitting gives cisC2H235Cl2_F.pgo.

5. Fit of the P(12) lines

The final step is to determine Bbar, which is straightforward as simulation of the P(12) lines is already quite good:


  1. The above plot is generated by using the transitions window to select transitions with lower state J = 12; note that the correct range was selected simulating the J = 12 transitions, and then pressing "All" in the transitions window. This is done automatically if "Plot All" is checked. Press "Add" to add these to the line list window, and then set up a search by selecting a single strong P(12) line, say qP6,6(12). As in the previous search, the previously assigned lines are included in the fit, so only a single line is required. The fitted parameters can now include Origin, A, Bbar and Bdelta; the "Std Dev" for these should again be cleared to avoid limiting the range. The file at this stage is saved as cisC2H235Cl2_G.pgo.
  2. Pressing search gives a very good fit as the first choice, and all three upper state rotational constants are now determined. The above process reassigns the blended lines we had excluded. These lines can be removed completely or assigned a larger "Std Dev" in the linelist window; removing them gives cisC2H235Cl2_H.pgo.

6. Completing the fit

The next step involves adding as many lines as possible to the fit, which can be done by walking down and up in J. As many predictions will now be close to the observations, a search need not be done, and a simple assign to nearest approach can be used, for example:

  1. Use the transitions window to add the P(11) lines to the line list window, and assign them to the nearest line with the "Nearest" button in the line list window. The "Nearest" button in the transitions window performs both these steps and additionally performs a complete fit cycle, and is particularly useful for walking along a series of transitions. Either of these assigns all the P(11) lines, though the residuals window suggests a couple are slightly off. If you are confident that these are simply blends, then draw a box round the points you want to keep (as shown below) then right click and select "Remove Points Outside".

  2. This process is easily repeated walking downwards in J; taking this down to P(5), where the Q branch lines start to obscure the P branch lines, gives cisC2H235Cl2_I.pgo.
  3. At this point switching to R branch lines gives an independent check of the assignments to date. Staring with R(5) and working upwards in J shows most predicted peaks matching, though it is less clear here than in the P branch region because of interference from the 35Cl37Cl species. Given the high probability of blends, the R branch lines were not included in the fit.
  4. The clearest unassigned transitions are now the the P branch - P(14), P(15) (partially obscured by a Q branch band head), and then P(19). At P(19) it is worth trying to float the quartic centrifugal distortion terms. Stepping up to P(30) gives cisC2H235Cl2_J.pgo. Stepping up to P(39) gives cisC2H235Cl2_K.pgo; the sextic centrifugal constants have been floated for this. There is also some evidence for localised perturbations, with some transitions being out of place, so we stop at this point.
In publishing the final fit, I recommend including a fit log file run with "PrintLevel" set to "Detail". This gives a complete set of information about the fit, including the correlation matrix and matrix elements used, which aids use of the fit results elsewhere and makes sure the fit can be reproduced. The "PrintLevel" setting is found in the top level object; reset the value to "Mininal" after producing the log to avoid slowing the program down by producing unnecessary output. The final log file is available as samples/autocis/cisC2H235Cl2.log; to produce this file the "Precision" setting (also in the top level object) was increased from the default value of 4 to 5. This increases the precision of some of the displayed values in the log, including the observed and calculated values.

C. C2H235Cl37Cl

The process here is given in outline; refer to the process above if you need reminding about the details.

1. Rough Alignment.

Assignment for the mixed isotopologue proceeds much as for the 35Cl2 species, with constants for both states initialized from the ground state microwave spectra (Leal et al, 1994), with some manual adjustment of the Origin and Bbar for rough agreement with the observed spectrum. This file is available as cisC2H235Cl37Clinitial.pgo. Identifying a region clear of the 35Cl2 species is tricky, but there is a region immediately to higher frequency of the 35Cl2 band head that looks promising, particularly as the 35Cl2 simulation only shows weak lines:


2. Initial fit to A and Bbar

In this case a three parameter search was used, using Ka = 6 and 7 lines for a range of J values.

  1. In the transitions window, select upper state Ka = 6, symmetry = E+O−, change "<>". With the aid of the Fortrat plot, adjust the plot range to select lower state J ≤ 25. The choice of the range of J is not crucial, but the idea is to give sufficient intense lines, but to avoid a region where centrifugal distortion is significant.
  2. While these are strong lines, of which a reasonable number might expect to appear in the fit, the region around the 35Cl2 band head is too crowded to give useful assignments, so after pressing "Add" in the transitions window, manually delete the R branch lines below 570.8. If there are too many lines in line list window, check you have the correct filter settings in the transitions window. The lines in the line list window can be sorted by frequency (if they are not already sorted) with More, Sort On, Frequency.
  3. Repeat the process for to add Ka = 7 lines, again deleting the R branch lines below 570.8.
  4. To set up a search requires three lines to be identified. Given the region immediately to high frequency of the 35Cl2 band head is clear, three R branch lines from this region are an obvious choice. A possible choice is qR6,10(16),  qR6,11(17) and qR7,11(17); move these to the top of the line list window with the move to top arrow button so they are adjacent, and then click and drag to select these three transitions.
  5. To set up the search use acceptance window of 0.001 cm−1 (the linewidth) as before and a search window of 0.3 cm−1. "Max Blends" could be 1 (as the Ka = 6 and 7 lines for a given J could overlap), and limiting the Origin search range to 0.1 is also required. Float Origin, A and Bbar. The file at this stage is available as cisC2H235Cl37Cl_A.pgo.
  6. Press Search - as there are a large number of possible assignments (6.3 × 106) you will be prompted if you want to continue. The search will take 5-15 minutes, depending on the speed of your computer. The file after the search (which includes the results of the search) is available as cisC2H235Cl37Cl_Aafter.pgo.
  7. Trying the results, the first one gives promising results in the region we have identified as clear:
    The others are all much worse, which might suggest using a search with a restricted search range on all of the parameters might be required to give more candidate fits.

3. Fitting A, Bbar and δ

  1. Taking the first fit - press "Fit" to  give the best values - we can proceed as for the main isotopologue, as we have essentially reached step 4. All the J" = 17 lines look reasonably close, suggesting a search on these for Origin, A and Bdelta with three lines selected. I suggest deleting all the previous assignments at this stage to allow for some minor re-assignments, and adding all J" = 17 lines to the line window for fitting to. The search saved in cisC2H235Cl37Cl_B.pgo has qR0,17(17), qR6,12(17) and qR13,5(17) selected, "Max Blends" = 3 and a search window of 0.1 cm−1. This range is probably rather wider than needed at this stage, but it is nevertheless reasonably fast. (Interestingly, using qR5,13(17) as one of the selected lines does not give good results, and subsequent work suggests some Ka = 5 lines are perturbed.)
  2. Fit number 1 is clearly the best and adjusting the fit using with the help of the residual plot yields a good fit to all the lines, available in cisC2H235Cl37Cl_C.pgo. (The qR5,13(17) is clearly slightly out of position based on this simulation; the intensities indicate it is not simply a blend. The other two lines excluded from this fit are simply blends.)
  3. Moving on to the R(18) sub-band we can now determine all 3 rotational constants with a quick search based on just one line, say qR6,13(18). Clearing the search ranges for all the parameters gives cisC2H235Cl37Cl_D.pgo and the search is now very quick, and the first fit is clearly better than any of the others.
  4. Moving on to R(16) the fit is confirmed, and the Nearest button in the transitions window can be used to add and fit these lines, though the plot range should be reduced to exclude the band head region. R(15) can similarly be added. After some tidying up, cisC2H235Cl37Cl_E.pgo results.
  5. Switching to the P branch region is a possible path at this point, as it is not possible to go to lower J in the R branch. While there is more interference from the main isotopologue, P(15) has sufficient lines showing for assignment. Assigning this, and stepping doen to P(8) yields good results (cisC2H235Cl37Cl_F.pgo), though a significant number of lines have been excluded as blends.
  6. At this stage the R branch transitions seem clearer, so try stepping upwards starting at R(19). Consider starting to float the centrifugal distortion parameters; in this case try floating these when R(22) is reached. It is then possible to walk the assignment up to R(30) fairly easily, at which point the strength and number of the 35Cl2 lines becomes a concern. A bit of editing is required at each J to check on the larger residuals. Keeping the largest individual error to around 0.00045 cm−1 gives a fit with an average error of 0.00017 cm−1, available in cisC2H235Cl37Cl_G.pgo.
The log file for the final fit is available as samples/autocis/cisC2H235Cl37Cl.log.

References.