package for:

   Assignment and Analysis of Broadband Spectra

 
         

       This is a package for graphical analysis of extremely broadband spectra with resolved rotational structure. The spectra can be pure rotational spectra, such as FASSST spectra, or rotation-vibration or vibronic spectra from Fourier transform interferometers, or laser spectrometers. Even if true broadband spectra are not available the package allows concatenation of many shorter spectra into a single spectrum and efficient operation on such a segmented spectrum. A brief description of the AABS package has been given in

Z.Kisiel, L.Pszczolkowski, I.R.Medvedev, M.Winnewisser, F.C.De Lucia, E.Herbst, J.Mol.Spectrosc. 233,231-243(2005)

and that paper can be used for citation. Since then the package has been used in many further studies, and a summary of some of the more advanced applications can be found in

Z.Kisiel, L.Pszczolkowski, B.J.Drouin, C.S.Brauer, S.Yu, J.C.Pearson, I.R.Medvedev, S.Fortman, C.Neese, J.Mol.Spectrosc. 270,134-144(2012)

       Complete (and continuously updated) documentation of the package is now provided in its own help file. The following is only intended to provide a summary of the main features of the package, and a direct route to the downloads:


        General description of the AABS package:
       At the core of the AABS package are two display programs:
  • SVIEW_L = viewer of the spectrum, based on program SVIEW
  • ASCP_L = viewer of predictions, based on program ASCP

        which are integrated with several other programs. The package also comprises of the utility program AC, which allows generation of dataset distribution plots that allow rapid overview of large spectroscopic datasets.

       ASCP_L is normally used as the active program, and the display of SVIEW_L is locked to it. Predictions of spectroscopic species of relevance to the current spectrum can be loaded into the program and displayed with various options for distinguishing between the various species. A special highlighting option by 'cloning' the current line allows highlighting of a transition sequence of interest. Frequency regions around successive predictions in this sequence can then easily be inspected in turn, and if there are suitable lines in the spectrum those can be measured. The frequency determined by SVIEW_L and quantum numbers from ASCP_L can be added to a specified datafile for the fitting program. When deviations from predictions are not too large then the analysis process involves only two keystrokes per line. Predictions and data for fitting in the standard of either SPFIT/SPCAT or ASFIT/ASROT packages can be used directly, and those from ERHAM can be used by means of several reformatting programs (instructions).

        An alternative mode of operation is to draw a Loomis-Wood type plot of strips of the experimental spectrum centred on successive highlighted lines. This display can either use the actual spectrum or its stick representation based on peakfinder results, which allows very fast operation. This mode is especially suitable for earlier stages of assignment. Measurements and addition of data to the fitting file can be made in a very economic way in both the main display mode and in the LW mode. requiring only two-three keystrokes per spectral line.


        AABS snapshots:
        Snapshots of the display for the basic mode of operation (make sure that your browser does not rescale the loaded picture, since this may affect the clarity of what you see):
  • snapaabs - standard alignment of the two programs as launched using the configuration files below. The predictions consist of four data files, which are a mixture of .ASR and .CAT files, and are for ground states of two different isomers and some excited vibrational states of diethyl ether. Different species are drawn in different colours and a transition sequence in one of these has been highlighted in white.
  • snapai - the summary of information on the loaded prediction data files. Eleven different files, consisting of a mix of .ASR and .CAT files have been read and their transitions merged and sorted for plotting.
  • The primary help system is as contained in the present AABS_HELP.CHM file, but it is also possible to display online help screens with Ctrl H. For the ASCP_L basic display mode these are: snapah1 - the main online help screen, snapah2 - the second help screen summarising the ASCP_L commands that are specific to linked operation with SVIEW_L, and snapah3 - the third help screen summarising the files that can be used by ASCP_L

         In addition to the basic mode the Loomis-Wood type mode offers extended display possibilities. The LW strips can be drawn as a simple stick representation of the spectrum, as open and filled triangle approximations to the spectrum and can also be from the actual spectrum. Several alternative colour schemes and output leading to PostScript/PDF diagrams are available.

  • snaplw - the preferred open triangle mode of the LW screen, which provides an optimum between clarity and speed of operation and has been adapted from the excellent Loomis-Wood program written in the Winnewisser group in Giessen. This plot plot obtained on pressing the F5 key while in the normal display, after having marked a transition sequence in the standard mode, as in the snapshot snapaabs above. The spectral strips can be easily scrolled in four directions, a movable cursor is available to select desired lines, and indication of assigned lines can be toggled on and off.
  • snaplwst, snaplwft - stick type and filled triangle versions of the LW display, which are toggled through by pressing the p key. Useful for more broadband, and more close in work, respectively.
  • snaplws - Loomis-Wood type plot using strips of the actual spectra, obtained by pressing the [ key in the LW display mode.
  • scheme1, scheme2, scheme3 - some of the different colour schemes for the LW display, which can selected with the he C key in the LW display mode.
  • snaplwt.pdf - result from output for the gle program, which is automatically generated for the Loomis-Wood display as above. Gle can then be used to compile the generated files into PostScript and PDF diagrams. Such diagram can also be generated in portrait orientation.
  • snaplws.pdf - PDF for a LW plot based on an actual spectrum
  • snaplwh - the help screen in the Loomis-Wood type plot

  


        The recommended installation procedure:
  • Create a directory called C:\ROT on your computer and place in it the five files: 
  • Place shortcuts to SVIEW_L and ASCP_L on the desktop. And this is (almost) all!
  • Actually this is not all for the more recent versions of Windows. You might need to unblock the files for unhindered use on your computer, since Windows will block them after downloading from the Internet.  In order to do this:
    • right click on the file in Windows Explorer or your file manager of choice,
    • select Properties,
    • click the Unblock button in the Security area at the bottom of the General tab.
  • You might also get the message "Msvcr71.DLL cannot be found" when you try to launch either of the two programs. If that is the case you also need the file MSVCR71.DLL, which is best placed in the same directory as the programs, namely C:\ROT.
  • NOTE: the name C:\ROT for the directory containing the program files is mandatory and cannot be changed.  The analysis projects themselves can, however, be in any directory of choice.
  • WINDOWS 10: there is a new default setting for borders around the program windows with the result that the current versions of SVIEW_L and ASCP_L (as of Aug2015) lose a few pixels on the bottom status line.  The suggested temporary solution is to use the XP compatibility mode, which is selected with the following actions ---> Right mouse click on the program icon->properties->compatibility tab->Compatibility Mode=Run this program in compatibility mode for: Windows XP (Service Pack 3)
  • WINDOWS 7: this Windows version allows the user to change the settings for borders around the program windows.  The default value is compatible with SVIEW_L and ASCP_L but if you notice missing/extra pixels the working area of these programs then set the borders explicitly using: ---> Right mouse click on the desktop->Personalize->Window Color->Advanced Appearance Settings->Item=Border Padding->set size=6.  An alternative entry point to these settings is through  Control panel->Personalization.
        On first time use on a new system you might perhaps also want to adjust the graphics size of the AABS programs to the size that you are prepared to devote to them on the desktop. The program windows are not freely scalable but their size is adjustable and is declared in the file AABS.CFG, which may need to be reedited.

       If you plan to use ASFIT/ASROT for fitting/prediction, as well as other programs from the PROSPE website, then it is recommended that these are also placed in the C:\ROT directory. For more convenient launching of these programs from the command line you can optionally add C:\ROT to your system path. One way of going this (on XP) is to go through the dialogue:

Control Panel->System->Advanced->Environment Variables-> PATH

and to append ;c:\rot to the value of that variable. Another way involves locating the file AUTOEXEC.NT, normally in C:\WINDOWS\SYSTEM32 and adding to it the line path=c:\rot if there was no previous such line in this file, and if there is one then append to it  ;c:\rot.

       

        You might want to download a complete sample project, and follow the associated mini-tutorial to check out some features of the package without the need for setting up a project from scratch.

 

        The recommended preparatory steps to running the package:
  • Create a directory which is to contain all work associated with analysis of a given spectrum.
  • Copy your broadband spectrum to this directory - it is recommended that the spectrum be in the compact binary mode used by SVIEW_L. This can easily be generated since SVIEW_L can read a spectrum as a two column ASCII file of point frequencies and intensities (preferably, but not necessarily, equally spaced in frequency). Binary file is then generated with the M option.
  • Generate peakfinder output for this spectrum if Loomis-Wood type plots are to be used for assignment. This is to be done by using the automatic peakfinder of SVIEW_L, which is invoked by specifying a negative value for the 0 option.
  • Make sure you have either SPFIT/SPCAT or ASFIT/ASROT running on your computer, the relevant executables can also be placed in directory C:\ROT
  • It is highly recommended that you have a text editor that is able to sense that the contents of an opened file has changed and it can then refresh it. The standard Notepad editor is not able to do this but, for example, the PSPAD editor can.
  • Edit a suitable version of the MOLNAM.INP file, which declares the names of prediction files to be displayed by ASCP_L.
  • When working with a segmented spectrum it is, optionally, possible to use a file called LIST to specify the frequency segments for which there is data. This file can either be created using SLIST (if the component spectra are available) or by reediting this LIST example - only the frequency entries are of relevance.
 

        The recommended way of launching the package:
  • From your favourite file manager drag and drop the spectral file onto the SVIEW_L icon on the desktop, then press ENTER
  • Drag and drop the MOLNAM.INP file onto the ASCP_L icon on the desktop. Press 2 ENTER for batch input, and then just ENTER as a data file name.
  • In the text editor open the data files associated with fitting the current spectroscopic species of interest as declared in SVIEW_L.INP. These might be either .LIN, .PAR, .FIT files for SPFIT, or .ASF, .RES files for ASFIT
  • Open a command prompt window, with the current directory set to the work directory for the current problem
  • The two viewing programs should have opened as two adjacent strips. Almost all operations are carried out from within ASCP_L, which controls the display of SVIEW_L as necessary. There are, however, two tuning tasks for dealing with the spectrum that it might be necessary to perform in SVIEW_L. One is setting the optimum width of the fitting window for determining line frequencies - expand a line profile with A/S keys and optimise using the O and 0 options. Another task is Y-axis scaling of the spectrum - use W/Z and 2/3 keys.
 

        Typical operation:
  • Click (or use ALT TAB) to make ASCP_L the active window - this should be the lower of the two strips. Note that there is minimal mousing around - almost all commands are issued from the keyboard, which is a much faster device and allows increased efficiency. It pays to study and learn the main keys for controlling the programs and two summary charts ASCP_L_KEYS.PDF and SVIEW_L_KEYS.PDF have been prepared to print and keep handy. Note that the navigation commands for the two programs are identical.
  • Move to the stick corresponding to a line from a line sequence of interest and highlight this sequence with t. It might actually be easier to just move to any line predicted for this spectroscopic species, use T to preselect a range of lines, and then find the desired type of line with left/right arrows. Subsequently t will highlight the sequence precisely.
  • Move along the lines in the highlighted sequence with left/right arrows and make measurements as necessary, mainly with F1 or F2. If a line in the spectrum is significantly off the cursor position you can move closer to it with 2/3 keys of ASCP_L and then measure.
  • You might want to check on the progress of accumulation of measurements in the fitting data file by moving to the text editor window. The data file is not locked by the AABS programs so that lines can be rearranged/tidied, the file saved, and further data will be appended to the modified file.
  • Go to the command line window and carry out fitting and prediction in your favoured way. It is recommended to browse through the results file from the fit prior to embarking on predictions. If working with SPFIT you might find it useful to reformat the .FIT file with program PIFORM, which improves readability and allows annotations on the data file. The fitting/prediction is not automated on purpose. It is hoped that in this way the user can spot any problems earlier and will take suitable corrective action, before it is too late.
  • Once new predictions are ready press ESC in ASCP_L, which updates predictions, as well as markers of lines already measured. To switch to a new spectroscopic species place the name of the new file for the fitting program in SVIEW_L.INP and update both SVIEW_L and ASCP_L by pressing ESC.
  • In more difficult cases launch the Loomis-Wood display by setting the cursor on a highlighted line and pressing F5. Use the help screen of this display for information. The steps above can be carried out as many times as necessary - it is not necessary to close the two display programs at any stage.

 
   

SVIEW_L = Spectral viewer
   
SVIEW_L.EXE The executable for Windows, to be placed in a directory named C:\ROT. The program uses dynamic memory allocation so that spectrum length is only limited by the hardware resources of the computer.

SVIEW_L reads spectra in the IFPAN binary format and in two column [frequency,intensity] ASCII format. ASCII to binary conversion is also possible.

  • The summary of active keys in SVIEW_L_KEYS.PDF provides a convenient overview of the possible actions.
  • The most complete documentation is available in AABS_HELP.CHM

NOTE: you might want to check the comments on use of the PC-Speaker made below.

   
SVIEW_L.HDR The header of the current source file. This contains the date of the current version and more documentation.
   

ASCP_L = Viewer of predictions
   
ASCP_L.EXE The executable for Windows, to be placed in a directory named C:\ROT. Dynamic memory allocation is now used so that memory can be allocated more efficiently for both small and large problems.

ASCP_L reads .ASR files from ASROT, .CAT files from SPCAT, .FRE files from the automatic peakfinder in SVIEW_L, and simple two column (frequency, intensity) ASCII files.

  • The summary of active keys in ASCP_L_KEYS.PDF provides a convenient overview of the possible actions.
  • The most complete documentation is available in AABS_HELP.CHM

NOTE: The two AABS programs make various beeping noises of confirmation/warning using the PC-Speaker channel. Support of this channel seems to vary these days. On desktops it is not too rare to find no device connected to the separate PC-Speaker output on the mainboard, because case manufacturers no longer put such a device in the case. The seller, when requested, will attach a small beeper to that connector.

On laptops this channel may be just another channel in the sound card, but often without active volume control. In such case the volume of the beeping sound may be controlled using the beep settings in SVIEW_L.INP.

It is also possible that the PC-Speaker channel is inactive/muted and may have to be activated in your Windows.

 

ASCP_L.HDR The header of the current source file. This contains the date of the current version and more documentation.

 

MOLNAM.INP A sample batch input file for ASCP_L to be reedited as necessary. This is the most convenient way of using this program when more than one file with predictions is to be loaded. This file can be edited with any text editor.

Note that mixed input from .ASR and .CAT files is declared in this example. In order to unify the intensity scales of the two programs you need to either increase the intensity scaling coefficient for the .CAT file by 4.87 or to divide that for the .ASR file by the same factor.

A legend for colour codes can be found in the description of the parent ASCP program. Colour codes greater than 10 allow user definable colours by means of their hexadecimal RGB value.

   
  Files required by both ASCP_L and SVIEW_L
   
ASCPEXCH.DLL Allows information to be exchanged between SVIEW_L and ASCP_L. This file is mandatory and has to be placed in C:\ROT. The two viewing programs can also work in standalone mode, but even then this DLL is necessary.
AABS.CFG The configuration file for graphics, to be placed in C:\ROT, the active settings in this version are for comfortable operation on a 1268x1024 pixel desktop. More information on the possible settings is given in the section on SVIEW.

In Windows7 (possibly also W8) you might sometimes find that the bottom descriptive line has several bottom pixels missing (such that the 'p' in 'H=help' is more like an 'o').  This results from your Windows configuration assigning
too narrow borders to the AABS program windows.  The solution is to:
  1. Right click on the desktop and select 'Personalize'
  2. Select 'Window color' in the bottom row of options
  3. Select 'Advanced appearance settings'
  4. Choose 'Item=Border Padding'
  5. Set 'Size=value' as required (typically 5 or 6)
AABS_HELP.CHM The comprehensive help file for the package, which is also to be placed in C:\ROT. The file is viewed by pressing the H key in either SVIEW_L or ASCP_L. The old internal help screens can still be displayed by pressing Ctrl H.

On some Windows systems viewing of CHM files may not be possible.  In particular, when this file is downloaded from the Internet the current Windows will block access to its contents as an added security measure (you get the message: "Navigation to the webpage was cancelled").  In order to unblock:

  • right click on the file in Windows Explorer or your file manager of choice
  • select Properties
  • click the Unblock button in the Security area at the bottom of the General tab.

You can read this Wikipedia entry for additional information on this standard and on alternative viewers.

SVIEW_L.INP The input file read by both SVIEW_L and ASCP_L which specifies several important parameters for linked operation under the AABS scheme. The file is to reside in the directory used for the current analysis and the key parameters are:
  • the name of the fitting data file to which measurements are to be appended. File extension specifies the fitting program: .LIN selects SPFIT and .ASF selects ASFIT
  • the name of the peakfinder file for Loomis-Wood type plots made with ASCP_L. This file is to be generated with the automatic peakfinder option of SVIEW_L
MSVCR71.DLL This file is only necessary if you are unable to launch the programs and the system prints a message that "Msvcr71.DLL cannot be found" . This DLL is best placed in C:\ROT.

The reason is that this file is no longer regarded as part of the operating system and is no longer distributed with Windows. Developers using Visual C++ .Net 2003 (as is the case here) are to distribute it with their application: see this Microsoft note.

   

Sample project and tutorial
   
LACTIC.ZIP An archive containing a complete AABS project for the mm-wave rotational spectrum of lactic acid as published in J.Mol.Spectrosc. 234, 106 (2005).

Once you have been through the installation and launching sections and are sure that SVIEW_L and ASCP_L will run on your machine, just unzip the project into a directory of your choice and then do the following (in the suggested order):

  1. drag the lactic_acid.spe file (the spectrum) to SVIEW_L and press ENTER in response to the file name query
  2. drag the la.inp file to ASCP_L and press 2 and then ENTER in response to the input mode query, and ENTER again in response to the next question
  3. The spectrum is a segmented spectrum and since the programs open in the centre of the declared frequency region it so happens in this case that the top window will show a horizontal line. Use the CTRL+ Left Arrow and CTRL+ Right Arrow shortcuts in ASCP_L to move to frequency regions for which the spectrum has been recorded

The project contains data files for the ground state of lactic acid and nine different excited vibrational states. You might want to press P in ASCP_L to change to "dataset colours" for better clarity, and press I for a legend on loaded datasets. The green dots are measured ground state lines as contained in the LA0.ASF file that is specified in the SVIEW_L.INP file.

To launch the Loomis-Wood display for a sequence of lines move the ASCP_L cursor to a line of your choice using the K and L keys, and possibly also the A and S keys. The parameters of the current line are displayed near the top of the program window. Then press t for "Highlighting by cloning" and type -2 ENTER. This will highlight a sequence of transitions with the Ka'' value and the selection rules of the current transition. Pressing F5 will then launch the LW-mode. Since the spectrum is segmented and moderately sparse you might not see too much, but you can increase the number of LW rows using the + key. Note that pressing H in any screen gives you on-line help.

If you want to see the line sequences in Fig.4 of the lactic acid paper then, while in the normal ASCP_L display, type F and then enter, say -234082.4 to centre the display on the band origin, move the cursor (if necessary) to the leading line in the band, then press t and type -3 ENTER to select bands of this type, which are defined by a common value of Kc. Pressing F5 then displays all such bands, of which there are six in the recorded spectrum. You might expect to see something like this, and you can generate a Postscript version of this display like this by using the G key and external compilation of the resulting files with the gle package.

la.009
la.010
la.011
Raw spectra in SVIEW_L binary standard for testing baseline subtraction, smoothing and concatenation operations.
la0_test.asf Abbreviated ground state data file for lactic acid for training the use of the ASFIT program and measurements with the AABS package (first check what is necessary to reduce the deviation of fit to unity)
   
  Legacy versions
   
ASCP_L_400k.EXE The last version of ASCP_L with static memory allocation for up to 400k lines.
   
SVIEW3_L.EXE, SVIEW6_L.EXE, SVIEW10_L.EXE, The last SVIEW_L executables based on static memory allocation for 3M, 6M and 10M point length spectra. Note that the 10M point program needs a lot of internal memory (up to 235 Mbytes).
   

  Accessory Programs
 

AC = Automatic Converter
  Automatic Conversion of output from a fitting program into a graphical plot of distribution of (obs-calc) values as a function of quantum numbers. Input can be from:
  • a .RES output file from ASFIT (option 2)
  • a .FIT file from SPFIT as reformatted by PIFORM
  • a .RES output file generated by ERHRES from output of ERHAM

The aim of this program is to allow rapid insight into the structure of large spectroscopic datasets.

AC.EXE Win32 executable
AC.FOR The source code
   
PQR.GLE The diagram description file for the gle program, using the data files produced by AC. The size of each marker is proportional to the value of the obs-calc difference, and red markers denote values greater than 3s. Purple crosses are for the relatively rare P-type transitions.

This file is a simple ASCII script that can be customised by editing in places indicate by the comments.

   
PQR.PS

PQR.PDF

The PostScript diagram obtained by first running AC on the data file TG.RES for tg-diethyl ether and then (for gle4.0.7 installation) issuing the command:

gle_ps pqr.gle

This data set was published in J.Mol.Spectrosc. 228, 314 (2004), and the plot allows some small defficiencies to be immediately spotted. For example, the lone Q-type line for K-1''=1 would not now be reported unless several supporting lines of the same type were available. Several other lone lines, well removed from the main line sequences, might also be accidental.

   
 

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