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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, C E.Herbst, J.Mol.Spectrosc. 233,231-243(2005)
and that paper can be used for citation.
NEW: 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 the downloads:
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A 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 can be in the standard of either SPFIT/SPCAT or ASFIT/ASROT packages.
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 in the basic mode actually uses stick
representation of peakfinder results instead of the actual spectrum,
which enables 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.
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| 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
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The recommended installation procedure for the package: |
- Create a directory
called C:\ROT on your computer and place in it the five
files:
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- Place shortcuts to SVIEW_L and ASCP_L on the desktop. And this is all!
- Actually this is not
all for the more recent versions of Windows in which you might 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.
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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.
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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.
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The recommended preparatory steps to running the package (so as to take
advantage of its main features): |
- Create a directory
which is to contain all work associated with analysis of a given
spectrum.
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- 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.
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- 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.
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- 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
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- 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.
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- Edit a suitable
version of the MOLNAM.INP file, which declares the names of prediction files to be
displayed by ASCP_L.
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- 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.
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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
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- 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.
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- 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
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- Open a command prompt
window, with the current directory set to the work directory for the
current problem
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- 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.
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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.
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- 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.
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- 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.
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- 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.
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- 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.
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- 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.
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- 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.
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SVIEW_L = Spectral viewer |
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| SVIEW_L.EXE |
The executable for Windows, to be
placed in a directory named C:\ROT. This version uses dynamic memory allocation so that
spectrum length is only limited by the hardware resources of the
computer. The summary of active keys in SVIEW_L_KEYS.PDF provides a convenient
overview of the possible actions.
SVIEW_L reads spectra in the IFPAN binary format and in two column [frequency,intensity]
ASCII format. ASCII to binary conversion is also possible.
NOTE: you might want to check the
comments on use of the PC-Speaker made below.
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| SVIEW_L.HDR |
The header of the current source
file. This contains the date of the current version and more
documentation. |
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ASCP_L = Viewer of predictions |
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| 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. The summary of active
keys in ASCP_L_KEYS.PDF provides a convenient
overview of the possible actions.
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.
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.
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| ASCP_L.HDR |
The header of the current source
file. This contains the date of the current version and more
documentation.
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| 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.
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Files required by both ASCP_L and SVIEW_L |
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| 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. |
| 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.
NOTE: this file is
used by AABS executables dated 16Feb2008 or later.
On some Windows systems viewing of CHM
files may not be possible. You can read this Wikipedia
entry for additional
information on this standard and on alternative viewers.
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| 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
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| 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.
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Sample project and tutorial |
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| 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):
- drag the lactic_acid.spe
file (the spectrum) to SVIEW_L and
press
ENTER
in response to the file name query
- 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
- 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.
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Legacy versions |
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| ASCP_L_400k.EXE |
The last version of ASCP_L with static
memory allocation for up to 400k lines. |
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| 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
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Accessory Programs |
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AC = Automatic Converter |
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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.
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| AC.EXE |
Win32 executable |
| AC.FOR |
The source code |
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| 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.
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| PQR.PS
PQR.PDF
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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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Back
to the table of programs
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