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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
transitons 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.
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However, 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
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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 (up to 235 Mbytes). |
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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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