XIAM
XIAM_mod
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XIAM is Version
2.5E
of
Holger
Hartwig's
IAM
internal
rotation
program for up to three
symmetric internal rotors and up to one quadrupolar nucleus
XIAM_mod is a modification by Sven Herbers providing two additional higher order internal rotation parameters
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The XIAM
program has been kindly deposited by Heinrich Maeder of the Kiel group who is currently its custodian and can
pass communications to Holger. Although Holger Hartwig can still be contacted he is now working outside academia.
The downloads section first contains the unchanged program distribution
package as received from Kiel, which is followed by some add-ons
resulting from the experience in using this program in Warsaw.
XIAM uses
the extended Internal Axis Method proposed by Woods to treat internal
rotation in an asymmetric top molecule and the principal features are:
- up to three symmetric internal rotors
- up to one quadrupolar nucleus with weakly
interacting nuclear quadrupole coupling
- centrifugal distortion up to sixth order for
the pure rotational part
- centrifugal distortion up to fourth order
between internal and overall rotation
- some top-top coupling terms for analysis of
excited states of internal rotation
- high speed of operation due to suitable
basis transformations and matrix factorisation
The
recommended reference for citing the use of XIAM is:
H.Hartwig and H.Dreizler, Z. Naturforsch 51a,
923-932
(1996).
Definition of the empirical internal rotation-overall rotation
distortion operator programmed into XIAM as terms Dpi2J, Dpi2K and Dpi2-. is in Eq.(6) of
N.Hansen, H.Mader and T.Bruhn, Molec. Phys. 97,
587-595
(1999).
XIAM_mod is a modification of XIAM
made by Sven Herbers, while working with Lam Nguyen
in Paris. This program has been kindly deposited by the author
and allows the use of two additional high order internal rotation
parameters Dc3K and Dc3-. The use of these parameters delivers a significant improvement in the deviation of fit, as has been demonstrated in comparison with standard XIAM for single and two internal rotor cases:
m-methylanisole: S.Herbers and V.L.Nguyen, J.Mol.Spectrosc. 370,
111289
(2020).
4-methylacetophenone: S.Herbers et al., J.Chem.Phys. 152, 074301 (2020).
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The official XIAM distribution package |
README.TXT |
Description of the distribution
package for the program, which consists of the four files in the
lefthand column of this table |
XIAM-V25.TXT |
The documentation file (slightly modified relative to the original, which is still available in the .TGZ file below)
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XIAM-25E.TGZ |
The
gnuzipped tar archive of the source files as received from Kiel. In the
Windows world this can be opened easily with a utility such as Total Commander. Note that input is to carry extension .xi and output
carries extension .xo |
EXAMPLES.TGZ |
The
gnuzipped tar archive containing input and output for several different
examples. These are:
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The official XIAM_mod distribution package |
XIAM_mod.exe
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The Windows executable, generated with gfortran. The recommended running procedure is
XIAM_mod<molnam.xi>molnam.xo
where molnam is the current molecule name.
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XIAM_mod.zip
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The distribution package as deposited. The
source files have been taken directly from the XIAM distribution
package, and the changes are:
- in iam.fi, iam.f, iamsys.f, which are associated with the new parameters, and are identified by the annotation !Herbers
- in line 958 of iamio.f, which is a correction to the evaluation of the error in the A rotational constant
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Hird.txt |
The updated Hird operator used in XIAM_mod (see XIAM-V25.TXT)
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EXAMPLES:
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Input and output files for the two molecules in the XIAM_mod reference papers:
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XIAM extras from the webmaster |
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SAMPLE.XI |
A commented sample
input file (for acetaldehyde), where some information from the
documentation has been put in using the commenting options allowed by
the program.
This commenting is only to serve as
quick reference for the available options and not as a substitute
reading the real documentation (and some papers!).
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XIAM.EXE |
Win95/98/NT
executable, compiled with the MSPS4 compiler, with array
dimensioning as in the distribution listings. Since this is a pure
number-crunching program the problems described in connection with
graphics are not applicable. |
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Modified XIAM |
XIAMALL.FOR |
This is a derivative
of the 'official' version of XIAM. This source file combines in one
file all the constituent source modules for the program, with the
exception of those directly below. Minimum descriptive commenting has
been placed at the top of this source, and in several other places.
The changes to the original source
are identified with zk or ! zk xiam4 in the comment field and these are either tweaks to the
output formats or changes making the fitting statistics more directly
comparable with those from SPFIT.
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IAM_.FOR
IAMDATA_.FOR
MGETX_.FOR
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These are source modules that are
combined with the main source on compilation by means of the INCLUDE statements in XIAMALL.FOR. All three
modules have to be placed in the same directory as XIAMALL.FOR.
The various PARAMETER statements at the top of the
IAM_.FOR file serve to configure the program but as Holger Hartwig
writes: please change the following parameters only if you really
know what you are doing !
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XIAM4.EXE |
An executable for a
Pentium IV generated by the Intel Visual Fortran Compiler ver.9.1,
using the options:
ifort -O3 -QxN
-static -exe:xiam4 xiamall.for
This version is tailored for large
single rotor datasets from mmw spectra (3000 lines and up to J=70)
and
will
use
up
to
228
Mb
of RAM so it should be run on a machine with
at least 0.5 Gb.
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XIAM5.EXE |
Compiled with the same compiler and compilation options as above, but with upper limit of 9999 on the number of lines.
As with the other versions of XIAM the program should be run from the
command line by using the pipeline construction, for example:
XIAM5 < molnam.xi > molnam.xo
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XIARES = converter of XIAM output
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The main purpose of this converter is to produce easier to read output from XIAM or XIAM_mod.
- Comments, which can be placed in the input file between the transitions but are
ignored in the original output, are now transferred to the reformatted
output
- All frequencies are converted to MHz and are in the usual order of obs, obs-calc and error
- Rotational constants are printed in MHz, quartic centrifugals
in kHz, sextics in Hz. Frequency units of other parameters are
converted to MHz, and all such values are printed in x.xxx(yy) or
[x.xxx] form.
- NEW (Feb 2024): clarification of standard deviation values since XIAM has a non-standard treatment for unequal weights.
XIARES is similar in concept to PIFORM, ERHRES and VIFORM, which also aim to convert output of the original programs into less cryptic form.
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XIARES.EXE |
Windows executable. Requires files molnam.xi and molnam.xo
to be available in the directory from which the program is
called. The prefix molnam is arbitrary and associated with the
problem under study, and the poutput is written to molnam.res.
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XIARES.FOR |
Fortran source.
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pyrcn.xi
pyrcn.xo
pyrcn.res
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XIAM input, output, and XIARES reformatted output for pyruvonitrile illustrating also the use of commenting in the input file that is allowed by XIAM |
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XA = XIAM to ASCP_L converter |
XA.FOR
XA.EXE
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This XIAM -> ASCP converter will
take XIAM predictive output and produce a file in the .ASR standard that
can be displayed by the stick display programs ASCP_L
(or the older ASCP). XA deals best with output produced with the ints=2 option, in which case the rigid rotor lines
are disregarded, and the intensity is taken from the total column.
ints=3 operation
is also possible but note that the rigid rotor lines are in this case
orders of magnitude stronger than the internal rotor lines.
The XA output is in the extended standard of the ASROT program, where the modification is by replacing the values in the branch and line strength columns by values of the remaining three of the six quantum numbers per asymmetric rotor level, as possible in SPFIT/SPCAT.
The
internal rotation labels Sn
Vm Bk are placed as n,m,k into the last
three quantum numbers of the lower state, while quantum numbers 4,5,6 of the upper state remain unfilled.
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to the table of programs
ERHAM |
Peter
Groner's
Effective Rotational HAMiltonian program for molecules
with up to two periodic large-amplitude motions
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This
program has been kindly deposited by its author, Peter Groner, from Department of Chemistry at the University of Missouri,
Kansas City (updated to a new
version in July 2013)
ERHAM sets up and solves the
"Effective rotational Hamiltonian for molecules with two periodic
large-amplitude motions". It allows to fit spectroscopic constants to
observed transition frequencies (usually to experimental precision) and
to predict the spectrum.
The reference for citing the use of ERHAM
is: P. Groner, J. Chem. Phys. 107,
4483-4498 (1997).
A review of the theory and the performance of the effective rotational Hamiltonian is also available: P. Groner, J. Mol.Spectrosc. 278,
52-67 (2012).
Principal
features:
- One or two internal rotors, not restricted to threefold
rotors
- Models and symmetry groups:
- Equivalent rotors: C2v, C2,
Cs
- Non-equivalent rotors: Cs, C1
- Single rotor: Cs, C1
- max(J) = 120
- Number of transitions in fit < 8191
- Modular input for “tunneling parameters”
- Tunneling energy parameters eqq
- Tunneling contributions to rotational and distortion
constants
- Quartic and sextic centrifugal distortion constants (A-reduction);
higher
order
CD
terms
may
be
defined
using the “tunneling parameter
input” which can also be used to define terms for the S-reduction
- Global fit of several non-interacting vibrational states to
the same r-vector parameters
- high speed of operation due to suitable
basis transformations and matrix factorisation
ERHAM has been
used in numerous investigations, which can be treated as worked
examples for the various areas of its applicability. Published
applications involving its author (GS = ground state, ETS = torsional
excited state):
- Dimethyl ether (GS): P.
Groner et al., Astrophys. J. 500, 1059-1063
(1998)
- 3-Methyl-1,2-butadiene (global fit of GS and 1st ETS): S. Bell et al., J. Phys. Chem. A 104,
514-520 (2000)
- Acetone (GS): P. Groner et al., Astrophys. J. Suppl.
Ser. 142, 145-151 (2002)
- Ethyl methyl ether (GS, nonequivalent): U. Fuchs et al., Astrophys.
J.
Suppl.
Ser. 144, 277-286 (2003)
- Dimethyl diselenide (GS, isotopomers with C2
or C1 symmetry): P. Groner et al., J. Mol.
Spectrosc. 226, 169-181 (2004)
- Acetone-13C (equivalent, non-equivalent): F. J.
Lovas & P. Groner, J. Mol. Spectrosc. 236,
173-177
(2006)
- Acetone (1st ETS): P.
Groner et al., J. Mol. Struct. 795, 173-178
(2006)
- Methyl carbamate (1 rotor, GS)
P. Groner et al., Astrophys. J. Suppl. Ser.
169, 28-36 (2007)
- Methyl formate-1-13C
(1 rotor, GS) A. Maeda et al., Astrophys. J. Suppl. Ser. 175, 138-146 (2008)
- Acetone (2nd ETS): P.
Groner et al., J. Mol. Spectrosc. 251,
180-184
(2008)
- CHClF2-H2O Chlorodifluoromethane-water (1 top - two-fold, GS): B.J. Bills et al., J. Mol. Spectrosc. 268,
7-15 (2011)
- 1,1-difluoroacetone (1 top, GS): G.S. Grubbs, II et al., J. Mol. Spectrosc. 280,
21-26 (2012)
- Dimethyl ether-d1 (1 top, 2 conformers, GS): C. Richard et al., A & A 552,
A117 (2013)
Other authors:
- Propane (GS & 2 ETS) Drouin et al. J.
Mol. Spectrosc. 240, 227-237 (2006)
- Pyruvic acid (1 rotor, GS &
several non-interacting excited states) Z. Kisiel et al., J.
Mol. Spectrosc. 241, 220-229 (2007)
- Methyl formate-12C
& -1-13C (1 rotor, ETS)
A. Maeda et al. J. Mol. Spectrosc. 251,
293-300 (2008)
- Pyruvic acid (1 rotor, GS &
several non-interacting excited states) Z. Kisiel et al., J.
Mol. Spectrosc. 241, 220-229 (2007)
- Dimethyl ether (GS) Endres et
al. A&A 504, 635-640 (2009)
- Pyruvonitrile (1 rotor, GS &
several non-interacting excited states) Krasnicki et al., J.
Mol.
Spectrosc. 260, 57-65 (2010)
- Dimethyl carbonate (GS): F.J. Lovas, et al., J.
Mol.
Spectrosc. 264, 10-18 (2010)
- Isopropenyl acetate (GS): H.L.V. Nguyen et al., J.
Mol.
Spectrosc. 264, 120-124 (2010)
- Dimethyl sulfate (GS): L.B. Favero et al., Chem. Phys. Lett. 517, 139-145 (2010)
- CF3(CF2)3O-CH3
& (CF3)2CFCF2OCH3 (1 top each,
GS): G. S. Grubbs, II, et al., J. Phys. Chem. A, 115, 1086–1091 (2011)
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The ERHAM package, version v16g-R3 of
July
2013 |
ERHAM.FOR |
Source listing.
This version of the program was described in a dedicated talk WH01 at
the 68th OSU International Symposium on Molecular Spectroscopy, June
17-21, 2013. Here is a PDF version of this presentation, while the original is available here.
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ERHAM.EXE |
Executable for Win32 systems |
ERHAM.TXT |
Documentation file.
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ac10x-r3.in
ac10x-r3.out
ac10x-r3.cat
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Input and output for acetone, lowest excited state
demonstrating some features specific to this version. The (abbreviated) .cat
file contains predictions in the format of the jpl catalog.
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Legacy: |
ERHAM.FOR
ERHAM.EXE
ERHAM.TXT
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Source listing, Win32 executable and the documentation file for ERHAM package, version v16g-R1 of Oct2009
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Input and output examples |
AC13C1G.IN
AC13C1G.OUT
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Acetone 13C1
ground state. | DMAG.IN
DMAG.OUT
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Dimethylallene,
Demaison et al., J.Mol.Spectrosc. 40,
445-460 (1971); 68, 97-113 (1977) |
DMDSEG.IN
DMDSEG.OUT
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Dimethyl diselenide 78Se80Se.
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ERHAM extras from the webmaster |
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ERHCONST.TXT |
Indices and names
for the ERHAM constants. Note that an extensive 'official' list is in Tables A1 and A2 of P.Groner, J.Mol.Spectrosc. 278,
52-67 (2012).
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ERHAM_AABS.TXT
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How to use ERHAM
with AABS (updated Feb2018) |
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ERHAMZ = tweaked version of ERHAM |
ERHAMZ_R3.FOR
ERHAMZ_R3.EXE
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This is a derivative of the
'official' version of ERHAM_v16g_R3 above with tweaks to some FORMAT
statements and with additional code for picking out worst lines in the
dataset.
All modifications are marked with the string ! zk in the comment columns.
The executable is generated by
the Intel Visual Fortran Compiler ver.11, using the
options :
ifort -nopdbfile -nodebug -traceback -arch:IA32 -O3 -Qsave -fpscomp:filesfromcmd erhamz_R3.for
and runs about 30% faster than the 'official' one.
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ERHAMZ_R3a.EXE |
This is a test version with the number of accepted transitions increased to ca 30000.
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LINERH = LIN to ERHam converter |
LINERH.FOR
LINERH.EXE
LINERH.INP
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Utility to convert lines from the .LIN format of SPFIT to a block suitable for use
in the ERHAM input file, or directly into an updated ERHAM input file. In both cases preceding versions of the ERHAM files are backed up.
The
steering file LINERH.INP holds
pertinent control information (to be reedited) and should reside in the
same directory as the input file.
NOTE: ERHAM
allows empty lines to be placed between transitions, so that lines in the .LIN file containing annotation beginning with '!' will generate output with an empty line preceding each such line.
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ERHRES = ERHam to RES converter |
ERHRES.FOR
ERHRES.EXE
ERHRES.INP
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The purpose of this utility is to convert ERHAM output into two useful files:
1/ A formatted .RES output similar to that from ASFIT
or PIFORM
with various enhanced readability features. This output:
- only includes the final cycle of fit,
- converts from J,N to J,Ka,Kc quantum number notation
- converts fitted parameters and their errors into more useful units
- prints parameters also in x.xxx(xx) form
- labels torsional parameters also according to the Bkpr notation
- prints the list of worst fitted lines, provided ERHAMZ_R3 was used
The file DMAG.RES is an example of using ERHAM followed by ERHRES.
The .RES file can
be used by the program AC
of the AABS
package for making dataset distribution plots.
2/ A .LIN file for direct use as the fitting file by the AABS package. If the .CAT file generated by ERHAM is used in the ASCP_L then measurements will be appended to this.LIN
file in the same quantum number format, namely IS1 and IS2 as the
fourth quantum number for the upper and lower level, respectively. mPrevious version of the .LIN file is backed up.
The operation sequence LINERH->ERHAMZ_R3->ERHRES should be neutral regarding the .LIN file. If there was no additional editing of the ERHAM input file then the .LIN file resulting from ERHRES should be identical to the one used as data for LINERH. On the other hand, manual editing of ERHAM input will be reflected in the .LIN file from ERHRES.
The end of .LIN line annotations can be of the same form as that recognised by PIFORM, although these are not yet completely actioned in the .RES output from ERHRES.
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ERHASR = ERHam to ASR converter |
ERHASR.FOR
ERHASR.EXE
ERHASR.INP |
Utility to convert ERHAM predictive output into the
form suitable for stick display programs ASCP_L
or ASCP.
The
steering
file
ERHASR.INP holds
pertinent control information (to be reedited) and should reside in the
same directory as the ERHAM output file.
This has been made obsolete by addition of .CAT output of ERHAM R3, so is retained for legacy purposes.
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to the table of programs
BARRIER |
Potential barrier for a single internal rotor from
torsional transitions or splittings (by Peter
Groner)
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Program to
determine the potential barrier for a single simple internal rotor from
torsional transitions or splittings. It is a simpler
offspring of program ASTOR described in P. Groner, et al., J. Mol. Struct. 142, 363-366 (1986).
BARRIER
has been created primarily to derive barriers to internal rotation for a
single rotor from the tunneling splittings determined by ERHAM.
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BARRIER |
Executable for Win systems.
This program is best launched from the command line (rather than by
clicking on its icon), since any error output can otherwise be
missed. An alternative useful for repetitive operation is to
create a file molrun with two lines containing the file names for input and output and then reuse the command:
BARRIER < molrun
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instructions |
Documentation file.
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Input and output examples |
C2H5D.in
C2H5D.out
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V3 example: monodeuterated ethane, CH3CH2D, as used in A.M.Daly et al., J.Mol.Spectrosc. 307,
27-32 (2015). | C2H5D-01.in
output
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As above, but with input abbreviated to the A-E splitting in the ground state and in the first excited torsional state.
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cdfm.in
cdfm-03.out
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V2 example: CHClF2...H2O cluster as used in B.J.Bills et al., J.Mol.Spectrosc. 268, 7-15 (2011).
Note that the splitting is entered twice in order for the program to
work, but this is effectively just one data point so there is no
meaningful error estimate.
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vinylSF5.in
vinylSF5.out |
V4 example: vinylsulfur pentafluoride, CH2=CH-SF5, as used in J.Chem.Phys. 149, 144304 (2018).
A-E and A-B splitting in the ground state is declared, but since A-E=E-B
there is only one independent data point available and there is no
meaningful error estimate.
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to the table of programs
BELGI |
The
BELGian Internal Rotor Program
of
Isabelle
Kleiner
et
al.
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This
program has been kindly deposited by its principal author, Isabelle Kleiner,
from Laboratoire Interuniversitaire des Systèmes
Atmosphériques, LISA, (Université paris 7 et Paris 12 et
CNRS, Créteil, France). The current BELGI repository
consists of three complementary packages:
- BELGI-Cs
-
program for molecules containing
an internal rotor (of C3v symmetry) which
can turn relative to the rest of the molecule (of Cs
symmetry)
- BELGI-C1
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program for molecules containing
an internal rotor (of C3v symmetry) which
can turn relative to the rest of the molecule (with no symmetry)
- several utility programs for
both versions of BELGI
This program has a long
history, detailed in the readme, and the authors (in chronological order)
are:
- I. Kleiner from Laboratoire
Interuniversitaire des Systèmes
Atmosphériques, LISA, (Université paris 7 et Paris 12 et
CNRS, Créteil, France)
- M. Godefroid from the "Laboratoire de Chimie
Quantique et Photophysique" , Free University of Brussels (Belgium),
- J. T. Hougen from the National Institute for
Standards and Technology (NIST, Gaithersburg, USA),
- L-H. Xu from Department of Physical Sciences,
University of New Brunswick,
- J. Ortigoso from Instituto de Estructura de la
Materia, CSIC (Madrid, Spain),
- V. Ilyushin from the Radio Astronomy Institute of
NASU, Kharkov (Ukraine)
- M. Carvajal-Zaera from the Departamento de Fisica
Aplicada, University of Huelva (Spain)
BELGI uses the
rho-axis system method (RAM), and allows the user to
calculate and fit the energies of transitions for molecules containing
an internal rotor (of C3v symmetry) which
can turn relative to the rest of the molecule (of Cs
symmetry).(BELGI-Cs) or a
molecular frame devoid of symmetry (BELGI-C1).
The reference for citing the use of BELGI-Cs
is:
- J. T. Hougen, I. Kleiner and M. Godefroid, J. Mol.
Spectrosc., 163, 559-586 (1994).
Extensive listing
of previous applications
of BELGI-Cs is
available and those papers contain many different examples of the use
of this program.
Principal characteristics of BELGI-Cs:
- Fit one internal rotor of C3v symmetry
(like
a
CH3 group), while the rest of the molecule possesses
a plane of symmetry (Cs).
- Jmax = 30
- Up to 80000 lines to fit or to calculate
- Up to 80 parameters of fit in each vibrational state
- Up to 2 vibrational states
- A two-step diagonalisation with:
- the diagonalisation of a 21x21 torsional matrix for
each K and s value (K is the projection of
J on the symmetry axis of the molecule and s
is the symmetry with s = 0 for the A states and s
= 1 for the E states), and
- the diagonalisation of the rotation, centrifugal
distortion and rotation-torsion coupling terms of the Hamiltonian
(dimension (9)*(2J+1) x (9)*(2J+1))
- A global fit of the A and E species
corresponding to ALL the torsional levels (up to the 9th
torsional state vt 0, 1…8)
The references for citing BELGI-C1
are:
- I. Kleiner and J. T. Hougen, J. Chem.
Phys. 119, 5505 (2003)
- R. J. Lavrich, A. R. Hight Walker, D. F. Plusquellic, I.
Kleiner, R.
D. Suenram, , J. T. Hougen and G. T. Fraser, J. Chem. Phys. , 119,
5497-5504
(2003).
You
can also check the listing and a listing of previous applications
of BELGI-Cs is given here.
Principal characteristics of BELGI-C1:
- can fit one internal rotor of C3v symmetry
(like
a
CH3 group), the rest of the molecule may not possess a
plan
of symmetry (C1). Complex algebra used.
- Jmax = 30
- Max 20000 lines to fit or to calculate
- Max 80 parameters to fit in each
vibrational states
- A two-step diagonalisation with:
- the
diagonalisation of a 21x21 torsional matrix for each K and s
value (K is the
projection of J on the
symmetry axis of the molecule and s
is the symmetry
with s = 0 for the A states and s
=1 for the E states) and
- the
diagonalisation of the rotation, centrifugal distortion and
rotation-torsion
coupling terms of the Hamiltonian (dimension (9)*(2J+1) x (9)*(2J+1))
- A Global fit of the A and E species
corresponding to ALL the torsional levels (up to the 9th
torsional
state vt 0, 1…8)
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The BELGI-Cs package |
BELGI-Cs.FOR |
Source listing. The program uses
two routines from the IMSL library that have to be provided at
compilation time. The two routines are DLSVRR for singular value
decomposition, and DLINRG for matrix inversion. |
BELGI-Cs.EXE |
Executable for Win32 systems. The
program assumes that the input is always in the file input.txt, and
writes to the default output device, which is normally the screen. If
you want to save the output to a file, say belgi.out, use the
command
belgi-cs>belgi.out
The program may spend a lot of time
without apparent output, so you can use the Task Manager to check CPU
usage. It also creates a file called DAT for its own use - this file is not
deleted by the program on completion of execution but will be replaced
on another run of BELGI.
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README_Cs.PDF |
The main
documentation file for the program, which includes discussion of its
features, internal structure, format of the input file, the meaning of
the parameters, and concludes with a special section on the history of BELGI development
and applications. |
CONSTANTS.TXT |
Table summarising the terms in the
vibration-rotation Hamiltonian that can be used in BELGI:
the
angular
momentum
operators
and
the
identifiers
for the associated
constants. |
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Input and output examples: |
INPUT.TXT
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Input file for methyl
carbamate,
H2NC(O)OCH3, ground and first
torsional states, J. Mol. Spectrosc., 240,
127
(2006). |
MECARB.OUT
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Output file for
methyl carbamate produced from the input above. |
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The BELGI-C1 package |
BELGI-C1.FOR |
Source
listing.
The
program
uses
two
routines
from
the IMSL library that have to be provided at
compilation time. The two routines are GETTIM for timing and DLINRG for matrix
inversion. |
BELGI-C1.EXE |
Executable
for
Win32
systems.
Run
in
the
same way as described for BELGI-Cs
above. The
program assumes that the input is always in the file input.txt, and
writes to the default output device, which is normally the screen. If
you want to save the output to a file, say belgi.out, use the
command
belgi-c1>belgi.out
The program may spend a lot of time
without apparent output, so you can use the Task Manager to check CPU
usage. It also creates a file called DAT for its own use - this file is not
deleted by the program on completion of execution but will be replaced
on another run of BELGI.
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README_C1.PDF |
Documentation.
Only the particularity
for the C1 code is described here, while for more general
information,
see also the read-me file for BELGI-Cs
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CONSTANTS.TXT
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The list of
parameters which can
be
floated |
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Input and output examples: |
INPUT.TXT |
Input file for
N-acetyl alanine
methyl
ester molecule (ADME) ground torsional state ( J. Chem. Phys. 125,
104312 (2006)) |
ADME.OUT |
Output file for the
input above.
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Utility
programs
for
BELGI |
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CONVERT =
to
convert
JKaKc quantisation (from input format used by
XIAM) into format of BELGI |
convert-a.for
convert-a.exe
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Source and WIN32
executable for the A-symmetry species. Just run the executable by
its name. Input and output are from files with compulsory names:
input file = XIAM-data-A-sept08.txt
output file = out-BELGI-A-sept08.txt
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convert-e.for
convert-e.exe |
Source and WIN32
executable for the E-symmetry species. Just run the
executable by its name. Input and output are from files with
compulsory names:
input file = XIAM-data-E-sept08.txt
output file = out-BELGI-E-sept08.txt |
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ABC =
to
convert
A,B,C,Dab,Dac,Dbc from BELGI (RAM quantities) to A,B,C (PAM quantities) |
abc.for
abc.exe |
Source and WIN32
executable. This program is to be executed using the pipeline
operation.
For screen output use the command:
abc<input_file_name
For disk output use the command: abc<input_file_name>output_file_name
Sample input file = RAMabcdADME
Sample output file = PAM-ADME
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MOMENTS =
to
calculate
guess input values for BELGI from masses and Cartesian coordinates of
atoms in the molecule |
moments.for
moments.exe |
Source and WIN32
executable. Just run the executable by its name. Input and
output are from files with compulsory names:
input file = TAPE5.txt
output file = TAPE6.txt
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RAM36
RAM36hf
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Vadim Ilyushin's program using the
Rho Axis Method for 3 and 6 fold barriers (hf version includes n.q. hypefine splitting)
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These
programs have been kindly deposited by their author, Vadim Ilyushin,
from the Institute of Radio Astronomy of the National Academy of Sciences of the Ukraine in Kharkov. The program is a derivative of BELGI and is characterised by considerable increase in the speed of operation. The RAM36 program was written in collaboration with Dr. J.T. Hougen (of NIST) and the
effectiveness of this collaboration was considerably enhanced by the
NIST exchange visitor program, and the help of this NIST program
is therefore gratefully acknowledged by the author.
RAM36 and RAM36hf are designed to deal with two general internal rotation cases:
- Sixfold rotation case with a C3v internal rotor and a C2v frame (such as toluene and nitromethane)
- Threefold rotation case with a C3v internal rotor and a Cs frame (such as acetic acid, acetamide or methyl formate)
The feature distinguishing the two programs is that RAM36 deals with the most common case of hyperfine-free transitions, while RAM36hf allows also inclusion of hyperfine structure from the presence of a single quadrupolar atom.
The reference for citing the use of RAM36 is:
- V.V.
Ilyushin, Z. Kisiel, L. Pszczółkowski, H. Mäder, J.T.
Hougen, “A New Torsion-Rotation Fitting Program for Molecules with
a Six-Fold Barrier: Application to the Microwave Spectrum of Toluene”, Journal of Molecular Spectroscopy 259, 26-38 (2010).
This paper describes both the program
and its application to the analysis of the lowest m-states in the
rotational spectrum of toluene, which is a rather demanding low-barrier case. Description of the steps taken to increase the speed of RAM36 operation relative to its predecessors is given in:
- V. V. Ilyushin, C. P. Endres, F. Lewen, S. Schlemmer, B. J. Drouin
"Submillimeter wave spectrum of acetic acid", Journal of Molecular
Spectroscopy 290, 31 - 41 (2013).
Another example of application of the sixfold barrier mode of RAM36 can be found in:
- V.V. Ilyushin, L.B. Favero, W.Caminati, J-U. Grabow
“Intertorsional Interactions Revealing Absolute Configurations: The V6
Internal Rotation Heavy-Top Case of Benzotrifluoride”, ChemPhysChem 11, 2589 – 2593.(2010).
An example of the use of RAM36 for a problem with a threefold barrier is described in:
- V.Ilyushin, R.Rizzato, L.Evangelisti, G.Feng, A.Maris,
S.Melandri, W.Caminati', “Almost free methyl top internal rotation:
rotational spectrum of 2-butynoic acid”, Journal of Molecular Spectroscopy 267, 186 - 190 (2011).
The references for citing the use of RAM3hf are:
- V.V.
Ilyushin, “Millimeter wave spectrum of nitromethane”, Journal of Molecular Spectroscopy 345, 64-69 (2018).
- A.Belloche,
A.A.Mescheheryakov, R.T.Garrod, V.V.Ilyushin, E.A.Alekseev,
R.A.Motiyenko, I.Margules, H.S.P.Muller, K.M.Menten, "Rotational
spectroscopy, tentative interstellar detection, and chemical modelling
of N-methylformamide", Astronomy & Astrophysics, 601, A49:41pp (2017).
The first paper describes a sixfold barrier case application, and the second describes a threefold barrier case application. Data files for both cases are provided below.
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The RAM36 package, version Dec
2012 |
RAM36.FOR |
Source listing.
RAM36 uses several routines from the LAPACK library that have to be
provided at compilation time. These routines are DSTEQR, DSYTRD, DORGTR,
DGETRF, DGETRI, and DGESVD. In order to
achieve the highest performance of the program it is recommended to use
specific-processor-optimized versions of the LAPACK library like Intel
Math Kernel Library (MKL) or AMD Core Math Library (ACML).
RAM36
also uses the DSBRDT routine from the Successive Band Reduction (SBR)
package [ C.H. Bischof, B. Lang, X.-.B. Sun, ACM Trans. Math. Software
26 (2000) 602-616.]. The source code is provided in the end of this file.
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RAM36.EXE |
Executable for Windows systems compiled with Intel Visual Fortran v.10 and making some use of the Intel multicore processor architecture.
The input should be in the file input.txt. This name is fixed so you might like to keep a copy of this file under a name related to the molecular problem.
The program should be run from the command prompt window opened in the
directory containing the input file. Use the pipeline command:
ram36>output
whereupon the results will be written to the file output. In this case the name of the output file is up to the user.
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READMERAM36.PDF |
Documentation
file for RAM36. |
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Input and output examples |
INPUT_TOLUENE
OUT_TOLUENE
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The input and output for the sixfold barrier toluene case, as in the reference paper.
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INPUT_2BA
OUT_2BA |
The input and output for the threefold barrier case of 2-butynoic acid. |
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The RAM36hf package, version 24 Feb
2020 |
RAM36hf.FOR |
Source listing. The notes given above in connection with the RAM36 source are also applicable in this case.
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RAM36hf.EXE |
Executable for Windows systems.
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READMERAM36hf.PDF
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Documentation
file for RAM36hf. |
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Input and output examples
| INPUT_nitromethane
OUT_nitromethane
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The input and output for the nitromethane sixfold barrier case as in the reference paper. (14N hyperfine).
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INPUT_Nmethylformamide
OUT_Nmethylformamide
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The input and output for the N-methylformamide threefold barrier case from the second reference paper (14N hyperfine). |
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RAM36 and RAM36hf extras from the webmaster |
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RAM36_USAGE.TXT
RAM36_AABS.TXT
runram36.bat
runram36hf.bat
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Instructions on how to use RAM36
together with the various extras provided below, and instructions on how to use it within AABS
Batch files allowing the use of generic file names such as MOLNAM.INP for the fit by means of the commands
runram36 molnam
runram36hf molnam
which will place the output in MOLNAM.OUT. See the first RAM36_USAGE_TXT file for details.
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VIFORM = reformatting of the fit output from RAM36 and RAM36hf |
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VIFORM.FOR
VIFORM.EXE
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Formatter of output from RAM36, and (NEW) also RAM36hf.
This program will convert output present in file molnam.out, where the choice of the string molnam is decided by the user after launching VIFORM.
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VIFORM
will produce:
- file molnam.res which is the principal reformatted output file similar to the .RES type files in the standard of the PIFORM
program and containing directly printable blocks of parameters of fit,
obs.-calc. lines, various data set statistics, correlation matrix and
lists of the worst fitting lines.
- files molnam.lin and molnam_frequency.lin, which are .LIN type files in the standard of the SPFIT program.
Any of these can be used by AABS as a data file for storing
measurements.
- additional files molnam_original.res and molnam_frequency.res
- file molnam.con with parameters of
fit and the errors written in the standard convention for tabulating
such values, and with a readable correlation matrix
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TOLUENE.INP
TOLUENE.OUT
TOLUENE.RES
TOLUENE.LIN TOLUENE.CON
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Some of the files associated with the fit of the toluene example above.
TOLUENE.INP and TOLUENE.OUT involve using
runram36 toluene
TOLUENE.RES, TOLUENE.LIN and TOLUENE.CON are produced by VIFORM on responding TOLUENE to its generic name question.
Note that the various annotations on transitions are preserved.
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VADASR = reformatting of predicttions from RAM36
VADCAT = reformatting of predictiions from RAM36 and RAM36hf |
VADASR.FOR
VADASR.EXE |
Utility to convert RAM36 predictive output into the
form suitable for the stick display program ASCP_L.
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This program requires predictive output from RAM36, obtained by setting
the first switch in the seventh line after the &&&END line
to +1 or -1. The PREDICTVT0.TXT file from RAM36 then has to be
copied to file VADASR.INP. If file PREDICTVT1.TXT was also generated then this can be appended to VADASR.INP..
The output will be written to file VADASR.OUT containing all of the predicted lines, as well as to individual files for each m state called:
m0.asr, m1.asr, m2.asr, m3.asr , m-3.asr ,... up to m-6.asr .
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VADCAT.FOR
VADCAT.EXE |
This program operates similarly to VADASR above but generates .CAT files, also for use with ASCP_L.
Output from both RAM36 and (NEW) RAM36hf can be converted and the source program is autodectected. Quantum numbers are placed in the .CAT file in the following order:
RAM36: J, Ka, Kc, m
RAM36hf: J, Ka, Kc, m, F
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TOL_ASCPL.INP |
The control file for ASCP_L
(option 2) allowing all of the m substate files produced for toluene to be read
and displayed. This file can be modified as necessary.
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LINVAD = converter from .LIN standard of SPFIT to frequency data block used by RAM36 and RAM36hf |
LINVAD.FOR
LINVAD.EXE
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Utility to convert lines from the .LIN format of SPFIT to a block suitable for use
in the input file to RAM36.and (NEW) RAM36hf.
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LINVAD.INP |
The control file (to be reedited) defining input and output file names for LINVAD. This should reside in the
same directory as the input file.
Note that slightly different versions of this file are required for RAM36.and RAM36HF.as described in the file.
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toluene_input.txt |
The output file from LINVAD containing the block of converted lines to be pasted into the RAM36 input file.
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VICONTR = extracting parameter contributions to measured lines from the EXPECTVT file(s) written by RAM36hf |
VICONTR.FOR
VICONTR.EXE |
This program extracts contributions from up to ten selected parameters of fit to transitions declared in the RAM36HF
fit. The program will also transfer transition commenting to
improve clarity of the output. The procedure for using VICONTR:
- Run RAM36HF
by setting to 1 the second parameter in the input file line defining
predictions (in last line above the block of frequencies). This
setting will produce the EXPECTVT0
file with the parameter contributions for all calculated lines and all
parameters of fit, so that it may be very large and with very long
lines.
- Run VIFORM, which will produce a .LIN file with complete end of line comments
- Fill out the VICONTR.INP file as required (see below).
- Run VICONTR
Note that VICONTR is only designed to work with RAM36HF, although it is possible to use it on RAM36 data, by converting those into a spinless RAM36HF input, as in the example below. |
VICONTR.INP |
The mandatory control file (to be reedited as
necessary). This version is for the worked example below, while a
physical value of the nuclear spin should be specified for actual RAM36HF data.
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Worked example of using VICONTR |
tol2010hf.inp
tol2010hf.out
expectvt0.txt
expectvt1.txt
tol2010hf.res
tol2010hf.lin
tol2010hf.log
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This shows how to use VICONTR on the example of data reported for toluene in J.Mol.Spectrosc.259, 26-38 (2010) and originally fitted with RAM36. The steps were as follows:
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The input tol2010hf.inp file results from conversion of the hyperfine free RAM36 version above by adding the columns for the F
quantum numbers, and filling those out with values equal to -1.0 (for
hyperfine free data). The order of parameters and transitions was
also unified with that in Tables 6 and 8 of the original paper.
- The
spin value in the first line of the file was set to 0.001. This
choice is not critical, but for technical reasons spin cannot be set to
zero, while any half integral value leads to unphysical values of F is various output files.
- The
two parameters directly above the block of transition frequencies were
set to -1,1. The first parameter enacts predictions for both Δm=0 and Δm ≠
0 selection rules (separate files). The second parameter enacts
calculation of the corresponding expectation value files.
- The tol2010hf.out file and the two EXPECT files are the result of refitting the toluene input with RAM36HF and are required for the next steps
- The .res and .lin files result from further processing of the .out file with VIFORM
- The tol2010hf.log file is the final result from VICONTR, using the VICONTR.INP
file above and upon online declaration that the contributions from the
parameters of fit: F, -2*RHO*F and 0.5*V6 should be listed
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SPFITint |
Can SPFIT be used to fit internal rotation ?
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This
is a recurring question and it is quite a reasonable one in view of the power of SPFIT and of the general nature of the way in which it allows the Hamiltonian to be constructed.
In short, the answer is YES, but the treatment may be less direct than you might like. Two alternative approaches are possible:
METHOD 1: Fourier series expansion based on the Mathieu equation description of the Internal Axis System (IAS) Hamiltonian for internal rotation [1]. The .PAR parameter file for SPFIT is set up by means of two preprocessor programs, first MOIAM (input file .INP), then IAMCALC (input file .IAM). This results in a .PAR file with an extensive set of linked parameters. This file is completely unreadable and its size can run to many Megabytes. Fortunately, in the final SPFIT output these expansions are brought together into the original leading parameters as specified in the .IAM file. Direct program documentation seems to be limited to that in moiam.c
and iamcalc.c
source codes, but there are quite a number of published applications to serve as worked examples. These include studies of HNO3 [2], methyl formate [3], propane [4], acetaldehyde [5], hydroxyacetone [6], and methyl carbamate [7]. Note that in [4] there is also a comparison of this way of using SPFIT with ERHAM.
- H.M.Pickett, J,Chem.Phys.107, 6732 (1997)
- D.T.Petkie, T.M.Goyette, P.Helminger, H.M.Pickett, F.C.De Lucia, J.Mol.Spectrosc. 208, 121 (2001); this appears to be the first explicit mention of MOIAM and IAMCALC in a publication.
- Methyl Formate = species c060003 in jpl spectral line catalog: PDF entry (includes a short description of IAMCALC), IAM file, PAR file (warning: 18MB) , LIN file
- B.J.Drouin, J.C.Pearson, A.Walters, V.Lattanzi, J.Mol.Spectrosc. 240, 227 (2006) = propane, species c044013 in jpl spectral line catalog: PDF entry, PAR file, LIN file
- Acetaldehyde = species c044003 in jpl spectral line catalog: PDF entry (includes a short description of IAMCALC), IAM file, PAR file (warning: 8.8MB) , LIN file
- A.J.Apponi, J.J.Hoy, D.T.Halfen, L.M.Ziurys, Astrophy. J. 652, 1787 (2006) = Hydrohxyacetone, species c074003 in jpl spectral line catalog: PDF entry, PAR file, LIN file
- Methyl Carbamate = species c075004 in jpl spectral line catalog: PDF entry (includes a short description of IAMCALC), PAR file (warning: 4MB), LIN file
- METHOD 2: Effective single state fits based on perturbation approximations. These will only work sensibly in specific cases but may be all that is required for the relatively small, low-J data sets obtained in supersonic expansion measurements. The approach is based on the Principal Axis Method approach (PAM) and depends on the fact that for a sizable threefold barrier the A states are sufficiently well treatable by the standard asymmetric rotor Hamiltonian. For the E states the torsion-rotation interaction may be sufficiently well described by terms of the type DaPa and their centrifugal distortion expansion, with the choice of terms depending on the orientation of the internal rotation axis relative
to the inertial axes. These terms have direct SPFIT
indices. The approach has been well described and used to treat
supersonic expansion data for o-chlorotoluene [1], and later for much higher-J, mmw data for pyruvic acid [2] and pyruvonitrile [3]. The discussion in Ref.[1] constitutes a nice tutorial in the use of the method, including how to derive the barrier height V3 from such fits by using tabulated perturbation coefficients in Appendix C of [4]. In [2-3] this method is compared to the results from XIAM and ERHAM and the advantages and disadvantages of this simple approach are discussed. The supplementary material for [2-3] also contains the input data files for SPFIT.
- D.Gerhard, A.Hellweg, I.Merke, W.Stahl, M.Baudelet, D.Petitprez, G.Wlodarczak, J.Mol.Spectrosc. 220, 234 (2003).
- Z.Kisiel, L.Pszczolkowski, E.Bialkowska-Jaworka, S.B.Charnley, J.Mol.Spectrosc. 241, 220 (2007).
- A.Krasnicki, Z.Kisiel, L.Pszczolkowski, J.Mol.Spectrosc. 260, 57 (2010).
- D.R.Herschbach, J.Chem.Phys. 31, 91 (1959).
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