| XIAM |
Version
2.5E
of
Holger
Hartwig's
IAM
internal
rotation program for up to three
symmetric internal rotors and up to one quadrupolar nucleus
|
This
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-:
N.Hansen, H.Mader and T.Bruhn, Molec. Phys. 97,
587-595
(1999).
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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 |
| 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 Windows 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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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
|
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 !
|
| 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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XA = Xiam to Ascp converter |
| XA.FOR
XA.EXE
|
This XIAM->ASCP converter will
take XIAM output and produce a file in the .ASR standard that
can be displayed by the stick display programs ASCP_L
or ASCP.
At the moment XA only
deals with output produced with the ints 3 option, the rigid rotor lines
are disregarded, and the intensity is taken from the total column. The
internal rotation labels Sn
Vm Bk are placed as n,m,k into the last
three quantum numbers of the lower state.
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| 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 October 2009)
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).
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, TES = 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
TES): 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 TES): 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 TES): P.
Groner et al., J. Mol. Spectrosc. 251,
180-184
(2008)
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) Kisiel et al., J.
Mol. Spectrosc. 241, 220-229 (2007)
- Methyl formate-12C
& -1-13C (1 rotor, TES)
Maeda et al. J. Mol. Spectrosc. 251,
293-300 (2008)
- Dimethyl ether (GS) Endres et
al. A&A 504, 635-640 (2009)
- Pyruvonitrile (1 rotor, GS &
several non-interacting excited states) Kisiel et al., J.
Mol. Spectrosc. 260, 57-65 (2010)
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The ERHAM package, version v16g-R1 of
Oct
2009 |
| ERHAM.FOR |
Source listing |
| ERHAM.EXE |
Executable for Win32 systems |
| ERHAM.TXT |
Documentation
file |
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Input and output examples |
| AC13C1G.IN
AC13C1G.OUT
|
Acetone 13C1
ground state |
| DMAG.IN
DMAG.OUT
|
Dimethylallene,
Demaison et al., J.Mol.Spectrosc. 40,
445-460 (1971); 68, 97-113 (1977) |
| DMDSEG.IN
DMDSEG.OUT
|
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 |
| ERHAM_AABS.TXT
|
How to use ERHAM
with AABS |
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ERHAMZ = tweaked version of ERHAM |
| ERHAMZ.FOR
ERHAMZ.EXE
|
This is a derivative of the
'official' version of ERHAM
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 for a Pentium IV as generated by
the Intel Visual Fortran Compiler ver.9.1, using the
options :
ifort -O3 -QxN
-static erhamz.for
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LINERH = LIN to ERHam converter |
| LINERH.FOR
LINERH.EXE
LINERH.INP
|
Utility to convert lines from the .LIN format of SPFIT to a block suitable for use
in ERHAM input file. The
steering file LINERH.INP holds
pertinent control information (to be reedited) and should reside in the
same directory as the input file. |
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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 input file. |
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ERHRES = ERHam to RES converter |
| ERHRES.FOR
ERHRES.EXE
ERHRES.INP
|
Utility to convert ERHAM output into the form
compatible with the .RES output of ASFIT
or PIFORM
with various enhanced readability features. 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.
In addition to the .RES
file ERHRES will also
generate a .LIN file for possible use
by SPFIT or by the ASCP_L
display program of AABS.
NOTE: ERHAM
allows empty lines to be placed between transitions, which are
transferred by ERHRES to
both the .RES output, and as
appropriate comments in the .LIN output,
for
later
use
by PIFORM.
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| BELGI |
The
BELGian Internal Rotor Program
of
Isabelle
Kleiner
et
al.
|
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
-
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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| |
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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.
|
| 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
|
Input file for methyl
carbamate,
H2NC(O)OCH3, ground and first
torsional states, J. Mol. Spectrosc., 240,
127
(2006). |
| MECARB.OUT
|
Output file for
methyl carbamate produced from the input above. |
| |
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.
|
| 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
|
| CONSTANTS.TXT
|
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
|
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
|
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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to the table of programs
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