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).

       
  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:

  XIAM extras from the webmaster
   
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!).

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.
   
  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.

      

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.

   
  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.

 

       

       

       

ERHAM

Peter Groner's Effective Rotational HAMiltonian program for molecules with up to two periodic large-amplitude motions

        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:
    1. Equivalent rotors: C2v, C2, Cs
    2. Non-equivalent rotors: Cs, C1
    3. 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)

              

       
  The ERHAM package, version v16g-R1 of Oct 2009
ERHAM.FOR Source listing
ERHAM.EXE Executable for Win32 systems
ERHAM.TXT Documentation file
   
  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.

  ERHAM extras from the webmaster
   
ERHCONST.TXT Indices and names for the ERHAM constants
ERHAM_AABS.TXT

     

How to use ERHAM with AABS
  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

   
  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.
   
  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.
   
  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.

   
 

       

       

     

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:
    1. 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
    2. 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:

  1. I. Kleiner and J. T. Hougen, J. Chem. Phys. 119, 5505 (2003) 
  2. 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:
    1. 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
    2. 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 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.
   
  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



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.



 Utility programs for BELGI




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



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



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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