XIAM

XIAM_mod

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


       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).


       
  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)
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:

The official XIAM_mod distribution package
XIAM_mod.exe
The Windows executable, generated with gfortran.  The recommended  running procedure is
        XIAM_mod<molnam.xi>molnam.xo
where molnam is the current molecule name.
XIAM_mod.zip
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
Hird.txt The updated Hird operator used in XIAM_mod (see XIAM-V25.TXT)
EXAMPLES:
Input and output files for the two molecules in the XIAM_mod reference papers:

  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.

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


XIARES = converter of XIAM output

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.
 XIARES is similar in concept to PIFORM, ERHRES and VIFORM, which also aim to convert output of the original programs into less cryptic form.
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.
XIARES.FOR  Fortran source.


  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


        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:
    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, 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)


       

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.
ERHAM.EXE Executable for Win32 systems
ERHAM.TXT Documentation file.
ac10x-r3.in
ac10x-r3.out
ac10x-r3.cat
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.


  Legacy:
ERHAM.FOR
ERHAM.EXE
ERHAM.TXT
Source listing, Win32 executable and the documentation file for ERHAM package, version v16g-R1 of Oct2009
   
  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.  Note that an extensive 'official' list is in Tables A1 and A2 of P.Groner, J.Mol.Spectrosc. 278, 52-67 (2012).

ERHAM_AABS.TXT

     

How to use ERHAM with AABS   (updated Feb2018)

ERHAMZ = tweaked version of ERHAM
ERHAMZ_R3.FOR

ERHAMZ_R3.EXE

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.

ERHAMZ_R3a.EXE This is a test version with the number of accepted transitions increased to ca 30000.
   

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 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.
   
  ERHRES = ERHam to RES converter
ERHRES.FOR
ERHRES.EXE
ERHRES.INP
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.

   

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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BARRIER

Potential barrier for a single internal rotor from
torsional transitions or splittings (by Peter Groner)


        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.

     

       
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
instructions Documentation file.


  Input and output examples
C2H5D.in
C2H5D.out
V3 example: monodeuterated ethane, CH3CH2D, as used in A.M.Daly et al., J.Mol.Spectrosc. 307, 27-32 (2015).
C2H5D-01.in
output
As above, but with input abbreviated to the A-E splitting in the ground state and in the first excited torsional state.
cdfm.in
cdfm-03.out
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.
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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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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RAM36
RAM36hf

Vadim Ilyushin's program using the  Rho Axis Method for 3 and 6 fold barriers (hf version includes n.q. hypefine splitting)


        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.

       
  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.

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.

READMERAM36.PDF Documentation file for RAM36.


Input and output examples
INPUT_TOLUENE OUT_TOLUENE 
The input and output for the sixfold barrier toluene case, as in the reference paper.
INPUT_2BA
OUT_2BA 
The input and output for the threefold barrier case of 2-butynoic acid.



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.
RAM36hf.EXE Executable for Windows systems.
READMERAM36hf.PDF
Documentation file for RAM36hf.


  Input and output examples
INPUT_nitromethane OUT_nitromethane

The input and output for the nitromethane sixfold barrier case as in the reference paper. (14N hyperfine).


INPUT_Nmethylformamide
OUT_Nmethylformamide
The input and output for the N-methylformamide threefold barrier case from the second reference paper (14N hyperfine).

  RAM36 and RAM36hf extras from the webmaster
   
RAM36_USAGE.TXT
RAM36_AABS.TXT

runram36.bat
runram36hf.bat

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.

  VIFORM = reformatting of the fit output from RAM36 and RAM36hf


VIFORM.FOR
VIFORM.EXE
Formatter of output from RAM36, and (NEW) also RAM36hf

This program will convert which output place placed in file called  molnam.out, where the choice of the string  molnam  is decided by the user aftter launching VIFORM.  

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
TOLUENE.INP
TOLUENE.OUT
TOLUENE.RES
TOLUENE.LIN TOLUENE.CON
 
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.
   
  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.

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.asrm2.asr, m3.asr , m-3.asr ,... up to m-6.asr .

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:
      RAM36J, Ka, Kc, m
      RAM36hfJ, Ka, Kc, m, F

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.
   
  LINVAD = converter from .LIN standard of SPFIT to frequency data block used by RAM36 and RAM36hf
LINVAD.FOR
LINVAD.EXE
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.

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.

toluene_input.txt The output file from LINVAD containing the block of converted lines to be pasted into the RAM36 input file.
   

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.

Worked example of using VICONTR
tol2010hf.inp
tol2010hf.out
expectvt0.txt
expectvt1.txt
tol2010hf.res
tol2010hf.lin

tol2010hf.log
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:
  • 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 ?


        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.

  1. H.M.Pickett,  J,Chem.Phys.107, 6732 (1997)
  2. 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.
  3. 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
  4. 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 entryPAR file, LIN file
  5. 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
  6. 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
  7. 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.
  1. D.Gerhard, A.Hellweg, I.Merke, W.Stahl, M.Baudelet, D.Petitprez, G.Wlodarczak, J.Mol.Spectrosc. 220, 234  (2003).
  2. Z.Kisiel, L.Pszczolkowski, E.Bialkowska-Jaworka, S.B.Charnley, J.Mol.Spectrosc. 241, 220 (2007).
  3. A.Krasnicki, Z.Kisiel, L.Pszczolkowski J.Mol.Spectrosc. 260, 57 (2010).
  4. D.R.Herschbach, J.Chem.Phys. 31, 91 (1959).

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