| PMIFST |
Principal Moments
of Inertia From
STructure
|
This program takes in either Cartesians or connectivity
definitions of molecular structure, calculates moments of
inertia etc., and allows viewing, 3-D rotation and
structural checks.
The original purpose has been to check the validity of
structural declarations and prediction of rotational
constants, but it is now also used as a rapid viewer for
inspection of structural results from various programs,
including STRFIT and various ab initio packages.
Principal features:
- use of Cartesians (in Angstroms or
bohr) or internal structural coordinates to
declare the molecule (note that the latter are
also used in the structure fitting program STRFIT)
- dummy atoms can be used to show,
among others, the orientation of the dipole
moment, orientation of the diagonal quadrupole
tensor etc.
- rotational constants of isotopic
species can be rapidly evaluated since nuclear
masses are easily modified on-line by using
common isotope notation i.e. 37Cl, 13C, etc.
- bonds, angles, dihedral angles can
be checked, including angles between bonds and
principal axes
- PostScript printout of molecule in
the displayed orientation is possible for those
familiar with the gle
graphics package.
- current limit on the number of
atoms is 200
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Current
version |
| PMIFST.FOR |
The listing - this is intended
for CVF6.5+
compilation |
| PMIFST.EXE |
CVF6.6A executable for
Win95/Pentium I upwards. Key properties
of the graphics, i.e. window size and the
display font are now read from the file PMIFST.CFG (below). The colour depth of
the display should be at least 8 bits
(256 colours). Running
conditions and installation are identical
to those discussed in connection with SVIEW
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| PMIFST.CFG |
Configuration
file for PMIFST, which has to reside in the
directory C:\ROT. |
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Examples |
| PMIFST.GIF |
Snapshot of a typical
display screen |
| CUBE.COR |
Simple Cartesian data |
| C70.COR |
Cartesian data in
atomic units from the ab initio
world - note that bond location fails if
you read this in as Angstrom data |
| PRMW.PMI |
CART type input for
pyrimidine...water complex - use of
mnemonics in a data file and use of dummy
atoms |
| SABKET.PMI |
CART type input - data
for the molecule which prompted creation
of this program. If you want to know
whether it was studied by rotational
spectroscopy, the answer is yes! See JACS
100, 8166, 1978. |
| SABKET.PS |
PostScript file
produced from the gle dump of a previewed orientation
of the structure in the file above |
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Legacy
versions |
| PMIFST_5.FOR |
The final
version for MSF5/VGA graphics |
| PMIFST_5.EXE |
Executable
for the above - it should run on all
versions of DOS/WIN which allow full
screen MS-DOS mode |
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| STRFIT |
STRucture FITting
to rotational data
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This program was originally written for determination of
effective structures of hydrogen bonded complexes. It is
based on the principles outlined by R.H.Schwendeman in "Structural
parameters from rotational spectra", a chapter
in "Critical evaluation of chemical and physical
structural information", D.R.Lide and M.A.Paul,
Eds., National Academy of Science, Washington, D.C.
(1974). For a similar approach see also:
P.Nosberger,A.Bauder, and Hs.H.Gunthard, "A
versatile method for molecular structure determinations
from ground state rotational constants", Chem.
Phys. 1, 418-425 (1973).
Although the program has been very useful in
determination of partial geometries, it can also be used
for complete geometry determination. When I wrote this
program it was natural for me to call it STRFIT, and I
only found out much later that this is the same name that
Schwendeman chose for one of his programs (the chapter in
Lide+Paul, p.107) - apologies for any confusion. In any
case the current program has been written completely
independently of its namesake.
This program can currently fit the following types of
geometry:
- r0 - from a
direct fit to the supplied ground state constants
- rz (r*
or rav) - from fit to supplied ground state
constants and harmonic vibration-rotation
contributions to moments of inertia calculated
with a program like VIBCA
- r0av or similar corrected geometry from fit
to supplied ground state constants and
vibration-rotation corrections from an external
model
- NEW: rm(1),
rm(2) , rm(1L),
rm(2L),
etc. - see J.K.G. Watson, A. Roytburg., W.
Ulrich, J. Mol. Spectrosc. 196,
102-119 (1999).
Principal features:
- internal coordinates (bond lengths
and angles) are fitted directly to moments of
inertia (not rotational constants) in a
nonlinear least-squares procedure
- rotational constants from many
isotopically substituted species can be used
simultaneously, it is also possible to fit to
linear combinations B+C and A+B
of rotational constants, as well as to planar
moments of inertia
- the geometry is declared in the
CART connectivity scheme used by PMIFST and can be checked by using that
program
- the fitted structure is echoed to
file STRFIT.PMI for direct inspection with PMIFST
- degenerate internal parameters
(i.e. those which have many repetitions owing to
symmetry) are easily specified
- isotopic changes in structural
parameters can be specified when sensible
- any parameter that can be fitted
can also be fixed at an assumed value if desired
Following
the extension of the program to fit the various rm(
) geometries of Watson the current reference for
citing the use of STRFIT is: Z. Kisiel, J. Mol. Spectrosc. 218,
58-67 (2003).
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| STRFIT.FOR |
The listing, to be compiled with
any 32-bit FORTRAN compiler. It is
recommended that the extension .STF be reserved for the data |
| STRFIT.EXE |
The
executable for Windows 95+. |
| |
Examples |
| OCSe.STF and OCSe.RES |
The data and results
files reproducing the rm(2)
fit for OCSe from Table 6 of the Watson,
Roytburg, Ulrich paper. |
| HCN.STF
and HCN.RES |
Reproduction of the rm(1L)
fit for HCN from Table 7 of the Watson,
Roytburg, Ulrich paper. Note the use of
commenting in the data file: any number
of comment lines beginning with a ! character are
allowed before any line declaring a
repeat count (such as NO OF PARAMETERS).
These comments are echoed to the output.
Annotations are also allowed past the
52nd column of all data lines past the
CART block - those are simply ignored on
input and will not be echoed to output.
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| H2O.STF
and H2O.RES |
Reproduction of the
'with cab' rm(2L)
fit for H2O
from Table 5 of the Watson, Roytburg,
Ulrich paper |
| O3.STF
and O3.RES |
Reproduction of the rm(2)
fit for ozone from Table 8 of the Watson,
Roytburg, Ulrich paper. The solution is
very well defined and there is no need to
preset the values of any of the c
or d parameters. |
| HNCO.STF, HNCO.RES |
Reproduction of the rm(2)
fit for HNCO from Table 9 of the Watson,
Roytburg, Ulrich paper |
| H2CCC.STF, H2CCC.RES |
Reproduction of the rm(2)
fit for H2CCC
from Table 10 of the Watson, Roytburg,
Ulrich paper |
| H2OHCL.STF, H2OHCL.RES |
The data and results
files for the rm(L)
fit for H2O...HCl
from column V, Table 6 of Z.Kisiel, J.Mol.Spectrosc.
218,
58-67 (2003).
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Older
examples |
| CHLPROP.STF |
The data
set for chloropropane (8 isotopomers),
set up on the basis of
Tobiason+Schwendeman J.Chem.Phys.
40,1014(1964) |
| CHLPROP.RES |
Abbreviated
results file for the above, which can be
compared with the results in Table 2 of
the Schwendeman chapter in the Lide, Paul
book |
| CHEX.STF |
The data
set for cyclohexane as set up in J.Mol.Struct.
350, 247 (1995) - note
the use of dummy atoms and repeated
coordinates |
| W2HCL.STF |
Data set
for the hydrogen bonded trimer (H2O)2HCl
- to fit the r* geometry as
published in J. Chem. Phys. 112,
5767-5776 (2000). The necessary
corrections are obtained with: GAMESS
->
FCONV -> VIBCA. |
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Back
to the table of programs
| KRA |
KRAitchman's
substitution coordinates
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| EVAL |
EVALuation of
internals from Cartesians
|
KRA embodies a standard implementation of
Kraitchman's equations for single isotopic substitution.
The equations are directly out of Gordy & Cook, and
the programmed possibilities are:
- on axis substitution in a
linear/symmetric top
- off-axis substitution in a
symmetric top
- substitution in an inertial plane
of an asymmetric top with several options of
using the planarity condition
- general substitution in an
asymmetric rotor
Errors in the determined coordinates are calculated from
propagation of uncertainties in the measured rotational
constants, and then the usually much larger Costain's
error is added (ie. dz=0.0015/|z| Angstr., see
C.C.Costain, Trans.Am.Crystallogr.Assoc. 2,
157-164(1966)).
EVAL is a simple tool to convert Cartesians and
their cited errors into internals and their errors. The
available internals are bond lengths, bond angles, and
dihedral angles, but since the errors on dihedrals have
not yet been required, they are not programmed in.
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KRA |
| KRA.FOR |
The listing, the data is best
kept in a file with extension .KRA, and the output is made to KRA.OUT |
| KRA.EXE |
Windows executable |
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| PRM.KRA |
The data set for
pyrimidine (4 isotopomers), as in J.Mol.Spectrosc.
195, 332-339(1999) |
| KRA.OUT |
Output for the above |
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EVAL |
| EVAL.FOR |
The listing, the data
is best assigned extension .EVA, output is to screen and to EVAL.OUT |
| EVAL.EXE |
Windows executable |
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| PRM.EVA |
The data set for
pyrimidine, which has been derived from a
prior run of KRA |
| EVAL.OUT |
Output for the above |
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Back
to the table of programs
| CORSCL |
Scaling of trial molecular geometry
declared in Cartesian coordinates
|
The main purpose of this program is to enhance the
accuracy of prediction of rotational spectra for isotopic
species of a molecule before its precise geometry has
been determined.
The program allows scaling of ab initio, ar any other,
trial geometry for the molecule to best reproduce
experimental rotational constants. The resulting scaled
geometry can then be used to evaluate rotational
constants for the isotopic species with the help of the PMIFST program.
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| CORSCL.FOR |
The listing. |
| CORSCL.EXE |
TheWindows executable. Input is
from two files: 1/
user specified file containint the trial
geometry in the .COR standard of PMIFST.
2/ a single line ASCII
file named CORSCL.INP, which contains the values of
rotational constants A,B,C
(in MHz) for the declared isotopic
species
The scaling factor is
determined online by trial and eror. Once
done the rescaled geometry is written to
file CORSCL.OUT for further use in PMIFST.
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| CAMPH.COR |
The sample
input file with trial geometry of the
camphor molecule from an ab initio
calculation. |
| CORSCL.INP |
Experimental rotational
constants for the isotopic species
declared in the file above. |
| CORSCL.OUT |
The output output file after a
session with CORSCL, which established that best
overall reproduction of experimental
moments of inertia is with scaling factor
of 1.0025. Note that this may not be the
most useful way of scaling as, for
example, for a prolate molecule you might
want to aim for best reproduction of B
and C, and might not care that
much about A. You can
check the results for camphor against the
actual experimental isotopic values in PCCP
5,820(2003)
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Back to the table of programs
| RGDFIT |
FITting of
coordinates of a RareGas
atom in a Dimer
with a molecule
|
This program embodies the simple idea that formation of a
dimer between a molecule and a rare-gas atom is
equivalent to adding a point mass to the molecule, so
that coordinates of the added atom can be calculated from
the moments of inertia of the molecule and of the dimer.
The geometry of the molecule is not explicitly required
in this step. The downside is of course sensitivity of
the derived coordinates to unavoidable vibration-rotation
contributions to moments of inertia, but if these can be
subtracted, the reliability will increase.
Exposition of the method has been given in Suenram,
Fraser, Lovas, J.Chem.Phys. 89,6141(1988)
and this particular program has been used to obtain the
results reported in Kisiel, Fowler, Legon, J.Chem.Phys.
95,2283(1991).
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| RGDFIT.FOR |
The listing, input is from a
file specified by the user (it is
recommended to use the molecule name as
file name, and Rg name for extension).
Output is to screen, and a printable copy
is also written to file RGDFIT.OUT |
| RGDFIT.EXE |
Windows executable |
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| VINF.AR |
Specimen data for the
Vinyl Fluoride-Argon dimer - in this case
there is a particularly high sensitivity
of results to the input data, Ar
complexes to more heavily fluorinated
ethylene gave more reliable results. See
the discussion in the KFL paper. |
| RGDFIT.OUT |
The output for the
data above. Note that for a general
molecule there are eight solutions to the
position of the Rg atom - the printout
assumes that the molecule is planar and
lists only the four distinguishable
solutions for such case - the other four
solutions can be obtained by changing the
sign of the Z-coordinate. |
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