|Procedures Details||<Prev Next>|
|Molecule||The Molecule; can be omitted if
there is only one molecule or the molecule directive is used.
|M'||The upper state Manifold; can be omitted if there is only one or two manifolds or the uppermanifold directive is used.|
|J'||Upper state total angular momentum (i.e. normally J, but F if hyperfine structure is
state. This can be a symmetry number (starting from 0) or name. The
symmetry names understood depend on the molecule type, but include "+",
"-" "e" and "f" for linear molecules. -1 in this field indicates that
the symmetry should be worked out from the text field at the end of the
|#'||Eigenvalue number for upper state. This indicates the rank of
the upper energy level in the list levels of the same J
and symmetry for the upper manifold (numbered staring from 1). 0 in
this field indicates the number should be worked out from the text
field at the end of the line.
|M''||The lower state Manifold; can be omitted if
there is only one or two manifolds or the lowermanifold directive is used. Note that
this is also allowed directly after the upper state manifold.
|J''||Lower state total angular momentum (i.e. normally J', but F" if hyperfine structure is included).|
|S''||Symmetry of lower state. This can be a symmetry number (starting from 0) or name. The symmetry names understood depend on the molecule type, but include "+", "-" "e" and "f" for linear molecules. -1 in this field indicates that the symmetry should be worked out from the text field at the end of the line.|
|#''||Eigenvalue number for lower state. This indicates the rank of the lower energy level in the list levels of the same J and symmetry for the lower manifold (numbered staring from 1). 0 in this field indicates the number should be worked out from the text field at the end of the line.|
|Frequency||The frequency of the transition or (for line intensity fits)
the intensity. The units are taken as set by PlotUnits of the Mixture, unless the units directive is used.
||The relative standard deviation of the observation, used to
derive the weight of the observation in the least squares fit. Only the
relative values are important, and typically 1 will be used for the
most accurate values, with larger values (perhaps 3 or 10) for blended
or weak transitions. A negative
or zero value or a single "-" character will cause the line to be
|(rest of line)
||If the eigenvalue numbers given above are >= 1, then
the rest of line is taken as a comment. If either or both eigenvalue
numbers are 0, then the comment should contain a string of the form:
: upper state quantum numbers - lower state quantum numbers
where the quantum numbers are in the format output by PGOPHER in line listings, and thus depend on the molecule type. The eigenvalue number will be worked out from this field.
LinearMolecule Excited 6 1 1 Ground 4 0 1 1006.0000 1.0 .005 0 : R( 4) : Excited v=1 6 e - Ground v=0 4 eWith only the essential fields:
6 1 1 4 0 1 1006.0000 1.0The spaces are not required either:
6 1 1 4 0 1 1006.0000 1.0Alternatively, the eigenvalue numbers can be set to 0, in which case the "Excited v=1 6 e - Ground v=0 4 e" string will be used to work out the quantum numbers.
LinearMolecule Excited 6 1 0 Ground 4 0 0 1006.0000 1.0 .005 0 : R( 4) : Excited v=1 6 e - Ground v=0 4 e
Parameter <Molecule> <Manifold> <State> <Parameter> = <Value> <Std Dev>The <Molecule>, <Manifold> and <Std Dev> entries are optional, as for normal line lists, though an appropriate value for the (relative) standard deviation is normally essential in this case.
Constrain <parameter> := <expression>where <expression> is an arbitrary expression in terms of other <parameter> names. In the simplest cases the parameters are specified using
though in most cases the names of the containing <object>'s will also be required on front to avoid ambiguity. To find the name of a parameter, right click on it in the constants window and select "Show Full Name". The name is also copied to the clipboard.
A typical example might look like
Constrain A.v=0.B := X.v=0.Bwhich would force two B values to be the same. The constraints are applied when the constraints are first read, and then at every appropriate stage of the fitting process. Note that if the parameter name contains special characters (< or >, for example) then quotes might be needed round the parameter name, as for example:
Constrain NH3.NH3.s.<0+|J+-^6|0+>.Value := "NH3.NH3.s.<0-|J+-^6|0->.Value"
(or end or -1)
||Stop reading from current file
or # or ;
||Lines starting with / # or ; are treated as comments and ignored; # and ; can also be used elsewhere in a line.|
||Read contents of filename (and then continue reading
current file). A blank filename
causes the current state to be saved, but reading continues normally. A
stop or end will causes the state to be
reset, giving the effect of an included file within one file.
||Include file in old PGOPHER format.
||Set the default molecule to molecule. (If there is only one
molecule in the mixture, the default will be initialized to this
||Set the default upper manifold
For this to work a default molecule must be set. If there are only one
or two manifolds present in the default molecule, this will be
initialized to the state with Initial
false or the higher energy manifold.
|lowermanifold manifold||Set the default lower manifold to manifold. For this to work a default molecule must be set. If there are only one or two manifolds present in the default molecule, this will be initialized to the state with Initial true or the lower energy manifold.|
||Set default upper state to name.
||Set default lower state to name.
||Set default symmetry to name. This may be required for
cases (such as symmetric tops) where two choose between two otherwise
degenerate transitions when using branch format.
|Force the (relative) standard
deviation of the
following observations to value.
value blank to leave
the standard deviations unchanged.
|Multiply the (relative) standard deviation of the following observations by value. Leave value blank to leave the (relative) standard deviations unchanged.|
|takeall||Include all lines, regardless of
the sign of their standard deviation. Standard deviations of zero are
forced to -1.
|takeobs||Include only lines with standard
deviations > 0, the default.
||Add value to the position of the
following observations. Leave value
blank to reset the offset to zero.
||Add value to the frequency offset of the following observations. Leave value blank to reset the offset to zero.|
||Multiply the position of the
following observations by value.
||Set the units of the following
observations. Unless this is set, the units are assumed to be the same
as the PlotUnits of the Mixture. If it is set, the
appropriate conversion will be performed.
|Set the External
observations. Unless one or more of these are set, the fields are taken
from the Simulation
settings in the Mixture.
||Offset the eigenvalue numbers of
the following observations. See Adjusting Eigenvalue
|upperindexoffsets ...||As for indexoffsets, but applied to the
upper state only.
|lowerindexoffsets ...||As for indexoffsets, but applied to the lower state only.|
||Add an additional condition to
including observations in the fit. See Selecting
||Discard the n outermost spins from the
calculations from the following observations. This works backwards down
the list S, I1, I2, ..., so nuclear
spins are discarded first. Omit n
to revert to using all spins. Note that n adds to the current number of
||(or color name). Mark the following
observations with colour name.
name blank to leave
the colour unset. See Determining Colours and
J ranges for the possible colours.
||Set the format for quantum
numbers as follows:
||State labels displayed at end of
line are calculated as they are fit, rather than using the strings read
from the file.
||Override displayed filename for
|pgopherversion version||Set the PGOPHER
version the line list file was created for. This allows for changes in
the input format in later versions of the program. Currently it only
affects asymmetric top line lists, where the definition of the numbers
defining rovibronic symmetry changed between version 5.1 and 5.2 as
described here. The version
string is of the form 5.1 or 5.1.144.
for the default,
(one photon) electric dipole transitions; specify rank = 0 for Raman or two photon
|correlation value offset||Set the correlation coefficient between the previous observation and the observation at offset from it. If offset is omitted, it defaults to -1, which sets the correlation coefficient between the previous two observations.|
|line||Following observations are line
||Following observations are line
||Following observations are lower
|Eupper||Following observations are upper state energies|
||Following observations are taken
in pairs as lower state combination differences
|CDupper||Following observations are taken in pairs as upper state combination differences|
||Mark start of region to search
for combination differences; requires
matching AutoCDupper or AutoCDlower directive.
||Convert preceding observations
to upper state combination differences;
present. The optional flag
controls the handling of observations that are not part of an upper
state combination difference:
||As for AutoCDupper, but convert to lower
state combination differences.
|indexoffsets||Clear any offsets.
|indexoffsets search||Use the transition comment at
the end of the line to determine the eigenvalue number.
|indexoffsets searchall||Use the transition comment at
the end of the line to determine the eigenvalue number and symmetry.
n1 n2 n3 ....
||Add to the eigenvalue number, as
||Frequency of observation (or
intensity for intensity fits)
|The (relative) standard
deviation of the observation
|J' J"||Upper and lower state total
angular momentum. (Note that the quantum numbers are never doubled)
||Upper and lower state symmetry number|
||Upper and lower state index
|E' E"||Upper and lower state energy.
Note this requires a calculation to be performed as each line is read,
and the selection could potentially change on each fit cycle.
||The transition intensity. As for state energies, this requires a calculation to be performed as each line is read, and the selection could potentially change on each fit cycle.|
NQN 3The layout is free format, in that the numbers can be separated by any number of spaces or tabs. All text after the relative standard deviation is treated as a comment. The quantum numbers are:
2 0 2 1 1 1 187.43463 1.0
1 1 0 1 0 1 21223.35986 1.0
2 1 1 2 0 2 22268.0897 1.0
A "branch" style label for a transition
can also be used, by replacing
all the upper and lower state quantum numbers with a branch label such
as P(2). The format should match that output by PGOPHER in the Line List Window
for the given molecule type.
The branch label should not contain spaces. For example, a simple
linear molecule input file
could look like:
P(2) 996.0000 1.0
P(1) 998.0000 1.0
R(0) 1002.0000 1.0
R(1) 1004.0000 1.0
R(2) 1006.0000 1.0
If the transition is a Raman transition, a multiphoton transition of
even rank or a magnetic dipole transition add a branchrank 0 directive before the
BranchTable P11 P22 P33 R11 R22 R33
8 - - - - - -
9 - 47126.7 47123.0 - - -
10 - 47120.9 47116.3 - - -
11 47123.0 47114.2 47108.9 - - 47131.0
12 47116.3 47106.1 47101.0 - 47128.7 47124.9
13 47108.9 47099.5 47092.6 47131.0 47123.0 47118.0
IncludeSPFITat the start of the file or, in a separate .lin file use a line containing:
IncludeSPFIT filename -3for a simple asymmetric top.
IncludeSPFIT * 3at the start of the file or:
IncludeSPFIT filename 3to include the contents of another file.
||Include both experimental and
||Include only experimental lines.
||Include only calculated lines.|
|mapupper n1 m.s
||Provide a mapping of state
numbers from the .par
file to PGOPHER states.
This is required for more complicated cases, typically involving
multiple states. Degenerate states in symmetric tops also require this,
as Pickett's programs treat this type state as pairs, while PGOPHER treats then as a single
state. n1 is the number in
the .par file. m.s
refer to the manifold (m) and
state (s) numbers in PGOPHER, numbered starting from
zero. s values >= 1000
indicate an alternate kl
assignment. The m. can be
omitted, in which case the manifold specified by uppermanifold is used.
Repeat the directive for every state number that requires changing. n2 values are taken mod 1000;
|maplower n1 m.s
||As for mapupper, but for the lower state.
||When fitting intensities, divide
input intensity by two where the transition is one of a normally
degenerate pair of levels, such as A1 and A2 in
non-degenerate vibronic states in C3v. PGOPHER always treats such
transitions as separate, but these sometimes appear merged into a
single line in .par and .mrg files.