|Procedures Details||<Prev Next>|
|Molecule||The Molecule; can be omitted if there
is only one molecule or the molecule directive
|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 included).
|S'||Symmetry of upper 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 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
directive is used.
||The standard deviation of the observation, used to derive
the weight of the observation in the least squares fit, in
the same units as the value in the previous column. Only the
relative values are important, and for simple use it is
sufficient to set this to 1for the most accurate
measurements, and use 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 ignored.
In calculating the average error for the fit (see the information about the log window) the residual is divided by the value given in this column, meaning that if the actual measurement error is given here the average error of the fit, which is then dimensionless, should be one. The setting this is essential if fitting data with very different accuracy, such as microwave and visible data for which the values differing by 104 or more might be appropriate.
|(rest of line)
||If the eigenvalue numbers given above are >= 1 and the
symmetries are not -1, then the rest of line is taken as a
comment. If either or both eigenvalue numbers are 0, or
symmetries 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 and or symmetry 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
In addition, the symmetries can be set to -1, in which case the "Excited v=1 6 e - Ground v=0 4 e" string will also be used to work out the quantum numbers:
LinearMolecule Excited 6 -1 0 Ground 4 -1 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, similar to normal line lists, though an appropriate value for the (relative) standard deviation is normally essential in this case. Also, if any of the <Molecule>, <Manifold> or <State> names are the same, both names must be given.
A general expression involving parameters can also be given; the
Expression <expression> = <Value> <Std Dev>
The <Std Dev> entry is optional; the = sign
with a space either size marks the end of the expression. The
expression can involve any parameter; these are typically
though <object> can be omitted for the
parameters in the default state or manifold, and additional
<object>. prefixes can be added to avoid ambiguity.
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"Additional dummy parameters can be added using a Variables object. See expressions for more on what is possible.
|stop (or end)
||Stop reading from current
|/ or #
||Lines starting with / # or ; are treated as comments and ignored; # and ; can also be used elsewhere in a line to indicate that the rest of the line is a comment.|
||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. Note that both "/" and "\" can be used as
directory separators in file names, regardless of the
system, and are converted into the standard for the system
before use. If the filename is <Linelist> then the contents of the line list window are included.
||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 anyway.)
||Set the default upper
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 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. In the standard
format the eigenvalue number is taken as within the
specified state only, and the state label is worked out and
then used to find the eigenvalue number subsequently. For
the alternative formats listed below it allows the state to
be specified where there is more than one in a manifold.
||Set default lower state to name. In the standard format the eigenvalue number is taken as within the specified state only, and the state label is worked out and then used to find the eigenvalue number subsequently. For the alternative formats listed below it allows the state to be specified where there is more than one in a manifold.|
||Set default symmetry to name. This may be
required for cases (such as symmetric tops) to choose
between two otherwise degenerate transitions when using
|Force the (relative) standard
deviation of the following observations to value. Leave 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.|
|Set the (relative) standard deviation of the
following observations to the observed value times x/100.
Most useful for intensity fitting. Leave x blank to
switch off this behaviour. Note that overridestddev and scalestddev are applied
after this calculation.
|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.
frequencyoffset variable name
|Add value to the position of the following
observations. Leave value
blank to reset the offset to zero. In the second form, name
is taken as a variable name (created automatically if
necessary in a Variables
object) and the offset is taken from this variable, which
may be fitted as with any other parameter. (An initial value
can be specified by adding ":= value" after name)
||Add value to the frequency offset of the following observations. Leave value blank to reset the offset to zero.|
frequencysvcale variable name
|Multiply the position of the following observations by value. Leave blank to reset the scale to 1. In the second form, name is taken as a variable name (created automatically if necessary in a Variables object) and the scaling factor is taken from this variable, which may be fitted as with any other parameter. (An initial value can be specified by adding ":= value" after name)|
||Set the units of the
following observations. If no directive is given, or the
units are omitted, the units are as specified by the PlotUnits of first Simulation of the
If it is set, the appropriate conversion will be performed.
Possible values include cm-1, cm1, MHz,
Kelvin, eV, sqrtcm1, cm-1/2, nmVac, nmAir, angVac, angAir.
nm, Å, Ang, Angstrom and Angstroms can also be used, implying vacuum wavelengths.
|intensityunits units||Set the units of the following intensity
observations. If no directive is given, or the units are
omitted, the units are as specified by the IntensityUnits
of the first Simulation
of the Mixture.
See this for a list of possible values.
|Set the External Field for the following
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 Numbers below.
|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 spins discarded.
||(or color name). Mark the
following observations with colour name. Leave 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 following observations
|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
||Specify the type of the transition to assume when specifying branches. Leave rank blank for the default, (one photon) electric dipole transitions; specify rank = 0 for Raman or two photon transitions. Magnetic dipole transitions also need rank = 0.|
|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.|
|linenumber n filename
||Set the effective line number and file name
of the next line in the file. This is used internally, and
may also be useful for files generated from other sources.
|MergeBlends on|off||If "on" or nothing follows the
directive then subsequent lines are scanned for blends. In
this mode an additional number is read at the end of each
line (the blend weight) and adjacent observations are
checked for the position being identical. If one or more
adjacent observations are found with identical positions,
then they are combined in fitting into a single effective
observation, with the calculated value being the average
(weighted by the blend weights) of the calculated positions
of the individual observations. The blend weights are
discarded for for observations that are not blends.
|line||Following observations are
||Following observations are
||Following observations are
lower state energies
|Eupper||Following observations are upper state energies|
|This can be used to specify that more than
one type of observation is present in the file. flags
can be one or more of:
||Following observations are
taken in pairs as lower state combination
|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.
observations to upper state combination
differences; starts at previous combination difference
directive, or start of file if none present. The optional flag controls the
handling of observations that are not part of an upper state
||As for AutoCDupper, but convert
to lower state combination
|indexoffsets||Clear any offsets.
|indexoffsets search||Use the transition comment at
the end of the observation line to determine the eigenvalue
|indexoffsets searchall||Use the transition comment at
the end of the observation line to determine the eigenvalue
number and symmetry.
||If "on" or nothing follows the
directive subsequent lines are assumed to start with a
molecule name, which is discarded and the default molecule
used instead. Use "off" to revert to the default
||If "upper", "lower" or "both"
is given, subsequent lines are assumed to contain the
specified manifold name(s), which are discarded. The text at
the end of the observation line is then used to identify the
state and manifold, with non-existent manifold names being
ignored provided the state name is unambiguous. If no flag
is given, revert to the default behaviour.
|indexoffsets n1 n2 n3 ....
||Add to the eigenvalue number,
as described below.
||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
||Upper and lower state symmetry number|
||Upper and lower state index
(Only useful if the state index is given in the file.)
|E' E"||Upper and lower state energy.a
||The transition intensity.a|
In addition the following molecule specific quantum numbers are
available, with ' or " added to indicate upper or lower state. Use
of these variables will also require a calculation on each line of
For asymmetric tops the standard quantum numbers Ka and
Kc are available.
For linear molecules:
||The Ω quantum number; note this is evaluated here taking Λ ≥ 0.|
|Fn||The spin component, 1 for F1, 2 for F2,
||The absolute value of K
|Kl||The sign of Kl
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
Where a state in either manifold has a non zero spin, replace J by N and add J on the end; for hyperfine
structure add F1...F on the end, so an open
shell asymmetric top with two nuclei would be N' Ka' Kc' J' F1' F' J" Ka" Kc" F1" F. This format is not
appropriate for vibrational structure type calculations, and
some of the more complicated cases for other calculation types
must be handled using the full standard format. Where multiple
states or manifolds are present, use uppermanifold,
directives (see above) as to indicate the required state. Use NQN 0 to revert to the
Fitting to energy levels is also possible by setting all the
quantum numbers for the unwanted state to "-".
When linear molecules and symmetric tops the selection rules
for rovibronic transitions, as set by the BranchRank directive, is used to
resolve ambiguities. If this is not sufficient, there are some
J' Fn'e J" Fn"f specifies Fn' e parity in the upper state and Fn" f parity in the lower state. The second item must be given without spaces, so an example might be:To specify J and Ω:
10 F1e 10 F2fThe e and f can be omitted in this case if there is only one one parity present.
J' Ω'e J" Ω"f specifies Ω' e parity in the upper state and Ω" f parity in the lower state. The second item must be given without spaces, so an example might be:For symmetric tops the sign of K is taken as the sign of Kl and the rovibronic symmetry can be added on the end of the K quantum number, as for example:
10 0e 10 1fThe e and f can't be omitted in this format (otherwise the format is assumed to be N' J' N" J").
2 -2A2" 3 3 63737.92In this case the upper state symmetry is specified as A2", and the sign of Kl is -1. In some cases this information is essential; for example the l component must be specified in E-E transitions. If either or both of the symmetry and sign are omitted, PGOPHER can often identify the specific transition by assuming it is an allowed transition, and also (if necessary) by minimising the change in the g quantum number used in determining rovibronic symmetry. The symmetry directive, which specifies a default symmetry can also help to pin down the transition. There are, however, some cases for any symmetric top, particularly transitions that have very low intensity, for which the full specification is required.
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 first line. For symmetric tops, the sign of Kl can be
specified immediately before K and the rovibronic
symmetry immediately after K, such as qQ+1A1(1) -
the lower state has the sign of Kl as +1, and has A1
rovibronic symmetry. Note that not all transitions can be
specified unambiguously using the branch format.
To allow for the easy shift of the assignment of a set of lines,
lines can be tabulated with a single running number, and the
branch given as a general expression involving the running number,
introduced with the BranchExpr directive. For example the
linear molecule P and R branches shown above could be expressed
BranchExpr P(J) 2 996.0000 1.0
1 998.0000 1.0
0 1002.0000 1.0
1 1004.0000 1.0
2 1006.0000 1.0
J in the branch string is replaced with the first number on the line. General expressions in terms of J can be used, so the R branch assignments can, for example, be shifted along by 1 using BranchExpr R(J+1). While J is used for the running number, it need not actually refer to J. An asymmetric top branch example is:
5 546.3561 1.0 # rR6,0(6) 7 7 1 - 6 6 0
6 546.9916 1.0 # rR6,2(7) 8 7 1 - 7 6 2
7 547.62667 1.0 # rR6,2(8) 9 7 3 - 8 6 2
8 548.26125 1.0 # rR6,4(9) 10 7 3 - 9 6 4
Note there are two expressions
here, one for Kc (=J-6+2-J%2) and one for
J" (=J+1). % in the expression for Kc
indicates modulus. In the above example the actual branch and J'
Ka' Kc' - J" Ka" Kc" are
indicated in the comments after the # on each line, though these
would normally be omitted. The corresponding information is,
however, displayed in the log when fitting.
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
BranchTable R2(J) R3(J-1) P2(J) P3(J-1)This is for the origin band of the Schumann-Runge band in O2.
3 49357.07 49357.37 49345.79
5 49349.06 49349.39 49331.21 49331.42
7 49336.03 49336.46 49311.69 49311.94
9 49318.02 49318.48 49287.18 49287.60
11 49294.99 49295.58 49257.76 49258.15
21 49105.02 - 49035.47 49036.55
Files from the ExoMol project can also be used as input to the fitting process; see Using ExoMol Files.
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
||Include only calculated lines.|
|mapupper n1 m.s
||Provide a mapping of state
numbers from the .par
file to PGOPHER
states. (See also the mapstate directive.) 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
||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.
treats such transitions as separate, but these sometimes
appear merged into a single line in .par and .mrg files.
|DiscardBlends TrueOrFalse||Blend fitting is not implemented at the
moment, and by default blends are treated as normal
transitions, and the blend weight is ignored. Use this
directive to discard blend transitions completely.
||Force quantum number format n. By
default it is automatically detected, but this can be used
if the autodetection fails.
||Provide a mapping of state numbers from the .par file to PGOPHER states.
Here n is the state number in the .par file, and name
is the PGOPHER state name. The current
implementation requires the PGOPHER state name to
be unique. See also mapupper and maplower.