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Linear Molecule

These are the settings for a linear molecule as a whole, i.e. those common to all states (but perhaps different for different isotopologues).


nNuclei Number of nuclei to calculate hyperfine structure for. Leave this at 0 unless you want the hyperfine structure simulated.
Jmin Minimum J to use in calculation - set to -1 (default) to use value from the species.
Jmax Maximum J to use in calculation - set to -1 (default) to use value from the species.
Colour Colour - set to "None" to take value from elsewhere as explained in Determining Colours and J ranges.
JAdjustSym If set, energy level plots and Fortrat diagrams will take account of the alternation in symmetry with J. For linear molecules a given energy level will typically alternate between + and - parity with J (hence the e/f notation). Note that this should be set to False if simulating hyperfine structure as otherwise confusing results can be obtained.
BlockMatrix Set to force check of Hamiltonian matrix for factorization into blocks before diagonalization. If blocks are found, these are diagonalized separately, ensuring states that have no connecting matrix elements are not accidentally mixed if the eigenvalues happen to be very close. In principle, if full use is made of symmetry and states are separated into separate manifolds as appropriate, this should not be necessary but can easily happen if selected terms in the Hamiltonian are zero or interactions between states are omitted.
AbsoluteE True if energies have not been offset. This is not the default for compatibility with previous versions, though perhaps should be for new calculations. Setting this false (the default) allows transitions with negative frequencies, which can occasionally be convenient for simulations involving a small spread of frequencies around a large central frequency where a large offset is applied to the upper state origin. This can give erroneous negative frequencies; while there is logic to detect common cases where this might arise, some calculations (typically involving near degenerate manifolds) require this to be set to true for correct operation.
Symmetric Set true if the molecule has a centre of symmetry, and g or u must be specified for individual states.
SymWt Statistical weight of symmetric rotational levels, or all levels if no centre of symmetry. See Making a linear molecule data file for how to set this up if there is a centre of symmetry. Note that any nucleus for which hyperfine structure is to be calculated should not be included in calculating the statistical weights - see under the linear nucleus settings for notes on the required calculation.

If there is no centre of symmetry this can be left at 1, unless nuclear spin states are required in the partition function. Versions of PGOPHER before 8.0.217 forced this, and loading old data files will set SymWt to 1.
AsymWt Statistical weight of asymmetric rotational levels. Ignored if no centre of symmetry.
RSquaredH Set to use the R2 Hamiltonian rather than the default N2 form.
ShowJ Show J in state label.
ShowOmega Show Omega in state label.
ShowN Show N in state label.
ShowFNumber Show F Number in state label.
Showef Show e/f symmetry in state label.


Abundance Abundance of this isotope; default is 1
AssumedOrigin Assumed energy origin for Boltzmann calculations; values > 1e50 (the default) imply an automatic estimate of the lowest populated energy level in the molecule.  This can normally be left at the default, except in unusual circumstances (most likely at very low temperatures) where it may be necessary to set it manually to the energy of the lowest level. It arises when the population, calculated as exp(-(E-AssumedOrigin)/kT)), overflows when the estimated assumed origin is significantly above the true lowest energy in the molecule. Predicted intensities will otherwise be independent of the value of the assumed origin unless the IntensityUnits are set to Arbitrary.
For linear molecules the lowest energy in any given state is estimated by taking the lowest value of:
Origin + A|Λ|Σ + 2/3λSS(3Σ2S(S+1))
which typically differ from the actual lowest energy by ~B.