Molecule

There can be one or more molecules within each species; there should be one molecule for each isotopomer or isotopologue. To add another molecule, either:

Right-click on the species you are adding to in the tree view and select "Add new...", then select a linear, symmetric top or asymmetric top molecule
Right click on a similar molecule entry (it must be of the same type) and select "copy", then right click where you want the new molecule to be and select paste.

The latter method is particularly effective for adding another isotope as the parameters and settings will be largely similar. Note that it is possible to copy and paste between independent copies of PGOPHER should you want to use a molecule from a completely different file as a starting point.

The settings given here are common to all different types of mixture. Details of other settings are given in the sections for linear, symmetric top, asymmetric top and vibrating molecules.

Settings

nNuclei	Number of nuclei to calculate hyperfine structure for. Leave this at 0 unless you want the hyperfine structure resolved.
Jmin	Minimum J to use in calculation - set to -1 (default) to use value from species.
Jmax	Maximum J to use in calculation - set to -1 (default) to use value from 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 that is often found. For example in linear molecules an energy level will typically alternate between + and - parity with J (hence the e/f notation).
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.

Parameters

Abundance Abundance of this isotopologue; 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 linear molecules at very low temperatures) where it may be necessary to set it manually to the energy of the lowest level. It arises as the population, calculated as exp(-(E-AssumedOrigin)/kT)) can overflow 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 or Squared.