Manual entry of the l matrix
If you want to set up an l
matrix, the most convenient starting point is importing the
required geometry and l
matrix directly from the output of selected ab initio
programs (see Importing l matrices
) or from a
simple force field analysis. If this is not possible, say if you
want to import an l
matrix from a source that PGOPHER
can't read directly, the following steps listed below are the
- The main menu item File, New,
Vibrational Structure will generate a basic settings for
two electronic states.
- Set the basic molecular information by clicking on "VibratingMolecule" and
Set the symmetry of the ground electronic state is set by
clicking on "X" and altering "Symmetry" as required. (The default is
Set the names of the nuclei by
right clicking on the "Nucleus1",
under X and
If you use the standard element names, possibly with a number
(e.g. H1, H2, Br) then the mass can be set by right clicking on
the nucleus and selecting "Set
Exact Mass". Alternatively, if an approximate mass is
entered (at "Mass")
"Set Exact Mass"
will find the corresponding exact mass. The names and masses
need only be set once, though they appear under a state, rather
than at the molecule level.
The geometry and l matrix are most
conveniently entered by right clicking on the state, "X" and selecting "l matrix...". This
brings up the l Matrix Window,
which will plot the molecular geometry, with the plot updating
as you enter it. Enter the equilibrium co-ordinates under "Equilibrium".
The l matrix can be entered in the same form; if "Mass Weighted" is
selected then the elements are l/sqrt(mass) with units of 1/sqrt(amu). The l matrix should be
orthogonal - the "Operate"
button contains tools to test and correct this, and the centre
Enter the ground state
frequencies and symmetries by clicking on "v1", "v2" ... in turn under "X". As for nuclear
masses, the symmetry of a mode only needs to be set in one
Repeat steps 3 and 5-7 above for
the excited state.
To make use of the l matrices for
Franck-Condon factors, "Calculate"
must be set to true under <A|FCF|X>.
- nModes - the
number of vibrational modes
- PointGroup -
the symmetry of the molecule
- nNuclei - the
number of nuclei