l Matrix Window
This window displays, and allows the
editing of, the equilibrium geometry and vibrational modes for an
electronic state. To bring up the window, right click on the state
and select "l Matrix...".
To display a particular normal mode, click on the appropriate
column. Rx, Ry and Rz are the
rotations around the x,
y and z axes and Tx, Ty and Tz are the
translations along the axes. They are calculated from the masses
and equilibrium geometries and can't be edited.
panel shows the atom positions, and a normal mode motion if
a mode is selected. a,
b, and c are the principal
inertial axes, which are calculated from the given atomic
||Drag to resize the upper and lower parts.
|Equilibrium positions of the atoms, in Å. These
should be with respect to the centre of mass; if not see
under the Operate button.
|Select matrix displayed and plotted in one of
- "Zero Point" is the displacements at the
classical limits of the zero point motion.
- "adm (/10)"
is the matrix M-½ l, and the
values correspond to relative atomic displacements, and
the units are 1/sqrt(atomic mass units).
- "l (/10)" is the l matrix; the values are
dimensionless. In this form the matrix should be
orthogonal; see under the Operate
button for options to check and correct this.
||Select plane to plot
||This controls the length of the arrows plotted on each
atom to show the motion of the atom in the selected normal
mode. The number is the multiple of the zero point motion,
assuming the motion is harmonic. If you can't see any
arrows, you may need to increase the value set here.
||Show Translational and Rotational normal modes. Note "Zero
Point" does not make sense for these, so the values
and plot are the same as "adm (/10)".
||Rotates the plotted image by the given angle
about the horizontal axis.
||This brings up a menu with the following options:
||Force update of the coordinates and l
matrix from all other objects and plot.
|Force update of the coordinates and l
matrix and show calculated state information in the log
||Adjust atomic co-ordinates in the Nuclear co-ordinates
objects so centre of mass is at the origin.
||Adjust the vibrational co-ordinates in Vibrational Modes objects
to be correctly normalized.
||Adjust vibrational co-ordinates in Vibrational Modes objects
to be orthogonal and correctly normalized. Also fixes centre
of mass if necessary.