Hfc display.m

Draws hyperfine tensors and their eigensystems. Two styles are implemented:

A. Ellipsoids (symmetric tensors only)

1. A unit sphere in a Cartesian space is scaled by abs(Axx) in the x direction, abs(Ayy) in the y direction and abs(Azz) in the z direction, where Axx, Ayy, Azz are the eigenvalues of the HFC tensor in units of milliTesla.

1. A set of axes is drawn inside the sphere with a red axis for a positive eigenvalue, and a blue axis for a negative one.

1. The sphere is translated to the point of corresponding nucleus and rotated into the molecular frame of reference.

B. Spherical harmonics (default)

1. The matrix is converted into irreducible spherical tensor operator coefficients.

1. The coefficients are placed in front of the corresponding spherical harmonics, which are plotted in three dimensions and translated to the point of the corresponding nucleus.

Syntax

    hfc_display(props,atoms,scaling_factor,conmatrix)

Arguments

                   props -  output of the quantum chemistry package output parser function

                   atoms -  a cell array of element symbols, indicating the atoms for which
                            the hyperfine coupling tensors should be visualized, e.g. {'C','H'}

          scaling_factor -  scaling factor, connecting the mT scale to the length units in 
                            Angstrom that are used in the molecule plot, usually of the order of 0.01

               conmatrix -  optional binary connectivity matrix, with 1 if a pair of atoms should be
                            connected by a bond in the resulting plot and zero otherwise. If you are 
                            happy with the default bond drawing threshold of 1.6 Angstrom, specify an
                            empty matrix here.

Returns

The function creates a figure.

Examples

The following figure is produced by /examples/visualisation/hfc_pyrene.m

Notes

1. Software OpenGL is forced internally because hardware OpenGL works badly with transparency in Matlab.
2. Antisymmetric components of the hyperfine coupling tensors are ignored.
3. Only Gaussian quantum chemistry package is supported at the moment - send an email to Ilya Kuprov if you are using something else.

See also

cst_display.m, volplot.m, molplot.m, conmat.m, gparse.m

Version 2.2, authors: Ilya Kuprov