Difference between revisions of "Hfc display.m"

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Draws hyperfine tensors and their eigensystems. Takes the props
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{{DISPLAYTITLE:hfc_display.m}} __NOTOC__
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structure from the output of [[gparse.m|gparse]] function. Every ellipsoid is drawn in the following way:
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Draws hyperfine tensors and their eigensystems. Two styles are implemented:
  
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1. A unit sphere in a Cartesian space is scaled by abs(Axx) in
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;A. Ellipsoids (symmetric tensors only):
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the x direction, abs(Ayy) in the y direction and abs(Azz) in
 
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the z direction, where Axx, Ayy, Azz are the eigenvalues of
 
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the HFC tensor in units of milliTesla.
 
  
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2. A set of axes is drawn inside the sphere with red axis for
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: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.
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positive eigenvalues and blue for negative ones.
 
  
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3. The sphere is translated to the point of corresponding atom
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:2. 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.
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and rotated into the molecular frame.
 
  
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Arguments:
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:3. The sphere is translated to the point of corresponding nucleus and rotated into the molecular frame of reference.
  
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                    props -  output of gparse function
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;B. Spherical harmonics (default):
  
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                    atoms -  a cell array of element symbols,
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:1. The matrix is converted into irreducible spherical tensor operator coefficients.
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                            indicating the atoms for which
 
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                            the hyperfine tensors should be
 
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                            visualized
 
  
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          scaling_factor -  a factor to scale the tensors
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:2. 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.
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                            by for visualization
 
  
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                conmatrix -  binary connectivity matrix, 1
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==Syntax==
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                            if a pair of atoms should be
 
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                            connected by a bond
 
  
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Note: software OpenGL is set as default, switch to hardware on
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    hfc_display(props,atoms,scaling,conmatrix,options)
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systems with good hardware graphics.
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==Parameters==
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              props - output of [[gparse.m]] function
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              atoms - a cell array of element symbols,
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                      indicating the atoms for which
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                      the hyperfine tensors should be
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                      visualised, e.g. {'C','H'}
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            scaling - a factor to scale the tensors
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                      by for visualisation
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          conmatrix - binary connectivity matrix, 1
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                      if a pair of atoms should be
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                      connected by a bond. If an em-
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                      pty vector is supplied, 1.6
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                      Angstrom cutoff distance is used
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      options.style - 'ellipsoids' or 'harmonics'
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    options.kill_iso - set to true() to eliminate the
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                      isotropic parts of tensors be-
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                      fore plotting
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==Examples==
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The following figure is produced by /examples/visualisation/hfc_pyrene.m - (left) ellipsoid plot; (right) spherical harmonic plot.
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[[File:hfc_pyrene.png]]
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==Notes==
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Only Gaussian quantum chemistry package is supported at the moment - send an email to [[Ilya Kuprov]] if you are using something else.
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==See also==
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[[cst_display.m]], [[volplot.m]], [[molplot.m]], [[conmat.m]], [[gparse.m]], [[efg_display.m]], [[Import,_export,_and_visualisation]]
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''Version 2.6, authors: [[Ilya Kuprov]]''

Latest revision as of 19:37, 6 June 2026

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.
2. 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.
3. 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.
2. 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,conmatrix,options)

Parameters

              props - output of gparse.m function

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

            scaling - a factor to scale the tensors
                      by for visualisation

          conmatrix - binary connectivity matrix, 1
                      if a pair of atoms should be
                      connected by a bond. If an em-
                      pty vector is supplied, 1.6 
                      Angstrom cutoff distance is used

      options.style - 'ellipsoids' or 'harmonics'

   options.kill_iso - set to true() to eliminate the
                      isotropic parts of tensors be-
                      fore plotting

Examples

The following figure is produced by /examples/visualisation/hfc_pyrene.m - (left) ellipsoid plot; (right) spherical harmonic plot.

Hfc pyrene.png

Notes

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, efg_display.m, Import,_export,_and_visualisation

Version 2.6, authors: Ilya Kuprov

Retrieved from "https://spindynamics.org/wiki/index.php?title=Hfc_display.m&oldid=9211"