Class Tensor

Method Details

• getType

  private static int getType(String type)

• getInfoIndex

  private static int getInfoIndex(String infoType)

• isFloatInfo

  public static boolean isFloatInfo(String infoType)

• getInfo

  public Object getInfo(String infoType)

  returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"

  Parameters:

  infoType -

  Returns:

  Object or null

• isotropy

  public float isotropy()

  isotropy = average of eigenvalues

  Returns:

  isotropy

• span

  public float span()

  width of the signal; |e2 - e0|

  Returns:

  unitless; >= 0

• skew

  public float skew()

  a measure of asymmetry.

  Returns:

  range [-1, 1]

• anisotropy

  public float anisotropy()

  anisotropy = directed distance from (center of two closest) to (the furthest)

  Returns:

  unitless number

• reducedAnisotropy

  public float reducedAnisotropy()

  reduced anisotropy = largest difference from isotropy (may be negative)

  Returns:

  unitless number

• asymmetry

  public float asymmetry()

  asymmetry = deviation from a symmetric tensor

  Returns:

  range [0,1]

• copyTensor

  public Tensor copyTensor()

• setFromAsymmetricTensor

  public Tensor setFromAsymmetricTensor(double[][] asymmetricTensor, String type, String id)

  Standard constructor for QM tensors

  Parameters:

  asymmetricTensor -

  type -

  id -

  Returns:

  this

• setFromEigenVectors

  public Tensor setFromEigenVectors(javajs.util.T3[] eigenVectors, float[] eigenValues, String type, String id, Tensor t)

  Standard constructor for charge and iso.

  Parameters:

  eigenVectors -

  eigenValues -

  type -

  id -

  t -

  Returns:

  this

• setFromAxes

  public Tensor setFromAxes(javajs.util.V3[] axes)

  Standard constructor for ellipsoids based on axes

  Parameters:

  axes -

  Returns:

  Tensor

• setFromThermalEquation

  public Tensor setFromThermalEquation(double[] coefs, String id)

  standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)

  Parameters:

  coefs -

  id -

  Returns:

  this

• setType

  public Tensor setType(String type)

  Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.

  Parameters:

  type -

  Returns:

  "this" for convenience only

• getFactoredValue

  public float getFactoredValue(int i)

  Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor

  Parameters:

  i -

  Returns:

  factored eigenvalue

• setAtomIndexes

  public void setAtomIndexes(int index1, int index2)

• isSelected

  public boolean isSelected(javajs.util.BS bsSelected, int iAtom)

• newTensorType

  private void newTensorType(javajs.util.V3[] vectors, float[] values, String type, String id)

  common processing of eigenvectors.

  Parameters:

  vectors -

  values -

  type -

  id -

• processType

  private void processType()

  Sets typeFactor, altType, isIsotropic, forThermalEllipsoid; type "iso" changed to "" here.

• sortAndNormalize

  private void sortAndNormalize()

  The expression: |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso| simply sorts the values from largest to smallest or smallest to largest, depending upon the direction of the asymmetry, always setting the last value to be the farthest from the mean. We use a simpler form here: |sigma_3 - sigma_1| >= |sigma_3 - sigma_2| >= |sigma_2 - sigma_1| which amounts to the same thing and is prettier. (Think about it!)

• isEquiv

  public boolean isEquiv(Tensor t)

• getEigenSort

  private static Comparator<? super Object> getEigenSort()

• toString

  public String toString()

  Overrides:

  toString in class Object