Field Detail

• ADP_FACTOR

  private static final float ADP_FACTOR

• MAGNETIC_SUSCEPTIBILITY_FACTOR

  private static final float MAGNETIC_SUSCEPTIBILITY_FACTOR

  See Also:

  Constant Field Values

• INTERACTION_FACTOR

  private static final float INTERACTION_FACTOR

  See Also:

  Constant Field Values

• tSort

  private static EigenSort tSort

• id

  public java.lang.String id

• type

  public java.lang.String type

• iType

  public int iType

• KNOWN_TYPES

  private static final java.lang.String KNOWN_TYPES

  See Also:

  Constant Field Values

• TYPE_OTHER

  public static final int TYPE_OTHER

  See Also:

  Constant Field Values

• TYPE_ISO

  public static final int TYPE_ISO

  See Also:

  Constant Field Values

• TYPE_ADP

  public static final int TYPE_ADP

  See Also:

  Constant Field Values

• TYPE_TLS_U

  public static final int TYPE_TLS_U

  See Also:

  Constant Field Values

• TYPE_TLS_R

  public static final int TYPE_TLS_R

  See Also:

  Constant Field Values

• TYPE_MS

  public static final int TYPE_MS

  See Also:

  Constant Field Values

• TYPE_EFG

  public static final int TYPE_EFG

  See Also:

  Constant Field Values

• TYPE_ISC

  public static final int TYPE_ISC

  See Also:

  Constant Field Values

• TYPE_CHARGE

  public static final int TYPE_CHARGE

  See Also:

  Constant Field Values

• TYPE_QUADRUPOLE

  public static final int TYPE_QUADRUPOLE

  See Also:

  Constant Field Values

• asymMatrix

  public double[][] asymMatrix

• symMatrix

  public double[][] symMatrix

• eigenVectors

  public javajs.util.V3[] eigenVectors

• eigenValues

  public float[] eigenValues

• parBorU

  public float[] parBorU

• altType

  public java.lang.String altType

• isIsotropic

  public boolean isIsotropic

• forThermalEllipsoid

  public boolean forThermalEllipsoid

• eigenSignMask

  public int eigenSignMask

• typeFactor

  private float typeFactor

• sortIso

  private boolean sortIso

• modelIndex

  public int modelIndex

• atomIndex1

  public int atomIndex1

• atomIndex2

  public int atomIndex2

• isModulated

  public boolean isModulated

• isUnmodulated

  public boolean isUnmodulated

• infoList

  private static final java.lang.String infoList

  See Also:

  Constant Field Values

Constructor Detail

• Tensor

  public Tensor()

  Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods. These had been static, but it turns out when that is the case, then JavaScript versions cannot be modularized to omit this class along with Eigen. So the general full constructor would look something like: new Tensor().setFrom...(....)

Method Detail

• getType

  private static int getType​(java.lang.String type)

• getInfoIndex

  private static int getInfoIndex​(java.lang.String infoType)

• isFloatInfo

  public static boolean isFloatInfo​(java.lang.String infoType)

• getInfo

  public java.lang.Object getInfo​(java.lang.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,
                                        java.lang.String type,
                                        java.lang.String id)

  Standard constructor for QM tensors

  Parameters:

  asymmetricTensor -

  type -

  id -

  Returns:

  this

• setFromEigenVectors

  public Tensor setFromEigenVectors​(javajs.util.V3[] eigenVectors,
                                    float[] eigenValues,
                                    java.lang.String type,
                                    java.lang.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,
                                       java.lang.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​(java.lang.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​(BS bsSelected,
                            int iAtom)

• newTensorType

  private void newTensorType​(javajs.util.V3[] vectors,
                             float[] values,
                             java.lang.String type,
                             java.lang.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 java.util.Comparator<? super java.lang.Object[]> getEigenSort()

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object