Class SymmetryOperation

Method Details

• setSigma

  void setSigma(String subsystemCode, javajs.util.Matrix sigma)

• setGamma

  private void setGamma(boolean isReverse)

• doFinalize

  void doFinalize()

• div12

  private static javajs.util.M4 div12(javajs.util.M4 op, int divisor)

• finalizeF

  private static float finalizeF(float m, int divisor)

• finalizeD

  private static double finalizeD(double m, int divisor)

• getXyz

  String getXyz(boolean normalized)

• getxyzTrans

  public String getxyzTrans(javajs.util.P3 t)

• dumpInfo

  String dumpInfo()

• dumpSeitz

  static final String dumpSeitz(javajs.util.M4 s, boolean isCanonical)

• setMatrixFromXYZ

  boolean setMatrixFromXYZ(String xyz, int modDim, boolean allowScaling)

• setDivisor

  private static int setDivisor(String xyz)

  Sets the divisor to 0 for n/9 or n/mm

  Parameters:

  xyz -

  Returns:

  0 or 12

• setModDim

  private void setModDim(int dim)

• setMatrix

  private void setMatrix(boolean isReverse)

• setFromMatrix

  boolean setFromMatrix(float[] offset, boolean isReverse)

• getMatrixFromXYZ

  public static javajs.util.M4 getMatrixFromXYZ(String xyz)

• getJmolCanonicalXYZ

  static String getJmolCanonicalXYZ(String xyz)

• getMatrixFromString

  static String getMatrixFromString(SymmetryOperation op, String xyz, float[] linearRotTrans, boolean allowScaling)

  Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format

  Parameters:

  op -

  xyz -

  linearRotTrans -

  allowScaling -

  Returns:

  canonized Jones-Faithful string

• replaceXn

  static String replaceXn(String xyz, int n)

• toDivisor

  private static final int toDivisor(float numer, int denom)

• xyzFraction12

  private static final String xyzFraction12(float n12ths, int denom, boolean allPositive, boolean halfOrLess)

• twelfthsOf

  static final String twelfthsOf(float n12ths)

• plusMinus

  private static String plusMinus(String strT, float x, String sx)

• normalizeTwelfths

  private static float normalizeTwelfths(float iValue, int divisor, boolean doNormalize)

• getXYZFromMatrix

  public static final String getXYZFromMatrix(javajs.util.M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)

• rotateAxes

  javajs.util.V3[] rotateAxes(javajs.util.V3[] vectors, UnitCell unitcell, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)

• fcoord2

  public String fcoord2(javajs.util.T3 p)

• fc2

  private String fc2(float f)

  Get string version of fraction when divisor == 0

  Parameters:

  f -

  Returns:

  "1/2" for example

• fcoord

  static String fcoord(javajs.util.T3 p)

  Get string version of fraction

  Parameters:

  p -

  Returns:

  "1/2" for example

• fc

  private static String fc(float x)

• approxF

  static float approxF(float f)

• getXYZFromRsVs

  static String getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)

• toString

  public String toString()

  Description copied from class: javajs.util.M4

  Returns a string that contains the values of this Matrix4f.

  Overrides:

  toString in class javajs.util.M4

  Returns:

  the String representation

• getMagneticOp

  float getMagneticOp()

  Magnetic spin is a pseudo (or "axial") vector. This means that it acts as a rotation, not a vector. When a rotation about x is passed through the mirror plane xz, it is reversed; when it is passed through the mirror plane yz, it is not reversed -- exactly opposite what you would imagine from a standard "polar" vector. For example, a vector perpendicular to a plane of symmetry (det=-1) will be flipped (m=1), while a vector parallel to that plane will not be flipped (m=-1) In addition, magnetic spin operations have a flag m=1 or m=-1 (m or -m) that indicates how the vector quantity changes with symmetry. This is called "time reversal" and stored here as timeReversal. To apply, timeReversal must be multiplied by the 3x3 determinant, which is always 1 (standard rotation) or -1 (rotation-inversion). This we store as magOp. See https://en.wikipedia.org/wiki/Pseudovector

  Returns:

  +1, -1, or 0

• setTimeReversal

  void setTimeReversal(int magRev)

  set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"

  Parameters:

  magRev -

• getCentering

  javajs.util.V3 getCentering()

  assumption here is that these are in order of sets, as in ITA

  Returns:

  centering

• fixMagneticXYZ

  String fixMagneticXYZ(javajs.util.M4 m, String xyz, boolean addMag)

• getInfo

  public Map<String,Object> getInfo()

• normalizeOperationToCentroid

  public static void normalizeOperationToCentroid(int dim, javajs.util.M4 m, javajs.util.P3[] atoms, int atomIndex, int count)

  Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.

  Parameters:

  dim -

  m -

  atoms -

  atomIndex - first index

  count - number of atoms

• getLatticeCentering

  public static javajs.util.Lst<javajs.util.P3> getLatticeCentering(SymmetryOperation[] ops)