Package org.jmol.symmetry

Class UnitCell

java.lang.Object
org.jmol.util.SimpleUnitCell
org.jmol.symmetry.UnitCell
All Implemented Interfaces:
Cloneable
public class UnitCell extends SimpleUnitCell implements Cloneable
a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry to be accessed generally only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.

  • Field Details

  • Method Details

    • fromOABC

      public static UnitCell fromOABC(T3[] oabc, boolean setRelative)
      A special constructor for spacially defined unit cells. Not used by readers.
      Parameters:
      oabc - [origin, Va, Vb, Vc]
      setRelative - a flag only set true for IsosurfaceMesh
      Returns:
      new unit cell

    • fromParams

      public static UnitCell fromParams(float[] params, boolean setRelative, float slop)
      Parameters:
      params -
      setRelative - only set true for JmolData and tensors
      slop -
      Returns:
      a new unit cell

    • getCanonicalCopyTrimmed

      public P3[] getCanonicalCopyTrimmed(P3 frac, float scale)

    • getConventionalUnitCell

      public T3[] getConventionalUnitCell(String latticeType, M3 primitiveToCrystal)
      return a conventional lattice from a primitive
      Parameters:
      latticeType - "A" "B" "C" "R" etc.
      primitiveToCrystal -
      Returns:
      [origin va vb vc]

    • getTensor

      public Tensor getTensor(Viewer vwr, float[] parBorU)

    • toTrm

      public static M4 toTrm(String transform, M4 trm)

    • getMatrixAndUnitCell

      public static T3[] getMatrixAndUnitCell(Viewer vwr, SimpleUnitCell uc, Object def, M4 retMatrix)
      Parameters:
      vwr - only needed for reciprocal axis and sqrt(...)
      uc - generally this or null
      def - String "abc;offset" or M3 or M4 or Object[M4]; if String, can be preceded by ! for "reverse of". For example, "!a-b,-5a-5b,-c;7/8,0,1/8" offset is optional, and can be a definition such as "a=3.40,b=4.30,c=5.02,alpha=90,beta=90,gamma=129" also allows for reciprocal lattice a*, b*, c
      retMatrix - if a string, return the 4x4 matrix corresponding to this definition; may be null to ignore
      Returns:
      [origin va vb vc]

    • getF2C

      public float[][] getF2C()

    • toUnitCellRnd

      public final void toUnitCellRnd(T3 pt, T3 offset)
      when offset is null, use the current cell, otherwise use the original unit cell
      Parameters:
      pt -
      offset -

    • getCenter

      public P3 getCenter(int periodicity)
      Takes into account subperiodic groups using BoxInfo.unitCubePoints P3.new3(0, 0, 0), // 0 P3.new3(0, 0, 1), // 1 c P3.new3(0, 1, 0), // 2 b P3.new3(0, 1, 1), // 3 bc P3.new3(1, 0, 0), // 4 a P3.new3(1, 0, 1), // 5 ac P3.new3(1, 1, 0), // 6 ab P3.new3(1, 1, 1), // 7 }; abc
      Parameters:
      periodicity -
      Returns:
      center

    • setSpinAxisAngle

      public void setSpinAxisAngle(A4 aa)

    • setSymmetryMinMax

      public static void setSymmetryMinMax(P3 c, P3 rmin, P3 rmax)

    • adjustRangeMinMax

      public void adjustRangeMinMax(T3[] oabc, float packingRange, P3i minXYZ, P3i maxXYZ, P3 rmin, P3 rmax, P3i newMin, P3i newMax)
      Parameters:
      oabc -
      packingRange - in Cartesian angstroms, usually 0.02, or NaN
      minXYZ - supercell lattice scaling minimum, may be null
      maxXYZ - supercell lattice scaling maximum, ignored if minXYZ is null
      rmin - preset minimum of range, or null
      rmax - preset maximum of range; ignored if rmin is null
      newMin -
      newMax -

    • toFractionalSpin

      public void toFractionalSpin(T3 v)

    • toCartesianSpin

      public void toCartesianSpin(T3 v)