Package org.jmol.symmetry

Class UnitCell

  • All Implemented Interfaces:
    java.lang.Cloneable
    class UnitCell
extends SimpleUnitCell
implements java.lang.Cloneable
    a class private to the org.jmol.symmetry package to be accessed 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 Detail

      • vertices

        private javajs.util.P3[] vertices

      • fractionalOffset

        private javajs.util.P3 fractionalOffset

      • allFractionalRelative

        private boolean allFractionalRelative
        this flag TRUE causes an update of matrixCtoFNoOffset each time an offset is changed so that it is updated and the two stay the same; set true only for isosurfaceMesh

      • cartesianOffset

        protected final javajs.util.P3 cartesianOffset

      • unitCellMultiplier

        protected javajs.util.T3 unitCellMultiplier
        a P3 or P4; the raw multiplier for the cell from UNITCELL {ijk ijk scale} UNITCELL {1iiijjjkkk 1iiijjjkkk scale} (encoded as a P4: {1iiijjjkkk 1iiijjjkkk scale 1kkkkkk} )

      • unitCellMultiplied

        private UnitCell unitCellMultiplied
        the multiplied, offset UnitCell derived from this UnitCell

      • moreInfo

        public javajs.util.Lst<java.lang.String> moreInfo

      • name

        public java.lang.String name

      • unitVectors

        private static final javajs.util.V3[] unitVectors

    • Constructor Detail

      • UnitCell

        private UnitCell()
        Indicate that this is a new unit cell, not one from a file.

    • Method Detail

      • fromOABC

        static UnitCell fromOABC​(javajs.util.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)
        Parameters:
        params -
        setRelative - only set true for JmolData and tensors
        Returns:
        a new unit cell

      • initOrientation

        void initOrientation​(javajs.util.M3 mat)

      • toUnitCell

        final void toUnitCell​(javajs.util.T3 pt,
                      javajs.util.T3 offset)
        when offset is null, use the current cell, otherwise use the original unit cell
        Parameters:
        pt -
        offset -

      • toUnitCellRnd

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

      • unitize

        public void unitize​(javajs.util.T3 pt)
        returns [0,1)
        Parameters:
        pt -

      • unitizeRnd

        public void unitizeRnd​(javajs.util.T3 pt)
        returns [0,1) with rounding to 0.0001
        Parameters:
        pt -

      • reset

        public void reset()

      • setOffset

        void setOffset​(javajs.util.T3 pt)

      • setCartesianOffset

        private void setCartesianOffset​(javajs.util.T3 origin)

      • getInfo

        java.util.Map<java.lang.String,​java.lang.Object> getInfo()

      • dumpInfo

        java.lang.String dumpInfo​(boolean isDebug,
                          boolean multiplied)

      • getUnitCellMultiplied

        UnitCell getUnitCellMultiplied()

      • getVertices

        javajs.util.P3[] getVertices()

      • getCartesianOffset

        javajs.util.P3 getCartesianOffset()

      • getFractionalOffset

        javajs.util.P3 getFractionalOffset()

      • getTensor

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

      • getCanonicalCopy

        javajs.util.P3[] getCanonicalCopy​(float scale,
                                  boolean withOffset)
        Parameters:
        scale -
        withOffset -
        Returns:
        points in Triangulator order

      • getScaledCell

        public javajs.util.P3[] getScaledCell​(boolean withOffset)

      • initUnitcellVertices

        private void initUnitcellVertices()

      • checkDistance

        public boolean checkDistance​(javajs.util.P3 f1,
                             javajs.util.P3 f2,
                             float distance,
                             float dx,
                             int iRange,
                             int jRange,
                             int kRange,
                             javajs.util.P3 ptOffset)
        Parameters:
        f1 -
        f2 -
        distance -
        dx -
        iRange -
        jRange -
        kRange -
        ptOffset - TODO
        Returns:
        TRUE if pt has been set.

      • getUnitCellMultiplier

        public javajs.util.T3 getUnitCellMultiplier()

      • getUnitCellVectors

        public javajs.util.P3[] getUnitCellVectors()

      • fix

        private float fix​(float x)

      • isSameAs

        public boolean isSameAs​(UnitCell uc)

      • hasOffset

        public boolean hasOffset()

      • getQuaternionRotation

        public javajs.util.Quat getQuaternionRotation​(java.lang.String abc)
        Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.
        Parameters:
        abc - ab bc ca
        Returns:
        quaternion

      • getV0abc

        public javajs.util.T3[] getV0abc​(java.lang.Object def,
                                 javajs.util.M4 retMatrix)
        Parameters:
        def - String "abc;offset" or M3 or M4 to origin; 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"
        retMatrix - if a string, return the M4 matrix corresponding to this definition
        Returns:
        [origin va vb vc] or null if invalid syntax, or null for allowNull and is identity

      • toFromPrimitive

        public boolean toFromPrimitive​(boolean toPrimitive,
                               char type,
                               javajs.util.T3[] uc,
                               javajs.util.M3 primitiveToCrystal)
        Parameters:
        toPrimitive - or assumed conventional
        type - P, R, A, B, C, I(BCC), or F(FCC)
        uc - either [origin, va, vb, vc] or just [va, vb, vc]
        primitiveToCrystal -
        Returns:
        true if successful

      • getConventionalUnitCell

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

      • getEquivPoints

        javajs.util.Lst<javajs.util.P3> getEquivPoints​(javajs.util.P3 pt,
                                               java.lang.String flags,
                                               javajs.util.M4[] ops,
                                               javajs.util.Lst<javajs.util.P3> list,
                                               int i0,
                                               int n0)
        Parameters:
        pt - the point to transform
        flags - "tofractional,fromfractional,packed"
        ops - space group operations
        list - the list to append to
        i0 - the starting index of the list
        n0 - the first point that is to be duplicated; prior points are just references for removing duplicates
        Returns:
        augmented list

      • checkDuplicate

        private static void checkDuplicate​(javajs.util.Lst<javajs.util.P3> list,
                                   int i0,
                                   int n0,
                                   int n)

      • normalize

        public void normalize​(javajs.util.V3 vtrans)

      • getState

        public java.lang.String getState()