Package org.jmol.util

Class SimpleUnitCell

  • Direct Known Subclasses:
    UnitCell
    public class SimpleUnitCell
extends java.lang.Object
    general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity

    • Constructor Summary

      Constructors 
      Modifier Constructor Description
      protected SimpleUnitCell()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static void addVectors​(float[] params)  
      static boolean checkPeriodic​(javajs.util.P3 pt)
      check atom position for range [0, 1) allowing for rounding
      static boolean checkUnitCell​(SymmetryInterface uc, javajs.util.P3 cell, javajs.util.P3 ptTemp)  
      static java.lang.String escapeMultiplier​(javajs.util.T3 pt)
      Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
      static float getCellWeight​(javajs.util.P3 pt)
      calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125 (vertex)
      javajs.util.T3 getFractionalOrigin()  
      float getInfo​(int infoType)  
      static javajs.util.T3[] getReciprocal​(javajs.util.T3[] abc, javajs.util.T3[] ret, float scale)
      Generate the reciprocal unit cell, scaled as desired
      float[] getUnitCellAsArray​(boolean vectorsOnly)  
      float[] getUnitCellParams()  
      static void ijkToPoint3f​(int nnn, javajs.util.P3 cell, int offset, int kcode)
      Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499
      protected void init​(float[] params)  
      boolean isPolymer()  
      boolean isSlab()  
      boolean isSupercell()  
      static boolean isValid​(float[] parameters)  
      static SimpleUnitCell newA​(float[] params)  
      static float normalizeXRnd​(float x)  
      static javajs.util.P4 ptToIJK​(javajs.util.T3 pt, int scale)
      Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
      private void setABC​(javajs.util.V3 va, javajs.util.V3 vb, javajs.util.V3 vc)  
      private void setCellParams()  
      static void setMinMaxLatticeParameters​(int dimension, javajs.util.P3i minXYZ, javajs.util.P3i maxXYZ, int kcode)  
      static javajs.util.T3[] setOabc​(java.lang.String abcabg, float[] params, javajs.util.T3[] ucnew)
      set cell vectors by string
      private void setParamsFromMatrix()  
      void toCartesian​(javajs.util.T3 pt, boolean ignoreOffset)  
      void toFractional​(javajs.util.T3 pt, boolean ignoreOffset)  
      void toFractionalM​(javajs.util.M4 m)  
      java.lang.String toString()  
      javajs.util.P3 toSupercell​(javajs.util.P3 fpt)
      convenience return only after changing fpt
      static void unitizeDim​(int dimension, javajs.util.T3 pt)  
      static void unitizeDimRnd​(int dimension, javajs.util.T3 pt)  
      static float unitizeX​(float x)  
      static float unitizeXRnd​(float x)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • unitCellParams

        protected float[] unitCellParams

      • matrixCartesianToFractional

        public javajs.util.M4 matrixCartesianToFractional

      • matrixFractionalToCartesian

        public javajs.util.M4 matrixFractionalToCartesian

      • volume

        public double volume

      • na

        private int na

      • nb

        private int nb

      • nc

        private int nc

      • a

        protected float a

      • b

        protected float b

      • c

        protected float c

      • alpha

        protected float alpha

      • beta

        protected float beta

      • gamma

        protected float gamma

      • cosAlpha

        protected double cosAlpha

      • sinAlpha

        protected double sinAlpha

      • cosBeta

        protected double cosBeta

      • sinBeta

        protected double sinBeta

      • cosGamma

        protected double cosGamma

      • sinGamma

        protected double sinGamma

      • cA_

        protected double cA_

      • cB_

        protected double cB_

      • a_

        protected double a_

      • b_

        protected double b_

      • c_

        protected double c_

      • dimension

        protected int dimension

      • fractionalOrigin

        private javajs.util.P3 fractionalOrigin

      • matrixCtoFNoOffset

        protected javajs.util.M4 matrixCtoFNoOffset

      • matrixFtoCNoOffset

        protected javajs.util.M4 matrixFtoCNoOffset

      • SLOP2

        private static final float SLOP2
        allowance for rounding in [0,1)
        See Also:
        Constant Field Values

    • Constructor Detail

      • SimpleUnitCell

        protected SimpleUnitCell()

    • Method Detail

      • isSupercell

        public boolean isSupercell()

      • isValid

        public static boolean isValid​(float[] parameters)

      • newA

        public static SimpleUnitCell newA​(float[] params)
        Parameters:
        params - len = 6 [a b c alpha beta gamma] len = 6 [a b -1 alpha beta gamma] // slab len = 6 [a -1 -1 alpha beta gamma] // polymer or len = 15 [-1 -1 -1 -1 -1 -1 va[3] vb[3] vc[3]] // vectors only or len = 15 [a -1 -1 -1 -1 -1 va[3] vb[3] vc[3]] // polymer, vectors only or len = 15 [a b -1 -1 -1 -1 va[3] vb[3] vc[3]] // slab, vectors only or len = 22 [a b c alpha beta gamma m00 m01 .. m33] // matrix included and/or len = 25 [...................... na nb nc] // supercell and/or len = 26 [...................... na nb nc scale] // scaled supercell
        Returns:
        a simple unit cell

      • init

        protected void init​(float[] params)

      • addVectors

        public static void addVectors​(float[] params)

      • setParamsFromMatrix

        private void setParamsFromMatrix()

      • setABC

        private void setABC​(javajs.util.V3 va,
                    javajs.util.V3 vb,
                    javajs.util.V3 vc)

      • setCellParams

        private void setCellParams()

      • getFractionalOrigin

        public javajs.util.T3 getFractionalOrigin()

      • toSupercell

        public javajs.util.P3 toSupercell​(javajs.util.P3 fpt)
        convenience return only after changing fpt
        Parameters:
        fpt -
        Returns:
        adjusted fpt

      • toCartesian

        public final void toCartesian​(javajs.util.T3 pt,
                              boolean ignoreOffset)

      • toFractionalM

        public void toFractionalM​(javajs.util.M4 m)

      • toFractional

        public final void toFractional​(javajs.util.T3 pt,
                               boolean ignoreOffset)

      • isPolymer

        public boolean isPolymer()

      • isSlab

        public boolean isSlab()

      • getUnitCellParams

        public final float[] getUnitCellParams()

      • getUnitCellAsArray

        public final float[] getUnitCellAsArray​(boolean vectorsOnly)

      • getInfo

        public final float getInfo​(int infoType)

      • ijkToPoint3f

        public static void ijkToPoint3f​(int nnn,
                                javajs.util.P3 cell,
                                int offset,
                                int kcode)
        Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499
        Parameters:
        nnn -
        cell -
        offset - 0 or 1 typically; < 0 means "apply no offset"
        kcode - Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}. Here, our offset -- initially 0 or 1 from the uccage renderer, but later -500 or -499 -- tells us which code we are looking at, the first one or the second one.

      • ptToIJK

        public static javajs.util.P4 ptToIJK​(javajs.util.T3 pt,
                                     int scale)
        Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
        Parameters:
        pt -
        scale - 1 for block of unit cells; 0 for one large supercell
        Returns:
        converted P4

      • escapeMultiplier

        public static java.lang.String escapeMultiplier​(javajs.util.T3 pt)
        Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
        Parameters:
        pt -
        Returns:
        String representation for state

      • getCellWeight

        public static float getCellWeight​(javajs.util.P3 pt)
        calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125 (vertex)
        Parameters:
        pt - // * @param tolerance fractional allowance to consider this on an edge
        Returns:
        weighting

      • getReciprocal

        public static javajs.util.T3[] getReciprocal​(javajs.util.T3[] abc,
                                             javajs.util.T3[] ret,
                                             float scale)
        Generate the reciprocal unit cell, scaled as desired
        Parameters:
        abc - [a,b,c] or [o,a,b,c]
        ret -
        scale - 0 for 2pi, teneral reciprocal lattice
        Returns:
        oabc

      • setOabc

        public static javajs.util.T3[] setOabc​(java.lang.String abcabg,
                                       float[] params,
                                       javajs.util.T3[] ucnew)
        set cell vectors by string
        Parameters:
        abcabg - "a=...,b=...,c=...,alpha=...,beta=..., gamma=..." or null
        params - to use if not null
        ucnew - to create and return; null if only to set params
        Returns:
        T3[4] origin, a, b c

      • setMinMaxLatticeParameters

        public static void setMinMaxLatticeParameters​(int dimension,
                                              javajs.util.P3i minXYZ,
                                              javajs.util.P3i maxXYZ,
                                              int kcode)
        Parameters:
        dimension -
        minXYZ -
        maxXYZ -
        kcode - Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}. Here, our offset -- initially 0 or 1 from the uccage renderer, but later -500 or -499 -- tells us which code we are looking at, the first one or the second one.

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • unitizeDim

        public static void unitizeDim​(int dimension,
                              javajs.util.T3 pt)

      • unitizeDimRnd

        public static void unitizeDimRnd​(int dimension,
                                 javajs.util.T3 pt)

      • unitizeX

        public static float unitizeX​(float x)

      • unitizeXRnd

        public static float unitizeXRnd​(float x)

      • normalizeXRnd

        public static float normalizeXRnd​(float x)

      • checkPeriodic

        public static boolean checkPeriodic​(javajs.util.P3 pt)
        check atom position for range [0, 1) allowing for rounding
        Parameters:
        pt -
        Returns:
        true if in [0, 1)

      • checkUnitCell

        public static boolean checkUnitCell​(SymmetryInterface uc,
                                    javajs.util.P3 cell,
                                    javajs.util.P3 ptTemp)