Package org.jmol.util

Class ModulationSet

java.lang.Object
javajs.util.T3
javajs.util.V3
org.jmol.util.Vibration
org.jmol.util.ModulationSet
All Implemented Interfaces:
Serializable, javajs.api.JSONEncodable, JmolModulationSet
public class ModulationSet extends Vibration implements JmolModulationSet
A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
Author:
Bob Hanson hansonr@stolaf.edu 8/9/2013
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    (package private) float[]
    axesLengths
    unit cell axes -- used in Modulation for calculating magnetic modulations
    private boolean
    enabled
    indicates state of modulated or unmodulated
    private double
    fileOcc
     
    private javajs.util.M3
    gammaE
     
    private javajs.util.Matrix
    gammaIinv
     
    Map<String,Float>
    htUij
    current value of anisotropic parameter modulation
    (package private) String
    id
    an identifier for this modulation
    private int
    iop
    the symmetry operation used to generate this atom
    private boolean
    isCommensurate
    commensurate modulations cannot be "undone" and they cannot be turned off
    private boolean
    isQ
     
    private boolean
    isSubsystem
    subsystems can deliver their own unique unit cell; they are commensurate
    private ModulationSet
    modCalc
    modCalc is used for calculations independent of what the current setting is
    private javajs.util.Lst<Modulation>
    mods
    the list of all modulations associated with this atom
    javajs.util.V3
    mxyz
    the modulated magnetic spin
    private int
    nOps
    the number of operators in this space group -- needed for occupancy calculation
    (package private) boolean
    occAbsolute
    for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations
    private double[]
    occParams
     
    private double
    occSiteMultiplicity
     
    private float
    occValue
    final occupancy value -- absolute; in range [0,1]
    (package private) javajs.util.P3
    ptTemp
     
    private javajs.util.P3
    qtOffset
     
    private javajs.util.P3
    r0
    the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself
    private javajs.util.Matrix
    rI
     
    private javajs.util.Matrix
    rsvs
    the matrix representation for this atom's symmetry operation
    private float
    scale
    an adjustable scaling factor, as for vibrations
    private javajs.util.Matrix
    sigma
     
    private float
    spinOp
    the spin operation for this atom: +1/0/-1
    private String
    strop
    a string description of the atom's symmetry operator
    private SymmetryInterface
    symmetry
    the space group appropriate to this atom
    private javajs.util.Matrix
    tau
     
    private javajs.util.Matrix
    tFactorInv
     
    private javajs.util.V3
    v0
     
    Vibration
    vib
    vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
    float
    vOcc
    the current value of the occupancy modulation

    Fields inherited from class org.jmol.util.Vibration

    modDim, modScale, showTrace, tracePt, twoPI, TYPE_SPIN, TYPE_VIBRATION

    Fields inherited from class javajs.util.T3

    x, y, z

  • Constructor Summary

    Constructors
    Constructor
    Description
    ModulationSet()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addTo(javajs.util.T3 a, float scale)
     
    void
    addUTens(String utens, float v)
     
    ModulationSet
    calculate(javajs.util.T3 tuv, boolean isQ)
    Calculate r_I internal d-space coordinate of an atom.
    void
    getInfo(Map<String,Object> info)
     
    private ModulationSet
    getModCalc()
     
    javajs.util.T3
    getModPoint(boolean asEnabled)
     
    Object
    getModulation(char type, javajs.util.T3 tuv, boolean occ100)
     
    private float
    getOccupancy(boolean checkCutoff)
     
    int
    getOccupancy100(boolean forVibVis)
     
    float
    getScale()
     
    String
    getState()
     
    SymmetryInterface
    getSubSystemUnitCell()
     
    javajs.util.V3
    getV3()
     
    Vibration
    getVibration(boolean forceNew)
     
    boolean
    isEnabled()
     
    boolean
    isNonzero()
     
    void
    scaleVibration(float m)
     
    javajs.util.T3
    setCalcPoint(javajs.util.T3 pt, javajs.util.T3 t456, float vibScale, float scale)
    get updated value for offset vector and for occupancy
    ModulationSet
    setMod(String id, javajs.util.P3 r00, javajs.util.P3 r0, int d, javajs.util.Lst<Modulation> mods, javajs.util.M3 gammaE, javajs.util.Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate)
    A collection of modulations for a specific atom.
    void
    setModTQ(javajs.util.T3 a, boolean isOn, javajs.util.T3 qtOffset, boolean isQ, float scale)
    Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
    void
    setMoment()
     
    float
    setOccupancy(double[] pt, double foccupancy, double siteMult)
    get the occupancy, first from the reader, then from renderer
    private void
    setVib(boolean isReset, float modulationScale)
     
    void
    setXYZ(javajs.util.T3 v)
     

    Methods inherited from class org.jmol.util.Vibration

    addTracePt, clone, setType, startTrace

    Methods inherited from class javajs.util.V3

    angle, new3, newV, newVsub

    Methods inherited from class javajs.util.T3

    add, add2, add3, ave, cross, distance, distanceSquared, dot, equals, floatToIntBits, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON, toString

    Methods inherited from class java.lang.Object

    finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • id

      String id
      an identifier for this modulation

    • r0

      private javajs.util.P3 r0
      the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself

    • symmetry

      private SymmetryInterface symmetry
      the space group appropriate to this atom

    • axesLengths

      float[] axesLengths
      unit cell axes -- used in Modulation for calculating magnetic modulations

    • nOps

      private int nOps
      the number of operators in this space group -- needed for occupancy calculation

    • iop

      private int iop
      the symmetry operation used to generate this atom

    • strop

      private String strop
      a string description of the atom's symmetry operator

    • spinOp

      private float spinOp
      the spin operation for this atom: +1/0/-1

    • rsvs

      private javajs.util.Matrix rsvs
      the matrix representation for this atom's symmetry operation

    • vib

      public Vibration vib
      vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.

    • mods

      private javajs.util.Lst<Modulation> mods
      the list of all modulations associated with this atom

    • isSubsystem

      private boolean isSubsystem
      subsystems can deliver their own unique unit cell; they are commensurate

    • isCommensurate

      private boolean isCommensurate
      commensurate modulations cannot be "undone" and they cannot be turned off

    • fileOcc

      private double fileOcc

    • occParams

      private double[] occParams

    • occSiteMultiplicity

      private double occSiteMultiplicity

    • occAbsolute

      boolean occAbsolute
      for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations

    • modCalc

      private ModulationSet modCalc
      modCalc is used for calculations independent of what the current setting is

    • mxyz

      public javajs.util.V3 mxyz
      the modulated magnetic spin

    • htUij

      public Map<String,Float> htUij
      current value of anisotropic parameter modulation

    • vOcc

      public float vOcc
      the current value of the occupancy modulation

    • occValue

      private float occValue
      final occupancy value -- absolute; in range [0,1]

    • qtOffset

      private javajs.util.P3 qtOffset

    • isQ

      private boolean isQ

    • enabled

      private boolean enabled
      indicates state of modulated or unmodulated

    • scale

      private float scale
      an adjustable scaling factor, as for vibrations

    • gammaE

      private javajs.util.M3 gammaE

    • gammaIinv

      private javajs.util.Matrix gammaIinv

    • sigma

      private javajs.util.Matrix sigma

    • tau

      private javajs.util.Matrix tau

    • rI

      private javajs.util.Matrix rI

    • tFactorInv

      private javajs.util.Matrix tFactorInv

    • ptTemp

      javajs.util.P3 ptTemp

    • v0

      private javajs.util.V3 v0

  • Constructor Details

    • ModulationSet

      public ModulationSet()

  • Method Details

    • getSubSystemUnitCell

      public SymmetryInterface getSubSystemUnitCell()
      Specified by:
      getSubSystemUnitCell in interface JmolModulationSet

    • isEnabled

      public boolean isEnabled()
      Specified by:
      isEnabled in interface JmolModulationSet

    • getScale

      public float getScale()
      Specified by:
      getScale in interface JmolModulationSet

    • setMod

      public ModulationSet setMod(String id, javajs.util.P3 r00, javajs.util.P3 r0, int d, javajs.util.Lst<Modulation> mods, javajs.util.M3 gammaE, javajs.util.Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate)
      A collection of modulations for a specific atom.
      Parameters:
      id -
      r00 - originating atom position prior to application of symmetry
      r0 - unmodulated (average) position after application of symmetry
      d -
      mods -
      gammaE -
      factors - including sigma and tFactor
      symmetry -
      iop -
      nOps -
      v - TODO
      isCommensurate - TODO
      Returns:
      this

    • calculate

      public ModulationSet calculate(javajs.util.T3 tuv, boolean isQ)
      Calculate r_I internal d-space coordinate of an atom.
      Parameters:
      tuv -
      isQ -
      Returns:
      this ModulationSet, with this.rI set to the coordinate

    • addUTens

      public void addUTens(String utens, float v)

    • setModTQ

      public void setModTQ(javajs.util.T3 a, boolean isOn, javajs.util.T3 qtOffset, boolean isQ, float scale)
      Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
      Specified by:
      setModTQ in interface JmolModulationSet
      Parameters:
      isOn -
      qtOffset -
      isQ -
      scale -

    • addTo

      public void addTo(javajs.util.T3 a, float scale)
      Specified by:
      addTo in interface JmolModulationSet

    • setVib

      private void setVib(boolean isReset, float modulationScale)

    • getState

      public String getState()
      Specified by:
      getState in interface JmolModulationSet

    • getModPoint

      public javajs.util.T3 getModPoint(boolean asEnabled)
      Specified by:
      getModPoint in interface JmolModulationSet

    • getModulation

      public Object getModulation(char type, javajs.util.T3 tuv, boolean occ100)
      Specified by:
      getModulation in interface JmolModulationSet

    • setCalcPoint

      public javajs.util.T3 setCalcPoint(javajs.util.T3 pt, javajs.util.T3 t456, float vibScale, float scale)
      get updated value for offset vector and for occupancy
      Overrides:
      setCalcPoint in class Vibration
      Returns:
      pt

    • getModCalc

      private ModulationSet getModCalc()

    • getInfo

      public void getInfo(Map<String,Object> info)
      Overrides:
      getInfo in class Vibration

    • setXYZ

      public void setXYZ(javajs.util.T3 v)
      Overrides:
      setXYZ in class Vibration

    • getVibration

      public Vibration getVibration(boolean forceNew)
      Specified by:
      getVibration in interface JmolModulationSet

    • getV3

      public javajs.util.V3 getV3()
      Specified by:
      getV3 in interface JmolModulationSet

    • scaleVibration

      public void scaleVibration(float m)
      Specified by:
      scaleVibration in interface JmolModulationSet

    • setMoment

      public void setMoment()
      Specified by:
      setMoment in interface JmolModulationSet

    • isNonzero

      public boolean isNonzero()
      Overrides:
      isNonzero in class Vibration

    • setOccupancy

      public float setOccupancy(double[] pt, double foccupancy, double siteMult)
      get the occupancy, first from the reader, then from renderer
      Parameters:
      pt -
      foccupancy -
      siteMult - or 0 is this is not relevant
      Returns:
      occupancy on [0,1]

    • getOccupancy100

      public int getOccupancy100(boolean forVibVis)
      Overrides:
      getOccupancy100 in class Vibration
      Parameters:
      forVibVis - used only in ModulationSet
      Returns:
      Integer.MIN_VALUE if not applicable, occupancy if enabled, -occupancy if not enabled

    • getOccupancy

      private float getOccupancy(boolean checkCutoff)