Field Detail

• id

  java.lang.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 java.lang.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 java.util.Map<java.lang.String,​java.lang.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 Detail

• ModulationSet

  public ModulationSet()

Method Detail

• 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​(java.lang.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​(java.lang.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 scale)

• getState

  public java.lang.String getState()

  Specified by:

  getState in interface JmolModulationSet

• getModPoint

  public javajs.util.T3 getModPoint​(boolean asEnabled)

  Specified by:

  getModPoint in interface JmolModulationSet

• getModulation

  public java.lang.Object getModulation​(char type,
                                        javajs.util.T3 tuv)

  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​(java.util.Map<java.lang.String,​java.lang.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 isTemp)

  Overrides:

  getOccupancy100 in class Vibration

  Parameters:

  isTemp - used only in ModulationSet

  Returns:

  Integer.MIN_VALUE if not applicable, occupancy if enabled, -occupancy if not enabled

• getOccupancy

  private float getOccupancy()