Field Detail

• cr

  protected AtomSetCollectionReader cr

• modDim

  protected int modDim

• modAxes

  protected java.lang.String modAxes

• modAverage

  protected boolean modAverage

• isCommensurate

  protected boolean isCommensurate

• commensurateSection1

  protected int commensurateSection1

• modPack

  private boolean modPack

• modVib

  private boolean modVib

• modType

  private java.lang.String modType

• modCell

  private java.lang.String modCell

• modDebug

  private boolean modDebug

• modSelected

  private int modSelected

• modLast

  private boolean modLast

• sigma

  private javajs.util.Matrix sigma

• htModulation

  private java.util.Map<java.lang.String,​double[]> htModulation

• htAtomMods

  private java.util.Map<java.lang.String,​javajs.util.Lst<Modulation>> htAtomMods

• iopLast

  private int iopLast

• gammaE

  private javajs.util.M3 gammaE

• nOps

  private int nOps

• haveOccupancy

  private boolean haveOccupancy

• atoms

  private Atom[] atoms

• ac

  private int ac

• haveAtomMods

  private boolean haveAtomMods

• modCoord

  private boolean modCoord

• finalized

  private boolean finalized

• symmetry

  private SymmetryInterface symmetry

• supercellSymmetry

  private SymmetryInterface supercellSymmetry

• legendres

  private javajs.util.Lst<java.lang.String> legendres

• atModel

  private java.lang.String atModel

• modMatrices

  private javajs.util.Matrix[] modMatrices

• qlist100

  private double[] qlist100

• qs

  private javajs.util.P3[] qs

• modCount

  private int modCount

• modTUV

  private javajs.util.T3 modTUV

• U_LIST

  private static final java.lang.String U_LIST

  See Also:

  Constant Field Values

• htSubsystems

  java.util.Map<java.lang.String,​Subsystem> htSubsystems

• minXYZ0

  private javajs.util.P3 minXYZ0

• maxXYZ0

  private javajs.util.P3 maxXYZ0

Constructor Detail

• MSRdr

  public MSRdr()

Method Detail

• getSigma

  javajs.util.Matrix getSigma()

• initialize

  public int initialize​(AtomSetCollectionReader r,
                        int modDim)
                 throws java.lang.Exception

  Specified by:

  initialize in interface MSInterface

  Throws:

  java.lang.Exception

• setSubsystemOptions

  private void setSubsystemOptions()

• setModDim

  protected void setModDim​(int ndim)

• addModulation

  public void addModulation​(java.util.Map<java.lang.String,​double[]> map,
                            java.lang.String id,
                            double[] pt,
                            int iModel)

  Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description

  Specified by:

  addModulation in interface MSInterface

  Parameters:

  map -

  id -

  pt -

  iModel -

• setModulation

  public void setModulation​(boolean isPost,
                            SymmetryInterface symmetry)
                     throws java.lang.Exception

  Both the Jana reader and the CIF reader will call this to set the modulation for a given model.

  Specified by:

  setModulation in interface MSInterface

  Throws:

  java.lang.Exception

• finalizeModulation

  public void finalizeModulation()

  Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.

  Specified by:

  finalizeModulation in interface MSInterface

• checkKey

  private java.lang.String checkKey​(java.lang.String key,
                                    boolean checkQ)

  Filter keys only for this model.

  Parameters:

  key -

  checkQ -

  Returns:

  trimmed key without model part or null

• getMod

  public double[] getMod​(java.lang.String key)

  Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.

  Specified by:

  getMod in interface MSInterface

  Parameters:

  key -

  Returns:

  modulation data

• getModulationMap

  public java.util.Map<java.lang.String,​double[]> getModulationMap()

  Specified by:

  getModulationMap in interface MSInterface

• setModulationForStructure

  private void setModulationForStructure​(int iModel,
                                         boolean isPost)
                                  throws java.lang.Exception

  Called when structure creation is complete and all modulation data has been collected.

  Parameters:

  iModel -

  isPost -

  Throws:

  java.lang.Exception

• initModForStructure

  private void initModForStructure​(int iModel)
                            throws java.lang.Exception

  Throws:

  java.lang.Exception

• fixLegendre

  private void fixLegendre()

• fixDouble

  private void fixDouble​(double[] pt)

• getQCoefs

  public double[] getQCoefs​(java.lang.String key)

  Specified by:

  getQCoefs in interface MSInterface

• getModType

  public char getModType​(java.lang.String key)

  Specified by:

  getModType in interface MSInterface

• calculateQCoefs

  private double[] calculateQCoefs​(double[] p)

  determine simple linear combination assuming simple -3 to 3 no more than two dimensions.

  Parameters:

  p -

  Returns:

  {i j k}

• approxInt

  private int approxInt​(float fn)

• toP3

  private javajs.util.P3 toP3​(double[] x)

• addAtomModulation

  private void addAtomModulation​(java.lang.String atomName,
                                 char axis,
                                 char type,
                                 double[] params,
                                 java.lang.String utens,
                                 double[] qcoefs)

  Create a list of modulations for each atom type (atom name).

  Parameters:

  atomName -

  axis -

  type -

  params -

  utens -

  qcoefs -

• addSubsystem

  public void addSubsystem​(java.lang.String code,
                           javajs.util.Matrix w)

  Specified by:

  addSubsystem in interface MSInterface

• addUStr

  private void addUStr​(Atom atom,
                       java.lang.String id,
                       float val)

• modulateAtom

  private void modulateAtom​(Atom a)

  The displacement will be set as the atom vibration vector; the string buffer will be appended with the t value for a given unit cell. Modulation generally involves x4 = q.r + t. Here we arbitrarily set t = modT = 0, but modT could be a FILTER option MODT=n. There would need to be one modT per dimension or modU, modV.

  Parameters:

  a -

• getAtomR0

  private javajs.util.P3 getAtomR0​(Atom atom)

• getAtomSymmetry

  public SymmetryInterface getAtomSymmetry​(Atom a,
                                           SymmetryInterface defaultSymmetry)

  When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.

  Specified by:

  getAtomSymmetry in interface MSInterface

• setSubsystem

  private void setSubsystem​(java.lang.String code,
                            Subsystem system)

• getMatrices

  private javajs.util.Matrix[] getMatrices​(Atom a)

• getSymmetry

  private SymmetryInterface getSymmetry​(Atom a)

• getSubsystem

  private Subsystem getSubsystem​(Atom a)

• setMinMax0

  public void setMinMax0​(javajs.util.P3 minXYZ,
                         javajs.util.P3 maxXYZ)

  Specified by:

  setMinMax0 in interface MSInterface

• expandMinMax

  private void expandMinMax​(javajs.util.P3 pt,
                            SymmetryInterface sym,
                            javajs.util.P3 minXYZ,
                            javajs.util.P3 maxXYZ)

• trimAtomSet

  private void trimAtomSet()

• getDefaultUnitCell

  private SymmetryInterface getDefaultUnitCell()

• getSymmetryFromCode

  public SymmetryInterface getSymmetryFromCode​(java.lang.String code)

  Specified by:

  getSymmetryFromCode in interface MSInterface

• addLatticeVector

  public boolean addLatticeVector​(javajs.util.Lst<float[]> lattvecs,
                                  java.lang.String data)
                           throws java.lang.Exception

  Specified by:

  addLatticeVector in interface MSInterface

  Throws:

  java.lang.Exception