Class MSRdr

Method Details

• getSigma

  javajs.util.Matrix getSigma()

• initialize

  public int initialize(AtomSetCollectionReader r, int modDim) throws Exception

  Specified by:

  initialize in interface MSInterface

  Throws:

  Exception

• setSubsystemOptions

  private void setSubsystemOptions()

• setModDim

  protected void setModDim(int ndim)

• addModulation

  public void addModulation(Map<String,double[]> map, 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 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:

  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 String checkKey(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(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 Map<String,double[]> getModulationMap()

  Specified by:

  getModulationMap in interface MSInterface

• setModulationForStructure

  private void setModulationForStructure(int iModel, boolean isPost) throws Exception

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

  Parameters:

  iModel -

  isPost -

  Throws:

  Exception

• initModForStructure

  private void initModForStructure(int iModel) throws Exception

  Throws:

  Exception

• fixLegendre

  private void fixLegendre()

• fixDoubleA

  private void fixDoubleA(double[] pt)

• getQCoefs

  public double[] getQCoefs(String key)

  Specified by:

  getQCoefs in interface MSInterface

• getModType

  public char getModType(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(String atomName, char axis, char type, double[] params, 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(String code, javajs.util.Matrix w)

  Specified by:

  addSubsystem in interface MSInterface

• addUStr

  private void addUStr(Atom atom, 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(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(String code)

  Specified by:

  getSymmetryFromCode in interface MSInterface

• addLatticeVector

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

  Specified by:

  addLatticeVector in interface MSInterface

  Throws:

  Exception