org.jmol.adapter.readers.cif.MSRdr

All Implemented Interfaces:: MSInterface

Direct Known Subclasses:: MSCifParser

public class MSRdr extends Object implements MSInterface

generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth, Legendre; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1

Author:: Bob Hanson hansonr@stolaf.edu

Field Summary

Fields

Modifier and Type

Field

Description

protected int

commensurateSection1

protected AtomSetCollectionReader

cr

protected boolean

isCommensurate

protected boolean

modAverage

protected String

modAxes

protected int

modDim
Constructor Summary

Constructors

Constructor

Description

MSRdr()
Method Summary

Modifier and Type

Method

Description

boolean

addLatticeVector(Lst<float[]> lattvecs, String data)

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

void

addSubsystem(String code, Matrix w)

void

finalizeModulation()

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

XtalSymmetry.FileSymmetry

getAtomSymmetry(Atom a, XtalSymmetry.FileSymmetry 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.

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.

char

getModType(String key)

Map<String,double[]>

getModulationMap()

double[]

getQCoefs(String key)

XtalSymmetry.FileSymmetry

getSymmetryFromCode(String code)

int

initialize(AtomSetCollectionReader r, int modDim)

void

setMinMax0(P3 minXYZ, P3 maxXYZ)

protected void

setModDim(int ndim)

void

setModulation(boolean isPost, XtalSymmetry.FileSymmetry symmetry)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- cr
  
  protected AtomSetCollectionReader cr
- modDim
  
  protected int modDim
- modAxes
  
  protected String modAxes
- modAverage
  
  protected boolean modAverage
- isCommensurate
  
  protected boolean isCommensurate
- commensurateSection1
  
  protected int commensurateSection1
Constructor Details
- MSRdr
  
  public MSRdr()
Method Details
- initialize
  
  public int initialize(AtomSetCollectionReader r, int modDim) throws Exception
  
  Specified by:
  
  initialize in interface MSInterface
  
  Throws:
  
  Exception
- 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, XtalSymmetry.FileSymmetry 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
- 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
- getQCoefs
  
  public double[] getQCoefs(String key)
  
  Specified by:
  
  getQCoefs in interface MSInterface
- getModType
  
  public char getModType(String key)
  
  Specified by:
  
  getModType in interface MSInterface
- addSubsystem
  
  public void addSubsystem(String code, Matrix w)
  
  Specified by:
  
  addSubsystem in interface MSInterface
- getAtomSymmetry
  
  public XtalSymmetry.FileSymmetry getAtomSymmetry(Atom a, XtalSymmetry.FileSymmetry 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
- setMinMax0
  
  public void setMinMax0(P3 minXYZ, P3 maxXYZ)
  
  Specified by:
  
  setMinMax0 in interface MSInterface
- getSymmetryFromCode
  
  public XtalSymmetry.FileSymmetry getSymmetryFromCode(String code)
  
  Specified by:
  
  getSymmetryFromCode in interface MSInterface
- addLatticeVector
  
  public boolean addLatticeVector(Lst<float[]> lattvecs, String data) throws Exception
  
  Specified by:
  
  addLatticeVector in interface MSInterface
  
  Throws:
  
  Exception

Class MSRdr

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

cr

modDim

modAxes

modAverage

isCommensurate

commensurateSection1

Constructor Details

MSRdr

Method Details

initialize

setModDim

addModulation

setModulation

finalizeModulation

getMod

getModulationMap

getQCoefs

getModType

addSubsystem

getAtomSymmetry

setMinMax0

getSymmetryFromCode

addLatticeVector