java.lang.Object

org.jmol.symmetry.Symmetry

org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry

All Implemented Interfaces:: SymmetryInterface

Enclosing class:: XtalSymmetry

public static class XtalSymmetry.FileSymmetry extends Symmetry

A class only used by adapter.smarter.XtalSymmetry while building the file-based model.

Field Summary

Fields

Modifier and Type

Field

Description

protected int

nSpins

protected String

spinFrameStr

Fields inherited from class org.jmol.symmetry.Symmetry
id, isBio, spaceGroup, spinFrameToCartXYZ, unitCell
Constructor Summary

Constructors

Constructor

Description

FileSymmetry()
Method Summary

Modifier and Type

Method

Description

void

addInversion()

boolean

addMagLatticeVectors(Lst<float[]> lattvecs)

void

addSpinLattice(Lst<String> lstSpinFrames, Map<String,String> mapSpinIdToUVW)

boolean

createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)

String

fcoord(T3 p)

void

getRotTransArrayAndXYZ(String xyz, float[] rotTransMatrix)

MMCifReader only

String

getSpaceGroupOperationCode(int iOp)

String

getSpaceGroupTitle()

Tensor

getTensor(Viewer vwr, float[] parBorU)

void

mapSpins(Map<String,String> map)

protected int

postSymmetrySetMagneticMoments(AtomSetCollection asc, boolean isCartesian)

At the end, we need to rescale the vectors using SpinFramePp.

protected void

preSymmetryFinalizeMoments(AtomSetCollectionReader acr, AtomSetCollection asc, String spinFrameStr, String spinFrameExt)

Scale the magnetic moments of magCIF and spinCIF files.

V3[]

rotateAxes(int iop, V3[] axes, P3 ptTemp, M3 mTemp)

void

setPrecision(float prec)

Lst<String>

setSpinList(String configuration)

void

toFractionalM(M4 m)

void

toUnitCellRnd(T3 pt, T3 offset)

void

twelfthify(P3 pt)

Methods inherited from class org.jmol.symmetry.Symmetry
addBioMoleculeOperation, addSpaceGroupOperation, adjustRangeMinMax, calculateCIPChiralityForAtoms, calculateCIPChiralityForSmiles, checkPeriodic, convertTransform, findSpaceGroup, fixUnitCell, geCIFWriterValue, generateCrystalClass, getAdditionalOperations, getAdditionalOperationsCount, getCanonicalCopy, getCartesianOffset, getCellRange, getCellWeight, getConstrainableEquivAtom, getCoordinatesAreFractional, getDimensionality, getEquivPointList, getEquivPoints, getFinalOperationCount, getFractionalOffset, getFractionalOrigin, getGroupType, getIntTableIndex, getIntTableNumber, getIntTableTransform, getInvariantSymops, getIterator, getLatticeCentering, getLatticeDesignation, getLatticeOp, getLatticeType, getMoreInfo, getOperationRsVs, getPeriodicity, getPointGroupInfo, getPointGroupName, getPrecision, getQuaternionRotation, getSiteMultiplicity, getSpaceGroup, getSpaceGroupClegId, getSpaceGroupInfo, getSpaceGroupInfoObj, getSpaceGroupJmolId, getSpaceGroupJSON, getSpaceGroupName, getSpaceGroupOperation, getSpaceGroupOperationCount, getSpaceGroupXyzOriginal, getSpinIndex, getSpinOp, getSpinSym, getState, getSubgroupJSON, getSymmetryInfoAtom, getSymmetryInfoStr, getSymmetryOperations, getSymopList, getTransform, getUnitCell, getUnitCellAsArray, getUnitCellCenter, getUnitCellDisplayName, getUnitCellInfo, getUnitCellInfoMap, getUnitCellInfoStr, getUnitCellInfoType, getUnitCellMultiplied, getUnitCellMultiplier, getUnitCellParams, getUnitCellState, getUnitCellVectors, getUnitCellVerticesNoOffset, getV0abc, getWyckoffPosition, haveUnitCell, initializeOrientation, isBio, isPolymer, isSimple, isSlab, isSupercell, isSymmetryCell, isWithinUnitCell, newSpaceGroupPoint, notInCentroid, removeDuplicates, saveOrRetrieveTransformMatrix, setFinalOperations, setLattice, setOffset, setOffsetPt, setPointGroup, setSpaceGroup, setSpaceGroupName, setSpaceGroupTo, setSpinAxisAngle, setSymmetryInfoFromFile, setUnitCell, setUnitCellFromParams, setViewer, staticCleanTransform, staticConvertOperation, staticGetMatrixTransform, staticGetTransformABC, staticToRationalXYZ, staticTransformSpaceGroup, toCartesian, toCartesianSpin, toFractional, toFractionalSpin, toFromPrimitive, toSupercell, toUnitCell, transformUnitCell, unitCellEquals, unitize, updatePointGroup

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

Field Details
- spinFrameStr
  
  protected String spinFrameStr
- nSpins
  
  protected int nSpins
Constructor Details
- FileSymmetry
  
  public FileSymmetry()
Method Details
- mapSpins
  
  public void mapSpins(Map<String,String> map)
- addMagLatticeVectors
  
  public boolean addMagLatticeVectors(Lst<float[]> lattvecs)
- addSpinLattice
  
  public void addSpinLattice(Lst<String> lstSpinFrames, Map<String,String> mapSpinIdToUVW)
- setSpinList
  
  public Lst<String> setSpinList(String configuration)
- createSpaceGroup
  
  public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
  
  Parameters:
  
  desiredSpaceGroupIndex -
  
  name -
  
  data - a Lst or Lst
  
  modDim - in [3+d] modulation dimension
  
  Returns:
  
  true if a known space group
- fcoord
  
  public String fcoord(T3 p)
- getRotTransArrayAndXYZ
  
  public void getRotTransArrayAndXYZ(String xyz, float[] rotTransMatrix)
  
  MMCifReader only
  
  Parameters:
  
  xyz -
  
  rotTransMatrix -
- getSpaceGroupOperationCode
  
  public String getSpaceGroupOperationCode(int iOp)
- getTensor
  
  public Tensor getTensor(Viewer vwr, float[] parBorU)
- getSpaceGroupTitle
  
  public String getSpaceGroupTitle()
- setPrecision
  
  public void setPrecision(float prec)
- toFractionalM
  
  public void toFractionalM(M4 m)
- toUnitCellRnd
  
  public void toUnitCellRnd(T3 pt, T3 offset)
- twelfthify
  
  public void twelfthify(P3 pt)
- addInversion
  
  public void addInversion()
- rotateAxes
  
  public V3[] rotateAxes(int iop, V3[] axes, P3 ptTemp, M3 mTemp)
- preSymmetryFinalizeMoments
  
  protected void preSymmetryFinalizeMoments(AtomSetCollectionReader acr, AtomSetCollection asc, String spinFrameStr, String spinFrameExt)
  
  Scale the magnetic moments of magCIF and spinCIF files. magCIF files have moments expressed as Bohr magnetons along the crystallographic axes. These have to be "fractionalized" in order to be properly handled by symmetry operations, then, in the end, turned into Cartesians (in setSpinVectors) It is not clear to me at all how this would be handled if there are subsystems. This method must be run PRIOR to applying symmetry and thus prior to creation of modulation sets.
  
  Parameters:
  
  acr -
  
  asc -
  
  spinFrameStr -
  
  spinFrameExt -
- postSymmetrySetMagneticMoments
  
  protected int postSymmetrySetMagneticMoments(AtomSetCollection asc, boolean isCartesian)
  
  At the end, we need to rescale the vectors using SpinFramePp.
  
  Parameters:
  
  asc -
  
  isCartesian - true only for FindSpinGroup JSON (FSGOutputReader)
  
  Returns:
  
  number of nonzero or incommensurate spins

Class XtalSymmetry.FileSymmetry

Field Summary

Fields inherited from class org.jmol.symmetry.Symmetry

Constructor Summary

Method Summary

Methods inherited from class org.jmol.symmetry.Symmetry

Methods inherited from class java.lang.Object

Field Details

spinFrameStr

nSpins

Constructor Details

FileSymmetry

Method Details

mapSpins

addMagLatticeVectors

addSpinLattice

setSpinList

createSpaceGroup

fcoord

getRotTransArrayAndXYZ

getSpaceGroupOperationCode

getTensor

getSpaceGroupTitle

setPrecision

toFractionalM

toUnitCellRnd

twelfthify

addInversion

rotateAxes

preSymmetryFinalizeMoments

postSymmetrySetMagneticMoments