org.jmol.symmetry.UnitCell

All Implemented Interfaces:: Cloneable

public class UnitCell extends SimpleUnitCell implements Cloneable

a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry to be accessed generally only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.

Field Summary

Fields

Modifier and Type

Field

Description

String

name

Fields inherited from class SimpleUnitCell
a, a_, alpha, b, b_, beta, c, c_, cA_, cB_, cosAlpha, cosBeta, cosGamma, dimension, DIMENSION_TYPE_ALL, dimensionType, gamma, HEX_TO_RHOMB, INFO_A, INFO_ALPHA, INFO_B, INFO_BETA, INFO_C, INFO_DIMENSION_TYPE, INFO_DIMENSIONS, INFO_GAMMA, INFO_IS_HEXAGONAL, INFO_IS_RHOMBOHEDRAL, INFO_VOLUME, matrixCartesianToFractional, matrixCtoFNoOffset, matrixFractionalToCartesian, matrixFtoCNoOffset, PARAM_COUNT, PARAM_M33, PARAM_M4, PARAM_OXYZ, PARAM_SCALE, PARAM_SLOP, PARAM_STD, PARAM_SUPERCELL, PARAM_VAX, PARAM_VBX, PARAM_VCX, PARAM_VCZ, RHOMB_TO_HEX, sinAlpha, sinBeta, sinGamma, slop, SLOP_PARAMS, SLOPDP, SLOPSP, toRadians, unitCellParams, volume
Method Summary

Modifier and Type

Method

Description

void

adjustRangeMinMax(T3[] oabc, float packingRange, P3i minXYZ, P3i maxXYZ, P3 rmin, P3 rmax, P3i newMin, P3i newMax)

static UnitCell

fromOABC(T3[] oabc, boolean setRelative)

A special constructor for spacially defined unit cells.

static UnitCell

fromParams(float[] params, boolean setRelative, float slop)

P3[]

getCanonicalCopyTrimmed(P3 frac, float scale)

P3

getCenter(int periodicity)

Takes into account subperiodic groups using BoxInfo.unitCubePoints P3.new3(0, 0, 0), // 0 P3.new3(0, 0, 1), // 1 c P3.new3(0, 1, 0), // 2 b P3.new3(0, 1, 1), // 3 bc P3.new3(1, 0, 0), // 4 a P3.new3(1, 0, 1), // 5 ac P3.new3(1, 1, 0), // 6 ab P3.new3(1, 1, 1), // 7 }; abc

T3[]

getConventionalUnitCell(String latticeType, M3 primitiveToCrystal)

return a conventional lattice from a primitive

float[][]

getF2C()

static T3[]

getMatrixAndUnitCell(Viewer vwr, SimpleUnitCell uc, Object def, M4 retMatrix)

Tensor

getTensor(Viewer vwr, float[] parBorU)

void

setSpinAxisAngle(A4 aa)

static void

setSymmetryMinMax(P3 c, P3 rmin, P3 rmax)

void

toCartesianSpin(T3 v)

void

toFractionalSpin(T3 v)

static M4

toTrm(String transform, M4 trm)

final void

toUnitCellRnd(T3 pt, T3 offset)

when offset is null, use the current cell, otherwise use the original unit cell

Methods inherited from class SimpleUnitCell
addVectors, approx0, escapeMultiplier, fillParams, getCellRange, getDimensionFromParams, getFractionalOrigin, getInfo, getInfoStr, getPrecision, getReciprocal, getUnitCellAsArray, getUnitCellParams, ijkToPoint3f, init, isHexagonal, isPolymer, isRhombohedral, isSlab, isSupercell, isValid, newA, newParams, parseCalc, parseCalcFunctions, parseSimpleMath, ptToIJK, setAbc, setAbcFromParams, setMinMaxLatticeParameters, setPrecision, toCartesian, toFractional, toFractionalM, toString, toSupercell, twelfthify, twelfthsOf, unitizeDim, unitizeDimRnd, unitizeX, unitizeXRnd

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- name
  
  public String name
Method Details
- fromOABC
  
  public static UnitCell fromOABC(T3[] oabc, boolean setRelative)
  
  A special constructor for spacially defined unit cells. Not used by readers.
  
  Parameters:
  
  oabc - [origin, Va, Vb, Vc]
  
  setRelative - a flag only set true for IsosurfaceMesh
  
  Returns:
  
  new unit cell
- fromParams
  
  public static UnitCell fromParams(float[] params, boolean setRelative, float slop)
  
  Parameters:
  
  params -
  
  setRelative - only set true for JmolData and tensors
  
  slop -
  
  Returns:
  
  a new unit cell
- getCanonicalCopyTrimmed
  
  public P3[] getCanonicalCopyTrimmed(P3 frac, float scale)
- getConventionalUnitCell
  
  public T3[] getConventionalUnitCell(String latticeType, M3 primitiveToCrystal)
  
  return a conventional lattice from a primitive
  
  Parameters:
  
  latticeType - "A" "B" "C" "R" etc.
  
  primitiveToCrystal -
  
  Returns:
  
  [origin va vb vc]
- getTensor
  
  public Tensor getTensor(Viewer vwr, float[] parBorU)
- toTrm
  
  public static M4 toTrm(String transform, M4 trm)
- getMatrixAndUnitCell
  
  public static T3[] getMatrixAndUnitCell(Viewer vwr, SimpleUnitCell uc, Object def, M4 retMatrix)
  
  Parameters:
  
  vwr - only needed for reciprocal axis and sqrt(...)
  
  uc - generally this or null
  
  def - String "abc;offset" or M3 or M4 or Object[M4]; if String, can be preceded by ! for "reverse of". For example, "!a-b,-5a-5b,-c;7/8,0,1/8" offset is optional, and can be a definition such as "a=3.40,b=4.30,c=5.02,alpha=90,beta=90,gamma=129" also allows for reciprocal lattice a*, b*, c
  
  retMatrix - if a string, return the 4x4 matrix corresponding to this definition; may be null to ignore
  
  Returns:
  
  [origin va vb vc]
- getF2C
  
  public float[][] getF2C()
- toUnitCellRnd
  
  public final void toUnitCellRnd(T3 pt, T3 offset)
  
  when offset is null, use the current cell, otherwise use the original unit cell
  
  Parameters:
  
  pt -
  
  offset -
- getCenter
  
  public P3 getCenter(int periodicity)
  
  Takes into account subperiodic groups using BoxInfo.unitCubePoints P3.new3(0, 0, 0), // 0 P3.new3(0, 0, 1), // 1 c P3.new3(0, 1, 0), // 2 b P3.new3(0, 1, 1), // 3 bc P3.new3(1, 0, 0), // 4 a P3.new3(1, 0, 1), // 5 ac P3.new3(1, 1, 0), // 6 ab P3.new3(1, 1, 1), // 7 }; abc
  
  Parameters:
  
  periodicity -
  
  Returns:
  
  center
- setSpinAxisAngle
  
  public void setSpinAxisAngle(A4 aa)
- setSymmetryMinMax
  
  public static void setSymmetryMinMax(P3 c, P3 rmin, P3 rmax)
- adjustRangeMinMax
  
  public void adjustRangeMinMax(T3[] oabc, float packingRange, P3i minXYZ, P3i maxXYZ, P3 rmin, P3 rmax, P3i newMin, P3i newMax)
  
  Parameters:
  
  oabc -
  
  packingRange - in Cartesian angstroms, usually 0.02, or NaN
  
  minXYZ - supercell lattice scaling minimum, may be null
  
  maxXYZ - supercell lattice scaling maximum, ignored if minXYZ is null
  
  rmin - preset minimum of range, or null
  
  rmax - preset maximum of range; ignored if rmin is null
  
  newMin -
  
  newMax -
- toFractionalSpin
  
  public void toFractionalSpin(T3 v)
- toCartesianSpin
  
  public void toCartesianSpin(T3 v)

Class UnitCell

Field Summary

Fields inherited from class SimpleUnitCell

Method Summary

Methods inherited from class SimpleUnitCell

Methods inherited from class Object

Field Details

name

Method Details

fromOABC

fromParams

getCanonicalCopyTrimmed

getConventionalUnitCell

getTensor

toTrm

getMatrixAndUnitCell

getF2C

toUnitCellRnd

getCenter

setSpinAxisAngle

setSymmetryMinMax

adjustRangeMinMax

toFractionalSpin

toCartesianSpin