Package org.jmol.symmetry
Class UnitCell
- java.lang.Object
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- org.jmol.util.SimpleUnitCell
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- org.jmol.symmetry.UnitCell
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- All Implemented Interfaces:
java.lang.Cloneable
class UnitCell extends SimpleUnitCell implements java.lang.Cloneable
a class private to the org.jmol.symmetry package to be accessed 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.
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Field Summary
Fields Modifier and Type Field Description private boolean
allFractionalRelative
this flag TRUE causes an update of matrixCtoFNoOffset each time an offset is changed so that it is updated and the two stay the same; set true only for isosurfaceMeshprotected javajs.util.P3
cartesianOffset
private javajs.util.P3
fractionalOffset
javajs.util.Lst<java.lang.String>
moreInfo
java.lang.String
name
private static double
twoP2
private UnitCell
unitCellMultiplied
the multiplied, offset UnitCell derived from this UnitCellprotected javajs.util.T3
unitCellMultiplier
a P3 or P4; the raw multiplier for the cell from UNITCELL {ijk ijk scale} UNITCELL {1iiijjjkkk 1iiijjjkkk scale} (encoded as a P4: {1iiijjjkkk 1iiijjjkkk scale 1kkkkkk} )private static javajs.util.V3[]
unitVectors
private javajs.util.P3[]
vertices
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Fields inherited from class org.jmol.util.SimpleUnitCell
a, a_, alpha, b, b_, beta, c, c_, cA_, cB_, cosAlpha, cosBeta, cosGamma, dimension, gamma, INFO_A, INFO_ALPHA, INFO_B, INFO_BETA, INFO_C, INFO_DIMENSIONS, INFO_GAMMA, matrixCartesianToFractional, matrixCtoFNoOffset, matrixFractionalToCartesian, matrixFtoCNoOffset, PARAM_COUNT, PARAM_M4, PARAM_SCALE, PARAM_STD, PARAM_SUPERCELL, PARAM_VABC, sinAlpha, sinBeta, sinGamma, SLOP, toRadians, unitCellParams, volume
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Constructor Summary
Constructors Modifier Constructor Description private
UnitCell()
Indicate that this is a new unit cell, not one from a file.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
private static void
checkDuplicate(javajs.util.Lst<javajs.util.P3> list, int i0, int n0, int n)
static UnitCell
cloneUnitCell(UnitCell uc)
(package private) java.lang.String
dumpInfo(boolean isDebug, boolean multiplied)
private float
fix(float x)
(package private) static UnitCell
fromOABC(javajs.util.T3[] oabc, boolean setRelative)
A special constructor for spacially defined unit cells.static UnitCell
fromParams(float[] params, boolean setRelative)
(package private) javajs.util.P3[]
getCanonicalCopy(float scale, boolean withOffset)
(package private) javajs.util.P3
getCartesianOffset()
javajs.util.T3[]
getConventionalUnitCell(java.lang.String latticeType, javajs.util.M3 primitiveToCrystal)
return a conventional lattice from a primitive(package private) javajs.util.Lst<javajs.util.P3>
getEquivPoints(javajs.util.P3 pt, java.lang.String flags, javajs.util.M4[] ops, javajs.util.Lst<javajs.util.P3> list, int i0, int n0)
(package private) javajs.util.P3
getFractionalOffset()
(package private) java.util.Map<java.lang.String,java.lang.Object>
getInfo()
javajs.util.Quat
getQuaternionRotation(java.lang.String abc)
Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.javajs.util.P3[]
getScaledCell(boolean withOffset)
java.lang.String
getState()
(package private) Tensor
getTensor(Viewer vwr, float[] parBorU)
(package private) UnitCell
getUnitCellMultiplied()
javajs.util.T3
getUnitCellMultiplier()
javajs.util.P3[]
getUnitCellVectors()
javajs.util.T3[]
getV0abc(java.lang.Object def)
(package private) javajs.util.P3[]
getVertices()
boolean
hasOffset()
(package private) void
initOrientation(javajs.util.M3 mat)
private void
initUnitcellVertices()
boolean
isSameAs(UnitCell uc)
void
normalize(javajs.util.V3 vtrans)
void
reset()
private void
setCartesianOffset(javajs.util.T3 origin)
(package private) void
setOffset(javajs.util.T3 pt)
boolean
toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] uc, javajs.util.M3 primitiveToCrystal)
(package private) void
toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
when offset is null, use the current cell, otherwise use the original unit cell(package private) void
toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset)
when offset is null, use the current cell, otherwise use the original unit cellvoid
unitize(javajs.util.T3 pt)
returns [0,1)void
unitizeRnd(javajs.util.T3 pt)
returns [0,1) with rounding to 0.0001-
Methods inherited from class org.jmol.util.SimpleUnitCell
addVectors, checkPeriodic, checkUnitCell, escapeMultiplier, getCellWeight, getFractionalOrigin, getInfo, getReciprocal, getUnitCellAsArray, getUnitCellParams, ijkToPoint3f, init, isPolymer, isSlab, isSupercell, isValid, newA, normalizeXRnd, ptToIJK, setMinMaxLatticeParameters, setOabc, toCartesian, toFractional, toFractionalM, toString, toSupercell, unitizeDim, unitizeDimRnd, unitizeX, unitizeXRnd
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Field Detail
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vertices
private javajs.util.P3[] vertices
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fractionalOffset
private javajs.util.P3 fractionalOffset
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allFractionalRelative
private boolean allFractionalRelative
this flag TRUE causes an update of matrixCtoFNoOffset each time an offset is changed so that it is updated and the two stay the same; set true only for isosurfaceMesh
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cartesianOffset
protected final javajs.util.P3 cartesianOffset
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unitCellMultiplier
protected javajs.util.T3 unitCellMultiplier
a P3 or P4; the raw multiplier for the cell from UNITCELL {ijk ijk scale} UNITCELL {1iiijjjkkk 1iiijjjkkk scale} (encoded as a P4: {1iiijjjkkk 1iiijjjkkk scale 1kkkkkk} )
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unitCellMultiplied
private UnitCell unitCellMultiplied
the multiplied, offset UnitCell derived from this UnitCell
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moreInfo
public javajs.util.Lst<java.lang.String> moreInfo
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name
public java.lang.String name
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twoP2
private static final double twoP2
- See Also:
- Constant Field Values
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unitVectors
private static final javajs.util.V3[] unitVectors
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Method Detail
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fromOABC
static UnitCell fromOABC(javajs.util.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
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fromParams
public static UnitCell fromParams(float[] params, boolean setRelative)
- Parameters:
params
-setRelative
- only set true for JmolData and tensors- Returns:
- a new unit cell
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initOrientation
void initOrientation(javajs.util.M3 mat)
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toUnitCell
final void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
when offset is null, use the current cell, otherwise use the original unit cell- Parameters:
pt
-offset
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toUnitCellRnd
final void toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset)
when offset is null, use the current cell, otherwise use the original unit cell- Parameters:
pt
-offset
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unitize
public void unitize(javajs.util.T3 pt)
returns [0,1)- Parameters:
pt
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unitizeRnd
public void unitizeRnd(javajs.util.T3 pt)
returns [0,1) with rounding to 0.0001- Parameters:
pt
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reset
public void reset()
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setOffset
void setOffset(javajs.util.T3 pt)
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setCartesianOffset
private void setCartesianOffset(javajs.util.T3 origin)
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getInfo
java.util.Map<java.lang.String,java.lang.Object> getInfo()
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dumpInfo
java.lang.String dumpInfo(boolean isDebug, boolean multiplied)
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getUnitCellMultiplied
UnitCell getUnitCellMultiplied()
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getVertices
javajs.util.P3[] getVertices()
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getCartesianOffset
javajs.util.P3 getCartesianOffset()
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getFractionalOffset
javajs.util.P3 getFractionalOffset()
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getCanonicalCopy
javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset)
- Parameters:
scale
-withOffset
-- Returns:
- points in Triangulator order
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getScaledCell
public javajs.util.P3[] getScaledCell(boolean withOffset)
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initUnitcellVertices
private void initUnitcellVertices()
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checkDistance
public boolean checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
- Parameters:
f1
-f2
-distance
-dx
-iRange
-jRange
-kRange
-ptOffset
- TODO- Returns:
- TRUE if pt has been set.
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getUnitCellMultiplier
public javajs.util.T3 getUnitCellMultiplier()
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getUnitCellVectors
public javajs.util.P3[] getUnitCellVectors()
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fix
private float fix(float x)
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isSameAs
public boolean isSameAs(UnitCell uc)
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hasOffset
public boolean hasOffset()
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getQuaternionRotation
public javajs.util.Quat getQuaternionRotation(java.lang.String abc)
Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.- Parameters:
abc
- ab bc ca- Returns:
- quaternion
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getV0abc
public javajs.util.T3[] getV0abc(java.lang.Object def)
- Parameters:
def
- String "abc;offset" or M3 or M4 to origin; 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"- Returns:
- [origin va vb vc]
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toFromPrimitive
public boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] uc, javajs.util.M3 primitiveToCrystal)
- Parameters:
toPrimitive
- or assumed conventionaltype
- P, R, A, B, C, I(BCC), or F(FCC)uc
- either [origin, va, vb, vc] or just [va, vb, vc]primitiveToCrystal
-- Returns:
- true if successful
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getConventionalUnitCell
public javajs.util.T3[] getConventionalUnitCell(java.lang.String latticeType, javajs.util.M3 primitiveToCrystal)
return a conventional lattice from a primitive- Parameters:
latticeType
- "A" "B" "C" "R" etc.primitiveToCrystal
-- Returns:
- [origin va vb vc]
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getEquivPoints
javajs.util.Lst<javajs.util.P3> getEquivPoints(javajs.util.P3 pt, java.lang.String flags, javajs.util.M4[] ops, javajs.util.Lst<javajs.util.P3> list, int i0, int n0)
- Parameters:
pt
- the point to transformflags
- "tofractional,fromfractional,packed"ops
- space group operationslist
- the list to append toi0
- the starting index of the listn0
- the first point that is to be duplicated; prior points are just references for removing duplicates- Returns:
- augmented list
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checkDuplicate
private static void checkDuplicate(javajs.util.Lst<javajs.util.P3> list, int i0, int n0, int n)
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normalize
public void normalize(javajs.util.V3 vtrans)
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getState
public java.lang.String getState()
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