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 JmolData, tensors, and isosurfaceMesh it is no longer clear to me exactly why this is necessary, and perhaps it is not for some of theseprotected javajs.util.P3
cartesianOffset
private javajs.util.P3
fractionalOffset
javajs.util.Lst<java.lang.String>
moreInfo
java.lang.String
name
private static double
twoP2
protected javajs.util.T3
unitCellMultiplier
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, sinAlpha, sinBeta, sinGamma, SLOP, toRadians, unitCellParams, volume
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Constructor Summary
Constructors Modifier Constructor Description private
UnitCell()
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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)
static UnitCell
cloneUnitCell(UnitCell uc)
(package private) java.lang.String
dumpInfo(boolean isFull)
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.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.java.lang.String
getState()
(package private) Tensor
getTensor(Viewer vwr, float[] parBorU)
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
reset()
private void
setCartesianOffset(javajs.util.T3 origin)
(package private) void
setOffset(javajs.util.T3 pt)
private static float
toFractionalX(float x)
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 cellvoid
unitize(javajs.util.T3 pt)
returns [0,1)-
Methods inherited from class org.jmol.util.SimpleUnitCell
escapeMultiplier, getCellWeight, getFractionalOrigin, getInfo, getReciprocal, getUnitCellAsArray, getUnitCellParams, ijkToPoint3f, init, isPolymer, isSlab, isSupercell, isValid, newA, setMinMaxLatticeParameters, setOabc, toCartesian, toFractional, toFractionalM, toString, toSupercell
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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 JmolData, tensors, and isosurfaceMesh it is no longer clear to me exactly why this is necessary, and perhaps it is not for some of these
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cartesianOffset
protected final javajs.util.P3 cartesianOffset
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unitCellMultiplier
protected javajs.util.T3 unitCellMultiplier
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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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unitize
public void unitize(javajs.util.T3 pt)
returns [0,1)- 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 isFull)
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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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toFractionalX
private static float toFractionalX(float x)
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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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getState
public java.lang.String getState()
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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.- Returns:
- [origin va vb vc]
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