Package org.jmol.symmetry
Class SymmetryOperation
- java.lang.Object
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- javajs.util.M34
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- javajs.util.M4
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- org.jmol.symmetry.SymmetryOperation
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public class SymmetryOperation extends javajs.util.M4
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Field Summary
Fields Modifier and Type Field Description private static javajs.util.P3
atomTest
private javajs.util.V3
centering
private boolean
doNormalize
"normalization" is the process of adjusting symmetry operator definitions such that the center of geometry of a molecule is within the 555 unit cell for each operation.private static java.lang.String[]
fortyeigths
(package private) int
index
private java.util.Hashtable<java.lang.String,java.lang.Object>
info
(package private) boolean
isBio
(package private) boolean
isCenteringOp
(package private) boolean
isFinalized
(package private) static java.lang.String[]
labelsXn
(package private) static java.lang.String[]
labelsXnSub
(package private) static java.lang.String[]
labelsXYZ
(package private) float[]
linearRotTrans
private float
magOp
(package private) int
modDim
private java.lang.String[]
myLabels
private int
opId
(package private) javajs.util.Matrix
rsvs
private javajs.util.Matrix
sigma
(package private) java.lang.String
subsystemCode
(package private) int
timeReversal
private static java.lang.String[]
twelfths
private boolean
unCentered
(package private) java.lang.String
xyz
(package private) java.lang.String
xyzOriginal
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Constructor Summary
Constructors Constructor Description SymmetryOperation(SymmetryOperation op, javajs.util.P3[] atoms, int atomIndex, int countOrId, boolean doNormalize)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) static float
approxF(float f)
private static javajs.util.M4
div12(javajs.util.M4 op)
(package private) void
doFinalize()
(package private) java.lang.String
dumpInfo()
(package private) static java.lang.String
dumpSeitz(javajs.util.M4 s, boolean isCanonical)
private static java.lang.String
fc(float x)
(package private) static java.lang.String
fcoord(javajs.util.T3 p)
(package private) java.lang.String
fixMagneticXYZ(javajs.util.M4 m, java.lang.String xyz, boolean addMag)
(package private) static java.lang.String
fortyEighthsOf(float n48ths)
(package private) javajs.util.V3
getCentering()
assumption here is that these are in order of sets, as in ITAjava.util.Map<java.lang.String,java.lang.Object>
getInfo()
(package private) float
getMagneticOp()
Magnetic spin is a pseudo (or "axial") vector.(package private) static java.lang.String
getMatrixFromString(SymmetryOperation op, java.lang.String xyz, float[] linearRotTrans, boolean allowScaling)
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 formatstatic javajs.util.M4
getMatrixFromXYZ(java.lang.String xyz)
(package private) java.lang.String
getXyz(boolean normalized)
static java.lang.String
getXYZFromMatrix(javajs.util.M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)
(package private) static java.lang.String
getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)
(package private) static void
newPoint(javajs.util.M4 m, javajs.util.P3 atom1, javajs.util.P3 atom2, int x, int y, int z)
private static float
normalize48ths(float iValue, boolean doNormalize)
private static float
normalizeTwelfths(float iValue, boolean doNormalize)
private static java.lang.String
plusMinus(java.lang.String strT, float x, java.lang.String sx)
(package private) static java.lang.String
replaceXn(java.lang.String xyz, int n)
(package private) javajs.util.V3[]
rotateAxes(javajs.util.V3[] vectors, UnitCell unitcell, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
(package private) boolean
setFromMatrix(float[] offset, boolean isReverse)
private void
setGamma(boolean isReverse)
rsvs is the superspace group rotation-translation matrix.private void
setMatrix(boolean isReverse)
(package private) boolean
setMatrixFromXYZ(java.lang.String xyz, int modDim, boolean allowScaling)
private void
setModDim(int dim)
static void
setOffset(javajs.util.M4 m, javajs.util.P3[] atoms, int atomIndex, int count)
(package private) void
setSigma(java.lang.String subsystemCode, javajs.util.Matrix sigma)
(package private) void
setTimeReversal(int magRev)
set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"java.lang.String
toString()
Returns a string that contains the values of this Matrix4f.(package private) static java.lang.String
twelfthsOf(float n12ths)
private static java.lang.String
xyzFraction12(float n12ths, boolean allPositive, boolean halfOrLess)
private static java.lang.String
xyzFraction48ths(float n48ths, boolean allPositive, boolean halfOrLess)
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Methods inherited from class javajs.util.M4
determinant4, equals, getColumn, getElement, getRotationScale, getRow, getTranslation, hashCode, invert, mul, mul2, newA16, newM4, newMV, rotTrans, rotTrans2, round, scale, setA, setAsXYRotation, setAsXZRotation, setAsYZRotation, setColumn4, setColumnA, setElement, setIdentity, setM4, setMV, setRotationScale, setRowA, setToAA, setToM3, setTranslation, setZero, sub, transform, transform2, transpose
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Field Detail
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xyzOriginal
java.lang.String xyzOriginal
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xyz
java.lang.String xyz
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doNormalize
private boolean doNormalize
"normalization" is the process of adjusting symmetry operator definitions such that the center of geometry of a molecule is within the 555 unit cell for each operation. It is carried out when "packed" is NOT issued and the lattice is given as {i j k} or when the lattice is given as {nnn mmm 1}
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isFinalized
boolean isFinalized
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opId
private int opId
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centering
private javajs.util.V3 centering
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atomTest
private static javajs.util.P3 atomTest
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myLabels
private java.lang.String[] myLabels
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modDim
int modDim
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linearRotTrans
float[] linearRotTrans
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rsvs
javajs.util.Matrix rsvs
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isBio
boolean isBio
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sigma
private javajs.util.Matrix sigma
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index
int index
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subsystemCode
java.lang.String subsystemCode
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timeReversal
int timeReversal
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twelfths
private static final java.lang.String[] twelfths
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fortyeigths
private static final java.lang.String[] fortyeigths
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labelsXYZ
static final java.lang.String[] labelsXYZ
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labelsXn
static final java.lang.String[] labelsXn
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labelsXnSub
static final java.lang.String[] labelsXnSub
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unCentered
private boolean unCentered
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isCenteringOp
boolean isCenteringOp
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magOp
private float magOp
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info
private java.util.Hashtable<java.lang.String,java.lang.Object> info
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Constructor Detail
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SymmetryOperation
SymmetryOperation(SymmetryOperation op, javajs.util.P3[] atoms, int atomIndex, int countOrId, boolean doNormalize)
- Parameters:
op
-atoms
-atomIndex
-countOrId
-doNormalize
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Method Detail
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setSigma
void setSigma(java.lang.String subsystemCode, javajs.util.Matrix sigma)
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setGamma
private void setGamma(boolean isReverse)
rsvs is the superspace group rotation-translation matrix. It is a (3 + modDim + 1) x (3 + modDim + 1) matrix from which we can extract all necessary parts;- Parameters:
isReverse
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doFinalize
void doFinalize()
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div12
private static javajs.util.M4 div12(javajs.util.M4 op)
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getXyz
java.lang.String getXyz(boolean normalized)
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newPoint
static void newPoint(javajs.util.M4 m, javajs.util.P3 atom1, javajs.util.P3 atom2, int x, int y, int z)
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dumpInfo
java.lang.String dumpInfo()
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dumpSeitz
static final java.lang.String dumpSeitz(javajs.util.M4 s, boolean isCanonical)
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setMatrixFromXYZ
boolean setMatrixFromXYZ(java.lang.String xyz, int modDim, boolean allowScaling)
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setModDim
private void setModDim(int dim)
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setMatrix
private void setMatrix(boolean isReverse)
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setFromMatrix
boolean setFromMatrix(float[] offset, boolean isReverse)
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getMatrixFromXYZ
public static javajs.util.M4 getMatrixFromXYZ(java.lang.String xyz)
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getMatrixFromString
static java.lang.String getMatrixFromString(SymmetryOperation op, java.lang.String xyz, float[] linearRotTrans, boolean allowScaling)
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format- Parameters:
op
-xyz
-linearRotTrans
-allowScaling
-- Returns:
- canonized Jones-Faithful string
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replaceXn
static java.lang.String replaceXn(java.lang.String xyz, int n)
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xyzFraction12
private static final java.lang.String xyzFraction12(float n12ths, boolean allPositive, boolean halfOrLess)
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xyzFraction48ths
private static final java.lang.String xyzFraction48ths(float n48ths, boolean allPositive, boolean halfOrLess)
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twelfthsOf
static final java.lang.String twelfthsOf(float n12ths)
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fortyEighthsOf
static final java.lang.String fortyEighthsOf(float n48ths)
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plusMinus
private static java.lang.String plusMinus(java.lang.String strT, float x, java.lang.String sx)
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normalizeTwelfths
private static float normalizeTwelfths(float iValue, boolean doNormalize)
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normalize48ths
private static float normalize48ths(float iValue, boolean doNormalize)
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getXYZFromMatrix
public static final java.lang.String getXYZFromMatrix(javajs.util.M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)
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setOffset
public static void setOffset(javajs.util.M4 m, javajs.util.P3[] atoms, int atomIndex, int count)
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rotateAxes
javajs.util.V3[] rotateAxes(javajs.util.V3[] vectors, UnitCell unitcell, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
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fcoord
static java.lang.String fcoord(javajs.util.T3 p)
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fc
private static java.lang.String fc(float x)
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approxF
static float approxF(float f)
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getXYZFromRsVs
static java.lang.String getXYZFromRsVs(javajs.util.Matrix rs, javajs.util.Matrix vs, boolean is12ths)
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toString
public java.lang.String toString()
Description copied from class:javajs.util.M4
Returns a string that contains the values of this Matrix4f.- Overrides:
toString
in classjavajs.util.M4
- Returns:
- the String representation
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getMagneticOp
float getMagneticOp()
Magnetic spin is a pseudo (or "axial") vector. This means that it acts as a rotation, not a vector. When a rotation about x is passed through the mirror plane xz, it is reversed; when it is passed through the mirror plane yz, it is not reversed -- exactly opposite what you would imagine from a standard "polar" vector. For example, a vector perpendicular to a plane of symmetry (det=-1) will be flipped (m=1), while a vector parallel to that plane will not be flipped (m=-1) In addition, magnetic spin operations have a flag m=1 or m=-1 (m or -m) that indicates how the vector quantity changes with symmetry. This is called "time reversal" and stored here as timeReversal. To apply, timeReversal must be multiplied by the 3x3 determinant, which is always 1 (standard rotation) or -1 (rotation-inversion). This we store as magOp. See https://en.wikipedia.org/wiki/Pseudovector- Returns:
- +1, -1, or 0
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setTimeReversal
void setTimeReversal(int magRev)
set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"- Parameters:
magRev
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getCentering
javajs.util.V3 getCentering()
assumption here is that these are in order of sets, as in ITA- Returns:
- centering
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fixMagneticXYZ
java.lang.String fixMagneticXYZ(javajs.util.M4 m, java.lang.String xyz, boolean addMag)
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getInfo
public java.util.Map<java.lang.String,java.lang.Object> getInfo()
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