org.jmol.util

Class ModulationSet

java.lang.Object

javajs.util.T3

javajs.util.V3

org.jmol.util.Vibration

org.jmol.util.ModulationSet

All Implemented Interfaces:

java.io.Serializable, javajs.api.JSONEncodable, JmolModulationSet

public class ModulationSet
extends Vibration
implements JmolModulationSet

A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy

Author:

Bob Hanson hansonr@stolaf.edu 8/9/2013

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private float[]	axesLengths
private boolean	enabled
private javajs.util.M3	gammaE
private javajs.util.Matrix	gammaIinv
java.util.Map<java.lang.String,java.lang.Float>	htUij
(package private) java.lang.String	id
private int	iop
private boolean	isQ
private boolean	isSubsystem
private javajs.util.Lst<Modulation>	mods
private ModulationSet	modTemp
javajs.util.V3	mxyz
(package private) javajs.util.P3	ptTemp
private javajs.util.P3	qtOffset
private javajs.util.P3	r0
private javajs.util.Matrix	rI
private javajs.util.Matrix	rsvs
private float	scale
private javajs.util.Matrix	sigma
private float	spinOp
private java.lang.String	strop
private SymmetryInterface	symmetry
private javajs.util.Matrix	tau
private javajs.util.Matrix	tFactorInv
private javajs.util.V3	v0
Vibration	vib vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
float	vOcc
float	vOcc0

Fields inherited from class org.jmol.util.Vibration

modDim, modScale, twoPI, TYPE_SPIN, TYPE_VIBRATION

Fields inherited from class javajs.util.T3

x, y, z

Constructor Summary

Constructors

Constructor and Description
ModulationSet()

Method Summary

Modifier and Type	Method and Description
void	addTo(javajs.util.T3 a, float scale)
void	addUTens(java.lang.String utens, float v)
ModulationSet	calculate(javajs.util.T3 tuv, boolean isQ) Calculate r_I internal d-space coordinate of an atom.
(package private) float[]	getAxesLengths()
void	getInfo(java.util.Map<java.lang.String,java.lang.Object> info)
javajs.util.T3	getModPoint(boolean asEnabled)
private void	getModTemp()
java.lang.Object	getModulation(char type, javajs.util.T3 tuv)
float	getScale()
java.lang.String	getState()
SymmetryInterface	getSubSystemUnitCell()
javajs.util.V3	getV3()
Vibration	getVibration(boolean forceNew)
boolean	isEnabled()
boolean	isNonzero()
void	scaleVibration(float m)
ModulationSet	setMod(java.lang.String id, javajs.util.P3 r00, javajs.util.P3 r0, int d, javajs.util.Lst<Modulation> mods, javajs.util.M3 gammaE, javajs.util.Matrix[] factors, int iop, SymmetryInterface symmetry, Vibration v) A collection of modulations for a specific atom.
void	setModTQ(javajs.util.T3 a, boolean isOn, javajs.util.T3 qtOffset, boolean isQ, float scale) Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
void	setMoment()
void	setTempPoint(javajs.util.T3 a, javajs.util.T3 t456, float vibScale, float scale)
private void	setVib(boolean isReset)
void	setXYZ(javajs.util.T3 v)

Methods inherited from class org.jmol.util.Vibration

clone, setType

Methods inherited from class javajs.util.V3

angle, new3, newV, newVsub

Methods inherited from class javajs.util.T3

add, add2, add3, ave, cross, distance, distanceSquared, dot, equals, floatToIntBits0, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

vOcc

public float vOcc

htUij

public java.util.Map<java.lang.String,java.lang.Float> htUij

vOcc0

public float vOcc0

id

java.lang.String id

mods

private javajs.util.Lst<Modulation> mods

iop

private int iop

r0

private javajs.util.P3 r0

vib

public Vibration vib

vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.

mxyz

public javajs.util.V3 mxyz

symmetry

private SymmetryInterface symmetry

gammaE

private javajs.util.M3 gammaE

gammaIinv

private javajs.util.Matrix gammaIinv

sigma

private javajs.util.Matrix sigma

tau

private javajs.util.Matrix tau

enabled

private boolean enabled

scale

private float scale

qtOffset

private javajs.util.P3 qtOffset

isQ

private boolean isQ

rI

private javajs.util.Matrix rI

modTemp

private ModulationSet modTemp

strop

private java.lang.String strop

isSubsystem

private boolean isSubsystem

tFactorInv

private javajs.util.Matrix tFactorInv

rsvs

private javajs.util.Matrix rsvs

spinOp

private float spinOp

ptTemp

javajs.util.P3 ptTemp

v0

private javajs.util.V3 v0

axesLengths

private float[] axesLengths

Constructor Detail

ModulationSet

public ModulationSet()

Method Detail

getScale

public float getScale()

Specified by:

getScale in interface JmolModulationSet

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface JmolModulationSet

setMod

public ModulationSet setMod(java.lang.String id,
                            javajs.util.P3 r00,
                            javajs.util.P3 r0,
                            int d,
                            javajs.util.Lst<Modulation> mods,
                            javajs.util.M3 gammaE,
                            javajs.util.Matrix[] factors,
                            int iop,
                            SymmetryInterface symmetry,
                            Vibration v)

A collection of modulations for a specific atom.

Parameters:

id -

r00 - originating atom position prior to application of symmetry

r0 - unmodulated (average) position after application of symmetry

d -

mods -

gammaE -

factors - including sigma and tFactor

iop -

symmetry -

v - TODO

Returns:

this

getSubSystemUnitCell

public SymmetryInterface getSubSystemUnitCell()

Specified by:

getSubSystemUnitCell in interface JmolModulationSet

calculate

public ModulationSet calculate(javajs.util.T3 tuv,
                               boolean isQ)

Calculate r_I internal d-space coordinate of an atom.

Parameters:

tuv -

isQ -

Returns:

this ModulationSet, with this.rI set to the coordinate

addUTens

public void addUTens(java.lang.String utens,
                     float v)

setModTQ

public void setModTQ(javajs.util.T3 a,
                     boolean isOn,
                     javajs.util.T3 qtOffset,
                     boolean isQ,
                     float scale)

Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.

Specified by:

setModTQ in interface JmolModulationSet

Parameters:

isOn -

qtOffset -

isQ -

scale -

addTo

public void addTo(javajs.util.T3 a,
                  float scale)

Specified by:

addTo in interface JmolModulationSet

setVib

private void setVib(boolean isReset)

getState

public java.lang.String getState()

Specified by:

getState in interface JmolModulationSet

getModPoint

public javajs.util.T3 getModPoint(boolean asEnabled)

Specified by:

getModPoint in interface JmolModulationSet

getModulation

public java.lang.Object getModulation(char type,
                                      javajs.util.T3 tuv)

Specified by:

getModulation in interface JmolModulationSet

setTempPoint

public void setTempPoint(javajs.util.T3 a,
                         javajs.util.T3 t456,
                         float vibScale,
                         float scale)

Overrides:

setTempPoint in class Vibration

getModTemp

private void getModTemp()

getInfo

public void getInfo(java.util.Map<java.lang.String,java.lang.Object> info)

Overrides:

getInfo in class Vibration

setXYZ

public void setXYZ(javajs.util.T3 v)

Overrides:

setXYZ in class Vibration

getVibration

public Vibration getVibration(boolean forceNew)

Specified by:

getVibration in interface JmolModulationSet

getV3

public javajs.util.V3 getV3()

Specified by:

getV3 in interface JmolModulationSet

scaleVibration

public void scaleVibration(float m)

Specified by:

scaleVibration in interface JmolModulationSet

setMoment

public void setMoment()

Specified by:

setMoment in interface JmolModulationSet

isNonzero

public boolean isNonzero()

Overrides:

isNonzero in class Vibration

getAxesLengths

float[] getAxesLengths()