Package 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:
Serializable
,JSONEncodable
,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:
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Field Summary
FieldsModifier and TypeFieldDescriptioncurrent value of anisotropic parameter modulationthe modulated magnetic spinvib is a spin vector when the model has modulation; otherwise an unmodulated vibration.float
the current value of the occupancy modulationFields inherited from class org.jmol.util.Vibration
modDim, modScale, showTrace, tracePt, twoPI, TYPE_SPIN, TYPE_VIBRATION, TYPE_WYCKOFF
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
void
Calculate r_I internal d-space coordinate of an atom.void
getModPoint
(boolean asEnabled) getModulation
(char type, T3 tuv, boolean occ100) int
getOccupancy100
(boolean forVibVis) float
getScale()
getState()
getV3()
getVibration
(boolean forceNew) boolean
boolean
void
scaleVibration
(float m) setCalcPoint
(T3 pt, T3 t456, float vibScale, float scale) get updated value for offset vector and for occupancysetMod
(String id, P3 r00, P3 r0, int d, Lst<Modulation> mods, M3 gammaE, Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate) A collection of modulations for a specific atom.void
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.void
float
setOccupancy
(double[] pt, double foccupancy, double siteMult) get the occupancy, first from the reader, then from renderervoid
Methods inherited from class org.jmol.util.Vibration
addTracePt, clone, setType, startTrace
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Field Details
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vib
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration. -
mxyz
the modulated magnetic spin -
htUij
current value of anisotropic parameter modulation -
vOcc
public float vOccthe current value of the occupancy modulation
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Constructor Details
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ModulationSet
public ModulationSet()
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Method Details
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getSubSystemUnitCell
- Specified by:
getSubSystemUnitCell
in interfaceJmolModulationSet
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isEnabled
public boolean isEnabled()- Specified by:
isEnabled
in interfaceJmolModulationSet
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getScale
public float getScale()- Specified by:
getScale
in interfaceJmolModulationSet
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setMod
public ModulationSet setMod(String id, P3 r00, P3 r0, int d, Lst<Modulation> mods, M3 gammaE, Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate) A collection of modulations for a specific atom.- Parameters:
id
-r00
- originating atom position prior to application of symmetryr0
- unmodulated (average) position after application of symmetryd
-mods
-gammaE
-factors
- including sigma and tFactorsymmetry
-iop
-nOps
-v
- TODOisCommensurate
- TODO- Returns:
- this
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calculate
Calculate r_I internal d-space coordinate of an atom.- Parameters:
tuv
-isQ
-- Returns:
- this ModulationSet, with this.rI set to the coordinate
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addUTens
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setModTQ
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.- Specified by:
setModTQ
in interfaceJmolModulationSet
- Parameters:
isOn
-qtOffset
-isQ
-scale
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addTo
- Specified by:
addTo
in interfaceJmolModulationSet
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getState
- Specified by:
getState
in interfaceJmolModulationSet
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getModPoint
- Specified by:
getModPoint
in interfaceJmolModulationSet
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getModulation
- Specified by:
getModulation
in interfaceJmolModulationSet
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setCalcPoint
get updated value for offset vector and for occupancy- Overrides:
setCalcPoint
in classVibration
- Returns:
- pt
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getInfo
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setXYZ
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getVibration
- Specified by:
getVibration
in interfaceJmolModulationSet
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getV3
- Specified by:
getV3
in interfaceJmolModulationSet
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scaleVibration
public void scaleVibration(float m) - Specified by:
scaleVibration
in interfaceJmolModulationSet
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setMoment
public void setMoment()- Specified by:
setMoment
in interfaceJmolModulationSet
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isNonzero
public boolean isNonzero() -
setOccupancy
public float setOccupancy(double[] pt, double foccupancy, double siteMult) get the occupancy, first from the reader, then from renderer- Parameters:
pt
-foccupancy
-siteMult
- or 0 is this is not relevant- Returns:
- occupancy on [0,1]
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getOccupancy100
public int getOccupancy100(boolean forVibVis) - Overrides:
getOccupancy100
in classVibration
- Parameters:
forVibVis
- used only in ModulationSet when calculating actual display offset- Returns:
- Integer.MIN_VALUE if not applicable, occupancy if enabled, -occupancy if not enabled
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