#include <PowderPattern.h>
Inheritance diagram for ObjCryst::PowderPattern::
Public Methods | |||
PowderPattern () | |||
PowderPattern (const PowderPattern &) | |||
~PowderPattern () | |||
virtual const string | GetClassName () const | ||
Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry. | |||
void | AddPowderPatternComponent (PowderPatternComponent &) | ||
Add a component (phase, backround) to this spectrum. More... | |||
unsigned int | GetNbPowderPatternComponent () const | ||
Number of components. | |||
const PowderPatternComponent & | GetPowderPatternComponent (const string &name) const | ||
Access to a component of the powder spectrum. | |||
const PowderPatternComponent & | GetPowderPatternComponent (const int) const | ||
Access to a component of the powder spectrum. | |||
PowderPatternComponent & | GetPowderPatternComponent (const string &name) | ||
Access to a component of the powder spectrum. | |||
PowderPatternComponent & | GetPowderPatternComponent (const int) | ||
Access to a component of the powder spectrum. | |||
void | SetPowderPatternPar (const double tthetaMin, const double tthetaStep, unsigned long nbPoint) | ||
\briefSet the powder spectrum angular range & resolution parameter. More... | |||
unsigned long | GetNbPoint () const | ||
Number of points ? | |||
void | SetRadiation (const Radiation &radiation) | ||
Set the radiation. | |||
const Radiation & | GetRadiation () const | ||
Neutron or x-ray experiment ? | |||
void | SetRadiationType (const RadiationType radiation) | ||
Set the radiation type. | |||
RadiationType | GetRadiationType () const | ||
Neutron or x-ray experiment ? | |||
void | SetWavelength (const double lambda) | ||
Set the wavelength of the experiment (in Angstroems). | |||
void | SetWavelength (const string &XRayTubeElementName, const double alpha12ratio=0.5) | ||
Set the wavelength of the experiment to that of an X-Ray tube. More... | |||
void | SetEnergy (const double energy) | ||
Set the energy of the experiment [in keV, lambda(A)=12398/E(keV)]. | |||
double | GetWavelength () const | ||
wavelength of the experiment (in Angstroems). | |||
void | SetUseFastLessPreciseFunc (const bool useItOrNot) | ||
Use of faster, less precise approximations to compute the powder spectrums This can be useful fot global optimization, but should be avoided for precise (eg derivative calculation) work. | |||
void | SetUseOnlyLowAngleData (const bool useOnlyLowAngle, const double angle) | ||
Set an option so that only low-amgle reflections (theta < angle) are used. More... | |||
const CrystVector_double & | GetPowderPatternCalc () const | ||
Get the calculated powder spectrum. | |||
const CrystVector_double & | GetPowderPatternObs () const | ||
Get the observed powder spectrum. | |||
const CrystVector_double & | GetPowderPatternObsSigma () const | ||
Get the sigma for each point of the observed powder spectrum. | |||
const CrystVector_double & | GetPowderPatternWeight () const | ||
Get the weight for each point of the powder spectrum. | |||
double | Get2ThetaMin () const | ||
Get the Minimum 2theta. | |||
double | Get2ThetaStep () const | ||
Get the step in 2theta. | |||
double | Get2ThetaMax () const | ||
Get the maximum 2theta. | |||
const RefinableObjClock & | GetClockPowderPatternCalc () const | ||
Last time the spectrum was calculated. | |||
const RefinableObjClock & | GetClockPowderPatternPar () const | ||
When were the spectrum parameters (2theta range, step) changed ? | |||
const RefinableObjClock & | GetClockPowderPatternRadiation () const | ||
When were the radiation parameter (radiation type, wavelength) changed ? | |||
void | Set2ThetaZero (const double newZero) | ||
Change Zero in 2Theta. | |||
void | Set2ThetaDisplacement (const double displacement) | ||
Change displacement correction ![]() | |||
void | Set2ThetaTransparency (const double transparency) | ||
Change transparency correction ![]() | |||
double | Get2ThetaCorr (const double ttheta) const | ||
Get the experimental 2theta from the theoretical value, taking into account all corrections (zero, transparency,..).
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long | Get2ThetaCorrPixel (const double ttheta) const | ||
Get the pixel number on the experimental spectrum, from the theoretical (uncorrected) value of 2theta, taking into account all corrections. (zero, transparency,..).
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void | ImportPowderPatternFullprof (const string &fullprofFileName) | ||
Import fullprof-style diffraction data. More... | |||
void | ImportPowderPatternPSI_DMC (const string &filename) | ||
Import powder spectrum, format DMC from PSI. | |||
void | ImportPowderPatternILL_D1A5 (const string &filename) | ||
Import powder spectrum, format from ILL D1A/D2B (format without counter info). | |||
void | ImportPowderPatternXdd (const string &fileName) | ||
Import *.xdd diffraction data (Topas,...). More... | |||
void | ImportPowderPatternSietronicsCPI (const string &fileName) | ||
Import *.cpi Sietronics diffraction data. More... | |||
void | ImportPowderPattern2ThetaObsSigma (const string &fileName, const int nbSkip=0) | ||
Import file with 3 columns 2Theta Iobs Sigma. More... | |||
void | ImportPowderPattern2ThetaObs (const string &fileName, const int nbSkip=0) | ||
Import file with 2 columns 2Theta Iobs. More... | |||
void | SetPowderPatternObs (const CrystVector_double &obs) | ||
Set observed powder spectrum from vector array. More... | |||
void | SavePowderPattern (const string &filename="powderPattern.out") const | ||
Save powder spectrum to one file, text format, 3 columns theta Iobs Icalc.If Iobs is missing, the column is omitted. position for all phases... More... | |||
void | PrintObsCalcData (ostream &os=cout) const | ||
Print to thee screen/console the observed and calculated spectrum (long, mostly useful for debugging). | |||
double | GetR () const | ||
Unweighted R-factor. More... | |||
double | GetRw () const | ||
Get the weighted R-factor. More... | |||
double | GetChiSq () const | ||
Return conventionnal Chi^2. More... | |||
void | FitScaleFactorForR () | ||
Fit the scale(s) factor of each component to minimize R. | |||
void | FitScaleFactorForRw () | ||
Fit the scale(s) factor of each component to minimize Rw. | |||
void | SetSigmaToSqrtIobs () | ||
Set sigma=sqrt(Iobs). | |||
void | SetWeightToInvSigmaSq (const double minRelatSigma=1e-3) | ||
Set w = 1/sigma^2. To filter too small or null intensities :If sigma< minRelatSigma* max(sigma), then w=1/(minRelatSigma* max(sigma))^2. | |||
void | SetWeightToSinTheta (const double power=1.) | ||
Set w = sin(theta). Not really usful, huh ? | |||
void | SetWeightToUnit () | ||
Set w = 1. | |||
void | SetWeightPolynomial (const double a, const double b, const double c, const double minRelatIobs=1e-3) | ||
Set w = 1/(a+ Iobs + b*Iobs^2+c*Iobs^3) To filter too small or null intensities: if Iobs < [minRelatIobs * max(Iobs)], then use Iobs=minRelatIobs * max(Iobs) to compute the weight. Typical values: a=2*min(Iobs) b=2/max(Iobs) c=0. | |||
void | Add2ThetaExcludedRegion (const double min2Theta, const double max2theta) | ||
Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be, as always, in radians. Does not work yet with integrated R factors. Note that the pattern is still computed in these regions. They are only ignored by statistics functions (R, Rws). | |||
unsigned int | GetNbCostFunction () const | ||
Number of Cost functions. | |||
const string & | GetCostFunctionName (const unsigned int) const | ||
Get a Cost function name from its id#. | |||
const string & | GetCostFunctionDescription (const unsigned int) const | ||
Get the (short) description of a cost function. | |||
virtual double | GetCostFunctionValue (const unsigned int) | ||
Get the current value of a cost function this should be const... | |||
virtual void | XMLOutput (ostream &os, int indent=0) const | ||
Output to stream in well-formed XML. More... | |||
virtual void | XMLInput (istream &is, const XMLCrystTag &tag) | ||
Input From stream. More... | |||
void | Prepare () | ||
Prepare everything (if necessary) for an optimization/calculation. | |||
Protected Methods | |||
void | CalcPowderPattern () const | ||
Calc the powder spectrum. | |||
virtual void | Init () | ||
Init parameters and options. | |||
Protected Attributes | |||
CrystVector_double | mPowderPatternCalc | ||
The calculated powder spectrum. It is mutable since it is completely defined by other parameters (eg it is not an 'independent parameter'). | |||
CrystVector_double | mPowderPatternBackgroundCalc | ||
The calculated powder spectrum part which corresponds to 'background' (eg non-scalable components). It is already included in mPowderPatternCalc. | |||
CrystVector_double | mPowderPatternObs | ||
The observed powder spectrum. | |||
CrystVector_double | mPowderPatternObsSigma | ||
The sigma of the observed spectrum. | |||
CrystVector_double | mPowderPatternWeight | ||
The weight for each point of the spectrum. | |||
double | m2ThetaMin | ||
2theta min and step for the spectrum. | |||
double | m2ThetaStep | ||
2theta min and step for the spectrum. | |||
unsigned long | mNbPoint | ||
Number of points in the spectrum. | |||
double | mWavelength | ||
The wavelength of the experiment, in Angstroems.
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Radiation | mRadiation | ||
The wavelength of the experiment, in Angstroems. | |||
RefinableObjClock | mClockPowderPatternPar | ||
When were the spectrum parameters (2theta range, step) changed ? | |||
RefinableObjClock | mClockPowderPatternRadiation | ||
When were the radiation parameter (radiation type, wavelength) changed ? | |||
RefinableObjClock | mClockPowderPatternCalc | ||
When was the powder spectrum last computed ? | |||
RefinableObjClock | mClockPowderPattern2ThetaCorr | ||
Corrections to 2Theta. | |||
RefinableObjClock | mClockScaleFactor | ||
Last modification of the scale factor. | |||
CrystVector_double | mExcludedRegionMin2Theta | ||
Min value for 2theta for all excluded regions. | |||
CrystVector_double | mExcludedRegionMax2Theta | ||
Max value for 2theta for all excluded regions. | |||
double | m2ThetaZero | ||
Zero correction : ![]() | |||
double | m2ThetaDisplacement | ||
Displacement correction :![]() | |||
double | m2ThetaTransparency | ||
Transparency correction : ![]() | |||
ObjRegistry< PowderPatternComponent > | mPowderPatternComponentRegistry | ||
The components (crystalline phases, background,...) of the powder spectrum. | |||
CrystVector_double | mScaleFactor | ||
The scale factors for each component. For unscalable phases, this is set to 1 (constant). | |||
bool | mUseFastLessPreciseFunc | ||
Use faster, less precise functions ? | |||
bool | mStatisticsExcludeBackground | ||
Should Statistics (R, Rw,..) exclude the background ? | |||
bool | mStatisticsUseIntegratedPeak | ||
Use integrated R & Rw factors (=>don't care about peak profiles) NOT IMPLEMENTED yet. Requires delicate tuning for the width of integration. | |||
CrystVector_int | mScalableComponentIndex | ||
To compute scale factors, which are the components (phases) that can be scaled ? | |||
CrystMatrix_double | mFitScaleFactorM | ||
Used to fit the components' scale factors. | |||
CrystMatrix_double | mFitScaleFactorB | ||
Used to fit the components' scale factors. | |||
CrystMatrix_double | mFitScaleFactorX | ||
Used to fit the components' scale factors. | |||
bool | mUseOnlyLowAngleData | ||
Flag forcing the use of only low-angle reflections. More... | |||
double | mUseOnlyLowAngleDataLimit | ||
Limit (theta angle, in radian) for the above option. More... |
This can also be used for simulation, using a fake Iobs. Supports multiple phases.
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Add a component (phase, backround) to this spectrum. It must have been allocated in the heap. The spectrum parameters (2theta min, step, nbpoints, wavelength, radiation type) of the component are automatically changed to that of the PowderPattern object. |
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Return conventionnal Chi^2.
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Unweighted R-factor.
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Get the weighted R-factor.
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Import file with 2 columns 2Theta Iobs.
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Import file with 3 columns 2Theta Iobs Sigma.
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Import fullprof-style diffraction data.
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Import *.cpi Sietronics diffraction data.
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Import *.xdd diffraction data (Topas,...).
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Save powder spectrum to one file, text format, 3 columns theta Iobs Icalc.If Iobs is missing, the column is omitted. position for all phases...
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Set observed powder spectrum from vector array. Note: powder spectrum parameters must have been set before calling this function, for example by calling DiffractionDataPowder::InitPowderPatternPar(). |
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\briefSet the powder spectrum angular range & resolution parameter. this will affect all components (phases) of the spectrum. Use this with caution, as the number of points must be correct with respect to the observed data (Iobs).
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Set an option so that only low-amgle reflections (theta < angle) are used. See DiffractionData::mUseOnlyLowAngleData
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Set the wavelength of the experiment to that of an X-Ray tube.
NOTE : if the name of the wavelength is generic (eg"Cu"), then the program considers that there are both Alpha1 and Alpha2, and thus automatically changes the WavelengthType to WAVELENGTH_ALPHA12. If instead either alpha1 or alpha2 (eg "CuA1") is asked for, the WavelengthType is set to WAVELENGTH_MONOCHROMATIC. In both cases, the radiation type is set to X-Ray. |
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Input From stream.
Reimplemented from ObjCryst::RefinableObj. |
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Output to stream in well-formed XML.
Reimplemented from ObjCryst::RefinableObj. |
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Flag forcing the use of only low-angle reflections. Mainly for use during global optimizations, or more generally when the program is far from the real structure. In this case high-angle reflection are not significant and only lead to slower calculations and also in fooling the optimization (bad agreement at low angle and good with the more numerous high-angle reflections). By default this is set to false. Practically, this means that any reflections below the limit is simply ignored, not calculated, not taken into account in statistics.
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Limit (theta angle, in radian) for the above option.
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