ObjCryst++
1.5CVS
|
Class to compute structure factors for a set of reflections and a Crystal. More...
Public Member Functions | |
ScatteringData (const ScatteringData &old) | |
virtual ScatteringData * | CreateCopy () const =0 |
So-called virtual copy constructor. | |
virtual void | SetHKL (const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l) |
input H,K,L | |
virtual void | GenHKLFullSpace2 (const REAL maxsithsl, const bool unique=false) |
Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. | |
virtual void | GenHKLFullSpace (const REAL maxTheta, const bool unique=false) |
Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. | |
RadiationType | GetRadiationType () const |
Neutron or x-ray experiment ? Wavelength ? | |
virtual const Radiation & | GetRadiation () const =0 |
Get the radiation object for this data. | |
virtual void | SetCrystal (Crystal &crystal) |
Set the crystal for this experiment. | |
const Crystal & | GetCrystal () const |
Const access to the data's crystal. | |
Crystal & | GetCrystal () |
Access to the data's crystal. | |
long | GetNbRefl () const |
Return the number of reflections in this experiment. | |
const CrystVector_REAL & | GetH () const |
Return the 1D array of H coordinates for all reflections. | |
const CrystVector_REAL & | GetK () const |
Return the 1D array of K coordinates for all reflections. | |
const CrystVector_REAL & | GetL () const |
Return the 1D array of L coordinates for all reflections. | |
const CrystVector_REAL & | GetH2Pi () const |
Return the 1D array of H coordinates for all reflections, multiplied by 2*pi. | |
const CrystVector_REAL & | GetK2Pi () const |
Return the 1D array of K coordinates for all reflections, multiplied by 2*pi. | |
const CrystVector_REAL & | GetL2Pi () const |
Return the 1D array of L coordinates for all reflections, multiplied by 2*pi. | |
const CrystVector_REAL & | GetReflX () const |
Return the 1D array of orthonormal x coordinates for all reflections (recipr. space) | |
const CrystVector_REAL & | GetReflY () const |
Return the 1D array of orthonormal y coordinates for all reflections (recipr. space) | |
const CrystVector_REAL & | GetReflZ () const |
Return the 1D array of orthonormal z coordinates for all reflections (recipr. space) | |
const CrystVector_REAL & | GetSinThetaOverLambda () const |
Return an array with ![]() | |
const CrystVector_REAL & | GetTheta () const |
Return an array with theta values for all reflections. | |
const RefinableObjClock & | GetClockTheta () const |
Clock the last time the sin(theta)/lambda and theta arrays were re-computed. | |
const CrystVector_REAL & | GetFhklCalcSq () const |
Returns the Array of calculated |F(hkl)|^2 for all reflections. | |
const CrystVector_REAL & | GetFhklCalcReal () const |
Access to real part of F(hkl)calc. | |
const CrystVector_REAL & | GetFhklCalcImag () const |
Access to imaginary part of F(hkl)calc. | |
const CrystVector_REAL & | GetFhklObsSq () const |
Returns the Array of observed |F(hkl)|^2 for all reflections. | |
const map< const ScatteringPower *, CrystVector_REAL > & | GetScatteringFactor () const |
Scattering factors for each ScatteringPower, as vectors with NbRefl elements. | |
CrystVector_REAL | GetWavelength () const |
wavelength of the experiment (in Angstroems) | |
void | SetIsIgnoringImagScattFact (const bool b) |
If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. | |
bool | IsIgnoringImagScattFact () const |
If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. | |
virtual void | PrintFhklCalc (ostream &os=cout) const |
Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections. | |
virtual void | PrintFhklCalcDetail (ostream &os=cout) const |
Print H, K, L sin(theta)/lambda theta F^2 Re(F) Im(F) [Re(F) Im(F)]_i, where [Re(F) Im(F)]_i are the real and imaginary contribution of the different scattering powers to the overall structure factor. | |
virtual void | BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false) |
This should be called by any optimization class at the begining of an optimization. | |
virtual void | EndOptimization () |
This should be called by any optimization class at the end of an optimization. | |
virtual void | SetApproximationFlag (const bool allow) |
Enable or disable numerical approximations. | |
virtual void | SetMaxSinThetaOvLambda (const REAL max) |
Set the maximum value for sin(theta)/lambda. | |
REAL | GetMaxSinThetaOvLambda () const |
Get the maximum value for sin(theta)/lambda. | |
virtual long | GetNbReflBelowMaxSinThetaOvLambda () const |
Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set. | |
const RefinableObjClock & | GetClockNbReflBelowMaxSinThetaOvLambda () const |
Clock the last time the number of reflections used was changed. | |
![]() | |
RefinableObj () | |
Constructor. | |
RefinableObj (const bool internalUseOnly) | |
Constructor. | |
RefinableObj (const RefinableObj &old) | |
Defined not implemented... | |
virtual | ~RefinableObj () |
Destructor. | |
virtual const string & | GetClassName () const |
Name for this class ("RefinableObj", "Crystal",...). | |
virtual const string & | GetName () const |
Name of the object. | |
virtual void | SetName (const string &name) |
Name of the object. | |
void | operator= (const RefinableObj &old) |
Defined not implemented... | |
void | PrepareForRefinement () const |
Find which parameters are used and not fixed, for a refinement /optimization. | |
void | FixAllPar () |
Fix All parameters. | |
void | UnFixAllPar () |
UnFix All parameters. | |
void | SetParIsFixed (const long parIndex, const bool fix) |
Fix/un-fix one parameter from its #. | |
void | SetParIsFixed (const string &parName, const bool fix) |
Fix/un-fix one parameter from its name. | |
void | SetParIsFixed (const RefParType *type, const bool fix) |
Fix/un-fix one family of parameters. | |
void | SetParIsUsed (const string &parName, const bool use) |
Set whether a parameter is used. | |
void | SetParIsUsed (const RefParType *type, const bool use) |
Set whether a family of parameters is used. | |
long | GetNbPar () const |
Total number of refinable parameter in the object. | |
long | GetNbParNotFixed () const |
Total number of non-fixed parameters. Is initialized by PrepareForRefinement() | |
RefinablePar & | GetPar (const long i) |
Access all parameters in the order they were inputted. | |
const RefinablePar & | GetPar (const long i) const |
Access all parameters in the order they were inputted. | |
RefinablePar & | GetPar (const string &name) |
Access all parameters from their name. | |
const RefinablePar & | GetPar (const string &name) const |
Access all parameters from their name. | |
RefinablePar & | GetPar (const REAL *) |
Access parameter from its adress. | |
const RefinablePar & | GetPar (const REAL *) const |
Access parameter from its adress. | |
long | GetParIndex (const string &name, const bool nothrow=false) const |
Get a parameter index (the order it was inputted) from its name. | |
long | GetParIndex (const REAL *, const bool nothrow=false) const |
Get a parameter index (the order it was inputted) from its adress. | |
RefinablePar & | GetParNotFixed (const long i) |
Access all parameters in the order they were inputted, skipping fixed parameters. | |
const RefinablePar & | GetParNotFixed (const long i) const |
Access all parameters in the order they were inputed, skipping fixed parameters. | |
void | AddPar (const RefinablePar &newRefPar) |
Add a refinable parameter. | |
void | AddPar (RefinablePar *newRefPar) |
Add a refinable parameter. | |
void | AddPar (RefinableObj &newRefParList, const bool copyParam=false) |
Add all the parameters in another RefinableObj. | |
vector< RefinablePar * >::iterator | RemovePar (RefinablePar *refPar) |
Remove a refinable parameter. | |
virtual void | Print () const |
unsigned long | CreateParamSet (const string name="") const |
Save the current set of refined values in a new set. | |
void | ClearParamSet (const unsigned long id) const |
Erase the param set with the given id, releasing memory. | |
void | SaveParamSet (const unsigned long id) const |
Save the current set of refined values over a previously-created set *of saved values. | |
void | RestoreParamSet (const unsigned long id) |
Restore a saved set of values. | |
const CrystVector_REAL & | GetParamSet (const unsigned long setId) const |
Access one save refpar set. | |
CrystVector_REAL & | GetParamSet (const unsigned long setId) |
Access one save refpar set. | |
REAL | GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const |
Access the (human) value of one refined parameter in a saved set of parameters. | |
const void | EraseAllParamSet () |
Erase all saved refpar sets. | |
const string & | GetParamSetName (const unsigned long setId) const |
Get the name associated to a refpar set. | |
void | SetLimitsAbsolute (const string &parName, const REAL min, const REAL max) |
Change the limits for a given parameter, giving absolute new limits. | |
void | SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max) |
Change the limits for a category of parameters, giving absolute new limits. | |
void | SetLimitsRelative (const string &parName, const REAL min, const REAL max) |
Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. | |
void | SetLimitsRelative (const RefParType *type, const REAL min, const REAL max) |
Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). | |
void | SetLimitsProportional (const string &parName, const REAL min, const REAL max) |
Change the limits for a given parameter, proportionnaly to the current value. | |
void | SetLimitsProportional (const RefParType *type, const REAL min, const REAL max) |
Change the limits for a category of parameters, proportionnaly to their current value. | |
void | SetGlobalOptimStep (const RefParType *type, const REAL step) |
Change the maximum step to use during Global Optimization algorithms. | |
ObjRegistry< RefinableObj > & | GetSubObjRegistry () |
Access to the registry of RefinableObj used by this object. | |
const ObjRegistry< RefinableObj > & | GetSubObjRegistry () const |
Access to the registry of RefinableObj used by this object. | |
virtual void | RegisterClient (RefinableObj &) const |
Register a new object using this object. | |
virtual void | DeRegisterClient (RefinableObj &) const |
Deregister an object (which not any more) using this object. | |
virtual const ObjRegistry < RefinableObj > & | GetClientRegistry () const |
Get the list of clients. | |
virtual ObjRegistry < RefinableObj > & | GetClientRegistry () |
Get the list of clients. | |
bool | IsBeingRefined () const |
Is the object being refined ? (Can be refined by one algorithm at a time only.) | |
virtual void | RandomizeConfiguration () |
Randomize Configuration (before a global optimization). | |
virtual void | GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst) |
Make a random move of the current configuration. | |
void | BeginGlobalOptRandomMove () |
Raise a flag, to be sure not to make a random change more than once in each RefinableObj. | |
virtual REAL | GetLogLikelihood () const |
Get -log(likelihood) of the current configuration for the object. | |
virtual unsigned int | GetNbLSQFunction () const |
Number of LSQ functions. | |
virtual const CrystVector_REAL & | GetLSQCalc (const unsigned int) const |
Get the current calculated value for the LSQ function. | |
virtual const CrystVector_REAL & | GetLSQObs (const unsigned int) const |
Get the observed values for the LSQ function. | |
virtual const CrystVector_REAL & | GetLSQWeight (const unsigned int) const |
Get the weight values for the LSQ function. | |
virtual const CrystVector_REAL & | GetLSQDeriv (const unsigned int, RefinablePar &) |
Get the first derivative values for the LSQ function, for a given parameter. | |
void | ResetParList () |
Re-init the list of refinable parameters, removing all parameters. | |
virtual void | XMLOutput (ostream &os, int indent=0) const |
Output to stream in well-formed XML. | |
virtual void | XMLInput (istream &is, const XMLCrystTag &tag) |
Input From stream. | |
virtual void | UpdateDisplay () const |
If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. | |
unsigned int | GetNbOption () const |
Number of Options for this object. | |
RefObjOpt & | GetOption (const unsigned int i) |
Access to the options. | |
const RefObjOpt & | GetOption (const unsigned int i) const |
const access to the options | |
virtual void | GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const |
Get the gene group assigned to each parameter. | |
void | SetDeleteRefParInDestructor (const bool b) |
Set this object not to delete its list of parameters when destroyed. | |
const RefinableObjClock & | GetRefParListClock () const |
What was the last time a RefinablePar was added/removed ? | |
virtual REAL | GetRestraintCost () const |
Get the restraint cost (overall penalty of all restraints) | |
void | AddRestraint (Restraint *pNewRestraint) |
Add a new restraint. | |
vector< Restraint * >::iterator | RemoveRestraint (Restraint *pRestraint) |
Remove a restraint from the list of known restraints. | |
virtual void | TagNewBestConfig () const |
During a global optimization, tells the object that the current config is the latest "best" config. | |
const RefinableObjClock & | GetClockMaster () const |
This clocks records any change in the object. See refinableObj::mClockMaster. |
Protected Member Functions | |
virtual void | PrepareHKLarrays () |
virtual CrystVector_long | SortReflectionBySinThetaOverLambda (const REAL maxSTOL=-1.) |
CrystVector_long | EliminateExtinctReflections () |
virtual void | CalcSinThetaLambda () const |
void | CalcScattFactor () const |
void | CalcTemperatureFactor () const |
virtual void | CalcResonantScattFactor () const |
void | CalcGlobalTemperatureFactor () const |
Compute the overall temperature factor affecting all reflections. | |
void | CalcStructFactor () const |
Compute the overall structure factor (real and imaginary part). | |
void | CalcGeomStructFactor () const |
Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal. | |
void | CalcLuzzatiFactor () const |
Calculate the Luzzati factor associated to each ScatteringPower and each reflection, for maximum likelihood optimization. | |
void | CalcStructFactVariance () const |
Calculate the variance associated to the calculated structure factor. | |
![]() | |
long | FindPar (const string &name) const |
Find a refinable parameter with a given name. | |
long | FindPar (const REAL *) const |
Find a refinable parameter from the adress of its value. | |
void | AddSubRefObj (RefinableObj &) |
void | RemoveSubRefObj (RefinableObj &) |
void | AddOption (RefObjOpt *opt) |
virtual void | Prepare () |
map< unsigned long, pair < CrystVector_REAL, string > >::iterator | FindParamSet (unsigned long id) const |
Find a parameter set with a given id (and check if it is there) |
Protected Attributes | |
long | mNbRefl |
Number of H,K,L reflections. | |
CrystVector_REAL | mH |
H,K,L coordinates. | |
CrystVector_REAL | mK |
CrystVector_REAL | mL |
CrystVector_long | mIntH |
H,K,L integer coordinates. | |
CrystVector_long | mIntK |
CrystVector_long | mIntL |
CrystVector_REAL | mH2Pi |
H,K,L coordinates, multiplied by 2PI. | |
CrystVector_REAL | mK2Pi |
CrystVector_REAL | mL2Pi |
CrystVector_REAL | mX |
reflection coordinates in an orthonormal base | |
CrystVector_REAL | mY |
CrystVector_REAL | mZ |
CrystVector_int | mMultiplicity |
Multiplicity for each reflections (mostly for powder diffraction) | |
CrystVector_int | mExpectedIntensityFactor |
Expected intensity factor for all reflections. | |
CrystVector_REAL | mFhklCalcReal |
real &imaginary parts of F(HKL)calc | |
CrystVector_REAL | mFhklCalcImag |
CrystVector_REAL | mFhklCalcSq |
F(HKL)^2 calc for each reflection. | |
Crystal * | mpCrystal |
Pointer to the crystal corresponding to this experiment. | |
REAL | mGlobalBiso |
Global Biso, affecting the overall structure factor for all reflections (but not the structure factors of individual atoms or type of atomes). | |
CrystVector_REAL | mGlobalTemperatureFactor |
Global Biso factor. | |
bool | mUseFastLessPreciseFunc |
Use faster, but less precise, approximations for functions? (integer *approximations to compute sin and cos in structure factors, and also *to compute interatomic distances). | |
CrystVector_REAL | mSinThetaLambda |
![]() | |
CrystVector_REAL | mTheta |
theta for the crystal and the HKL in ReciprSpace (in radians) | |
map< const ScatteringPower *, REAL > | mvFprime |
Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value. | |
map< const ScatteringPower *, REAL > | mvFsecond |
map< const ScatteringPower *, CrystVector_REAL > | mvTemperatureFactor |
Thermic factors for each ScatteringPower, as vectors with NbRefl elements. | |
map< const ScatteringPower *, CrystVector_REAL > | mvScatteringFactor |
Scattering factors for each ScatteringPower, as vectors with NbRefl elements. | |
map< const ScatteringPower *, CrystVector_REAL > | mvRealGeomSF |
Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements. | |
map< const ScatteringPower *, CrystVector_REAL > | mvImagGeomSF |
RefinableObjClock | mClockHKL |
Clock for the list of hkl. | |
RefinableObjClock | mClockStructFactor |
Clock for the structure factor. | |
RefinableObjClock | mClockStructFactorSq |
Clock for the square modulus of the structure factor. | |
RefinableObjClock | mClockTheta |
Clock the last time theta was computed. | |
RefinableObjClock | mClockScattFactor |
Clock the last time scattering factors were computed. | |
RefinableObjClock | mClockScattFactorResonant |
Clock the last time resonant scattering factors were computed. | |
RefinableObjClock | mClockGeomStructFact |
Clock the last time the geometrical structure factors were computed. | |
RefinableObjClock | mClockThermicFact |
Clock the last time temperature factors were computed. | |
RefinableObjClock | mClockGlobalBiso |
last time the global Biso factor was modified | |
RefinableObjClock | mClockGlobalTemperatureFact |
last time the global temperature factor was computed | |
bool | mIgnoreImagScattFact |
Ignore imaginary part of scattering factor. | |
REAL | mMaxSinThetaOvLambda |
Maximum sin(theta)/lambda for all calculations (10 by default). | |
long | mNbReflUsed |
Number of reflections which are below the max. | |
RefinableObjClock | mClockNbReflUsed |
Clock recording the last time the number of reflections used has increased. | |
map< const ScatteringPower *, CrystVector_REAL > | mvLuzzatiFactor |
The Luzzati 'D' factor for each scattering power and each reflection. | |
CrystVector_REAL | mFhklCalcVariance |
The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor. | |
RefinableObjClock | mClockLuzzatiFactor |
RefinableObjClock | mClockFhklCalcVariance |
CrystVector_REAL | mFhklObsSq |
Observed squared structure factors (zero-sized if none) | |
RefinableObjClock | mClockFhklObsSq |
Last time observed squared structure factors were altered. | |
![]() | |
string | mName |
Name for this RefinableObject. Should be unique, at least in the same scope.+. | |
vector< RefinablePar * > | mvpRefPar |
Vector of pointers to the refinable parameters. | |
vector< Restraint * > | mvpRestraint |
Vector of pointers to the restraints for this object. | |
map< unsigned long, pair < CrystVector_REAL, string > > | mvpSavedValuesSet |
Map of (index,pointers to arrays) used to save sets of values for all parameters. | |
long | mNbRefParNotFixed |
Total of not-fixed parameters. | |
CrystVector_long | mRefparNotFixedIndex |
Index of not-fixed parameters. | |
int | mOptimizationDepth |
Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. | |
ObjRegistry< RefinableObj > | mSubObjRegistry |
Registry of RefinableObject needed for this object (owned by this object or not) | |
ObjRegistry< RefinableObj > | mClientObjRegistry |
Registry of RefinableObject using this object. | |
ObjRegistry< RefObjOpt > | mOptionRegistry |
List of options for this object. | |
bool | mDeleteRefParInDestructor |
If true (the default), then all RefinablePar will be deleted when the the object is deleted. | |
RefinableObjClock | mRefParListClock |
Last time the RefinableParList was modified (a parameter added or removed). | |
bool | mRandomMoveIsDone |
CrystVector_REAL | mLSQDeriv |
Temporary array used to return derivative values of the LSQ function for given parameters. | |
RefinableObjClock | mClockMaster |
Master clock, which is changed whenever the object has been altered. |
Class to compute structure factors for a set of reflections and a Crystal.
This class only computes structure factor, but no intensity. i.e. it does not include any correction such as absorption, Lorentz or Polarization.
Does this really need to be a RefinableObj ?
|
virtual |
This should be called by any optimization class at the begining of an optimization.
This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.
allowApproximations,: | if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives. |
enableRestraints:\xrefitem | deprecated 28. |
Reimplemented from ObjCryst::RefinableObj.
Reimplemented in ObjCryst::PowderPatternDiffraction.
|
protected |
Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal.
|
protectedvirtual |
get f' and f" for ScatteringPower of the crystal, at the exp. wavelength
This could be specialized for multi-wavelength experiments...
|
protected |
Get scattering factors for all ScatteringPower & reflections
|
protectedvirtual |
Compute sin(theta)/lambda as well a orthonormal coordinates for all reflections. theta and tan(theta), are also re-computed, provided a wavelength has been supplied.
|
protected |
Compute the overall structure factor (real and imaginary part).
*This function is \e optimized \e for \e speed (geometrical structure factors are *computed for all atoms and all reflections in two loops, avoiding re-calculation). *So use this function for repetitive calculations. *This function recognizes the type of radiation (XRay or neutron) and *uses the corresponding scattering factor/length.
|
protected |
Calculate the variance associated to the calculated structure factor.
|
protected |
Compute thermic factors for all ScatteringPower & reflections
|
protected |
Get rid of extinct reflections. Useful after GenHKLFullSpace(). Do not use this if you have a list of observed reflections !
Currently done using (brute-force) numerical evaluation. Should rather use SpaceGroup info... To do !
|
virtual |
This should be called by any optimization class at the end of an optimization.
This also affects all sub-objects.
Reimplemented from ObjCryst::RefinableObj.
Reimplemented in ObjCryst::PowderPatternDiffraction.
|
virtual |
Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.
maxsithsl:maximum | sin(theta)/lambda=1/2d value |
unique,: | if set to true, only unique reflections will be listed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor. |
The multiplicity is always stored in ScatteringData::mMultiplicity.
|
virtual |
Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value.
maxTheta:maximum | theta value |
unique,: | if set to true, only unique reflections will be listed. Bijvoet (Friedel) pairs are NOT merged, for 'anomalous' reasons, unless you have chosen to ignore the imaginary part of the scattering factor. |
The multiplicity is always stored in ScatteringData::mMultiplicity.
const CrystVector_REAL& ObjCryst::ScatteringData::GetH2Pi | ( | ) | const |
Return the 1D array of H coordinates for all reflections, multiplied by 2*pi.
Should be private
const CrystVector_REAL& ObjCryst::ScatteringData::GetK2Pi | ( | ) | const |
Return the 1D array of K coordinates for all reflections, multiplied by 2*pi.
Should be private
const CrystVector_REAL& ObjCryst::ScatteringData::GetL2Pi | ( | ) | const |
Return the 1D array of L coordinates for all reflections, multiplied by 2*pi.
Should be private
|
virtual |
Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set.
Reimplemented in ObjCryst::PowderPatternDiffraction.
bool ObjCryst::ScatteringData::IsIgnoringImagScattFact | ( | ) | const |
If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.
|
protectedvirtual |
This function is called after H,K and L arrays have been initialized or modified.
|
virtual |
Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections.
|
virtual |
Enable or disable numerical approximations.
This can be used for global optimization to get faster calculations. Depending on the type of object, this may do something or not (it does not do anything in a base RefinableObj, except calling this function for all sub-objects).
Also see:
Reimplemented from ObjCryst::RefinableObj.
Reimplemented in ObjCryst::PowderPatternDiffraction.
|
virtual |
|
virtual |
input H,K,L
h,k,l,: | REAL arrays (vectors with NbRefl elements -same size), *with the h, k and l coordinates of all reflections. |
void ObjCryst::ScatteringData::SetIsIgnoringImagScattFact | ( | const bool | b | ) |
If true, then the imaginary part of the scattering factor is ignored during Structure factor computation.
(default value=false)
|
virtual |
Set the maximum value for sin(theta)/lambda.
All data (reflections,..) still exist but are ignored for all calculations.
Reimplemented in ObjCryst::PowderPatternDiffraction.
|
protectedvirtual |
sort reflections by theta values (also get rid of [0,0,0] if present) If maxSTOL >0, then only reflections where sin(theta)/lambda<maxSTOL are kept
Reimplemented in ObjCryst::DiffractionDataSingleCrystal.
|
protected |
Expected intensity factor for all reflections.
|
mutableprotected |
The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor.
Actually this is the variance on both real and imaginary parts.
|
protected |
Ignore imaginary part of scattering factor.
This can be used either to speed up computation, or when f" has a small effect on calculated intensities, mostly for powder diffraction (GenHKLFullSpace will not generate Friedel pairs, reducing the number of reflections by a factor up to 2 for some structures).
Practically this makes f"=0 during computation. The real resonant contribution (f') is not affected.
This may be removed later on...
|
protected |
Maximum sin(theta)/lambda for all calculations (10 by default).
This keeps all data in memory, but only the part which is below the max is calculated.
This affects the computing of structure factors, intensities (for single crystal and powder patterns), R and Rw.
The reflections must be sorted by increasing sin(theta)/lambda for this to work correctly.
|
mutableprotected |
Number of reflections which are below the max.
This is updated automatically from ScatteringData::mMaxSinThetaOvLambda
|
protected |
Pointer to the crystal corresponding to this experiment.
This gives an access to the UB matrix for the crystal, as well as to the list of Scatterer.
|
protected |
Use faster, but less precise, approximations for functions? (integer *approximations to compute sin and cos in structure factors, and also *to compute interatomic distances).
This is activated by global optimization algortithms, only during the optimization.
|
mutableprotected |
Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value.
For multi-wavelength support this should be changed to a vector... or to a matrix to take into account anisotropy of anomalous scattering...