FOX/ObjCryst++
1.10.X (development)
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The basic atom scatterer, in a crystal. More...
Public Member Functions | |
Atom () | |
Default constructor. More... | |
Atom (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow) | |
Atom constructor. More... | |
Atom (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow, const REAL popu) | |
Atom constructor. More... | |
Atom (const Atom &old) | |
Copy constructor. | |
virtual Atom * | CreateCopy () const |
~Atom () | |
Destructor... | |
virtual const string & | GetClassName () const |
Name for this class ("RefinableObj", "Crystal",...). More... | |
virtual void | operator= (const Atom &rhs) |
void | Init (const REAL x, const REAL y, const REAL z, const string &name, const ScatteringPower *pow, const REAL popu=1) |
initialize the atom (used for arrays of atoms). More... | |
virtual int | GetNbComponent () const |
Number of components in the scatterer (eg number of point scatterers) | |
virtual const ScatteringComponentList & | GetScatteringComponentList () const |
Get the list of all scattering components for this scatterer. More... | |
virtual string | GetComponentName (const int i) const |
Name for the i-th component of this scatterer. More... | |
virtual void | Print () const |
Print some info about the scatterer (ideally this should be one line...). | |
REAL | GetMass () const |
Returns the molar mass of the atom. More... | |
REAL | GetRadius () const |
Returns the radius (in Angstroems) of the atom. More... | |
virtual ostream & | POVRayDescription (ostream &os, const CrystalPOVRayOptions &options) const |
XMLOutput a description of the scatterer for POVRay. More... | |
virtual void | GLInitDisplayList (const bool onlyIndependentAtoms=false, const REAL xMin=-.1, const REAL xMax=1.1, const REAL yMin=-.1, const REAL yMax=1.1, const REAL zMin=-.1, const REAL zMax=1.1, const bool displayEnantiomer=false, const bool displayNames=false, const bool hideHydrogens=false) const |
bool | IsDummy () const |
Is this a dummy atom ? (ie no ScatteringPower) Dummy atoms should not exist ! | |
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... | |
const ScatteringPower & | GetScatteringPower () const |
Get the ScatteringPowerAtom corresponding to this atom. | |
virtual void | GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const |
Get the gene group assigned to each parameter. More... | |
Public Member Functions inherited from ObjCryst::Scatterer | |
Scatterer () | |
Constructor. | |
Scatterer (const Scatterer &old) | |
Copy Constructor. | |
virtual | ~Scatterer () |
Destructor. | |
REAL | GetX () const |
X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
REAL | GetY () const |
Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
REAL | GetZ () const |
Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
REAL | GetOccupancy () const |
Get the occupancy of the scatterer (0. More... | |
virtual void | SetX (const REAL x) |
X coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
virtual void | SetY (const REAL y) |
Y coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
virtual void | SetZ (const REAL z) |
Z coordinate (fractionnal) of the scatterer (for complex scatterers, this corresponds to the position of one atom of the Scatterer, ideally it should be near the center of the Scatterer. More... | |
virtual void | SetOccupancy (const REAL occupancy) |
Change the occupancy of the scatterer (0. More... | |
operator string () const | |
Conversion function. More... | |
virtual const string & | GetColour () const |
Colour associated to this scatterer (using POVRay names) More... | |
virtual const float * | GetColourRGB () const |
Colour associated to this scatterer, 3 RGB Coordinates. | |
const RefinableObjClock & | GetClockScatterer () const |
Last time anything in the scatterer was changed (atoms, positions, scattering power) | |
RefinableObjClock & | GetClockScatterer () |
Last time anything in the scatterer was changed (atoms, positions, scattering power) | |
void | SetCrystal (Crystal &) |
Set the crystal in which is included this Scatterer. | |
const Crystal & | GetCrystal () const |
In which crystal is this Scatterer included ? | |
Crystal & | GetCrystal () |
In which crystal is this Scatterer included ? | |
Public Member Functions inherited from ObjCryst::RefinableObj | |
RefinableObj () | |
Constructor. | |
RefinableObj (const bool internalUseOnly) | |
Constructor. More... | |
RefinableObj (const RefinableObj &old) | |
Defined not implemented... More... | |
virtual | ~RefinableObj () |
Destructor. | |
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... More... | |
void | PrepareForRefinement () const |
Find which parameters are used and not fixed, for a refinement /optimization. More... | |
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. More... | |
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. | |
RefinablePar & | GetParNotFixed (const long i) |
Access all parameters in the order they were inputted, skipping fixed parameters. More... | |
const RefinablePar & | GetParNotFixed (const long i) const |
Access all parameters in the order they were inputed, skipping fixed parameters. More... | |
void | AddPar (const RefinablePar &newRefPar) |
Add a refinable parameter. More... | |
void | AddPar (RefinablePar *newRefPar) |
Add a refinable parameter. More... | |
void | AddPar (RefinableObj &newRefParList, const bool copyParam=false) |
Add all the parameters in another RefinableObj. More... | |
vector< RefinablePar * >::iterator | RemovePar (RefinablePar *refPar) |
Remove a refinable parameter. More... | |
unsigned long | CreateParamSet (const string name="") const |
Save the current set of refined values in a new set. More... | |
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. More... | |
void | RestoreParamSet (const unsigned long id) |
Restore a saved set of values. More... | |
const CrystVector_REAL & | GetParamSet (const unsigned long setId) const |
Access one save refpar set. More... | |
CrystVector_REAL & | GetParamSet (const unsigned long setId) |
Access one save refpar set. More... | |
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. More... | |
const void | EraseAllParamSet () |
Erase all saved refpar sets. More... | |
const string & | GetParamSetName (const unsigned long setId) const |
Get the name associated to a refpar set. More... | |
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. More... | |
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). More... | |
void | SetLimitsProportional (const string &parName, const REAL min, const REAL max) |
Change the limits for a given parameter, proportionnaly to the current value. More... | |
void | SetLimitsProportional (const RefParType *type, const REAL min, const REAL max) |
Change the limits for a category of parameters, proportionnaly to their current value. More... | |
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. More... | |
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 | BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false) |
This should be called by any optimization class at the begining of an optimization. More... | |
virtual void | EndOptimization () |
This should be called by any optimization class at the end of an optimization. More... | |
virtual void | SetApproximationFlag (const bool allow) |
Enable or disable numerical approximations. More... | |
virtual void | RandomizeConfiguration () |
Randomize Configuration (before a global optimization). More... | |
virtual void | GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst) |
Make a random move of the current configuration. More... | |
void | BeginGlobalOptRandomMove () |
Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More... | |
virtual REAL | GetLogLikelihood () const |
Get -log(likelihood) of the current configuration for the object. More... | |
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. More... | |
virtual std::map< RefinablePar *, CrystVector_REAL > & | GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar) |
Get the first derivative for the LSQ function for each parameter supplied in a list. More... | |
void | ResetParList () |
Re-init the list of refinable parameters, removing all parameters. More... | |
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. More... | |
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 | |
void | SetDeleteRefParInDestructor (const bool b) |
Set this object not to delete its list of parameters when destroyed. More... | |
const RefinableObjClock & | GetRefParListClock () const |
What was the last time a RefinablePar was added/removed ? More... | |
virtual REAL | GetRestraintCost () const |
Get the restraint cost (overall penalty of all restraints) More... | |
void | AddRestraint (Restraint *pNewRestraint) |
Add a new restraint. More... | |
vector< Restraint * >::iterator | RemoveRestraint (Restraint *pRestraint) |
Remove a restraint from the list of known restraints. More... | |
virtual void | TagNewBestConfig () const |
During a global optimization, tells the object that the current config is the latest "best" config. More... | |
const RefinableObjClock & | GetClockMaster () const |
This clocks records any change in the object. See refinableObj::mClockMaster. | |
Private Member Functions | |
virtual void | InitRefParList () |
Prepare refinable parameters for the scatterer object. | |
Private Attributes | |
ScatteringComponentList | mScattCompList |
The list of scattering components. | |
const ScatteringPower * | mpScattPowAtom |
The ScatteringPowerAtom associated to that atom. | |
Additional Inherited Members | |
Protected Member Functions inherited from ObjCryst::Scatterer | |
virtual void | InitRGBColour () |
Get RGB Colour coordinates from Colour Name. More... | |
const RefinableObjClock & | GetClockScattCompList () const |
Last time the ScatteringComponentList was generated. | |
Protected Member Functions inherited from ObjCryst::RefinableObj | |
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 inherited from ObjCryst::Scatterer | |
CrystVector_REAL | mXYZ |
coordinates of the scatterer (or of its center..) | |
REAL | mOccupancy |
Occupancy : 0 <= occ <= 1 For a multi-atom scatterer (polyhedron,..), this is the overall occupancy of the scatterer (affects all components of the scatterer). | |
string | mColourName |
Colour for this scatterer (from POVRay) | |
float | mColourRGB [3] |
Colour for this scatterer using RGB. | |
RefinableObjClock | mClockScatterer |
Last time anything (number of atoms, positions, scattering power) was changed. | |
RefinableObjClock | mClockScattCompList |
Crystal * | mpCryst |
The crystal in which the Scatterer is This is needed so that we can know which scattering powers are available in the crystal, and also to convert fractionnal to orthonormal coordinates (for some scatterers only). More... | |
Protected Attributes inherited from ObjCryst::RefinableObj | |
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. More... | |
map< unsigned long, pair < CrystVector_REAL, string > > | mvpSavedValuesSet |
Map of (index,pointers to arrays) used to save sets of values for all parameters. More... | |
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. More... | |
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. More... | |
ObjRegistry< RefObjOpt > | mOptionRegistry |
List of options for this object. More... | |
bool | mDeleteRefParInDestructor |
If true (the default), then all RefinablePar will be deleted when the the object is deleted. More... | |
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. More... | |
std::map< unsigned int, std::map< RefinablePar *, CrystVector_REAL > > | mLSQ_FullDeriv |
Temporary map to return the derivative of the LSQ function versus a list of parameters. More... | |
RefinableObjClock | mClockMaster |
Master clock, which is changed whenever the object has been altered. More... | |
The basic atom scatterer, in a crystal.
This class records the position of the atom, and has a pointer to its ScatteringPowerAtom.
ObjCryst::Atom::Atom | ( | ) |
Default constructor.
The Atom must be initialized thereafter using Atom::Init()
ObjCryst::Atom::Atom | ( | const REAL | x, |
const REAL | y, | ||
const REAL | z, | ||
const string & | name, | ||
const ScatteringPower * | pow | ||
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Atom constructor.
x,y,z | : fractional coordinates of the atom |
pow | : the ScatteringPower associated to this atom. Must be allocated separately. |
name | : name of the atom ('Ta1','Sm2', 'Tungsten_1'...). The name can have any format but spaces should be avoided. |
ObjCryst::Atom::Atom | ( | const REAL | x, |
const REAL | y, | ||
const REAL | z, | ||
const string & | name, | ||
const ScatteringPower * | pow, | ||
const REAL | popu | ||
) |
Atom constructor.
x,y,z | : fractional coordinates of the atom |
popu | : the population of the atom (0.0->1.0) This should take into account the multiplicity of the atom. For an atom in group P2 and on the 2 axis, this should be set to 0.5, unless you are using the dynamical occupancy correction (recommended for global optimizations). See Crystal::CalcDynPopCorr() and Crystal::mUseDynPopCorr |
pow | : the ScatteringPower associated to this atom. Must be allocated separatly. |
name | : name of the atom ('Ta1','Sm2', 'Tungsten_1'...). The name can have any format but spaces should be avoided (just a precaution) |
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so-called Virtual copy constructor, needed to make copies of arrays of Scatterers
Implements ObjCryst::Scatterer.
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Name for this class ("RefinableObj", "Crystal",...).
This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry
Reimplemented from ObjCryst::Scatterer.
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Name for the i-th component of this scatterer.
If the component is an Atom, Then the name is that of the atom. Else, it is the name of the scatterer plus the component number in the scatterer plus the name of the ScatteringPower.
Implements ObjCryst::Scatterer.
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Get the gene group assigned to each parameter.
Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life.
The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique.
obj | the , supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object. |
groupIndex | a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned). |
firstGroup | this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group. |
Reimplemented from ObjCryst::RefinableObj.
REAL ObjCryst::Atom::GetMass | ( | ) | const |
Returns the molar mass of the atom.
Values are extracted from the 'atominfo' package, which uses data from the CRC Handbook of Chemistry & Physics, 63rd & 70th editions The Mass is actually extracted from the ScatteringPowerAtom.
REAL ObjCryst::Atom::GetRadius | ( | ) | const |
Returns the radius (in Angstroems) of the atom.
Values are extracted from the 'atominfo' package, which uses data from the ICSD/CRYSTIN Manual The Radius is extracted from the ScatteringPowerAtom.
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Get the list of all scattering components for this scatterer.
This is the most important function of this class, giving the list of scattering positions along with the associated ScatteringPower.
Implements ObjCryst::Scatterer.
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Create an OpenGL Display List of the scatterer. This should only be called by a Crystal object.
noSymmetrics | if false (the default), then all symmetrics are shown in the 3D display, within the limits defined by the min/max parameters \ param xMin,xMax,yMin,yMax,zMin,zMax: in fractionnal coordinates, the region in which we want scaterrer to be displayed. The test is made on the center of the scatterer (eg a ZScatterer (molecule) will not be 'cut' on the border). |
displayNames | if true, only the names of the scatterers will be displayed, at the position of the scatterers (to actually see them, they will have to be translated with respect to the drawing of the scatterers). |
hideHydrogens | if true, do not display hydrogens/deuterium and their bonds |
Implements ObjCryst::Scatterer.
void ObjCryst::Atom::Init | ( | const REAL | x, |
const REAL | y, | ||
const REAL | z, | ||
const string & | name, | ||
const ScatteringPower * | pow, | ||
const REAL | popu = 1 |
||
) |
initialize the atom (used for arrays of atoms).
x,y,z | : fractional coordinates of the atom |
pow | : the ScatteringPower associated to this atom. Must be allocated separately. |
name | : name of the atom ('Ta1','Sm2', 'Tungsten_1'...). |
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XMLOutput a description of the scatterer for POVRay.
Implements ObjCryst::Scatterer.
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Input From stream.
Reimplemented from ObjCryst::RefinableObj.
Definition at line 454 of file ObjCryst/IO.cpp.
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Output to stream in well-formed XML.
Reimplemented from ObjCryst::RefinableObj.
Definition at line 423 of file ObjCryst/IO.cpp.