The CIFData class holds all the information from a single data_ block from a cif file. More...

Classes
struct	CIFAtom
	Atom record. More...

Public Member Functions
void	ExtractAll (const bool verbose=false)
	Extract lattice parameters, spacegroup (symbol or number), atomic positions, chemical name and formula if available. More...

void	ExtractName (const bool verbose=false)
	Extract name & formula for the crystal. More...

void	ExtractUnitCell (const bool verbose=false)
	Extract unit cell.

void	ExtractSpacegroup (const bool verbose=false)
	Extract spacegroup number or symbol.

void	ExtractAtomicPositions (const bool verbose=false)
	Extract all atomic positions. More...

void	ExtractAnisotropicADPs (const bool verbose=false)
	Extract anisotropic atomic displacement parameters. Isotropic ADPs.

void	ExtractPowderPattern (const bool verbose=false)
	Extract Powder Diffraction data, with Iobs, sigma(Iobs) and either 2theta or time-of-flight position. More...

void	ExtractSingleCrystalData (const bool verbose=false)
	Extract single crystal data, with Iobs, sigma(Iobs) and h,k,l. More...

void	Cartesian2FractionalCoord ()
	Generate fractional coordinates from cartesian ones for all atoms CIFData::CalcMatrices() must be called first.

void	Fractional2CartesianCoord ()
	Generate cartesian coordinates from fractional ones for all atoms CIFData::CalcMatrices() must be called first.

void	f2c (REAL &x, REAL &y, REAL &z)
	Convert from fractional to cartesian coordinates CIFData::CalcMatrices() must be called first.

void	c2f (REAL &x, REAL &y, REAL &z)
	Convert from cartesia to fractional coordinates CIFData::CalcMatrices() must be called first.

void	CalcMatrices (const bool verbose=false)
	Calculate real space transformation matrices requires unit cell parameters.

Public Attributes
std::list< std::string >	mvComment
	Comments from CIF file, in the order they were read.

std::map< ci_string, std::string >	mvItem
	Individual CIF items.

std::map< std::set< ci_string > , std::map< ci_string, std::vector< std::string > > >	mvLoop
	CIF Loop data.

std::vector< REAL >	mvLatticePar
	Lattice parameters, in ansgtroem and degrees - vector size is 0 if no parameters have been obtained yet. More...

std::string	mSpacegroupNumberIT
	Spacegroup number from International Tables (_space_group_IT_number), or -1.

std::string	mSpacegroupSymbolHall
	Spacegroup Hall symbol (or empty string) (_space_group_name_Hall)

std::string	mSpacegroupHermannMauguin
	Spacegroup Hermann-Mauguin symbol (or empty string) (_space_group_name_H-M_alt)

std::set< string >	mvSymmetry_equiv_pos_as_xyz
	Map of _symmetry_equiv_pos_as_xyz strings.

std::string	mName
	Crystal name. Or empty string if none is available.

std::string	mFormula
	Formula. Or empty string if none is available.

std::vector< CIFAtom >	mvAtom
	Atoms, if any are found.

REAL	mOrthMatrix [3][3]
	Fractionnal2Cartesian matrix.

REAL	mOrthMatrixInvert [3][3]
	Cartesian2Fractionnal matrix.

std::vector< REAL >	mPowderPatternObs
	Powder pattern data.

std::vector< REAL >	mPowderPatternX

std::vector< REAL >	mPowderPatternSigma

CrystVector_long	mH
	Single crystal data.

CrystVector_long	mK

CrystVector_long	mL

CrystVector_REAL	mIobs
	Single crystal data.

CrystVector_REAL	mSigma

WavelengthType	mDataType
	Is this X-Ray 2theta, time-of-flight ?

REAL	mWavelength
	Wavelength.

Detailed Description

The CIFData class holds all the information from a single data_ block from a cif file.

It is a placeholder for all comments, item and loop data, as raw strings copied from a cif file.

It is also used to interpret this data to extract parts of the cif data, i.e. only part of the core cif dictionnary are recognized. CIF tags currently recognized include ("tag1 > tag2" means tag1 is preferred to tag2 when extracting the info, only one is reported):

crystal name: chemical_name_systematic > _chemical_name_mineral > _chemical_name_structure_type > _chemical_name_common
crystal formula: _chemical_formula_analytical > _chemical_formula_structural > _chemical_formula_iupac > _chemical_formula_moiety
unit cell: _cell_length{a,b,c} ; cell_angle{alpha,beta,gamma}
spacegroup number: space_group_IT_number > _symmetry_Int_Tables_number
spacegroup Hall symbol: _space_group_name_Hall > _symmetry_space_group_name_Hall
spacegroup Hermann-Mauguin symbol:_space_group_name_H-M_alt > _symmetry_space_group_name_H-M
atom coordinates: _atom_site_fract{x} ; atom_site_Cartn{x,y,z}
atom occupancy: atom_site_occupancy
atom label & symbol: _atom_site_type_symbol ; _atom_site_label
atom adps: _atom_site_aniso{U,B}_{11,22,33,12,13,23} > atom_site{U,B}_iso_or_equiv

Cartesian coordinates are stored in Angstroems, angles in radians.

To import PowderPattern data, the following tags are used:

observed intensity: pd_meas_counts_total > _pd_meas_intensity_total > _pd_proc_intensity_total > _pd_proc_intensity_net
uncertainty on intensity: deducted from _pd_proc_ls_weight or square root of intensity
coordinates: _pd_proc_2theta_corrected > _pd_meas_angle_2theta > _pd_meas_time_of_flight > _pd_proc_2theta_range{min,max,inc}
intensity normalizer (optional): _pd_meas_intensity_monitor > _pd_meas_step_count_time

If another data field is needed, it is possible to directly access the string data (CIFData::mvComment , CIFData::mvItem and CIFData::mvLoop) to search for the correct tags.

Definition at line 62 of file CIF.h.

Member Function Documentation

void ObjCryst::CIFData::ExtractAll ( const bool verbose = false )

Extract lattice parameters, spacegroup (symbol or number), atomic positions, chemical name and formula if available.

All other data is ignored

Definition at line 26 of file CIF.cpp.

void ObjCryst::CIFData::ExtractAtomicPositions ( const bool verbose = false )

Extract all atomic positions.

Will generate cartesian from fractional coordinates or vice-versa if only cartesian coordinates are available.

Definition at line 233 of file CIF.cpp.

void ObjCryst::CIFData::ExtractName ( const bool verbose = false )

Extract name & formula for the crystal.

Crystal formula

Definition at line 143 of file CIF.cpp.

void ObjCryst::CIFData::ExtractPowderPattern ( const bool verbose = false )

Extract Powder Diffraction data, with Iobs, sigma(Iobs) and either 2theta or time-of-flight position.

Now find the data

Definition at line 468 of file CIF.cpp.

void ObjCryst::CIFData::ExtractSingleCrystalData ( const bool verbose = false )

Extract single crystal data, with Iobs, sigma(Iobs) and h,k,l.

Now find the data

Definition at line 570 of file CIF.cpp.

Member Data Documentation

std::vector<REAL> ObjCryst::CIFData::mvLatticePar

Lattice parameters, in ansgtroem and degrees - vector size is 0 if no parameters have been obtained yet.

Definition at line 111 of file CIF.h.

The documentation for this class was generated from the following files:

Classes

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation