A class representing a region of atoms in a crystal lattice. More...

#include <crystal.h>

Public Member Functions
void	resize (size_t n)
	Resizes the region to contain the given number of atoms.

size_t	size () const

Public Attributes
Mat3N	frac_pos
	The fractional coordinates of the atoms in the region, expressed as a matrix of size (3, n), where n is the number of atoms.

Mat3N	cart_pos
	The cartesian coordinates of the atoms in the region, expressed as a matrix of size (3, n), where n is the number of atoms.

IVec	asym_idx
	The indices of the asymmetric units containing the atoms in the region, expressed as a vector of size n.

IVec	uc_idx
	The indices of the uc units containing the atoms in the region, expressed as a vector of size n.

IMat3N	hkl
	The cell index of this atom.

IVec	atomic_numbers
	The atomic numbers of the atoms in the region, expressed as a vector of size n.

IVec	symop
	The symmetry operations applied to the atoms in the region, expressed as a vector of size n.

IVec	disorder_group
	Disorder group.

Detailed Description

A class representing a region of atoms in a crystal lattice.

A crystal atom region is a collection of atoms in a crystal lattice, characterized by their fractional and cartesian coordinates, their atomic numbers, and their symmetry operations.

Member Function Documentation

◆ resize()

void occ::crystal::CrystalAtomRegion::resize ( size_t n )

inline

Resizes the region to contain the given number of atoms.

Parameters

n	The new size of the region, i.e., the number of atoms it will contain.

◆ size()

size_t occ::crystal::CrystalAtomRegion::size ( ) const

inline

/fitting/fit.py

Returns the number of atoms in the region.

Returns: The size of the region, i.e., the number of atoms it contains.

Member Data Documentation

◆ asym_idx

IVec occ::crystal::CrystalAtomRegion::asym_idx

The indices of the asymmetric units containing the atoms in the region, expressed as a vector of size n.

Each element of the vector represents the index of the asymmetric unit that contains the corresponding atom.

◆ atomic_numbers

IVec occ::crystal::CrystalAtomRegion::atomic_numbers

The atomic numbers of the atoms in the region, expressed as a vector of size n.

◆ cart_pos

Mat3N occ::crystal::CrystalAtomRegion::cart_pos

The cartesian coordinates of the atoms in the region, expressed as a matrix of size (3, n), where n is the number of atoms.

Each column of the matrix represents the (x, y, z) coordinates of an atom, expressed in angstroms.

◆ disorder_group

IVec occ::crystal::CrystalAtomRegion::disorder_group

Disorder group.

◆ frac_pos

Mat3N occ::crystal::CrystalAtomRegion::frac_pos

The fractional coordinates of the atoms in the region, expressed as a matrix of size (3, n), where n is the number of atoms.

Each column of the matrix represents the (x, y, z) coordinates of an atom, expressed as a fraction of the unit cell dimensions.

◆ hkl

IMat3N occ::crystal::CrystalAtomRegion::hkl

The cell index of this atom.

◆ symop

IVec occ::crystal::CrystalAtomRegion::symop

The symmetry operations applied to the atoms in the region, expressed as a vector of size n.

Each element of the vector represents the symmetry operation that maps the corresponding atom to its equivalent position in the unit cell.

◆ uc_idx

IVec occ::crystal::CrystalAtomRegion::uc_idx

The indices of the uc units containing the atoms in the region, expressed as a vector of size n.