occ::crystal::AsymmetricUnit Struct Reference

A class representing an asymmetric unit of a crystal structure. More...

#include <asymmetric_unit.h>

Public Member Functions
	AsymmetricUnit ()
	Constructs an empty asymmetric unit.
	AsymmetricUnit (const Mat3N &positions, const IVec &atomic_numbers)
	Constructs an asymmetric unit from the given positions and atomic numbers.
	AsymmetricUnit (const Mat3N &positions, const IVec &atomic_numbers, const std::vector< std::string > &labels)
	Constructs an asymmetric unit from the given positions, atomic numbers, and labels.
std::string	chemical_formula () const
	Returns the chemical formula of the asymmetric unit.
Vec	covalent_radii () const
	Returns the covalent radii of the atoms in the asymmetric unit.
Vec	vdw_radii () const
	Returns the van der Waals radii of the atoms in the asymmetric unit.
void	generate_default_labels ()
	Generates default labels for the atoms in the unit cell.
size_t	size () const
	Returns the number of atoms in the unit cell.
void	resize (Eigen::Index n)
	Resize every member to hold n atoms.
bool	is_consistent () const
	Whether every member is sized consistently with the atom count.
void	ensure_consistent ()
	Give any inconsistently sized member its default, sized to the atom count.

Public Attributes
Mat3N	positions
	The positions of the atoms in the unit cell, expressed as a matrix of size (3, n), where n is the number of atoms.
IVec	atomic_numbers
	The atomic numbers of the atoms in the unit cell, expressed as a vector of size n.
Vec	occupations
	The occupations of the atoms in the unit cell, expressed as a vector of size n.
Vec	charges
	The charges of the atoms in the unit cell, expressed as a vector of size n.
Mat6N	adps
	The anisotropic displacement parameters of the atoms in the unit cell, expressed as a (6, N) matrix matrix of columns of (u11, u22, u33, u12, u13, u23)
std::vector< std::string >	labels
	The labels of the atoms in the unit cell, expressed as a vector of strings of size n.

Detailed Description

A class representing an asymmetric unit of a crystal structure.

An asymmetric unit is a building block of a crystal lattice, and it contains a set of atoms with their positions, atomic numbers, occupations, charges, and labels.

Constructor & Destructor Documentation

AsymmetricUnit() [1/3]

occ::crystal::AsymmetricUnit::AsymmetricUnit ( )

inline

Constructs an empty asymmetric unit.

AsymmetricUnit() [2/3]

occ::crystal::AsymmetricUnit::AsymmetricUnit	(	const Mat3N &	positions,
		const IVec &	atomic_numbers
	)

Constructs an asymmetric unit from the given positions and atomic numbers.

Parameters

positions	The positions of the atoms in the unit cell, 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.
atomic_numbers	The atomic numbers of the atoms in the unit cell, expressed as a vector of size n.

AsymmetricUnit() [3/3]

occ::crystal::AsymmetricUnit::AsymmetricUnit	(	const Mat3N &	positions,
		const IVec &	atomic_numbers,
		const std::vector< std::string > &	labels
	)

Constructs an asymmetric unit from the given positions, atomic numbers, and labels.

Parameters

positions	The positions of the atoms in the unit cell, 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.
atomic_numbers	The atomic numbers of the atoms in the unit cell, expressed as a vector of size n.
labels	The labels of the atoms in the unit cell, expressed as a vector of strings of size n. Each string represents the label of the corresponding atom.

Member Function Documentation

chemical_formula()

std::string occ::crystal::AsymmetricUnit::chemical_formula

(

)

const

Returns the chemical formula of the asymmetric unit.

The chemical formula is a string that represents the composition of the unit cell, using the symbols of the chemical elements. For example, "H2O" or "CuZn"

Returns

The chemical formula of the asymmetric unit.

covalent_radii()

Vec occ::crystal::AsymmetricUnit::covalent_radii

(

)

const

Returns the covalent radii of the atoms in the asymmetric unit.

The covalent radii of an atom is a measure of the size of its atomic nucleus, and it is typically used to calculate the distances between atoms in a molecule.

Returns

A vector of size n containing the covalent radii of the atoms in the unit cell, in the same order as their atomic numbers.

ensure_consistent()

void occ::crystal::AsymmetricUnit::ensure_consistent

(

)

Give any inconsistently sized member its default, sized to the atom count.

Idempotent, and a no-op when the asymmetric unit is already consistent. Because the members are public, code can build an AsymmetricUnit by default-constructing it and resizing only the members it cares about; this restores the invariant that the rest of the library relies on. Crystal calls it on construction.

Does not touch a member that is already correctly sized, so real data is never overwritten.

generate_default_labels()

void occ::crystal::AsymmetricUnit::generate_default_labels

(

)

Generates default labels for the atoms in the unit cell.

The default labels are assigned based on the chemical element of each atom, using the standard one- or two-letter symbol followed by a number. For example, "C1", "N2", "Fe3".

is_consistent()

bool occ::crystal::AsymmetricUnit::is_consistent

(

)

const

Whether every member is sized consistently with the atom count.

resize()

void occ::crystal::AsymmetricUnit::resize

(

Eigen::Index

n

)

Resize every member to hold n atoms.

Members that carry no information of their own are given their neutral default: occupancy 1, charge 0, zero ADPs. Labels are cleared, since a meaningful default needs the atomic numbers – call generate_default_labels() after filling those in.

Prefer this over resizing positions and atomic_numbers by hand: the members are public, so a partial resize silently leaves the rest inconsistent, and consumers then index out of bounds.

size()

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

inline

Returns the number of atoms in the unit cell.

Returns

The size of the unit cell, i.e., the number of atoms it contains.

vdw_radii()

Vec occ::crystal::AsymmetricUnit::vdw_radii

(

)

const

Returns the van der Waals radii of the atoms in the asymmetric unit.

Returns

A vector of size n containing the van der Waals radii of the atoms in the unit cell, in the same order as their atomic numbers.

Member Data Documentation

adps

Mat6N occ::crystal::AsymmetricUnit::adps

The anisotropic displacement parameters of the atoms in the unit cell, expressed as a (6, N) matrix matrix of columns of (u11, u22, u33, u12, u13, u23)

atomic_numbers

IVec occ::crystal::AsymmetricUnit::atomic_numbers

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

charges

Vec occ::crystal::AsymmetricUnit::charges

The charges of the atoms in the unit cell, expressed as a vector of size n.

labels

std::vector<std::string> occ::crystal::AsymmetricUnit::labels

The labels of the atoms in the unit cell, expressed as a vector of strings of size n.

Each string represents the label of the corresponding atom.

occupations

Vec occ::crystal::AsymmetricUnit::occupations

The occupations of the atoms in the unit cell, expressed as a vector of size n.

positions

Mat3N occ::crystal::AsymmetricUnit::positions

The positions of the atoms in the unit cell, 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.

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The documentation for this struct was generated from the following file:

• /home/runner/work/occ/occ/include/occ/crystal/asymmetric_unit.h