atom.h File Reference

#include <cstdint>
#include <iostream>
#include <set>
#include <vector>
#include <map>
#include <glm/glm.hpp>
#include <element.h>
#include <colour.h>

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Classes
class	Atom
	An atom structure. More...

Functions
std::ostream &	operator<< (std::ostream &o, Atom &atom)
	Print an atom to std::ostream.
glm::vec3	getCenter (const std::vector< Atom > &atoms)
	Calculate the centre of mass.
void	center (std::vector< Atom > &atoms)
	Subtract the centre of mass of some Atoms.
void	centerOn (std::vector< Atom > &atoms, uint64_t index)
	Centre on a particular Atom.
void	translate (std::vector< Atom > &atoms, glm::vec3 r)
glm::vec3	min (const std::vector< Atom > &atoms)
	Calculate the minimum positions of some Atoms.
glm::vec3	max (const std::vector< Atom > &atoms)
	Calculate the maximum positions of some Atoms.
glm::vec3	extent (const std::vector< Atom > &atoms)
	Calculate the extent of some Atoms.
std::set< Element >	uniqueElements (const std::vector< Atom > &atoms)
	Determine the unique elements in a list of Atom.
float	largest (const std::vector< Atom > &atoms)
	Calculate the largest Atom.
std::multimap< Element, uint64_t >	elementIndices (const std::vector< Atom > &atoms)
	Obtain indices of each element.
void	applyColours (std::vector< Atom > &atoms, const std::map< uint64_t, glm::vec4 > &colours)
	Apply colours by index.
void	applySizes (std::vector< Atom > &atoms, const std::vector< float > sizes)
	Apply sizes by index.

Function Documentation

applyColours()

void applyColours	(	std::vector< Atom > &	atoms,
		const std::map< uint64_t, glm::vec4 > &	colours
	)

Apply colours by index.

Parameters

atoms	the Atoms to colour.
colours	the partial map of indices to colours.

applySizes()

void applySizes	(	std::vector< Atom > &	atoms,
		const std::vector< float >	sizes
	)

Apply sizes by index.

Parameters

atoms	the Atoms to colour.
colours	the atom sizes.

center()

void center

(

std::vector< Atom > &

atoms

)

Subtract the centre of mass of some Atoms.

Parameters

atoms

the Atom list to centre.

centerOn()

void centerOn	(	std::vector< Atom > &	atoms,
		uint64_t	index
	)

Centre on a particular Atom.

Parameters

atoms	the Atom list to centre.
index	the Atom index to centre on.

elementIndices()

std::multimap< Element, uint64_t > elementIndices

(

const std::vector< Atom > &

atoms

)

Obtain indices of each element.

Parameters

atoms

the atoms to index.

Returns

std::multimap<Element, uint64_t> the indices of each element type.

extent()

glm::vec3 extent

(

const std::vector< Atom > &

atoms

)

Calculate the extent of some Atoms.

Parameters

atoms

the Atom list.

Returns

glm::vec3 the extent (max-min).

getCenter()

glm::vec3 getCenter

(

const std::vector< Atom > &

atoms

)

Calculate the centre of mass.

Parameters

atoms

the Atom list to centre.

Returns

glm::vec3 the Atoms centers of mass.

largest()

float largest

(

const std::vector< Atom > &

atoms

)

Calculate the largest Atom.

Parameters

atoms

the Atom list.

Returns

float the largest Atom.

max()

glm::vec3 max

(

const std::vector< Atom > &

atoms

)

Calculate the maximum positions of some Atoms.

Parameters

atoms

the Atom list.

Returns

glm::vec3 the maximum position.

min()

glm::vec3 min

(

const std::vector< Atom > &

atoms

)

Calculate the minimum positions of some Atoms.

Parameters

atoms

the Atom list.

Returns

glm::vec3 the minimum position.

operator<<()

std::ostream & operator<<	(	std::ostream &	o,
		Atom &	atom
	)

Print an atom to std::ostream.

Remarks

Prints and atoms element symbol and position.

Parameters

o	output stream.
atom	atom to print.

Returns

std::ostream& the resulting output stream.

translate()

void translate	(	std::vector< Atom > &	atoms,
		glm::vec3	r
	)

uniqueElements()

std::set< Element > uniqueElements

(

const std::vector< Atom > &

atoms

)

Determine the unique elements in a list of Atom.

Parameters

atoms

the atoms to check.

Returns

std::set<Element> the set of elements.