File AtomCollection.h

Copyright

This code is licensed under the 3-clause BSD license.

Copyright ETH Zurich, Laboratory for Physical Chemistry, Reiher Group.

See LICENSE.txt for details.

namespace Scine

This header file contains functions that allow for common notation for common things that can be done at a different degree of derivatives.

This header contains alias definitions defining which classes to use for the different degrees of derivatives.

namespace Utils
class AtomCollection
#include <AtomCollection.h>

A Collection of Atoms.

Has the same functionality as a std::vector<Atom>, but is implemented as a composition of a ElementTypeCollection and a PositionCollection.

Public Types

using iterator = AtomCollectionIterator

Public Functions

AtomCollection(int N = 0)

Construct a new AtomCollection object.

All atoms will be created and as type: None and be placed at (0,0,0).

Parameters

  • N: The number of atoms.

AtomCollection(ElementTypeCollection elements, PositionCollection positions)

Construct a new AtomCollection object.

Parameters

  • elements: The elements of the atoms.

  • positions: The positions of the atoms.

void setElements(ElementTypeCollection elements)

Update all Elements.

The new data must have the correct size, this function does not resize the data objects.

Parameters

  • elements: The new collection of Elements.

void setPositions(PositionCollection positions)

Update all positions.

The new data must have the correct size, this function does not resize the data objects.

Parameters

  • positions: The new positions.

const ElementTypeCollection &getElements() const

Get the Elements object.

Return

const ElementTypeCollection&

const PositionCollection &getPositions() const

Get the Positions object.

Return

const PositionCollection&

void setElement(int i, ElementType e)

Set the Element of one existing atom.

This function can not access/create new atoms that are not present yet.

Parameters

  • i: The index of the atom.

  • e: The new Element.

void setPosition(int i, const Position &p)

Set the Position of one existing atom.

This function can not access/create new atoms that are not present yet.

Parameters

  • i: The index of the atom.

  • p: The new Position.

ElementType getElement(int i) const

Get the Element of a single atom.

Return

ElementType The Element of atom i.

Parameters

  • i: The index of the atom.

Position getPosition(int i) const

Get the Position of a a single atom.

Return

Position The Position of atom i.

Parameters

  • i: The index of the atom.

int size() const

Getter for thw collection size.

Return

int Returns the number of atoms in the collection.

iterator begin() const

The start of the collection iterator.

Return

iterator The iterator.

iterator end() const

The end of the collection iterator.

Return

iterator The iterator.

void clear()

Clears all content and resizes data objects to size 0;.

void resize(int n)

Resizes the data obejects to the given size.

Parameters

  • n: The number of atoms to resize to.

void push_back(const Atom &atom)

Appends one atom to the collectio via copy.

Parameters

  • atom: The atom.

Atom operator[](int i) const

Operator overlaod, getter by position.

Return

Atom That atom at position i.

Parameters

  • i: The position.

Atom at(int i) const

Getter by position.

Return

Atom That atom at position i.

Parameters

  • i: The position.

bool operator==(const AtomCollection &other) const

Performs in-order comparison of both the contained element types and positions.

Note

The positions are fuzzy-compared with Eigen’s isApprox function and must therefore not be exactly equal.

Return

Whether both atomcollection contain the same information

Parameters

bool operator!=(const AtomCollection &other) const

Negates.

See

operator ==

Private Members

ElementTypeCollection elements_
PositionCollection positions_
class AtomCollectionIterator : public std::iterator<std::bidirectional_iterator_tag, Atom>
#include <AtomCollection.h>

Custom iterator typename for AtomCollection.

Public Functions

AtomCollectionIterator(AtomCollection const *ac = nullptr, int num = 0)
AtomCollectionIterator &operator++()
AtomCollectionIterator operator++(int)
AtomCollectionIterator &operator--()
AtomCollectionIterator operator--(int)
bool operator==(AtomCollectionIterator other) const
bool operator!=(AtomCollectionIterator other) const
value_type operator*() const

Private Members

AtomCollection const *ac_
int num_