.. index:: pair: class; SuperCell
.. _doxid-class_super_cell:

class SuperCell
===============

.. toctree::
	:hidden:

Overview
~~~~~~~~

The :ref:`SuperCell <doxid-class_super_cell>` defines the size, shape and boundary condx of a simulation. :ref:`More...<details-class_super_cell>`


.. ref-code-block:: cpp
	:class: doxyrest-overview-code-block

	#include <SuperCell.h>
	
	class SuperCell {
	public:
		// fields
	
		bool :ref:`periodic<doxid-class_super_cell_1a0d6bf20f355df1aa29ecb8e6ea537b32>`[3];
		:ref:`Vec<doxid-class_vec>` :ref:`vectors<doxid-class_super_cell_1affa5638859c2084f5a450d36af59e3d0>`[3];
		:ref:`Vec<doxid-class_vec>` :ref:`inverse<doxid-class_super_cell_1a77573e78c599ebb8f891ae6f9d85ff6f>`[3];
		double :ref:`heights<doxid-class_super_cell_1ab4c7d986c2e94dde9f0d58720304d2a1>`[3];
		:ref:`Vec<doxid-class_vec>` :ref:`translations<doxid-class_super_cell_1af0dc9eb3a0b6f5f0a49f47d850a92305>`[27];

		// construction
	
		:ref:`SuperCell<doxid-class_super_cell_1ab0ef5f42969cf74b2deb2e5955bd0347>`(const :ref:`Vec<doxid-class_vec>` v[3], const bool p[3]);
		:ref:`SuperCell<doxid-class_super_cell_1affe2302533e36eaafb1d1409cfbde8d6>`(const SuperCell* original);

		// methods
	
		void :ref:`SetAtoms<doxid-class_super_cell_1a4fe2eaed02cbcdc085c7e284f401822f>`(:ref:`Atoms<doxid-class_atoms>`* a);
		void :ref:`TransformToScaledSpace<doxid-class_super_cell_1a2bb2250269179109e468d8525d6a331b>`(:ref:`Vec<doxid-class_vec>`* positions, int nAtoms) const;
		void :ref:`TransformToRealSpace<doxid-class_super_cell_1a48d9131fabb02b140869e850a258c586>`(:ref:`Vec<doxid-class_vec>`* positions, int nAtoms) const;
		void :ref:`ClosestLatticeSiteIndices<doxid-class_super_cell_1a32a151f35cd7018194a864bb9043c8a2>`(int intVector[3], :ref:`Vec<doxid-class_vec>`& diff) const;
		double :ref:`GetVolume<doxid-class_super_cell_1a7670c6a88e62fc1faf9b9e321004af99>`() const;
		void :ref:`SetBasis<doxid-class_super_cell_1a5c441b1a4cbd6b116c78e382821ef285>`(const :ref:`Vec<doxid-class_vec>` v[3]);
		:ref:`Vec<doxid-class_vec>` :ref:`GetBasis<doxid-class_super_cell_1a7123e525b79c1a645e9be9431e8fef95>`(int a);
		void :ref:`SetPeriodic<doxid-class_super_cell_1a0b138a7d8c44c535219b186b10135ee8>`(const bool newperiodic[3]);
	};
.. _details-class_super_cell:

Detailed Documentation
~~~~~~~~~~~~~~~~~~~~~~

The :ref:`SuperCell <doxid-class_super_cell>` defines the size, shape and boundary condx of a simulation.

The :ref:`SuperCell <doxid-class_super_cell>` serves two purposes. The most important is the computational box of a simulation: it defines the size, shape and boundary conditions of the simulation. A second use is for the unit cell of the lattice in the elements of a Quasicontinuum simulation.

Fields
------

.. index:: pair: variable; periodic
.. _doxid-class_super_cell_1a0d6bf20f355df1aa29ecb8e6ea537b32:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	bool periodic[3]

Periodic boundary conditions along the 3 axes?

.. index:: pair: variable; vectors
.. _doxid-class_super_cell_1affa5638859c2084f5a450d36af59e3d0:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`Vec<doxid-class_vec>` vectors[3]

The basis vectors.

.. index:: pair: variable; inverse
.. _doxid-class_super_cell_1a77573e78c599ebb8f891ae6f9d85ff6f:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`Vec<doxid-class_vec>` inverse[3]

The inverse of the vectors matrix.

.. index:: pair: variable; heights
.. _doxid-class_super_cell_1ab4c7d986c2e94dde9f0d58720304d2a1:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	double heights[3]

The heights of the supercell.

.. index:: pair: variable; translations
.. _doxid-class_super_cell_1af0dc9eb3a0b6f5f0a49f47d850a92305:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`Vec<doxid-class_vec>` translations[27]

The 27 possible translations due to the periodic boundaries.

Construction
------------

.. index:: pair: function; SuperCell
.. _doxid-class_super_cell_1ab0ef5f42969cf74b2deb2e5955bd0347:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	SuperCell(const :ref:`Vec<doxid-class_vec>` v[3], const bool p[3])

Create a new supercell with basis vectors :ref:`Vec <doxid-class_vec>` and periodicity p.

.. index:: pair: function; SuperCell
.. _doxid-class_super_cell_1affe2302533e36eaafb1d1409cfbde8d6:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	SuperCell(const SuperCell* original)

Copy constructor.

Methods
-------

.. index:: pair: function; SetAtoms
.. _doxid-class_super_cell_1a4fe2eaed02cbcdc085c7e284f401822f:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void SetAtoms(:ref:`Atoms<doxid-class_atoms>`* a)

Set the atoms associated with the supercell.

.. index:: pair: function; TransformToScaledSpace
.. _doxid-class_super_cell_1a2bb2250269179109e468d8525d6a331b:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void TransformToScaledSpace(:ref:`Vec<doxid-class_vec>`* positions, int nAtoms) const

In-place transformation of positions from real to scaled space.

.. index:: pair: function; TransformToRealSpace
.. _doxid-class_super_cell_1a48d9131fabb02b140869e850a258c586:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void TransformToRealSpace(:ref:`Vec<doxid-class_vec>`* positions, int nAtoms) const

In-place transformation of positions from scaled to real space.

.. index:: pair: function; ClosestLatticeSiteIndices
.. _doxid-class_super_cell_1a32a151f35cd7018194a864bb9043c8a2:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void ClosestLatticeSiteIndices(int intVector[3], :ref:`Vec<doxid-class_vec>`& diff) const

Quasicontinuum only: convert position to closest lattice site.

When the supercell is used in a QC simulation to represent the crystal lattice of an element, this function is used to convert the position of an atom into lattice coordinates.

.. index:: pair: function; GetVolume
.. _doxid-class_super_cell_1a7670c6a88e62fc1faf9b9e321004af99:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	double GetVolume() const

Get the volume of the supercell.

.. index:: pair: function; SetBasis
.. _doxid-class_super_cell_1a5c441b1a4cbd6b116c78e382821ef285:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void SetBasis(const :ref:`Vec<doxid-class_vec>` v[3])

Change the basis. The atoms are not moved. Should only be called from the atoms.

.. index:: pair: function; GetBasis
.. _doxid-class_super_cell_1a7123e525b79c1a645e9be9431e8fef95:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	:ref:`Vec<doxid-class_vec>` GetBasis(int a)

Get the basis vectors.

.. index:: pair: function; SetPeriodic
.. _doxid-class_super_cell_1a0b138a7d8c44c535219b186b10135ee8:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	void SetPeriodic(const bool newperiodic[3])

Set the periodicity. USE WITH CAUTION!

Change the periodicity of the supercell. Other classes may not notice that this has happened. This cannot be done after the atoms have been assigned a Potential.