#include <BoxGeometry.hpp>

Public Member Functions
	BoxGeometry ()

	BoxGeometry (BoxGeometry const &rhs)

void	set_periodic (unsigned coord, bool val)
	Set periodicity for direction.

constexpr bool	periodic (unsigned coord) const
	Check periodicity in direction.

Utils::Vector3d const &	length () const
	Box length.

Utils::Vector3d const &	length_inv () const
	Inverse box length.

Utils::Vector3d const &	length_half () const
	Half box length.

void	set_length (Utils::Vector3d const &box_l)
	Set box side lengths.

double	volume () const
	Box volume.

template<typename T >
T	get_mi_coord (T a, T b, unsigned coord) const
	Get the minimum-image distance between two coordinates.

template<typename T >
Utils::Vector< T, 3 >	get_mi_vector (const Utils::Vector< T, 3 > &a, const Utils::Vector< T, 3 > &b) const
	Get the minimum-image vector between two coordinates.

BoxType	type () const

void	set_type (BoxType type)

LeesEdwardsBC const &	lees_edwards_bc () const

void	set_lees_edwards_bc (LeesEdwardsBC bc)

void	lees_edwards_update (double pos_offset, double shear_velocity)
	Update the Lees-Edwards parameters of the box geometry for the current simulation time.

Utils::Vector3d	velocity_difference (Utils::Vector3d const &x, Utils::Vector3d const &y, Utils::Vector3d const &u, Utils::Vector3d const &v) const
	Calculate the velocity difference including the Lees-Edwards velocity.

void	fold_position (Utils::Vector3d &pos, Utils::Vector3i &image_box) const
	Fold coordinates to primary simulation box in-place.

auto	folded_position (Utils::Vector3d const &pos) const
	Calculate coordinates folded to primary simulation box.

auto	folded_image_box (Utils::Vector3d const &pos, Utils::Vector3i const &image_box) const
	Calculate image box of coordinates folded to primary simulation box.

auto	image_shift (Utils::Vector3i const &image_box) const
	Calculate image box shift vector.

auto	unfolded_position (Utils::Vector3d const &pos, Utils::Vector3i const &image_box) const
	Unfold particle coordinates to image box.

Detailed Description

Definition at line 98 of file BoxGeometry.hpp.

Constructor & Destructor Documentation

◆ BoxGeometry() [1/2]

BoxGeometry::BoxGeometry ( )

inline

Definition at line 100 of file BoxGeometry.hpp.

References CUBOID, set_length(), set_periodic(), and set_type().

◆ BoxGeometry() [2/2]

BoxGeometry::BoxGeometry ( BoxGeometry const & rhs )

inline

Definition at line 107 of file BoxGeometry.hpp.

References length(), periodic(), set_length(), set_periodic(), and type().

Member Function Documentation

◆ fold_position()

void BoxGeometry::fold_position	(	Utils::Vector3d &	pos,
		Utils::Vector3i &	image_box
	)		const

inline

Fold coordinates to primary simulation box in-place.

Lees-Edwards offset is ignored.

Parameters

[in,out]	pos	coordinates to fold
[in,out]	image_box	image box offset

Definition at line 267 of file BoxGeometry.hpp.

References Algorithm::periodic_fold().

Referenced by fold_and_reset(), LeesEdwards::Push::operator()(), AtomDecomposition::resort(), serialize_and_reduce(), and vs_relative_update_particles().

◆ folded_image_box()

auto BoxGeometry::folded_image_box	(	Utils::Vector3d const &	pos,
		Utils::Vector3i const &	image_box
	)		const

inline

Calculate image box of coordinates folded to primary simulation box.

Parameters

[in]	pos	coordinates
[in]	image_box	image box to fold

Returns: Folded image box.

Definition at line 306 of file BoxGeometry.hpp.

References Algorithm::periodic_fold().

Referenced by Writer::H5md::File::write().

◆ folded_position()

auto BoxGeometry::folded_position ( Utils::Vector3d const & pos ) const

inline

Calculate coordinates folded to primary simulation box.

Parameters

[in] pos coordinates to fold

Returns: Folded coordinates.

Definition at line 289 of file BoxGeometry.hpp.

References Algorithm::periodic_fold().

Referenced by gather_particle_data(), is_valid_position(), LB::ParticleCoupling::kernel(), positions_in_halo(), and Writer::H5md::File::write().

◆ get_mi_coord()

template<typename T >

T BoxGeometry::get_mi_coord	(	T	a,
		T	b,
		unsigned	coord
	)		const

inline

Get the minimum-image distance between two coordinates.

Parameters

a	Coordinate of the terminal point.
b	Coordinate of the initial point.
coord	Direction

Returns: Shortest distance from b to a across periodic images, i.e. a - b. Can be negative.

Definition at line 192 of file BoxGeometry.hpp.

References coord().

Referenced by get_mi_vector().

◆ get_mi_vector()

template<typename T >

Utils::Vector< T, 3 > BoxGeometry::get_mi_vector	(	const Utils::Vector< T, 3 > &	a,
		const Utils::Vector< T, 3 > &	b
	)		const

inline

Get the minimum-image vector between two coordinates.

Template Parameters

T	Floating point type.

Parameters

a	Coordinate of the terminal point.
b	Coordinate of the initial point.

Returns: Vector from b to a that minimizes the distance across periodic images, i.e. a - b.

Definition at line 210 of file BoxGeometry.hpp.

References CUBOID, LeesEdwardsBC::distance(), get_mi_coord(), LEES_EDWARDS, lees_edwards_bc(), Algorithm::periodic_fold(), LeesEdwardsBC::shear_plane_normal, and type().

Referenced by add_bonded_force(), add_bonded_two_body_force(), add_oif_global_forces(), calc_bonded_energy(), calc_bonded_four_body_force(), calc_bonded_three_body_force(), calc_bonded_three_body_pressure_tensor(), calc_bonded_virial_pressure_tensor(), IBMTribend::calc_forces(), OifLocalForcesBond::calc_forces(), calc_oif_mesh(), calculate_positional_correction(), calculate_velocity_correction(), calculate_vs_relate_to_params(), elc_data::dielectric_layers_contribution(), image_sum(), IBMTribend::initialize(), IBMTriel::initialize(), and is_valid_position().

◆ image_shift()

auto BoxGeometry::image_shift ( Utils::Vector3i const & image_box ) const

inline

Calculate image box shift vector.

Definition at line 320 of file BoxGeometry.hpp.

◆ lees_edwards_bc()

LeesEdwardsBC const & BoxGeometry::lees_edwards_bc ( ) const

inline

Definition at line 231 of file BoxGeometry.hpp.

Referenced by get_mi_vector(), lees_edwards_vel_shift(), positions_in_halo_impl(), LeesEdwards::shear_direction(), LeesEdwards::velocity_shift(), LeesEdwards::verlet_list_offset(), and Writer::H5md::File::write().

◆ lees_edwards_update()

void BoxGeometry::lees_edwards_update	(	double	pos_offset,
		double	shear_velocity
	)

inline

Update the Lees-Edwards parameters of the box geometry for the current simulation time.

Definition at line 238 of file BoxGeometry.hpp.

References LEES_EDWARDS, LeesEdwardsBC::pos_offset, LeesEdwardsBC::shear_velocity, and type().

Referenced by LeesEdwards::LeesEdwards::update_box_params().

◆ length()

Utils::Vector3d const & BoxGeometry::length ( ) const

inline

Box length.

Returns: Return vector of side-lengths of the box.

Definition at line 154 of file BoxGeometry.hpp.

Referenced by BoxGeometry(), dipolar_energy_correction(), dipolar_force_corrections(), get_simulation_box(), image_sum(), RegularDecomposition::max_cutoff(), LeesEdwards::Push::operator()(), positions_in_halo_impl(), prepare_sc_cache(), random_position(), setup_PoQ(), setup_PQ(), ParticlePropertyRange::unfolded_pos_range(), and Writer::H5md::write_box().

◆ length_half()

Utils::Vector3d const & BoxGeometry::length_half ( ) const

inline

Half box length.

Returns: Return vector of half side-lengths of the box.

Definition at line 166 of file BoxGeometry.hpp.

Referenced by velocity_difference().

◆ length_inv()

Utils::Vector3d const & BoxGeometry::length_inv ( ) const

inline

Inverse box length.

Returns: Return vector of inverse side-lengths of the box.

Definition at line 160 of file BoxGeometry.hpp.

Referenced by add_PQ_force(), dipolar_energy_correction(), dipolar_force_corrections(), prepare_sc_cache(), setup_PoQ(), and setup_PQ().

◆ periodic()

constexpr bool BoxGeometry::periodic ( unsigned coord ) const

inlineconstexpr

Check periodicity in direction.

Parameters

coord Direction to check

Returns: true iff periodic in direction.

Definition at line 145 of file BoxGeometry.hpp.

References coord().

Referenced by BoxGeometry(), get_n_cut(), and get_simulation_box().

◆ set_lees_edwards_bc()

void BoxGeometry::set_lees_edwards_bc ( LeesEdwardsBC bc )

inline

Definition at line 232 of file BoxGeometry.hpp.

◆ set_length()

void BoxGeometry::set_length ( Utils::Vector3d const & box_l )

inline

Set box side lengths.

Parameters

box_l Length that should be set.

Definition at line 172 of file BoxGeometry.hpp.

Referenced by BoxGeometry(), and BoxGeometry().

◆ set_periodic()

void BoxGeometry::set_periodic	(	unsigned	coord,
		bool	val
	)

inline

Set periodicity for direction.

Parameters

coord	The coordinate to set the periodicity for.
val	True if this direction should be periodic.

Definition at line 137 of file BoxGeometry.hpp.

References coord().

Referenced by BoxGeometry(), and BoxGeometry().

◆ set_type()

void BoxGeometry::set_type ( BoxType type )

inline

Definition at line 229 of file BoxGeometry.hpp.

References type().

Referenced by BoxGeometry().

◆ type()

BoxType BoxGeometry::type ( ) const

inline

Definition at line 228 of file BoxGeometry.hpp.

Referenced by BoxGeometry(), get_mi_vector(), LB::ParticleCoupling::kernel(), lees_edwards_update(), lees_edwards_vel_shift(), positions_in_halo_impl(), set_type(), LeesEdwards::LeesEdwards::update_box_params(), velocity_difference(), LeesEdwards::velocity_shift(), LeesEdwards::verlet_list_offset(), and vs_relative_update_particles().

◆ unfolded_position()

auto BoxGeometry::unfolded_position	(	Utils::Vector3d const &	pos,
		Utils::Vector3i const &	image_box
	)		const

inline

Unfold particle coordinates to image box.

Definition at line 325 of file BoxGeometry.hpp.

Referenced by add_oif_global_forces(), OifLocalForcesBond::calc_forces(), calc_oif_mesh(), GatherPos::kernel(), and GatherCom::kernel().

◆ velocity_difference()

Utils::Vector3d BoxGeometry::velocity_difference	(	Utils::Vector3d const &	x,
		Utils::Vector3d const &	y,
		Utils::Vector3d const &	u,
		Utils::Vector3d const &	v
	)		const

inline

Calculate the velocity difference including the Lees-Edwards velocity.

Definition at line 245 of file BoxGeometry.hpp.

References LEES_EDWARDS, length_half(), Utils::sgn(), LeesEdwardsBC::shear_plane_normal, and type().

Referenced by dpd_pair_force().

◆ volume()

double BoxGeometry::volume ( ) const

inline

Box volume.

Returns: Return the volume of the box.

Definition at line 182 of file BoxGeometry.hpp.

References Utils::product().

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

BoxGeometry.hpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ BoxGeometry() [1/2]

◆ BoxGeometry() [2/2]

Member Function Documentation

◆ fold_position()

◆ folded_image_box()

◆ folded_position()

◆ get_mi_coord()

◆ get_mi_vector()

◆ image_shift()

◆ lees_edwards_bc()

◆ lees_edwards_update()

◆ length()

◆ length_half()

◆ length_inv()

◆ periodic()

◆ set_lees_edwards_bc()

◆ set_length()

◆ set_periodic()

◆ set_type()

◆ type()

◆ unfolded_position()

◆ velocity_difference()

◆ volume()