#include <Face.h>

Public Member Functions
	Face ()

	~Face ()

bool	checkTetraIntersection (Face *f2)

bool	checkTetraIntersection (Face f2, scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

scalar	getTetraIntersectionVolume (Face *f2)

scalar	getTetraIntersectionVolume (Face f2, scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

scalar	checkTetraIntersectionAndGetVolume (Face *f2)

scalar	checkTetraIntersectionAndGetVolume (Face f2, scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

void	getTetraIntersectionVolumeAndArea (Face *f2, geoscalar &vol, geoscalar &area)

void	getTetraIntersectionVolumeAndArea (Face f2, geoscalar &vol, geoscalar &area, scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

bool	getTetraIntersectionVolumeTotalGradientAndShapeFunctions (Face *f2, geoscalar dr, grr3(&dVdr), geoscalar &vol, grr4(&phi1), grr4(&phi2))

bool	getTetraIntersectionVolumeTotalGradientAndShapeFunctions (Face f2, geoscalar dr, grr3(&dVdr), geoscalar &vol, grr4(&phi1), grr4(&phi2), scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

int	init (int index, tetra_element_linear e, mesh_node n0, mesh_node n1, mesh_node n2, mesh_node oposite, SecondOrderFunctions::stu centroid_stu, Blob daddy_blob, SimulationParams *params)

int	init (int index, mesh_node n0, mesh_node n1, mesh_node n2, mesh_node opposite, Blob daddy_blob, SimulationParams params)

void	set_ssint_interaction_type (int ssint_interaction_type)

int	build_opposite_node ()

void	calc_area_normal_centroid ()

void	set_kinetic_state (bool state)

vector3 *	get_centroid ()

void	print_centroid ()

void	print_nodes ()

scalar	get_area ()

void	barycentric_calc_point (scalar b1, scalar b2, scalar b3, vector3 *p)

void	barycentric_calc_point_f2 (scalar b1, scalar b2, scalar b3, vector3 p, scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

scalar	average_phi ()

scalar	get_normal_flux ()

void	add_force_to_node (int i, vector3 *f)

template<class brr3 >
void	add_force_to_node (int i, brr3(&f))

void	add_force_to_node_atomic (int i, vector3 *f)

void	zero_force ()

void	set_ssint_xz_interaction_flag (bool state)

template<class brr3 >
void	vec3Vec3SubsToArr3Mod (Face f2, brr3(&w), scalar blob_corr, int f1_daddy_blob_index, int f2_daddy_blob_index)

bool	is_ssint_active ()

bool	is_kinetic_active ()

scalar	length_of_longest_edge ()

Data Fields
mesh_node *	n [4]

int	index

tetra_element_linear *	e

int	ssint_interaction_type

scalar	area_0

scalar	area

vector3	normal

vector3	centroid

vector3	force [4]

SecondOrderFunctions::stu	centroid_stu

bool	ssint_xz_interaction_flag

bool	kinetically_active

Blob *	daddy_blob


int	num_blobs

Private Attributes
int	stuff

bool	dealloc_n3

Constructor & Destructor Documentation

◆ Face()

Face::Face ( )

◆ ~Face()

Face::~Face ( )

Member Function Documentation

◆ add_force_to_node() [1/2]

void Face::add_force_to_node	(	int	i,
		vector3 *	f
	)

Referenced by Blob::apply_ctforces(), VdW_solver::do_gensoft_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_steric_interaction(), and VdW_solver::do_sticky_xz_interaction().

◆ add_force_to_node() [2/2]

template<class brr3 >

void Face::add_force_to_node	(	int	i,
		brr3 &	f
	)

◆ add_force_to_node_atomic()

void Face::add_force_to_node_atomic	(	int	i,
		vector3 *	f
	)

◆ average_phi()

scalar Face::average_phi ( )

Returns the average electrostatic potential of this face

◆ barycentric_calc_point()

void Face::barycentric_calc_point	(	scalar	b1,
		scalar	b2,
		scalar	b3,
		vector3 *	p
	)

Calculate the point p on this triangle given the barycentric coordinates b1, b2, b3. Altered to act periodically around box boundaries.

Referenced by BEM_Poisson_Boltzmann::build_BEM_matrices(), VdW_solver::do_gensoft_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_sticky_xz_interaction(), GaussianQuadrature_tri::integrate_face_to_face(), and GaussianQuadrature_tri::integrate_point_to_face().

◆ barycentric_calc_point_f2()

void Face::barycentric_calc_point_f2	(	scalar	b1,
		scalar	b2,
		scalar	b3,
		vector3 *	p,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

Referenced by VdW_solver::do_gensoft_interaction(), and VdW_solver::do_lj_interaction().

◆ build_opposite_node()

int Face::build_opposite_node ( )

Referenced by Blob::add_steric_nodes().

◆ calc_area_normal_centroid()

void Face::calc_area_normal_centroid ( )

Referenced by build_opposite_node(), Blob::calc_all_centroids(), and init().

◆ checkTetraIntersection() [1/2]

bool Face::checkTetraIntersection ( Face * f2 )

Check whether the tetrahedron formed by this face an the opposite linear node does intersect with the corresponding tetrahedron in f2 Returns true if there is intersection. Uses the "Fast Tetrahedron-Tetrahedron Overlap Algorithm". It calls some private functions.

Referenced by GenSoftSSINT_solver::do_interaction(), Steric_solver::do_interaction(), and LJSteric_solver::do_interaction().

◆ checkTetraIntersection() [2/2]

bool Face::checkTetraIntersection	(	Face *	f2,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ checkTetraIntersectionAndGetVolume() [1/2]

scalar Face::checkTetraIntersectionAndGetVolume ( Face * f2 )

Check whether the tetrahedron formed by this face an the opposite linear node does intersect with the corresponding tetrahedron in f2. If so, return the overlapping volume, otherwise return 0. Uses the "Fast Tetrahedron-Tetrahedron Overlap Algorithm" for checking if interaction occurs.

◆ checkTetraIntersectionAndGetVolume() [2/2]

scalar Face::checkTetraIntersectionAndGetVolume	(	Face *	f2,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ get_area()

scalar Face::get_area ( )

Referenced by Blob::apply_ctforces().

◆ get_centroid()

vector3 * Face::get_centroid ( )

Referenced by print_centroid().

◆ get_normal_flux()

scalar Face::get_normal_flux ( )

Referenced by Blob::solve_poisson().

◆ getTetraIntersectionVolume() [1/2]

scalar Face::getTetraIntersectionVolume ( Face * f2 )

Get the volume that the enclose the intersection of the tetrahedron formed by this face an the opposite linear node with the corresponding tetrahedron in f2. It calls volumeIntersection, at volumeIntersection.h

◆ getTetraIntersectionVolume() [2/2]

scalar Face::getTetraIntersectionVolume	(	Face *	f2,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ getTetraIntersectionVolumeAndArea() [1/2]

void Face::getTetraIntersectionVolumeAndArea	(	Face *	f2,
		geoscalar &	vol,
		geoscalar &	area
	)

Get the volume and area that the enclose the intersection of the tetrahedron formed by this face an the opposite linear node with the corresponding tetrahedron in f2. It calls volumeIntersection, at volumeIntersection.h

◆ getTetraIntersectionVolumeAndArea() [2/2]

void Face::getTetraIntersectionVolumeAndArea	(	Face *	f2,
		geoscalar &	vol,
		geoscalar &	area,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ getTetraIntersectionVolumeTotalGradientAndShapeFunctions() [1/2]

bool Face::getTetraIntersectionVolumeTotalGradientAndShapeFunctions	(	Face *	f2,
		geoscalar	dr,
		grr3 &	dVdr,
		geoscalar &	vol,
		grr4 &	phi1,
		grr4 &	phi2
	)

Get the volume that enclose the intersection of the tetrahedron formed by this face an the opposite linear node with the corresponding tetrahedron in f2. In addition, return the gradient of this volume, calculated as dV/dx,dV/dy,dV/dz, and the internal coordinates of the point where the force is applied. It calls 4 times volumeIntersection. This version works well for the double loop i<j.

Referenced by VdW_solver::do_steric_interaction().

◆ getTetraIntersectionVolumeTotalGradientAndShapeFunctions() [2/2]

bool Face::getTetraIntersectionVolumeTotalGradientAndShapeFunctions	(	Face *	f2,
		geoscalar	dr,
		grr3 &	dVdr,
		geoscalar &	vol,
		grr4 &	phi1,
		grr4 &	phi2,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ init() [1/2]

int Face::init	(	int	index,
		tetra_element_linear *	e,
		mesh_node *	n0,
		mesh_node *	n1,
		mesh_node *	n2,
		mesh_node *	oposite,
		SecondOrderFunctions::stu	centroid_stu,
		Blob *	daddy_blob,
		SimulationParams *	params
	)

Referenced by Blob::load_surface(), and Blob::load_surface_no_topology().

◆ init() [2/2]

int Face::init	(	int	index,
		mesh_node *	n0,
		mesh_node *	n1,
		mesh_node *	n2,
		mesh_node *	opposite,
		Blob *	daddy_blob,
		SimulationParams *	params
	)

◆ is_kinetic_active()

bool Face::is_kinetic_active ( )

Referenced by VdW_solver::solve().

◆ is_ssint_active()

bool Face::is_ssint_active ( )

◆ length_of_longest_edge()

scalar Face::length_of_longest_edge ( )

Referenced by Blob::calc_rest_state_info().

◆ print_centroid()

void Face::print_centroid ( )

◆ print_nodes()

void Face::print_nodes ( )

◆ set_kinetic_state()

void Face::set_kinetic_state ( bool state )

Referenced by Blob::kinetically_set_faces().

◆ set_ssint_interaction_type()

void Face::set_ssint_interaction_type ( int ssint_interaction_type )

Referenced by Blob::load_ssint().

◆ set_ssint_xz_interaction_flag()

void Face::set_ssint_xz_interaction_flag ( bool state )

Referenced by VdW_solver::solve_sticky_wall().

◆ vec3Vec3SubsToArr3Mod()

template<class brr3 >

template void Face::vec3Vec3SubsToArr3Mod< grr3 >	(	Face *	f2,
		brr3 &	w,
		scalar *	blob_corr,
		int	f1_daddy_blob_index,
		int	f2_daddy_blob_index
	)

◆ zero_force()

void Face::zero_force ( )

Referenced by build_opposite_node(), Face(), init(), Blob::zero_force(), and ~Face().

Field Documentation

◆ area

scalar Face::area

Last calculated area (by most recent call to calc_area_normal_centroid())

Referenced by build_opposite_node(), calc_area_normal_centroid(), VdW_solver::do_gensoft_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_sticky_xz_interaction(), BEM_Poisson_Boltzmann::gauss_quadrature_4_point(), get_area(), Blob::get_ssint_area(), getTetraIntersectionVolumeAndArea(), init(), GaussianQuadrature_tri::integrate_face_to_face(), and GaussianQuadrature_tri::integrate_point_to_face().

◆ area_0

scalar Face::area_0

Initial, equilibrium area of this face

Referenced by Face(), init(), Blob::load_surface(), Blob::load_surface_no_topology(), and ~Face().

◆ centroid

vector3 Face::centroid

Last calculated centroid (by most recent call to calc_area_normal_centroid())

Referenced by BEM_Poisson_Boltzmann::build_BEM_matrices(), build_opposite_node(), calc_area_normal_centroid(), VdW_solver::consider_interaction(), get_centroid(), BEM_Poisson_Boltzmann::perform_integrals_for_lookup_cell_relative(), and BEM_Poisson_Boltzmann::perform_integrals_for_lookup_cell_self().

◆ centroid_stu

SecondOrderFunctions::stu Face::centroid_stu

Stores the natural (shape function) coords of the centroid of this face in the parent element

Referenced by get_normal_flux(), and init().

◆ daddy_blob

Blob* Face::daddy_blob

Referenced by VdW_solver::consider_interaction(), VdW_solver::do_gensoft_interaction(), LJSteric_solver::do_interaction(), GenSoftSSINT_solver::do_interaction(), Steric_solver::do_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_steric_interaction(), Face(), init(), VdW_solver::solve(), and ~Face().

◆ dealloc_n3

bool Face::dealloc_n3

private

Referenced by build_opposite_node(), Face(), and ~Face().

◆ e

tetra_element_linear* Face::e

Pointer to the element this is a face of

Referenced by Face(), get_normal_flux(), init(), and ~Face().

◆ force

vector3 Face::force[4]

Stores the current force applied to this face. The first 3 "vectors" are to those surface nodes that define this face, while the last one belongs to the opposite node of the linear tetrahedron

Referenced by add_force_to_node(), add_force_to_node_atomic(), Blob::aggregate_forces_and_solve(), and zero_force().

◆ index

int Face::index

Index of this face

Referenced by init().

◆ kinetically_active

bool Face::kinetically_active

Referenced by Face(), is_kinetic_active(), set_kinetic_state(), and ~Face().

◆ n

mesh_node* Face::n[4]

The first 3 pointers are to those surface nodes that define this face, while the last one belongs to the opposite node of the linear tetrahedron

Referenced by Blob::aggregate_forces_and_solve(), average_phi(), barycentric_calc_point(), barycentric_calc_point_f2(), BEM_Poisson_Boltzmann::build_BEM_matrices(), build_opposite_node(), calc_area_normal_centroid(), checkTetraIntersection(), checkTetraIntersectionAndGetVolume(), VdW_solver::consider_interaction(), Face(), get_area(), get_centroid(), getTetraIntersectionVolume(), getTetraIntersectionVolumeAndArea(), getTetraIntersectionVolumeTotalGradientAndShapeFunctions(), Blob::init(), init(), length_of_longest_edge(), Blob::move(), print_nodes(), Blob::solve_poisson(), vec3Vec3SubsToArr3Mod(), and ~Face().

◆ normal

vector3 Face::normal

Last calculated normal (by most recent call to calc_area_normal_centroid())

Referenced by build_opposite_node(), calc_area_normal_centroid(), VdW_solver::consider_interaction(), VdW_solver::do_sticky_xz_interaction(), BEM_Poisson_Boltzmann::gauss_quadrature_4_point(), and get_normal_flux().

◆ num_blobs

int Face::num_blobs

vdw measurement info

Referenced by barycentric_calc_point_f2(), checkTetraIntersection(), checkTetraIntersectionAndGetVolume(), Face(), getTetraIntersectionVolume(), getTetraIntersectionVolumeAndArea(), getTetraIntersectionVolumeTotalGradientAndShapeFunctions(), init(), vec3Vec3SubsToArr3Mod(), and ~Face().

◆ ssint_interaction_type

int Face::ssint_interaction_type

Van der Waals interaction type

Referenced by VdW_solver::do_gensoft_interaction(), VdW_solver::do_lj_interaction(), VdW_solver::do_sticky_xz_interaction(), Face(), is_ssint_active(), set_ssint_interaction_type(), and ~Face().

◆ ssint_xz_interaction_flag

bool Face::ssint_xz_interaction_flag

Referenced by Face(), set_ssint_xz_interaction_flag(), and ~Face().

◆ stuff

int Face::stuff