VdW_solver Class Reference

#include <VdW_solver.h>

Inheritance diagram for VdW_solver:

Data Structures
struct	adjacent_cell_lookup_table_entry
struct	tri_gauss_point

Public Member Functions
	VdW_solver ()
	~VdW_solver ()
int	init (NearestNeighbourLinkedListCube *surface_face_lookup, vector3 *box_size, SSINT_matrix *ssint_matrix, scalar &steric_factor, int num_blobs, int inc_self_ssint, string ssint_type_string, scalar &steric_dr, int calc_kinetics, bool working_w_static_blobs)
int	solve (scalar *blob_corr)
int	solve_sticky_wall (scalar h)
scalar	get_field_energy (int i, int j)
void	reset_fieldenergy ()

Protected Member Functions
bool	consider_interaction (Face *f1, int l_index_i, int motion_state_i, LinkedListNode< Face > *l_j, scalar *blob_corr)
virtual void	do_interaction (Face *f1, Face *f2, scalar *blob_corr)
bool	do_steric_interaction (Face *f1, Face *f2, scalar *blob_corr)
void	do_lj_interaction (Face *f1, Face *f2, scalar *blob_corr)
void	do_gensoft_interaction (Face *f1, Face *f2, scalar *blob_corr)
void	do_sticky_xz_interaction (Face *f, bool bottom_wall, scalar dim_y)
void	calc_lj_force_pair_matrix (vector3(&force_pair_matrix)[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&p)[num_tri_gauss_quad_points], vector3(&q)[num_tri_gauss_quad_points], scalar &Rmin, scalar &Emin, scalar &energy)
void	calc_ljinterpolated_force_pair_matrix (vector3(&force_pair_matrix)[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&p)[num_tri_gauss_quad_points], vector3(&q)[num_tri_gauss_quad_points], scalar &Rmin, scalar &Emin, scalar &energy)
void	calc_gensoft_force_pair_matrix (vector3(&force_pair_matrix)[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&p)[num_tri_gauss_quad_points], vector3(&q)[num_tri_gauss_quad_points], scalar &Rmin, scalar &Emin, scalar &k0, scalar &energy)
void	calc_lj_factors (scalar &mag_r, int index_k, int index_l, scalar &Emin, scalar &Rmin_6, scalar &force_mag, scalar &e)
void	calc_ljinterpolated_factors (scalar &mag_r, int index_k, int index_l, scalar &Emin, scalar &Rmini, scalar &force_mag, scalar &e)
void	calc_gensoft_factors (scalar &mag_r, int index_k, int index_l, scalar &Emin, scalar &Rmin_2, scalar &Rmin_3, scalar &k0, scalar &force_mag, scalar &e)
scalar	distance2 (vector3 &p, vector3 &q)
scalar	dot (vector3 *p, vector3 *q)
scalar	dot_with_normal (vector3 *p, vector3 *q, vector3 *n)
scalar	minimum_image (scalar delta, scalar size)

Protected Attributes
int	total_num_surface_faces
NearestNeighbourLinkedListCube *	surface_face_lookup
vector3	box_size
SSINT_matrix *	ssint_matrix
scalar **	fieldenergy
int	num_blobs
int	inc_self_ssint
	whether to include interactions between faces within the same blob, or not. More...
int	calc_kinetics
bool	working_w_static_blobs
scalar	steric_factor
	Proportionality factor to the Steric repulsion. More...
scalar	steric_dr
	Constant to calculate the numerical derivative. More...
int	ssint_type

Static Protected Attributes
static const int	adjacent_cell_lookup_table [27][3]
static const int	num_tri_gauss_quad_points = 3
static const tri_gauss_point	gauss_points []

Constructor & Destructor Documentation

VdW_solver()

VdW_solver::VdW_solver

(

)

~VdW_solver()

VdW_solver::~VdW_solver

(

)

Member Function Documentation

calc_gensoft_factors()

void VdW_solver::calc_gensoft_factors ( scalar &  mag_r, int  index_k, int  index_l, scalar &  Emin, scalar &  Rmin_2, scalar &  Rmin_3, scalar &  k0, scalar &  force_mag, scalar &  e  )

protected

Referenced by calc_gensoft_force_pair_matrix().

calc_gensoft_force_pair_matrix()

void VdW_solver::calc_gensoft_force_pair_matrix ( vector3(&)  force_pair_matrix[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&)  p[num_tri_gauss_quad_points], vector3(&)  q[num_tri_gauss_quad_points], scalar &  Rmin, scalar &  Emin, scalar &  k0, scalar &  energy  )

protected

Referenced by do_gensoft_interaction().

calc_lj_factors()

void VdW_solver::calc_lj_factors ( scalar &  mag_r, int  index_k, int  index_l, scalar &  Emin, scalar &  Rmin_6, scalar &  force_mag, scalar &  e  )

protected

Given (mag_r), get LJ force magnitude (force_mag) and energy (e)

Referenced by calc_lj_force_pair_matrix(), and calc_ljinterpolated_force_pair_matrix().

calc_lj_force_pair_matrix()

void VdW_solver::calc_lj_force_pair_matrix ( vector3(&)  force_pair_matrix[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&)  p[num_tri_gauss_quad_points], vector3(&)  q[num_tri_gauss_quad_points], scalar &  Rmin, scalar &  Emin, scalar &  energy  )

protected

Referenced by do_lj_interaction().

calc_ljinterpolated_factors()

void VdW_solver::calc_ljinterpolated_factors ( scalar &  mag_r, int  index_k, int  index_l, scalar &  Emin, scalar &  Rmini, scalar &  force_mag, scalar &  e  )

protected

Given (mag_r), get LJ_interpolated force magnitude (force_mag) and energy (e)

Referenced by calc_ljinterpolated_force_pair_matrix().

calc_ljinterpolated_force_pair_matrix()

void VdW_solver::calc_ljinterpolated_force_pair_matrix ( vector3(&)  force_pair_matrix[num_tri_gauss_quad_points][num_tri_gauss_quad_points], vector3(&)  p[num_tri_gauss_quad_points], vector3(&)  q[num_tri_gauss_quad_points], scalar &  Rmin, scalar &  Emin, scalar &  energy  )

protected

Referenced by do_lj_interaction().

consider_interaction()

bool VdW_solver::consider_interaction ( Face *  f1, int  l_index_i, int  motion_state_i, LinkedListNode< Face > *  l_j, scalar *  blob_corr  )

protected

Referenced by solve().

distance2()

scalar VdW_solver::distance2 ( vector3 &  p, vector3 &  q  )

protected

Referenced by calc_gensoft_force_pair_matrix(), calc_lj_force_pair_matrix(), and calc_ljinterpolated_force_pair_matrix().

do_gensoft_interaction()

void VdW_solver::do_gensoft_interaction ( Face *  f1, Face *  f2, scalar *  blob_corr  )

protected

Referenced by GenSoftSSINT_solver::do_interaction().

do_interaction()

void VdW_solver::do_interaction ( Face *  f1, Face *  f2, scalar *  blob_corr  )

protectedvirtual

Alters interaction calculations to apply periodic boundary conditions

Reimplemented in GenSoftSSINT_solver, LJSteric_solver, and Steric_solver.

Referenced by solve().

do_lj_interaction()

void VdW_solver::do_lj_interaction ( Face *  f1, Face *  f2, scalar *  blob_corr  )

protected

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

do_steric_interaction()

bool VdW_solver::do_steric_interaction ( Face *  f1, Face *  f2, scalar *  blob_corr  )

protected

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

do_sticky_xz_interaction()

void VdW_solver::do_sticky_xz_interaction ( Face *  f, bool  bottom_wall, scalar  dim_y  )

protected

Referenced by solve_sticky_wall().

dot()

scalar VdW_solver::dot ( vector3 *  p, vector3 *  q  )

protected

dot_with_normal()

scalar VdW_solver::dot_with_normal ( vector3 *  p, vector3 *  q, vector3 *  n  )

protected

get_field_energy()

scalar VdW_solver::get_field_energy	(	int	i,
		int	j
	)

Referenced by World::make_measurements(), and World::write_detailed_measurements_to_file().

init()

int VdW_solver::init	(	NearestNeighbourLinkedListCube *	surface_face_lookup,
		vector3 *	box_size,
		SSINT_matrix *	ssint_matrix,
		scalar &	steric_factor,
		int	num_blobs,
		int	inc_self_ssint,
		string	ssint_type_string,
		scalar &	steric_dr,
		int	calc_kinetics,
		bool	working_w_static_blobs
	)

Referenced by World::init().

minimum_image()

scalar VdW_solver::minimum_image ( scalar  delta, scalar  size  )

protected

reset_fieldenergy()

void VdW_solver::reset_fieldenergy

(

)

Zero measurement stuff, AKA fieldenergy

Referenced by solve().

solve()

int VdW_solver::solve

(

scalar *

blob_corr

)

Solve VdW

Referenced by World::run().

solve_sticky_wall()

int VdW_solver::solve_sticky_wall

(

scalar

h

)

Allow protein VdW interactions along the top and bottom x-z planes

Referenced by World::run().

Field Documentation

adjacent_cell_lookup_table

const int VdW_solver::adjacent_cell_lookup_table

staticprotected

Initial value:

= {
    {-1, -1, -1},
    {-1, -1, 0},
    {-1, -1, +1},
    {-1, 0, -1},
    {-1, 0, 0},
    {-1, 0, +1},
    {-1, +1, -1},
    {-1, +1, 0},
    {-1, +1, +1},
    {0, -1, -1},
    {0, -1, 0},
    {0, -1, +1},
    {0, 0, -1},
    {0, 0, 0},
    {0, 0, +1},
    {0, +1, -1},
    {0, +1, 0},
    {0, +1, +1},
    {+1, -1, -1},
    {+1, -1, 0},
    {+1, -1, +1},
    {+1, 0, -1},
    {+1, 0, 0},
    {+1, 0, +1},
    {+1, +1, -1},
    {+1, +1, 0},
    {+1, +1, +1}
}

Referenced by solve().

box_size

vector3 VdW_solver::box_size

protected

Referenced by VdW_solver(), and ~VdW_solver().

calc_kinetics

int VdW_solver::calc_kinetics

protected

Referenced by init(), and solve().

fieldenergy

scalar** VdW_solver::fieldenergy

protected

Referenced by do_gensoft_interaction(), do_lj_interaction(), do_steric_interaction(), get_field_energy(), init(), reset_fieldenergy(), VdW_solver(), and ~VdW_solver().

gauss_points

const VdW_solver::tri_gauss_point VdW_solver::gauss_points

staticprotected

Initial value:

= {
    
    {   0.333333333333333,
        {0.666666666666667, 0.166666666666667, 0.166666666666667}
    },
    {   0.333333333333333,
        {0.166666666666667, 0.666666666666667, 0.166666666666667}
    },
    {   0.333333333333333,
        {0.166666666666667, 0.166666666666667, 0.666666666666667}
    }

    

    
}

Referenced by calc_gensoft_factors(), calc_lj_factors(), calc_ljinterpolated_factors(), do_gensoft_interaction(), do_lj_interaction(), and do_sticky_xz_interaction().

inc_self_ssint

int VdW_solver::inc_self_ssint

protected

whether to include interactions between faces within the same blob, or not.

Referenced by consider_interaction(), and init().

num_blobs

int VdW_solver::num_blobs

protected

Referenced by consider_interaction(), get_field_energy(), init(), reset_fieldenergy(), VdW_solver(), and ~VdW_solver().

num_tri_gauss_quad_points

const int VdW_solver::num_tri_gauss_quad_points = 3

staticprotected

Referenced by calc_gensoft_force_pair_matrix(), calc_lj_force_pair_matrix(), calc_ljinterpolated_force_pair_matrix(), do_gensoft_interaction(), do_lj_interaction(), and do_sticky_xz_interaction().

ssint_matrix

SSINT_matrix* VdW_solver::ssint_matrix

protected

Referenced by do_gensoft_interaction(), do_lj_interaction(), do_sticky_xz_interaction(), and init().

ssint_type

int VdW_solver::ssint_type

protected

Referenced by consider_interaction(), do_lj_interaction(), init(), VdW_solver(), and ~VdW_solver().

steric_dr

scalar VdW_solver::steric_dr

protected

Constant to calculate the numerical derivative.

Referenced by do_steric_interaction(), and init().

steric_factor

scalar VdW_solver::steric_factor

protected

Proportionality factor to the Steric repulsion.

Referenced by do_steric_interaction(), and init().

surface_face_lookup

NearestNeighbourLinkedListCube* VdW_solver::surface_face_lookup

protected

Referenced by init(), solve(), solve_sticky_wall(), VdW_solver(), and ~VdW_solver().

total_num_surface_faces

int VdW_solver::total_num_surface_faces

protected

Referenced by solve(), VdW_solver(), and ~VdW_solver().

working_w_static_blobs

bool VdW_solver::working_w_static_blobs

protected

Referenced by consider_interaction(), init(), and solve().

---

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

• VdW_solver.h
• VdW_solver.cpp