#include <VdW_solver.h>
|
| VdW_solver () |
|
| ~VdW_solver () |
|
int | init (NearestNeighbourLinkedListCube *surface_face_lookup, vector3 *box_size, LJ_matrix *lj_matrix, scalar &vdw_steric_factor, int num_blobs, int inc_self_vdw, string vdw_type_string, scalar &vdw_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 () |
|
|
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_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 &vdw_r_eq, scalar &vdw_eps, 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 &vdw_r_eq, scalar &vdw_eps, scalar &energy) |
|
void | calc_lj_factors (scalar &mag_r, int index_k, int index_l, scalar &vdw_eps, scalar &vdw_r_eq_6, scalar &force_mag, scalar &e) |
|
void | calc_ljinterpolated_factors (scalar &mag_r, int index_k, int index_l, scalar &vdw_eps, scalar &vdw_r_eqi, 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) |
|
§ VdW_solver()
VdW_solver::VdW_solver |
( |
| ) |
|
§ ~VdW_solver()
VdW_solver::~VdW_solver |
( |
| ) |
|
§ calc_lj_factors()
§ 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 & |
vdw_r_eq, |
|
|
scalar & |
vdw_eps, |
|
|
scalar & |
energy |
|
) |
| |
|
protected |
§ calc_ljinterpolated_factors()
void VdW_solver::calc_ljinterpolated_factors |
( |
scalar & |
mag_r, |
|
|
int |
index_k, |
|
|
int |
index_l, |
|
|
scalar & |
vdw_eps, |
|
|
scalar & |
vdw_r_eqi, |
|
|
scalar & |
force_mag, |
|
|
scalar & |
e |
|
) |
| |
|
protected |
§ 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 & |
vdw_r_eq, |
|
|
scalar & |
vdw_eps, |
|
|
scalar & |
energy |
|
) |
| |
|
protected |
§ consider_interaction()
§ distance2()
§ do_interaction()
void VdW_solver::do_interaction |
( |
Face * |
f1, |
|
|
Face * |
f2, |
|
|
scalar * |
blob_corr |
|
) |
| |
|
protectedvirtual |
§ do_lj_interaction()
void VdW_solver::do_lj_interaction |
( |
Face * |
f1, |
|
|
Face * |
f2, |
|
|
scalar * |
blob_corr |
|
) |
| |
|
protected |
§ do_steric_interaction()
bool VdW_solver::do_steric_interaction |
( |
Face * |
f1, |
|
|
Face * |
f2, |
|
|
scalar * |
blob_corr |
|
) |
| |
|
protected |
§ do_sticky_xz_interaction()
void VdW_solver::do_sticky_xz_interaction |
( |
Face * |
f, |
|
|
bool |
bottom_wall, |
|
|
scalar |
dim_y |
|
) |
| |
|
protected |
§ dot()
§ dot_with_normal()
§ get_field_energy()
scalar VdW_solver::get_field_energy |
( |
int |
i, |
|
|
int |
j |
|
) |
| |
§ init()
§ minimum_image()
§ reset_fieldenergy()
void VdW_solver::reset_fieldenergy |
( |
| ) |
|
Zero measurement stuff, AKA fieldenergy
Referenced by solve().
§ solve()
int VdW_solver::solve |
( |
scalar * |
blob_corr | ) |
|
§ 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().
§ 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
§ calc_kinetics
int VdW_solver::calc_kinetics |
|
protected |
§ fieldenergy
scalar** VdW_solver::fieldenergy |
|
protected |
§ gauss_points
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_lj_factors(), calc_ljinterpolated_factors(), do_lj_interaction(), and do_sticky_xz_interaction().
§ inc_self_vdw
int VdW_solver::inc_self_vdw |
|
protected |
§ lj_matrix
§ num_blobs
int VdW_solver::num_blobs |
|
protected |
§ num_tri_gauss_quad_points
const int VdW_solver::num_tri_gauss_quad_points = 3 |
|
staticprotected |
§ steric_dr
§ steric_factor
scalar VdW_solver::steric_factor |
|
protected |
§ surface_face_lookup
§ total_num_surface_faces
int VdW_solver::total_num_surface_faces |
|
protected |
§ vdw_type
§ working_w_static_blobs
bool VdW_solver::working_w_static_blobs |
|
protected |
The documentation for this class was generated from the following files: