#include <VdW_solver.h>
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 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 [] |
VdW_solver::VdW_solver | ( | ) |
VdW_solver::~VdW_solver | ( | ) |
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Referenced by calc_gensoft_force_pair_matrix().
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Referenced by do_gensoft_interaction().
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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().
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Referenced by do_lj_interaction().
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Given (mag_r), get LJ_interpolated force magnitude (force_mag) and energy (e)
Referenced by calc_ljinterpolated_force_pair_matrix().
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Referenced by do_lj_interaction().
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Referenced by solve().
Referenced by GenSoftSSINT_solver::do_interaction().
Alters interaction calculations to apply periodic boundary conditions
Reimplemented in GenSoftSSINT_solver, LJSteric_solver, and Steric_solver.
Referenced by solve().
Referenced by LJSteric_solver::do_interaction(), and do_interaction().
Referenced by solve_sticky_wall().
scalar VdW_solver::get_field_energy | ( | int | i, |
int | j | ||
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Referenced by World::make_measurements(), and World::write_detailed_measurements_to_file().
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().
void VdW_solver::reset_fieldenergy | ( | ) |
Zero measurement stuff, AKA fieldenergy
Referenced by solve().
int VdW_solver::solve | ( | scalar * | blob_corr | ) |
Solve VdW
Referenced by World::run().
int VdW_solver::solve_sticky_wall | ( | scalar | h | ) |
Allow protein VdW interactions along the top and bottom x-z planes
Referenced by World::run().
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Referenced by solve().
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Referenced by VdW_solver(), and ~VdW_solver().
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Referenced by calc_gensoft_factors(), calc_lj_factors(), calc_ljinterpolated_factors(), do_gensoft_interaction(), do_lj_interaction(), and do_sticky_xz_interaction().
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whether to include interactions between faces within the same blob, or not.
Referenced by consider_interaction(), and init().
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Referenced by consider_interaction(), get_field_energy(), init(), reset_fieldenergy(), VdW_solver(), and ~VdW_solver().
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Referenced by do_gensoft_interaction(), do_lj_interaction(), do_sticky_xz_interaction(), and init().
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Referenced by consider_interaction(), do_lj_interaction(), init(), VdW_solver(), and ~VdW_solver().
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Constant to calculate the numerical derivative.
Referenced by do_steric_interaction(), and init().
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Proportionality factor to the Steric repulsion.
Referenced by do_steric_interaction(), and init().
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Referenced by init(), solve(), solve_sticky_wall(), VdW_solver(), and ~VdW_solver().
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Referenced by solve(), VdW_solver(), and ~VdW_solver().
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Referenced by consider_interaction(), init(), and solve().