rod_math_v9.h File Reference

#include <cmath>
#include <iostream>
#include <assert.h>
#include "dimensions.h"
#include <stdlib.h>
#include <boost/math/special_functions/fpclassify.hpp>

Go to the source code of this file.

Namespaces
	rod

Macros
#define	OUT
	This is used to denote when a function modifies one of its parameters. More...
#define	_USE_MATH_DEFINES
	This has to come before including cmath. More...
#define	OMP_SIMD_INTERNAL   _Pragma("omp simd")
#define	vec3d(x)   for(int x = 0; x < 3; ++ x)
	Shorthand to loop over elements of our 1d arrays representing 3d vectors. More...

Functions
void	rod::rod_abort (std::string message)
void	rod::print_array (std::string array_name, float array[], int length)
void	rod::print_array (std::string array_name, double array[], int length)
void	rod::normalize (float in[3], OUT float out[3])
void	rod::normalize_unsafe (float in[3], OUT float out[3])
float	rod::absolute (float in[3])
void	rod::cross_product (float a[3], float b[3], float out[3])
void	rod::cross_product_unsafe (float a[3], float b[3], float out[3])
void	rod::get_rotation_matrix (float a[3], float b[3], float rotation_matrix[9])
void	rod::apply_rotation_matrix (float vec[3], float matrix[9], OUT float rotated_vec[3])
void	rod::apply_rotation_matrix_row (float vec[3], float matrix[9], OUT float rotated_vec[3])
void	rod::matmul_3x3_3x3 (float a[9], float b[9], OUT float out[9])
void	rod::get_p_i (float curr_r[3], float next_r[3], OUT float p_i[3])
void	rod::rodrigues_rotation (float v[3], float k[3], float theta, OUT float v_rot[3])
float	rod::safe_cos (float in)
float	rod::get_l_i (float p_i[3], float p_im1[3])
float	rod::get_signed_angle (float m1[3], float m2[3], float l[3])
void	rod::perpendicularize (float m_i[3], float p_i[3], OUT float m_i_prime[3])
void	rod::update_m1_matrix (float m_i[3], float p_i[3], float p_i_prime[3], float m_i_prime[3])
float	rod::get_stretch_energy (float k, float p_i[3], float p_i_equil[3])
void	rod::parallel_transport (float m[3], float m_prime[3], float p_im1[3], float p_i[3])
float	rod::get_twist_energy (float beta, float m_i[3], float m_im1[3], float m_i_equil[3], float m_im1_equil[3], float p_im1[3], float p_i[3], float p_im1_equil[3], float p_i_equil[3])
void	rod::get_kb_i (float p_im1[3], float p_i[3], float e_im1_equil[3], float e_i_equil[3], OUT float kb_i[3])
void	rod::get_omega_j_i (float kb_i[3], float n_j[3], float m_j[3], OUT float omega_j_i[2])
float	rod::get_bend_energy (float omega_i_im1[2], float omega_i_im1_equil[2], float B_equil[4])
float	rod::get_bend_energy_from_p (float p_im1[3], float p_i[3], float p_im1_equil[3], float p_i_equil[3], float n_im1[3], float m_im1[3], float n_im1_equil[3], float m_im1_equil[3], float n_i[3], float m_i[3], float n_i_equil[3], float m_i_equil[3], float B_i_equil[4], float B_im1_equil[4])
float	rod::get_weights (float a[3], float b[3])
void	rod::get_mutual_element_inverse (float pim1[3], float pi[3], float weight, OUT float mutual_element[3])
void	rod::get_mutual_axes_inverse (float mim1[3], float mi[3], float weight, OUT float m_mutual[3])
float	rod::get_bend_energy_mutual_parallel_transport (float p_im1[3], float p_i[3], float p_im1_equil[3], float p_i_equil[3], float n_im1[3], float m_im1[3], float n_im1_equil[3], float m_im1_equil[3], float n_i[3], float m_i[3], float n_i_equil[3], float m_i_equil[3], float B_i_equil[4], float B_im1_equil[4])
float	rod::get_translational_friction (float viscosity, float radius, bool rotational)
float	rod::get_rotational_friction (float viscosity, float radius, float length, bool safe)
float	rod::get_force (float bend_energy, float stretch_energy, float delta_x)
float	rod::get_torque (float twist_energy, float delta_theta)
float	rod::get_delta_r (float friction, float timestep, float force, float noise, float external_force)
float	rod::get_noise (float timestep, float kT, float friction, float random_number)
void	rod::load_p (float p[4][3], float *r, int offset)
void	rod::load_m (float m_loaded[4][3], float *m, int offset)
void	rod::normalize_all (float p[4][3])
void	rod::absolute_all (float p[4][3], float absolutes[4])
void	rod::cross_all (float p[4][3], float m[4][3], OUT float n[4][3])
void	rod::delta_e_all (float p[4][3], float new_p[4][3], OUT float delta_p[4][3])
void	rod::update_m1_all (float m[4][3], float absolutes[4], float t[4][3], float delta_e[4][3], OUT float m_out[4][3])
void	rod::update_m1_matrix_all (float m[4][3], float p[4][3], float p_prime[4][3], OUT float m_prime[4][3], int start_cutoff, int end_cutoff)
void	rod::fix_m1_all (float m[4][3], float new_t[4][3])
void	rod::update_and_fix_m1_all (float old_e[4][3], float new_e[4][3], float m[4][3])
void	rod::set_cutoff_values (int e_i_node_no, int length, OUT int start_cutoff, int end_cutoff)
bool	rod::not_simulation_destroying (float x)
bool	rod::not_simulation_destroying (float x[3])
void	rod::load_B_all (float B[4][4], float *B_matrix, int offset)
void	rod::make_diagonal_B_matrix (float B, OUT float B_matrix[4])
void	rod::set_cutoff_values (int p_i_node_no, int num_nodes, OUT int *start_cutoff, int *end_cutoff)
float	rod::get_absolute_length_from_array (float *array, int node_no, int length)
void	rod::get_centroid_generic (float *r, int length, OUT float centroid[3])
void	rod::get_perturbation_energy (float perturbation_amount, int perturbation_dimension, float B_equil[4], float *material_params, int start_cutoff, int end_cutoff, int p_i_node_no, float *r_all, float *r_all_equil, float *m_all, float *m_all_equil, float energies[3])

Variables
static const bool	rod::debug_nan = false
const double	rod::boltzmann_constant = 1.3806503e-23/mesoDimensions::Energy
static const int	rod::x = 0
static const int	rod::y = 1
static const int	rod::z = 2
static const int	rod::im2 = 0
	index of i-2nd thing More...
static const int	rod::im1 = 1
	index of i-1st thing More...
static const int	rod::i = 2
	index of ith thing More...
static const int	rod::ip1 = 3
	index of i+1th thing More...
static const float	rod::rod_software_version = 0.3

Macro Definition Documentation

_USE_MATH_DEFINES

#define _USE_MATH_DEFINES

This has to come before including cmath.

OMP_SIMD_INTERNAL

#define OMP_SIMD_INTERNAL   _Pragma("omp simd")

OUT

#define OUT

This is used to denote when a function modifies one of its parameters.

Referenced by rod::get_bend_energy_mutual_parallel_transport(), and rod::Rod_blob_interface::position_rod_from_blob().

vec3d

#define vec3d

(

x

)

for(int x = 0; x < 3; ++ x)

Shorthand to loop over elements of our 1d arrays representing 3d vectors.

Referenced by ffea_test::arbitrary_equilibrium_bend(), ffea_test::connection_energy(), ffea_test::connection_propagation(), rod::Rod_blob_interface::do_connection_timestep(), rod::equil_attachment_node_from_J(), rod::get_absolute_length_from_array(), rod::Rod_blob_interface::get_attachment_material_axis(), rod::Rod_blob_interface::get_attachment_node(), rod::Rod_blob_interface::get_attachment_node_pos(), rod::get_attachment_node_pos(), rod::Rod::get_centroid(), rod::Rod_blob_interface::get_element_id(), rod::get_kb_i(), rod::get_mutual_axes_inverse(), rod::get_mutual_element_inverse(), rod::Rod_blob_interface::get_node_energy(), rod::get_p_i(), ffea_test::identify_face(), rod::load_p(), rod::normalize(), rod::normalize_unsafe(), rod::perpendicularize(), rod::points_out_of_tet(), rod::Rod_blob_interface::position_blob_from_rod(), rod::Rod_blob_interface::position_rod_ends(), rod::Rod_blob_interface::position_rod_from_blob(), rod::precise_normalize(), rod::QR_decompose_gram_schmidt(), rod::rescale_attachment_node(), rod::Rod_blob_interface::Rod_blob_interface(), rod::rodrigues_rotation(), rod::rotate_tet(), rod::Rod_blob_interface::select_face_nodes(), rod::Rod_blob_interface::set_edge_vecs(), and rod::Rod_blob_interface::set_tet().