rod_structure.h

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// 
//  This file is part of the FFEA simulation package
//  
//  Copyright (c) by the Theory and Development FFEA teams,
//  as they appear in the README.md file. 
// 
//  FFEA is free software: you can redistribute it and/or modify
//  it under the terms of the GNU General Public License as published by
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU General Public License for more details.
// 
//  You should have received a copy of the GNU General Public License
//  along with FFEA.  If not, see <http://www.gnu.org/licenses/>.
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/*
 *      rod_structure.h
 *  Author: Rob Welch, University of Leeds
 *  Email: py12rw@leeds.ac.uk
 */
#ifndef ROD_STRUCTURE
#define ROD_STRUCTURE

#include <iostream>
#include <fstream>
#include <cassert>
#include <boost/algorithm/string.hpp>
#include <string>
#include <vector>
#include "rod_math_v9.h"
#include <omp.h>
#include "RngStream.h"
#include <stdio.h>

namespace rod {

std::vector <float> stof_vec (std::vector <std::string> vec_in, int length);
struct Rod
{
  int length; 
  int num_elements; 
  int num_rods; 
  int rod_no; 
  int line_start = 0; 
  double rod_version = 999.999; 
  bool computed_rest_energy = false;
  
  float viscosity = 1; 
  float timestep = 0.002;
  float kT = 0; 
  float perturbation_amount = 0.01; 
  float translational_friction;
  float rotational_friction; 
  float * equil_r; 
  float * equil_m; 
  float * current_r; 
  float * current_m; 
  float * perturbed_x_energy_positive; 
  float * perturbed_y_energy_positive;
  float * perturbed_z_energy_positive;
  float * twisted_energy_positive;
  float * perturbed_x_energy_negative; 
  float * perturbed_y_energy_negative;
  float * perturbed_z_energy_negative;
  float * twisted_energy_negative;
  float * material_params; 
  float * B_matrix; 
  float * applied_forces; 
  bool * pinned_nodes; 
  bool interface_at_start = false; 
  bool interface_at_end = false; 
  bool restarting = false; 
  float bending_response_factor;
  float spring_constant_factor;
  float twist_constant_factor;
  float viscosity_constant_factor;
  
  std::string rod_filename;
  FILE * file_ptr;
  int frame_no = 0;
  int step_no = 0;
  Rod (int length, int set_rod_no);
  Rod (std::string path, int set_rod_no);
  Rod set_units();
  Rod compute_rest_energy ();
  Rod do_timestep(RngStream rng[]);
  Rod add_force(float force[4], int node_index);
  Rod pin_node(bool pin_state, int node_index);
  Rod load_header (std::string filename);
  Rod load_contents (std::string filename);
  Rod write_frame_to_file ();
  Rod write_array (float * array_ptr, int array_len, float unit_scale_factor);
  Rod write_mat_params_array(float *array_ptr, int array_len, float stretch_scale_factor, float twist_scale_factor, float length_scale_factor);
  Rod change_filename(std::string new_filename);
  Rod equilibrate_rod(RngStream rng[]);
  Rod translate_rod(float* r, float translation_vec[3]);
  Rod rotate_rod(float euler_angles[3]);
  Rod scale_rod(float scale);
  Rod get_centroid(float *r, float centroid[3]);
  Rod get_min_max(float *r, OUT float min[3], float max[3]);
  Rod get_p(int index, OUT float p[3], bool equil);
};

} //end namespace
#endif