SimulationParams.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
//  the Free Software Foundation, either version 3 of the License, or
//  (at your option) any later version.
// 
//  FFEA is distributed in the hope that it will be useful,
//  but WITHOUT ANY WARRANTY; without even the implied warranty of
//  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/>.
// 
//  To help us fund FFEA development, we humbly ask that you cite 
//  the research papers on the package.
//

#ifndef PARAMS_H_INCLUDED
#define PARAMS_H_INCLUDED

#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <time.h>
#include <vector>
#include <map>
#include <iostream>
#include <boost/algorithm/string.hpp>
#include <boost/filesystem.hpp>
#include <boost/lexical_cast.hpp>

#include "FFEA_return_codes.h"
#include "FFEA_user_info.h"
#include "mat_vec_types.h"
#include "dimensions.h"
#include "FFEA_input_reader.h"

#define WALL_TYPE_PBC 0
#define WALL_TYPE_HARD 1
#define WALL_TYPE_STOP 2

#define UNSET 0
#define SET 1
#define DEFAULT 2

using namespace std;
namespace b_fs = boost::filesystem;

struct PreComp_params {
  vector<string> types; 
  string folder; 
  int inputData; 
  scalar dist_to_m;
  scalar E_to_J;
};


class SimulationParams {
public:
    scalar dt; 
    long long num_steps; 
    int check; 
    int num_blobs; 
    int num_rods; 
    int num_interfaces; 
    int *num_conformations; 
    int *num_states; 
    int state_array_size;
    int conformation_array_size;
    int rng_seed; 

    scalar kT; 

    int max_iterations_cg; 
    scalar epsilon2; 

    int es_update; 
    int es_N_x; 
    int es_N_y; 
    int es_N_z; 
    int move_into_box;  
    int restrict_motion[3]; 
    int num_dimensions;  
    scalar es_h; 

    scalar kappa; 

    scalar epsilon_0; 
    scalar dielec_ext; 

    int restart; 

    int calc_ssint; 
    int inc_self_ssint; 
    string ssint_type;  
    int calc_es; 
    int calc_noise; 
    int calc_stokes; 
    int calc_kinetics;  
    int calc_preComp; 
    int calc_springs; 
    int calc_ctforces; 
    int force_pbc; 
    int kinetics_update; 
    int wall_x_1;
    int wall_x_2;
    int wall_y_1;
    int wall_y_2;
    int wall_z_1;
    int wall_z_2;

    int sticky_wall_xz;

    scalar stokes_visc;

    int calc_steric; 
    scalar steric_factor; 
    scalar ssint_cutoff; 
    geoscalar steric_dr; 

    string FFEA_script_filename;
    b_fs::path FFEA_script_path, FFEA_script_basename;
    string trajectory_out_fname;
    string kinetics_out_fname;
    string measurement_out_fname;
    string detailed_meas_out_fname;
    string ssint_in_fname;
    string bsite_in_fname;
    string icheckpoint_fname;  
    string ocheckpoint_fname;  
    string ctforces_fname; 
    string springs_fname; 
    string trajectory_beads_fname; 

    SimulationParams();

    ~SimulationParams();

    int validate(int sim_mode);

    int parse_param_assignment(char *str);

    int extract_params(vector<string> script_vector);

    int assign(string lvalue, string rvalue);

    int get_max_num_states();

    int kinetics_out_fname_set;
    int trajbeads_fname_set; 

    void write_to_file(FILE *fout, PreComp_params &pc_params);

private:
    int trajectory_out_fname_set;
    int measurement_out_fname_set;
    int icheckpoint_fname_set;
    int ocheckpoint_fname_set;
    int ssint_in_fname_set;
    int bsite_in_fname_set;

    int checkFileName(string oFile);

    string RemoveFileExtension(const string& FileName);
};
#endif