neutrals.h

// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
// Full license can be found in License.md
 
#ifndef INCLUDE_NEUTRALS_H_
#define INCLUDE_NEUTRALS_H_
 
/**************************************************************
 * \class Neutrals
 *
 * \brief Defines the neutral states
 * 
 * The Neutrals class defines the neutrals states as well as a bunch
 * of derived states and source/loss terms.  The initial temperature
 * structure as well as the lower boundary densities can be set
 * through the planet input file.
 *
 * \author Aaron Ridley
 *
 * \date 2021/03/28 
 *
 **************************************************************/
 
#include <string>
#include <vector>
 
class Neutrals {
 
 public:
 
 
  struct species_chars {
 
    std::string cName;
 
    precision_t mass;
 
    precision_t vibe;
 
    int DoAdvect;
 
    arma_cube density_scgc;
 
    std::vector<float> diff0;
    std::vector<float> diff_exp;
 
    std::vector<float> neutral_ion;
 
    precision_t thermal_cond;
    precision_t thermal_exp;
 
    int iEuvAbsId_;
    int nEuvIonSpecies;
    std::vector<int> iEuvIonId_;
    std::vector<int> iEuvIonSpecies_;
 
    int nAuroraIonSpecies;
    std::vector<int> iAuroraIonSpecies_;
    float Aurora_Coef;
 
    // --------------------------------------------------
    // Some derived quantities:
    arma_cube rho_alt_int_scgc;
 
    arma_cube chapman_scgc;
 
    arma_cube scale_height_scgc;
 
    // --------------------------------------------------
    // Sources and Losses:
 
    arma_cube ionization_scgc;
 
    arma_cube sources_scgc;
    
    arma_cube losses_scgc;
 
    precision_t lower_bc_density;
  };
 
  // bulk quantities (states):
 
  arma_cube density_scgc;
 
  std::vector<arma_cube> velocity_vcgc;
 
  arma_cube temperature_scgc;
 
  arma_cube rho_scgc;
 
  arma_cube mean_major_mass_scgc;
 
  arma_cube pressure_scgc;
 
  arma_cube sound_scgc;
 
  arma_cube Cv_scgc;
 
  arma_cube gamma_scgc;
 
  arma_cube kappa_scgc;
 
  std::vector<species_chars> species;
  
  precision_t max_chapman = 1.0e26;
 
  // Source terms:
 
  arma_cube conduction_scgc;
 
  arma_cube heating_euv_scgc;
 
  precision_t heating_efficiency;
 
  float *initial_temperatures, *initial_altitudes;
  int nInitial_temps = 0;
 
  // names and units
  std::string density_name = "Neutral Bulk Density";
  std::string density_unit = "(/m3)";
 
  std::vector<std::string> velocity_name;
  std::string velocity_unit = "(m/s)";
 
  std::string temperature_name = "Temperature";
  std::string temperature_unit = "(K)";
 
  // --------------------------------------------------------------------
  // Functions:
 
  /**********************************************************************
     \brief Initialize the neutrals
     \param grid The grid to define the neutrals on
     \param input info about how user has configured things
     \param report allow reporting to occur
   **/
  Neutrals(Grid grid, Inputs input, Report report);
 
  /**********************************************************************
     \brief Creates the variables within the species_chars structure
     \param grid The grid to define the neutrals on
     \param input info about how user has configured things
     \param report allow reporting to occur
   **/
  species_chars create_species(Grid grid);
 
  /**********************************************************************
     \brief Read in the planet-specific file
 
     This file specifies the species to model, their masses, 
     diffusion coefficients and all of the other things needed
     for specifying the neutrals.
 
     \param input info about how user has configured things
     \param report allow reporting to occur
   **/
  int read_planet_file(Inputs input, Report report);
 
  /**********************************************************************
     \brief Sets the initial conditions of the neutrals
     \param grid The grid to define the neutrals on
     \param input info about how user has configured things
     \param report allow reporting to occur
   **/
  int initial_conditions(Grid grid, Inputs input, Report report);
 
  /**********************************************************************
     \brief temporary function to set neutral densities with in the model
 
     This function integrates the species densities from the bottom
     of the model using a hydrostatic approximation and the bulk
     temperature.  It is temporary until we get a vertical solver.
 
     \param grid The grid to define the neutrals on
     \param report allow reporting to occur
   **/
  void fill_with_hydrostatic(Grid grid, Report report);
 
  /**********************************************************************
     \brief Calculate the bulk mass density from individual species densities
     \param report allow reporting to occur
   **/
  void calc_mass_density(Report &report);
 
  /**********************************************************************
     \brief Calculate the bulk specific heat from individual species
     \param report allow reporting to occur
   **/
  void calc_specific_heat(Report &report);
 
  /**********************************************************************
     \brief Calculate the chapman integrals for the individual species
     \param grid The grid to define the neutrals on
     \param report allow reporting to occur
   **/
  void calc_chapman(Grid grid, Report &report);
 
  /**********************************************************************
     \brief Calculate the neutral bulk vertical thermal conduction
     \param grid The grid to define the neutrals on
     \param time The times within the model (dt is needed)
     \param report allow reporting to occur
   **/
  void calc_conduction(Grid grid, Times time, Report &report);
 
  /**********************************************************************
     \brief Add all of the neutral source terms to each of the equations
     \param time The times within the model (dt is needed)
     \param report allow reporting to occur
   **/
  void add_sources(Times time, Report &report);
 
  /**********************************************************************
     \brief Set boundary conditions for the neutrals
     \param report allow reporting to occur
   **/
  void set_bcs(Report &report);
  int get_species_id(std::string name, Report &report);
};
 
#endif  // INCLUDE_NEUTRALS_H_