balance.hh

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 * 
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 * 
 * This program 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.
 *
 * 
 * @file    balance.hh
 * @brief   
 */

#ifndef BALANCE_HH_
#define BALANCE_HH_


#include "la/distribution.hh"
#include "transport/substance.hh"
#include "petscmat.h"
#include "fields/unit_si.hh"
#include "tools/time_marks.hh"

class RegionDB;
class TimeGovernor;
class TimeStep;




/**
 * Design of balance class - serves as storage and writer.
 * Equations themselves call methods of Balance that add/modify mass, source and flux
 * of various quantities and generate output.
 *
 * One instance of Balance can handle several conservative quantities of the same type
 * (e.g. mass of several substances or their phases).
 *
 * The mass, flux and source are calculated as follows:
 *
 *  m(q,r) =  ( M'(q) * solution + mv(q) )[r]
 *  f(q,r) = -( R' * ( F(q) * solution + fv(q) ) )[r]
 *  s(q,r) =  ( S'(q) * solution + sv(q) )[r]
 *
 * where M' stands for matrix transpose,
 *
 *  m(q,r)...mass of q-th substance in region r
 *  f(q,r)...incoming flux of q-th substance in region r
 *  s(q,r)...source of q-th substance in region r
 *
 * and
 *
 *  M(q)...region_mass_matrix_      n_dofs x n_bulk_regions
 *  F(q)...be_flux_matrix_          n_boundary_edges x n_dofs
 *  S(q)...region_source_matrix_    n_dofs x n_bulk_regions
 *  SV(q)..region_source_rhs_       n_dofs x n_bulk_regions
 *  mv(q)..region_mass_vec_         n_bulk_regions
 *  fv(q)..be_flux_vec_             n_boundary_edges
 *  sv(q)..region_source_vec_       n_bulk_regions
 *  R......region_be_matrix_        n_boundary_edges x n_boundary_regions
 * 
 * Remark: Matrix F and the vector fv are such that F*solution+fv produces _outcoming_ fluxes per boundary edge.
 * However we write to output _incoming_ flux due to users' convention and consistently with input interface.
 *
 * Note that it holds:
 *
 *  sv(q) = column sum of SV(q)
 *
 * Except for that, we also provide information on positive/negative flux and source:
 *
 *  fp(q,r) = ( R' * EFP(q) )[r],   EFP(q)[e] = max{ 0, ( F(q) * solution + fv(q) )[e] }
 *  fn(q,r) = ( R' * EFN(q) )[r],   EFN(q)[e] = min{ 0, ( F(q) * solution + fv(q) )[e] }
 *  sp(q,r) = sum_{i in DOFS } max{ 0, ( S(q)[i,r] * solution[i] + SV(q)[i,r] ) }
 *  sn(q,r) = sum_{i in DOFS } min{ 0, ( S(q)[i,r] * solution[i] + SV(q)[i,r] ) }
 *
 * where
 *
 *  fp(q,r)...positive (inward) flux of q-th quantity in region r
 *  fn(q,r)...negative (outward) flux of q-th quantity in region r
 *  sp(q,r)...positive source (spring) of q-th quantity in region r
 *  sn(q,r)...negative source (sink) of q-th quantity in region r
 *
 * Remark: The matrix R is needed only for calculation of signed fluxes.
 * The reason is that to determine sign, we decompose flux to sum of local contributions
 * per each boundary element and check its sign. It is not possible to decompose flux
 * using shape functions, since their normal derivatives may have any sign.
 *
 *
 *
 * Output values (if not relevant, zero is supplied):
 *
 * #time    bulk_region     quantity 0    0       0        mass source source_in source_out 0               0                 0
 * #time    boundary_region quantity flux flux_in flux_out 0    0      0         0          0               0                 0
 * #time    ALL             quantity flux flux_in flux_out mass source source_in source_out integrated_flux integrated_source error
 *
 * error = current_mass - (initial_mass + integrated_source - integrated_flux)
 *
 */
class Balance {
public:

    /**
     * Class for storing internal data about conservative quantities handled by the Balance object.
     * In the future we may store additional data or support definition of derived quantities
     * (e.g. linear combinations of quantities).
     */
    class Quantity {
    public:

        Quantity(const unsigned int index, const string &name)
            : name_(name),
              index_(index)
        {}

        /// Name of quantity (for output).
        string name_;

        /// Internal index within list of quantities.
        const unsigned int index_;

    };

    /**
     * Possible formats of output file.
     */
    enum OutputFormat
    {
        legacy,//!< legacy
        txt,   //!< csv
        gnuplot//!< gnuplot
    };

    /// Main balance input record type.
    static const Input::Type::Record & get_input_type();

    /// Input selection for file format.
    static const Input::Type::Selection & get_format_selection_input_type();


    /**
     * Constructor.
     * @param file_prefix  Prefix of output file name.
     * @param mesh         Mesh.
     */
    Balance(const std::string &file_prefix, const Mesh *mesh);

    /**
     * Destructor.
     */
    ~Balance();

    /**
     * Initialize the balance object according to the input.
     * The balance output time marks are set according to the already existing output time marks of the same equation.
     * So, this method must be called after Output::
     *
     * @param in_rec       Input record of balance.
     * @param tg           TimeGovernor of the equation. We need just equation mark type.
     *
     */
    void init_from_input(const Input::Record &in_rec, TimeGovernor &tg);

    /// Setter for units of conserved quantities.
    void units(const UnitSI &unit);

    /// Getter for cumulative_.
    inline bool cumulative() const { return cumulative_; }


    /**
     * Define a single conservative quantity.
     * @param name Name of the quantity.
     * @return     Quantity's internal index.
     */
    unsigned int add_quantity(const string &name);

    /**
     * Define a set of conservative quantities.
     * @param names List of quantities' names.
     * @return      List of quantities' indices.
     */
    std::vector<unsigned int> add_quantities(const std::vector<string> &names);

    /**
     * Allocates matrices and vectors for balance.
     * @param n_loc_dofs            Number of solution dofs on the local process.
     * @param max_dofs_per_boundary Number of dofs contributing to one boundary edge.
     */
    void allocate(unsigned int n_loc_dofs,
            unsigned int max_dofs_per_boundary);


    /// Returns true if the given time step is marked for the balance output.
    bool is_current(const TimeStep &step);

    /**
     * This method must be called before assembling the matrix for computing mass.
     * It actually erases the matrix.
     */
    void start_mass_assembly(unsigned int quantity_idx);

    /// Variant of the start_mass_assembly() method for a set of quantities.
    inline void start_mass_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            start_mass_assembly(idx);
    }

    /**
     * This method must be called before assembling the matrix and vector for fluxes.
     * It actually erases the matrix and vector.
     */
    void start_flux_assembly(unsigned int quantity_idx);

    /// Variant of the start_flux_assembly() method for a set of quantities.
    inline void start_flux_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            start_flux_assembly(idx);
    }

    /**
     * This method must be called before assembling the matrix and vectors for sources.
     * It actually erases the matrix and vectors.
     */
    void start_source_assembly(unsigned int quantity_idx);

    /// Variant of the start_source_assembly() method for a set of quantities.
    inline void start_source_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            start_source_assembly(idx);
    }

    /**
     * Adds elements into matrix for computing mass.
     * @param quantity_idx  Index of quantity.
     * @param region_idx    Index of bulk region.
     * @param dof_indices   Dof indices to be added.
     * @param values        Values to be added.
     */
    void add_mass_matrix_values(unsigned int quantity_idx,
            unsigned int region_idx,
            const std::vector<int> &dof_indices,
            const std::vector<double> &values);

    /**
     * Adds elements into matrix for computing (outgoing) flux.
     * @param quantity_idx  Index of quantity.
     * @param elem_idx      Local index of boundary edge.
     * @param dof_indices   Dof indices to be added.
     * @param values        Values to be added.
     */
    void add_flux_matrix_values(unsigned int quantity_idx,
            unsigned int elem_idx,
            const std::vector<int> &dof_indices,
            const std::vector<double> &values);

    /**
     * Adds elements into matrix for computing source.
     * @param quantity_idx  Index of quantity.
     * @param region_idx    Index of bulk region.
     * @param dof_indices   Dof indices to be added.
     * @param values        Values to be added.
     */
    void add_source_matrix_values(unsigned int quantity_idx,
            unsigned int region_idx,
            const std::vector<int> &dof_indices,
            const std::vector<double> &values);
    
    /**
     * Adds element into vector for computing mass.
     * @param quantity_idx  Index of quantity.
     * @param region_idx    Index of bulk region.
     * @param value         Value to be added.
     */
    void add_mass_vec_value(unsigned int quantity_idx,
            unsigned int region_idx,
            double value);

    /**
     * Adds element into vector for computing (outgoing) flux.
     * @param quantity_idx  Index of quantity.
     * @param elem_idx      Local index of boundary edge.
     * @param value         Value to be added.
     */
    void add_flux_vec_value(unsigned int quantity_idx,
            unsigned int elem_idx,
            double value);

    /**
     * Adds elements into vector for computing source.
     * @param quantity_idx  Index of quantity.
     * @param region_idx    Index of bulk region.
     * @param dof_indices   Dof indices to be added.
     * @param values        Values to be added.
     */
    void add_source_vec_values(unsigned int quantity_idx,
            unsigned int region_idx,
            const std::vector<int> &dof_values,
            const std::vector<double> &values);

    /// This method must be called after assembling the matrix for computing mass.
    void finish_mass_assembly(unsigned int quantity_idx);

    /// Variant of the finish_mass_assembly() method for a set of quantities.
    inline void finish_mass_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            finish_mass_assembly(idx);
    }

    /// This method must be called after assembling the matrix and vector for computing flux.
    void finish_flux_assembly(unsigned int quantity_idx);

    /// Variant of the finish_flux_assembly() method for a set of quantities.
    inline void finish_flux_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            finish_flux_assembly(idx);
    }

    /// This method must be called after assembling the matrix and vectors for computing source.
    void finish_source_assembly(unsigned int quantity_idx);

    /// Variant of the finish_source_assembly() method for a set of quantities.
    inline void finish_source_assembly(std::vector<unsigned int> q_idx_vec)
    {
        for (auto idx : q_idx_vec)
            finish_source_assembly(idx);
    }

    /**
     * Updates cumulative quantities for balance.
     * This method can be called in substeps even if no output is generated.
     * It calculates the sum of source over time interval.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     * @param dt            Actual time step.
     */
    void calculate_cumulative_sources(unsigned int quantity_idx,
            const Vec &solution,
            double dt);

    /**
     * Updates cumulative quantities for balance.
     * This method can be called in substeps even if no output is generated.
     * It calculates the sum of (incoming) flux over time interval.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     * @param dt            Actual time step.
     */
    void calculate_cumulative_fluxes(unsigned int quantity_idx,
            const Vec &solution,
            double dt);

    /**
     * Calculates actual mass and save it to given vector.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     * @param output_array  Vector of output masses per region.
     */
    void calculate_mass(unsigned int quantity_idx,
            const Vec &solution,
            vector<double> &output_array);

    /**
     * Calculates actual mass and save it to internal vector.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     */
    void calculate_mass(unsigned int quantity_idx,
            const Vec &solution)
    {
        calculate_mass(quantity_idx, solution, masses_[quantity_idx]);
    }

    /**
     * Calculates actual (incoming) flux.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     */
    void calculate_flux(unsigned int quantity_idx,
            const Vec &solution);

    /**
     * Calculates actual source.
     * @param quantity_idx  Index of quantity.
     * @param solution      Solution vector.
     */
    void calculate_source(unsigned int quantity_idx,
            const Vec &solution);

    /**
    * Adds provided values to the cumulative sources.
    * @param quantity_idx Index of quantity.
    * @param sources Sources per region.
    * @param dt Actual time step.
    */
    void add_cumulative_source(unsigned int quantity_idx, double source);

    /// Perform output to file for given time instant.
    void output(double time);

private:
    /// Size of column in output (used if delimiter is space)
    static const unsigned int output_column_width = 20;
    /**
     * Postponed allocation and initialization to allow calling setters in arbitrary order.
     * In particular we need to perform adding of output times after the output time marks are set.
     * On the other hand we need to read the input before we make the allocation.
     *
     * The initialization is done during the first call of any start_*_assembly method.
     */
    void lazy_initialize();

    /// Perform output in old format (for compatibility)
    void output_legacy(double time);

    /// Perform output in csv format
    void output_csv(double time, char delimiter, const std::string& comment_string, unsigned int repeat = 0);

    /// Perform output in yaml format
    void output_yaml(double time);

    /// Return part of output represented by zero values. Count of zero values is given by cnt parameter.
    std::string csv_zero_vals(unsigned int cnt, char delimiter);

    /// Print output header
    void format_csv_output_header(char delimiter, const std::string& comment_string);

    /// Format string value of csv output. Wrap string into quotes and if delimiter is space, align text to column.
    std::string format_csv_val(std::string val, char delimiter, bool initial = false);

    /// Format double value of csv output. If delimiter is space, align text to column.
    std::string format_csv_val(double val, char delimiter, bool initial = false);


    /// Allocation parameters. Set by the allocate method used in the lazy_initialize.
    unsigned int n_loc_dofs_;
    unsigned int max_dofs_per_boundary_;


    /// Save prefix passed in in constructor.
    std::string file_prefix_;

    /// File path for output_ stream.
    FilePath balance_output_file_;

    /// Handle for file for output in given OutputFormat of balance and total fluxes over individual regions and region sets.
    ofstream output_;

    // The same as the previous case, but for output in YAML format.
    ofstream output_yaml_;

    /// Format of output file.
    OutputFormat output_format_;

    /// Names of conserved quantities.
    std::vector<Quantity> quantities_;

    const Mesh *mesh_;

    /// Units of conserved quantities.
    UnitSI units_;


    /// Matrices for calculation of mass (n_dofs x n_bulk_regions).
    Mat *region_mass_matrix_;

    /// Matrices for calculation of flux (n_boundary_edges x n_dofs).
    Mat *be_flux_matrix_;

    /// Matrices for calculation of source (n_dofs x n_bulk_regions).
    Mat *region_source_matrix_;

    /// Matrices for calculation of signed source (n_dofs x n_bulk_regions).
    Mat *region_source_rhs_;

    /// Vectors for calculation of flux (n_boundary_edges).
    Vec *be_flux_vec_;
    
    /// Vectors for calculation of mass (n_bulk_regions).
    Vec *region_mass_vec_;

    /// Vectors for calculation of source (n_bulk_regions).
    Vec *region_source_vec_;

    /**
     * Auxiliary matrix for transfer of quantities between boundary edges and regions
     * (n_boundary_edges x n_boundary_regions).
     */
    Mat region_be_matrix_;

    /// auxiliary vectors for summation of matrix columns
    Vec ones_, ones_be_;

    /// Number of boundary region for each local boundary edge.
    std::vector<unsigned int> be_regions_;

    /// Offset for local part of vector of boundary edges.
    int be_offset_;


    // Vectors storing mass and balances of fluxes and volumes.
    // substance, phase, region
    std::vector<std::vector<double> > fluxes_;
    std::vector<std::vector<double> > fluxes_in_;
    std::vector<std::vector<double> > fluxes_out_;
    std::vector<std::vector<double> > masses_;
    std::vector<std::vector<double> > sources_;
    std::vector<std::vector<double> > sources_in_;
    std::vector<std::vector<double> > sources_out_;

    // Sums of the above vectors over phases and regions
    std::vector<double> sum_fluxes_;
    std::vector<double> sum_fluxes_in_;
    std::vector<double> sum_fluxes_out_;
    std::vector<double> sum_masses_;
    std::vector<double> sum_sources_;
    std::vector<double> sum_sources_in_;
    std::vector<double> sum_sources_out_;
    std::vector<double> initial_mass_;

    // time integrated quantities
    std::vector<double> integrated_sources_;
    std::vector<double> integrated_fluxes_;
    std::vector<double> increment_fluxes_;
    std::vector<double> increment_sources_;

    /// initial time
    double initial_time_;

    /// time of last calculated balance
    double last_time_;

    /// TimeMark type for balance output of particular equation.
    TimeMark::Type balance_output_type_;

    /// TimeMark type for output of particular equation.
    TimeMark::Type output_mark_type_;

    /// true before calculating the mass at initial time, otherwise false
    bool initial_;

    /// if true then cumulative balance is computed
    bool cumulative_;

    /// true before allocating necessary internal structures (Petsc matrices etc.)
    bool allocation_done_;

    /// If the balance is on. Balance is off in the case of no balance output time marks.
    bool balance_on_;

    /// Add output time marks to balance output time marks.
    bool add_output_times_;


    /// MPI rank.
    int rank_;

    /// hold count of line printed into output_
    unsigned int output_line_counter_;

    /// marks whether YAML output has printed header
    bool output_yaml_header_;




};





#endif // BALANCE_HH_