assembly_richards.hh

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/*
 * assembly_lmh.hh
 *
 *  Created on: Apr 30, 2016
 *      Author: jb
 */

#ifndef SRC_FLOW_ASSEMBLY_LMH_HH_
#define SRC_FLOW_ASSEMBLY_LMH_HH_

#include "system/index_types.hh"
#include "flow/assembly_lmh.hh"
#include "soil_models.hh"
#include "coupling/balance.hh"

#include "badiff.h"


/**
 * Prove of concept for general assembly scheme.
 * Ideas:
 * - Local assembly class for given DIM provides assembly methods for:
 *   - local assembly on elements of dimension DIM
 *   - local assembly on edges/faces of neighbouring elemnts of dimension DIM
 *   - local assembly of interactiong elements DIM and OTHER_DIM with OTHER_DIM < DIM
 * - Such class template would be necessary to create particular instance of Assembler class, that
 *   takes job of pass through the mesh, precomputing necessary fields, etc.
 *   This allows to manage order of assembled entities in arbitrary way in order to use caches and vectorisation efficiently.
 * - Separate local assembly template would be necessary for every pass through the mesh, but it may delegate its actions
 *   to a single general local assembly class.
 * - The local assembly class gets an Accessor object for particular domain of the assembly, i.e. ElementAccessor for element assembly,
 *   FaceAccessor for interface intergrals assembly, and InteractionAccessor for assembly of interaction of two elements, e.g. for XFEM
 *   there may be an interaction between every 3D element within the enrichment with appropriate 1D elemnt on the well.
 *   These accessors provides methods to access fields values as well as the DOF indices on the element(s).
 * - Results of the assembly are passed to the global linear algebra objects collected in the RichardSystem class, global indices
 *   (which are still local indicies of the single process) provided by accessors are used.
 *
 *
 * TODO:
 * - finish functional Richards model
 * - move whole internals of the assembly_mh_matrix into local assembly classes
 * - mean while: imporve accessors, imporve mesh and DOF handler interface; possibly create new mesh implementation used in Darcy first and then
 *   apply it to other equations
 */


template<int dim>
class AssemblyRichards : public AssemblyLMH<dim> {
public:

    typedef std::shared_ptr<RichardsLMH::EqData> AssemblyDataPtrRichards;

    AssemblyRichards(AssemblyDataPtrRichards data)
    : AssemblyLMH<dim>(data),
      ad_(data),
      genuchten_on(false),
      cross_section(1.0),
      cr_disc_dofs(dim+1)
    {}

protected:
    void reset_soil_model(const DHCellAccessor& dh_cell) {
        ElementAccessor<3> ele = dh_cell.elm();
        genuchten_on = (ad_->genuchten_p_head_scale.field_result({ele.region()}) != result_zeros);
        if (genuchten_on) {
            SoilData soil_data;
            soil_data.n =  ad_->genuchten_n_exponent.value(ele.centre(), ele);
            soil_data.alpha = ad_->genuchten_p_head_scale.value(ele.centre(), ele);
            soil_data.Qr = ad_->water_content_residual.value(ele.centre(), ele);
            soil_data.Qs = ad_->water_content_saturated.value(ele.centre(), ele);
            soil_data.Ks = ad_->conductivity.value(ele.centre(), ele);
            //soil_data.cut_fraction = 0.99; // set by model

            ad_->soil_model_->reset(soil_data);
        }
    }

    double compute_conductivity(ElementAccessor<3> ele)
    {
        double conductivity = 0;
        if (genuchten_on) {
            for (unsigned int i=0; i<ele->n_sides(); i++)
            {
                double phead = ad_->p_edge_solution[ this->loc_schur_.row_dofs[i] ];
                conductivity += ad_->soil_model_->conductivity(phead);
            }
            conductivity /= ele->n_sides();
        }
        else {
            conductivity = this->ad_->conductivity.value(ele.centre(), ele);
        }
        return conductivity;
    }

    void update_water_content(const DHCellAccessor& dh_cell) {

        // dof indices for edge pressure must be updated
        // since update_water_content is called also outside assemble cycle (init condition)
        update_dofs(dh_cell);

        reset_soil_model(dh_cell);
        const ElementAccessor<3> ele = dh_cell.elm();
        double storativity = ad_->storativity.value(ele.centre(), ele)
                             + ad_->extra_storativity.value(ele.centre(), ele);
        VectorMPI water_content_vec = ad_->water_content_ptr->vec();

        for (unsigned int i=0; i<ele->n_sides(); i++) {
            double capacity = 0;
            double water_content = 0;
            double phead = ad_->p_edge_solution[ edge_indices_[i] ];
            if (genuchten_on) {

                  fadbad::B<double> x_phead(phead);
                  fadbad::B<double> evaluated( ad_->soil_model_->water_content_diff(x_phead) );
                  evaluated.diff(0,1);
                  water_content = evaluated.val();
                  capacity = x_phead.d(0);
            }
            ad_->capacity[ cr_disc_dofs[i] ] = capacity + storativity;
            water_content_vec[ cr_disc_dofs[i] ] = water_content + storativity * phead;
        }
    }

    void assemble_sides(const DHCellAccessor& dh_cell) override
    {
        reset_soil_model(dh_cell);
        const ElementAccessor<3> ele = dh_cell.elm();
        cross_section = ad_->cross_section.value(ele.centre(), ele);

        double conductivity = compute_conductivity(ele);
        double scale = 1 / cross_section / conductivity;
        this->assemble_sides_scale(dh_cell,scale);
    }

    /***
     * Called from assembly_local_matrix, assumes precomputed:
     * cross_section, genuchten_on, soil_model
     */
    void assemble_source_term(const DHCellAccessor& dh_cell) override
    {
        update_water_content(dh_cell);
        const ElementAccessor<3> ele = dh_cell.elm();
        
        // set lumped source
        double diagonal_coef = ele.measure() * cross_section / ele->n_sides();
        double source_diagonal = diagonal_coef * 
                        ( ad_->water_source_density.value(ele.centre(), ele)
                        + ad_->extra_source.value(ele.centre(), ele));

        VectorMPI water_content_vec = ad_->water_content_ptr->vec();

        for (unsigned int i=0; i<ele->n_sides(); i++)
        {

            const int local_side = cr_disc_dofs[i];
            if (this->dirichlet_edge[i] == 0) {

                double capacity = ad_->capacity[local_side];
                double water_content_diff = -water_content_vec[local_side] + ad_->water_content_previous_time[local_side];
                double mass_diagonal = diagonal_coef * capacity;

                /*
                DebugOut().fmt("w diff: {:g}  mass: {:g} w prev: {:g} w time: {:g} c: {:g} p: {:g} z: {:g}",
                      water_content_diff,
                      mass_diagonal * ad_->p_edge_solution[local_edge],
                     -ad_->water_content_previous_it[local_side],
                      ad_->water_content_previous_time[local_side],
                      capacity,
                      ad_->p_edge_solution[local_edge],
                      ele.centre()[0] );
                */


                double mass_rhs = mass_diagonal * ad_->p_edge_solution[ this->loc_schur_.row_dofs[i] ] / ad_->time_step_
                                  + diagonal_coef * water_content_diff / ad_->time_step_;

//                 DBGCOUT(<< "source [" << loc_system_.row_dofs[this->loc_edge_dofs[i]] << ", " << loc_system_.row_dofs[this->loc_edge_dofs[i]]
//                             << "] mat: " << -mass_diagonal/this->ad_->time_step_
//                             << " rhs: " << -source_diagonal - mass_rhs
//                             << "\n");
                this->loc_system_.add_value(this->loc_edge_dofs[i], this->loc_edge_dofs[i],
                                            -mass_diagonal/ad_->time_step_,
                                            -source_diagonal - mass_rhs);
            }

            ad_->balance->add_mass_values(ad_->water_balance_idx, dh_cell, {local_side},
                                          {0.0}, diagonal_coef*water_content_vec[local_side]);
            ad_->balance->add_source_values(ad_->water_balance_idx, ele.region().bulk_idx(),
                                            {this->loc_system_.row_dofs[this->loc_edge_dofs[i]]},
                                            {0},{source_diagonal});
        }

    }

    /// Updates DoFs for edge pressure vector (dh CR) and for water content vector (dh CR_disc)
    /// Be sure to call it before @p update_water_content().
    void update_dofs(const DHCellAccessor& dh_cell)
    {
        edge_indices_ = dh_cell.cell_with_other_dh(ad_->dh_cr_.get()).get_loc_dof_indices();
        cr_disc_dofs = dh_cell.cell_with_other_dh(ad_->dh_cr_disc_.get()).get_loc_dof_indices();
    }
    
    void postprocess_velocity_specific(const DHCellAccessor& dh_cell, arma::vec& solution,
                                       double edge_scale, double edge_source_term) override
    {   
        update_water_content(dh_cell);
        
        const ElementAccessor<3> ele = dh_cell.elm();

        VectorMPI water_content_vec = ad_->water_content_ptr->vec();
        
        for (unsigned int i=0; i<ele->n_sides(); i++) {
            
            double water_content = water_content_vec[ cr_disc_dofs[i] ];
            double water_content_previous_time = ad_->water_content_previous_time[ cr_disc_dofs[i] ];
            
            solution[this->loc_side_dofs[i]]
                += edge_source_term - edge_scale * (water_content - water_content_previous_time) / ad_->time_step_;
        }
         
        IntIdx p_dof = dh_cell.cell_with_other_dh(ad_->dh_p_.get()).get_loc_dof_indices()(0);
        ad_->conductivity_ptr->vec()[p_dof] = compute_conductivity(ele);
    }

    AssemblyDataPtrRichards ad_;

    bool genuchten_on;
    double cross_section;
    LocDofVec cr_disc_dofs;  ///< Dofs of discontinuous fields on element edges.
    LocDofVec edge_indices_; ///< Dofs of discontinuous fields on element edges.
};



#endif /* SRC_FLOW_ASSEMBLY_LMH_HH_ */