assembly_reaction.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    assembly_reaction.hh
 * @brief
 */
 
#ifndef ASSEMBLY_REACTION_HH_
#define ASSEMBLY_REACTION_HH_
 
#include "coupling/generic_assembly.hh"
#include "coupling/assembly_base.hh"
#include "reaction/dual_porosity.hh"
#include "reaction/isotherm.hh"
#include "fem/fe_p.hh"
#include "quadrature/quadrature_lib.hh"
//#include "coupling/balance.hh"
#include "fem/element_cache_map.hh"
 
 
 
template <unsigned int dim, class TEqData>
class InitConditionAssemblyDp : public AssemblyBasePatch<dim>
{
public:
    typedef typename TEqData::EqFields EqFields;
    typedef TEqData EqData;
 
    static constexpr const char * name() { return "Dp_InitCondition_Assembly"; }
 
    /// Constructor.
    InitConditionAssemblyDp(EqData *eq_data, AssemblyInternals *asm_internals)
    : AssemblyBasePatch<dim>(0, asm_internals), eq_fields_(eq_data->eq_fields_.get()), eq_data_(eq_data),
      mass_integral_( this->create_bulk_integral(this->quad_) )  {
        this->used_fields_ += eq_fields_->init_conc_immobile;
    }
 
    /// Destructor.
    ~InitConditionAssemblyDp() {}
 
    /// Initialize auxiliary vectors and other data members
    void initialize() {}
 
 
    /// Assemble integral over element
    inline void cell_integral(DHCellAccessor cell, unsigned int element_patch_idx)
    {
        ASSERT_EQ(cell.dim(), dim).error("Dimension of element mismatch!");
 
        dof_p0_ = cell.get_loc_dof_indices()[0];
        auto p = *( mass_integral_->points(element_patch_idx).begin() );
 
        //setting initial solid concentration for substances involved in adsorption
        for (unsigned int sbi = 0; sbi < eq_data_->substances_.size(); sbi++)
        {
            eq_fields_->conc_immobile_fe[sbi]->vec().set( dof_p0_, eq_fields_->init_conc_immobile[sbi](p) );
        }
    }
 
 
private:
    /// Data objects shared with Elasticity
    EqFields *eq_fields_;
    EqData *eq_data_;
 
    /// Sub field set contains fields used in calculation.
    FieldSet used_fields_;
 
    IntIdx dof_p0_;                                           ///< Index of local DOF
 
    std::shared_ptr<BulkIntegralAcc<dim>> mass_integral_;     ///< Bulk integral of assembly class
 
    template < template<IntDim...> class DimAssembly>
    friend class GenericAssembly;
};
 
template <unsigned int dim, class TEqData>
class ReactionAssemblyDp : public AssemblyBasePatch<dim>
{
public:
    typedef typename TEqData::EqFields EqFields;
    typedef TEqData EqData;
 
    static constexpr const char * name() { return "Dp_InitCondition_Assembly"; }
 
    /// Constructor.
    ReactionAssemblyDp(EqData *eq_data, AssemblyInternals *asm_internals)
    : AssemblyBasePatch<dim>(0, asm_internals), eq_fields_(eq_data->eq_fields_.get()), eq_data_(eq_data),
      mass_integral_( this->create_bulk_integral(this->quad_) )  {
        this->used_fields_ += eq_fields_->porosity;
        this->used_fields_ += eq_fields_->porosity_immobile;
        this->used_fields_ += eq_fields_->diffusion_rate_immobile;
    }
 
    /// Destructor.
    ~ReactionAssemblyDp() {}
 
    /// Initialize auxiliary vectors and other data members
    void initialize() {}
 
 
    /// Assemble integral over element
    inline void cell_integral(DHCellAccessor cell, unsigned int element_patch_idx)
    {
        ASSERT_EQ(cell.dim(), dim).error("Dimension of element mismatch!");
 
        auto p = *( mass_integral_->points(element_patch_idx).begin() );
 
        // if porosity_immobile == 0 then mobile concentration stays the same
        // and immobile concentration cannot change
        por_immob_ = eq_fields_->porosity_immobile(p);
        if (por_immob_ == 0.0) return;
 
        // get data from fields
        dof_p0_ = cell.get_loc_dof_indices()[0];
        por_mob_ = eq_fields_->porosity(p);
        arma::Col<double> diff_vec(eq_data_->substances_.size());
        for (sbi_=0; sbi_<eq_data_->substances_.size(); sbi_++) // Optimize: SWAP LOOPS
            diff_vec[sbi_] = eq_fields_->diffusion_rate_immobile[sbi_](p);
 
        temp_exponent_ = (por_mob_ + por_immob_) / (por_mob_ * por_immob_) * eq_data_->time_->dt();
 
        for (sbi_ = 0; sbi_ < eq_data_->substances_.size(); sbi_++) //over all substances
        {
            exponent_ = diff_vec[sbi_] * temp_exponent_;
            //previous values
            previous_conc_mob_ = eq_fields_->conc_mobile_fe[sbi_]->vec().get(dof_p0_);
            previous_conc_immob_ = eq_fields_->conc_immobile_fe[sbi_]->vec().get(dof_p0_);
 
            // ---compute average concentration------------------------------------------
            conc_average_ = ((por_mob_ * previous_conc_mob_) + (por_immob_ * previous_conc_immob_))
                           / (por_mob_ + por_immob_);
 
            conc_max_ = std::max(previous_conc_mob_-conc_average_, previous_conc_immob_-conc_average_);
 
            // the following 2 conditions guarantee:
            // 1) stability of forward Euler's method
            // 2) the error of forward Euler's method will not be large
            if(eq_data_->time_->dt() <= por_mob_*por_immob_/(max(diff_vec)*(por_mob_+por_immob_)) &&
                conc_max_ <= (2*eq_data_->scheme_tolerance_/(exponent_*exponent_)*conc_average_))               // forward euler
            {
                temp_ = diff_vec[sbi_]*(previous_conc_immob_ - previous_conc_mob_) * eq_data_->time_->dt();
                // ---compute concentration in mobile area
                conc_mob_ = temp_ / por_mob_ + previous_conc_mob_;
 
                // ---compute concentration in immobile area
                conc_immob_ = -temp_ / por_immob_ + previous_conc_immob_;
            }
            else                                                        //analytic solution
            {
                temp_ = exp(-exponent_);
                // ---compute concentration in mobile area
                conc_mob_ = (previous_conc_mob_ - conc_average_) * temp_ + conc_average_;
 
                // ---compute concentration in immobile area
                conc_immob_ = (previous_conc_immob_ - conc_average_) * temp_ + conc_average_;
            }
 
            eq_fields_->conc_mobile_fe[sbi_]->vec().set(dof_p0_, conc_mob_);
            eq_fields_->conc_immobile_fe[sbi_]->vec().set(dof_p0_, conc_immob_);
        }
    }
 
 
private:
    /// Data objects shared with Elasticity
    EqFields *eq_fields_;
    EqData *eq_data_;
 
    /// Sub field set contains fields used in calculation.
    FieldSet used_fields_;
 
    unsigned int sbi_;                                     ///< Index of substance
    IntIdx dof_p0_;                                        ///< Index of local DOF
    double conc_average_;                                  ///< weighted (by porosity) average of concentration
    double conc_mob_, conc_immob_;                         ///< new mobile and immobile concentration
    double previous_conc_mob_, previous_conc_immob_;       ///< mobile and immobile concentration in previous time step
    double conc_max_;                                      ///< difference between concentration and average concentration
    double por_mob_, por_immob_;                           ///< mobile and immobile porosity
    double exponent_, temp_exponent_, temp_;               ///< Precomputed values
    std::shared_ptr<BulkIntegralAcc<dim>> mass_integral_;  ///< Bulk integral of assembly class
 
    template < template<IntDim...> class DimAssembly>
    friend class GenericAssembly;
};
 
template <unsigned int dim, class TEqData>
class InitConditionAssemblySorp : public AssemblyBasePatch<dim>
{
public:
    typedef typename TEqData::EqFields EqFields;
    typedef TEqData EqData;
 
    static constexpr const char * name() { return "Sorp_InitCondition_Assembly"; }
 
    /// Constructor.
    InitConditionAssemblySorp(EqData *eq_data, AssemblyInternals *asm_internals)
    : AssemblyBasePatch<dim>(0, asm_internals), eq_fields_(eq_data->eq_fields_.get()), eq_data_(eq_data),
      mass_integral_( this->create_bulk_integral(this->quad_) )  {
        this->used_fields_ += eq_fields_->init_conc_solid;
    }
 
    /// Destructor.
    ~InitConditionAssemblySorp() {}
 
    /// Initialize auxiliary vectors and other data members
    void initialize() {}
 
 
    /// Assemble integral over element
    inline void cell_integral(DHCellAccessor cell, unsigned int element_patch_idx)
    {
        ASSERT_EQ(cell.dim(), dim).error("Dimension of element mismatch!");
 
        dof_p0_ = cell.get_loc_dof_indices()[0];
        auto p = *( mass_integral_->points(element_patch_idx).begin() );
 
        //setting initial solid concentration for substances involved in adsorption
        for (unsigned int sbi = 0; sbi < eq_data_->n_substances_; sbi++)
        {
            eq_fields_->conc_solid_fe[ eq_data_->substance_global_idx_[sbi] ]->vec().set( dof_p0_, eq_fields_->init_conc_solid[sbi](p) );
        }
    }
 
 
private:
    /// Data objects shared with Elasticity
    EqFields *eq_fields_;
    EqData *eq_data_;
 
    /// Sub field set contains fields used in calculation.
    FieldSet used_fields_;
 
    IntIdx dof_p0_;                                        ///< Index of local DOF
    std::shared_ptr<BulkIntegralAcc<dim>> mass_integral_;  ///< Bulk integral of assembly class
 
    template < template<IntDim...> class DimAssembly>
    friend class GenericAssembly;
};
 
template <unsigned int dim, class TEqData>
class ReactionAssemblySorp : public AssemblyBasePatch<dim>
{
public:
    typedef typename TEqData::EqFields EqFields;
    typedef TEqData EqData;
 
    static constexpr const char * name() { return "Sorp_Reaction_Assembly"; }
 
    /// Constructor.
    ReactionAssemblySorp(EqData *eq_data, AssemblyInternals *asm_internals)
    : AssemblyBasePatch<dim>(0, asm_internals), eq_fields_(eq_data->eq_fields_.get()), eq_data_(eq_data),
      mass_integral_( this->create_bulk_integral(this->quad_) )  {
        this->used_fields_ += eq_fields_->scale_aqua;
        this->used_fields_ += eq_fields_->scale_sorbed;
        this->used_fields_ += eq_fields_->no_sorbing_surface_cond;
        this->used_fields_ += eq_fields_->sorption_type;
        this->used_fields_ += eq_fields_->distribution_coefficient;
        this->used_fields_ += eq_fields_->isotherm_other;
    }
 
    /// Destructor.
    ~ReactionAssemblySorp() {}
 
    /// Initialize auxiliary vectors and other data members
    void initialize() {}
 
 
    /// Assemble integral over element
    inline void cell_integral(DHCellAccessor cell, unsigned int element_patch_idx)
    {
        ASSERT_EQ(cell.dim(), dim).error("Dimension of element mismatch!");
 
        unsigned int i_subst, subst_id;
        auto p = *( mass_integral_->points(element_patch_idx).begin() );
 
        reg_idx_ = cell.elm().region().bulk_idx();
        dof_p0_ = cell.get_loc_dof_indices()[0];
 
        double scale_aqua = eq_fields_->scale_aqua(p);
        double scale_sorbed = eq_fields_->scale_sorbed(p);
        double no_sorbing_surface_cond = eq_fields_->no_sorbing_surface_cond(p);
 
        for(i_subst = 0; i_subst < eq_data_->n_substances_; i_subst++)
        {
            subst_id = eq_data_->substance_global_idx_[i_subst];
 
            Isotherm & isotherm = eq_data_->isotherms[reg_idx_][i_subst];
 
            bool limited_solubility_on = eq_data_->solubility_vec_[i_subst] > 0.0;
 
            // in case of no sorbing surface, set isotherm type None
            if( no_sorbing_surface_cond <= std::numeric_limits<double>::epsilon())
            {
                isotherm.reinit(Isotherm::none, false, eq_data_->solvent_density_,
                                scale_aqua, scale_sorbed,
                                0,0,0);
            } else {
                if ( scale_sorbed <= 0.0)
                    THROW( SorptionBase::ExcNotPositiveScaling() << SorptionBase::EI_Subst(i_subst) );
 
                isotherm.reinit(Isotherm::SorptionType(eq_fields_->sorption_type[i_subst](p)),
                                limited_solubility_on, eq_data_->solvent_density_,
                                scale_aqua, scale_sorbed,
                                eq_data_->solubility_vec_[i_subst],
                                eq_fields_->distribution_coefficient[i_subst](p),
                                eq_fields_->isotherm_other[i_subst](p));
            }
 
            double c_aqua = eq_fields_->conc_mobile_fe[subst_id]->vec().get(dof_p0_);
            double c_sorbed = eq_fields_->conc_solid_fe[subst_id]->vec().get(dof_p0_);
            isotherm.compute(c_aqua, c_sorbed);
            eq_fields_->conc_mobile_fe[subst_id]->vec().set(dof_p0_, c_aqua);
            eq_fields_->conc_solid_fe[subst_id]->vec().set(dof_p0_, c_sorbed);
 
            // update maximal concentration per region (optimization for interpolation)
            if(eq_data_->table_limit_[i_subst] < 0)
                eq_data_->max_conc[reg_idx_][i_subst] = std::max(eq_data_->max_conc[reg_idx_][i_subst],
                                                      eq_fields_->conc_mobile_fe[subst_id]->vec().get(dof_p0_));
        }
    }
 
 
private:
    /// Data objects shared with Elasticity
    EqFields *eq_fields_;
    EqData *eq_data_;
 
    /// Sub field set contains fields used in calculation.
    FieldSet used_fields_;
 
    IntIdx dof_p0_;                                        ///< Index of local DOF
    int reg_idx_;                                          ///< Bulk region idx
    //unsigned int sbi_;                                     ///< Index of substance
    std::shared_ptr<BulkIntegralAcc<dim>> mass_integral_;  ///< Bulk integral of assembly class
 
 
    template < template<IntDim...> class DimAssembly>
    friend class GenericAssembly;
};
 
#endif /* ASSEMBLY_REACTION_HH_ */