kinetic_block_visitor.hpp

Go to the documentation of this file.

/*
 * Copyright 2023 Blue Brain Project, EPFL.
 * See the top-level LICENSE file for details.
 *
 * SPDX-License-Identifier: Apache-2.0
 */
 
#pragma once
 
/**
 * \file
 * \brief \copybrief nmodl::visitor::KineticBlockVisitor
 */
 
#include <memory>
#include <string>
#include <unordered_map>
#include <unordered_set>
#include <vector>
 
#include "visitors/ast_visitor.hpp"
 
namespace nmodl {
namespace visitor {
 
/**
 * \addtogroup visitor_classes
 * \{
 */
 
/**
 * \class KineticBlockVisitor
 * \brief %Visitor for kinetic block statements
 *
 * Replaces each KINETIC block with a DERIVATIVE block
 * containing a system of ODEs that is equivalent to
 * the original set of reaction statements
 *
 * Note: assumes that the order of statements between the first and last
 * reaction statement (those starting with "~") does not matter.
 *
 * If there is a CONSERVE statement it is rewritten in an equivalent
 * form which is then be used by the SympySolver visitor to replace
 * the ODE for the last state variable on the LHS of the CONSERVE statement
 *
 */
class KineticBlockVisitor: public AstVisitor {
  private:
    /// update stoichiometric matrices with reaction var term
    void process_reac_var(const std::string& varname, int count = 1);
 
    /// update CONSERVE statement with reaction var term
    void process_conserve_reac_var(const std::string& varname, int count = 1);
 
    /// stochiometric matrices nu_L, nu_R
    /// forwards/backwards fluxes k_f, k_b
    /// (see kinetic_schemes.ipynb notebook for details)
    struct RateEqs {
        std::vector<std::vector<int>> nu_L;
        std::vector<std::vector<int>> nu_R;
        std::vector<std::string> k_f;
        std::vector<std::string> k_b;
    } rate_eqs;
 
    /// multiplicative factors for ODEs from COMPARTMENT statements
    std::vector<std::string> compartment_factors;
 
    /// additive constant terms for ODEs from reaction statements like ~ x << (a)
    std::vector<std::string> additive_terms;
 
    /// multiplicate constant terms for fluxes from non-state vars as reactants
    /// e.g. reaction statements like ~ x <-> c (a,a)
    /// where c is not a state var, which is equivalent to the ODE
    /// x' = a * (c - x)
    std::vector<std::string> non_state_var_fflux;
    std::vector<std::string> non_state_var_bflux;
 
    /// generated set of fluxes and ODEs
    std::vector<std::string> fflux;
    std::vector<std::string> bflux;
    std::vector<std::string> odes;
 
    /// current expressions for the `fflux`, `bflux` variables that can be used in the mod file
    /// and that are determined by the preceeding kinetic reaction statement, i.e. their
    /// value changes depending on their location inside the kinetic block
    std::string modfile_fflux;
    std::string modfile_bflux;
 
    /// number of state variables
    int state_var_count = 0;
 
    /// state variables vector
    std::vector<std::string> state_var;
 
    /// unordered_map from state variable to corresponding index
    std::unordered_map<std::string, int> state_var_index;
 
    /// unordered_map from array state variable to its size (for summing over each element of any
    /// array state vars in a CONSERVE statement)
    std::unordered_map<std::string, int> array_state_var_size;
 
    /// true if we are visiting a reaction statement
    bool in_reaction_statement = false;
 
    /// true if we are visiting the left hand side of reaction statement
    bool in_reaction_statement_lhs = false;
 
    /// true if we are visiting a CONSERVE statement
    bool in_conserve_statement = false;
 
    /// counts the number of CONSERVE statements in Kinetic blocks
    int conserve_statement_count = 0;
 
    /// conserve statement equation as string
    std::string conserve_equation_str;
 
    /// conserve statement: current state variable being processed
    std::string conserve_equation_statevar;
 
    /// conserve statement: current state var multiplicative factor being processed
    std::string conserve_equation_factor;
 
    /// current statement index
    int i_statement = 0;
 
    /// vector of kinetic block nodes
    std::vector<ast::KineticBlock*> kinetic_blocks;
 
    /// statements to remove from block
    std::unordered_set<ast::Statement*> statements_to_remove;
 
    /// current statement block being visited
    ast::StatementBlock* current_statement_block = nullptr;
 
  public:
    KineticBlockVisitor() = default;
    inline int get_conserve_statement_count() const {
        return conserve_statement_count;
    }
 
    void visit_wrapped_expression(ast::WrappedExpression& node) override;
    void visit_reaction_operator(ast::ReactionOperator& node) override;
    void visit_react_var_name(ast::ReactVarName& node) override;
    void visit_reaction_statement(ast::ReactionStatement& node) override;
    void visit_conserve(ast::Conserve& node) override;
    void visit_compartment(ast::Compartment& node) override;
    void visit_statement_block(ast::StatementBlock& node) override;
    void visit_kinetic_block(ast::KineticBlock& node) override;
    void visit_program(ast::Program& node) override;
};
 
/** \} */  // end of visitor_classes
 
}  // namespace visitor
}  // namespace nmodl