Visitor for kinetic block statements More...

Detailed Description

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

Definition at line 47 of file kinetic_block_visitor.hpp.

#include <kinetic_block_visitor.hpp>

Inheritance diagram for nmodl::visitor::KineticBlockVisitor:

Classes
struct	RateEqs
	stochiometric matrices nu_L, nu_R forwards/backwards fluxes k_f, k_b (see kinetic_schemes.ipynb notebook for details) More...

Public Member Functions
	KineticBlockVisitor ()=default

int	get_conserve_statement_count () const

void	visit_wrapped_expression (ast::WrappedExpression &node) override
	visit node of type ast::WrappedExpression More...

void	visit_reaction_operator (ast::ReactionOperator &node) override
	visit node of type ast::ReactionOperator More...

void	visit_react_var_name (ast::ReactVarName &node) override
	visit node of type ast::ReactVarName More...

void	visit_reaction_statement (ast::ReactionStatement &node) override
	visit node of type ast::ReactionStatement More...

void	visit_conserve (ast::Conserve &node) override
	visit node of type ast::Conserve More...

void	visit_compartment (ast::Compartment &node) override
	visit node of type ast::Compartment More...

void	visit_statement_block (ast::StatementBlock &node) override
	visit node of type ast::StatementBlock More...

void	visit_kinetic_block (ast::KineticBlock &node) override
	visit node of type ast::KineticBlock More...

void	visit_program (ast::Program &node) override
	visit node of type ast::Program More...

Public Member Functions inherited from nmodl::visitor::AstVisitor
void	visit_node (ast::Node &node) override
	visit node of type ast::Node More...

void	visit_statement (ast::Statement &node) override
	visit node of type ast::Statement More...

void	visit_expression (ast::Expression &node) override
	visit node of type ast::Expression More...

void	visit_block (ast::Block &node) override
	visit node of type ast::Block More...

void	visit_identifier (ast::Identifier &node) override
	visit node of type ast::Identifier More...

void	visit_number (ast::Number &node) override
	visit node of type ast::Number More...

void	visit_string (ast::String &node) override
	visit node of type ast::String More...

void	visit_integer (ast::Integer &node) override
	visit node of type ast::Integer More...

void	visit_float (ast::Float &node) override
	visit node of type ast::Float More...

void	visit_double (ast::Double &node) override
	visit node of type ast::Double More...

void	visit_boolean (ast::Boolean &node) override
	visit node of type ast::Boolean More...

void	visit_name (ast::Name &node) override
	visit node of type ast::Name More...

void	visit_prime_name (ast::PrimeName &node) override
	visit node of type ast::PrimeName More...

void	visit_indexed_name (ast::IndexedName &node) override
	visit node of type ast::IndexedName More...

void	visit_var_name (ast::VarName &node) override
	visit node of type ast::VarName More...

void	visit_argument (ast::Argument &node) override
	visit node of type ast::Argument More...

void	visit_react_var_name (ast::ReactVarName &node) override
	visit node of type ast::ReactVarName More...

void	visit_read_ion_var (ast::ReadIonVar &node) override
	visit node of type ast::ReadIonVar More...

void	visit_write_ion_var (ast::WriteIonVar &node) override
	visit node of type ast::WriteIonVar More...

void	visit_nonspecific_cur_var (ast::NonspecificCurVar &node) override
	visit node of type ast::NonspecificCurVar More...

void	visit_electrode_cur_var (ast::ElectrodeCurVar &node) override
	visit node of type ast::ElectrodeCurVar More...

void	visit_range_var (ast::RangeVar &node) override
	visit node of type ast::RangeVar More...

void	visit_global_var (ast::GlobalVar &node) override
	visit node of type ast::GlobalVar More...

void	visit_pointer_var (ast::PointerVar &node) override
	visit node of type ast::PointerVar More...

void	visit_random_var (ast::RandomVar &node) override
	visit node of type ast::RandomVar More...

void	visit_bbcore_pointer_var (ast::BbcorePointerVar &node) override
	visit node of type ast::BbcorePointerVar More...

void	visit_extern_var (ast::ExternVar &node) override
	visit node of type ast::ExternVar More...

void	visit_param_block (ast::ParamBlock &node) override
	visit node of type ast::ParamBlock More...

void	visit_independent_block (ast::IndependentBlock &node) override
	visit node of type ast::IndependentBlock More...

void	visit_assigned_block (ast::AssignedBlock &node) override
	visit node of type ast::AssignedBlock More...

void	visit_state_block (ast::StateBlock &node) override
	visit node of type ast::StateBlock More...

void	visit_initial_block (ast::InitialBlock &node) override
	visit node of type ast::InitialBlock More...

void	visit_constructor_block (ast::ConstructorBlock &node) override
	visit node of type ast::ConstructorBlock More...

void	visit_destructor_block (ast::DestructorBlock &node) override
	visit node of type ast::DestructorBlock More...

void	visit_statement_block (ast::StatementBlock &node) override
	visit node of type ast::StatementBlock More...

void	visit_derivative_block (ast::DerivativeBlock &node) override
	visit node of type ast::DerivativeBlock More...

void	visit_linear_block (ast::LinearBlock &node) override
	visit node of type ast::LinearBlock More...

void	visit_non_linear_block (ast::NonLinearBlock &node) override
	visit node of type ast::NonLinearBlock More...

void	visit_discrete_block (ast::DiscreteBlock &node) override
	visit node of type ast::DiscreteBlock More...

void	visit_function_table_block (ast::FunctionTableBlock &node) override
	visit node of type ast::FunctionTableBlock More...

void	visit_function_block (ast::FunctionBlock &node) override
	visit node of type ast::FunctionBlock More...

void	visit_procedure_block (ast::ProcedureBlock &node) override
	visit node of type ast::ProcedureBlock More...

void	visit_net_receive_block (ast::NetReceiveBlock &node) override
	visit node of type ast::NetReceiveBlock More...

void	visit_solve_block (ast::SolveBlock &node) override
	visit node of type ast::SolveBlock More...

void	visit_breakpoint_block (ast::BreakpointBlock &node) override
	visit node of type ast::BreakpointBlock More...

void	visit_before_block (ast::BeforeBlock &node) override
	visit node of type ast::BeforeBlock More...

void	visit_after_block (ast::AfterBlock &node) override
	visit node of type ast::AfterBlock More...

void	visit_ba_block (ast::BABlock &node) override
	visit node of type ast::BABlock More...

void	visit_for_netcon (ast::ForNetcon &node) override
	visit node of type ast::ForNetcon More...

void	visit_kinetic_block (ast::KineticBlock &node) override
	visit node of type ast::KineticBlock More...

void	visit_unit_block (ast::UnitBlock &node) override
	visit node of type ast::UnitBlock More...

void	visit_constant_block (ast::ConstantBlock &node) override
	visit node of type ast::ConstantBlock More...

void	visit_neuron_block (ast::NeuronBlock &node) override
	visit node of type ast::NeuronBlock More...

void	visit_unit (ast::Unit &node) override
	visit node of type ast::Unit More...

void	visit_double_unit (ast::DoubleUnit &node) override
	visit node of type ast::DoubleUnit More...

void	visit_local_var (ast::LocalVar &node) override
	visit node of type ast::LocalVar More...

void	visit_limits (ast::Limits &node) override
	visit node of type ast::Limits More...

void	visit_number_range (ast::NumberRange &node) override
	visit node of type ast::NumberRange More...

void	visit_constant_var (ast::ConstantVar &node) override
	visit node of type ast::ConstantVar More...

void	visit_binary_operator (ast::BinaryOperator &node) override
	visit node of type ast::BinaryOperator More...

void	visit_unary_operator (ast::UnaryOperator &node) override
	visit node of type ast::UnaryOperator More...

void	visit_reaction_operator (ast::ReactionOperator &node) override
	visit node of type ast::ReactionOperator More...

void	visit_paren_expression (ast::ParenExpression &node) override
	visit node of type ast::ParenExpression More...

void	visit_binary_expression (ast::BinaryExpression &node) override
	visit node of type ast::BinaryExpression More...

void	visit_diff_eq_expression (ast::DiffEqExpression &node) override
	visit node of type ast::DiffEqExpression More...

void	visit_unary_expression (ast::UnaryExpression &node) override
	visit node of type ast::UnaryExpression More...

void	visit_non_lin_equation (ast::NonLinEquation &node) override
	visit node of type ast::NonLinEquation More...

void	visit_lin_equation (ast::LinEquation &node) override
	visit node of type ast::LinEquation More...

void	visit_function_call (ast::FunctionCall &node) override
	visit node of type ast::FunctionCall More...

void	visit_watch (ast::Watch &node) override
	visit node of type ast::Watch More...

void	visit_ba_block_type (ast::BABlockType &node) override
	visit node of type ast::BABlockType More...

void	visit_unit_def (ast::UnitDef &node) override
	visit node of type ast::UnitDef More...

void	visit_factor_def (ast::FactorDef &node) override
	visit node of type ast::FactorDef More...

void	visit_valence (ast::Valence &node) override
	visit node of type ast::Valence More...

void	visit_unit_state (ast::UnitState &node) override
	visit node of type ast::UnitState More...

void	visit_local_list_statement (ast::LocalListStatement &node) override
	visit node of type ast::LocalListStatement More...

void	visit_model (ast::Model &node) override
	visit node of type ast::Model More...

void	visit_define (ast::Define &node) override
	visit node of type ast::Define More...

void	visit_include (ast::Include &node) override
	visit node of type ast::Include More...

void	visit_param_assign (ast::ParamAssign &node) override
	visit node of type ast::ParamAssign More...

void	visit_assigned_definition (ast::AssignedDefinition &node) override
	visit node of type ast::AssignedDefinition More...

void	visit_conductance_hint (ast::ConductanceHint &node) override
	visit node of type ast::ConductanceHint More...

void	visit_expression_statement (ast::ExpressionStatement &node) override
	visit node of type ast::ExpressionStatement More...

void	visit_protect_statement (ast::ProtectStatement &node) override
	visit node of type ast::ProtectStatement More...

void	visit_from_statement (ast::FromStatement &node) override
	visit node of type ast::FromStatement More...

void	visit_while_statement (ast::WhileStatement &node) override
	visit node of type ast::WhileStatement More...

void	visit_if_statement (ast::IfStatement &node) override
	visit node of type ast::IfStatement More...

void	visit_else_if_statement (ast::ElseIfStatement &node) override
	visit node of type ast::ElseIfStatement More...

void	visit_else_statement (ast::ElseStatement &node) override
	visit node of type ast::ElseStatement More...

void	visit_watch_statement (ast::WatchStatement &node) override
	visit node of type ast::WatchStatement More...

void	visit_mutex_lock (ast::MutexLock &node) override
	visit node of type ast::MutexLock More...

void	visit_mutex_unlock (ast::MutexUnlock &node) override
	visit node of type ast::MutexUnlock More...

void	visit_conserve (ast::Conserve &node) override
	visit node of type ast::Conserve More...

void	visit_compartment (ast::Compartment &node) override
	visit node of type ast::Compartment More...

void	visit_lon_diffuse (ast::LonDiffuse &node) override
	visit node of type ast::LonDiffuse More...

void	visit_reaction_statement (ast::ReactionStatement &node) override
	visit node of type ast::ReactionStatement More...

void	visit_lag_statement (ast::LagStatement &node) override
	visit node of type ast::LagStatement More...

void	visit_constant_statement (ast::ConstantStatement &node) override
	visit node of type ast::ConstantStatement More...

void	visit_table_statement (ast::TableStatement &node) override
	visit node of type ast::TableStatement More...

void	visit_suffix (ast::Suffix &node) override
	visit node of type ast::Suffix More...

void	visit_useion (ast::Useion &node) override
	visit node of type ast::Useion More...

void	visit_nonspecific (ast::Nonspecific &node) override
	visit node of type ast::Nonspecific More...

void	visit_electrode_current (ast::ElectrodeCurrent &node) override
	visit node of type ast::ElectrodeCurrent More...

void	visit_range (ast::Range &node) override
	visit node of type ast::Range More...

void	visit_global (ast::Global &node) override
	visit node of type ast::Global More...

void	visit_random_var_list (ast::RandomVarList &node) override
	visit node of type ast::RandomVarList More...

void	visit_pointer (ast::Pointer &node) override
	visit node of type ast::Pointer More...

void	visit_bbcore_pointer (ast::BbcorePointer &node) override
	visit node of type ast::BbcorePointer More...

void	visit_external (ast::External &node) override
	visit node of type ast::External More...

void	visit_thread_safe (ast::ThreadSafe &node) override
	visit node of type ast::ThreadSafe More...

void	visit_verbatim (ast::Verbatim &node) override
	visit node of type ast::Verbatim More...

void	visit_line_comment (ast::LineComment &node) override
	visit node of type ast::LineComment More...

void	visit_block_comment (ast::BlockComment &node) override
	visit node of type ast::BlockComment More...

void	visit_ontology_statement (ast::OntologyStatement &node) override
	visit node of type ast::OntologyStatement More...

void	visit_program (ast::Program &node) override
	visit node of type ast::Program More...

void	visit_nrn_state_block (ast::NrnStateBlock &node) override
	visit node of type ast::NrnStateBlock More...

void	visit_eigen_newton_solver_block (ast::EigenNewtonSolverBlock &node) override
	visit node of type ast::EigenNewtonSolverBlock More...

void	visit_eigen_linear_solver_block (ast::EigenLinearSolverBlock &node) override
	visit node of type ast::EigenLinearSolverBlock More...

void	visit_cvode_block (ast::CvodeBlock &node) override
	visit node of type ast::CvodeBlock More...

void	visit_longitudinal_diffusion_block (ast::LongitudinalDiffusionBlock &node) override
	visit node of type ast::LongitudinalDiffusionBlock More...

void	visit_wrapped_expression (ast::WrappedExpression &node) override
	visit node of type ast::WrappedExpression More...

void	visit_derivimplicit_callback (ast::DerivimplicitCallback &node) override
	visit node of type ast::DerivimplicitCallback More...

void	visit_solution_expression (ast::SolutionExpression &node) override
	visit node of type ast::SolutionExpression More...

void	visit_update_dt (ast::UpdateDt &node) override
	visit node of type ast::UpdateDt More...

Public Member Functions inherited from nmodl::visitor::Visitor
virtual	~Visitor ()=default

Private Member Functions
void	process_reac_var (const std::string &varname, int count=1)
	update stoichiometric matrices with reaction var term More...

void	process_conserve_reac_var (const std::string &varname, int count=1)
	update CONSERVE statement with reaction var term More...

void	set_compartment_factor (int var_index, const std::string &factor)

void	compute_compartment_factor (ast::Compartment &node, const ast::Name &name)

void	compute_indexed_compartment_factor (ast::Compartment &node, const ast::Name &name)

void	unroll_kinetic_blocks (ast::Program &node)
	Unroll loops in KINETIC blocks. More...

Private Attributes
struct nmodl::visitor::KineticBlockVisitor::RateEqs	rate_eqs

std::vector< std::string >	compartment_factors
	multiplicative factors for ODEs from COMPARTMENT statements More...

std::vector< std::string >	additive_terms
	additive constant terms for ODEs from reaction statements like ~ x << (a) More...

std::vector< std::string >	non_state_var_fflux
	multiplicate constant terms for fluxes from non-state vars as reactants e.g. More...

std::vector< std::string >	non_state_var_bflux

std::vector< std::string >	fflux
	generated set of fluxes and ODEs More...

std::vector< std::string >	bflux

std::vector< std::string >	odes

std::string	modfile_fflux
	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. More...

std::string	modfile_bflux

int	state_var_count = 0
	number of state variables More...

std::vector< std::string >	state_var
	state variables vector More...

std::unordered_map< std::string, int >	state_var_index
	unordered_map from state variable to corresponding index More...

std::unordered_map< std::string, int >	array_state_var_size
	unordered_map from array state variable to its size (for summing over each element of any array state vars in a CONSERVE statement) More...

bool	in_reaction_statement = false
	true if we are visiting a reaction statement More...

bool	in_reaction_statement_lhs = false
	true if we are visiting the left hand side of reaction statement More...

bool	in_conserve_statement = false
	true if we are visiting a CONSERVE statement More...

int	conserve_statement_count = 0
	counts the number of CONSERVE statements in Kinetic blocks More...

std::string	conserve_equation_str
	conserve statement equation as string More...

std::string	conserve_equation_statevar
	conserve statement: current state variable being processed More...

std::string	conserve_equation_factor
	conserve statement: current state var multiplicative factor being processed More...

int	i_statement = 0
	current statement index More...

std::vector< ast::KineticBlock * >	kinetic_blocks
	vector of kinetic block nodes More...

std::unordered_set< ast::Statement * >	statements_to_remove
	statements to remove from block More...

ast::StatementBlock *	current_statement_block = nullptr
	current statement block being visited More...

Constructor & Destructor Documentation

◆ KineticBlockVisitor()

nmodl::visitor::KineticBlockVisitor::KineticBlockVisitor ( )

default

Member Function Documentation

◆ compute_compartment_factor()

void nmodl::visitor::KineticBlockVisitor::compute_compartment_factor	(	ast::Compartment &	node,
		const ast::Name &	name
	)

private

Definition at line 161 of file kinetic_block_visitor.cpp.

◆ compute_indexed_compartment_factor()

void nmodl::visitor::KineticBlockVisitor::compute_indexed_compartment_factor	(	ast::Compartment &	node,
		const ast::Name &	name
	)

private

Definition at line 178 of file kinetic_block_visitor.cpp.

◆ get_conserve_statement_count()

int nmodl::visitor::KineticBlockVisitor::get_conserve_statement_count ( ) const

inline

Definition at line 148 of file kinetic_block_visitor.hpp.

◆ process_conserve_reac_var()

void nmodl::visitor::KineticBlockVisitor::process_conserve_reac_var	(	const std::string &	varname,
		int	count = `1`
	)

private

update CONSERVE statement with reaction var term

Definition at line 68 of file kinetic_block_visitor.cpp.

◆ process_reac_var()

void nmodl::visitor::KineticBlockVisitor::process_reac_var	(	const std::string &	varname,
		int	count = `1`
	)

private

update stoichiometric matrices with reaction var term

Definition at line 27 of file kinetic_block_visitor.cpp.

◆ set_compartment_factor()

void nmodl::visitor::KineticBlockVisitor::set_compartment_factor	(	int	var_index,
		const std::string &	factor
	)

private

Definition at line 149 of file kinetic_block_visitor.cpp.

◆ unroll_kinetic_blocks()

void nmodl::visitor::KineticBlockVisitor::unroll_kinetic_blocks ( ast::Program & node )

private

Unroll loops in KINETIC blocks.

The subsequent processing in KineticBlockVisitor fails if there's any reaction equation inside a FROM .. TO .. block. The solution is to unroll any loops first to satisfy the assumption.

Definition at line 647 of file kinetic_block_visitor.cpp.

◆ visit_compartment()

void nmodl::visitor::KineticBlockVisitor::visit_compartment ( ast::Compartment & node )

overridevirtual

visit node of type ast::Compartment

Implements nmodl::visitor::Visitor.

Definition at line 202 of file kinetic_block_visitor.cpp.

◆ visit_conserve()

void nmodl::visitor::KineticBlockVisitor::visit_conserve ( ast::Conserve & node )

overridevirtual

visit node of type ast::Conserve

Implements nmodl::visitor::Visitor.

Definition at line 107 of file kinetic_block_visitor.cpp.

◆ visit_kinetic_block()

void nmodl::visitor::KineticBlockVisitor::visit_kinetic_block ( ast::KineticBlock & node )

overridevirtual

visit node of type ast::KineticBlock

Implements nmodl::visitor::Visitor.

Definition at line 403 of file kinetic_block_visitor.cpp.

◆ visit_program()

void nmodl::visitor::KineticBlockVisitor::visit_program ( ast::Program & node )

overridevirtual

visit node of type ast::Program

Implements nmodl::visitor::Visitor.

Definition at line 682 of file kinetic_block_visitor.cpp.

◆ visit_react_var_name()

void nmodl::visitor::KineticBlockVisitor::visit_react_var_name ( ast::ReactVarName & node )

overridevirtual

visit node of type ast::ReactVarName

Implements nmodl::visitor::Visitor.

Definition at line 229 of file kinetic_block_visitor.cpp.

◆ visit_reaction_operator()

void nmodl::visitor::KineticBlockVisitor::visit_reaction_operator ( ast::ReactionOperator & node )

overridevirtual

visit node of type ast::ReactionOperator

Implements nmodl::visitor::Visitor.

Definition at line 219 of file kinetic_block_visitor.cpp.

◆ visit_reaction_statement()

void nmodl::visitor::KineticBlockVisitor::visit_reaction_statement ( ast::ReactionStatement & node )

overridevirtual

visit node of type ast::ReactionStatement

check if reaction statement is a single state variable

Implements nmodl::visitor::Visitor.

Definition at line 251 of file kinetic_block_visitor.cpp.

◆ visit_statement_block()

void nmodl::visitor::KineticBlockVisitor::visit_statement_block ( ast::StatementBlock & node )

overridevirtual

visit node of type ast::StatementBlock

Implements nmodl::visitor::Visitor.

Definition at line 394 of file kinetic_block_visitor.cpp.

◆ visit_wrapped_expression()

void nmodl::visitor::KineticBlockVisitor::visit_wrapped_expression ( ast::WrappedExpression & node )

overridevirtual

visit node of type ast::WrappedExpression

Implements nmodl::visitor::Visitor.

Definition at line 374 of file kinetic_block_visitor.cpp.

Member Data Documentation

◆ additive_terms

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::additive_terms

private

additive constant terms for ODEs from reaction statements like ~ x << (a)

Definition at line 80 of file kinetic_block_visitor.hpp.

◆ array_state_var_size

std::unordered_map<std::string, int> nmodl::visitor::KineticBlockVisitor::array_state_var_size

private

unordered_map from array state variable to its size (for summing over each element of any array state vars in a CONSERVE statement)

Definition at line 111 of file kinetic_block_visitor.hpp.

◆ bflux

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::bflux

private

Definition at line 91 of file kinetic_block_visitor.hpp.

◆ compartment_factors

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::compartment_factors

private

multiplicative factors for ODEs from COMPARTMENT statements

Definition at line 77 of file kinetic_block_visitor.hpp.

◆ conserve_equation_factor

std::string nmodl::visitor::KineticBlockVisitor::conserve_equation_factor

private

conserve statement: current state var multiplicative factor being processed

Definition at line 132 of file kinetic_block_visitor.hpp.

◆ conserve_equation_statevar

std::string nmodl::visitor::KineticBlockVisitor::conserve_equation_statevar

private

conserve statement: current state variable being processed

Definition at line 129 of file kinetic_block_visitor.hpp.

◆ conserve_equation_str

std::string nmodl::visitor::KineticBlockVisitor::conserve_equation_str

private

conserve statement equation as string

Definition at line 126 of file kinetic_block_visitor.hpp.

◆ conserve_statement_count

int nmodl::visitor::KineticBlockVisitor::conserve_statement_count = 0

private

counts the number of CONSERVE statements in Kinetic blocks

Definition at line 123 of file kinetic_block_visitor.hpp.

◆ current_statement_block

ast::StatementBlock* nmodl::visitor::KineticBlockVisitor::current_statement_block = nullptr

private

current statement block being visited

Definition at line 144 of file kinetic_block_visitor.hpp.

◆ fflux

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::fflux

private

generated set of fluxes and ODEs

Definition at line 90 of file kinetic_block_visitor.hpp.

◆ i_statement

int nmodl::visitor::KineticBlockVisitor::i_statement = 0

private

current statement index

Definition at line 135 of file kinetic_block_visitor.hpp.

◆ in_conserve_statement

bool nmodl::visitor::KineticBlockVisitor::in_conserve_statement = false

private

true if we are visiting a CONSERVE statement

Definition at line 120 of file kinetic_block_visitor.hpp.

◆ in_reaction_statement

bool nmodl::visitor::KineticBlockVisitor::in_reaction_statement = false

private

true if we are visiting a reaction statement

Definition at line 114 of file kinetic_block_visitor.hpp.

◆ in_reaction_statement_lhs

bool nmodl::visitor::KineticBlockVisitor::in_reaction_statement_lhs = false

private

true if we are visiting the left hand side of reaction statement

Definition at line 117 of file kinetic_block_visitor.hpp.

◆ kinetic_blocks

std::vector<ast::KineticBlock*> nmodl::visitor::KineticBlockVisitor::kinetic_blocks

private

vector of kinetic block nodes

Definition at line 138 of file kinetic_block_visitor.hpp.

◆ modfile_bflux

std::string nmodl::visitor::KineticBlockVisitor::modfile_bflux

private

Definition at line 98 of file kinetic_block_visitor.hpp.

◆ modfile_fflux

std::string nmodl::visitor::KineticBlockVisitor::modfile_fflux

private

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

Definition at line 97 of file kinetic_block_visitor.hpp.

◆ non_state_var_bflux

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::non_state_var_bflux

private

Definition at line 87 of file kinetic_block_visitor.hpp.

◆ non_state_var_fflux

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::non_state_var_fflux

private

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)

Definition at line 86 of file kinetic_block_visitor.hpp.

◆ odes

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::odes

private

Definition at line 92 of file kinetic_block_visitor.hpp.

◆ rate_eqs

struct nmodl::visitor::KineticBlockVisitor::RateEqs nmodl::visitor::KineticBlockVisitor::rate_eqs

private

◆ state_var

std::vector<std::string> nmodl::visitor::KineticBlockVisitor::state_var

private

state variables vector

Definition at line 104 of file kinetic_block_visitor.hpp.

◆ state_var_count

int nmodl::visitor::KineticBlockVisitor::state_var_count = 0

private

number of state variables

Definition at line 101 of file kinetic_block_visitor.hpp.

◆ state_var_index

std::unordered_map<std::string, int> nmodl::visitor::KineticBlockVisitor::state_var_index

private

unordered_map from state variable to corresponding index

Definition at line 107 of file kinetic_block_visitor.hpp.

◆ statements_to_remove

std::unordered_set<ast::Statement*> nmodl::visitor::KineticBlockVisitor::statements_to_remove

private

statements to remove from block

Definition at line 141 of file kinetic_block_visitor.hpp.

The documentation for this class was generated from the following files:

/home/runner/work/nmodl/nmodl/src/visitors/kinetic_block_visitor.hpp
/home/runner/work/nmodl/nmodl/src/visitors/kinetic_block_visitor.cpp

Detailed Description

Classes

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ KineticBlockVisitor()

Member Function Documentation

◆ compute_compartment_factor()

◆ compute_indexed_compartment_factor()

◆ get_conserve_statement_count()

◆ process_conserve_reac_var()

◆ process_reac_var()

◆ set_compartment_factor()

◆ unroll_kinetic_blocks()

◆ visit_compartment()

◆ visit_conserve()

◆ visit_kinetic_block()

◆ visit_program()

◆ visit_react_var_name()

◆ visit_reaction_operator()

◆ visit_reaction_statement()

◆ visit_statement_block()

◆ visit_wrapped_expression()

Member Data Documentation

◆ additive_terms

◆ array_state_var_size

◆ bflux

◆ compartment_factors

◆ conserve_equation_factor

◆ conserve_equation_statevar

◆ conserve_equation_str

◆ conserve_statement_count

◆ current_statement_block

◆ fflux

◆ i_statement

◆ in_conserve_statement

◆ in_reaction_statement

◆ in_reaction_statement_lhs

◆ kinetic_blocks

◆ modfile_bflux

◆ modfile_fflux

◆ non_state_var_bflux

◆ non_state_var_fflux

◆ odes

◆ rate_eqs

◆ state_var

◆ state_var_count

◆ state_var_index

◆ statements_to_remove