Initial attempt at implementing VERBATIM.

docs/contents/longitudinal_diffusion.rst

@@ -0,0 +1,33 @@
+Longitudinal Diffusion
+======================
+
+The idea behind ``LONGITUDINAL_DIFFUSION`` is to allow a ``STATE`` variable to
+diffuse along a section, i.e. from one segment into a neighbouring segment.
+
+This problem is solved by registering callbacks. In particular, NEURON needs to
+be informed of the volume and diffusion rate. Additionally, the implicit
+time-stepping requires information about certain derivatives.
+
+Implementation in NMODL
+-----------------------
+
+The following ``KINETIC`` block
+
+  .. code-block::
+
+    KINETIC state {
+        COMPARTMENT vol {X}
+        LONGITUDINAL_DIFFUSION mu {X}
+
+        ~ X << (ica)
+    }
+
+Will undergo two transformations. The first is to create a system of ODEs that
+can be solved. This consumed the AST node. However, to print the code for
+longitudinal diffusion we require information from the ``COMPARTMENT`` and
+``LONGITUDINAL_DIFFUSION`` statements. This is why there's a second
+transformation, that runs before the other transformation, to extract the
+required information and store it a AST node called
+``LONGITUDINAL_DIFFUSION_BLOCK``. This block can then be converted into an
+"info" object, which is then used to print the callbacks.
+

docs/index.rst

@@ -24,6 +24,7 @@ About NMODL
    contents/pointers
    contents/cable_equations
    contents/globals
+   contents/longitudinal_diffusion
 
 .. toctree::
    :maxdepth: 3

src/codegen/codegen_coreneuron_cpp_visitor.cpp

@@ -115,6 +115,21 @@ std::string CodegenCoreneuronCppVisitor::process_verbatim_token(const std::strin
     return get_variable_name(token, use_instance);
 }
 
+void CodegenCoreneuronCppVisitor::visit_verbatim(const Verbatim& node) {
+    const auto& text = node.get_statement()->eval();
+    printer->add_line("// VERBATIM");
+    const auto& result = process_verbatim_text(text);
+
+    const auto& statements = stringutils::split_string(result, '\n');
+    for (const auto& statement: statements) {
+        const auto& trimed_stmt = stringutils::trim_newline(statement);
+        if (trimed_stmt.find_first_not_of(' ') != std::string::npos) {
+            printer->add_line(trimed_stmt);
+        }
+    }
+    printer->add_line("// ENDVERBATIM");
+}
+
 
 /**
  * \details This can be override in the backend. For example, parameters can be constant
@@ -343,28 +358,6 @@ void CodegenCoreneuronCppVisitor::print_abort_routine() const {
 /****************************************************************************************/
 
 
-void CodegenCoreneuronCppVisitor::print_top_verbatim_blocks() {
-    if (info.top_verbatim_blocks.empty()) {
-        return;
-    }
-    print_namespace_stop();
-
-    printer->add_newline(2);
-    print_using_namespace();
-
-    printing_top_verbatim_blocks = true;
-
-    for (const auto& block: info.top_verbatim_blocks) {
-        printer->add_newline(2);
-        block->accept(*this);
-    }
-
-    printing_top_verbatim_blocks = false;
-
-    print_namespace_start();
-}
-
-
 void CodegenCoreneuronCppVisitor::print_function_prototypes() {
     if (info.functions.empty() && info.procedures.empty()) {
         return;
@@ -869,7 +862,13 @@ std::string CodegenCoreneuronCppVisitor::get_variable_name(const std::string& na
     auto i =
         std::find_if(codegen_int_variables.begin(), codegen_int_variables.end(), index_comparator);
     if (i != codegen_int_variables.end()) {
-        return int_variable_name(*i, varname, use_instance);
+        auto full_name = int_variable_name(*i, varname, use_instance);
+        auto pos = position_of_int_var(varname);
+
+        if (info.semantics[pos].name == naming::RANDOM_SEMANTIC) {
+            return "(nrnran123_State*) " + full_name;
+        }
+        return full_name;
     }
 
     // global variable
@@ -1677,7 +1676,7 @@ void CodegenCoreneuronCppVisitor::print_instance_variable_setup() {
         printer->push_block("for (int id = 0; id < nodecount; id++)");
         for (const auto& var: info.random_variables) {
             const auto& name = get_variable_name(var->get_name());
-            printer->fmt_line("nrnran123_deletestream((nrnran123_State*){});", name);
+            printer->fmt_line("nrnran123_deletestream({});", name);
         }
         printer->pop_block();
     }

src/codegen/codegen_coreneuron_cpp_visitor.hpp

@@ -122,7 +122,6 @@ class CodegenCoreneuronCppVisitor: public CodegenCppVisitor {
      */
     std::string process_verbatim_token(const std::string& token);
 
-
     /**
      * Check if variable is qualified as constant
      * \param name The name of variable
@@ -324,12 +323,6 @@ class CodegenCoreneuronCppVisitor: public CodegenCppVisitor {
     /****************************************************************************************/
 
 
-    /**
-     * Print top level (global scope) verbatim blocks
-     */
-    void print_top_verbatim_blocks();
-
-
     /**
      * Print function and procedures prototype declaration
      */
@@ -424,7 +417,7 @@ class CodegenCoreneuronCppVisitor: public CodegenCppVisitor {
      * \param text The verbatim code to be processed
      * \return     The code with all variables renamed as needed
      */
-    std::string process_verbatim_text(std::string const& text) override;
+    std::string process_verbatim_text(std::string const& text);
 
 
     /**
@@ -963,6 +956,7 @@ class CodegenCoreneuronCppVisitor: public CodegenCppVisitor {
 
     void visit_derivimplicit_callback(const ast::DerivimplicitCallback& node) override;
     void visit_for_netcon(const ast::ForNetcon& node) override;
+    void visit_verbatim(const ast::Verbatim& node) override;
     void visit_watch_statement(const ast::WatchStatement& node) override;
 
     ParamVector functor_params() override;

src/codegen/codegen_cpp_visitor.cpp

@@ -13,6 +13,7 @@
 #include "ast/all.hpp"
 #include "codegen/codegen_helper_visitor.hpp"
 #include "codegen/codegen_utils.hpp"
+#include "utils/string_utils.hpp"
 #include "visitors/defuse_analyze_visitor.hpp"
 #include "visitors/rename_visitor.hpp"
 #include "visitors/symtab_visitor.hpp"
@@ -519,12 +520,6 @@ void CodegenCppVisitor::print_function_call(const FunctionCall& node) {
         }
     }
 
-    // first argument to random functions need to be type casted
-    // from void* to nrnran123_State*.
-    if (is_random_function && !arguments.empty()) {
-        printer->add_text("(nrnran123_State*)");
-    }
-
     print_vector_elements(arguments, ", ");
     printer->add_text(')');
 }
@@ -639,6 +634,28 @@ void CodegenCppVisitor::print_namespace_stop() {
 }
 
 
+void CodegenCppVisitor::print_top_verbatim_blocks() {
+    if (info.top_verbatim_blocks.empty()) {
+        return;
+    }
+    print_namespace_stop();
+
+    printer->add_newline(2);
+    print_using_namespace();
+
+    printing_top_verbatim_blocks = true;
+
+    for (const auto& block: info.top_verbatim_blocks) {
+        printer->add_newline(2);
+        block->accept(*this);
+    }
+
+    printing_top_verbatim_blocks = false;
+
+    print_namespace_start();
+}
+
+
 /****************************************************************************************/
 /*                         Printing routines for code generation                        */
 /****************************************************************************************/
@@ -1048,22 +1065,6 @@ void CodegenCppVisitor::visit_function_call(const FunctionCall& node) {
 }
 
 
-void CodegenCppVisitor::visit_verbatim(const Verbatim& node) {
-    const auto& text = node.get_statement()->eval();
-    printer->add_line("// VERBATIM");
-    const auto& result = process_verbatim_text(text);
-
-    const auto& statements = stringutils::split_string(result, '\n');
-    for (const auto& statement: statements) {
-        const auto& trimed_stmt = stringutils::trim_newline(statement);
-        if (trimed_stmt.find_first_not_of(' ') != std::string::npos) {
-            printer->add_line(trimed_stmt);
-        }
-    }
-    printer->add_line("// ENDVERBATIM");
-}
-
-
 void CodegenCppVisitor::visit_update_dt(const ast::UpdateDt& node) {
     // dt change statement should be pulled outside already
 }

src/codegen/codegen_cpp_visitor.hpp

@@ -169,6 +169,10 @@ struct ShadowUseStatement {
     std::string rhs;
 };
 
+inline std::string get_name(ast::Ast const* sym) {
+    return sym->get_node_name();
+}
+
 inline std::string get_name(const std::shared_ptr<symtab::Symbol>& sym) {
     return sym->get_name();
 }
@@ -1031,14 +1035,6 @@ class CodegenCppVisitor: public visitor::ConstAstVisitor {
      */
     virtual std::string nrn_thread_internal_arguments() = 0;
 
-    /**
-     * Process a verbatim block for possible variable renaming
-     * \param text The verbatim code to be processed
-     * \return     The code with all variables renamed as needed
-     */
-    virtual std::string process_verbatim_text(std::string const& text) = 0;
-
-
     /**
      * Arguments for register_mech or point_register_mech function
      */
@@ -1453,6 +1449,11 @@ class CodegenCppVisitor: public visitor::ConstAstVisitor {
      */
     void print_nmodl_constants();
 
+    /**
+     * Print top level (global scope) verbatim blocks
+     */
+    void print_top_verbatim_blocks();
+
 
     /****************************************************************************************/
     /*                            Overloaded visitor routines                               */
@@ -1478,7 +1479,6 @@ class CodegenCppVisitor: public visitor::ConstAstVisitor {
     void visit_unary_operator(const ast::UnaryOperator& node) override;
     void visit_unit(const ast::Unit& node) override;
     void visit_var_name(const ast::VarName& node) override;
-    void visit_verbatim(const ast::Verbatim& node) override;
     void visit_while_statement(const ast::WhileStatement& node) override;
     void visit_update_dt(const ast::UpdateDt& node) override;
     void visit_protect_statement(const ast::ProtectStatement& node) override;

src/codegen/codegen_helper_visitor.cpp

@@ -9,8 +9,10 @@
 
 #include <algorithm>
 #include <cmath>
+#include <memory>
 
 #include "ast/all.hpp"
+#include "ast/constant_var.hpp"
 #include "codegen/codegen_naming.hpp"
 #include "parser/c11_driver.hpp"
 #include "visitors/visitor_utils.hpp"
@@ -853,5 +855,62 @@ void CodegenHelperVisitor::visit_after_block(const ast::AfterBlock& node) {
     info.before_after_blocks.push_back(&node);
 }
 
+std::shared_ptr<ast::Compartment> find_compartment(const ast::LongitudinalDiffusionBlock& node,
+                                                   const std::string& var_name) {
+    const auto& compartment_block = node.get_compartment_statements();
+    for (const auto& stmt: compartment_block->get_statements()) {
+        auto comp = std::dynamic_pointer_cast<ast::Compartment>(stmt);
+
+        auto species = comp->get_species();
+        auto it = std::find_if(species.begin(), species.end(), [&var_name](auto var) {
+            return var->get_node_name() == var_name;
+        });
+
+        if (it != species.end()) {
+            return comp;
+        }
+    }
+
+    return nullptr;
+}
+
+void CodegenHelperVisitor::visit_longitudinal_diffusion_block(
+    const ast::LongitudinalDiffusionBlock& node) {
+    auto longitudinal_diffusion_block = node.get_longitudinal_diffusion_statements();
+    for (auto stmt: longitudinal_diffusion_block->get_statements()) {
+        auto diffusion = std::dynamic_pointer_cast<ast::LonDiffuse>(stmt);
+        auto rate_index_name = diffusion->get_index_name();
+        auto rate_expr = diffusion->get_rate();
+        auto species = diffusion->get_species();
+
+        auto process_compartment = [](const std::shared_ptr<ast::Compartment>& compartment)
+            -> std::pair<std::shared_ptr<ast::Name>, std::shared_ptr<ast::Expression>> {
+            std::shared_ptr<ast::Expression> volume_expr;
+            std::shared_ptr<ast::Name> volume_index_name;
+            if (!compartment) {
+                volume_index_name = nullptr;
+                volume_expr = std::make_shared<ast::Double>("1.0");
+            } else {
+                volume_index_name = compartment->get_index_name();
+                volume_expr = std::shared_ptr<ast::Expression>(compartment->get_volume()->clone());
+            }
+            return {std::move(volume_index_name), std::move(volume_expr)};
+        };
+
+        for (auto var: species) {
+            std::string state_name = var->get_value()->get_value();
+            auto compartment = find_compartment(node, state_name);
+            auto [volume_index_name, volume_expr] = process_compartment(compartment);
+
+            info.longitudinal_diffusion_info.insert(
+                {state_name,
+                 LongitudinalDiffusionInfo(volume_index_name,
+                                           std::shared_ptr<ast::Expression>(volume_expr),
+                                           rate_index_name,
+                                           std::shared_ptr<ast::Expression>(rate_expr->clone()))});
+        }
+    }
+}
+
 }  // namespace codegen
 }  // namespace nmodl

src/codegen/codegen_helper_visitor.hpp

@@ -115,6 +115,7 @@ class CodegenHelperVisitor: public visitor::ConstAstVisitor {
     void visit_verbatim(const ast::Verbatim& node) override;
     void visit_before_block(const ast::BeforeBlock& node) override;
     void visit_after_block(const ast::AfterBlock& node) override;
+    void visit_longitudinal_diffusion_block(const ast::LongitudinalDiffusionBlock& node) override;
 };
 
 /** @} */  // end of codegen_details