transform kernels and convolutions using a transformer before code ge…

…neration [noci]

pynestml/transformers/convolutions_transformer.py

@@ -35,6 +35,7 @@
 from pynestml.codegeneration.printers.unitless_sympy_simple_expression_printer import UnitlessSympySimpleExpressionPrinter
 from pynestml.frontend.frontend_configuration import FrontendConfiguration
 from pynestml.meta_model.ast_assignment import ASTAssignment
+from pynestml.meta_model.ast_block import ASTBlock
 from pynestml.meta_model.ast_data_type import ASTDataType
 from pynestml.meta_model.ast_declaration import ASTDeclaration
 from pynestml.meta_model.ast_equations_block import ASTEquationsBlock
@@ -46,6 +47,7 @@
 from pynestml.meta_model.ast_node import ASTNode
 from pynestml.meta_model.ast_node_factory import ASTNodeFactory
 from pynestml.meta_model.ast_simple_expression import ASTSimpleExpression
+from pynestml.meta_model.ast_small_stmt import ASTSmallStmt
 from pynestml.meta_model.ast_variable import ASTVariable
 from pynestml.symbols.predefined_functions import PredefinedFunctions
 from pynestml.symbols.real_type_symbol import RealTypeSymbol
@@ -86,6 +88,53 @@ def __init__(self, options: Optional[Mapping[str, Any]] = None):
         self._ode_toolbox_variable_printer._expression_printer = self._ode_toolbox_printer
         self._ode_toolbox_function_call_printer._expression_printer = self._ode_toolbox_printer
 
+    def add_restore_kernel_variables_to_start_of_timestep(self, model, solvers_json):
+        r"""For each integrate_odes() call in the model, append statements restoring the kernel variables to the values at the start of the timestep"""
+
+        var_names = []
+        for solver_dict in solvers_json:
+            if solver_dict is None:
+                continue
+
+            for var_name, expr in solver_dict["initial_values"].items():
+                var_names.append(var_name)
+
+        class IntegrateODEsFunctionCallVisitor(ASTVisitor):
+            all_args = None
+
+            def __init__(self):
+                super().__init__()
+
+            def visit_small_stmt(self, node: ASTSmallStmt):
+                self._visit(node)
+
+            def visit_simple_expression(self, node: ASTSimpleExpression):
+                self._visit(node)
+
+            def _visit(self, node):
+                if node.is_function_call() and node.get_function_call().get_name() == PredefinedFunctions.INTEGRATE_ODES:
+                    parent_stmt = node.get_parent()
+                    parent_block = parent_stmt.get_parent()
+                    assert isinstance(parent_block, ASTBlock)
+                    idx = parent_block.stmts.index(parent_stmt)
+
+                    for i, var_name in enumerate(var_names):
+                        var = ASTNodeFactory.create_ast_variable(var_name + "__at_start_of_timestep", type_symbol=RealTypeSymbol)
+                        var.update_scope(parent_block.get_scope())
+                        expr = ASTNodeFactory.create_ast_simple_expression(variable=var)
+                        ast_assignment = ASTNodeFactory.create_ast_assignment(lhs=ASTUtils.get_variable_by_name(model, var_name),
+                                                                               is_direct_assignment=True,
+                                                                               expression=expr, source_position=ASTSourceLocation.get_added_source_position())
+                        ast_assignment.update_scope(parent_block.get_scope())
+                        ast_small_stmt = ASTNodeFactory.create_ast_small_stmt(assignment=ast_assignment)
+                        ast_small_stmt.update_scope(parent_block.get_scope())
+                        ast_stmt = ASTNodeFactory.create_ast_stmt(small_stmt=ast_small_stmt)
+                        ast_stmt.update_scope(parent_block.get_scope())
+
+                        parent_block.stmts.insert(idx + i + 1, ast_stmt)
+
+        model.accept(IntegrateODEsFunctionCallVisitor())
+
     def add_kernel_variables_to_integrate_odes_calls(self, model, solvers_json):
         for solver_dict in solvers_json:
             if solver_dict is None:
@@ -124,7 +173,7 @@ def add_temporary_kernel_variables_copy(self, model, solvers_json):
         scope = model.get_update_blocks()[0].scope
 
         for var_name in var_names:
-            var = ASTNodeFactory.create_ast_variable(var_name + "__tmp", type_symbol=RealTypeSymbol)
+            var = ASTNodeFactory.create_ast_variable(var_name + "__at_start_of_timestep", type_symbol=RealTypeSymbol)
             var.scope = scope
             expr = ASTNodeFactory.create_ast_simple_expression(variable=ASTUtils.get_variable_by_name(model, var_name))
             ast_declaration = ASTNodeFactory.create_ast_declaration(variables=[var],
@@ -163,6 +212,7 @@ def transform(self, models: Union[ASTNode, Sequence[ASTNode]]) -> Union[ASTNode,
             self.replace_convolve_calls_with_buffers_(model)
             self.remove_kernel_definitions_from_equations_blocks(model)
             self.add_kernel_variables_to_integrate_odes_calls(model, solvers_json)
+            self.add_restore_kernel_variables_to_start_of_timestep(model, solvers_json)
             self.add_temporary_kernel_variables_copy(model, solvers_json)
             self.add_integrate_odes_call_for_kernel_variables(model, solvers_json)
             self.add_kernel_equations(model, solvers_json)
@@ -438,6 +488,32 @@ def generate_kernel_buffers(self, model: ASTModel) -> Mapping[ASTKernel, ASTInpu
 
         return kernel_buffers
 
+    def add_kernel_equations(self, model, solver_dicts):
+        if not model.get_equations_blocks():
+            ASTUtils.create_equations_block()
+
+        assert len(model.get_equations_blocks()) <= 1
+
+        equations_block = model.get_equations_blocks()[0]
+
+        for solver_dict in solver_dicts:
+            if solver_dict is None:
+                continue
+
+            for var_name, expr_str in solver_dict["update_expressions"].items():
+                expr = ModelParser.parse_expression(expr_str)
+                expr.update_scope(model.get_scope())
+                expr.accept(ASTSymbolTableVisitor())
+
+                var = ASTNodeFactory.create_ast_variable(var_name, differential_order=1, source_position=ASTSourceLocation.get_added_source_position())
+                var.update_scope(equations_block.get_scope())
+                ast_ode_equation = ASTNodeFactory.create_ast_ode_equation(lhs=var, rhs=expr, source_position=ASTSourceLocation.get_added_source_position())
+                ast_ode_equation.update_scope(equations_block.get_scope())
+                equations_block.declarations.append(ast_ode_equation)
+
+        model.accept(ASTParentVisitor())
+        model.accept(ASTSymbolTableVisitor())
+
     def remove_kernel_definitions_from_equations_blocks(self, model: ASTModel) -> ASTDeclaration:
         r"""
         Removes all kernels in equations blocks.

pynestml/utils/ast_utils.py

@@ -456,6 +456,9 @@ def create_equations_block(cls, model: ASTModel) -> ASTModel:
             block = ASTNodeFactory.create_ast_equations_block(list(),
                                                               ASTSourceLocation.get_added_source_position())
             model.get_body().get_body_elements().append(block)
+
+        model.accept(ASTParentVisitor())
+
         return model
 
     @classmethod