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Improve COMPARTMENT names & documentation. #1498

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Oct 3, 2024
Merged

Improve COMPARTMENT names & documentation. #1498

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12 changes: 6 additions & 6 deletions src/language/nmodl.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1527,18 +1527,18 @@
- Compartment:
nmodl: COMPARTMENT
members:
- name:
brief: "TODO"
- index_name:
brief: "Name of the index variable in volume expression"
type: Name
optional: true
prefix: {value: " "}
suffix: {value: ","}
- expression:
brief: "TODO"
- volume:
brief: "The volume of the compartment"
type: Expression
prefix: {value: " "}
- names:
brief: "TODO"
- species:
brief: "The names of the species that reside in this compartment"
type: Name
vector: true
prefix: {value: " {"}
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14 changes: 7 additions & 7 deletions src/visitors/kinetic_block_visitor.cpp
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Expand Up @@ -164,7 +164,7 @@ void KineticBlockVisitor::compute_compartment_factor(ast::Compartment& node,
const auto it = state_var_index.find(var_name);
if (it != state_var_index.cend()) {
int var_index = it->second;
auto expr = node.get_expression();
auto expr = node.get_volume();
std::string expression = to_nmodl(expr);

set_compartment_factor(var_index, expression);
Expand All @@ -178,7 +178,7 @@ void KineticBlockVisitor::compute_compartment_factor(ast::Compartment& node,
void KineticBlockVisitor::compute_indexed_compartment_factor(ast::Compartment& node,
const ast::Name& name) {
auto array_var_name = name.get_node_name();
auto index_name = node.get_name()->get_node_name();
auto index_name = node.get_index_name()->get_node_name();

auto pattern = fmt::format("^{}\\[([0-9]*)\\]$", array_var_name);
std::regex re(pattern);
Expand All @@ -189,8 +189,8 @@ void KineticBlockVisitor::compute_indexed_compartment_factor(ast::Compartment& n

if (matches) {
int index_value = std::stoi(m[1]);
auto volume_expr = node.get_expression();
auto expr = std::shared_ptr<ast::Expression>(node.get_expression()->clone());
auto volume_expr = node.get_volume();
auto expr = std::shared_ptr<ast::Expression>(volume_expr->clone());
IndexRemover(index_name, index_value).visit_expression(*expr);

std::string expression = to_nmodl(*expr);
Expand All @@ -203,9 +203,9 @@ void KineticBlockVisitor::visit_compartment(ast::Compartment& node) {
// COMPARTMENT block has an expression, and a list of state vars it applies to.
// For each state var, the rhs of the differential eq should be divided by the expression.
// Here we store the expressions in the compartment_factors vector
logger->debug("KineticBlockVisitor :: COMPARTMENT expr: {}", to_nmodl(node.get_expression()));
for (const auto& name_ptr: node.get_names()) {
if (node.get_name() == nullptr) {
logger->debug("KineticBlockVisitor :: COMPARTMENT expr: {}", to_nmodl(node.get_volume()));
for (const auto& name_ptr: node.get_species()) {
if (node.get_index_name() == nullptr) {
compute_compartment_factor(node, *name_ptr);
} else {
compute_indexed_compartment_factor(node, *name_ptr);
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