diff --git a/crates/fayalite/src/sim.rs b/crates/fayalite/src/sim.rs
index 10fbb92..988afca 100644
--- a/crates/fayalite/src/sim.rs
+++ b/crates/fayalite/src/sim.rs
@@ -6429,7 +6429,7 @@ impl_to_sim_value_for_int_value!(SIntValue, SInt, SIntType);
 struct SimulationImpl {
     state: interpreter::State,
     io: Expr<Bundle>,
-    uninitialized_inputs: HashSet<Target>,
+    uninitialized_inputs: HashMap<Target, Vec<Target>>,
     io_targets: HashMap<Target, CompiledValue<CanonicalType>>,
     made_initial_step: bool,
     needs_settle: bool,
@@ -6483,37 +6483,52 @@ impl SimulationImpl {
             .field("clocks_triggered", clocks_triggered)
             .finish_non_exhaustive()
     }
-    fn parse_io(&mut self, target: Target, value: CompiledValue<CanonicalType>) {
+    /// returns `true` if `target` or any sub-targets are uninitialized inputs
+    fn parse_io(&mut self, target: Target, value: CompiledValue<CanonicalType>) -> bool {
         self.io_targets.insert(target, value);
         match value.layout.body {
             CompiledTypeLayoutBody::Scalar => match target.flow() {
-                Flow::Source => {}
+                Flow::Source => false,
                 Flow::Sink => {
-                    self.uninitialized_inputs.insert(target);
+                    self.uninitialized_inputs.insert(target, vec![]);
+                    true
                 }
                 Flow::Duplex => unreachable!(),
             },
             CompiledTypeLayoutBody::Array { .. } => {
                 let value = value.map_ty(Array::from_canonical);
+                let mut sub_targets = Vec::new();
                 for index in 0..value.layout.ty.len() {
-                    self.parse_io(
-                        target.join(
-                            TargetPathElement::from(TargetPathArrayElement { index })
-                                .intern_sized(),
-                        ),
-                        value.element(index),
+                    let sub_target = target.join(
+                        TargetPathElement::from(TargetPathArrayElement { index }).intern_sized(),
                     );
+                    if self.parse_io(sub_target, value.element(index)) {
+                        sub_targets.push(sub_target);
+                    }
+                }
+                if sub_targets.is_empty() {
+                    false
+                } else {
+                    self.uninitialized_inputs.insert(target, sub_targets);
+                    true
                 }
             }
             CompiledTypeLayoutBody::Bundle { .. } => {
                 let value = value.map_ty(Bundle::from_canonical);
+                let mut sub_targets = Vec::new();
                 for BundleField { name, .. } in value.layout.ty.fields() {
-                    self.parse_io(
-                        target.join(
-                            TargetPathElement::from(TargetPathBundleField { name }).intern_sized(),
-                        ),
-                        value.field_by_name(name),
+                    let sub_target = target.join(
+                        TargetPathElement::from(TargetPathBundleField { name }).intern_sized(),
                     );
+                    if self.parse_io(sub_target, value.field_by_name(name)) {
+                        sub_targets.push(sub_target);
+                    }
+                }
+                if sub_targets.is_empty() {
+                    false
+                } else {
+                    self.uninitialized_inputs.insert(target, sub_targets);
+                    true
                 }
             }
         }
@@ -6522,7 +6537,7 @@ impl SimulationImpl {
         let mut retval = Self {
             state: State::new(compiled.insns),
             io: compiled.io.to_expr(),
-            uninitialized_inputs: HashSet::new(),
+            uninitialized_inputs: HashMap::new(),
             io_targets: HashMap::new(),
             made_initial_step: false,
             needs_settle: true,
@@ -6791,6 +6806,35 @@ impl SimulationImpl {
         };
         panic!("simulator read/write expression must not have dynamic array indexes");
     }
+    fn mark_target_as_initialized(&mut self, mut target: Target) {
+        fn remove_target_and_children(
+            uninitialized_inputs: &mut HashMap<Target, Vec<Target>>,
+            target: Target,
+        ) {
+            let Some(children) = uninitialized_inputs.remove(&target) else {
+                return;
+            };
+            for child in children {
+                remove_target_and_children(uninitialized_inputs, child);
+            }
+        }
+        remove_target_and_children(&mut self.uninitialized_inputs, target);
+        while let Some(target_child) = target.child() {
+            let parent = target_child.parent();
+            for child in self
+                .uninitialized_inputs
+                .get(&*parent)
+                .map(|v| &**v)
+                .unwrap_or(&[])
+            {
+                if self.uninitialized_inputs.contains_key(child) {
+                    return;
+                }
+            }
+            target = *parent;
+            self.uninitialized_inputs.remove(&target);
+        }
+    }
     #[track_caller]
     fn read_helper(&mut self, io: Expr<CanonicalType>) -> CompiledValue<CanonicalType> {
         let Some(target) = io.target() else {
@@ -6810,7 +6854,7 @@ impl SimulationImpl {
                     self.settle();
                 }
                 Flow::Sink => {
-                    if self.uninitialized_inputs.contains(&*target) {
+                    if self.uninitialized_inputs.contains_key(&*target) {
                         panic!("can't read from an uninitialized input");
                     }
                 }
@@ -6833,7 +6877,7 @@ impl SimulationImpl {
             Flow::Duplex => unreachable!(),
         }
         if !self.made_initial_step {
-            self.uninitialized_inputs.remove(&*target);
+            self.mark_target_as_initialized(*target);
         }
         self.needs_settle = true;
         compiled_value
@@ -7136,11 +7180,11 @@ pub struct Simulation<T: BundleType> {
     io: Expr<T>,
 }
 
-struct SortedSetDebug<'a, T>(&'a HashSet<T>);
+struct SortedSetDebug<'a, T, V>(&'a HashMap<T, V>);
 
-impl<T: fmt::Debug> fmt::Debug for SortedSetDebug<'_, T> {
+impl<T: fmt::Debug, V> fmt::Debug for SortedSetDebug<'_, T, V> {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        let mut entries = Vec::from_iter(self.0.iter().map(|v| {
+        let mut entries = Vec::from_iter(self.0.iter().map(|(v, _)| {
             if f.alternate() {
                 format!("{v:#?}")
             } else {
diff --git a/crates/fayalite/tests/sim.rs b/crates/fayalite/tests/sim.rs
index bea7d93..a249235 100644
--- a/crates/fayalite/tests/sim.rs
+++ b/crates/fayalite/tests/sim.rs
@@ -255,8 +255,14 @@ fn test_shift_register() {
     let mut sim = Simulation::new(shift_register());
     let mut writer = RcWriter::default();
     sim.add_trace_writer(VcdWriterDecls::new(writer.clone()));
-    sim.write_clock(sim.io().cd.clk, false);
-    sim.write_reset(sim.io().cd.rst, true);
+    sim.write(
+        sim.io().cd,
+        #[hdl]
+        ClockDomain {
+            clk: false.to_clock(),
+            rst: true.to_sync_reset(),
+        },
+    );
     sim.write_bool(sim.io().d, false);
     sim.advance_time(SimDuration::from_micros(1));
     sim.write_clock(sim.io().cd.clk, true);