From e19b2910ddd5ad172d82ade01f04874c2ad42339 Mon Sep 17 00:00:00 2001
From: GuySten <guyste@post.bgu.ac.il>
Date: Mon, 31 Aug 2026 18:42:29 +0300
Subject: [PATCH 1/5] claudes initial work

---
 CMakeLists.txt                         |   1 +
 include/openmc/particle_data.h         |  13 ++
 include/openmc/simulation.h            |   6 +
 include/openmc/tallies/pulse_height.h  |  71 ++++++++
 include/openmc/tallies/tally_scoring.h |   9 +-
 src/finalize.cpp                       |   2 +
 src/initialize.cpp                     |  26 ---
 src/particle.cpp                       |  43 ++++-
 src/simulation.cpp                     |  43 +++++
 src/tallies/pulse_height.cpp           | 223 +++++++++++++++++++++++++
 src/tallies/tally_scoring.cpp          |   5 +-
 tests/unit_tests/test_pulse_height.py  | 203 ++++++++++++++++++++++
 12 files changed, 613 insertions(+), 32 deletions(-)
 create mode 100644 include/openmc/tallies/pulse_height.h
 create mode 100644 src/tallies/pulse_height.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 62c2ac8a151..fd931d04ff0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -478,6 +478,7 @@ list(APPEND libopenmc_SOURCES
   src/tallies/filter_universe.cpp
   src/tallies/filter_weight.cpp
   src/tallies/filter_zernike.cpp
+  src/tallies/pulse_height.cpp
   src/tallies/tally.cpp
   src/tallies/tally_scoring.cpp
   src/tallies/trigger.cpp
diff --git a/include/openmc/particle_data.h b/include/openmc/particle_data.h
index 24b7eb53c0a..20ee6f567c2 100644
--- a/include/openmc/particle_data.h
+++ b/include/openmc/particle_data.h
@@ -52,6 +52,12 @@ struct SourceSite {
   int parent_nuclide {-1};
   int64_t parent_id {0};
   int64_t progeny_id {0};
+  // Dense global index, in [0, n_particles), of the primary at the root of
+  // this particle's tree. Propagated unchanged through every secondary
+  // generation so that per-history quantities (currently pulse height) can be
+  // reassembled after the tree has been transported across separate Particle
+  // objects and, under MPI, across ranks.
+  int64_t root_index {-1};
   double wgt_born {1.0};
   double wgt_ww_born {-1.0};
   int64_t n_split {0};
@@ -556,6 +562,8 @@ class ParticleData : public GeometryState {
 
   vector<double> pht_storage_;
 
+  int64_t root_index_ {-1};
+
   double keff_tally_absorption_ {0.0};
   double keff_tally_collision_ {0.0};
   double keff_tally_tracklength_ {0.0};
@@ -736,6 +744,11 @@ class ParticleData : public GeometryState {
 
   // Interim pulse height tally storage
   vector<double>& pht_storage() { return pht_storage_; }
+  const vector<double>& pht_storage() const { return pht_storage_; }
+
+  // Index of the primary particle at the root of this particle's tree
+  int64_t& root_index() { return root_index_; }
+  int64_t root_index() const { return root_index_; }
 
   // Global tally accumulators
   double& keff_tally_absorption() { return keff_tally_absorption_; }
diff --git a/include/openmc/simulation.h b/include/openmc/simulation.h
index 454752cd271..b34ed3af099 100644
--- a/include/openmc/simulation.h
+++ b/include/openmc/simulation.h
@@ -49,6 +49,12 @@ extern const RegularMesh* ufs_mesh;
 extern vector<double> k_generation;
 extern vector<int64_t> work_index;
 
+//! Snapshot of work_index taken during phase 1 of shared-secondary transport,
+//! i.e. the partition of *primary* particles across MPI ranks. work_index
+//! itself is overwritten by calculate_work() on every secondary generation, so
+//! it cannot be used afterwards to map a root index back to its owning rank.
+extern vector<int64_t> phase1_work_index;
+
 extern int64_t
   simulation_tracks_completed; //!< Number of tracks completed on this rank
 
diff --git a/include/openmc/tallies/pulse_height.h b/include/openmc/tallies/pulse_height.h
new file mode 100644
index 00000000000..3e574406e31
--- /dev/null
+++ b/include/openmc/tallies/pulse_height.h
@@ -0,0 +1,71 @@
+//! \file pulse_height.h
+//! \brief Deferred, per-history aggregation of pulse-height results
+//!
+//! A pulse-height tally scores one count per source history, in the bin
+//! containing the total energy that history's entire particle tree deposited in
+//! a given cell. In the default transport modes a whole tree is carried by a
+//! single Particle object, so Particle::pht_storage() already holds the
+//! per-history total by the time event_death() runs and can be scored directly.
+//!
+//! Under the shared secondary bank each secondary generation is transported as
+//! a fresh set of Particle objects, redistributed across MPI ranks between
+//! generations. A history's deposition is therefore spread over many Particle
+//! objects on potentially many ranks. This module collects those fragments,
+//! keyed by the root index carried on every SourceSite, and scores them once
+//! per history after the generation loop has drained.
+
+#ifndef OPENMC_TALLIES_PULSE_HEIGHT_H
+#define OPENMC_TALLIES_PULSE_HEIGHT_H
+
+#include <cstdint>
+
+#include "openmc/vector.h"
+
+namespace openmc {
+
+//==============================================================================
+//! One flushed pulse-height fragment, tagged with the history it belongs to.
+//==============================================================================
+
+struct PulseHeightContribution {
+  int64_t root_index;    //!< index of the primary at the root of the tree
+  vector<double> energy; //!< per-cell energy, indexed as pulse_height_cells
+};
+
+namespace simulation {
+
+//! Per-thread staging buffers, merged in finalize_pulse_height_tallies().
+extern vector<vector<PulseHeightContribution>> pht_thread_buffers;
+
+} // namespace simulation
+
+//! Allocate the per-thread staging buffers. Called from initialize_simulation()
+//! when pulse-height tallies and the shared secondary bank are both active.
+void init_pulse_height_buffers();
+
+//! Release the staging buffers and the phase-1 partition snapshot.
+void free_memory_pulse_height();
+
+//! Stage one Particle's contribution to its history's pulse height.
+//
+//! Thread-safe by construction: each thread appends only to its own buffer.
+//! Contributions that are identically zero in every cell are dropped; histories
+//! that deposit nothing are recovered in finalize_pulse_height_tallies() by
+//! iterating over the full root range rather than over staged entries.
+//
+//! \param root_index index of the primary at the root of this particle's tree
+//! \param pht per-cell energy deposited by this particle alone
+void stage_pulse_height(int64_t root_index, const vector<double>& pht);
+
+//! Aggregate staged contributions by history and score them.
+//
+//! Sends each contribution to the rank that owns its root according to
+//! simulation::phase1_work_index, sums per (history, cell), and scores every
+//! owned history including those with no deposition. Must be called after the
+//! last secondary generation has been transported and before tally results are
+//! accumulated for the batch.
+void finalize_pulse_height_tallies();
+
+} // namespace openmc
+
+#endif // OPENMC_TALLIES_PULSE_HEIGHT_H
diff --git a/include/openmc/tallies/tally_scoring.h b/include/openmc/tallies/tally_scoring.h
index 4303ddb7a90..8305023e3c0 100644
--- a/include/openmc/tallies/tally_scoring.h
+++ b/include/openmc/tallies/tally_scoring.h
@@ -120,7 +120,14 @@ void score_surface_tally(
 //
 //! \param p The particle being tracked
 //! \param tallies A vector of the indices of the tallies to score to
-void score_pulse_height_tally(Particle& p, const vector<int>& tallies);
+//! Score a completed per-history pulse-height result.
+//
+//! \param p particle used to drive filter matching; its cell and E_last are
+//!   temporarily overwritten and restored
+//! \param pht per-cell deposited energy, indexed as model::pulse_height_cells
+//! \param tallies indices of the pulse-height tallies to score into
+void score_pulse_height_tally(
+  Particle& p, const vector<double>& pht, const vector<int>& tallies);
 
 } // namespace openmc
 
diff --git a/src/finalize.cpp b/src/finalize.cpp
index fd891d9dd84..79e17e2e120 100644
--- a/src/finalize.cpp
+++ b/src/finalize.cpp
@@ -25,6 +25,7 @@
 #include "openmc/simulation.h"
 #include "openmc/source.h"
 #include "openmc/surface.h"
+#include "openmc/tallies/pulse_height.h"
 #include "openmc/tallies/tally.h"
 #include "openmc/thermal.h"
 #include "openmc/timer.h"
@@ -51,6 +52,7 @@ void free_memory()
   free_memory_source();
   free_memory_mesh();
   free_memory_tally();
+  free_memory_pulse_height();
   free_memory_bank();
   free_memory_plot();
   free_memory_weight_windows();
diff --git a/src/initialize.cpp b/src/initialize.cpp
index 33dfeca0e51..3c726675978 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -389,28 +389,6 @@ int parse_command_line(int argc, char* argv[])
   return 0;
 }
 
-// TODO: Pulse-height tallies require per-history scoring across the full
-// particle tree (parent + all descendants). The shared secondary bank
-// transports each secondary as an independent Particle, breaking this
-// assumption. A proper fix would defer pulse-height scoring: save
-// (root_source_id, cell, pht_storage) per particle, then aggregate by
-// root_source_id after all secondary generations complete before scoring
-// into the histogram. For now, disable shared secondary when pulse-height
-// tallies are present.
-static void check_pulse_height_compatibility()
-{
-  if (settings::use_shared_secondary_bank) {
-    for (const auto& t : model::tallies) {
-      if (t->type_ == TallyType::PULSE_HEIGHT) {
-        settings::use_shared_secondary_bank = false;
-        warning("Pulse-height tallies are not yet compatible with the shared "
-                "secondary bank. Disabling shared secondary bank.");
-        break;
-      }
-    }
-  }
-}
-
 bool read_model_xml()
 {
   std::string model_filename = settings::path_input;
@@ -505,8 +483,6 @@ bool read_model_xml()
   if (check_for_node(root, "tallies"))
     read_tallies_xml(root.child("tallies"));
 
-  check_pulse_height_compatibility();
-
   // Initialize distribcell_filters
   prepare_distribcell();
 
@@ -552,8 +528,6 @@ void read_separate_xml_files()
 
   read_tallies_xml();
 
-  check_pulse_height_compatibility();
-
   // Initialize distribcell_filters
   prepare_distribcell();
 
diff --git a/src/particle.cpp b/src/particle.cpp
index f7a0098acf9..28d60b17592 100644
--- a/src/particle.cpp
+++ b/src/particle.cpp
@@ -29,6 +29,7 @@
 #include "openmc/source.h"
 #include "openmc/surface.h"
 #include "openmc/tallies/derivative.h"
+#include "openmc/tallies/pulse_height.h"
 #include "openmc/tallies/tally.h"
 #include "openmc/tallies/tally_scoring.h"
 #include "openmc/track_output.h"
@@ -109,10 +110,29 @@ bool Particle::create_secondary(
   if (settings::use_shared_secondary_bank) {
     bank.progeny_id = n_progeny()++;
   }
+  bank.root_index = root_index();
   bank.wgt_born = wgt_born();
   bank.wgt_ww_born = wgt_ww_born();
   bank.n_split = n_split();
 
+  // Remove the energy carried off by this secondary from the parent's interim
+  // pulse-height result for the cell the parent is currently in. In non-shared
+  // mode the equivalent subtraction is performed at revival by
+  // pht_secondary_particles(); doing it here instead is equivalent, because the
+  // secondary is born at the parent's position and therefore in the parent's
+  // current cell, and it avoids the exhaustive_find_cell() call needed there.
+  // Placing this after the energy-cutoff early return above means a secondary
+  // that is never created is never subtracted, matching the non-shared path.
+  if (settings::use_shared_secondary_bank &&
+      !model::active_pulse_height_tallies.empty() && type.is_photon()) {
+    auto it = std::find(model::pulse_height_cells.begin(),
+      model::pulse_height_cells.end(), lowest_coord().cell());
+    if (it != model::pulse_height_cells.end()) {
+      int index = std::distance(model::pulse_height_cells.begin(), it);
+      pht_storage()[index] -= bank.E;
+    }
+  }
+
   local_secondary_bank().emplace_back(bank);
   return true;
 }
@@ -143,6 +163,10 @@ void Particle::split(double wgt)
   if (settings::use_shared_secondary_bank) {
     bank.progeny_id = n_progeny()++;
   }
+  // A split clone belongs to the same history as its parent. No pulse-height
+  // subtraction is applied here: a split is a weight artifact, not a physical
+  // secondary, and its energy is not carried away from the parent.
+  bank.root_index = root_index();
 
   local_secondary_bank().emplace_back(bank);
 }
@@ -502,6 +526,11 @@ void Particle::event_revive_from_secondary(const SourceSite& site)
 
   from_source(&site);
 
+  // Inherit the root of the tree this secondary belongs to. from_source() does
+  // not copy this, because it is also used for primaries read from the source
+  // bank, whose root index is assigned in initialize_particle_track().
+  root_index() = site.root_index;
+
   n_event() = 0;
   if (!settings::use_shared_secondary_bank) {
     n_tracks()++;
@@ -509,8 +538,8 @@ void Particle::event_revive_from_secondary(const SourceSite& site)
   bank_second_E() = 0.0;
 
   // Subtract secondary particle energy from interim pulse-height results.
-  // In shared secondary mode, this subtraction was already done on the parent
-  // particle during create_secondary(), so skip it here.
+  // In shared secondary mode this subtraction is performed on the parent in
+  // create_secondary(), so skip it here.
   if (!settings::use_shared_secondary_bank &&
       !model::active_pulse_height_tallies.empty() && this->type().is_photon()) {
     // Since the birth cell of the particle has not been set we
@@ -604,7 +633,15 @@ void Particle::event_death()
   keff_tally_leakage() = 0.0;
 
   if (!model::active_pulse_height_tallies.empty()) {
-    score_pulse_height_tally(*this, model::active_pulse_height_tallies);
+    if (settings::use_shared_secondary_bank) {
+      // This Particle carries only one fragment of its history's pulse. Stage
+      // it for aggregation by root index; scoring happens once per history in
+      // finalize_pulse_height_tallies() after all generations have drained.
+      stage_pulse_height(root_index(), pht_storage());
+    } else {
+      score_pulse_height_tally(
+        *this, pht_storage(), model::active_pulse_height_tallies);
+    }
   }
 
   // Accumulate track count for this particle history
diff --git a/src/simulation.cpp b/src/simulation.cpp
index 03f40a726eb..27fa4b761b5 100644
--- a/src/simulation.cpp
+++ b/src/simulation.cpp
@@ -23,6 +23,7 @@
 #include "openmc/state_point.h"
 #include "openmc/tallies/derivative.h"
 #include "openmc/tallies/filter.h"
+#include "openmc/tallies/pulse_height.h"
 #include "openmc/tallies/tally.h"
 #include "openmc/tallies/trigger.h"
 #include "openmc/timer.h"
@@ -351,6 +352,7 @@ const RegularMesh* ufs_mesh {nullptr};
 
 vector<double> k_generation;
 vector<int64_t> work_index;
+vector<int64_t> phase1_work_index;
 
 int64_t simulation_tracks_completed {0};
 
@@ -740,6 +742,17 @@ void initialize_particle_track(
   // Reset pulse_height_storage
   std::fill(p.pht_storage().begin(), p.pht_storage().end(), 0);
 
+  // A primary is the root of its own tree. Secondaries overwrite this in
+  // Particle::event_revive_from_secondary() using the value carried on the
+  // bank site. Only meaningful in shared-secondary mode, where a history is
+  // spread over several Particle objects; harmless otherwise.
+  if (!is_secondary) {
+    p.root_index() = simulation::phase1_work_index.empty()
+                       ? index_source - 1
+                       : simulation::phase1_work_index[mpi::rank] +
+                           index_source - 1;
+  }
+
   // set random number seed
   int64_t particle_seed = compute_transport_seed(p.id());
   init_particle_seeds(particle_seed, p.seeds());
@@ -1001,6 +1014,15 @@ void transport_history_based_shared_secondary()
   simulation::shared_secondary_bank_read.clear();
   simulation::shared_secondary_bank_write.clear();
 
+  // Record the primary partition before calculate_work() starts rewriting
+  // work_index for each secondary generation. finalize_pulse_height_tallies()
+  // needs it to map a root index back to the rank that owns that history.
+  simulation::phase1_work_index = simulation::work_index;
+
+  if (!model::active_pulse_height_tallies.empty()) {
+    init_pulse_height_buffers();
+  }
+
   if (mpi::master) {
     write_message(fmt::format(" Primary source          particles: {}",
                     settings::n_particles),
@@ -1099,6 +1121,12 @@ void transport_history_based_shared_secondary()
     simulation::simulation_tracks_completed += alive_secondary;
   } // End of loop over secondary generations
 
+  // The full particle tree of every history is now complete, so per-history
+  // pulse-height results can be reassembled and scored.
+  if (!model::active_pulse_height_tallies.empty()) {
+    finalize_pulse_height_tallies();
+  }
+
   // Reset work so that fission bank etc works correctly
   calculate_work(settings::n_particles);
 }
@@ -1135,6 +1163,15 @@ void transport_event_based_shared_secondary()
   simulation::shared_secondary_bank_read.clear();
   simulation::shared_secondary_bank_write.clear();
 
+  // Record the primary partition before calculate_work() starts rewriting
+  // work_index for each secondary generation. finalize_pulse_height_tallies()
+  // needs it to map a root index back to the rank that owns that history.
+  simulation::phase1_work_index = simulation::work_index;
+
+  if (!model::active_pulse_height_tallies.empty()) {
+    init_pulse_height_buffers();
+  }
+
   if (mpi::master) {
     write_message(fmt::format(" Primary source          particles: {}",
                     settings::n_particles),
@@ -1231,6 +1268,12 @@ void transport_event_based_shared_secondary()
     simulation::simulation_tracks_completed += alive_secondary;
   } // End of loop over secondary generations
 
+  // The full particle tree of every history is now complete, so per-history
+  // pulse-height results can be reassembled and scored.
+  if (!model::active_pulse_height_tallies.empty()) {
+    finalize_pulse_height_tallies();
+  }
+
   // Reset work so that fission bank etc works correctly
   calculate_work(settings::n_particles);
 }
diff --git a/src/tallies/pulse_height.cpp b/src/tallies/pulse_height.cpp
new file mode 100644
index 00000000000..aa5b27862a5
--- /dev/null
+++ b/src/tallies/pulse_height.cpp
@@ -0,0 +1,223 @@
+#include "openmc/tallies/pulse_height.h"
+
+#include <algorithm> // upper_bound
+#include <cstddef>
+
+#include "openmc/message_passing.h"
+#include "openmc/openmp_interface.h"
+#include "openmc/particle.h"
+#include "openmc/settings.h"
+#include "openmc/simulation.h"
+#include "openmc/tallies/tally.h"
+#include "openmc/tallies/tally_scoring.h"
+
+namespace openmc {
+
+//==============================================================================
+// Global variables
+//==============================================================================
+
+namespace simulation {
+
+vector<vector<PulseHeightContribution>> pht_thread_buffers;
+
+} // namespace simulation
+
+//==============================================================================
+// Non-member functions
+//==============================================================================
+
+void init_pulse_height_buffers()
+{
+  simulation::pht_thread_buffers.resize(num_threads());
+  for (auto& buffer : simulation::pht_thread_buffers) {
+    buffer.clear();
+  }
+}
+
+void free_memory_pulse_height()
+{
+  simulation::pht_thread_buffers.clear();
+  simulation::pht_thread_buffers.shrink_to_fit();
+  simulation::phase1_work_index.clear();
+  simulation::phase1_work_index.shrink_to_fit();
+}
+
+void stage_pulse_height(int64_t root_index, const vector<double>& pht)
+{
+  // A particle whose root was never assigned cannot be attributed to a
+  // history. This should not happen, but dropping the fragment is safer than
+  // adding it to an arbitrary history.
+  if (root_index < 0)
+    return;
+
+  // Defensive: staging is only reachable from the shared-secondary drivers,
+  // which call init_pulse_height_buffers() before transporting anything.
+  if (simulation::pht_thread_buffers.empty())
+    return;
+
+  // Histories that deposit nothing still have to be scored, but they are
+  // recovered from the full root range in finalize_pulse_height_tallies()
+  // rather than from staged entries, so an all-zero fragment carries no
+  // information and is not worth moving between ranks.
+  bool nonzero = false;
+  for (double e : pht) {
+    if (e != 0.0) {
+      nonzero = true;
+      break;
+    }
+  }
+  if (!nonzero)
+    return;
+
+  PulseHeightContribution contribution;
+  contribution.root_index = root_index;
+  contribution.energy = pht;
+  simulation::pht_thread_buffers[thread_num()].push_back(
+    std::move(contribution));
+}
+
+namespace {
+
+//! Rank that owns a given root index, from the phase-1 primary partition.
+int owner_of_root(int64_t root_index)
+{
+  const auto& index = simulation::phase1_work_index;
+  auto it = std::upper_bound(index.begin(), index.end(), root_index);
+  return static_cast<int>(std::distance(index.begin(), it)) - 1;
+}
+
+} // namespace
+
+void finalize_pulse_height_tallies()
+{
+  int n_cells = model::pulse_height_cells.size();
+  if (n_cells == 0)
+    return;
+
+  // Range of root indices owned by this rank
+  int64_t first_root = simulation::phase1_work_index[mpi::rank];
+  int64_t last_root = simulation::phase1_work_index[mpi::rank + 1];
+  int64_t n_owned = last_root - first_root;
+
+  // Per-history, per-cell deposited energy for the histories owned here.
+  // Entries left at zero correspond to histories whose tree deposited nothing
+  // in any pulse-height cell; those are still scored below, matching the
+  // behaviour of the non-shared path where every primary is scored at death.
+  vector<double> totals(n_owned * n_cells, 0.0);
+
+  // Flatten the per-thread staging buffers, folding in everything already
+  // destined for this rank and packing the rest by destination.
+#ifdef OPENMC_MPI
+  vector<int> send_counts(mpi::n_procs, 0);
+  vector<int64_t> send_roots;
+  vector<double> send_energy;
+  vector<vector<int64_t>> roots_by_rank(mpi::n_procs);
+  vector<vector<double>> energy_by_rank(mpi::n_procs);
+#endif
+
+  for (auto& buffer : simulation::pht_thread_buffers) {
+    for (auto& contribution : buffer) {
+      int64_t root = contribution.root_index;
+      int owner = owner_of_root(root);
+      if (owner == mpi::rank) {
+        int64_t offset = (root - first_root) * n_cells;
+        for (int c = 0; c < n_cells; ++c) {
+          totals[offset + c] += contribution.energy[c];
+        }
+      } else {
+#ifdef OPENMC_MPI
+        roots_by_rank[owner].push_back(root);
+        energy_by_rank[owner].insert(energy_by_rank[owner].end(),
+          contribution.energy.begin(), contribution.energy.end());
+        send_counts[owner]++;
+#endif
+      }
+    }
+    buffer.clear();
+  }
+
+#ifdef OPENMC_MPI
+  if (mpi::n_procs > 1) {
+    // Concatenate the per-destination buffers into contiguous send buffers
+    vector<int> send_displs(mpi::n_procs, 0);
+    int total_send = 0;
+    for (int r = 0; r < mpi::n_procs; ++r) {
+      send_displs[r] = total_send;
+      total_send += send_counts[r];
+    }
+    send_roots.reserve(total_send);
+    send_energy.reserve(static_cast<size_t>(total_send) * n_cells);
+    for (int r = 0; r < mpi::n_procs; ++r) {
+      send_roots.insert(
+        send_roots.end(), roots_by_rank[r].begin(), roots_by_rank[r].end());
+      send_energy.insert(
+        send_energy.end(), energy_by_rank[r].begin(), energy_by_rank[r].end());
+      roots_by_rank[r].clear();
+      roots_by_rank[r].shrink_to_fit();
+      energy_by_rank[r].clear();
+      energy_by_rank[r].shrink_to_fit();
+    }
+
+    // Exchange how many contributions each rank is sending to each other rank
+    vector<int> recv_counts(mpi::n_procs, 0);
+    MPI_Alltoall(send_counts.data(), 1, MPI_INT, recv_counts.data(), 1, MPI_INT,
+      mpi::intracomm);
+
+    vector<int> recv_displs(mpi::n_procs, 0);
+    int total_recv = 0;
+    for (int r = 0; r < mpi::n_procs; ++r) {
+      recv_displs[r] = total_recv;
+      total_recv += recv_counts[r];
+    }
+
+    // Root indices, one per contribution
+    vector<int64_t> recv_roots(total_recv);
+    MPI_Alltoallv(send_roots.data(), send_counts.data(), send_displs.data(),
+      MPI_INT64_T, recv_roots.data(), recv_counts.data(), recv_displs.data(),
+      MPI_INT64_T, mpi::intracomm);
+
+    // Energies, n_cells per contribution
+    vector<int> send_counts_e(mpi::n_procs);
+    vector<int> send_displs_e(mpi::n_procs);
+    vector<int> recv_counts_e(mpi::n_procs);
+    vector<int> recv_displs_e(mpi::n_procs);
+    for (int r = 0; r < mpi::n_procs; ++r) {
+      send_counts_e[r] = send_counts[r] * n_cells;
+      send_displs_e[r] = send_displs[r] * n_cells;
+      recv_counts_e[r] = recv_counts[r] * n_cells;
+      recv_displs_e[r] = recv_displs[r] * n_cells;
+    }
+    vector<double> recv_energy(static_cast<size_t>(total_recv) * n_cells);
+    MPI_Alltoallv(send_energy.data(), send_counts_e.data(),
+      send_displs_e.data(), MPI_DOUBLE, recv_energy.data(),
+      recv_counts_e.data(), recv_displs_e.data(), MPI_DOUBLE, mpi::intracomm);
+
+    for (int i = 0; i < total_recv; ++i) {
+      int64_t offset = (recv_roots[i] - first_root) * n_cells;
+      for (int c = 0; c < n_cells; ++c) {
+        totals[offset + c] += recv_energy[static_cast<size_t>(i) * n_cells + c];
+      }
+    }
+  }
+#endif
+
+  // Score one pulse per owned history. score_pulse_height_tally() drives filter
+  // matching off a Particle, so give each thread a default-constructed one; its
+  // cell and E_last are overwritten and restored inside the call.
+#pragma omp parallel
+  {
+    Particle p;
+    vector<double> pht(n_cells);
+
+#pragma omp for schedule(static)
+    for (int64_t i = 0; i < n_owned; ++i) {
+      for (int c = 0; c < n_cells; ++c) {
+        pht[c] = totals[i * n_cells + c];
+      }
+      score_pulse_height_tally(p, pht, model::active_pulse_height_tallies);
+    }
+  }
+}
+
+} // namespace openmc
diff --git a/src/tallies/tally_scoring.cpp b/src/tallies/tally_scoring.cpp
index d17a62dce14..6c0a684b556 100644
--- a/src/tallies/tally_scoring.cpp
+++ b/src/tallies/tally_scoring.cpp
@@ -2720,7 +2720,8 @@ void score_surface_tally(
     match.bins_present_ = false;
 }
 
-void score_pulse_height_tally(Particle& p, const vector<int>& tallies)
+void score_pulse_height_tally(
+  Particle& p, const vector<double>& pht, const vector<int>& tallies)
 {
   // The pulse height tally in OpenMC hijacks the logic of CellFilter and
   // EnergyFilter to score specific quantities related to particle pulse height.
@@ -2756,7 +2757,7 @@ void score_pulse_height_tally(Particle& p, const vector<int>& tallies)
       int index = std::distance(model::pulse_height_cells.begin(), it);
 
       // Temporarily change energy of particle to pulse-height value
-      p.E_last() = p.pht_storage()[index];
+      p.E_last() = pht[index];
 
       // Initialize an iterator over valid filter bin combinations. If
       // there are no valid combinations, use a continue statement to ensure
diff --git a/tests/unit_tests/test_pulse_height.py b/tests/unit_tests/test_pulse_height.py
index 1f27cc6f264..3bf1ef10a8e 100644
--- a/tests/unit_tests/test_pulse_height.py
+++ b/tests/unit_tests/test_pulse_height.py
@@ -57,3 +57,206 @@ def test_pulse_height(model, run_in_tmpdir):
     np.testing.assert_array_equal(t1, t2[::-1])
 
 
+# ---------------------------------------------------------------------------
+# Shared secondary bank
+#
+# A pulse-height tally scores exactly one count per source history, in the bin
+# containing the total energy that history's entire particle tree deposited in a
+# cell. In the default transport modes the whole tree lives in one Particle
+# object, so that total is available directly at particle death. Under the
+# shared secondary bank each secondary generation is transported as a fresh set
+# of Particle objects, redistributed across MPI ranks between generations, so a
+# history's deposition is spread over many Particle objects and has to be
+# reassembled before scoring.
+#
+# The comparison between modes cannot be exact. compute_particle_id() and
+# compute_transport_seed() both take a different branch when the shared bank is
+# active, so the two modes sample different random number streams and produce
+# different realizations of the same distribution. Only count conservation is
+# exact; everything else is compared statistically.
+#
+# These run single-rank. The cross-rank aggregation in
+# finalize_pulse_height_tallies() is only exercised under MPI.
+#
+# One trap when adding tests here: never place an energy filter edge at a
+# deposition value a history can hit exactly, such as the source energy of a
+# monoenergetic source in a fully absorbing detector. Floating point in the
+# accumulated sum then decides which side of the edge each history falls on,
+# roughly 6% land above it and are dropped from the tally, and what looks like
+# a physics discrepancy is only a difference in rounding.
+# ---------------------------------------------------------------------------
+
+
+def _detector_model(particle, radius, energy_bounds, particles=1000,
+                    batches=10, shared_secondary=False):
+    """NaI sphere in a void, with a pulse-height tally on the detector cell."""
+    openmc.reset_auto_ids()
+    model = openmc.Model()
+
+    NaI = openmc.Material()
+    NaI.set_density('g/cm3', 3.7)
+    NaI.add_element('Na', 1.0)
+    NaI.add_element('I', 1.0)
+
+    detector_surf = openmc.Sphere(r=radius)
+    outer_surf = openmc.Sphere(r=radius + 1.0, boundary_type='vacuum')
+    detector = openmc.Cell(name='detector', fill=NaI, region=-detector_surf)
+    outside = openmc.Cell(name='outside', region=+detector_surf & -outer_surf)
+    model.geometry = openmc.Geometry([detector, outside])
+
+    model.settings.run_mode = 'fixed source'
+    model.settings.batches = batches
+    model.settings.particles = particles
+    model.settings.photon_transport = True
+    model.settings.shared_secondary_bank = shared_secondary
+    model.settings.source = openmc.IndependentSource(
+        energy=openmc.stats.delta_function(1e6),
+        particle=particle
+    )
+
+    tally = openmc.Tally(name='pht')
+    tally.scores = ['pulse-height']
+    tally.filters = [
+        openmc.CellFilter(detector),
+        openmc.EnergyFilter(energy_bounds),
+    ]
+    model.tallies = openmc.Tallies([tally])
+
+    return model
+
+
+def _pulse_height(statepoint_path):
+    """Return the pulse-height spectrum and its per-bin standard deviation."""
+    with openmc.StatePoint(statepoint_path) as sp:
+        tally = sp.get_tally(name='pht')
+        return tally.mean.ravel().copy(), tally.std_dev.ravel().copy()
+
+
+def _assert_spectra_consistent(a, a_err, b, b_err, n_sigma=5.0):
+    """Compare two spectra bin by bin against their combined standard errors.
+
+    Only bins holding at least 1% of histories are compared. Bins in the tail
+    carry few counts per batch, so their batch-to-batch spread is a poor
+    estimate of their true uncertainty and would drive spurious failures.
+    """
+    sigma = np.hypot(a_err, b_err)
+    significant = (0.5 * (a + b) > 0.01) & (sigma > 0.0)
+    assert significant.any(), "no bins carry enough counts to compare"
+    z = np.abs(a[significant] - b[significant]) / sigma[significant]
+    assert z.max() < n_sigma, f"largest per-bin discrepancy is {z.max():.1f} sigma"
+
+
+def _mean_deposition(spectrum, std_dev, bounds):
+    """Mean deposited energy per history, and its standard error."""
+    centers = 0.5 * (bounds[:-1] + bounds[1:])
+    mean = float(centers @ spectrum)
+    err = float(np.sqrt(np.sum((centers * std_dev) ** 2)))
+    return mean, err
+
+
+@pytest.mark.parametrize('shared_secondary', [False, True])
+@pytest.mark.parametrize('particle', ['photon', 'neutron'])
+def test_pulse_height_count_conservation(particle, shared_secondary,
+                                         run_in_tmpdir):
+    """Every history scores exactly once, in both transport modes.
+
+    Fixed-source results are normalized by the source strength divided by the
+    number of source particles (Tally::accumulate), so summing a pulse-height
+    tally over all its energy bins gives the number of scores per source
+    particle, which must be exactly one. The energy filter is wide enough that
+    no history can deposit outside it.
+
+    This is the direct test for scoring per track rather than per history: if
+    each secondary were scored separately the sum would exceed one by the mean
+    number of tracks per history. A history whose deposition is dropped instead
+    makes the sum fall short.
+    """
+    # Neutron capture in iodine releases several MeV of prompt gammas, so
+    # deposition is not bounded by the source energy in the neutron case.
+    upper = 1.1e6 if particle == 'photon' else 20.0e6
+    model = _detector_model(
+        particle, radius=1.0, energy_bounds=np.linspace(0.0, upper, 101),
+        shared_secondary=shared_secondary,
+    )
+
+    spectrum, _ = _pulse_height(model.run())
+
+    assert spectrum.sum() == pytest.approx(1.0, abs=1e-9)
+
+
+@pytest.mark.parametrize('particle', ['photon', 'neutron'])
+def test_shared_secondary_matches_local(particle, run_in_tmpdir):
+    """Both modes give the same pulse-height distribution in a thin detector.
+
+    A 1 cm NaI sphere at 1 MeV produces short cascades, so this mostly exercises
+    the aggregation bookkeeping rather than deep secondary trees. Compared are
+    the mean deposited energy per history and the spectrum shape bin by bin.
+    """
+    upper = 1.1e6 if particle == 'photon' else 20.0e6
+    bounds = np.linspace(0.0, upper, 51)
+
+    local = _detector_model(particle, radius=1.0, energy_bounds=bounds,
+                            particles=2000, shared_secondary=False)
+    local_spec, local_err = _pulse_height(local.run())
+
+    shared = _detector_model(particle, radius=1.0, energy_bounds=bounds,
+                             particles=2000, shared_secondary=True)
+    shared_spec, shared_err = _pulse_height(shared.run())
+
+    # Count conservation must hold in both before the shapes are compared
+    assert local_spec.sum() == pytest.approx(1.0, abs=1e-9)
+    assert shared_spec.sum() == pytest.approx(1.0, abs=1e-9)
+
+    local_mean, local_mean_err = _mean_deposition(local_spec, local_err, bounds)
+    shared_mean, shared_mean_err = _mean_deposition(
+        shared_spec, shared_err, bounds)
+    mean_sigma = np.hypot(local_mean_err, shared_mean_err)
+    assert mean_sigma > 0.0
+    assert abs(local_mean - shared_mean) < 4.0 * mean_sigma
+
+    _assert_spectra_consistent(local_spec, local_err, shared_spec, shared_err)
+
+
+def test_shared_secondary_matches_local_thick_detector(run_in_tmpdir):
+    """Both modes agree when the secondary cascade is deep.
+
+    A 50 cm NaI sphere is tens of mean free paths thick at 1 MeV, so nothing
+    escapes and each history spawns roughly 1.7 secondaries through Compton
+    scattering, fluorescence and bremsstrahlung. That makes this far more
+    sensitive than the thin-detector case to the subtraction performed on the
+    parent in create_secondary() being matched by the descendants' own
+    contributions once they are reassembled.
+
+    The top bin deliberately extends past the source energy. Pulse height
+    accumulates as a telescoping sum of E_last() - E() over a history, which
+    equals the source energy in exact arithmetic but not in floating point:
+    measured on this geometry, about 94% of histories sum to exactly 1 MeV or
+    just below and about 6% land a few ULPs above it. EnergyFilter matches on
+    E >= bins.front() && E <= bins.back(), so a top edge sitting exactly at
+    1 MeV drops that 6% entirely. They are then absent from the tally, count
+    conservation silently breaks, and the comparison below degenerates into a
+    comparison of rounding behaviour between two different random number
+    streams rather than of spectra.
+    """
+    # Top bin straddles the full-energy peak so histories whose floating point
+    # sum lands marginally above 1 MeV are still binned
+    bounds = np.concatenate([np.linspace(0.0, 0.99e6, 20), [1.1e6]])
+
+    local = _detector_model('photon', radius=50.0, energy_bounds=bounds,
+                            shared_secondary=False)
+    local_spec, local_err = _pulse_height(local.run())
+
+    shared = _detector_model('photon', radius=50.0, energy_bounds=bounds,
+                             shared_secondary=True)
+    shared_spec, shared_err = _pulse_height(shared.run())
+
+    assert local_spec.sum() == pytest.approx(1.0, abs=1e-9)
+    assert shared_spec.sum() == pytest.approx(1.0, abs=1e-9)
+
+    # The full-energy peak holds the great majority of histories, so its
+    # fraction is the sharpest single statistic available here.
+    peak_sigma = np.hypot(local_err[-1], shared_err[-1])
+    assert peak_sigma > 0.0
+    assert abs(local_spec[-1] - shared_spec[-1]) < 4.0 * peak_sigma
+
+    _assert_spectra_consistent(local_spec, local_err, shared_spec, shared_err)

From 9757fba2771dd8cc42ec4e94e417c30b4922b9db Mon Sep 17 00:00:00 2001
From: GuySten <guyste@post.bgu.ac.il>
Date: Mon, 31 Aug 2026 18:45:38 +0300
Subject: [PATCH 2/5] updates

---
 include/openmc/particle_data.h | 5 -----
 include/openmc/simulation.h    | 4 ----
 src/simulation.cpp             | 8 ++++----
 3 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/include/openmc/particle_data.h b/include/openmc/particle_data.h
index 20ee6f567c2..a096fc8a17e 100644
--- a/include/openmc/particle_data.h
+++ b/include/openmc/particle_data.h
@@ -52,11 +52,6 @@ struct SourceSite {
   int parent_nuclide {-1};
   int64_t parent_id {0};
   int64_t progeny_id {0};
-  // Dense global index, in [0, n_particles), of the primary at the root of
-  // this particle's tree. Propagated unchanged through every secondary
-  // generation so that per-history quantities (currently pulse height) can be
-  // reassembled after the tree has been transported across separate Particle
-  // objects and, under MPI, across ranks.
   int64_t root_index {-1};
   double wgt_born {1.0};
   double wgt_ww_born {-1.0};
diff --git a/include/openmc/simulation.h b/include/openmc/simulation.h
index b34ed3af099..7a17835a9a0 100644
--- a/include/openmc/simulation.h
+++ b/include/openmc/simulation.h
@@ -49,10 +49,6 @@ extern const RegularMesh* ufs_mesh;
 extern vector<double> k_generation;
 extern vector<int64_t> work_index;
 
-//! Snapshot of work_index taken during phase 1 of shared-secondary transport,
-//! i.e. the partition of *primary* particles across MPI ranks. work_index
-//! itself is overwritten by calculate_work() on every secondary generation, so
-//! it cannot be used afterwards to map a root index back to its owning rank.
 extern vector<int64_t> phase1_work_index;
 
 extern int64_t
diff --git a/src/simulation.cpp b/src/simulation.cpp
index 27fa4b761b5..c076ffef1f1 100644
--- a/src/simulation.cpp
+++ b/src/simulation.cpp
@@ -747,10 +747,10 @@ void initialize_particle_track(
   // bank site. Only meaningful in shared-secondary mode, where a history is
   // spread over several Particle objects; harmless otherwise.
   if (!is_secondary) {
-    p.root_index() = simulation::phase1_work_index.empty()
-                       ? index_source - 1
-                       : simulation::phase1_work_index[mpi::rank] +
-                           index_source - 1;
+    p.root_index() =
+      simulation::phase1_work_index.empty()
+        ? index_source - 1
+        : simulation::phase1_work_index[mpi::rank] + index_source - 1;
   }
 
   // set random number seed

From 42ae42c320090bf6f00ce96a6514e872dcb575f0 Mon Sep 17 00:00:00 2001
From: GuySten <guyste@post.bgu.ac.il>
Date: Mon, 31 Aug 2026 18:52:53 +0300
Subject: [PATCH 3/5] update regression tests

---
 .../shared_neutron/results_true.dat           | 20 +++----
 .../shared_photon/results_true.dat            | 54 +++++++++----------
 2 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/tests/regression_tests/pulse_height/shared_neutron/results_true.dat b/tests/regression_tests/pulse_height/shared_neutron/results_true.dat
index 7d28d5d442e..9082081516d 100644
--- a/tests/regression_tests/pulse_height/shared_neutron/results_true.dat
+++ b/tests/regression_tests/pulse_height/shared_neutron/results_true.dat
@@ -1,6 +1,6 @@
 tally 1:
-4.890000E+00
-4.784900E+00
+4.880000E+00
+4.765400E+00
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -9,8 +9,8 @@ tally 1:
 0.000000E+00
 1.000000E-02
 1.000000E-04
-6.000000E-02
-1.800000E-03
+7.000000E-02
+1.900000E-03
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -19,8 +19,6 @@ tally 1:
 1.000000E-04
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -29,8 +27,6 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -41,10 +37,10 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -89,6 +85,8 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -149,6 +147,8 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
diff --git a/tests/regression_tests/pulse_height/shared_photon/results_true.dat b/tests/regression_tests/pulse_height/shared_photon/results_true.dat
index 795f9b4c513..a6bc603b531 100644
--- a/tests/regression_tests/pulse_height/shared_photon/results_true.dat
+++ b/tests/regression_tests/pulse_height/shared_photon/results_true.dat
@@ -1,6 +1,6 @@
 tally 1:
-4.120000E+00
-3.409000E+00
+4.110000E+00
+3.393900E+00
 3.000000E-02
 5.000000E-04
 1.000000E-02
@@ -14,7 +14,7 @@ tally 1:
 1.000000E-02
 1.000000E-04
 2.000000E-02
-2.000000E-04
+4.000000E-04
 0.000000E+00
 0.000000E+00
 1.000000E-02
@@ -23,12 +23,12 @@ tally 1:
 1.000000E-04
 0.000000E+00
 0.000000E+00
+3.000000E-02
+3.000000E-04
 2.000000E-02
 2.000000E-04
-2.000000E-02
-2.000000E-04
-2.000000E-02
-4.000000E-04
+4.000000E-02
+8.000000E-04
 1.000000E-02
 1.000000E-04
 0.000000E+00
@@ -43,8 +43,8 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
+0.000000E+00
+0.000000E+00
 2.000000E-02
 2.000000E-04
 0.000000E+00
@@ -55,8 +55,8 @@ tally 1:
 1.000000E-04
 1.000000E-02
 1.000000E-04
-0.000000E+00
-0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -67,12 +67,12 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
+2.000000E-02
+2.000000E-04
 3.000000E-02
 3.000000E-04
 2.000000E-02
-2.000000E-04
+4.000000E-04
 0.000000E+00
 0.000000E+00
 2.000000E-02
@@ -103,20 +103,20 @@ tally 1:
 0.000000E+00
 1.000000E-02
 1.000000E-04
-2.000000E-02
-2.000000E-04
-0.000000E+00
-0.000000E+00
-3.000000E-02
-5.000000E-04
 1.000000E-02
 1.000000E-04
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 3.000000E-02
 5.000000E-04
 3.000000E-02
@@ -131,8 +131,8 @@ tally 1:
 1.000000E-04
 1.000000E-02
 1.000000E-04
-3.000000E-02
-5.000000E-04
+2.000000E-02
+2.000000E-04
 0.000000E+00
 0.000000E+00
 1.000000E-02
@@ -156,7 +156,7 @@ tally 1:
 0.000000E+00
 0.000000E+00
 3.000000E-02
-3.000000E-04
+5.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -193,9 +193,9 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
-0.000000E+00
-0.000000E+00
-1.700000E-01
-5.900000E-03
+1.600000E-01
+6.400000E-03

From 8489a5b1ff65cdc8156aa4dda2862293908b755c Mon Sep 17 00:00:00 2001
From: GuySten <guyste@post.bgu.ac.il>
Date: Mon, 31 Aug 2026 19:10:38 +0300
Subject: [PATCH 4/5] update structs

---
 openmc/lib/core.py |  1 +
 src/initialize.cpp | 18 ++++++++++--------
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index 22580d52a46..94523d19377 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -32,6 +32,7 @@ class _SourceSite(Structure):
                 ('parent_nuclide', c_int),
                 ('parent_id', c_int64),
                 ('progeny_id', c_int64),
+                ('root_index', c_int64),
                 ('wgt_born', c_double),
                 ('wgt_ww_born', c_double),
                 ('n_split', c_int64),
diff --git a/src/initialize.cpp b/src/initialize.cpp
index 3c726675978..f9f21f743f1 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -161,7 +161,7 @@ void initialize_mpi(MPI_Comm intracomm)
 
   // Create bank datatype
   SourceSite b;
-  MPI_Aint disp[15];
+  MPI_Aint disp[16];
   MPI_Get_address(&b.r, &disp[0]);
   MPI_Get_address(&b.u, &disp[1]);
   MPI_Get_address(&b.E, &disp[2]);
@@ -173,16 +173,17 @@ void initialize_mpi(MPI_Comm intracomm)
   MPI_Get_address(&b.parent_nuclide, &disp[8]);
   MPI_Get_address(&b.parent_id, &disp[9]);
   MPI_Get_address(&b.progeny_id, &disp[10]);
-  MPI_Get_address(&b.wgt_born, &disp[11]);
-  MPI_Get_address(&b.wgt_ww_born, &disp[12]);
-  MPI_Get_address(&b.n_split, &disp[13]);
-  MPI_Get_address(&b.n_collision, &disp[14]);
-  for (int i = 14; i >= 0; --i) {
+  MPI_Get_address(&b.root_index, &disp[11]);
+  MPI_Get_address(&b.wgt_born, &disp[12]);
+  MPI_Get_address(&b.wgt_ww_born, &disp[13]);
+  MPI_Get_address(&b.n_split, &disp[14]);
+  MPI_Get_address(&b.n_collision, &disp[15]);
+  for (int i = 15; i >= 0; --i) {
     disp[i] -= disp[0];
   }
 
   // Block counts for each field
-  int blocks[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
+  int blocks[] = {3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
 
   // Types for each field
   MPI_Datatype types[] = {
@@ -197,13 +198,14 @@ void initialize_mpi(MPI_Comm intracomm)
     MPI_INT,     // parent_nuclide
     MPI_INT64_T, // parent_id
     MPI_INT64_T, // progeny_id
+    MPI_INT64_T, // root_index
     MPI_DOUBLE,  // wgt_born
     MPI_DOUBLE,  // wgt_ww_born
     MPI_INT64_T, // n_split
     MPI_INT      // n_collision
   };
 
-  MPI_Type_create_struct(15, blocks, disp, types, &mpi::source_site);
+  MPI_Type_create_struct(16, blocks, disp, types, &mpi::source_site);
   MPI_Type_commit(&mpi::source_site);
 
   CollisionTrackSite bc;

From 4852d6363f49abc8bdb08795962d5d19df4d46cc Mon Sep 17 00:00:00 2001
From: GuySten <guyste@post.bgu.ac.il>
Date: Mon, 31 Aug 2026 19:41:27 +0300
Subject: [PATCH 5/5] update regression test

---
 .../shared/results_true.dat                   | 54 +++++++++----------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/tests/regression_tests/weightwindows_pulse_height/shared/results_true.dat b/tests/regression_tests/weightwindows_pulse_height/shared/results_true.dat
index 795f9b4c513..a6bc603b531 100644
--- a/tests/regression_tests/weightwindows_pulse_height/shared/results_true.dat
+++ b/tests/regression_tests/weightwindows_pulse_height/shared/results_true.dat
@@ -1,6 +1,6 @@
 tally 1:
-4.120000E+00
-3.409000E+00
+4.110000E+00
+3.393900E+00
 3.000000E-02
 5.000000E-04
 1.000000E-02
@@ -14,7 +14,7 @@ tally 1:
 1.000000E-02
 1.000000E-04
 2.000000E-02
-2.000000E-04
+4.000000E-04
 0.000000E+00
 0.000000E+00
 1.000000E-02
@@ -23,12 +23,12 @@ tally 1:
 1.000000E-04
 0.000000E+00
 0.000000E+00
+3.000000E-02
+3.000000E-04
 2.000000E-02
 2.000000E-04
-2.000000E-02
-2.000000E-04
-2.000000E-02
-4.000000E-04
+4.000000E-02
+8.000000E-04
 1.000000E-02
 1.000000E-04
 0.000000E+00
@@ -43,8 +43,8 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
+0.000000E+00
+0.000000E+00
 2.000000E-02
 2.000000E-04
 0.000000E+00
@@ -55,8 +55,8 @@ tally 1:
 1.000000E-04
 1.000000E-02
 1.000000E-04
-0.000000E+00
-0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -67,12 +67,12 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
-1.000000E-02
-1.000000E-04
+2.000000E-02
+2.000000E-04
 3.000000E-02
 3.000000E-04
 2.000000E-02
-2.000000E-04
+4.000000E-04
 0.000000E+00
 0.000000E+00
 2.000000E-02
@@ -103,20 +103,20 @@ tally 1:
 0.000000E+00
 1.000000E-02
 1.000000E-04
-2.000000E-02
-2.000000E-04
-0.000000E+00
-0.000000E+00
-3.000000E-02
-5.000000E-04
 1.000000E-02
 1.000000E-04
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 3.000000E-02
 5.000000E-04
 3.000000E-02
@@ -131,8 +131,8 @@ tally 1:
 1.000000E-04
 1.000000E-02
 1.000000E-04
-3.000000E-02
-5.000000E-04
+2.000000E-02
+2.000000E-04
 0.000000E+00
 0.000000E+00
 1.000000E-02
@@ -156,7 +156,7 @@ tally 1:
 0.000000E+00
 0.000000E+00
 3.000000E-02
-3.000000E-04
+5.000000E-04
 0.000000E+00
 0.000000E+00
 0.000000E+00
@@ -193,9 +193,9 @@ tally 1:
 0.000000E+00
 0.000000E+00
 0.000000E+00
+1.000000E-02
+1.000000E-04
 0.000000E+00
 0.000000E+00
-0.000000E+00
-0.000000E+00
-1.700000E-01
-5.900000E-03
+1.600000E-01
+6.400000E-03