From 4e3350ebcf685547795f5fa2ce5a7275d3d766f5 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Mon, 5 Jul 2021 12:35:14 -0500
Subject: [PATCH 01/18] Adding a function to determine the instance of a cell
 at any level of Particle::coords.

---
 include/openmc/geometry.h | 11 +++++++++++
 src/geometry.cpp          | 39 +++++++++++++++++++++++++--------------
 2 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/include/openmc/geometry.h b/include/openmc/geometry.h
index 0ba29ef48..8590e33e1 100644
--- a/include/openmc/geometry.h
+++ b/include/openmc/geometry.h
@@ -40,6 +40,17 @@ inline bool coincident(double d1, double d2) {
 
 bool check_cell_overlap(Particle& p, bool error=true);
 
+//==============================================================================
+//! Get the cell instance for a particle at the specified universe level
+//!
+//! \param p A particle for which to compute the instance using
+//!   it's vector of LocalCoord.
+//! \param level The level (zero indexed) of the geometry where the instance should be computed.
+//! \return The instance of the cell at the specified level.
+//==============================================================================
+
+int cell_instance_at_level(const Particle& p, int level);
+
 //==============================================================================
 //! Locate a particle in the geometry tree and set its geometry data fields.
 //!
diff --git a/src/geometry.cpp b/src/geometry.cpp
index c93e1940b..1cbb74935 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -65,6 +65,30 @@ bool check_cell_overlap(Particle& p, bool error)
 
 //==============================================================================
 
+int cell_instance_at_level(const Particle& p, int level) {
+  if (level > p.n_coord()) {
+    fatal_error(fmt::format("Cell instance at level {} requested, but only {} levels exist in the model.", level, p.n_coord()));
+  }
+  // determine the cell instance
+  Cell& c {*model::cells[p.coord(level).cell]};
+  int instance = 0;
+  for (int i = 0; i < level; i++) {
+    const auto& c_i {*model::cells[p.coord(i).cell]};
+    if (c_i.type_ == Fill::UNIVERSE) {
+      instance += c_i.offset_[c.distribcell_index_];
+    } else if (c_i.type_ == Fill::LATTICE) {
+      auto& lat {*model::lattices[p.coord(i + 1).lattice]};
+      const auto& i_xyz {p.coord(i + 1).lattice_i};
+      if (lat.are_valid_indices(i_xyz)) {
+        instance += lat.offset(c.distribcell_index_, i_xyz);
+      }
+    }
+  }
+  return instance;
+}
+
+//==============================================================================
+
 bool
 find_cell_inner(Particle& p, const NeighborList* neighbor_list)
 {
@@ -130,22 +154,9 @@ find_cell_inner(Particle& p, const NeighborList* neighbor_list)
       // Found a material cell which means this is the lowest coord level.
 
       // Find the distribcell instance number.
-      int offset = 0;
       if (c.distribcell_index_ >= 0) {
-        for (int i = 0; i < p.n_coord(); i++) {
-          const auto& c_i {*model::cells[p.coord(i).cell]};
-          if (c_i.type_ == Fill::UNIVERSE) {
-            offset += c_i.offset_[c.distribcell_index_];
-          } else if (c_i.type_ == Fill::LATTICE) {
-            auto& lat {*model::lattices[p.coord(i + 1).lattice]};
-            const auto& i_xyz {p.coord(i + 1).lattice_i};
-            if (lat.are_valid_indices(i_xyz)) {
-              offset += lat.offset(c.distribcell_index_, i_xyz);
-            }
-          }
-        }
+        p.cell_instance() = cell_instance_at_level(p, p.n_coord() - 1);
       }
-      p.cell_instance() = offset;
 
       // Set the material and temperature.
       p.material_last() = p.material();

From 39c52dcf94639a3bb9c8ca02a3e47aac032d08d8 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Wed, 28 Jul 2021 17:49:33 -0500
Subject: [PATCH 02/18] Incorporate cell instance levels into plotting. Return
 C_NONE if it is not a distributed cell.

---
 src/geometry.cpp | 5 +++++
 src/plot.cpp     | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/geometry.cpp b/src/geometry.cpp
index 1cbb74935..563e5467b 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -66,11 +66,16 @@ bool check_cell_overlap(Particle& p, bool error)
 //==============================================================================
 
 int cell_instance_at_level(const Particle& p, int level) {
+  // throw error if the requested level is too deep for the geometry
   if (level > p.n_coord()) {
     fatal_error(fmt::format("Cell instance at level {} requested, but only {} levels exist in the model.", level, p.n_coord()));
   }
+
   // determine the cell instance
   Cell& c {*model::cells[p.coord(level).cell]};
+
+  if (c.distribcell_index_ == C_NONE) return C_NONE;
+
   int instance = 0;
   for (int i = 0; i < level; i++) {
     const auto& c_i {*model::cells[p.coord(i).cell]};
diff --git a/src/plot.cpp b/src/plot.cpp
index 999cf3d29..c3ef36467 100644
--- a/src/plot.cpp
+++ b/src/plot.cpp
@@ -47,7 +47,7 @@ IdData::set_value(size_t y, size_t x, const Particle& p, int level) {
     data_(y, x, 1) = NOT_FOUND;
   } else {
     data_(y, x, 0) = model::cells.at(p.coord(level).cell)->id_;
-    data_(y, x, 1) = p.cell_instance();
+    data_(y, x, 1) = level == p.n_coord() - 1 ?  p.cell_instance() : cell_instance_at_level(p, level);
   }
 
   // set material data

From 058e5a9094a8f7c35d40263f198bfffda9d9efc6 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sat, 17 Jul 2021 15:46:52 -0500
Subject: [PATCH 03/18] Allowing cell instance filters for non material-filled
 cells.

---
 include/openmc/tallies/filter_cell_instance.h |  5 +++++
 src/tallies/filter_cell_instance.cpp          | 21 ++++++++++++++++++-
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/include/openmc/tallies/filter_cell_instance.h b/include/openmc/tallies/filter_cell_instance.h
index dee9b8bea..a2a204db6 100644
--- a/include/openmc/tallies/filter_cell_instance.h
+++ b/include/openmc/tallies/filter_cell_instance.h
@@ -46,6 +46,8 @@ public:
 
   void set_cell_instances(gsl::span<CellInstance> instances);
 
+  void set_geom_level(int32_t level);
+
 private:
   //----------------------------------------------------------------------------
   // Data members
@@ -55,6 +57,9 @@ private:
 
   //! A map from cell/instance indices to filter bin indices.
   std::unordered_map<CellInstance, gsl::index, CellInstanceHash> map_;
+
+  //! Level in the geometry to check for the cell instance
+  int32_t geom_level_ {-1};
 };
 
 } // namespace openmc
diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index c41077631..c5a88dc7a 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -7,6 +7,7 @@
 #include "openmc/capi.h"
 #include "openmc/cell.h"
 #include "openmc/error.h"
+#include "openmc/geometry.h"
 #include "openmc/xml_interface.h"
 
 namespace openmc {
@@ -53,7 +54,7 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
     Expects(x.index_cell >= 0);
     Expects(x.index_cell < model::cells.size());
     const auto& c {model::cells[x.index_cell]};
-    if (c->type_ != Fill::MATERIAL) {
+    if (c->type_ != Fill::MATERIAL && geom_level_ < 0) {
       throw std::invalid_argument{fmt::format(
         "Cell {} is not filled with a material. Only material cells can be "
         "used in a cell instance filter.", c->id_)};
@@ -65,12 +66,30 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
   n_bins_ = cell_instances_.size();
 }
 
+void
+CellInstanceFilter::set_geom_level(int32_t level) {
+  Expects(level >= 0);
+  geom_level_ = level;
+}
+
 void
 CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
                          FilterMatch& match) const
 {
   gsl::index index_cell = p.coord(p.n_coord() - 1).cell;
   gsl::index instance = p.cell_instance();
+
+  if (geom_level_ >= 0) {
+    // if the particle has fewer levels than the cell we're looking for,
+    // return no bins
+    if (p.coord(geom_level_).cell == C_NONE) return;
+
+    // otherwise use the cell at the requested level
+    // and compute the cell instance for this particle's position
+    index_cell = p.coord(geom_level_).cell;
+    instance = cell_instance_at_level(p, geom_level_);
+  }
+
   auto search = map_.find({index_cell, instance});
   if (search != map_.end()) {
     int index_bin = search->second;

From ca5dc796b9bf5abd298e4f29a6de863590a4fefb Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 10:53:14 -0500
Subject: [PATCH 04/18] Updating error messages. Adding cell instance cells to
 our distribcell set.

---
 include/openmc/tallies/filter_cell_instance.h | 2 +-
 src/geometry.cpp                              | 4 ++--
 src/geometry_aux.cpp                          | 4 ++++
 src/tallies/filter_cell_instance.cpp          | 6 +++---
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/include/openmc/tallies/filter_cell_instance.h b/include/openmc/tallies/filter_cell_instance.h
index a2a204db6..a3fbad181 100644
--- a/include/openmc/tallies/filter_cell_instance.h
+++ b/include/openmc/tallies/filter_cell_instance.h
@@ -59,7 +59,7 @@ private:
   std::unordered_map<CellInstance, gsl::index, CellInstanceHash> map_;
 
   //! Level in the geometry to check for the cell instance
-  int32_t geom_level_ {-1};
+  int32_t geom_level_ {C_NONE};
 };
 
 } // namespace openmc
diff --git a/src/geometry.cpp b/src/geometry.cpp
index 563e5467b..7eb731660 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -67,8 +67,8 @@ bool check_cell_overlap(Particle& p, bool error)
 
 int cell_instance_at_level(const Particle& p, int level) {
   // throw error if the requested level is too deep for the geometry
-  if (level > p.n_coord()) {
-    fatal_error(fmt::format("Cell instance at level {} requested, but only {} levels exist in the model.", level, p.n_coord()));
+  if (level > model::n_coord_levels) {
+    fatal_error(fmt::format("Cell instance at level {} requested, but only {} levels exist in the geometry.", level, p.n_coord()));
   }
 
   // determine the cell instance
diff --git a/src/geometry_aux.cpp b/src/geometry_aux.cpp
index af6ebac9f..9d3062901 100644
--- a/src/geometry_aux.cpp
+++ b/src/geometry_aux.cpp
@@ -319,9 +319,13 @@ prepare_distribcell()
   std::unordered_set<int32_t> distribcells;
   for (auto& filt : model::tally_filters) {
     auto* distrib_filt = dynamic_cast<DistribcellFilter*>(filt.get());
+    auto* cell_inst_filt = dynamic_cast<CellInstanceFilter*>(filt.get());
     if (distrib_filt) {
       distribcells.insert(distrib_filt->cell());
     }
+    if (cell_inst_filt) {
+      for (const auto& c_inst : cell_inst_filt->cell_instances()) distribcells.insert(c_inst.index_cell);
+    }
   }
 
   // By default, add material cells to the list of distributed cells
diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index c5a88dc7a..ba70b06bb 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -56,8 +56,8 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
     const auto& c {model::cells[x.index_cell]};
     if (c->type_ != Fill::MATERIAL && geom_level_ < 0) {
       throw std::invalid_argument{fmt::format(
-        "Cell {} is not filled with a material. Only material cells can be "
-        "used in a cell instance filter.", c->id_)};
+        "Cell {} is not filled with a material. A geometry level must be specified to"
+        "use cells filled with a universe or lattice.", c->id_)};
     }
     cell_instances_.push_back(x);
     map_[x] = cell_instances_.size() - 1;
@@ -82,7 +82,7 @@ CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
   if (geom_level_ >= 0) {
     // if the particle has fewer levels than the cell we're looking for,
     // return no bins
-    if (p.coord(geom_level_).cell == C_NONE) return;
+    if (p.n_coord() - 1 < geom_level_ || p.coord(geom_level_).cell == C_NONE) return;
 
     // otherwise use the cell at the requested level
     // and compute the cell instance for this particle's position

From 885ed95facc879334b170d92bf6191ec3b202e60 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 11:28:39 -0500
Subject: [PATCH 05/18] Adding geometry_level to the cell instance filter XML
 output.

---
 openmc/filter.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/openmc/filter.py b/openmc/filter.py
index e46effa7b..2edca37ba 100644
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -550,6 +550,8 @@ class CellInstanceFilter(Filter):
         Unique identifier for the filter
     num_bins : Integral
         The number of filter bins
+    geometry_level : Integral
+        Geometry level of the specified cell (used to compute instances in the simulation)
 
     See Also
     --------
@@ -559,6 +561,7 @@ class CellInstanceFilter(Filter):
     def __init__(self, bins, filter_id=None):
         self.bins = bins
         self.id = filter_id
+        self._geom_level = None
 
     @Filter.bins.setter
     def bins(self, bins):
@@ -570,6 +573,15 @@ class CellInstanceFilter(Filter):
             pairs[i, 1] = instance
         self._bins = pairs
 
+    @property
+    def geometry_level(self):
+        return self._geometry_level
+
+    @geometry_level.setter
+    def geometry_level(self, val):
+        cv.check_type('geometry level', val, Integral)
+        self._geometry_level = val
+
     def get_pandas_dataframe(self, data_size, stride, **kwargs):
         """Builds a Pandas DataFrame for the Filter's bins.
 
@@ -618,7 +630,8 @@ class CellInstanceFilter(Filter):
         element = ET.Element('filter')
         element.set('id', str(self.id))
         element.set('type', self.short_name.lower())
-
+        if self.geometry_level:
+            element.set('geometry_level', self.geometry_level)
         subelement = ET.SubElement(element, 'bins')
         subelement.text = ' '.join(str(i) for i in self.bins.ravel())
         return element

From 991c3d1f76d63e73b022261cf19d48e536f2c461 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 11:29:00 -0500
Subject: [PATCH 06/18] Adding read of 'geometry_level' for cell instance
 filters.

---
 src/tallies/filter_cell_instance.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index ba70b06bb..568a989f0 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -38,6 +38,10 @@ CellInstanceFilter::from_xml(pugi::xml_node node)
     instances.push_back({index, instance});
   }
 
+  if (check_for_node(node, "geometry_level")) {
+    this->set_geom_level(std::stoi(get_node_value(node, "geometry_level")));
+  }
+
   this->set_cell_instances(instances);
 }
 

From 4c55737a9421607b612caceb33a5d1937809c9e2 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 14:55:23 -0500
Subject: [PATCH 07/18] Better method for supporting non-material filled cells.

---
 include/openmc/tallies/filter_cell_instance.h |  6 +++
 src/tallies/filter_cell_instance.cpp          | 50 +++++++++++--------
 2 files changed, 36 insertions(+), 20 deletions(-)

diff --git a/include/openmc/tallies/filter_cell_instance.h b/include/openmc/tallies/filter_cell_instance.h
index a3fbad181..89f8d18af 100644
--- a/include/openmc/tallies/filter_cell_instance.h
+++ b/include/openmc/tallies/filter_cell_instance.h
@@ -55,11 +55,17 @@ private:
   //! The indices of the cells binned by this filter.
   vector<CellInstance> cell_instances_;
 
+  //! The set of cells used in this filter
+  std::unordered_set<int32_t> cells_;
+
   //! A map from cell/instance indices to filter bin indices.
   std::unordered_map<CellInstance, gsl::index, CellInstanceHash> map_;
 
   //! Level in the geometry to check for the cell instance
   int32_t geom_level_ {C_NONE};
+
+  //! Indicates if filter uses only material-filled cells
+  bool material_cells_only_;
 };
 
 } // namespace openmc
diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index 568a989f0..a4476d739 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -57,17 +57,20 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
   for (auto& x : instances) {
     Expects(x.index_cell >= 0);
     Expects(x.index_cell < model::cells.size());
-    const auto& c {model::cells[x.index_cell]};
-    if (c->type_ != Fill::MATERIAL && geom_level_ < 0) {
-      throw std::invalid_argument{fmt::format(
-        "Cell {} is not filled with a material. A geometry level must be specified to"
-        "use cells filled with a universe or lattice.", c->id_)};
-    }
     cell_instances_.push_back(x);
+    cells_.insert(x.index_cell);
     map_[x] = cell_instances_.size() - 1;
   }
 
   n_bins_ = cell_instances_.size();
+
+  material_cells_only_ = true;
+  for (const auto& cell_inst : cell_instances_) {
+    const auto& c = *model::cells[cell_inst.index_cell];
+    if (c.type_ == Fill::MATERIAL) continue;
+    material_cells_only_ = false;
+    break;
+  }
 }
 
 void
@@ -83,22 +86,29 @@ CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
   gsl::index index_cell = p.coord(p.n_coord() - 1).cell;
   gsl::index instance = p.cell_instance();
 
-  if (geom_level_ >= 0) {
-    // if the particle has fewer levels than the cell we're looking for,
-    // return no bins
-    if (p.n_coord() - 1 < geom_level_ || p.coord(geom_level_).cell == C_NONE) return;
-
-    // otherwise use the cell at the requested level
-    // and compute the cell instance for this particle's position
-    index_cell = p.coord(geom_level_).cell;
-    instance = cell_instance_at_level(p, geom_level_);
+  if (cells_.count(index_cell) > 0) {
+    auto search = map_.find({index_cell, instance});
+    if (search != map_.end()) {
+      int index_bin = search->second;
+      match.bins_.push_back(index_bin);
+      match.weights_.push_back(1.0);
+    }
   }
 
-  auto search = map_.find({index_cell, instance});
-  if (search != map_.end()) {
-    int index_bin = search->second;
-    match.bins_.push_back(index_bin);
-    match.weights_.push_back(1.0);
+  if (!material_cells_only_) {
+    for (int i = 0; i < p.n_coord() - 1; i++) {
+      gsl::index index_cell = p.coord(i).cell;
+      // if this cell isn't used on the filter, move on
+      if (cells_.count(index_cell) == 0) continue;
+
+      // if this cell is used in the filter, check the instance as well
+      gsl::index instance = cell_instance_at_level(p, i);
+      auto search = map_.find({index_cell, instance});
+      if (search != map_.end()) {
+        match.bins_.push_back(search->second);
+        match.bins_.push_back(1.0);
+      }
+    }
   }
 }
 

From 8d4c6f87083878dcebb507f80b05f0ff0c027b60 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 14:57:58 -0500
Subject: [PATCH 08/18] Reverting changes to the cell instance filter Python
 object.

---
 openmc/filter.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/openmc/filter.py b/openmc/filter.py
index 2edca37ba..e46effa7b 100644
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -550,8 +550,6 @@ class CellInstanceFilter(Filter):
         Unique identifier for the filter
     num_bins : Integral
         The number of filter bins
-    geometry_level : Integral
-        Geometry level of the specified cell (used to compute instances in the simulation)
 
     See Also
     --------
@@ -561,7 +559,6 @@ class CellInstanceFilter(Filter):
     def __init__(self, bins, filter_id=None):
         self.bins = bins
         self.id = filter_id
-        self._geom_level = None
 
     @Filter.bins.setter
     def bins(self, bins):
@@ -573,15 +570,6 @@ class CellInstanceFilter(Filter):
             pairs[i, 1] = instance
         self._bins = pairs
 
-    @property
-    def geometry_level(self):
-        return self._geometry_level
-
-    @geometry_level.setter
-    def geometry_level(self, val):
-        cv.check_type('geometry level', val, Integral)
-        self._geometry_level = val
-
     def get_pandas_dataframe(self, data_size, stride, **kwargs):
         """Builds a Pandas DataFrame for the Filter's bins.
 
@@ -630,8 +618,7 @@ class CellInstanceFilter(Filter):
         element = ET.Element('filter')
         element.set('id', str(self.id))
         element.set('type', self.short_name.lower())
-        if self.geometry_level:
-            element.set('geometry_level', self.geometry_level)
+
         subelement = ET.SubElement(element, 'bins')
         subelement.text = ' '.join(str(i) for i in self.bins.ravel())
         return element

From 930fb20010d1c1b6d2a6cfc8a3f7c9ce90405cdd Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 15:03:08 -0500
Subject: [PATCH 09/18] Removing geom_level form cell instance filter.

---
 src/tallies/filter_cell_instance.cpp | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index a4476d739..0db6c7d21 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -38,10 +38,6 @@ CellInstanceFilter::from_xml(pugi::xml_node node)
     instances.push_back({index, instance});
   }
 
-  if (check_for_node(node, "geometry_level")) {
-    this->set_geom_level(std::stoi(get_node_value(node, "geometry_level")));
-  }
-
   this->set_cell_instances(instances);
 }
 
@@ -51,6 +47,7 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
   // Clear existing cells
   cell_instances_.clear();
   cell_instances_.reserve(instances.size());
+  cells_.clear();
   map_.clear();
 
   // Update cells and mapping
@@ -73,12 +70,6 @@ CellInstanceFilter::set_cell_instances(gsl::span<CellInstance> instances)
   }
 }
 
-void
-CellInstanceFilter::set_geom_level(int32_t level) {
-  Expects(level >= 0);
-  geom_level_ = level;
-}
-
 void
 CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
                          FilterMatch& match) const

From 3114c935629fd6812bcb04cbd0115a4b776d5f49 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 20:01:21 -0500
Subject: [PATCH 10/18] Adding an extra layer to the geometry to test the cell
 instance filter regression test for a universe-filled cell.

---
 .../filter_cellinstance/inputs_true.dat       | 21 ++++++++++---------
 .../filter_cellinstance/test.py               |  8 +++++--
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/tests/regression_tests/filter_cellinstance/inputs_true.dat b/tests/regression_tests/filter_cellinstance/inputs_true.dat
index 5abf73433..5df992627 100644
--- a/tests/regression_tests/filter_cellinstance/inputs_true.dat
+++ b/tests/regression_tests/filter_cellinstance/inputs_true.dat
@@ -2,18 +2,19 @@
 <geometry>
   <cell id="1" material="1" region="-1" universe="1" />
   <cell id="2" material="2" region="1" universe="1" />
-  <cell id="3" material="1" region="-2" universe="2" />
-  <cell id="4" material="2" region="2" universe="2" />
-  <cell fill="3" id="5" region="3 -4 5 -6" universe="4" />
-  <lattice id="3">
+  <cell fill="1" id="3" universe="2" />
+  <cell id="4" material="1" region="-2" universe="3" />
+  <cell id="5" material="2" region="2" universe="3" />
+  <cell fill="4" id="6" region="3 -4 5 -6" universe="5" />
+  <lattice id="4">
     <pitch>2 2</pitch>
     <dimension>4 4</dimension>
     <lower_left>-4 -4</lower_left>
     <universes>
-1 2 2 2 
-2 1 2 2 
-2 2 1 2 
-2 2 2 1 </universes>
+2 3 3 3 
+3 2 3 3 
+3 3 2 3 
+3 3 3 2 </universes>
   </lattice>
   <surface coeffs="0.0 0.0 0.7" id="1" type="z-cylinder" />
   <surface coeffs="0.0 0.0 0.5" id="2" type="z-cylinder" />
@@ -48,10 +49,10 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tallies>
   <filter id="1" type="cellinstance">
-    <bins>3 0 3 1 3 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 3 10 3 11 2 0 2 1 2 2 2 3</bins>
+    <bins>4 0 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 4 10 4 11 2 0 2 1 2 2 2 3 3 0 3 1 3 2 3 3</bins>
   </filter>
   <filter id="2" type="cellinstance">
-    <bins>2 3 2 2 2 1 2 0 3 11 3 10 3 9 3 8 3 7 3 6 3 5 3 4 3 3 3 2 3 1 3 0</bins>
+    <bins>3 3 3 2 3 1 3 0 2 3 2 2 2 1 2 0 4 11 4 10 4 9 4 8 4 7 4 6 4 5 4 4 4 3 4 2 4 1 4 0</bins>
   </filter>
   <tally id="1">
     <filters>1</filters>
diff --git a/tests/regression_tests/filter_cellinstance/test.py b/tests/regression_tests/filter_cellinstance/test.py
index dc00394fc..bd708788c 100644
--- a/tests/regression_tests/filter_cellinstance/test.py
+++ b/tests/regression_tests/filter_cellinstance/test.py
@@ -22,7 +22,10 @@ def model():
     cyl1 = openmc.ZCylinder(r=0.7)
     c1 = openmc.Cell(fill=m1, region=-cyl1)
     c2 = openmc.Cell(fill=m2, region=+cyl1)
-    u1 = openmc.Universe(cells=[c1, c2])
+    # intermediate universe
+    ui = openmc.Universe(cells=[c2])
+    ci = openmc.Cell(fill=ui)
+    u1 = openmc.Universe(cells=[c1, ci])
 
     cyl2 = openmc.ZCylinder(r=0.5)
     c3 = openmc.Cell(fill=m1, region=-cyl2)
@@ -50,7 +53,8 @@ def model():
     model.settings.source = openmc.Source(space=openmc.stats.Point())
 
     instances = ([(c3, i) for i in range(c3.num_instances)] +
-                 [(c2, i) for i in range(c2.num_instances)])
+                 [(c2, i) for i in range(c2.num_instances)] +
+                 [(ci, i) for i in range(ci.num_instances)])
     f1 = openmc.CellInstanceFilter(instances)
     f2 = openmc.CellInstanceFilter(instances[::-1])
     t1 = openmc.Tally()

From f5651337e1275f485d5c2c9af6411c10a0d19ff0 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 29 Jul 2021 20:02:15 -0500
Subject: [PATCH 11/18] Correction to match's weights vector.

---
 src/tallies/filter_cell_instance.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index 0db6c7d21..d846aa294 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -97,7 +97,7 @@ CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
       auto search = map_.find({index_cell, instance});
       if (search != map_.end()) {
         match.bins_.push_back(search->second);
-        match.bins_.push_back(1.0);
+        match.weights_.push_back(1.0);
       }
     }
   }

From 82719c0fdeb53f6da73b96bf10d62376c7f917e3 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 30 Jul 2021 10:33:19 -0500
Subject: [PATCH 12/18] Updating cell instance regression test to include a
 higher level cell tally.

---
 .../filter_cellinstance/inputs_true.dat       |  2 +-
 .../filter_cellinstance/results_true.dat      | 16 +++++++
 .../filter_cellinstance/test.py               | 45 +++++++++++++------
 tests/testing_harness.py                      |  4 ++
 4 files changed, 53 insertions(+), 14 deletions(-)

diff --git a/tests/regression_tests/filter_cellinstance/inputs_true.dat b/tests/regression_tests/filter_cellinstance/inputs_true.dat
index 5df992627..f9d3ca58d 100644
--- a/tests/regression_tests/filter_cellinstance/inputs_true.dat
+++ b/tests/regression_tests/filter_cellinstance/inputs_true.dat
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='utf-8'?>
 <geometry>
-  <cell id="1" material="1" region="-1" universe="1" />
+  <cell id="1" material="1" region="-1" universe="2" />
   <cell id="2" material="2" region="1" universe="1" />
   <cell fill="1" id="3" universe="2" />
   <cell id="4" material="1" region="-2" universe="3" />
diff --git a/tests/regression_tests/filter_cellinstance/results_true.dat b/tests/regression_tests/filter_cellinstance/results_true.dat
index 053ecf576..c6832c6e1 100644
--- a/tests/regression_tests/filter_cellinstance/results_true.dat
+++ b/tests/regression_tests/filter_cellinstance/results_true.dat
@@ -33,6 +33,14 @@ tally 1:
 2.015188E+02
 9.951936E+00
 2.345815E+01
+1.061333E+01
+2.508486E+01
+2.767786E+01
+1.781264E+02
+2.898957E+01
+2.015188E+02
+9.951936E+00
+2.345815E+01
 tally 2:
 9.951936E+00
 2.345815E+01
@@ -42,6 +50,14 @@ tally 2:
 1.781264E+02
 1.061333E+01
 2.508486E+01
+9.951936E+00
+2.345815E+01
+2.898957E+01
+2.015188E+02
+2.767786E+01
+1.781264E+02
+1.061333E+01
+2.508486E+01
 6.794395E-02
 1.135006E-03
 1.299309E-01
diff --git a/tests/regression_tests/filter_cellinstance/test.py b/tests/regression_tests/filter_cellinstance/test.py
index bd708788c..ccd547f91 100644
--- a/tests/regression_tests/filter_cellinstance/test.py
+++ b/tests/regression_tests/filter_cellinstance/test.py
@@ -2,8 +2,27 @@ import openmc
 import openmc.model
 import pytest
 
+from numpy.testing import assert_array_almost_equal
+
 from tests.testing_harness import PyAPITestHarness
 
+class CellInstanceFilterTest(PyAPITestHarness):
+
+    def _compare_results(self):
+        with openmc.StatePoint(self.statepoint_name) as sp:
+            # we expect the tally results for the instances of
+            # cells 2 and 3 to be the same as 2 is nested
+            # in a universe directly under 3
+            t1 = sp.tallies[1]
+            f1 = sp.filters[1]
+            c2_bins = [tuple(tuple(i) for i in f1.bins if i[0] == 2)]
+            c2_mean = t1.get_values(filters=[openmc.CellInstanceFilter], filter_bins=c2_bins)
+            c3_bins = [tuple(tuple(i) for i in f1.bins if i[0] == 3)]
+            c3_mean = t1.get_values(filters=[openmc.CellInstanceFilter], filter_bins=c3_bins)
+            assert_array_almost_equal(c2_mean, c3_mean)
+
+        return super()._compare_results()
+
 
 @pytest.fixture
 def model():
@@ -23,23 +42,23 @@ def model():
     c1 = openmc.Cell(fill=m1, region=-cyl1)
     c2 = openmc.Cell(fill=m2, region=+cyl1)
     # intermediate universe
-    ui = openmc.Universe(cells=[c2])
-    ci = openmc.Cell(fill=ui)
-    u1 = openmc.Universe(cells=[c1, ci])
+    u1 = openmc.Universe(cells=[c2])
+    c3 = openmc.Cell(fill=u1)
+    u2 = openmc.Universe(cells=[c1, c3])
 
     cyl2 = openmc.ZCylinder(r=0.5)
-    c3 = openmc.Cell(fill=m1, region=-cyl2)
-    c4 = openmc.Cell(fill=m2, region=+cyl2)
-    u2 = openmc.Universe(cells=[c3, c4])
+    c4 = openmc.Cell(fill=m1, region=-cyl2)
+    c5 = openmc.Cell(fill=m2, region=+cyl2)
+    u3 = openmc.Universe(cells=[c4, c5])
 
     lat = openmc.RectLattice()
     lat.lower_left = (-4, -4)
     lat.pitch = (2, 2)
     lat.universes = [
-        [u1, u2, u2, u2],
-        [u2, u1, u2, u2],
-        [u2, u2, u1, u2],
-        [u2, u2, u2, u1]
+        [u2, u3, u3, u3],
+        [u3, u2, u3, u3],
+        [u3, u3, u2, u3],
+        [u3, u3, u3, u2]
     ]
     box = openmc.model.rectangular_prism(8.0, 8.0, boundary_type='reflective')
     main_cell = openmc.Cell(fill=lat, region=box)
@@ -52,9 +71,9 @@ def model():
     model.settings.particles = 1000
     model.settings.source = openmc.Source(space=openmc.stats.Point())
 
-    instances = ([(c3, i) for i in range(c3.num_instances)] +
+    instances = ([(c4, i) for i in range(c4.num_instances)] +
                  [(c2, i) for i in range(c2.num_instances)] +
-                 [(ci, i) for i in range(ci.num_instances)])
+                 [(c3, i) for i in range(c3.num_instances)])
     f1 = openmc.CellInstanceFilter(instances)
     f2 = openmc.CellInstanceFilter(instances[::-1])
     t1 = openmc.Tally()
@@ -69,5 +88,5 @@ def model():
 
 
 def test_cell_instance(model):
-    harness = PyAPITestHarness('statepoint.5.h5', model)
+    harness = CellInstanceFilterTest('statepoint.5.h5', model)
     harness.main()
diff --git a/tests/testing_harness.py b/tests/testing_harness.py
index 48f121d45..92d34ccdc 100644
--- a/tests/testing_harness.py
+++ b/tests/testing_harness.py
@@ -115,6 +115,10 @@ class TestHarness:
 
         return outstr
 
+    @property
+    def statepoint_name(self):
+        return self._sp_name
+
     def _write_results(self, results_string):
         """Write the results to an ASCII file."""
         with open('results_test.dat', 'w') as fh:

From f5f087ef07ea53016e843924436aed11039051e6 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 30 Jul 2021 10:41:25 -0500
Subject: [PATCH 13/18] Moving import and adding comment to test.

---
 tests/regression_tests/filter_cellinstance/test.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/regression_tests/filter_cellinstance/test.py b/tests/regression_tests/filter_cellinstance/test.py
index ccd547f91..3f5fa54b2 100644
--- a/tests/regression_tests/filter_cellinstance/test.py
+++ b/tests/regression_tests/filter_cellinstance/test.py
@@ -1,11 +1,11 @@
+from numpy.testing import assert_array_almost_equal
 import openmc
 import openmc.model
 import pytest
 
-from numpy.testing import assert_array_almost_equal
-
 from tests.testing_harness import PyAPITestHarness
 
+
 class CellInstanceFilterTest(PyAPITestHarness):
 
     def _compare_results(self):
@@ -41,7 +41,7 @@ def model():
     cyl1 = openmc.ZCylinder(r=0.7)
     c1 = openmc.Cell(fill=m1, region=-cyl1)
     c2 = openmc.Cell(fill=m2, region=+cyl1)
-    # intermediate universe
+    # intermediate universe containing only cell 2
     u1 = openmc.Universe(cells=[c2])
     c3 = openmc.Cell(fill=u1)
     u2 = openmc.Universe(cells=[c1, c3])

From b2efde103307cba6e7b2f797a74b742a6666a690 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 30 Jul 2021 10:41:53 -0500
Subject: [PATCH 14/18] Removing unused method declaration.

---
 include/openmc/tallies/filter_cell_instance.h | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/include/openmc/tallies/filter_cell_instance.h b/include/openmc/tallies/filter_cell_instance.h
index 89f8d18af..789a4151e 100644
--- a/include/openmc/tallies/filter_cell_instance.h
+++ b/include/openmc/tallies/filter_cell_instance.h
@@ -46,8 +46,6 @@ public:
 
   void set_cell_instances(gsl::span<CellInstance> instances);
 
-  void set_geom_level(int32_t level);
-
 private:
   //----------------------------------------------------------------------------
   // Data members
@@ -61,9 +59,6 @@ private:
   //! A map from cell/instance indices to filter bin indices.
   std::unordered_map<CellInstance, gsl::index, CellInstanceHash> map_;
 
-  //! Level in the geometry to check for the cell instance
-  int32_t geom_level_ {C_NONE};
-
   //! Indicates if filter uses only material-filled cells
   bool material_cells_only_;
 };

From b42a04cc7614d2c68b6ba707df0f588984a0d981 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 30 Jul 2021 10:42:11 -0500
Subject: [PATCH 15/18] Adding comment to cell_instance_at_level.

---
 src/geometry.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/geometry.cpp b/src/geometry.cpp
index 7eb731660..f38f649f3 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -74,6 +74,7 @@ int cell_instance_at_level(const Particle& p, int level) {
   // determine the cell instance
   Cell& c {*model::cells[p.coord(level).cell]};
 
+  // quick exit if this cell doesn't have distribcell instances
   if (c.distribcell_index_ == C_NONE) return C_NONE;
 
   int instance = 0;

From 595a00d8d5a291413a00d4bd4eda04580d68cf7f Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 30 Jul 2021 10:42:52 -0500
Subject: [PATCH 16/18] Lowering nesting of check for non-material-filled cell
 instances.

---
 src/tallies/filter_cell_instance.cpp | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/tallies/filter_cell_instance.cpp b/src/tallies/filter_cell_instance.cpp
index d846aa294..0dcc4b094 100644
--- a/src/tallies/filter_cell_instance.cpp
+++ b/src/tallies/filter_cell_instance.cpp
@@ -86,19 +86,19 @@ CellInstanceFilter::get_all_bins(const Particle& p, TallyEstimator estimator,
     }
   }
 
-  if (!material_cells_only_) {
-    for (int i = 0; i < p.n_coord() - 1; i++) {
-      gsl::index index_cell = p.coord(i).cell;
-      // if this cell isn't used on the filter, move on
-      if (cells_.count(index_cell) == 0) continue;
+  if (material_cells_only_) return;
 
-      // if this cell is used in the filter, check the instance as well
-      gsl::index instance = cell_instance_at_level(p, i);
-      auto search = map_.find({index_cell, instance});
-      if (search != map_.end()) {
-        match.bins_.push_back(search->second);
-        match.weights_.push_back(1.0);
-      }
+  for (int i = 0; i < p.n_coord() - 1; i++) {
+    gsl::index index_cell = p.coord(i).cell;
+    // if this cell isn't used on the filter, move on
+    if (cells_.count(index_cell) == 0) continue;
+
+    // if this cell is used in the filter, check the instance as well
+    gsl::index instance = cell_instance_at_level(p, i);
+    auto search = map_.find({index_cell, instance});
+    if (search != map_.end()) {
+      match.bins_.push_back(search->second);
+      match.weights_.push_back(1.0);
     }
   }
 }

From 822858dfbbdfee9a290150627618f54da29b2dd0 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Mon, 2 Aug 2021 16:39:10 -0500
Subject: [PATCH 17/18] Update include/openmc/geometry.h

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 include/openmc/geometry.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/openmc/geometry.h b/include/openmc/geometry.h
index 8590e33e1..617921f45 100644
--- a/include/openmc/geometry.h
+++ b/include/openmc/geometry.h
@@ -44,7 +44,7 @@ bool check_cell_overlap(Particle& p, bool error=true);
 //! Get the cell instance for a particle at the specified universe level
 //!
 //! \param p A particle for which to compute the instance using
-//!   it's vector of LocalCoord.
+//!   its coordinates
 //! \param level The level (zero indexed) of the geometry where the instance should be computed.
 //! \return The instance of the cell at the specified level.
 //==============================================================================

From 404dc1ecc9571aab924ea404212c38e2735da5a9 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Mon, 2 Aug 2021 17:38:27 -0500
Subject: [PATCH 18/18] Ensuring Particle::cell_instance_ is set to zero if not
 a distribcell.

---
 src/geometry.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/geometry.cpp b/src/geometry.cpp
index f38f649f3..8f5bda38f 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -77,6 +77,7 @@ int cell_instance_at_level(const Particle& p, int level) {
   // quick exit if this cell doesn't have distribcell instances
   if (c.distribcell_index_ == C_NONE) return C_NONE;
 
+  // compute the cell's instance
   int instance = 0;
   for (int i = 0; i < level; i++) {
     const auto& c_i {*model::cells[p.coord(i).cell]};
@@ -159,6 +160,7 @@ find_cell_inner(Particle& p, const NeighborList* neighbor_list)
     if (c.type_ == Fill::MATERIAL) {
       // Found a material cell which means this is the lowest coord level.
 
+      p.cell_instance() = 0;
       // Find the distribcell instance number.
       if (c.distribcell_index_ >= 0) {
         p.cell_instance() = cell_instance_at_level(p, p.n_coord() - 1);