From 5c78cd62594c96181dc149d2c99b1ec75098d737 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Mon, 10 Jun 2019 19:46:11 -0500
Subject: [PATCH] Correcting a couple of issues in setting the OVERLAP value
 and color.

---
 include/openmc/plot.h | 4 ++--
 src/geometry.cpp      | 5 ++++-
 src/plot.cpp          | 7 +++++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/include/openmc/plot.h b/include/openmc/plot.h
index 1d8ac0ea1..d762cad70 100644
--- a/include/openmc/plot.h
+++ b/include/openmc/plot.h
@@ -108,7 +108,7 @@ public:
   Position width_; //!< Plot width in geometry
   PlotBasis basis_; //!< Plot basis (XY/XZ/YZ)
   std::array<size_t, 3> pixels_; //!< Plot size in pixels
-  bool check_overlaps_ = false;
+  bool color_overlaps_ = true;
   int level_; //!< Plot universe level
 };
 
@@ -176,7 +176,7 @@ T PlotBase::get_map() const {
         if (found_cell) {
           data.set_value(y, x, p, j);
         }
-        if (check_overlaps_ && check_cell_overlap(&p, false)) {
+        if (color_overlaps_ && check_cell_overlap(&p, false)) {
           data.set_overlap(y, x);
         }
       } // inner for
diff --git a/src/geometry.cpp b/src/geometry.cpp
index 4169a5420..ce118c0e0 100644
--- a/src/geometry.cpp
+++ b/src/geometry.cpp
@@ -44,12 +44,15 @@ bool check_cell_overlap(Particle* p, bool error)
     for (auto index_cell : univ.cells_) {
       Cell& c = *model::cells[index_cell];
       if (c.contains(p->coord_[j].r, p->coord_[j].u, p->surface_)) {
-        if (error && index_cell != p->coord_[j].cell) {
+        if (index_cell != p->coord_[j].cell) {
+          if (error) {
           std::stringstream err_msg;
           err_msg << "Overlapping cells detected: " << c.id_ << ", "
                   << model::cells[p->coord_[j].cell]->id_ << " on universe "
                   << univ.id_;
           fatal_error(err_msg);
+          }
+          return true;
         }
         ++model::overlap_check_count[index_cell];
       }
diff --git a/src/plot.cpp b/src/plot.cpp
index 0ec26473e..d53a12805 100644
--- a/src/plot.cpp
+++ b/src/plot.cpp
@@ -53,7 +53,7 @@ IdData::set_value(size_t y, size_t x, const Particle& p, int level) {
 }
 
 void IdData::set_overlap(size_t y, size_t x) {
-  data_(y, x) = OVERLAP;
+  xt::view(data_, y, x, xt::all()) = OVERLAP;
 }
 
 PropertyData::PropertyData(size_t h_res, size_t v_res)
@@ -154,7 +154,10 @@ void create_ppm(Plot pl)
       auto id = ids.data_(y, x, pl.color_by_);
       // no setting needed if not found
       if (id == NOT_FOUND) { continue; }
-      if (id == OVERLAP) data(x,y) = RED;
+      if (id == OVERLAP) {
+        data(x,y) = RED;
+        continue;
+      }
       if (PlotColorBy::cells == pl.color_by_) {
         data(x,y) = pl.colors_[model::cell_map[id]];
       } else if (PlotColorBy::mats == pl.color_by_) {