From adf7077a01b6661316b4db94e11fa4d51f0b995d Mon Sep 17 00:00:00 2001
From: helen-brooks <helen.brooks@ukaea.uk>
Date: Fri, 29 Jan 2021 14:33:43 +0000
Subject: [PATCH] Refactor read_input_xml so that all non-trivial functionality
 is containined in public functions.

---
 include/openmc/cross_sections.h |  3 +++
 include/openmc/geometry_aux.h   |  7 +------
 src/cross_sections.cpp          | 23 +++++++++++++++++++++++
 src/geometry_aux.cpp            |  6 +-----
 src/initialize.cpp              | 21 ++++-----------------
 5 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/include/openmc/cross_sections.h b/include/openmc/cross_sections.h
index 3afcf6b177..aa1ba3661a 100644
--- a/include/openmc/cross_sections.h
+++ b/include/openmc/cross_sections.h
@@ -70,6 +70,9 @@ void read_ce_cross_sections(const std::vector<std::vector<double>>& nuc_temps,
 //! Read cross_sections.xml and populate data libraries
 void read_ce_cross_sections_xml();
 
+//! Load nuclide and thermal scattering data
+void finalize_cross_sections();
+
 void library_clear();
 
 } // namespace openmc
diff --git a/include/openmc/geometry_aux.h b/include/openmc/geometry_aux.h
index 5ff05e7a7d..43e4e71cdf 100644
--- a/include/openmc/geometry_aux.h
+++ b/include/openmc/geometry_aux.h
@@ -46,14 +46,9 @@ void get_temperatures(std::vector<std::vector<double>>& nuc_temps,
 
 //==============================================================================
 //! \brief Perform final setup for geometry
-//!
-//! \param[out] nuc_temps  Vector of temperatures for each nuclide
-//! \param[out] thermal_temps Vector of tempratures for each thermal scattering
-//!   table
 //==============================================================================
 
-void finalize_geometry(std::vector<std::vector<double>>& nuc_temps,
-  std::vector<std::vector<double>>& thermal_temps);
+void finalize_geometry();
 
 //==============================================================================
 //! Figure out which Universe is the root universe.
diff --git a/src/cross_sections.cpp b/src/cross_sections.cpp
index b82a690e6d..dc071cbac9 100644
--- a/src/cross_sections.cpp
+++ b/src/cross_sections.cpp
@@ -7,6 +7,7 @@
 #include "openmc/dagmc.h"
 #endif
 #include "openmc/error.h"
+#include "openmc/geometry_aux.h"
 #include "openmc/file_utils.h"
 #include "openmc/hdf5_interface.h"
 #include "openmc/material.h"
@@ -17,6 +18,7 @@
 #include "openmc/settings.h"
 #include "openmc/simulation.h"
 #include "openmc/string_utils.h"
+#include "openmc/timer.h"
 #include "openmc/thermal.h"
 #include "openmc/xml_interface.h"
 #include "openmc/wmp.h"
@@ -323,6 +325,27 @@ void read_ce_cross_sections_xml()
   }
 }
 
+void finalize_cross_sections(){
+  if (settings::run_mode != RunMode::PLOTTING) {
+    simulation::time_read_xs.start();
+    if (settings::run_CE) {
+      // Determine desired temperatures for each nuclide and S(a,b) table
+      double_2dvec nuc_temps(data::nuclide_map.size());
+      double_2dvec thermal_temps(data::thermal_scatt_map.size());
+      get_temperatures(nuc_temps, thermal_temps);
+
+      // Read continuous-energy cross sections from HDF5
+      read_ce_cross_sections(nuc_temps, thermal_temps);
+    } else {
+      // Create material macroscopic data for MGXS
+      set_mg_interface_nuclides_and_temps();
+      data::mg.init();
+      mark_fissionable_mgxs_materials();
+    }
+    simulation::time_read_xs.stop();
+  }
+}
+
 void library_clear() {
   data::libraries.clear();
   data::library_map.clear();
diff --git a/src/geometry_aux.cpp b/src/geometry_aux.cpp
index eff7016ab8..e2b079ba79 100644
--- a/src/geometry_aux.cpp
+++ b/src/geometry_aux.cpp
@@ -242,8 +242,7 @@ get_temperatures(std::vector<std::vector<double>>& nuc_temps,
 
 //==============================================================================
 
-void finalize_geometry(std::vector<std::vector<double>>& nuc_temps,
-  std::vector<std::vector<double>>& thermal_temps)
+void finalize_geometry()
 {
   // Perform some final operations to set up the geometry
   adjust_indices();
@@ -253,9 +252,6 @@ void finalize_geometry(std::vector<std::vector<double>>& nuc_temps,
   // Assign temperatures to cells that don't have temperatures already assigned
   assign_temperatures();
 
-  // Determine desired temperatures for each nuclide and S(a,b) table
-  get_temperatures(nuc_temps, thermal_temps);
-
   // Determine number of nested coordinate levels in the geometry
   model::n_coord_levels = maximum_levels(model::root_universe);
 }
diff --git a/src/initialize.cpp b/src/initialize.cpp
index 6594417de9..2c645ace1b 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -257,24 +257,11 @@ void read_input_xml()
   read_materials_xml();
   read_geometry_xml();
 
-  // Convert user IDs -> indices, assign temperatures
-  double_2dvec nuc_temps(data::nuclide_map.size());
-  double_2dvec thermal_temps(data::thermal_scatt_map.size());
-  finalize_geometry(nuc_temps, thermal_temps);
+  // Final geometry setup and assign temperatures
+  finalize_geometry();
 
-  if (settings::run_mode != RunMode::PLOTTING) {
-    simulation::time_read_xs.start();
-    if (settings::run_CE) {
-      // Read continuous-energy cross sections
-      read_ce_cross_sections(nuc_temps, thermal_temps);
-    } else {
-      // Create material macroscopic data for MGXS
-      set_mg_interface_nuclides_and_temps();
-      data::mg.init();
-      mark_fissionable_mgxs_materials();
-    }
-    simulation::time_read_xs.stop();
-  }
+  // Finalize cross sections having assigned temperatures
+  finalize_cross_sections();
 
   read_tallies_xml();