Support for a single model.xml file

include/openmc/cross_sections.h

@@ -62,6 +62,11 @@ extern vector<Library> libraries;
 //! libraries
 void read_cross_sections_xml();
 
+//! Read cross sections file (either XML or multigroup H5) and populate data
+//! libraries
+//! \param[in] root node of the cross_sections.xml
+void read_cross_sections_xml(pugi::xml_node root);
+
 //! Load nuclide and thermal scattering data from HDF5 files
 //
 //! \param[in] nuc_temps Temperatures for each nuclide in [K]

include/openmc/file_utils.h

@@ -3,14 +3,31 @@
 
 #include <fstream> // for ifstream
 #include <string>
+#include <sys/stat.h>
 
 namespace openmc {
 
+// TODO: replace with std::filesystem when switch to C++17 is made
+//! Determine if a path is a directory
+//! \param[in] path Path to check
+//! \return Whether the path is a directory
+inline bool dir_exists(const std::string& path)
+{
+  struct stat s;
+  if (stat(path.c_str(), &s) != 0) return false;
+
+  return s.st_mode & S_IFDIR;
+}
+
 //! Determine if a file exists
 //! \param[in] filename Path to file
 //! \return Whether file exists
 inline bool file_exists(const std::string& filename)
 {
+  // rule out file being a path to a directory
+  if (dir_exists(filename))
+    return false;
+
   std::ifstream s {filename};
   return s.good();
 }

include/openmc/geometry_aux.h

@@ -10,6 +10,7 @@
 #include <vector>
 
 #include "openmc/vector.h"
+#include "openmc/xml_interface.h"
 
 namespace openmc {
 
@@ -19,8 +20,13 @@ extern std::unordered_map<int32_t, std::unordered_map<int32_t, int32_t>>
 extern std::unordered_map<int32_t, int32_t> universe_level_counts;
 } // namespace model
 
+//! Read geometry from XML file
 void read_geometry_xml();
 
+//! Read geometry from XML node
+//! \param[in] root node of geometry XML element
+void read_geometry_xml(pugi::xml_node root);
+
 //==============================================================================
 //! Replace Universe, Lattice, and Material IDs with indices.
 //==============================================================================

include/openmc/initialize.h

@@ -1,6 +1,8 @@
 #ifndef OPENMC_INITIALIZE_H
 #define OPENMC_INITIALIZE_H
 
+#include <string>
+
 #ifdef OPENMC_MPI
 #include "mpi.h"
 #endif
@@ -11,7 +13,13 @@ int parse_command_line(int argc, char* argv[]);
 #ifdef OPENMC_MPI
 void initialize_mpi(MPI_Comm intracomm);
 #endif
-void read_input_xml();
+
+//! Read material, geometry, settings, and tallies from a single XML file
+bool read_model_xml();
+//! Read inputs from separate XML files
+void read_separate_xml_files();
+//! Write some output that occurs right after initialization
+void initial_output();
 
 } // namespace openmc
 

include/openmc/material.h

@@ -221,6 +221,10 @@ double density_effect(const vector<double>& f, const vector<double>& e_b_sq,
 //! Read material data from materials.xml
 void read_materials_xml();
 
+//! Read material data XML node
+//! \param[in] root node of materials XML element
+void read_materials_xml(pugi::xml_node root);
+
 void free_memory_material();
 
 } // namespace openmc

include/openmc/plot.h

@@ -279,6 +279,10 @@ void voxel_finalize(hid_t dspace, hid_t dset, hid_t memspace);
 //! Read plot specifications from a plots.xml file
 void read_plots_xml();
 
+//! Read plot specifications from an XML Node
+//! \param[in] XML node containing plot info
+void read_plots_xml(pugi::xml_node root);
+
 //! Clear memory
 void free_memory_plot();
 

include/openmc/settings.h

@@ -127,9 +127,12 @@ extern double weight_survive;      //!< Survival weight after Russian roulette
 //==============================================================================
 
 //! Read settings from XML file
-//! \param[in] root XML node for <settings>
 void read_settings_xml();
 
+//! Read settings from XML node
+//! \param[in] root XML node for <settings>
+void read_settings_xml(pugi::xml_node root);
+
 void free_memory_settings();
 
 } // namespace openmc

include/openmc/tallies/tally.h

@@ -48,10 +48,10 @@ class Tally {
   void set_nuclides(const vector<std::string>& nuclides);
 
   //! returns vector of indices corresponding to the tally this is called on
-  const vector<int32_t>& filters() const { return filters_; } 
+  const vector<int32_t>& filters() const { return filters_; }
 
   //! \brief Returns the tally filter at index i
-  int32_t filters(int i) const { return filters_[i]; } 
+  int32_t filters(int i) const { return filters_[i]; }
 
   void set_filters(gsl::span<Filter*> filters);
 
@@ -178,6 +178,10 @@ extern double global_tally_leakage;
 //! Read tally specification from tallies.xml
 void read_tallies_xml();
 
+//! Read tally specification from an XML node
+//! \param[in] root node of tallies XML element
+void read_tallies_xml(pugi::xml_node root);
+
 //! \brief Accumulate the sum of the contributions from each history within the
 //! batch to a new random variable
 void accumulate_tallies();

openmc/_xml.py

@@ -1,22 +1,40 @@
-def clean_indentation(element, level=0, spaces_per_level=2):
-    """
-    copy and paste from https://effbot.org/zone/element-lib.htm#prettyprint
-    it basically walks your tree and adds spaces and newlines so the tree is
-    printed in a nice way
+def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True):
+    """Set indentation of XML element and its sub-elements.
+    Copied and pasted from https://effbot.org/zone/element-lib.htm#prettyprint.
+    It walks your tree and adds spaces and newlines so the tree is
+    printed in a nice way.
+
+    Parameters
+    ----------
+    level : int
+        Indentation level for the element passed in (default 0)
+    spaces_per_level : int
+        Number of spaces per indentation level (default 2)
+    trailing_indent : bool
+        Whether or not to add indentation after closing the element
+
     """
     i = "\n" + level*spaces_per_level*" "
 
+    # ensure there's always some tail for the element passed in
+    if not element.tail:
+        element.tail = ""
+
     if len(element):
         if not element.text or not element.text.strip():
             element.text = i + spaces_per_level*" "
-        if not element.tail or not element.tail.strip():
+        if trailing_indent and (not element.tail or not element.tail.strip()):
             element.tail = i
         for sub_element in element:
+            # `trailing_indent` is intentionally not forwarded to the recursive
+            # call. Any child element of the topmost element should add
+            # indentation at the end to ensure its parent's indentation is
+            # correct.
             clean_indentation(sub_element, level+1, spaces_per_level)
         if not sub_element.tail or not sub_element.tail.strip():
             sub_element.tail = i
     else:
-        if level and (not element.tail or not element.tail.strip()):
+        if trailing_indent and level and (not element.tail or not element.tail.strip()):
             element.tail = i
 
 

openmc/cell.py

@@ -650,7 +650,7 @@ def from_xml_element(cls, elem, surfaces, materials, get_universe):
         surfaces : dict
             Dictionary mapping surface IDs to :class:`openmc.Surface` instances
         materials : dict
-            Dictionary mapping material IDs to :class:`openmc.Material`
+            Dictionary mapping material ID strings to :class:`openmc.Material`
             instances (defined in :math:`openmc.Geometry.from_xml`)
         get_universe : function
             Function returning universe (defined in

openmc/executor.py

@@ -9,7 +9,7 @@
 def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
                            plot=False, restart_file=None, threads=None,
                            tracks=False, event_based=None,
-                           openmc_exec='openmc', mpi_args=None):
+                           openmc_exec='openmc', mpi_args=None, path_input=None):
     """Converts user-readable flags in to command-line arguments to be run with
     the OpenMC executable via subprocess.
 
@@ -42,6 +42,9 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
     mpi_args : list of str, optional
         MPI execute command and any additional MPI arguments to pass,
         e.g. ['mpiexec', '-n', '8'].
+    path_input : str or Pathlike
+        Path to a single XML file or a directory containing XML files for the
+        OpenMC executable to read.
 
     .. versionadded:: 0.13.0
 
@@ -82,6 +85,9 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None,
     if mpi_args is not None:
         args = mpi_args + args
 
+    if path_input is not None:
+        args += [path_input]
+
     return args
 
 
@@ -118,7 +124,7 @@ def _run(args, output, cwd):
         raise RuntimeError(error_msg)
 
 
-def plot_geometry(output=True, openmc_exec='openmc', cwd='.'):
+def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None):
     """Run OpenMC in plotting mode
 
     Parameters
@@ -129,17 +135,23 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.'):
         Path to OpenMC executable
     cwd : str, optional
         Path to working directory to run in
+    path_input : str
+        Path to a single XML file or a directory containing XML files for the
+        OpenMC executable to read.
 
     Raises
     ------
     RuntimeError
         If the `openmc` executable returns a non-zero status
 
     """
-    _run([openmc_exec, '-p'], output, cwd)
+    args = [openmc_exec, '-p']
+    if path_input is not None:
+        args += [path_input]
+    _run(args, output, cwd)
 
 
-def plot_inline(plots, openmc_exec='openmc', cwd='.'):
+def plot_inline(plots, openmc_exec='openmc', cwd='.', path_input=None):
     """Display plots inline in a Jupyter notebook.
 
     .. versionchanged:: 0.13.0
@@ -155,6 +167,9 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'):
         Path to OpenMC executable
     cwd : str, optional
         Path to working directory to run in
+    path_input : str
+        Path to a single XML file or a directory containing XML files for the
+        OpenMC executable to read.
 
     Raises
     ------
@@ -171,15 +186,16 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'):
     openmc.Plots(plots).export_to_xml(cwd)
 
     # Run OpenMC in geometry plotting mode
-    plot_geometry(False, openmc_exec, cwd)
+    plot_geometry(False, openmc_exec, cwd, path_input)
 
     if plots is not None:
         images = [_get_plot_image(p, cwd) for p in plots]
         display(*images)
 
 
 def calculate_volumes(threads=None, output=True, cwd='.',
-                      openmc_exec='openmc', mpi_args=None):
+                      openmc_exec='openmc', mpi_args=None,
+                      path_input=None):
     """Run stochastic volume calculations in OpenMC.
 
     This function runs OpenMC in stochastic volume calculation mode. To specify
@@ -210,6 +226,10 @@ def calculate_volumes(threads=None, output=True, cwd='.',
     cwd : str, optional
         Path to working directory to run in. Defaults to the current working
         directory.
+    path_input : str or Pathlike
+        Path to a single XML file or a directory containing XML files for the
+        OpenMC executable to read.
+
 
     Raises
     ------
@@ -223,14 +243,16 @@ def calculate_volumes(threads=None, output=True, cwd='.',
     """
 
     args = _process_CLI_arguments(volume=True, threads=threads,
-                                  openmc_exec=openmc_exec, mpi_args=mpi_args)
+                                  openmc_exec=openmc_exec, mpi_args=mpi_args,
+                                  path_input=path_input)
 
     _run(args, output, cwd)
 
 
 def run(particles=None, threads=None, geometry_debug=False,
         restart_file=None, tracks=False, output=True, cwd='.',
-        openmc_exec='openmc', mpi_args=None, event_based=False):
+        openmc_exec='openmc', mpi_args=None, event_based=False,
+        path_input=None):
     """Run an OpenMC simulation.
 
     Parameters
@@ -239,17 +261,17 @@ def run(particles=None, threads=None, geometry_debug=False,
         Number of particles to simulate per generation.
     threads : int, optional
         Number of OpenMP threads. If OpenMC is compiled with OpenMP threading
-        enabled, the default is implementation-dependent but is usually equal
-        to the number of hardware threads available (or a value set by the
+        enabled, the default is implementation-dependent but is usually equal to
+        the number of hardware threads available (or a value set by the
         :envvar:`OMP_NUM_THREADS` environment variable).
     geometry_debug : bool, optional
         Turn on geometry debugging during simulation. Defaults to False.
     restart_file : str, optional
         Path to restart file to use
     tracks : bool, optional
-        Enables the writing of particles tracks. The number of particle
-        tracks written to tracks.h5 is limited to 1000 unless
-        Settings.max_tracks is set. Defaults to False.
+        Enables the writing of particles tracks. The number of particle tracks
+        written to tracks.h5 is limited to 1000 unless Settings.max_tracks is
+        set. Defaults to False.
     output : bool
         Capture OpenMC output from standard out
     cwd : str, optional
@@ -258,13 +280,17 @@ def run(particles=None, threads=None, geometry_debug=False,
     openmc_exec : str, optional
         Path to OpenMC executable. Defaults to 'openmc'.
     mpi_args : list of str, optional
-        MPI execute command and any additional MPI arguments to pass,
-        e.g. ['mpiexec', '-n', '8'].
+        MPI execute command and any additional MPI arguments to pass, e.g.
+        ['mpiexec', '-n', '8'].
     event_based : bool, optional
         Turns on event-based parallelism, instead of default history-based
 
         .. versionadded:: 0.12
 
+    path_input : str or Pathlike
+        Path to a single XML file or a directory containing XML files for the
+        OpenMC executable to read.
+
     Raises
     ------
     RuntimeError
@@ -275,6 +301,7 @@ def run(particles=None, threads=None, geometry_debug=False,
     args = _process_CLI_arguments(
         volume=False, geometry_debug=geometry_debug, particles=particles,
         restart_file=restart_file, threads=threads, tracks=tracks,
-        event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args)
+        event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args,
+        path_input=path_input)
 
     _run(args, output, cwd)