Addressing some comments from PR

include/openmc/initialize.h

@@ -11,8 +11,12 @@ int parse_command_line(int argc, char* argv[]);
 #ifdef OPENMC_MPI
 void initialize_mpi(MPI_Comm intracomm);
 #endif
+
+//! Read material, geometry, settings, and tallies from a single XML file
 bool read_model_xml();
-void read_input_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

openmc/geometry.py

@@ -256,9 +256,9 @@ class Geometry:
         ----------
         path : str, optional
             Path to geometry XML file
-        materials : dict
-            Dictionary mapping material ID strings to :class:`openmc.Material`
-            instances (defined in :math:`openmc.Geometry.from_xml`)
+        materials : openmc.Materials or None
+            Materials used to assign to cells. If None, an attempt is made to
+            generate it from the materials.xml file.
 
         Returns
         -------

openmc/model/model.py

@@ -205,8 +205,24 @@ class Model:
                 self._plots.append(plot)
 
     @classmethod
-    def from_xml(cls, *args, separate_xmls=True, **kwargs):
-        if separate_xmls:
+    def from_xml(cls, *args, path='model.xml', separate_xmls=True, **kwargs):
+        """Generate geometry from XML file
+
+        Parameters
+        ----------
+        path : str, optional
+            Path to model XML file
+        separate_xmls : bool
+            Whether or not to read from a single or separate XML files
+
+        Returns
+        -------
+        openmc.Geometry
+            Geometry object
+
+        """
+
+        if separate_xmls or not Path(path).exists():
             return cls.from_separate_xmls(*args, **kwargs)
         else:
             return cls.from_model_xml(*args, **kwargs)
@@ -228,7 +244,7 @@ class Model:
         model.settings = openmc.Settings.from_xml_element(root.find('settings'))
         model.materials = openmc.Materials.from_xml_element(root.find('materials'))
         materials = {str(m.id): m for m in model.materials}
-        model.geometry = .Geometry.from_xml_element(root.find('geometry'), materials)
+        model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), materials)
 
         # gather meshses from other classes before reading the tally node
         meshes = {}
@@ -442,8 +458,8 @@ class Model:
                 depletion_operator.cleanup_when_done = True
                 depletion_operator.finalize()
 
-    def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True):
-        """Export model to separate XML files.
+    def export_to_xml(self, directory='.', remove_surfs=False, separate_xmls=True, filename='model.xml'):
+        """Export model to an XML file(s).
 
         Parameters
         ----------
@@ -453,6 +469,8 @@ class Model:
         remove_surfs : bool
             Whether or not to remove redundant surfaces from the geometry when
             exporting.
+        filename : str
+            Name of the single XML file to create (only used :math:`separate_xmls` if False)
 
             .. versionadded:: 0.13.1
 
@@ -460,11 +478,15 @@ class Model:
             Whether or not to write a single model.xml file or many XML files.
         """
         if separate_xmls:
-            self.export_to_separate_xmls(directory, remove_surfs)
+            if filename != 'model.xml':
+                warnings.warn('Export filename parameter {filename} is ignored '
+                              'because the model is being written to separate XML files.')
+            self._export_to_separate_xmls(directory, remove_surfs)
         else:
-            self.export_to_single_xml(directory, remove_surfs)
+            filename = Path(directory) / Path(filename)
+            self._export_to_single_xml(filename, remove_surfs)
 
-    def export_to_separate_xmls(self, directory='.', remove_surfs=False):
+    def _export_to_separate_xmls(self, directory='.', remove_surfs=False):
         """Export model to separate XML files.
 
         Parameters
@@ -501,7 +523,7 @@ class Model:
         if self.plots:
             self.plots.export_to_xml(d)
 
-    def export_to_single_xml(self, directory='.', remove_surfs=False):
+    def _export_to_single_xml(self, path='model.xml', remove_surfs=False):
         """Export model to XML files.
 
         Parameters
@@ -516,10 +538,9 @@ class Model:
             .. versionadded:: 0.13.1
         """
         # Create directory if required
-        d = Path(directory)
-        if not d.is_dir():
-            d.mkdir(parents=True)
-        d /= 'model.xml'
+        xml_path = Path(path)
+        if not xml_path.parent.exists:
+            raise RuntimeError(f'The directory "{xml_path}" does not exist.')
 
         if remove_surfs:
             warnings.warn("remove_surfs kwarg will be deprecated soon, please "
@@ -541,7 +562,7 @@ class Model:
             materials = openmc.Materials(self.geometry.get_all_materials()
                                          .values())
 
-        with open(d, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh:
+        with open(xml_path, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh:
             # write the XML header
             fh.write("<?xml version='1.0' encoding='utf-8'?>\n")
             fh.write("<model>\n")

openmc/plots.py

@@ -911,6 +911,12 @@ class Plots(cv.CheckedList):
 
     def to_xml_element(self):
         """Create a 'plots' element to be written to an XML file.
+
+        Returns
+        -------
+        element : xml.etree.ElementTree.Element
+            XML element containing all plot elements
+
         """
         # Reset xml element tree
         self._plots_file.clear()

src/initialize.cpp

@@ -106,7 +106,7 @@ int openmc_init(int argc, char* argv[], const void* intracomm)
   openmc::openmc_set_seed(DEFAULT_SEED);
 
   // Read XML input files
-  if (!read_model_xml()) read_input_xml();
+  if (!read_model_xml()) read_separate_xml_files();
 
   // Write some initial output under the header if needed
   initial_output();
@@ -371,7 +371,7 @@ bool read_model_xml() {
   return true;
 }
 
-void read_input_xml()
+void read_separate_xml_files()
 {
   read_settings_xml();
   read_cross_sections_xml();

tests/unit_tests/test_model.py

@@ -530,21 +530,20 @@ def test_calc_volumes(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
 
     test_model.finalize_lib()
 
-def test_model_xml():
+def test_model_xml(run_in_tmpdir):
 
-    with cdtemp():
-        # load a model from examples
-        pwr_model = openmc.examples.pwr_core()
+    # load a model from examples
+    pwr_model = openmc.examples.pwr_core()
 
-        # export to separate XMLs manually
-        pwr_model.settings.export_to_xml('settings_ref.xml')
-        pwr_model.materials.export_to_xml('materials_ref.xml')
-        pwr_model.geometry.export_to_xml('geometry_ref.xml')
+    # export to separate XMLs manually
+    pwr_model.settings.export_to_xml('settings_ref.xml')
+    pwr_model.materials.export_to_xml('materials_ref.xml')
+    pwr_model.geometry.export_to_xml('geometry_ref.xml')
 
-        # now write and read a model.xml file
-        pwr_model.export_to_xml(separate_xmls=False)
-        new_model = openmc.Model.from_xml(separate_xmls=False)
+    # now write and read a model.xml file
+    pwr_model.export_to_xml(separate_xmls=False)
+    new_model = openmc.Model.from_xml(separate_xmls=False)
 
-        # make sure we can also export this again to separate
-        # XML files
-        new_model.export_to_xml(separate_xmls=True)
+    # make sure we can also export this again to separate
+    # XML files
+    new_model.export_to_xml(separate_xmls=True)