From 2e716589a14d2465ab4a494e12ddf86172af72e3 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 3 Nov 2022 23:57:22 -0500
Subject: [PATCH] Other bug fixes

---
 openmc/geometry.py    | 32 ++++++++++++++++----------------
 openmc/model/model.py |  6 +++---
 openmc/plots.py       |  7 ++++---
 3 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/openmc/geometry.py b/openmc/geometry.py
index b4f8046bd2..d036df9c74 100644
--- a/openmc/geometry.py
+++ b/openmc/geometry.py
@@ -204,24 +204,24 @@ class Geometry:
             surfaces[s1].periodic_surface = surfaces[s2]
 
         # Add any DAGMC universes
-        for elem in elem.findall('dagmc_universe'):
-            dag_univ = openmc.DAGMCUniverse.from_xml_element(elem)
+        for e in elem.findall('dagmc_universe'):
+            dag_univ = openmc.DAGMCUniverse.from_xml_element(e)
             universes[dag_univ.id] = dag_univ
 
         # Dictionary that maps each universe to a list of cells/lattices that
         # contain it (needed to determine which universe is the elem)
         child_of = defaultdict(list)
 
-        for elem in elem.findall('lattice'):
-            lat = openmc.RectLattice.from_xml_element(elem, get_universe)
+        for e in elem.findall('lattice'):
+            lat = openmc.RectLattice.from_xml_element(e, get_universe)
             universes[lat.id] = lat
             if lat.outer is not None:
                 child_of[lat.outer].append(lat)
             for u in lat.universes.ravel():
                 child_of[u].append(lat)
 
-        for elem in elem.findall('hex_lattice'):
-            lat = openmc.HexLattice.from_xml_element(elem, get_universe)
+        for e in elem.findall('hex_lattice'):
+            lat = openmc.HexLattice.from_xml_element(e, get_universe)
             universes[lat.id] = lat
             if lat.outer is not None:
                 child_of[lat.outer].append(lat)
@@ -235,15 +235,8 @@ class Geometry:
                         for u in ring:
                             child_of[u].append(lat)
 
-        # Create dictionary to easily look up materials
-        if materials is None:
-            filename = Path(path).parent / 'materials.xml'
-            materials = openmc.Materials.from_xml(str(filename))
-        mats = {str(m.id): m for m in materials}
-        mats['void'] = None
-
-        for elem in elem.findall('cell'):
-            c = openmc.Cell.from_xml_element(elem, surfaces, mats, get_universe)
+        for e in elem.findall('cell'):
+            c = openmc.Cell.from_xml_element(e, surfaces, materials, get_universe)
             if c.fill_type in ('universe', 'lattice'):
                 child_of[c.fill].append(c)
 
@@ -276,7 +269,14 @@ class Geometry:
         tree = ET.parse(path)
         root = tree.getroot()
 
-        return cls.from_xml_element(root, materials)
+         # Create dictionary to easily look up materials
+        if materials is None:
+            filename = Path(path).parent / 'materials.xml'
+            materials = openmc.Materials.from_xml(str(filename))
+        mats = {str(m.id): m for m in materials}
+        mats['void'] = None
+
+        return cls.from_xml_element(root, mats)
 
     def find(self, point):
         """Find cells/universes/lattices which contain a given point
diff --git a/openmc/model/model.py b/openmc/model/model.py
index 2193084c36..a839dc8f0c 100644
--- a/openmc/model/model.py
+++ b/openmc/model/model.py
@@ -208,11 +208,11 @@ class Model:
                 self._plots.append(plot)
 
     @classmethod
-    def from_xml(cls, separate_xmls=True, **kwargs):
+    def from_xml(cls, *args, separate_xmls=True, **kwargs):
         if separate_xmls:
-            return cls.from_separate_xmls(**kwargs)
+            return cls.from_separate_xmls(*args, **kwargs)
         else:
-            return cls.from_model_xml(**kwargs)
+            return cls.from_model_xml(*args, **kwargs)
 
     @classmethod
     def from_model_xml(cls, path='model.xml'):
diff --git a/openmc/plots.py b/openmc/plots.py
index badea2e586..b1f1927876 100644
--- a/openmc/plots.py
+++ b/openmc/plots.py
@@ -919,6 +919,7 @@ class Plots(cv.CheckedList):
 
         # Clean the indentation in the file to be user-readable
         clean_indentation(self._plots_file)
+        reorder_attributes(self._plots_file)  # TODO: Remove when support is Python 3.8+
 
         return self._plots_file
 
@@ -936,8 +937,8 @@ class Plots(cv.CheckedList):
         if p.is_dir():
             p /= 'plots.xml'
 
+        self.to_xml_element()
         # Write the XML Tree to the plots.xml file
-        reorder_attributes(self._plots_file)  # TODO: Remove when support is Python 3.8+
         tree = ET.ElementTree(self._plots_file)
         tree.write(str(p), xml_declaration=True, encoding='utf-8')
 
@@ -958,8 +959,8 @@ class Plots(cv.CheckedList):
         """
         # Generate each plot
         plots = cls()
-        for elem in elem.findall('plot'):
-            plots.append(Plot.from_xml_element(elem))
+        for e in elem.findall('plot'):
+            plots.append(Plot.from_xml_element(e))
         return plots
 
     @classmethod