Merge pull request #1247 from drewejohnson/dep-chain-file

Read depletion_chain information from main cross section file

openmc/data/library.py

@@ -1,5 +1,6 @@
 import os
 import xml.etree.ElementTree as ET
+import pathlib
 
 import h5py
 
@@ -48,19 +49,30 @@ class DataLibrary(EqualityMixin):
 
         Parameters
         ----------
-        filename : str
+        filename : str or Path
             Path to the file to be registered.
+            If an ``xml`` file, treat as the depletion chain file without
+            materials.
 
         """
-        # Support pathlib
-        # TODO: Remove when support is Python 3.6+ only
-        filename = str(filename)
+        if not isinstance(filename, pathlib.Path):
+            path = pathlib.Path(filename)
+        else:
+            path = filename
 
-        with h5py.File(filename, 'r') as h5file:
-            filetype = h5file.attrs['filetype'].decode()[5:]
-            materials = list(h5file)
+        if path.suffix == '.xml':
+            filetype = 'depletion_chain'
+            materials = []
+        elif path.suffix == '.h5':
+            with h5py.File(path, 'r') as h5file:
+                filetype = h5file.attrs['filetype'].decode()[5:]
+                materials = list(h5file)
+        else:
+            raise ValueError(
+                "File type {} not supported by {}"
+                .format(path.name, self.__class__.__name__))
 
-        library = {'path': filename, 'type': filetype, 'materials': materials}
+        library = {'path': str(path), 'type': filetype, 'materials': materials}
         self.libraries.append(library)
 
     def export_to_xml(self, path='cross_sections.xml'):
@@ -85,8 +97,11 @@ class DataLibrary(EqualityMixin):
             dir_element.text = os.path.realpath(common_dir)
 
         for library in self.libraries:
-            lib_element = ET.SubElement(root, "library")
-            lib_element.set('materials', ' '.join(library['materials']))
+            if library['type'] == "depletion_chain":
+                lib_element = ET.SubElement(root, "depletion_chain")
+            else:
+                lib_element = ET.SubElement(root, "library")
+                lib_element.set('materials', ' '.join(library['materials']))
             lib_element.set('path', os.path.relpath(library['path'], common_dir))
             lib_element.set('type', library['type'])
 
@@ -106,7 +121,7 @@ class DataLibrary(EqualityMixin):
         ----------
         path : str, optional
             Path to XML file to read. If not provided, the
-            `OPENMC_CROSS_SECTIONS` environment variable will be  used.
+            :envvar:`OPENMC_CROSS_SECTIONS` environment variable will be  used.
 
         Returns
         -------
@@ -146,4 +161,13 @@ class DataLibrary(EqualityMixin):
                        'materials': materials}
             data.libraries.append(library)
 
+        # get depletion chain data
+
+        dep_node = root.find("depletion_chain")
+        if dep_node is not None:
+            filename = os.path.join(directory, dep_node.attrib['path'])
+            library = {'path': filename, 'type': 'depletion_chain',
+                       'materials': []}
+            data.libraries.append(library)
+
         return data

openmc/deplete/abc.py

@@ -8,7 +8,10 @@ from collections import namedtuple
 import os
 from pathlib import Path
 from abc import ABCMeta, abstractmethod
+from xml.etree import ElementTree as ET
+from warnings import warn
 
+from openmc.data import DataLibrary
 from .chain import Chain
 
 OperatorResult = namedtuple('OperatorResult', ['k', 'rates'])
@@ -43,8 +46,9 @@ class TransportOperator(metaclass=ABCMeta):
     Parameters
     ----------
     chain_file : str, optional
-        Path to the depletion chain XML file.  Defaults to the
-        :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+        Path to the depletion chain XML file.  Defaults to the file
+        listed under ``depletion_chain`` in
+        :envvar:`OPENMC_CROSS_SECTIONS` environment variable.
 
     Attributes
     ----------
@@ -62,8 +66,21 @@ class TransportOperator(metaclass=ABCMeta):
         if chain_file is None:
             chain_file = os.environ.get("OPENMC_DEPLETE_CHAIN", None)
             if chain_file is None:
-                raise IOError("No chain specified, either manually or in "
-                              "environment variable OPENMC_DEPLETE_CHAIN.")
+                data = DataLibrary.from_xml()
+                # search for depletion_chain path from end of list
+                for lib in reversed(data.libraries):
+                    if lib['type'] == 'depletion_chain':
+                        break
+                else:
+                    raise IOError(
+                        "No chain specified, either manually or "
+                        "under depletion_chain in environment variable "
+                        "OPENMC_CROSS_SECTIONS.")
+                chain_file = lib['path']
+            else:
+                warn("Use of OPENMC_DEPLETE_CHAIN is deprecated in favor "
+                     "of adding depletion_chain to OPENMC_CROSS_SECTIONS",
+                     FutureWarning)
         self.chain = Chain.from_xml(chain_file)
 
     @abstractmethod

openmc/deplete/chain.py

@@ -107,7 +107,8 @@ class Chain(object):
     yield sublibrary files. The depletion chain used during a depletion
     simulation is indicated by either an argument to
     :class:`openmc.deplete.Operator` or through the
-    :envvar:`OPENMC_DEPLETE_CHAIN` environment variable.
+    ``depletion_chain`` item in the :envvar:`OPENMC_CROSS_SECTIONS`
+    environment variable.
 
     Attributes
     ----------

openmc/deplete/operator.py

@@ -64,8 +64,9 @@ class Operator(TransportOperator):
     settings : openmc.Settings
         OpenMC Settings object
     chain_file : str, optional
-        Path to the depletion chain XML file.  Defaults to the
-        :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+        Path to the depletion chain XML file.  Defaults to the file
+        listed under ``depletion_chain`` in
+        :envvar:`OPENMC_CROSS_SECTIONS` environment variable.
     prev_results : ResultsList, optional
         Results from a previous depletion calculation. If this argument is
         specified, the depletion calculation will start from the latest state

openmc/model/model.py

@@ -133,8 +133,9 @@ class Model(object):
             Array of timesteps in units of [s]. Note that values are not
             cumulative.
         chain_file : str, optional
-            Path to the depletion chain XML file.  Defaults to the
-            :envvar:`OPENMC_DEPLETE_CHAIN` environment variable if it exists.
+            Path to the depletion chain XML file.  Defaults to the chain
+            found under the ``depletion_chain`` in the
+            :envvar:`OPENMC_CROSS_SECTIONS` environment variable if it exists.
         method : str
              Integration method used for depletion (e.g., 'cecm', 'predictor')
         **kwargs

tests/unit_tests/test_data_misc.py

@@ -2,6 +2,7 @@
 
 from collections.abc import Mapping
 import os
+from pathlib import Path
 
 import numpy as np
 import pytest
@@ -33,6 +34,30 @@ def test_data_library(tmpdir):
     assert new_lib.libraries[-1]['type'] == 'thermal'
 
 
+def test_depletion_chain_data_library(run_in_tmpdir):
+    dep_lib = openmc.data.DataLibrary.from_xml()
+    prev_len = len(dep_lib.libraries)
+    chain_path = Path(__file__).parents[1] / "chain_simple.xml"
+    dep_lib.register_file(chain_path)
+    assert len(dep_lib.libraries) == prev_len + 1
+    # Inspect
+    dep_dict = dep_lib.libraries[-1]
+    assert dep_dict['materials'] == []
+    assert dep_dict['type'] == 'depletion_chain'
+    assert dep_dict['path'] == str(chain_path)
+
+    out_path = "cross_section_chain.xml"
+    dep_lib.export_to_xml(out_path)
+
+    dep_import = openmc.data.DataLibrary.from_xml(out_path)
+    for lib in reversed(dep_import.libraries):
+        if lib['type'] == 'depletion_chain':
+            break
+    else:
+        raise IndexError("depletion_chain not found in exported DataLibrary")
+    assert os.path.exists(lib['path'])
+
+
 def test_linearize():
     """Test linearization of a continuous function."""
     x, y = openmc.data.linearize([-1., 1.], lambda x: 1 - x*x)

tests/unit_tests/test_deplete_operator.py

@@ -0,0 +1,70 @@
+"""Basic unit tests for openmc.deplete.Operator instantiation
+
+Modifies and resets environment variable OPENMC_CROSS_SECTIONS
+to a custom file with new depletion_chain node
+"""
+
+from os import environ
+from unittest import mock
+from pathlib import Path
+
+import pytest
+from openmc.deplete.abc import TransportOperator
+from openmc.deplete.chain import Chain
+
+BARE_XS_FILE = "bare_cross_sections.xml"
+CHAIN_PATH = Path(__file__).parents[1] / "chain_simple.xml"
+
+
+@pytest.fixture()
+def bare_xs(run_in_tmpdir):
+    """Create a very basic cross_sections file, return simple Chain.
+
+    """
+
+    bare_xs_contents = """<?xml version="1.0"?>
+<cross_sections>
+  <depletion_chain path="{}" />
+</cross_sections>
+""".format(CHAIN_PATH)
+
+    with open(BARE_XS_FILE, "w") as out:
+        out.write(bare_xs_contents)
+
+    yield
+
+
+class BareDepleteOperator(TransportOperator):
+    """Very basic class for testing the initialization."""
+
+    # declare abstract methods so object can be created
+    def __call__(self, *args, **kwargs):
+        pass
+
+    def initial_condition(self):
+        pass
+
+    def get_results_info(self):
+        pass
+
+
+@mock.patch.dict(environ, {"OPENMC_CROSS_SECTIONS": BARE_XS_FILE})
+def test_operator_init(bare_xs):
+    """The test will set and unset environment variable OPENMC_CROSS_SECTIONS
+    to point towards a temporary dummy file. This file will be removed
+    at the end of the test, and only contains a
+    depletion_chain node."""
+    # force operator to read from OPENMC_CROSS_SECTIONS
+    bare_op = BareDepleteOperator(chain_file=None)
+    act_chain = bare_op.chain
+    ref_chain = Chain.from_xml(CHAIN_PATH)
+    assert len(act_chain) == len(ref_chain)
+    for name in ref_chain.nuclide_dict:
+        # compare openmc.deplete.Nuclide objects
+        ref_nuc = ref_chain[name]
+        act_nuc = act_chain[name]
+        for prop in [
+                'name', 'half_life', 'decay_energy', 'reactions',
+                'decay_modes', 'yield_data', 'yield_energies',
+                ]:
+            assert getattr(act_nuc, prop) == getattr(ref_nuc, prop), prop