Merge pull request #1301 from drewejohnson/feat-op-dilute

Allow user control over initial concentration for trace isotopes

docs/source/io_formats/depletion_results.rst

@@ -44,3 +44,10 @@ The current version of the depletion results file format is 1.0.
 **/reactions/<name>/**
 
 :Attributes: - **index** (*int*) -- Index user in results for this reaction
+
+.. note::
+
+    The reaction rates for some isotopes not originally present may
+    be non-zero, but should be negligible compared to other atoms.
+    This can be controlled by changing the
+    :class:`openmc.deplete.Operator` ``dilute_initial`` attribute.

openmc/deplete/abc.py

@@ -10,11 +10,12 @@ from pathlib import Path
 from abc import ABC, abstractmethod
 from xml.etree import ElementTree as ET
 from warnings import warn
+from numbers import Real
 
 from numpy import nonzero, empty
 
 from openmc.data import DataLibrary, JOULE_PER_EV
-from openmc.checkvalue import check_type
+from openmc.checkvalue import check_type, check_greater_than
 from .chain import Chain
 
 OperatorResult = namedtuple('OperatorResult', ['k', 'rates'])
@@ -55,17 +56,21 @@ class TransportOperator(ABC):
     fission_q : dict, optional
         Dictionary of nuclides and their fission Q values [eV]. If not given,
         values will be pulled from the ``chain_file``.
+    dilute_initial : float, optional
+        Initial atom density [atoms/cm^3] to add for nuclides that are zero
+        in initial condition to ensure they exist in the decay chain.
+        Only done for nuclides with reaction rates.
+        Defaults to 1.0e3.
 
     Attributes
     ----------
     dilute_initial : float
-        Initial atom density to add for nuclides that are zero in initial
-        condition to ensure they exist in the decay chain.  Only done for
-        nuclides with reaction rates. Defaults to 1.0e3.
-
+        Initial atom density [atoms/cm^3] to add for nuclides that are zero
+        in initial condition to ensure they exist in the decay chain.
+        Only done for nuclides with reaction rates.
     """
-    def __init__(self, chain_file=None, fission_q=None):
-        self.dilute_initial = 1.0e3
+    def __init__(self, chain_file=None, fission_q=None, dilute_initial=1.0e3):
+        self.dilute_initial = dilute_initial
         self.output_dir = '.'
 
         # Read depletion chain
@@ -89,6 +94,17 @@ class TransportOperator(ABC):
                      FutureWarning)
         self.chain = Chain.from_xml(chain_file, fission_q)
 
+    @property
+    def dilute_initial(self):
+        """Initial atom density for nuclides with zero initial concentration"""
+        return self._dilute_initial
+
+    @dilute_initial.setter
+    def dilute_initial(self, value):
+        check_type("dilute_initial", value, Real)
+        check_greater_than("dilute_initial", value, 0.0, equality=True)
+        self._dilute_initial = value
+
     @abstractmethod
     def __call__(self, vec, print_out=True):
         """Runs a simulation.

openmc/deplete/operator.py

@@ -76,6 +76,11 @@ class Operator(TransportOperator):
     fission_q : dict, optional
         Dictionary of nuclides and their fission Q values [eV]. If not given,
         values will be pulled from the ``chain_file``.
+    dilute_initial : float, optional
+        Initial atom density [atoms/cm^3] to add for nuclides that are zero
+        in initial condition to ensure they exist in the decay chain.
+        Only done for nuclides with reaction rates.
+        Defaults to 1.0e3.
 
     Attributes
     ----------
@@ -84,9 +89,9 @@ class Operator(TransportOperator):
     settings : openmc.Settings
         OpenMC settings object
     dilute_initial : float
-        Initial atom density to add for nuclides that are zero in initial
-        condition to ensure they exist in the decay chain. Only done for
-        nuclides with reaction rates. Defaults to 1.0e3.
+        Initial atom density [atoms/cm^3] to add for nuclides that
+        are zero in initial condition to ensure they exist in the decay
+        chain. Only done for nuclides with reaction rates.
     output_dir : pathlib.Path
         Path to output directory to save results.
     round_number : bool
@@ -110,11 +115,11 @@ class Operator(TransportOperator):
         Results from a previous depletion calculation
     diff_burnable_mats : bool
         Whether to differentiate burnable materials with multiple instances
-
     """
     def __init__(self, geometry, settings, chain_file=None, prev_results=None,
-                 diff_burnable_mats=False, fission_q=None):
-        super().__init__(chain_file, fission_q)
+                 diff_burnable_mats=False, fission_q=None,
+                 dilute_initial=1.0e3):
+        super().__init__(chain_file, fission_q, dilute_initial)
         self.round_number = False
         self.settings = settings
         self.geometry = geometry

openmc/deplete/results_list.py

@@ -26,7 +26,15 @@ class ResultsList(list):
                 self.append(Results.from_hdf5(fh, i))
 
     def get_atoms(self, mat, nuc):
-        """Get nuclide concentration over time from a single material
+        """Get number of nuclides over time from a single material
+
+        .. note::
+
+            Initial values for some isotopes that do not appear in
+            initial concentrations may be non-zero, depending on the
+            value of :class:`openmc.deplete.Operator` ``dilute_initial``.
+            The :class:`openmc.deplete.Operator` adds isotopes according
+            to this setting, which can be set to zero.
 
         Parameters
         ----------
@@ -56,6 +64,14 @@ class ResultsList(list):
     def get_reaction_rate(self, mat, nuc, rx):
         """Get reaction rate in a single material/nuclide over time
 
+        .. note::
+
+            Initial values for some isotopes that do not appear in
+            initial concentrations may be non-zero, depending on the
+            value of :class:`openmc.deplete.Operator` ``dilute_initial``
+            The :class:`openmc.deplete.Operator` adds isotopes according
+            to this setting, which can be set to zero.
+
         Parameters
         ----------
         mat : str