Allow user control over Operator.dilute_initial

Users can now pass dilute_initial as an input
argument into the Operator, and directly set
Operator.dilute_initial. Documentation was updated to
include units on the initial default concentration, which
is 1000 atoms per cubic centimeter. The user is allowed
to set this value to zero.

Notes have been added to ResultsList.get_atoms
and get_reaction_rate methods, indicating why there may
be non-zero values when pulling data for isotopes not
initially present.
A similar note was added to the depletion_results.h5
io format file.

Closes #1288

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