Fission Product Model with Explicit Fission Products for all Depletab…

…le Components (#1067)

* Update the fission product model to fix a bug where all
nuclides were not being initialized in non-fuel depletable
components when using the `explicitFissionProducts` model.

Add testing for the updated implementation.

* Update release notes

* Bug fix

* Update interactDistributeState

* Skip nuclides with 0 ndens in reaction rate calc

* Black formatting

* Add limiter on the interactCoupled method for the LatticePhysicsInterface to only run coupled cross section generation at time node 0.

* Address reviewer comment

* Update docstring

* Add dummy nuclides for all XS types

* Fix dummy nuclides for ISOTXS

* Improve test coverage.

* More test coverage

* Black formatting

* Rename files to test file path case sensitivity on Linux

* Update expected filename to be all caps

* One last name update. Sorry, can't test this locally on Windows!

Co-authored-by: Arrielle Opotowsky <c-aopotowsky@terrapower.com>
Co-authored-by: Michael Jarrett <mjarrett@terrapower.com>

armi/nuclearDataIO/cccc/isotxs.py

@@ -133,6 +133,59 @@ def compareNuclideXS(nuc1, nuc2, tolerance=0.0, verbose=False):
     return equal
 
 
+def addDummyNuclidesToLibrary(lib, dummyNuclides):
+    """
+    This method adds DUMMY nuclides to the current ISOTXS library.
+
+    Parameters
+    ----------
+    lib : obj
+        ISOTXS library object
+
+    dummyNuclides: list
+        List of DUMMY nuclide objects that will be copied and added to the GAMISO file
+
+    Notes
+    -----
+    Since MC2-3 does not write DUMMY nuclide information for GAMISO files, this is necessary to provide a
+    consistent set of nuclide-level data across all the nuclides in a
+    :py:class:`~armi.nuclearDataIO.xsLibraries.XSLibrary`.
+    """
+    if not dummyNuclides:
+        runLog.important("No dummy nuclide data provided to be added to {}".format(lib))
+        return False
+    elif len(lib.xsIDs) > 1:
+        runLog.warning(
+            "Cannot add dummy nuclide data to ISOTXS library {} containing data for more than 1 XS ID.".format(
+                lib
+            )
+        )
+        return False
+
+    dummyNuclideKeysAddedToLibrary = []
+    for dummyNuclide in dummyNuclides:
+        dummyKey = dummyNuclide.nucLabel
+        if len(lib.xsIDs):
+            dummyKey += lib.xsIDs[0]
+        if dummyKey in lib:
+            continue
+
+        newDummy = xsNuclides.XSNuclide(lib, dummyKey)
+        # Copy isotxs metadata from the isotxs metadata of the given dummy nuclide
+        for kk, vv in dummyNuclide.isotxsMetadata.items():
+            if kk in ["jj", "jband"]:
+                newDummy.isotxsMetadata[kk] = {}
+                for mm in vv:
+                    newDummy.isotxsMetadata[kk][mm] = 1
+            else:
+                newDummy.isotxsMetadata[kk] = vv
+
+        lib[dummyKey] = newDummy
+        dummyNuclideKeysAddedToLibrary.append(dummyKey)
+
+    return any(dummyNuclideKeysAddedToLibrary)
+
+
 class _IsotxsIO(cccc.Stream):
     """
     A semi-abstract stream for reading and writing to a :py:class:`~armi.nuclearDataIO.isotxs.Isotxs`.
@@ -313,10 +366,10 @@ def _computeNuclideRecordOffset(self):
         This is not used within ARMI, because it can compute it arbitrarily. Other codes use this to seek to a
         specific position within an ISOTXS file.
         """
-        recordsPerNuclude = [
+        recordsPerNuclide = [
             self._computeNumIsotxsRecords(nuc) for nuc in self._lib.nuclides
         ]
-        return [sum(recordsPerNuclude[0:ii]) for ii in range(len(self._lib))]
+        return [sum(recordsPerNuclide[0:ii]) for ii in range(len(self._lib))]
 
     def _computeNumIsotxsRecords(self, nuclide):
         """Compute the number of ISOTXS records for a specific nuclide."""

armi/nuclearDataIO/cccc/tests/test_gamiso.py

@@ -24,7 +24,7 @@
 
 THIS_DIR = os.path.dirname(__file__)
 FIXTURE_DIR = os.path.join(THIS_DIR, "..", "..", "tests", "fixtures")
-GAMISO_AA = os.path.join(FIXTURE_DIR, "mc2v3-AA.gamiso")
+GAMISO_AA = os.path.join(FIXTURE_DIR, "AA.GAMISO")
 
 
 class TestGamiso(unittest.TestCase):

armi/nuclearDataIO/tests/.gitignore

@@ -1,6 +1,3 @@
-*isotxs*
-*gamiso*
-*pmatrx*
 *dlayxs*
 *.out
 *.sum

armi/nuclearDataIO/tests/test_xsLibraries.py

@@ -40,18 +40,18 @@
 # CCCC fixtures are less fancy than these merging ones.
 FIXTURE_DIR_CCCC = os.path.join(os.path.dirname(isotxs.__file__), "tests", "fixtures")
 
-ISOTXS_AA = os.path.join(FIXTURE_DIR, "mc2v3-AA.isotxs")
-ISOTXS_AB = os.path.join(FIXTURE_DIR, "mc2v3-AB.isotxs")
+ISOTXS_AA = os.path.join(FIXTURE_DIR, "ISOAA")
+ISOTXS_AB = os.path.join(FIXTURE_DIR, "ISOAB")
 ISOTXS_AA_AB = os.path.join(FIXTURE_DIR, "combined-AA-AB.isotxs")
 ISOTXS_LUMPED = os.path.join(FIXTURE_DIR, "combined-and-lumped-AA-AB.isotxs")
 
-PMATRX_AA = os.path.join(FIXTURE_DIR, "mc2v3-AA.pmatrx")
-PMATRX_AB = os.path.join(FIXTURE_DIR, "mc2v3-AB.pmatrx")
+PMATRX_AA = os.path.join(FIXTURE_DIR, "AA.PMATRX")
+PMATRX_AB = os.path.join(FIXTURE_DIR, "AB.PMATRX")
 PMATRX_AA_AB = os.path.join(FIXTURE_DIR, "combined-AA-AB.pmatrx")
 PMATRX_LUMPED = os.path.join(FIXTURE_DIR, "combined-and-lumped-AA-AB.pmatrx")
 
-GAMISO_AA = os.path.join(FIXTURE_DIR, "mc2v3-AA.gamiso")
-GAMISO_AB = os.path.join(FIXTURE_DIR, "mc2v3-AB.gamiso")
+GAMISO_AA = os.path.join(FIXTURE_DIR, "AA.GAMISO")
+GAMISO_AB = os.path.join(FIXTURE_DIR, "AB.GAMISO")
 GAMISO_AA_AB = os.path.join(FIXTURE_DIR, "combined-AA-AB.gamiso")
 GAMISO_LUMPED = os.path.join(FIXTURE_DIR, "combined-and-lumped-AA-AB.gamiso")
 
@@ -260,7 +260,7 @@ def test_mergeFailsWithNonIsotxsFiles(self):
                 lib = xsLibraries.IsotxsLibrary()
                 xsLibraries.mergeXSLibrariesInWorkingDirectory(lib)
                 self.assertIn(
-                    f"Ignoring file {dummyFileName} in the merging of ISOXX files",
+                    f"{dummyFileName} in the merging of ISOXX files",
                     log.getStdoutValue(),
                 )
         finally:
@@ -401,8 +401,6 @@ def assert_contains_only(self, container, shouldBeThere, shouldNotBeThere):
         self.assertEqual(set(), container & set(shouldNotBeThere))
 
 
-# LOOK OUT, THIS GETS DELETED LATER ON SO IT DOESN'T RUN... IT IS AN ABSTRACT CLASS!!
-# LOOK OUT, THIS GETS DELETED LATER ON SO IT DOESN'T RUN... IT IS AN ABSTRACT CLASS!!
 # LOOK OUT, THIS GETS DELETED LATER ON SO IT DOESN'T RUN... IT IS AN ABSTRACT CLASS!!
 class TestXSlibraryMerging(unittest.TestCase, TempFileMixin):
     """A shared class that defines tests that should be true for all IsotxsLibrary merging."""
@@ -604,6 +602,57 @@ def getLibLumpedPath(self):
         return GAMISO_LUMPED
 
 
+class Combined_merge_Tests(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.isotxsAA = None
+        cls.isotxsAB = None
+        cls.gamisoAA = None
+        cls.gamisoAB = None
+        cls.pmatrxAA = None
+        cls.pmatrxAB = None
+        cls.libCombined = None
+
+    @classmethod
+    def tearDownClass(cls):
+        cls.isotxsAA = None
+        cls.isotxsAB = None
+        cls.gamisoAA = None
+        cls.gamisoAB = None
+        cls.pmatrxAA = None
+        cls.pmatrxAB = None
+        cls.libCombined = None
+        del cls.isotxsAA
+        del cls.isotxsAB
+        del cls.gamisoAA
+        del cls.gamisoAB
+        del cls.pmatrxAA
+        del cls.pmatrxAB
+        del cls.libCombined
+
+    def setUp(self):
+        # load a library that is in the ARMI tree. This should
+        # be a small library with LFPs, Actinides, structure, and coolant
+        for attrName, path, readFunc in [
+            ("isotxsAA", ISOTXS_AA, isotxs.readBinary),
+            ("gamisoAA", GAMISO_AA, gamiso.readBinary),
+            ("pmatrxAA", PMATRX_AA, pmatrx.readBinary),
+            ("isotxsAB", ISOTXS_AB, isotxs.readBinary),
+            ("gamisoAB", GAMISO_AB, gamiso.readBinary),
+            ("pmatrxAB", PMATRX_AB, pmatrx.readBinary),
+            ("libCombined", ISOTXS_AA_AB, isotxs.readBinary),
+        ]:
+            if getattr(self.__class__, attrName) is None:
+                setattr(self.__class__, attrName, readFunc(path))
+
+    def test_mergeAllXSLibFiles(self):
+        lib = xsLibraries.IsotxsLibrary()
+        xsLibraries.mergeXSLibrariesInWorkingDirectory(
+            lib, xsLibrarySuffix="", mergeGammaLibs=True, alternateDirectory=FIXTURE_DIR
+        )
+        self.assertEqual(set(lib.nuclideLabels), set(self.libCombined.nuclideLabels))
+
+
 # Remove the abstract class, so that it does not run (all tests would fail)
 del TestXSlibraryMerging
 

armi/nuclearDataIO/xsLibraries.py

@@ -27,6 +27,7 @@
 from armi import runLog
 from armi.nucDirectory import nuclideBases
 from armi.nuclearDataIO.nuclearFileMetadata import NuclideXSMetadata, RegionXSMetadata
+from armi.nuclearDataIO import xsNuclides
 from armi.utils import properties
 
 _ISOTXS_EXT = "ISO"
@@ -144,10 +145,22 @@ def getISOTXSLibrariesToMerge(xsLibrarySuffix, xsLibFileNames):
     return isosToMerge
 
 
-def mergeXSLibrariesInWorkingDirectory(lib, xsLibrarySuffix="", mergeGammaLibs=False):
+def mergeXSLibrariesInWorkingDirectory(
+    lib,
+    xsLibrarySuffix="",
+    mergeGammaLibs=False,
+    alternateDirectory=None,
+):
     """
     Merge neutron (ISOTXS) and gamma (GAMISO/PMATRX) library data into the provided library.
 
+    Notes
+    -----
+    Convention is for fuel XS id to come first alphabetically (A, B, C, etc.) and then be
+    followed by non-fuel. This should allow `referenceDummyNuclide` to be defined before
+    it is needed by a non-fuel cross section, but if the convention is not followed then
+    this could cause an issue.
+
     Parameters
     ----------
     lib : obj
@@ -161,18 +174,25 @@ def mergeXSLibrariesInWorkingDirectory(lib, xsLibrarySuffix="", mergeGammaLibs=F
     mergeGammaLibs : bool, optional
         If True, the GAMISO and PMATRX files that correspond to the ISOTXS library will be merged. Note: if these
         files do not exist this will fail.
+
+    alternateDirectory : str, optional
+        An alternate directory in which to search for files other than the working directory. The main purpose
+        of this is for testing, but it could also be useful to users.
     """
     # pylint: disable=import-outside-toplevel) ; avoid cyclic import with isotxs bringing this in for data structure
     from armi.nuclearDataIO.cccc import isotxs
     from armi.nuclearDataIO.cccc import gamiso
     from armi.nuclearDataIO.cccc import pmatrx
     from armi import nuclearDataIO
 
+    baseDir = alternateDirectory or os.getcwd()
+    globPath = os.path.join(baseDir, _ISOTXS_EXT + "*")
     xsLibFiles = getISOTXSLibrariesToMerge(
-        xsLibrarySuffix, [iso for iso in glob.glob(_ISOTXS_EXT + "*")]
+        xsLibrarySuffix, [iso for iso in glob.glob(globPath)]
     )
     librariesToMerge = []
     neutronVelocities = {}  # Dictionary of neutron velocities from each ISOTXS file
+    referenceDummyNuclides = None
     for xsLibFilePath in sorted(xsLibFiles):
         try:
             xsID = re.search("ISO([A-Z0-9]{2})", xsLibFilePath).group(
@@ -197,21 +217,48 @@ def mergeXSLibrariesInWorkingDirectory(lib, xsLibrarySuffix="", mergeGammaLibs=F
                 )
             )
             continue
+
         neutronLibrary = isotxs.readBinary(xsLibFilePath)
         neutronVelocities[xsID] = neutronLibrary.neutronVelocity
-        librariesToMerge.append(neutronLibrary)
+
+        dummyNuclidesInNeutron = [
+            nuc
+            for nuc in neutronLibrary.nuclides
+            if isinstance(nuc._base, nuclideBases.DummyNuclideBase)
+        ]
+        if not dummyNuclidesInNeutron:
+            runLog.info(f"Adding dummy nuclides to library {xsID}")
+            addedDummyData = isotxs.addDummyNuclidesToLibrary(
+                neutronLibrary, referenceDummyNuclides
+            )  # Add DUMMY nuclide data not produced by MC2-3
+            isotxsLibraryPath = os.path.join(
+                baseDir,
+                nuclearDataIO.getExpectedISOTXSFileName(
+                    suffix=xsLibrarySuffix, xsID=xsID
+                ),
+            )
+            isotxsDummyPath = isotxsLibraryPath
+            isotxs.writeBinary(neutronLibrary, isotxsDummyPath)
+            neutronLibraryDummyData = isotxs.readBinary(isotxsDummyPath)
+            librariesToMerge.append(neutronLibraryDummyData)
+            dummyNuclidesInNeutron = referenceDummyNuclides
+        else:
+            librariesToMerge.append(neutronLibrary)
+            if not referenceDummyNuclides:
+                referenceDummyNuclides = dummyNuclidesInNeutron
+
         if mergeGammaLibs:
-            dummyNuclides = [
-                nuc
-                for nuc in neutronLibrary.nuclides
-                if isinstance(nuc._base, nuclideBases.DummyNuclideBase)
-            ]
-
-            gamisoLibraryPath = nuclearDataIO.getExpectedGAMISOFileName(
-                suffix=xsLibrarySuffix, xsID=xsID
+            gamisoLibraryPath = os.path.join(
+                baseDir,
+                nuclearDataIO.getExpectedGAMISOFileName(
+                    suffix=xsLibrarySuffix, xsID=xsID
+                ),
             )
-            pmatrxLibraryPath = nuclearDataIO.getExpectedPMATRXFileName(
-                suffix=xsLibrarySuffix, xsID=xsID
+            pmatrxLibraryPath = os.path.join(
+                baseDir,
+                nuclearDataIO.getExpectedPMATRXFileName(
+                    suffix=xsLibrarySuffix, xsID=xsID
+                ),
             )
 
             # Check if the gamiso and pmatrx data paths exist with the xs library suffix so that
@@ -226,18 +273,20 @@ def mergeXSLibrariesInWorkingDirectory(lib, xsLibrarySuffix="", mergeGammaLibs=F
                     f"Attempting to find GAMISO/PMATRX data with "
                     f"only XS ID {xsID} instead."
                 )
-                gamisoLibraryPath = nuclearDataIO.getExpectedGAMISOFileName(xsID=xsID)
-                pmatrxLibraryPath = nuclearDataIO.getExpectedPMATRXFileName(xsID=xsID)
+                gamisoLibraryPath = os.path.join(
+                    baseDir, nuclearDataIO.getExpectedGAMISOFileName(xsID=xsID)
+                )
+                pmatrxLibraryPath = os.path.join(
+                    baseDir, nuclearDataIO.getExpectedPMATRXFileName(xsID=xsID)
+                )
 
             # GAMISO data
             gammaLibrary = gamiso.readBinary(gamisoLibraryPath)
             addedDummyData = gamiso.addDummyNuclidesToLibrary(
-                gammaLibrary, dummyNuclides
+                gammaLibrary, dummyNuclidesInNeutron
             )  # Add DUMMY nuclide data not produced by MC2-3
             if addedDummyData:
-                gamisoDummyPath = os.path.abspath(
-                    os.path.join(os.getcwd(), gamisoLibraryPath)
-                )
+                gamisoDummyPath = gamisoLibraryPath
                 gamiso.writeBinary(gammaLibrary, gamisoDummyPath)
                 gammaLibraryDummyData = gamiso.readBinary(gamisoDummyPath)
                 librariesToMerge.append(gammaLibraryDummyData)
@@ -247,12 +296,10 @@ def mergeXSLibrariesInWorkingDirectory(lib, xsLibrarySuffix="", mergeGammaLibs=F
             # PMATRX data
             pmatrxLibrary = pmatrx.readBinary(pmatrxLibraryPath)
             addedDummyData = pmatrx.addDummyNuclidesToLibrary(
-                pmatrxLibrary, dummyNuclides
+                pmatrxLibrary, dummyNuclidesInNeutron
             )  # Add DUMMY nuclide data not produced by MC2-3
             if addedDummyData:
-                pmatrxDummyPath = os.path.abspath(
-                    os.path.join(os.getcwd(), pmatrxLibraryPath)
-                )
+                pmatrxDummyPath = pmatrxLibraryPath
                 pmatrx.writeBinary(pmatrxLibrary, pmatrxDummyPath)
                 pmatrxLibraryDummyData = pmatrx.readBinary(pmatrxDummyPath)
                 librariesToMerge.append(pmatrxLibraryDummyData)