Added XML Schema chain validation functionality

openmc/deplete/chain.py

@@ -17,7 +17,8 @@
 
 import lxml.etree as ET
 import scipy.sparse as sp
-
+import xmlschema
+
 from openmc.checkvalue import check_type, check_greater_than, PathLike
 from openmc.data import gnds_name, zam
 from openmc.exceptions import DataError
@@ -26,6 +27,8 @@
 import openmc.data
 
 
+# Name of the XML schema file
+XML_SCHEMA = "openmc_chain_schemas.xsd"
 # tuple of (possible MT values, secondaries)
 ReactionInfo = namedtuple('ReactionInfo', ('mts', 'secondaries'))
 
@@ -544,7 +547,7 @@ def from_xml(cls, filename, fission_q=None):
 
         """
         chain = cls()
-
+        Chain.validate(filename)
         if fission_q is not None:
             check_type("fission_q", fission_q, Mapping)
         else:
@@ -1043,19 +1046,23 @@ def fission_yields(self, yields):
                 yields = [yields]
             check_type("fission_yields", yields, Iterable, Mapping)
         self._fission_yields = yields
-
-    def validate(self, strict=True, quiet=False, tolerance=1e-4):
+
+    @staticmethod
+    def validate(filename, strict=True, quiet=False, tolerance = None):
         """Search for possible inconsistencies
 
         The following checks are performed for all nuclides present:
-
-            1) For all non-fission reactions, does the sum of branching
+
+            1) The XML file structure is validated against an XMLSchema 
+            2) For all non-fission reactions, does the sum of branching
                ratios equal about one?
-            2) For fission reactions, does the sum of fission yield
+            3) For fission reactions, does the sum of fission yield
                fractions equal about two?
 
         Parameters
         ----------
+        filename : str
+            Path of the XML file that needs to be validated
         strict : bool, optional
             Raise exceptions at the first inconsistency if true.
             Otherwise mark a warning
@@ -1084,16 +1091,40 @@ def validate(self, strict=True, quiet=False, tolerance=1e-4):
         --------
         openmc.deplete.Nuclide.validate
         """
-        check_type("tolerance", tolerance, Real)
-        check_greater_than("tolerance", tolerance, 0.0, True)
+        msg_func = ("Nuclide {name} caused the following error: {e}").format
+        xml_tree = ET.parse(filename)
+        schema_info =  Path(__file__).parent / XML_SCHEMA
         valid = True
-        # Sort through nuclides by name
-        for name in sorted(self.nuclide_dict):
-            stat = self[name].validate(strict, quiet, tolerance)
-            if quiet and not stat:
-                return stat
-            valid = valid and stat
-        return valid
+        if tolerance:
+            check_type("tolerance", tolerance, Real)
+            check_greater_than("tolerance", tolerance, 0.0, True)
+            xsd_text = schema_info.read_text()
+            schema_info = re.sub(r"0\.0001", str(tolerance), xsd_text)
+
+        schema = xmlschema.XMLSchema11(schema_info)
+        # Get all the validation errors
+        errors = list(schema.iter_errors(xml_tree))
+        if errors:
+            for e in errors:
+                # Get the element that caused the error
+                elem = e.elem
+                parent = elem
+                # Find parent Nuclide tag
+                while parent is not None and parent.tag != "nuclide":
+                    parent = parent.getparent()
+                # Get Nuclide name
+                name = parent.get("name") 
+                msg = msg_func(name=name, e=e.message)
+                if strict:
+                    raise ValueError(msg)
+                elif quiet:
+                    valid = False
+                    continue
+                else:
+                    warn(msg)
+                    valid = False
+
+        return valid 
 
     def reduce(self, initial_isotopes, level=None):
         """Reduce the size of the chain by following transmutation paths

openmc/deplete/openmc_chain_schemas.xsd

@@ -0,0 +1,142 @@
+<?xml version="1.0"?>
+<xs:schema 
+    xmlns:xs="http://www.w3.org/2001/XMLSchema"
+    xmlns:vc="http://www.w3.org/2007/XMLSchema-versioning"
+    vc:minVersion="1.1">
+    <xs:annotation>
+        <xs:documentation>
+            Author: Lorenzo Canzian, newcleo Spa, Italy
+            Date: 2025-09-25
+        </xs:documentation>
+    </xs:annotation>
+
+    <xs:element name="depletion_chain" type="chain"/> 
+
+    <xs:complexType name="chain">
+        <xs:annotation>
+            <xs:documentation xml:lang="en">Inside the depletion chain (root tag) one can have unlimited nuclide tags</xs:documentation>
+        </xs:annotation>
+        <xs:sequence>
+            <xs:element name="nuclide" type="nuclideinfo" maxOccurs="unbounded"/>
+
+        </xs:sequence>
+    </xs:complexType>
+
+    <xs:simpleType name="dataListType">
+        <xs:list itemType="xs:double"/>
+    </xs:simpleType>
+
+    <xs:complexType name="nuclideinfo">
+
+        <xs:choice maxOccurs="unbounded">
+            <xs:annotation>
+                <xs:documentation xml:lang="en">Each nuclide can have multiple possibile interactions, so there are unlimited choices between different kind of tags</xs:documentation>
+            </xs:annotation>
+            <xs:element name="decay" maxOccurs="unbounded" minOccurs="0">
+                <xs:annotation>
+                    <xs:documentation xml:lang="en">Decay tag contains informations about the decay channel of the nuclide. We have three attributes:
+                        type of decay, target produced, branching ratio. Type of decays include (name, (A_change, Z_change))
+                        0: ('gamma', (0, 0)),
+                        1: ('beta-', (0, 1)),
+                        2: ('ec/beta+', (0, -1)),
+                        3: ('IT', (0, 0)),
+                        4: ('alpha', (-4, -2)),
+                        5: ('n', (-1, 0)),
+                        6: ('sf', None),
+                        7: ('p', (-1, -1)),
+                        8: ('e-', (0, 0)),
+                        9: ('xray', (0, 0)),    
+                        10: ('unknown', None)
+                    </xs:documentation>
+                </xs:annotation>
+                <xs:complexType>                    
+                    <xs:attribute name="type" type="xs:string" use="required"/>
+                    <xs:attribute name="target" type="xs:string" use="optional"/>
+                    <xs:attribute name="branching_ratio" type="xs:decimal" use="required"/>                    
+                </xs:complexType>
+            </xs:element>
+
+            <xs:element name="reaction" maxOccurs="unbounded" minOccurs="0">
+                <xs:annotation>
+                    <xs:documentation xml:lang="en">Reaction tag contains informations about the transmutation channel of the nuclide. There are four possible attributes:
+                    type of reaction, target produced, Q value, branching ratio. Reactions are written as (n,2n), (n,fission),(n,gamma),(n,p), etc...
+                    </xs:documentation>
+                </xs:annotation>
+                <xs:complexType>                        
+                    <xs:attribute name="type" type="xs:string" use="required"/>
+                    <xs:attribute name="target" type="xs:string" use="optional"/>                
+                    <xs:attribute name="Q" type="xs:decimal" use="optional"/>  
+                    <xs:attribute name="branching_ratio" type="xs:decimal" use="optional"/>    
+                </xs:complexType>
+            </xs:element>
+
+            <xs:element name="source" maxOccurs="unbounded" minOccurs="0">
+                <xs:annotation>
+                    <xs:documentation xml:lang="en">Source tag contains informations about other particles produced during decays of the nuclide. There are three attributes:
+                    type, particle produced, interpolation. We also have another nested tag named parameter which contain the parameters linked to the particle emission
+                    </xs:documentation>
+                </xs:annotation>
+                <xs:complexType>                                   
+                    <xs:sequence>         
+                        <xs:element name="parameters">
+                            <xs:annotation>
+                                <xs:documentation xml:lang="en">First half are photon energies (in eV), second half are intensities (probabilities of emission)</xs:documentation>
+                            </xs:annotation>                      
+                            <xs:simpleType>
+                                <xs:list itemType="xs:string"/>
+                            </xs:simpleType>
+                        </xs:element>
+                    </xs:sequence>
+                    <xs:attribute name="type" type="xs:string" use="required"/>
+                    <xs:attribute name="particle" type="xs:string" use="required"/>  
+                    <xs:attribute name="interpolation" type="xs:string" use="optional"/>  
+                </xs:complexType>
+            </xs:element>
+
+            <xs:element name="neutron_fission_yields" maxOccurs="unbounded" minOccurs="0">
+            <xs:annotation>
+                <xs:documentation xml:lang="en">Fission_yields tag contains informations about the products of a fission and the relative fission yields
+                </xs:documentation>
+            </xs:annotation>
+            <xs:complexType>
+                <xs:sequence minOccurs="0">
+                <xs:element name="energies" minOccurs="0">
+                    <xs:simpleType>
+                        <xs:list itemType="xs:double"/>
+                    </xs:simpleType>
+                </xs:element>
+                <xs:element name="fission_yields" maxOccurs="unbounded" minOccurs="0">
+                    <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="products" minOccurs="0">
+                        <xs:simpleType>
+                            <xs:list itemType="xs:string"/>
+                        </xs:simpleType>
+                        </xs:element>
+                        <xs:element name="data" minOccurs="0">
+                            <xs:complexType>
+                                    <xs:simpleContent>
+                                        <xs:extension base="dataListType">
+                                            <xs:assert test="abs(sum(for $x in tokenize(., '\s+') return number($x)) - 2) &lt; 0.0001"/>
+                                        </xs:extension>
+                                    </xs:simpleContent>
+                                </xs:complexType>
+                        </xs:element>
+                    </xs:sequence>
+                    <xs:attribute name="energy" type="xs:double"/>
+                    </xs:complexType>
+                </xs:element>
+                </xs:sequence>
+                <xs:attribute name="parent" type="xs:string" use="optional"/>
+            </xs:complexType>
+            </xs:element>
+        </xs:choice>
+        <xs:attribute name="name" type="xs:string" use="required"/>
+        <xs:attribute name="half_life" type="xs:string" use="optional"/>
+        <xs:attribute name="decay_modes" type="xs:integer" use="optional"/>
+        <xs:attribute name="decay_energy" type="xs:decimal" use="optional"/>
+        <xs:attribute name="reactions" type="xs:integer" use="optional"/>
+        <xs:assert test="not(decay) or abs(sum(decay/@branching_ratio) - 1) &lt; 0.001" />
+        <xs:assert test="not(reaction) or abs(sum(reaction/@branching_ratio) - 1) &lt; 0.001 or sum(reaction/@branching_ratio) &lt; 0.001" />
+    </xs:complexType>
+</xs:schema>

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     "uncertainties",
     "setuptools",
     "endf",
+    "xmlschema"
 ]
 
 [project.optional-dependencies]

tests/chain_simple.xml

@@ -28,7 +28,7 @@
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
         <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>1.093250e-04 2.087260e-04 2.780820e-02 6.759540e-03 2.392300e-02 4.356330e-05</data>
+        <data>1.093250e-04 2.087260e-04 2.780820e-02 6.759540e-03 2.392300e-02 1.9411915633</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>
@@ -41,7 +41,7 @@
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
         <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>6.142710e-5 1.483250e-04 0.0292737 0.002566345 0.0219242 4.9097e-6</data>
+        <data>6.142710e-5 1.483250e-04 0.0292737 0.002566345 0.0219242 1.9460259097</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>
@@ -53,8 +53,8 @@
     <neutron_fission_yields>
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
-        <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>4.141120e-04 7.605360e-04 0.0135457 0.00026864 0.0024432 3.7100E-07</data>
+        <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135 Am241</products>
+        <data>4.141120e-04 7.605360e-04 0.0135457 0.00026864 0.0024432 1.982567371</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>

tests/chain_simple_decay.xml

@@ -33,7 +33,7 @@
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
         <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>1.093250e-04 2.087260e-04 2.780820e-02 6.759540e-03 2.392300e-02 4.356330e-05</data>
+        <data>1.093250e-04 2.087260e-04 2.780820e-02 6.759540e-03 2.392300e-02 1.94119120899</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>
@@ -46,7 +46,7 @@
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
         <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>6.142710e-5 1.483250e-04 0.0292737 0.002566345 0.0219242 4.9097e-6</data>
+        <data>6.142710e-5 1.483250e-04 0.0292737 0.002566345 0.0219242 1.9458259979</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>
@@ -59,7 +59,7 @@
       <energies>2.53000e-02</energies>
       <fission_yields energy="2.53000e-02">
         <products>Gd157 Gd156 I135 Xe135 Xe136 Cs135</products>
-        <data>4.141120e-04 7.605360e-04 0.0135457 0.00026864 0.0024432 3.7100E-07</data>
+        <data>4.141120e-04 7.605360e-04 0.0135457 0.00026864 0.0024432 1.982567812</data>
       </fission_yields>
     </neutron_fission_yields>
   </nuclide>