mirror of
https://github.com/Cantera/cantera.git
synced 2025-02-25 18:55:29 -06:00
[ctml2yaml] Combine duplicate section ids
If a reactionData or speciesData node has a duplicated id attribute, combine the duplicate sections together. If duplicate reaction id attributes or species names are found, either warn or raise an error.
This commit is contained in:
Bryan W. Weber
@@ -2059,21 +2059,14 @@ def create_species_from_data_node(ctml_tree: etree.Element) -> Dict[str, List[Sp
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for species_data_node in ctml_tree.iterfind("speciesData"):
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this_data_node_id = species_data_node.get("id", "")
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if this_data_node_id in species:
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raise ValueError(
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"Duplicate speciesData id found: '{}'".format(this_data_node_id)
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warnings.warn(
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"Duplicate 'speciesData' id found: '{}'. Only the first section will "
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"be included in the output file.".format(this_data_node_id)
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)
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this_node_species = [] # type: List[Species]
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for species_node in species_data_node.iterfind("species"):
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this_species = Species(species_node)
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for s in this_node_species:
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if this_species.attribs["name"] == s.attribs["name"]:
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raise ValueError(
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"Duplicate specification of species '{}' in node '{}'".format(
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this_species.attribs["name"], this_data_node_id
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)
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)
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this_node_species.append(this_species)
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species[this_data_node_id] = this_node_species
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continue
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species[this_data_node_id] = [
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Species(s) for s in species_data_node.iterfind("species")
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]
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return species
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@@ -2084,18 +2077,19 @@ def create_reactions_from_data_node(
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"""Take a reactionData node and return a dictionary of Reaction objects."""
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reactions = {} # type: Dict[str, List[Reaction]]
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for reactionData_node in ctml_tree.iterfind("reactionData"):
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this_data_node_id = reactionData_node.get("id", "")
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if this_data_node_id in reactions:
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raise ValueError(
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"Duplicate reactionData id found: '{}'".format(this_data_node_id)
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)
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node_motz_wise = False
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if reactionData_node.get("motz_wise", "").lower() == "true":
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node_motz_wise = True
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this_node_reactions = [] # type: List[Reaction]
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for reaction_node in reactionData_node.iterfind("reaction"):
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this_node_reactions.append(Reaction(reaction_node, node_motz_wise))
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reactions[this_data_node_id] = this_node_reactions
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this_data_node_id = reactionData_node.get("id", "")
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if this_data_node_id in reactions:
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warnings.warn(
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"Duplicate 'reactionData' id found: '{}'. Only the first section will "
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"be included in the output file.".format(this_data_node_id)
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)
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continue
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reactions[this_data_node_id] = [
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Reaction(r, node_motz_wise) for r in reactionData_node.iterfind("reaction")
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]
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return reactions
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@@ -1186,3 +1186,15 @@ class ctml2yamlTest(utilities.CanteraTest):
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ctmlPhase, yamlPhase = self.checkConversion("Li_Liquid")
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self.checkThermo(ctmlPhase, yamlPhase, [300, 500])
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def test_duplicate_section_ids(self):
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with self.assertWarnsRegex(UserWarning, "Duplicate 'speciesData' id"):
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ctml2yaml.convert(
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Path(self.test_data_dir).joinpath("duplicate-speciesData-ids.xml"),
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Path(self.test_work_dir).joinpath("duplicate-speciesData-ids.yaml")
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)
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with self.assertWarnsRegex(UserWarning, "Duplicate 'reactionData' id"):
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ctml2yaml.convert(
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Path(self.test_data_dir).joinpath("duplicate-reactionData-ids.xml"),
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Path(self.test_work_dir).joinpath("duplicate-reactionData-ids.yaml")
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)
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89
test/data/duplicate-reactionData-ids.xml
Normal file
89
test/data/duplicate-reactionData-ids.xml
Normal file
@@ -0,0 +1,89 @@
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<?xml version="1.0"?>
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<ctml>
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<validate reactions="yes" species="yes"/>
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<!-- phase gas -->
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<phase dim="3" id="gas">
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<elementArray datasrc="elements.xml">H C</elementArray>
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<speciesArray datasrc="#species_data">R1A R1B</speciesArray>
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<reactionArray datasrc="#reaction_data"/>
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<state>
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<temperature units="K">300.0</temperature>
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<pressure units="Pa">101325.0</pressure>
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</state>
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<thermo model="IdealGas"/>
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<kinetics model="GasKinetics"/>
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<transport model="None"/>
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</phase>
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<!-- species definitions -->
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<speciesData id="species_data">
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<!-- species R1A -->
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<species name="R1A">
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<atomArray>H:4 C:1 </atomArray>
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
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1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
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-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
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</NASA>
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</thermo>
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</species>
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<!-- species R1B -->
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<species name="R1B">
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<atomArray>H:4 C:1 </atomArray>
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
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1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
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-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
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</NASA>
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</thermo>
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</species>
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</speciesData>
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<reactionData id="reaction_data">
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<!-- reaction 0001 -->
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<reaction id="0001">
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<equation>R1A [=] R1B</equation>
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<rateCoeff>
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<Arrhenius>
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<A>1.000000E+09</A>
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<b>0.0</b>
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<E units="cal/mol">20000.000000</E>
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</Arrhenius>
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</rateCoeff>
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<reactants>R1A:1.0</reactants>
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<products>R1B:1.0</products>
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</reaction>
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</reactionData>
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<reactionData id="reaction_data">
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<!-- reaction 0001 -->
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<reaction id="0001">
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<equation>R1B [=] R1A</equation>
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<rateCoeff>
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<Arrhenius>
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<A>1.000000E+09</A>
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<b>0.0</b>
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<E units="cal/mol">20000.000000</E>
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</Arrhenius>
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</rateCoeff>
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<reactants>R1B:1.0</reactants>
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<products>R1A:1.0</products>
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</reaction>
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</reactionData>
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</ctml>
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57
test/data/duplicate-speciesData-ids.xml
Normal file
57
test/data/duplicate-speciesData-ids.xml
Normal file
@@ -0,0 +1,57 @@
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<?xml version="1.0"?>
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<ctml>
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<validate reactions="yes" species="yes"/>
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<!-- phase gas -->
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<phase dim="3" id="gas">
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<elementArray datasrc="elements.xml">H</elementArray>
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<speciesArray datasrc="#species_data">H H</speciesArray>
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<state>
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<temperature units="K">300.0</temperature>
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<pressure units="Pa">101325.0</pressure>
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</state>
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<thermo model="IdealGas"/>
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<kinetics model="none"/>
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<transport model="None"/>
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</phase>
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<!-- species definitions -->
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<speciesData id="species_data">
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<!-- species H -->
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<species name="H">
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<atomArray>H:1 </atomArray>
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
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-9.277323320E-22, 2.547365990E+04, -4.466828530E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
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4.981973570E-22, 2.547365990E+04, -4.466829140E-01</floatArray>
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</NASA>
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</thermo>
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</species>
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</speciesData>
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<speciesData id="species_data">
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<!-- species H -->
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<species name="H">
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<atomArray>H:1 </atomArray>
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
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-9.277323320E-22, 2.547365990E+04, -4.466828530E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
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4.981973570E-22, 2.547365990E+04, -4.466829140E-01</floatArray>
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</NASA>
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</thermo>
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</species>
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</speciesData>
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</ctml>
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@@ -25,12 +25,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.344331120E+00, 7.980520750E-03, -1.947815100E-05, 2.015720940E-08,
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2.344331120E+00, 7.980520750E-03, -1.947815100E-05, 2.015720940E-08,
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-7.376117610E-12, -9.179351730E+02, 6.830102380E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.337279200E+00, -4.940247310E-05, 4.994567780E-07, -1.795663940E-10,
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3.337279200E+00, -4.940247310E-05, 4.994567780E-07, -1.795663940E-10,
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2.002553760E-14, -9.501589220E+02, -3.205023310E+00</floatArray>
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</NASA>
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</thermo>
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@@ -42,12 +42,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
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2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
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-9.277323320E-22, 2.547365990E+04, -4.466828530E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
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2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
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4.981973570E-22, 2.547365990E+04, -4.466829140E-01</floatArray>
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</NASA>
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</thermo>
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@@ -59,12 +59,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.168267100E+00, -3.279318840E-03, 6.643063960E-06, -6.128066240E-09,
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3.168267100E+00, -3.279318840E-03, 6.643063960E-06, -6.128066240E-09,
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2.112659710E-12, 2.912225920E+04, 2.051933460E+00</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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2.569420780E+00, -8.597411370E-05, 4.194845890E-08, -1.001777990E-11,
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2.569420780E+00, -8.597411370E-05, 4.194845890E-08, -1.001777990E-11,
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1.228336910E-15, 2.921757910E+04, 4.784338640E+00</floatArray>
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</NASA>
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</thermo>
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@@ -76,12 +76,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.782456360E+00, -2.996734160E-03, 9.847302010E-06, -9.681295090E-09,
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3.782456360E+00, -2.996734160E-03, 9.847302010E-06, -9.681295090E-09,
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3.243728370E-12, -1.063943560E+03, 3.657675730E+00</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.282537840E+00, 1.483087540E-03, -7.579666690E-07, 2.094705550E-10,
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3.282537840E+00, 1.483087540E-03, -7.579666690E-07, 2.094705550E-10,
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-2.167177940E-14, -1.088457720E+03, 5.453231290E+00</floatArray>
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</NASA>
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</thermo>
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@@ -93,12 +93,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.992015430E+00, -2.401317520E-03, 4.617938410E-06, -3.881133330E-09,
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3.992015430E+00, -2.401317520E-03, 4.617938410E-06, -3.881133330E-09,
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1.364114700E-12, 3.615080560E+03, -1.039254580E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.092887670E+00, 5.484297160E-04, 1.265052280E-07, -8.794615560E-11,
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3.092887670E+00, 5.484297160E-04, 1.265052280E-07, -8.794615560E-11,
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1.174123760E-14, 3.858657000E+03, 4.476696100E+00</floatArray>
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</NASA>
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</thermo>
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@@ -110,12 +110,12 @@
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<thermo>
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<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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4.198640560E+00, -2.036434100E-03, 6.520402110E-06, -5.487970620E-09,
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4.198640560E+00, -2.036434100E-03, 6.520402110E-06, -5.487970620E-09,
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1.771978170E-12, -3.029372670E+04, -8.490322080E-01</floatArray>
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</NASA>
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<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
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<floatArray name="coeffs" size="7">
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3.033992490E+00, 2.176918040E-03, -1.640725180E-07, -9.704198700E-11,
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3.033992490E+00, 2.176918040E-03, -1.640725180E-07, -9.704198700E-11,
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1.682009920E-14, -3.000429710E+04, 4.966770100E+00</floatArray>
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</NASA>
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</thermo>
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@@ -154,7 +154,8 @@
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<products>H2O:1.0</products>
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</reaction>
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<reaction reversible="no" id="0002" negative_orders="yes">
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<!-- reaction 0003 -->
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<reaction reversible="no" id="0003" negative_orders="yes">
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<equation>H2 + 0.5 O2 =] H2O</equation>
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<order species="H2">1.0</order>
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<order species="O2">-0.25</order>
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