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[yaml2ck] Fix explicit third body reaction output
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Prior to this fix, third body efficiencies were erroneously specified
for third body reactions with explicit collision partners (see #1415).
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@ischoegl @speth
ischoegl authored and speth committed Jan 4, 2023
1 parent 2ce92ea commit 957dd24
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Showing 5 changed files with 45 additions and 17 deletions.
3 changes: 2 additions & 1 deletion interfaces/cython/cantera/yaml2ck.py
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Original file line number Diff line number Diff line change
Expand Up @@ -472,7 +472,8 @@ def build_reactions_text(reactions: Iterable[ct.Reaction]):
else:
raise ValueError(f"Unknown reaction type: '{reac.reaction_type}'")

if reac.third_body is not None:
third = reac.third_body
if third is not None and third.name == "M" and len(third.efficiencies):
reaction_lines.append(
" ".join(
f"{spec}/{value:.3E}/"
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3 changes: 3 additions & 0 deletions test/data/explicit-third-bodies.inp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,9 @@ REACTIONS
R1A+R1B+m = P1+H+M 3.0E19 -2.0 1900 ! An end of line comment
DUPLICATE

R1A+R1B+R2 = P1+H+R2 3.0E19 -2.0 1900 ! An end of line comment
DUPLICATE

R1A+R1B(+ M ) = P1+H(+m) 1.0E18 -2.0 1000
LOW/4.0E25 -3.0 0/
R2/0.0/ SP)X/0/
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42 changes: 28 additions & 14 deletions test/data/explicit-third-bodies.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<phase dim="3" id="gas">
<elementArray datasrc="elements.xml">H C Ar</elementArray>
<speciesArray datasrc="#species_data">
H R1A R1B P1 R2
H R1A R1B P1 R2
SP)X</speciesArray>
<reactionArray datasrc="#reaction_data"/>
<state>
Expand All @@ -27,12 +27,12 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
2.500000000E+00, 7.053328190E-13, -1.995919640E-15, 2.300816320E-18,
-9.277323320E-22, 2.547365990E+04, -4.466828530E-01</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
2.500000010E+00, -2.308429730E-11, 1.615619480E-14, -4.735152350E-18,
4.981973570E-22, 2.547365990E+04, -4.466829140E-01</floatArray>
</NASA>
</thermo>
Expand All @@ -44,12 +44,12 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
</NASA>
</thermo>
Expand All @@ -61,12 +61,12 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
</NASA>
</thermo>
Expand All @@ -78,12 +78,12 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
</NASA>
</thermo>
Expand All @@ -95,12 +95,12 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
</NASA>
</thermo>
Expand All @@ -112,20 +112,20 @@
<thermo>
<NASA Tmax="1000.0" Tmin="200.0" P0="100000.0">
<floatArray name="coeffs" size="7">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmax="3500.0" Tmin="1000.0" P0="100000.0">
<floatArray name="coeffs" size="7">
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
7.485149500E-02, 1.339094670E-02, -5.732858090E-06, 1.222925350E-09,
-1.018152300E-13, -9.468344590E+03, 1.843731800E+01</floatArray>
</NASA>
</thermo>
</species>
</speciesData>
<reactionData id="reaction_data">

<!-- reaction 0001 -->
<!-- reaction 0001a -->
<reaction duplicate="yes" reversible="yes" type="threeBody" id="0001">
<equation>R1A + R1B + M [=] P1 + H + M</equation>
<rateCoeff>
Expand All @@ -139,6 +139,20 @@
<products>H:1 P1:1.0</products>
</reaction>

<!-- reaction 0001b -->
<reaction duplicate="yes" reversible="yes" type="threeBody" id="0001">
<equation>R1A + R1B + R2 [=] P1 + H + R2</equation>
<rateCoeff>
<Arrhenius>
<A>3.000000E+13</A>
<b>-2.0</b>
<E units="cal/mol">1900.000000</E>
</Arrhenius>
</rateCoeff>
<reactants>R1B:1 R1A:1.0</reactants>
<products>H:1 P1:1.0</products>
</reaction>

<!-- reaction 0002 -->
<reaction duplicate="yes" reversible="yes" type="falloff" id="0002">
<equation>R1A + R1B (+ M) [=] P1 + H (+ M)</equation>
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3 changes: 3 additions & 0 deletions test/data/explicit-third-bodies.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,9 @@ reactions:
type: three-body
rate-constant: {A: 3.0e+13, b: -2.0, Ea: 1900.0 cal/mol}
duplicate: true
- equation: R1A + R1B + R2 <=> P1 + H + R2
rate-constant: {A: 3.0e+13, b: -2.0, Ea: 1900.0 cal/mol}
duplicate: true
- equation: R1A + R1B (+ M) <=> P1 + H (+ M)
type: falloff
high-P-rate-constant: {A: 1.0e+15, b: -2.0, Ea: 1000.0 cal/mol}
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11 changes: 9 additions & 2 deletions test/python/test_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -559,7 +559,7 @@ def convert(
thermo: str | Path | None = None,
transport: str | Path | None = None,
permissive: bool = False,
) -> None:
) -> str:
if mech is not None:
mech, thermo, transport = self._convert_to_ck(
input_file,
Expand All @@ -578,6 +578,7 @@ def convert(
quiet=True,
permissive=permissive,
)
return mech

def check_conversion(self, basename, cls=ct.Solution, **kwargs):
# The round-trip YAML->CK->YAML will always have the single phase name 'gas'
Expand Down Expand Up @@ -689,7 +690,13 @@ def test_phase_id(self):

def test_third_body_reactions(self):
input_file = self.test_data_path / "explicit-third-bodies.yaml"
self.convert(input_file)
mech = self.convert(input_file)
with open(mech) as fid:
lines = fid.readlines()
for i, line in enumerate(lines):
if line.startswith("R1A + R1B"):
next = lines[i + 1]
assert next.startswith("LOW") or next.strip() == "DUPLICATE"
ck_phase, yaml_phase = self.check_conversion(input_file)
self.check_kinetics(
ck_phase, yaml_phase, [300, 800, 1450, 2800], [5e3, 1e5, 2e6]
Expand Down

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