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Fix Chebyshev rate constant when using local quantity units #600

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Mar 1, 2019
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Fix Chebyshev rate constant when using local quantity units #600

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10 changes: 8 additions & 2 deletions interfaces/cython/cantera/ck2cti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,8 @@
'KJOULES/MOL': 'kJ/mol',
'KJOULES/MOLE': 'kJ/mol'}

Avogadro = 6.02214129e23 # in molec/mol; value consistent with ct_defs.h.

_open = open
if sys.version_info[0] == 2:
string_types = (str, unicode)
Expand Down Expand Up @@ -580,7 +582,7 @@ class Chebyshev(KineticsModel):

"""

def __init__(self, coeffs=None, kunits='', **kwargs):
def __init__(self, coeffs=None, **kwargs):
KineticsModel.__init__(self, **kwargs)
if coeffs is not None:
self.coeffs = np.array(coeffs, np.float64)
Expand All @@ -590,7 +592,6 @@ def __init__(self, coeffs=None, kunits='', **kwargs):
self.coeffs = None
self.degreeT = 0
self.degreeP = 0
self.kunits = kunits

def isPressureDependent(self):
"""
Expand Down Expand Up @@ -1499,6 +1500,11 @@ def parseExpression(expression, dest):
for p in range(chebyshev.degreeP):
chebyshev.coeffs[t,p] = chebyshevCoeffs[index]
index += 1
if quantity_units == 'mol' and self.quantity_units == 'molec':
chebyshev.coeffs[0, 0] -= np.log10(Avogadro)*quantity_dim
elif quantity_units == 'molec' and self.quantity_units == 'mol':
chebyshev.coeffs[0, 0] += np.log10(Avogadro)*quantity_dim

reaction.kinetics = chebyshev
elif pdepArrhenius is not None:
reaction.kinetics = PDepArrhenius(
Expand Down
2 changes: 1 addition & 1 deletion interfaces/cython/cantera/test/test_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -506,7 +506,7 @@ def test_diamond(self):

def test_pdep(self):
gas = ct.Solution('pdep-test.cti')
self.assertEqual(gas.n_reactions, 6)
self.assertEqual(gas.n_reactions, 7)

def test_invalid(self):
try:
Expand Down
47 changes: 43 additions & 4 deletions test/data/pdep-test.cti
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,8 @@ units(length='cm', time='s', quantity='mol', act_energy='cal/mol')

ideal_gas(name='gas',
elements="H C",
species="""H R1A R1B P1 R2
P2A P2B R3 P3A P3B
R4 P4 R5 P5A P5B
R6 P6A P6B""",
species="""H R1A R1B P1 R2 P2A P2B R3 P3A P3B R4
P4 R5 P5A P5B R6 P6A P6B R7 P7A P7B""",
reactions='all',
initial_state=state(temperature=300.0, pressure=OneAtm))

Expand Down Expand Up @@ -211,6 +209,39 @@ species(name='P6B',
1.22292535E-09, -1.01815230E-13, -9.46834459E+03,
1.84373180E+01])))

species(name='R7',
atoms='C:2 H:7',
thermo=(NASA([200.00, 1000.00],
[ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05,
-4.84743026E-08, 1.66693956E-11, -1.02466476E+04,
-4.64130376E+00]),
NASA([1000.00, 3500.00],
[ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06,
1.22292535E-09, -1.01815230E-13, -9.46834459E+03,
1.84373180E+01])))

species(name='P7A',
atoms='C:1 H:4',
thermo=(NASA([200.00, 1000.00],
[ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05,
-4.84743026E-08, 1.66693956E-11, -1.02466476E+04,
-4.64130376E+00]),
NASA([1000.00, 3500.00],
[ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06,
1.22292535E-09, -1.01815230E-13, -9.46834459E+03,
1.84373180E+01])))

species(name='P7B',
atoms='C:1 H:4',
thermo=(NASA([200.00, 1000.00],
[ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05,
-4.84743026E-08, 1.66693956E-11, -1.02466476E+04,
-4.64130376E+00]),
NASA([1000.00, 3500.00],
[ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06,
1.22292535E-09, -1.01815230E-13, -9.46834459E+03,
1.84373180E+01])))

#-------------------------------------------------------------------------------
# Reaction data
#-------------------------------------------------------------------------------
Expand Down Expand Up @@ -265,3 +296,11 @@ chebyshev_reaction('R6 <=> P6A + P6B',
[-2.93660e-01, 2.85680e-01, -9.33730e-03, -4.01020e-03],
[-2.26210e-01, 1.69190e-01, 4.85810e-03, -2.38030e-03],
[-1.43220e-01, 7.71110e-02, 1.27080e-02, -6.41540e-04]])
# Reaction 7
chebyshev_reaction('R7 + H <=> P7A + P7B',
Tmin=300.0, Tmax=2000.0,
Pmin=(0.009869232667160128, 'atm'), Pmax=(98.69232667160128, 'atm'),
coeffs=[[ 3.20681e+01, -1.13970e+00, -1.20590e-01, 1.60340e-02],
[ 1.97640e+00, 1.00370e+00, 7.28650e-03, -3.04320e-02],
[ 3.17700e-01, 2.68890e-01, 9.48060e-02, -7.63850e-03],
[-3.12850e-02, -3.94120e-02, 4.43750e-02, 1.44580e-02]])
23 changes: 23 additions & 0 deletions test/data/pdep-test.inp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ R3 P3A P3B
R4 P4
R5 P5A P5B
R6 P6A P6B
R7 P7A P7B
END

THERMO ALL
Expand Down Expand Up @@ -95,6 +96,19 @@ P6B C 1H 4 G 200.000 3500.000 1000.000 1
7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4

R7 C 2H 7 G 200.000 3500.000 1000.000 1
7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
P7A C 1H 4 G 200.000 3500.000 1000.000 1
7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
P7B C 1H 4 G 200.000 3500.000 1000.000 1
7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13 2
-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05 3
-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00 4
END

REACTIONS
Expand Down Expand Up @@ -149,4 +163,13 @@ CHEB / -2.3294000e-01 4.0190000e-01 -2.6073000e-02 -5.0486000e-03 /
CHEB / -2.9366000e-01 2.8568000e-01 -9.3373000e-03 -4.0102000e-03 /
CHEB / -2.2621000e-01 1.6919000e-01 4.8581000e-03 -2.3803000e-03 /
CHEB / -1.4322000e-01 7.7111000e-02 1.2708000e-02 -6.4154000e-04 /

! Bimolecular CHEB with local quantity units
R7+H=P7A+P7B 1.0E0 0.0 0.0
units / molec /
tcheb / 300.0 2000.0 / pcheb / 0.009869232667160128 98.69232667160128 /
cheb / 4 4 8.2883000e+00 -1.1397000e+00 -1.2059000e-01 1.6034000e-02 /
cheb / 1.9764000e+00 1.0037000e+00 7.2865000e-03 -3.0432000e-02 /
cheb / 3.1770000e-01 2.6889000e-01 9.4806000e-02 -7.6385000e-03 /
cheb / -3.1285000e-02 -3.9412000e-02 4.4375000e-02 1.4458000e-02 /
END
75 changes: 71 additions & 4 deletions test/data/pdep-test.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,8 @@
<phase dim="3" id="gas">
<elementArray datasrc="elements.xml">H C</elementArray>
<speciesArray datasrc="#species_data">
H R1A R1B P1 R2
P2A P2B R3 P3A P3B
R4 P4 R5 P5A P5B
R6 P6A P6B</speciesArray>
H R1A R1B P1 R2 P2A P2B R3 P3A P3B R4
P4 R5 P5A P5B R6 P6A P6B R7 P7A P7B</speciesArray>
<reactionArray datasrc="#reaction_data"/>
<state>
<temperature units="K">300.0</temperature>
Expand Down Expand Up @@ -328,6 +326,57 @@
</NASA>
</thermo>
</species>

<!-- species R7 -->
<species name="R7">
<atomArray>C:2 H:7 </atomArray>
<thermo>
<NASA Tmin="200.0" Tmax="1000.0" P0="100000.0">
<floatArray size="7" name="coeffs">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmin="1000.0" Tmax="3500.0" P0="100000.0">
<floatArray size="7" name="coeffs">
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>

<!-- species P7A -->
<species name="P7A">
<atomArray>C:1 H:4 </atomArray>
<thermo>
<NASA Tmin="200.0" Tmax="1000.0" P0="100000.0">
<floatArray size="7" name="coeffs">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmin="1000.0" Tmax="3500.0" P0="100000.0">
<floatArray size="7" name="coeffs">
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>

<!-- species P7B -->
<species name="P7B">
<atomArray>C:1 H:4 </atomArray>
<thermo>
<NASA Tmin="200.0" Tmax="1000.0" P0="100000.0">
<floatArray size="7" name="coeffs">
5.149876130E+00, -1.367097880E-02, 4.918005990E-05, -4.847430260E-08,
1.666939560E-11, -1.024664760E+04, -4.641303760E+00</floatArray>
</NASA>
<NASA Tmin="1000.0" Tmax="3500.0" P0="100000.0">
<floatArray size="7" name="coeffs">
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">

Expand Down Expand Up @@ -518,5 +567,23 @@
<reactants>R6:1.0</reactants>
<products>P6A:1.0 P6B:1</products>
</reaction>

<!-- reaction 0007 -->
<reaction id="0007" reversible="yes" type="chebyshev">
<equation>R7 + H [=] P7A + P7B</equation>
<rateCoeff>
<Tmin>300.0</Tmin>
<Tmax>2000.0</Tmax>
<Pmin units="atm">0.009869232667160128</Pmin>
<Pmax units="atm">98.69232667160128</Pmax>
<floatArray name="coeffs" degreeT="4" degreeP="4">
2.90681e+01, -1.13970e+00, -1.20590e-01, 1.60340e-02,
1.97640e+00, 1.00370e+00, 7.28650e-03, -3.04320e-02,
3.17700e-01, 2.68890e-01, 9.48060e-02, -7.63850e-03,
-3.12850e-02, -3.94120e-02, 4.43750e-02, 1.44580e-02</floatArray>
</rateCoeff>
<reactants>R7:1.0 H:1</reactants>
<products>P7A:1.0 P7B:1</products>
</reaction>
</reactionData>
</ctml>
30 changes: 18 additions & 12 deletions test/kinetics/pdep.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -57,14 +57,14 @@ Kinetics* PdepTest::kin_ = NULL;

TEST_F(PdepTest, reactionCounts)
{
EXPECT_EQ((size_t) 6, kin_->nReactions());
EXPECT_EQ((size_t) 7, kin_->nReactions());
}

TEST_F(PdepTest, PlogLowPressure)
{
// Test that P-log reactions have the right low-pressure limit
set_TP(500.0, 1e-7);
vector_fp kf(6);
vector_fp kf(7);
kin_->getFwdRateConstants(&kf[0]);

// Pre-exponential factor decreases by 10^3 for second-order reaction
Expand All @@ -84,7 +84,7 @@ TEST_F(PdepTest, PlogHighPressure)
{
// Test that P-log reactions have the right high-pressure limit
set_TP(500.0, 1e10);
vector_fp kf(6);
vector_fp kf(7);
kin_->getFwdRateConstants(&kf[0]);

// Pre-exponential factor decreases by 10^3 for second-order reaction
Expand All @@ -100,7 +100,7 @@ TEST_F(PdepTest, PlogDuplicatePressures)
{
// Test that multiple rate expressions are combined when necessary
set_TP(500.0, 1e10);
vector_fp kf(6);
vector_fp kf(7);

kin_->getFwdRateConstants(&kf[0]);
double kf1 = k(1.3700e+14, -0.79, 17603.0) + k(1.2800e+03, 1.71, 9774.0);
Expand All @@ -115,7 +115,7 @@ TEST_F(PdepTest, PlogCornerCases)
// Test rate evaluation at the corner cases where the pressure
// is exactly of the specified interpolation values
set_TP(500.0, 101325);
vector_fp kf(6);
vector_fp kf(7);
kin_->getFwdRateConstants(&kf[0]);

double kf0 = k(4.910800e+28, -4.8507, 24772.8);
Expand All @@ -130,7 +130,7 @@ TEST_F(PdepTest, PlogCornerCases)
TEST_F(PdepTest, PlogIntermediatePressure1)
{
set_TP(1100.0, 20*101325);
vector_fp ropf(6);
vector_fp ropf(7);
kin_->getFwdRatesOfProgress(&ropf[0]);

// Expected rates computed using Chemkin
Expand All @@ -144,7 +144,7 @@ TEST_F(PdepTest, PlogIntermediatePressure1)
TEST_F(PdepTest, PlogIntermediatePressure2)
{
thermo_->setState_TP(1100.0, 0.5*101325);
vector_fp ropf(6);
vector_fp ropf(7);
kin_->getFwdRatesOfProgress(&ropf[0]);

EXPECT_NEAR(5.244649e+02, ropf[0], 5e-2);
Expand All @@ -156,7 +156,7 @@ TEST_F(PdepTest, PlogIntermediatePressure2)
TEST_F(PdepTest, PlogIntermediatePressure3)
{
thermo_->setState_TP(800.0, 70*101325);
vector_fp ropf(6);
vector_fp ropf(7);
kin_->getFwdRatesOfProgress(&ropf[0]);

EXPECT_NEAR(2.274501e+04, ropf[0], 1e+1);
Expand All @@ -168,31 +168,37 @@ TEST_F(PdepTest, PlogIntermediatePressure3)
TEST_F(PdepTest, ChebyshevIntermediate1)
{
// Test Chebyshev rates in the normal interpolation region
vector_fp kf(6);
vector_fp kf(7);

set_TP(1100.0, 20 * 101325);
kin_->getFwdRateConstants(&kf[0]);
// Expected rates computed using RMG-py
EXPECT_NEAR(3.130698657e+06, kf[4], 1e-1);
EXPECT_NEAR(1.187949573e+00, kf[5], 1e-7);

// Rate for a reaction specified as "molec" instead of "mol" should
// be higher by a factor of the Avogadro constant (in mol, not kmol).
// Accuracy is limited by the low precision used by ck2cti
EXPECT_NEAR(kf[4], kf[6]/(Avogadro*1e-3), 5e2);
}

TEST_F(PdepTest, ChebyshevIntermediate2)
{
// Test Chebyshev rates in the normal interpolation region
vector_fp kf(6);
vector_fp kf(7);

set_TP(400.0, 0.1 * 101325);
kin_->getFwdRateConstants(&kf[0]);
// Expected rates computed using RMG-py
EXPECT_NEAR(1.713599902e+05, kf[4], 1e-3);
EXPECT_NEAR(9.581780687e-24, kf[5], 1e-31);
EXPECT_NEAR(kf[4], kf[6]/(Avogadro*1e-3), 1e2);
}

TEST_F(PdepTest, ChebyshevIntermediateROP)
{
set_TP(1100.0, 30 * 101325);
vector_fp ropf(6);
vector_fp ropf(7);
// Expected rates computed using Chemkin
kin_->getFwdRatesOfProgress(&ropf[0]);
EXPECT_NEAR(4.552930e+03, ropf[4], 1e-1);
Expand All @@ -201,7 +207,7 @@ TEST_F(PdepTest, ChebyshevIntermediateROP)

TEST_F(PdepTest, ChebyshevEdgeCases)
{
vector_fp kf(6);
vector_fp kf(7);

// Minimum P
set_TP(500.0, 1000.0);
Expand Down