[ck2cti] Added ability to convert falloff reactions with explicit third bodies

For reactions written as: R1+R2(+S1)=P1(+S1), the implication is that the third-body efficiencies for all colliders besides S1 are zero.
2013-01-11 22:56:05 +00:00 · 2013-01-11 22:56:05 +00:00 · 994acf84ea
commit 994acf84ea
parent 121f039ea1
4 changed files with 289 additions and 15 deletions
--- a/interfaces/python/ck2cti.py
+++ b/interfaces/python/ck2cti.py
@ -34,6 +34,7 @@ import logging
 import types
 import os.path
 import numpy as np
+import re

 UNIT_OPTIONS = {'CAL/': 'cal/mol',
                'CAL/MOL': 'cal/mol',
@ -228,6 +229,7 @@ class Reaction(object):
        self.reversible = reversible
        self.duplicate = duplicate
        self.fwdOrders = fwdOrders if fwdOrders is not None else {}
+        self.thirdBody = None

    def _coeff_string(self, coeffs):
        L = []
@ -236,8 +238,11 @@ class Reaction(object):
                L.append('{0} {1}'.format(stoichiometry, species))
            else:
                L.append(str(species))
+        expression = ' + '.join(L)
+        if self.thirdBody:
+            expression += ' (+ {0})'.format(self.thirdBody)

-        return ' + '.join(L)
+        return expression

    @property
    def reactantString(self):
@ -483,7 +488,7 @@ class Chebyshev(KineticsModel):
        return True

    def to_cti(self, reactantstr, arrow, productstr, indent=0):
-        rxnstr = reactantstr + ' (+ M)' + arrow + productstr + ' (+ M)'
+        rxnstr = reactantstr + arrow + productstr
        prefix = ' '*(indent+19)
        lines = ['chebyshev_reaction({0!r},'.format(rxnstr),
                 prefix + 'Tmin={0.Tmin}, Tmax={0.Tmax},'.format(self),
@ -588,7 +593,7 @@ class Lindemann(ThirdBody):
        self.arrheniusLow = arrheniusLow

    def to_cti(self, reactantstr, arrow, productstr, indent=0):
-        rxnstr = reactantstr + ' (+ M)' + arrow + productstr + ' (+ M)'
+        rxnstr = reactantstr + arrow + productstr
        prefix = ' '*(indent + 17)
        lines = ['falloff_reaction({0!r},'.format(rxnstr)]
        lines.append(prefix + 'kf={0},'.format(self.arrheniusHigh.rateStr()))
@ -662,7 +667,7 @@ class Troe(Lindemann):
        self.T2 = T2

    def to_cti(self, reactantstr, arrow, productstr, indent=0):
-        rxnstr = reactantstr + ' (+ M)' + arrow + productstr + ' (+ M)'
+        rxnstr = reactantstr + arrow + productstr
        prefix = ' '*17
        lines = ['falloff_reaction({0!r},'.format(rxnstr),
                 prefix + 'kf={0},'.format(self.arrheniusHigh.rateStr()),
@ -713,7 +718,7 @@ class Sri(Lindemann):
        self.E = E

    def to_cti(self, reactantstr, arrow, productstr, indent=0):
-        rxnstr = reactantstr + ' (+ M)' + arrow + productstr + ' (+ M)'
+        rxnstr = reactantstr + arrow + productstr
        prefix = ' '*17
        lines = ['falloff_reaction({0!r},'.format(rxnstr),
                 prefix + 'kf={0},'.format(self.arrheniusHigh.rateStr()),
@ -942,16 +947,26 @@ def readKineticsEntry(entry, speciesDict, energyUnits, moleculeUnits):
    else:
        raise InputParseError("Failed to find reactant/product delimiter in reaction string.")

-    reactants = reactants.replace('(+M)','')
-    reactants = reactants.replace('(+m)','')
-    products = products.replace('(+M)','')
-    products = products.replace('(+m)','')
-
    # Create a new Reaction object for this reaction
    reaction = Reaction(reactants=[], products=[], reversible=reversible)

    def parseExpression(expression, dest):
-        thirdBody = False
+        falloff3b = None
+        thirdBody = False  # simple third body reaction (non-falloff)
+
+        # Look for third-body species for falloff reactions
+        if re.search(r'\(\+[Mm]\)', expression):
+            falloff3b = 'M'
+            expression = re.sub(r'(\(\+[Mm]\))', '', expression)
+        elif re.search(r'\(\+.*\)', expression):
+            # See if it matches a known species
+            for species in speciesDict:
+                if re.search(r'\(\+%s\)' % re.escape(species), expression):
+                    falloff3b = species
+                    expression = re.sub(r'(\(\+%s\))' % re.escape(species),
+                                        '', expression)
+                    break
+
        for term in expression.split('+'):
            term = term.strip()
            if not term[0].isalpha():
@ -970,14 +985,20 @@ def readKineticsEntry(entry, speciesDict, energyUnits, moleculeUnits):
            if species == 'M' or species == 'm':
                thirdBody = True
            elif species not in speciesDict:
-                raise InputParseError('Unexpected species "{0}" in reaction {1}.'.format(species, reaction))
+                raise InputParseError('Unexpected species "{0}" in reaction expression "{1}".'.format(species, expression))
            else:
                dest.append((stoichiometry, speciesDict[species]))

-        return thirdBody
+        return falloff3b, thirdBody

-    thirdBody = parseExpression(reactants, reaction.reactants)
-    parseExpression(products, reaction.products)
+    falloff_3b_r, thirdBody = parseExpression(reactants, reaction.reactants)
+    falloff_3b_p, thirdBody = parseExpression(products, reaction.products)
+
+    if falloff_3b_r != falloff_3b_p:
+        raise InputParseError('Third bodies do not match: "{0}" and "{1}" in'
+            ' reaction entry:\n\n{2}'.format(falloff_3b_r, falloff_3b_p, entry))
+
+    reaction.thirdBody = falloff_3b_r

    # Determine the appropriate units for k(T) and k(T,P) based on the number of reactants
    # This assumes elementary kinetics for all reactions
--- a/test/data/explicit-third-bodies.inp
+++ b/test/data/explicit-third-bodies.inp
@ -0,0 +1,38 @@
+ELEMENTS
+H  C   AR
+END
+
+SPECIES
+H
+R1A R1B P1
+R2 SP)X
+END
+
+THERMO
+   300.000  1000.000  5000.000
+SP)X                    C   1H   3          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
+
+R1A+R1B+m = P1+H+M                  3.0E19   -2.0   1900
+  DUPLICATE
+
+R1A+R1B(+ M ) = P1+H(+m)            1.0E18   -2.0   1000
+  LOW/4.0E25 -3.0 0/
+  R2/0.0/ SP)X/0/
+  DUPLICATE
+
+R1A+R1B(+R2) = P1+H(+ R2)          2.0E18   -3.0   1200
+  LOW/3.0E25 -2.0 0/
+  DUPLICATE
+
+! A really pathological species name
+R1A+R1B(+SP)X) = P1+H(+SP)X)      3.0E18   -1.0   1400
+  LOW/1.0E25 -1.0 0/
+  DUPLICATE
+
+END
--- a/test/data/explicit-third-bodies.xml
+++ b/test/data/explicit-third-bodies.xml
@ -0,0 +1,205 @@
+<?xml version="1.0"?>
+<ctml>
+  <validate reactions="yes" species="yes"/>
+
+  <!-- phase gas     -->
+  <phase dim="3" id="gas">
+    <elementArray datasrc="elements.xml">H C Ar</elementArray>
+    <speciesArray datasrc="#species_data">
+      H     R1A   R1B   P1    R2    
+      SP)X</speciesArray>
+    <reactionArray datasrc="#reaction_data"/>
+    <state>
+      <temperature units="K">300.0</temperature>
+      <pressure units="Pa">101325.0</pressure>
+    </state>
+    <thermo model="IdealGas"/>
+    <kinetics model="GasKinetics"/>
+    <transport model="None"/>
+  </phase>
+
+  <!-- species definitions     -->
+  <speciesData id="species_data">
+
+    <!-- species H    -->
+    <species name="H">
+      <atomArray>H:1 </atomArray>
+      <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, 
+             -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, 
+             4.981973570E-22,   2.547365990E+04,  -4.466829140E-01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+
+    <!-- species R1A    -->
+    <species name="R1A">
+      <atomArray>H:4 C:1 </atomArray>
+      <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, 
+             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, 
+             -1.018152300E-13,  -9.468344590E+03,   1.843731800E+01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+
+    <!-- species R1B    -->
+    <species name="R1B">
+      <atomArray>H:4 C:1 </atomArray>
+      <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, 
+             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, 
+             -1.018152300E-13,  -9.468344590E+03,   1.843731800E+01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+
+    <!-- species P1    -->
+    <species name="P1">
+      <atomArray>H:7 C:2 </atomArray>
+      <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, 
+             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, 
+             -1.018152300E-13,  -9.468344590E+03,   1.843731800E+01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+
+    <!-- species R2    -->
+    <species name="R2">
+      <atomArray>H:7 C:2 </atomArray>
+      <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, 
+             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, 
+             -1.018152300E-13,  -9.468344590E+03,   1.843731800E+01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+
+    <!-- species SP)X    -->
+    <species name="SP)X">
+      <atomArray>H:3 C:1 </atomArray>
+      <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, 
+             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, 
+             -1.018152300E-13,  -9.468344590E+03,   1.843731800E+01</floatArray>
+        </NASA>
+      </thermo>
+    </species>
+  </speciesData>
+  <reactionData id="reaction_data">
+
+    <!-- reaction 0001    -->
+    <reaction duplicate="yes" reversible="yes" type="threeBody" id="0001">
+      <equation>R1A + R1B + M [=] P1 + H + M</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>
+      <rateCoeff>
+        <Arrhenius>
+           <A>1.000000E+15</A>
+           <b>-2.0</b>
+           <E units="cal/mol">1000.000000</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+           <A>4.000000E+19</A>
+           <b>-3.0</b>
+           <E units="cal/mol">0.000000</E>
+        </Arrhenius>
+        <efficiencies default="1.0">SP)X:0.0 R2:0.0</efficiencies>
+        <falloff type="Lindemann"/>
+      </rateCoeff>
+      <reactants>R1B:1 R1A:1.0</reactants>
+      <products>H:1 P1:1.0</products>
+    </reaction>
+
+    <!-- reaction 0003    -->
+    <reaction duplicate="yes" reversible="yes" type="falloff" id="0003">
+      <equation>R1A + R1B (+ R2) [=] P1 + H (+ R2)</equation>
+      <rateCoeff>
+        <Arrhenius>
+           <A>2.000000E+15</A>
+           <b>-3.0</b>
+           <E units="cal/mol">1200.000000</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+           <A>3.000000E+19</A>
+           <b>-2.0</b>
+           <E units="cal/mol">0.000000</E>
+        </Arrhenius>
+        <efficiencies default="0.0">R2:1.0</efficiencies>
+        <falloff type="Lindemann"/>
+      </rateCoeff>
+      <reactants>R1B:1 R1A:1.0</reactants>
+      <products>H:1 P1:1.0</products>
+    </reaction>
+
+    <!-- reaction 0004    -->
+    <reaction duplicate="yes" reversible="yes" type="falloff" id="0004">
+      <equation>R1A + R1B (+ SP)X) [=] P1 + H (+ SP)X)</equation>
+      <rateCoeff>
+        <Arrhenius>
+           <A>3.000000E+15</A>
+           <b>-1.0</b>
+           <E units="cal/mol">1400.000000</E>
+        </Arrhenius>
+        <Arrhenius name="k0">
+           <A>1.000000E+19</A>
+           <b>-1.0</b>
+           <E units="cal/mol">0.000000</E>
+        </Arrhenius>
+        <efficiencies default="0.0">SP)X:1.0</efficiencies>
+        <falloff type="Lindemann"/>
+      </rateCoeff>
+      <reactants>R1B:1 R1A:1.0</reactants>
+      <products>H:1 P1:1.0</products>
+    </reaction>
+  </reactionData>
+</ctml>
--- a/test/python/testConvert.py
+++ b/test/python/testConvert.py
@ -124,6 +124,16 @@ class chemkinConverterTest(utilities.CanteraTest):
                                        'sri-falloff.cti')
        self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])

+    def test_explicit_third_bodies(self):
+        if os.path.exists('explicit-third-bodies.cti'):
+            os.path.remove('explicit-third-bodies.cti')
+        ck2cti.convertMech('../data/explicit-third-bodies.inp',
+                           thermoFile='../data/dummy-thermo.dat', quiet=True)
+
+        ref, gas = self.checkConversion('explicit-third-bodies.cti',
+                                        '../data/explicit-third-bodies.xml')
+        self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
+
    def test_explicit_reverse_rate(self):
        if os.path.exists('explicit-reverse-rate.cti'):
            os.remove('explicit-reverse-rate.cti')