[unittests] Fix ch4_ion.yaml

The content of ch4_ion.yaml now matches ch4_ion.cti (the file was re-created
using cti2yaml)

test/data/ch4_ion.yaml

@@ -1,142 +1,237 @@
+generator: cti2yaml
+cantera-version: 2.5.0a4
+date: Mon, 10 Aug 2020 12:55:00 +0000
+input-files: [ch4_ion.cti]
+
 units: {length: cm, quantity: mol, activation-energy: cal/mol}
 
 phases:
 - name: gas
   thermo: ideal-gas
+  elements: [O, H, C, N, E]
+  species:
+  - gri30.yaml/species: [H, O, OH, HO2, H2O2, C, CH, CH2, CH2(S), CH3, HCO,
+      CH2O, CH3O]
+  - species: [H2, O2, H2O, CH4, CO, CO2, N2, HCO+, H3O+, E, O2-]
+  skip-undeclared-third-bodies: true
+  kinetics: gas
+  reactions:
+  - gri30.yaml/reactions: declared-species
+  - reactions: declared-species
   transport: ionized-gas
-  species: [O2, H2O, CO2, N2, H3O+, E, O2-]
-  state: {T: 300, P: 1 atm}
+  state:
+    T: 300.0
+    P: 1.01325e+05
 
 species:
+- name: H2
+  composition: {H: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12,
+      -917.935173, 0.683010238]
+    - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14,
+      -950.158922, -3.20502331]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 2.92
+    well-depth: 38.0
+    polarizability: 0.455
+    rotational-relaxation: 280.0
+  note: TPIS78
 - name: O2
   composition: {O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [3.78245636E+00, -2.99673416E-03, 9.84730201E-06, -9.68129509E-09,
-       3.24372837E-12, -1.06394356E+03, 3.65767573E+00]
-    - [3.28253784E+00, 1.48308754E-03, -7.57966669E-07, 2.09470555E-10,
-       -2.16717794E-14, -1.08845772E+03, 5.45323129E+00]
+    - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12,
+      -1063.94356, 3.65767573]
+    - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14,
+      -1088.45772, 5.45323129]
   transport:
     model: gas
     geometry: linear
     diameter: 3.46
-    well-depth: 107.40
+    well-depth: 107.4
     polarizability: 1.131
-    rotational-relaxation: 3.80
-    note: TPIS89
-
+    rotational-relaxation: 3.8
+  note: TPIS89
 - name: H2O
   composition: {H: 2, O: 1}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [4.19864056E+00, -2.03643410E-03, 6.52040211E-06, -5.48797062E-09,
-       1.77197817E-12, -3.02937267E+04, -8.49032208E-01]
-    - [3.03399249E+00, 2.17691804E-03, -1.64072518E-07, -9.70419870E-11,
-       1.68200992E-14, -3.00042971E+04, 4.96677010E+00]
+    - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12,
+      -3.02937267e+04, -0.849032208]
+    - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14,
+      -3.00042971e+04, 4.9667701]
   transport:
     model: gas
     geometry: nonlinear
-    diameter: 2.60
-    well-depth: 572.40
+    diameter: 2.6
+    well-depth: 572.4
     dipole: 1.84
     polarizability: 1.053
-    rotational-relaxation: 4.00
-    note: L 8/89
-
+    rotational-relaxation: 4.0
+  note: L 8/89
+- name: CH4
+  composition: {C: 1, H: 4}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11,
+      -1.02466476e+04, -4.64130376]
+    - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13,
+      -9468.34459, 18.437318]
+  transport:
+    model: gas
+    geometry: nonlinear
+    diameter: 3.75
+    well-depth: 141.4
+    polarizability: 2.6
+    rotational-relaxation: 13.0
+  note: L 8/88
+- name: CO
+  composition: {C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13,
+      -1.4344086e+04, 3.50840928]
+    - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14,
+      -1.41518724e+04, 7.81868772]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.65
+    well-depth: 98.1
+    polarizability: 1.95
+    rotational-relaxation: 1.8
+  note: TPIS79
 - name: CO2
   composition: {C: 1, O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 1000, 3500]
+    temperature-ranges: [200.0, 1000.0, 3500.0]
     data:
-    - [2.35677352E+00, 8.98459677E-03, -7.12356269E-06, 2.45919022E-09,
-       -1.43699548E-13, -4.83719697E+04, 9.90105222E+00]
-    - [3.85746029E+00, 4.41437026E-03, -2.21481404E-06, 5.23490188E-10,
-       -4.72084164E-14, -4.87591660E+04, 2.27163806E+00]
+    - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13,
+      -4.83719697e+04, 9.90105222]
+    - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14,
+      -4.8759166e+04, 2.27163806]
   transport:
     model: gas
     geometry: linear
     diameter: 3.76
-    well-depth: 244.00
+    well-depth: 244.0
     polarizability: 2.65
-    rotational-relaxation: 2.10
-    note: L 7/88
-
+    rotational-relaxation: 2.1
+  note: L 7/88
 - name: N2
   composition: {N: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [300, 1000, 5000]
+    temperature-ranges: [300.0, 1000.0, 5000.0]
     data:
-    - [3.29867700E+00, 1.40824040E-03, -3.96322200E-06, 5.64151500E-09,
-       -2.44485400E-12, -1.02089990E+03, 3.95037200E+00]
-    - [2.92664000E+00, 1.48797680E-03, -5.68476000E-07, 1.00970380E-10,
-       -6.75335100E-15, -9.22797700E+02, 5.98052800E+00]
+    - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12,
+      -1020.8999, 3.950372]
+    - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15,
+      -922.7977, 5.980528]
   transport:
     model: gas
     geometry: linear
     diameter: 3.62
     well-depth: 97.53
     polarizability: 1.76
-    rotational-relaxation: 4.00
+    rotational-relaxation: 4.0
     dispersion-coefficient: 2.995
     quadrupole-polarizability: 3.602
-    note: 121286
-
+  note: '121286'
+- name: HCO+
+  composition: {H: 1, C: 1, O: 1, E: -1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [2.4739736, 8.671559e-03, -1.00315e-05, 6.7170527e-09, -1.7872674e-12,
+      9.9146608e+04, 8.17571187]
+    - [3.741188, 3.3441517e-03, -1.2397121e-06, 2.1189388e-10, -1.370415e-14,
+      9.8884078e+04, 2.07861357]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.59
+    well-depth: 498.0
+    polarizability: 1.356
+    dispersion-coefficient: 0.416
+  note: J12/70
 - name: H3O+
   composition: {H: 3, O: 1, E: -1}
   thermo:
     model: NASA7
-    temperature-ranges: [298.15, 1000, 6000]
+    temperature-ranges: [298.15, 1000.0, 6000.0]
     data:
-    - [3.79295270E+00, -9.10854000E-04, 1.16363549E-05, -1.21364887E-08,
-       4.26159663E-12, 7.07512401E+04, 1.47156856E+00]
-    - [2.49647716E+00, 5.72844920E-03, -1.83953281E-06, 2.73577439E-10,
-       -1.54093985E-14, 7.09729113E+04, 7.45850779E+00]
+    - [3.7929527, -9.10854e-04, 1.16363549e-05, -1.21364887e-08, 4.26159663e-12,
+      7.07512401e+04, 1.47156856]
+    - [2.49647716, 5.7284492e-03, -1.83953281e-06, 2.73577439e-10, -1.54093985e-14,
+      7.09729113e+04, 7.45850779]
   transport:
     model: gas
     geometry: nonlinear
     diameter: 3.15
     well-depth: 106.2
     dipole: 1.417
     polarizability: 0.897
-    rotational-relaxation: 0.0
-    note: TPIS89
-
+  note: TPIS89
 - name: O2-
   composition: {E: 1, O: 2}
   thermo:
     model: NASA7
-    temperature-ranges: [298.15, 1000.00, 6000]
+    temperature-ranges: [298.15, 1000.0, 6000.0]
     data:
-    - [3.66442522E+00, -9.28741138E-04, 6.45477082E-06, -7.7470338E-09,
-       2.93332662E-12, -6.87076983E+03, 4.35140681E+00]
-    - [3.95666294E+00, 5.98141823E-04, -2.12133905E-07, 3.63267581E-11,
-       -2.24989228E-15, -7.06287229E+03, 2.27871017E+00]
+    - [3.66442522, -9.28741138e-04, 6.45477082e-06, -7.7470338e-09, 2.93332662e-12,
+      -6870.76983, 4.35140681]
+    - [3.95666294, 5.98141823e-04, -2.12133905e-07, 3.63267581e-11, -2.24989228e-15,
+      -7062.87229, 2.27871017]
   transport:
     model: gas
     geometry: linear
     diameter: 3.33
     well-depth: 136.5
     polarizability: 1.424
-    note: L4/89
-
+  note: L4/89
 - name: E
   composition: {E: 1}
   thermo:
     model: NASA7
-    temperature-ranges: [200, 3000]
+    temperature-ranges: [200.0, 1000.0, 6000.0]
     data:
-    - [2.5E+00, 0.0, 0.0, 0.0, 0.0, -7.45375000E+02, -1.17246902E+01]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, -11.7246902]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, -11.7246902]
   transport:
     model: gas
     geometry: atom
     diameter: 2.05
     well-depth: 145.0
     polarizability: 0.667
-    rotational-relaxation: 0.0
-    note: gas L10/92
+  note: gas L10/92
+
+reactions:
+- equation: CH + O => HCO+ + E  # Reaction 1
+  rate-constant: {A: 2.51e+11, b: 0.0, Ea: 1700}
+- equation: HCO+ + H2O => H3O+ + CO  # Reaction 2
+  rate-constant: {A: 1.51e+15, b: 0.0, Ea: 0.0}
+- equation: H3O+ + E => H2O + H  # Reaction 3
+  rate-constant: {A: 2.29e+18, b: -0.5, Ea: 0.0}
+- equation: H3O+ + E => OH + H + H  # Reaction 4
+  rate-constant: {A: 7.95e+21, b: -1.4, Ea: 0.0}
+- equation: H3O+ + E => H2 + OH  # Reaction 5
+  rate-constant: {A: 1.25e+19, b: -0.5, Ea: 0.0}
+- equation: H3O+ + E =>  O + H2 + H  # Reaction 6
+  rate-constant: {A: 6.0e+17, b: -0.3, Ea: 0.0}