[WIP] Commit yaml files

SConstruct

@@ -1518,7 +1518,7 @@ cdefine('CT_USE_DEMANGLE', 'has_demangle')
 config_h_build = env.Command('build/src/config.h.build',
                              'include/cantera/base/config.h.in',
                        ConfigBuilder(configh))
-# This separate copy operation, which SCons will skip of config.h.build is
+# This separate copy operation, which SCons will skip if config.h.build is
 # unmodified, prevents unnecessary rebuilds of the precompiled header
 config_h = env.Command('include/cantera/base/config.h',
                        'build/src/config.h.build',
@@ -1585,44 +1585,9 @@ for xml in mglob(env, 'data/inputs', 'xml'):
     if xml.name not in convertedInputFiles:
         build(env.Command(dest, xml.path, Copy('$TARGET', '$SOURCE')))
 
-# Convert input files from Chemkin format to YAML
-ck_sources = [
-    dict(output='gri30.yaml', input='data/inputs/gri30.inp',
-         thermo='data/thermo/gri30_thermo.dat',
-         transport='data/transport/gri30_tran.dat',
-         phase='gri30'),
-    dict(output='air.yaml', input='data/inputs/air.inp',
-         transport='data/transport/gri30_tran.dat',
-         phase='air'),
-    dict(output='airNASA9.yaml', input='data/inputs/airNASA9.inp',
-         thermo='data/thermo/airDataNASA9.dat',
-         phase='airNASA9'),
-    dict(output='h2o2.yaml', input='data/inputs/h2o2.inp',
-         transport='data/transport/gri30_tran.dat',
-         phase='ohmech'),
-    dict(output='silane.yaml', input='data/inputs/silane.inp')
-]
-
-for mech in ck_sources:
-    convertedInputFiles.add(mech['output'])
-    cmd = ('$python_cmd_esc interfaces/cython/cantera/ck2yaml.py'
-           ' --quiet --no-validate --input=$SOURCE --output=$TARGET')
-    if 'thermo' in mech:
-        cmd += ' --thermo=' + mech['thermo']
-    if 'transport' in mech:
-        cmd += ' --transport=' + mech['transport']
-    if 'phase' in mech:
-        cmd += ' --name=' + mech['phase']
-    b = build(env.Command('build/data/{}'.format(mech['output']), mech['input'], cmd))
-    env.Depends(b, 'interfaces/cython/cantera/ck2yaml.py')
-
-# preprocess input files (cti -> yaml)
-for cti in mglob(env, 'data/inputs', 'cti'):
-    outName = os.path.splitext(cti.name)[0] + '.yaml'
-    if outName not in convertedInputFiles:
-        b = build(env.Command('build/data/{}'.format(outName), cti.path,
-                              '$python_cmd_esc interfaces/cython/cantera/cti2yaml.py $SOURCE $TARGET'))
-        env.Depends(b, 'interfaces/cython/cantera/cti2yaml.py')
+for yaml in mglob(env, "data", "yaml"):
+    dest = pjoin("build", "data", yaml.name)
+    build(env.Command(dest, yaml.path, Copy("$TARGET", "$SOURCE")))
 
 if addInstallActions:
     # Put headers in place
@@ -1890,7 +1855,7 @@ if any(target.startswith('test') for target in COMMAND_LINE_TARGETS):
         test_py_int = env.Command('#build/python_local/cantera/__init__.py',
                                   '#interfaces/python_minimal/cantera/__init__.py',
                                   Copy('$TARGET', '$SOURCE'))
-        for script in ['ctml_writer', 'ck2cti']:
+        for script in ['ctml_writer', 'ck2cti', 'ck2yaml', 'ctml2yaml']:
             s = env.Command('#build/python_local/cantera/{}.py'.format(script),
                             '#interfaces/cython/cantera/{}.py'.format(script),
                             Copy('$TARGET', '$SOURCE'))

data/KOH.yaml

@@ -0,0 +1,81 @@
+description: |-
+  A collection of potassium, oxygen, and hydrogen phases. Includes
+  charged species in addition to neutral species.
+
+generator: cti2yaml
+cantera-version: 2.5.0a3
+date: Wed, 11 Dec 2019 16:59:04 -0500
+input-files: [KOH.cti]
+
+units: {length: cm, quantity: mol, activation-energy: cal/mol}
+
+phases:
+- name: KOH_plasma
+  thermo: ideal-gas
+  elements: [K, O, H, E]
+  species:
+  - nasa_gas.yaml/species: all
+  skip-undeclared-elements: true
+  state:
+    T: 300.0
+    P: 1.01325e+05
+- name: K_solid
+  thermo: fixed-stoichiometry
+  elements: [K]
+  species:
+  - nasa_condensed.yaml/species: [K(cr)]
+  density: 0.86 g/cm^3
+- name: K_liquid
+  thermo: fixed-stoichiometry
+  elements: [K]
+  species:
+  - nasa_condensed.yaml/species: [K(L)]
+  density: 1.0 g/cm^3
+- name: KOH_a
+  thermo: fixed-stoichiometry
+  elements: [K, O, H]
+  species:
+  - nasa_condensed.yaml/species: [KOH(a)]
+  density: 2.04 g/cm^3
+- name: KOH_b
+  thermo: fixed-stoichiometry
+  elements: [K, O, H]
+  species:
+  - nasa_condensed.yaml/species: [KOH(b)]
+  density: 1.0 g/cm^3
+- name: KOH_liquid
+  thermo: fixed-stoichiometry
+  elements: [K, O, H]
+  species:
+  - nasa_condensed.yaml/species: [KOH(L)]
+  density: 1.0 g/cm^3
+- name: K2O2_solid
+  thermo: fixed-stoichiometry
+  elements: [K, O]
+  species:
+  - nasa_condensed.yaml/species: [K2O2(s)]
+  density: 1.0 g/cm^3
+- name: K2O_solid
+  thermo: fixed-stoichiometry
+  elements: [K, O]
+  species:
+  - nasa_condensed.yaml/species: [K2O(s)]
+  density: 1.0 g/cm^3
+- name: KO2_solid
+  thermo: fixed-stoichiometry
+  elements: [K, O]
+  species:
+  - nasa_condensed.yaml/species: [KO2(s)]
+  density: 1.0 g/cm^3
+- name: ice
+  thermo: fixed-stoichiometry
+  elements: [H, O]
+  species:
+  - nasa_condensed.yaml/species: [H2O(s)]
+  density: 0.917 g/cm^3
+- name: liquid_water
+  thermo: fixed-stoichiometry
+  elements: [H, O]
+  species:
+  - nasa_condensed.yaml/species: [H2O(L)]
+  density: 1.0 g/cm^3

data/air.yaml

@@ -0,0 +1,182 @@
+description: |-
+  Ideal gas properties of air. Includes several reactions among
+  the included species.
+
+generator: ck2yaml
+input-files: [air.inp, gri30_tran.dat]
+cantera-version: 2.5.0a3
+date: Wed, 11 Dec 2019 16:59:03 -0500
+
+units: {length: cm, time: s, quantity: mol, activation-energy: cal/mol}
+
+phases:
+- name: air
+  thermo: ideal-gas
+  elements: [O, N, Ar]
+  species: [O, O2, N, NO, NO2, N2O, N2, AR]
+  kinetics: gas
+  transport: mixture-averaged
+  state: {T: 300.0, P: 1 atm}
+
+species:
+- name: O
+  composition: {O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [3.1682671, -3.27931884e-03, 6.64306396e-06, -6.12806624e-09, 2.11265971e-12,
+      2.91222592e+04, 2.05193346]
+    - [2.56942078, -8.59741137e-05, 4.19484589e-08, -1.00177799e-11, 1.22833691e-15,
+      2.92175791e+04, 4.78433864]
+    note: L1/90
+  transport:
+    model: gas
+    geometry: atom
+    well-depth: 80.0
+    diameter: 2.75
+- name: O2
+  composition: {O: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [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]
+    note: TPIS89
+  transport:
+    model: gas
+    geometry: linear
+    well-depth: 107.4
+    diameter: 3.458
+    polarizability: 1.6
+    rotational-relaxation: 3.8
+- name: N
+  composition: {N: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 6000.0]
+    data:
+    - [2.5, 0.0, 0.0, 0.0, 0.0, 5.6104637e+04, 4.1939087]
+    - [2.4159429, 1.7489065e-04, -1.1902369e-07, 3.0226245e-11, -2.0360982e-15,
+      5.6133773e+04, 4.6496096]
+    note: L6/88
+  transport:
+    model: gas
+    geometry: atom
+    well-depth: 71.4
+    diameter: 3.298
+    note: '*'
+- name: NO
+  composition: {N: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 6000.0]
+    data:
+    - [4.2184763, -4.638976e-03, 1.1041022e-05, -9.3361354e-09, 2.803577e-12,
+      9844.623, 2.2808464]
+    - [3.2606056, 1.1911043e-03, -4.2917048e-07, 6.9457669e-11, -4.0336099e-15,
+      9920.9746, 6.3693027]
+    note: RUS78
+  transport:
+    model: gas
+    geometry: linear
+    well-depth: 97.53
+    diameter: 3.621
+    polarizability: 1.76
+    rotational-relaxation: 4.0
+- name: NO2
+  composition: {N: 1, O: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 6000.0]
+    data:
+    - [3.9440312, -1.585429e-03, 1.6657812e-05, -2.0475426e-08, 7.8350564e-12,
+      2896.6179, 6.3119917]
+    - [4.8847542, 2.1723956e-03, -8.2806906e-07, 1.574751e-10, -1.0510895e-14,
+      2316.4983, -0.11741695]
+    note: L7/88
+  transport:
+    model: gas
+    geometry: nonlinear
+    well-depth: 200.0
+    diameter: 3.5
+    rotational-relaxation: 1.0
+    note: '*'
+- name: N2O
+  composition: {N: 2, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 6000.0]
+    data:
+    - [2.2571502, 0.011304728, -1.3671319e-05, 9.6819806e-09, -2.9307182e-12,
+      8741.7744, 10.757992]
+    - [4.8230729, 2.6270251e-03, -9.5850874e-07, 1.6000712e-10, -9.7752303e-15,
+      8073.4048, -2.2017207]
+    note: L7/88
+  transport:
+    model: gas
+    geometry: linear
+    well-depth: 232.4
+    diameter: 3.828
+    rotational-relaxation: 1.0
+    note: '*'
+- name: N2
+  composition: {N: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [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]
+    note: '121286'
+  transport:
+    model: gas
+    geometry: linear
+    well-depth: 97.53
+    diameter: 3.621
+    polarizability: 1.76
+    rotational-relaxation: 4.0
+- name: AR
+  composition: {Ar: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.366]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.366]
+    note: '120186'
+  transport:
+    model: gas
+    geometry: atom
+    well-depth: 136.5
+    diameter: 3.33
+
+reactions:
+- equation: 2 O + M <=> O2 + M  # Reaction 1
+  type: three-body
+  rate-constant: {A: 1.2e+17, b: -1.0, Ea: 0.0}
+  efficiencies: {AR: 0.83}
+- equation: N + NO <=> N2 + O  # Reaction 2
+  rate-constant: {A: 2.7e+13, b: 0.0, Ea: 355.0}
+- equation: N + O2 <=> NO + O  # Reaction 3
+  rate-constant: {A: 9.0e+09, b: 1.0, Ea: 6500.0}
+- equation: N2O + O <=> N2 + O2  # Reaction 4
+  rate-constant: {A: 1.4e+12, b: 0.0, Ea: 1.081e+04}
+- equation: N2O + O <=> 2 NO  # Reaction 5
+  rate-constant: {A: 2.9e+13, b: 0.0, Ea: 2.315e+04}
+- equation: N2O (+M) <=> N2 + O (+M)  # Reaction 6
+  type: falloff
+  low-P-rate-constant: {A: 6.37e+14, b: 0.0, Ea: 5.664e+04}
+  high-P-rate-constant: {A: 7.91e+10, b: 0.0, Ea: 5.602e+04}
+  efficiencies: {AR: 0.625}
+- equation: NO + O + M <=> NO2 + M  # Reaction 7
+  type: three-body
+  rate-constant: {A: 1.06e+20, b: -1.41, Ea: 0.0}
+  efficiencies: {AR: 0.7}
+- equation: NO2 + O <=> NO + O2  # Reaction 8
+  rate-constant: {A: 3.9e+12, b: 0.0, Ea: -240.0}