Merge branch 'main' into ext_prec

Cantera · Dec 22, 2023 · a78547c · a78547c
2 parents 96bd8af + 87317b7
commit a78547c
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Showing 8 changed files with 143 additions and 30 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -65,7 +65,7 @@ jobs:
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.8', '3.10', '3.11']
+        python-version: ['3.8', '3.10', '3.11', '3.12']
         os: ['ubuntu-20.04', 'ubuntu-22.04']
       fail-fast: false
     env:
@@ -157,7 +157,7 @@ jobs:
     timeout-minutes: 90
     strategy:
       matrix:
-        python-version: ['3.8', '3.10', '3.11']
+        python-version: ['3.8', '3.10', '3.11', '3.12']
       fail-fast: false
     env:
       PYTHON_CMD: "python${{ matrix.python-version }}"
@@ -189,7 +189,7 @@ jobs:
         brew link --force --overwrite python@${{ matrix.python-version }}
         brew install --display-times scons
     - name: Upgrade pip
-      run: $PYTHON_CMD -m pip install -U pip 'setuptools>=47.0.0,<48' wheel
+      run: $PYTHON_CMD -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
       run: |
         $PYTHON_CMD -m pip install ruamel.yaml numpy cython pandas pytest pytest-github-actions-annotate-failures pint
@@ -379,7 +379,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-20.04", "ubuntu-22.04"]
-        python-version: ['3.8', '3.10', '3.11']
+        python-version: ['3.8', '3.10', '3.11', '3.12']
       fail-fast: false
     env:
       HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
@@ -423,7 +423,7 @@ jobs:
           -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +
         env:
           # The ignore setting here is due to a new warning introduced in Matplotlib==3.6.0
-          PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing"
+          PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing,ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:"
           MPLBACKEND: Agg
       - name: Save the results file for inspection
         uses: actions/upload-artifact@v3
@@ -517,7 +517,7 @@ jobs:
       matrix:
         os: ["windows-2022"]
         vs-toolset: ["14.1", "14.3"]
-        python-version: ["3.8", "3.10", "3.11"]
+        python-version: ["3.8", "3.10", "3.11", "3.12"]
         include:
         - python-version: 3.8
           fmt-ver: 10
@@ -595,7 +595,7 @@ jobs:
     strategy:
       matrix:
         vs-toolset: ['14.2']
-        python-version: ["3.8", "3.10", "3.11"]
+        python-version: ["3.8", "3.10", "3.11", "3.12"]
       fail-fast: false
     steps:
       - uses: actions/checkout@v3

diff --git a/SConstruct b/SConstruct
@@ -1720,7 +1720,7 @@ env['python_cmd_esc'] = quoted(env['python_cmd'])
 # Python Package Settings
 python_min_version = parse_version("3.8")
 # Newest Python version not supported/tested by Cantera
-python_max_p1_version = parse_version("3.12")
+python_max_p1_version = parse_version("3.13")
 # The string is used to set python_requires in setup.cfg.in
 env["py_requires_ver_str"] = f">={python_min_version}"
 if env["python_sdist"] or env["package_build"]:

diff --git a/interfaces/cython/cantera/ck2yaml.py b/interfaces/cython/cantera/ck2yaml.py
@@ -1991,13 +1991,14 @@ def write_yaml(self, name='gas', out_name='mech.yaml'):
 
             # Write the individual species data
             all_species = list(self.species_list)
+            for surf in self.surfaces:
+                all_species.extend(surf.species_list)
+
             for species in all_species:
                 if species.composition is None:
                     raise InputError('No thermo data found for '
-                                     'species {!r}'.format(species.label))
+                                     f'species {species.label!r}')
 
-            for surf in self.surfaces:
-                all_species.extend(surf.species_list)
             speciesMap = BlockMap([('species', all_species)])
             speciesMap.yaml_set_comment_before_after_key('species', before='\n')
             emitter.dump(speciesMap, dest)
@@ -2043,6 +2044,19 @@ def convert_mech(input_file, thermo_file=None, transport_file=None,
         else:
             phase_name = None
 
+        if surface_file:
+            parser.files.append(surface_file)
+            surface_file = os.path.expanduser(surface_file)
+            if not os.path.exists(surface_file):
+                raise IOError('Missing input file: {0!r}'.format(surface_file))
+            try:
+                # Read input mechanism files
+                parser.load_chemkin_file(surface_file, surface=True)
+            except Exception as err:
+                logger.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
+                               surface_file, parser.line_number, err))
+                raise
+
         if thermo_file:
             parser.files.append(thermo_file)
             thermo_file = os.path.expanduser(thermo_file)
@@ -2070,19 +2084,6 @@ def convert_mech(input_file, thermo_file=None, transport_file=None,
                 if s.transport is None:
                     raise InputError("No transport data for species '{}'.", s)
 
-        if surface_file:
-            parser.files.append(surface_file)
-            surface_file = os.path.expanduser(surface_file)
-            if not os.path.exists(surface_file):
-                raise IOError('Missing input file: {0!r}'.format(surface_file))
-            try:
-                # Read input mechanism files
-                parser.load_chemkin_file(surface_file, surface=True)
-            except Exception as err:
-                logger.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
-                               surface_file, parser.line_number, err))
-                raise
-
         if extra_file:
             parser.files.append(extra_file)
             extra_file = os.path.expanduser(extra_file)
@@ -2104,10 +2105,14 @@ def convert_mech(input_file, thermo_file=None, transport_file=None,
         # Write output file
         surface_names = parser.write_yaml(name=phase_name, out_name=out_name)
         if not quiet:
-            nReactions = len(parser.reactions) + sum(len(surf.reactions) for surf in parser.surfaces)
-            logger.info('Wrote YAML mechanism file to {0!r}.'.format(out_name))
-            logger.info('Mechanism contains {0} species and {1} reactions.'.format(
-                        len(parser.species_list), nReactions))
+            nSpecies = len(parser.species_list)
+            nReactions = len(parser.reactions)
+            for surf in parser.surfaces:
+                nSpecies += len(surf.species_list)
+                nReactions += len(surf.reactions)
+            logger.info(f'Wrote YAML mechanism file to {out_name!r}.')
+            logger.info(f'Mechanism contains {nSpecies} species and {nReactions} '
+                        'reactions.')
         return parser, surface_names
 
     def show_duplicate_reactions(self, error_message):

diff --git a/interfaces/sourcegen/sourcegen/_orchestrate.py b/interfaces/sourcegen/sourcegen/_orchestrate.py
@@ -23,8 +23,8 @@ def generate_source(lang: str, out_dir: str):
     config = {}
     if config_path.exists():
         with config_path.open() as config_file:
-            yaml = ruamel.yaml.YAML(typ='safe', pure=True)
-            config = yaml.load(config_file)
+            reader = ruamel.yaml.YAML(typ="safe")
+            config = reader.load(config_file)
 
     ignore_files: List[str] = config.get("ignore_files", [])
     ignore_funcs: Dict[str, List[str]] = config.get("ignore_funcs", {})

diff --git a/test/data/surface2-gas.inp b/test/data/surface2-gas.inp
@@ -0,0 +1,5 @@
+ELEMENTS H O PT END
+
+SPECIES
+  H H2 H2O H2O2 HO2 O O2 OH
+END
diff --git a/test/data/surface2-thermo.dat b/test/data/surface2-thermo.dat
@@ -0,0 +1,59 @@
+THERMO
+  300.0   1000.0   3000.0
+H                 120186H   1               G  0300.00   5000.00  1000.00      1
+ 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00    2
+ 0.02547162E+06-0.04601176E+01 0.02500000E+02 0.00000000E+00 0.00000000E+00    3
+ 0.00000000E+00 0.00000000E+00 0.02547162E+06-0.04601176E+01                   4
+H2                121286H   2               G  0300.00   5000.00  1000.00      1
+ 0.02991423E+02 0.07000644E-02-0.05633828E-06-0.09231578E-10 0.15827519E-14    2
+-0.08350340E+04-0.13551101E+01 0.03298124E+02 0.08249441E-02-0.08143015E-05    3
+-0.09475434E-09 0.04134872E-11-0.10125209E+04-0.03294094E+02                   4
+H2O                20387H   2O   1          G  0300.00   5000.00  1000.00      1
+ 0.02672145E+02 0.03056293E-01-0.08730260E-05 0.12009964E-09-0.06391618E-13    2
+-0.02989921E+06 0.06862817E+02 0.03386842E+02 0.03474982E-01-0.06354696E-04    3
+ 0.06968581E-07-0.02506588E-10-0.03020811E+06 0.02590232E+02                   4
+H2O2              120186H   2O   2          G  0300.00   5000.00  1000.00      1
+ 0.04573167E+02 0.04336136E-01-0.14746888E-05 0.02348903E-08-0.14316536E-13    2
+-0.01800696E+06 0.05011369E+01 0.03388753E+02 0.06569226E-01-0.14850125E-06    3
+-0.04625805E-07 0.02471514E-10-0.01766314E+06 0.06785363E+02                   4
+HO2                20387H   1O   2          G  0300.00   5000.00  1000.00      1
+ 0.04072191E+02 0.02131296E-01-0.05308145E-05 0.06112269E-09-0.02841164E-13    2
+-0.15797270E+03 0.03476029E+02 0.02979963E+02 0.04996697E-01-0.03790997E-04    3
+ 0.02354192E-07-0.08089024E-11 0.01762273E+04 0.09222724E+02                   4
+O                 120186O   1               G  0300.00   5000.00  1000.00      1
+ 0.02542059E+02-0.02755061E-03-0.03102803E-07 0.04551067E-10-0.04368051E-14    2
+ 0.02923080E+06 0.04920308E+02 0.02946428E+02-0.16381665E-02 0.02421031E-04    3
+-0.16028431E-08 0.03890696E-11 0.02914764E+06 0.02963995E+02                   4
+O2                121386O   2               G  0300.00   5000.00  1000.00      1
+ 0.03697578E+02 0.06135197E-02-0.12588420E-06 0.01775281E-09-0.11364354E-14    2
+-0.12339301E+04 0.03189165E+02 0.03212936E+02 0.11274864E-02-0.05756150E-05    3
+ 0.13138773E-08-0.08768554E-11-0.10052490E+04 0.06034737E+02                   4
+OH                121286O   1H   1          G  0300.00   5000.00  1000.00      1
+ 0.02882730E+02 0.10139743E-02-0.02276877E-05 0.02174683E-09-0.05126305E-14    2
+ 0.03886888E+05 0.05595712E+02 0.03637266E+02 0.01850910E-02-0.16761646E-05    3
+ 0.02387202E-07-0.08431442E-11 0.03606781E+05 0.13588605E+01                   4
+O_Pt               92491O   1PT  1          I    300.00   3000.00 1000.00      1
+ 0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13    2
+-0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05    3
+-0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01                   4
+O2_Pt              92491O   2PT  3          I    300.00   3000.00 1000.00      1
+ 0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13    2
+-0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05    3
+-0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01                   4
+H_Pt               92491H   1PT  1          I    300.00   3000.00 1000.00      1
+ 0.10696996E+01 0.15432230E-02-0.15500922E-06-0.16573165E-09 0.38359347E-13    2
+-0.50546128E+04-0.71555238E+01-0.13029877E+01 0.54173199E-02 0.31277972E-06    3
+-0.32328533E-08 0.11362820E-11-0.42277075E+04 0.58743238E+01                   4
+H2O_Pt             92491O   1H   2PT  1     I    300.00   3000.00 1000.00      1
+ 0.25803051E+01 0.49570827E-02-0.46894056E-06-0.52633137E-09 0.11998322E-12    2
+-0.38302234E+05-0.17406322E+02-0.27651553E+01 0.13315115E-01 0.10127695E-05    3
+-0.71820083E-08 0.22813776E-11-0.36398055E+05 0.12098145E+02                   4
+OH_Pt              92491O   1H   1PT  1     I    300.00   3000.00 1000.00      1
+ 0.18249973E+01 0.32501565E-02-0.31197541E-06-0.34603206E-09 0.79171472E-13    2
+-0.26685492E+05-0.12280891E+02-0.20340881E+01 0.93662683E-02 0.66275214E-06    3
+-0.52074887E-08 0.17088735E-11-0.25319949E+05 0.89863186E+01                   4
+_Pt_                    PT  1               S    300.0    3000.0  1000.0       1
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00    2
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00    3
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00                   4
+END
diff --git a/test/data/surface2.inp b/test/data/surface2.inp
@@ -0,0 +1,32 @@
+SITE/PT_SURFACE/    SDEN/2.72E-9/
+_Pt_ H_Pt O2_Pt/3/ H2O_Pt OH_Pt O_Pt
+END
+
+ REACTIONS      JOULES/MOLE      MWON
+ H2 + 2_Pt_  => 2H_Pt                        4.4579E+10  0.5   0.0
+					  FORD/_Pt_  1/
+ 2H_Pt        => H2 + 2_Pt_                  3.70E+21   0.00   67400.0
+                                        COV/H_Pt 0.0    0.0    -6000.0/
+                                        COV/OH_Pt 0.0    1.0    -3000.0/
+ H  +  _Pt_  => H_Pt                           1.00    0.0   0.0
+                                          STICK
+ O2 +  2_Pt_ => 2O_Pt                        1.80E+21   -0.5   0.0
+    DUPLICATE
+ O2 +  2_Pt_ => 2O_Pt                        0.023    0.00       0.00
+    DUPLICATE         STICK       MWOFF
+ 2O_Pt        => O2 + 2_Pt_                  3.70E+21   0.00   213200.0
+					COV/O_Pt 0.0    0.0   -60000.0/
+ O + _Pt_    => O_Pt                           1.00    0.0    0.0
+                                          STICK
+                                          MWON
+ H2O  + _Pt_ => H2O_Pt                         0.75    0.0    0.0
+                                          STICK
+ H2O_Pt       => H2O  + _Pt_                   1.0E+13   0.00  40300.0
+ OH  +  _Pt_ => OH_Pt                          1.00    0.0    0.0
+					  STICK
+ OH_Pt        => OH  +  _Pt_                   1.0E+13   0.00   192800.0
+ H_Pt + O_Pt  =  OH_Pt + _Pt_                  3.70E+21  0.00    11500.0
+ H_Pt + OH_Pt =  H2O_Pt + _Pt_                 3.70E+21  0.00    17400.0
+ OH_Pt + OH_Pt = H2O_Pt + O_Pt                  3.70E+21  0.00    48200.0
+ O2_Pt = O2 + 3 _Pt_                           3.70E+21  0.00    11500.0
+END
diff --git a/test/python/test_convert.py b/test/python/test_convert.py
@@ -440,6 +440,18 @@ def test_surface_mech2(self):
         self.assertEqual(covdeps["OH_Pt"]["m"], 1.0)
         self.assertNear(covdeps["H_Pt"]["E"], -6e6)
 
+    def test_surface_mech3(self):
+        # This tests the case where the thermo data for both the gas and surface are
+        # combined in a file separate from the gas and surface definitions.
+
+        output = self.convert('surface2-gas.inp', thermo='surface2-thermo.dat',
+                              surface='surface2.inp', output='surface2')
+        surf = ct.Interface(output, 'PT_SURFACE')
+
+        assert surf.n_species == 6
+        assert surf.n_reactions ==  15
+        assert surf.reaction(4).duplicate is True
+
     def test_third_body_plus_falloff_reactions(self):
         output = self.convert("third_body_plus_falloff_reaction.inp")
         gas = ct.Solution(output)