Merge pull request #550 from pbauman/thermochem-parsing-part2-antioch

Thermochemsity Parsing Refactoring Part 2: Antioch

CHANGES

@@ -1,9 +1,22 @@
 Version 0.9.0 (in progress)
    * C++11 compiler now required
    * Minimum libMesh git hash for this release is: 2d9b8bc
+   * Minimum Antioch git hash is now: e17822d
    * Use factory pattern for DiffSolver, now support
      specifying DiffSolver type in inputfile,
      add support for libMesh::PetscDiffSolver
+   * Refactor thermochemistry input options parsing.
+     See master_example_inputfile.in for details. Backward
+     compatibility with the input file will be maintained
+     for one release.
+   * Add Full support for Antioch XML parser for parsing
+     Antioch thermochemistry and transport data
+   * Update Cantera transport to respect transport model
+     specified in the XML file.
+   * Updated ozone_flame example with run scripts for both
+     Antioch and Cantera versions. Also updated to illustrate
+     overriding input options on the command line and AMR
+     for the final step.
 
 Version 0.8.0
    * Minimum libMesh git hash for this release is: 8be0a4e

README.md

@@ -38,11 +38,10 @@ Optional Packages
 -----------------
 
 To enable the reacting low Mach Navier-Stokes physics class, GRINS must be compiled with
-an external chemistry library. While [Cantera](http://code.google.com/p/cantera/) is
-partially supported, [Antioch](https://github.com/libantioch/antioch) is fully
-supported.
+an external chemistry library. Both [Cantera](http://code.google.com/p/cantera/) and
+[Antioch](https://github.com/libantioch/antioch) are fully supported.
 
-The current required minimum hash for using Antioch is libantioch/antioch@ad78595 (libantioch/antioch#240).
+The current required minimum hash for using Antioch is libantioch/antioch@e17822d (libantioch/antioch#265).
 
 
 Building GRINS 

examples/master_example_inputfile.in

@@ -173,9 +173,6 @@
         # Notify that we're using Cantera
         thermochemistry_library = 'cantera'
 
-        # Species in this gas mixture
-        species = 'N2 N C CN'
-
         [./Cantera]
            # Specify the mixture to be used. This is the "mixture" or "phase"
            # given in the chemical_data file. The user must set this
@@ -197,37 +194,63 @@
    # Arbitrary material name. Here we describe input parameters related
    # to the Antioch thermochemistry library. These are used for reacting
    # flow Physics. Note that units here *must* be SI.
+   # Although we support ASCII input to Antioch, XML format is much preferred.
+   # The parsing type is determined by the suffix on the chemical data file:
+   # .dat --> ASCII
+   # .xml --> XML
+   # .chemkin --> CHEMKIN (not yet supported)
    [./AntiochMaterial]
       [./GasMixture]
          # Notify that we're using Antioch
          thermochemistry_library = 'antioch'
 
-         # Species in this gas mixture
-         species = 'N2 N C CN'
-
-         # Path to file containing kinetics data.
-         kinetics_data = 'datafile.xml'
-
          # Antioch model specification
          [./Antioch]
 
+           # For XML, we assume you have all kinetics, thermo, and transport data
+           # (modulo Blotter or Sutherland data, which are specified in separate files).
+           # For the thermo, we will query the XML file to determine whether it's NASA7
+           # or NASA9. NASA models are always used for the chemistry and if
+           # thermo_model (see below) is ideal_gas, then that NASA model will
+           # also be used there.
+           chemical_data = 'datafile.xml'
+
+           # Specify the mixture to be used. This is the "mixture" or "phase"
+           # given in the chemical_data file if it's an xml file.
+           # The user must set this when using an XML file since the data file
+           # may contain more than one mixture. If using ASCII parsing, this
+           # variable is not used and not needed.
+           gas_mixture = 'air4sp'
+
+
            # The type of transport model. Currently accepted values
            # are: constant, mixture_averaged
            transport_model = 'constant'
 
            # Model used for computing thermodynamic quantities.
-           # Currently accepted values are: cea, stat_mech
-           # Note: CEA data is internally used to the kinetics
-           #       calculation and this option will not effect that.
-           thermo_model = 'cea'
+           # Currently accepted values are: ideal_gas, stat_mech
+           #
+           # ideal_gas corresponds to assuming electronic states are not populated
+           # and vibrational are partially populated and computed by taking the NASA
+           # curve fit value for the total and subtracting the translational and
+           # vibrational energy. This is a common model in combustion applications.
+           #
+           # stat_mech will use statistical mechanics relations to compute translational,
+           # rotational, vibrational, and electronic energies. Note these strongly depend
+           # on having the correct modes/degenercies for vibrational and electronic states
+           # for each species.
+           thermo_model = 'ideal_gas'
 
            # Model used for computing viscosity.
            # Currently accepted values are:
            #   constant (only valid with transport_model = constant)
            #   blottner (transport_model = mixture_averaged, requires blottner_data)
            #   sutherland (transport_model = mixture_averaged, requires sutherland_data),
-           #   kinetics_theory (transport_model = mixture_averaged, requires transport_data, requires
-           #                    thermal_conductivity_model and mass_diffusivity_model to  be kinetics_theory)
+           #   kinetics_theory (* transport_model = mixture_averaged,
+           #                    * requires transport_data if using ASCII parsing or have data in XML file
+           #                      if using XML parsing
+           #                    * requires thermal_conductivity_model and mass_diffusivity_model
+           #                      to  be kinetics_theory)
            #
            # For viscosity_model = 'constant', the viscosity value
            # will be parsed from [Materials/material-name/Viscosity/value]
@@ -238,8 +261,11 @@
            #   constant (only valid with transport_model = constant)
            #   constant_prandtl
            #   eucken (transport_model = mixture_averaged, requires thermo_model = stat_mech)
-           #   kinetics_theory (transport_model = mixture_averaged, requires transport_data, requires
-           #                    viscosity_model and mass_diffusivity_model to be kinetics_theory)
+           #   kinetics_theory (* transport_model = mixture_averaged,
+           #                    * requires transport_data if using ASCII parsing or have data in XML file
+           #                      if using XML parsing 
+           #                    * requires viscosity_model and mass_diffusivity_model
+           #                      to be kinetics_theory)
            #
            # For thermal_conductivity_model = 'constant', the conductivity value
            # will be parsed from [Materials/material-name/ThermalConductivity/value]
@@ -251,8 +277,11 @@
            # Model used for computing mass diffusivity
            # Currently accepted values are:
            #   constant_lewis (transport_model = mixture_averaged, constant)
-           #   kinetics_theory (transport_model = mixture_averaged, requires transport_data, requires
-           #                    viscosity_model and thermal_conductivity_model to be kinetics_theory)
+           #   kinetics_theory (* transport_model = mixture_averaged,
+           #                    * requires transport_data if using ASCII parsing or have data in XML file
+           #                      if using XML parsing
+           #                    * requires viscosity_model and thermal_conductivity_model
+           #                      to be kinetics_theory)
            #
            # For  mass_diffusivity_model = 'constant_lewis', the lewis number
            # will be parsed from [Materials/material-name/LewisNumber/value]

src/physics/include/grins/antioch_instantiation_macro.h

@@ -41,18 +41,20 @@
                                    Antioch::EuckenThermalConductivity<Antioch::StatMechThermodynamics<libMesh::Real> >, \
                                    Antioch::ConstantLewisDiffusivity<libMesh::Real> >; \
   template class GRINS::class_name<curve_fit,                           \
-                                   Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit>, libMesh::Real>, \
+                                   Antioch::IdealGasThermo<curve_fit,libMesh::Real>, \
                                    Antioch::SutherlandViscosity<libMesh::Real>, \
-                                   Antioch::EuckenThermalConductivity<Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit>, libMesh::Real> >, \
+                                   Antioch::EuckenThermalConductivity<Antioch::IdealGasThermo<curve_fit,libMesh::Real> >, \
                                    Antioch::ConstantLewisDiffusivity<libMesh::Real> >; \
   template class GRINS::class_name<curve_fit,                           \
-                                   Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit>, libMesh::Real>, \
+                                   Antioch::IdealGasThermo<curve_fit,libMesh::Real>, \
                                    Antioch::BlottnerViscosity<libMesh::Real>, \
-                                   Antioch::EuckenThermalConductivity<Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit>, libMesh::Real> >, \
+                                   Antioch::EuckenThermalConductivity<Antioch::IdealGasThermo<curve_fit,libMesh::Real> >, \
                                    Antioch::ConstantLewisDiffusivity<libMesh::Real> >
 
 #define INSTANTIATE_ANTIOCH_TRANSPORT(class_name)                       \
-  INSTANTIATE_ANTIOCH_TRANSPORT_RAW(class_name,Antioch::CEACurveFit<libMesh::Real>)
+  INSTANTIATE_ANTIOCH_TRANSPORT_RAW(class_name,Antioch::CEACurveFit<libMesh::Real>); \
+  INSTANTIATE_ANTIOCH_TRANSPORT_RAW(class_name,Antioch::NASA7CurveFit<libMesh::Real>); \
+  INSTANTIATE_ANTIOCH_TRANSPORT_RAW(class_name,Antioch::NASA9CurveFit<libMesh::Real>)
 
 #ifdef ANTIOCH_HAVE_GSL
 #define INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT_RAW(class_name,curve_fit) \
@@ -62,13 +64,15 @@
                                    Antioch::KineticsTheoryThermalConductivity<Antioch::StatMechThermodynamics<libMesh::Real>,libMesh::Real>, \
                                    Antioch::MolecularBinaryDiffusion<libMesh::Real,Antioch::GSLSpliner> >; \
   template class GRINS::class_name<curve_fit,                           \
-                                   Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit>, libMesh::Real>, \
+                                   Antioch::IdealGasThermo<curve_fit,libMesh::Real>, \
                                    Antioch::KineticsTheoryViscosity<libMesh::Real,Antioch::GSLSpliner>, \
-                                   Antioch::KineticsTheoryThermalConductivity<Antioch::IdealGasMicroThermo<Antioch::NASAEvaluator<libMesh::Real,curve_fit> >,libMesh::Real>, \
+                                   Antioch::KineticsTheoryThermalConductivity<Antioch::IdealGasThermo<curve_fit,libMesh::Real>, libMesh::Real>, \
                                    Antioch::MolecularBinaryDiffusion<libMesh::Real,Antioch::GSLSpliner> >
 
 #define INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT(class_name)       \
-  INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT_RAW(class_name,Antioch::CEACurveFit<libMesh::Real>)
+  INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT_RAW(class_name,Antioch::CEACurveFit<libMesh::Real>); \
+  INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT_RAW(class_name,Antioch::NASA7CurveFit<libMesh::Real>); \
+  INSTANTIATE_ANTIOCH_KINETICS_THEORY_TRANSPORT_RAW(class_name,Antioch::NASA9CurveFit<libMesh::Real>)
 
 #endif // ANTIOCH_HAVE_GSL