[Transport] Add gas phase transport parameters to Species objects

include/cantera/thermo/Species.h

@@ -4,11 +4,13 @@
 #define CT_SPECIES_H
 
 #include "cantera/base/ct_defs.h"
+#include "cantera/base/smart_ptr.h"
 
 namespace Cantera
 {
 
 class SpeciesThermoInterpType;
+class TransportData;
 
 //! Contains data about a single chemical species
 /*!
@@ -49,6 +51,8 @@ public:
     //! The effective size [m] of the species
     double size;
 
+    shared_ptr<TransportData> transport;
+
 protected:
     //! Thermodynamic data for the species
     SpeciesThermoInterpType* thermo_;

include/cantera/transport/TransportData.h

@@ -0,0 +1,76 @@
+//! @file TransportData.h
+
+#ifndef CT_TRANSPORTDATA_H
+#define CT_TRANSPORTDATA_H
+
+#include "cantera/base/ct_defs.h"
+
+namespace Cantera
+{
+
+class Species;
+
+//! Base class for transport data for a single species
+class TransportData
+{
+public:
+    TransportData() {}
+    explicit TransportData(const std::string& name);
+    virtual ~TransportData() {}
+
+    virtual void validate(const Species& species) {}
+
+    //! The name of the species
+    std::string name;
+};
+
+//! Transport data for a single gas-phase species which can be used in
+//! mixture-averaged or multicomponent transport models.
+class GasTransportData : public TransportData
+{
+public:
+    GasTransportData();
+
+    GasTransportData(const std::string& name, const std::string& geometry,
+                     double diameter, double well_depth, double dipole=0.0,
+                     double polarizability=0.0, double rot_relax=0.0,
+                     double acentric=0.0);
+
+    //! Set the parameters using "customary" units: diameter in Angstroms, well
+    //! depth in Kelvin, dipole in Debye, and polarizability in Angstroms^3.
+    //! These are the units used in in CK-style input files.
+    void setCustomaryUnits(const std::string& name, const std::string& geometry,
+                           double diameter, double well_depth, double dipole=0.0,
+                           double polarizability=0.0, double rot_relax=0.0,
+                           double acentric=0.0);
+
+    virtual void validate(const Species& species);
+
+    //! A string specifying the molecular geometry. One of `atom`, `linear`, or
+    //! `nonlinear`.
+    std::string geometry;
+
+    //! The Lennard-Jones collision diameter [m]
+    double diameter;
+
+    //! The Lennard-Jones well depth [J]
+    double well_depth;
+
+    //! The permanent dipole moment of the molecule [Coulomb-m]. Default 0.0.
+    double dipole;
+
+    //! The polarizability of the molecule [m^3]. Default 0.0.
+    double polarizability;
+
+    //! The rotational relaxation number (the number of collisions it takes to
+    //! equilibrate the rotational degrees of freedom with the temperature).
+    //! Default 0.0.
+    double rotational_relaxation;
+
+    // Pitzer's acentric factor [dimensionless]. Default 0.0.
+    double acentric_factor;
+};
+
+}
+
+#endif

src/thermo/Species.cpp

@@ -35,6 +35,7 @@ Species::Species(const Species& other)
     , composition(other.composition)
     , charge(other.charge)
     , size(other.size)
+    , transport(other.transport)
 {
     if (other.thermo_) {
         thermo_ = other.thermo_->duplMyselfAsSpeciesThermoInterpType();
@@ -52,6 +53,7 @@ Species& Species::operator=(const Species& other)
     composition = other.composition;
     charge = other.charge;
     size = other.size;
+    transport = other.transport;
     delete thermo_;
     if (other.thermo_) {
         thermo_ = other.thermo_->duplMyselfAsSpeciesThermoInterpType();

src/thermo/ThermoFactory.cpp

@@ -52,6 +52,8 @@
 #include "cantera/thermo/MixedSolventElectrolyte.h"
 #include "cantera/thermo/IdealSolnGasVPSS.h"
 
+#include "cantera/transport/TransportData.h"
+
 #include "cantera/base/stringUtils.h"
 
 using namespace std;
@@ -621,7 +623,37 @@ bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
         vp_ptr->createInstallPDSS(k, s, phaseNode_ptr);
     } else {
         SpeciesThermoInterpType* st = newSpeciesThermoInterpType(s);
-        th.addSpecies(Species(s["name"], comp_map, st, chrg, sz));
+        Species sp(s["name"], comp_map, st, chrg, sz);
+
+        // Read gas-phase transport data, if provided
+        if (s.hasChild("transport") &&
+                s.child("transport")["model"] == "gas_transport") {
+            XML_Node& tr = s.child("transport");
+
+            string geometry, dummy;
+            getString(tr, "geometry", geometry, dummy);
+
+            double diam = getFloat(tr, "LJ_diameter");
+            double welldepth = getFloat(tr, "LJ_welldepth");
+
+            double dipole = 0.0;
+            getOptionalFloat(tr, "dipoleMoment", dipole);
+
+            double polar = 0.0;
+            getOptionalFloat(tr, "polarizability", polar);
+
+            double rot = 0.0;
+            getOptionalFloat(tr, "rotRelax", rot);
+            double acentric = 0.0;
+            getOptionalFloat(tr, "acentric_factor", acentric);
+
+            GasTransportData* gastran = new GasTransportData;
+            gastran->setCustomaryUnits(sp.name, geometry, diam, welldepth,
+                                   dipole, polar, rot, acentric);
+            sp.transport.reset(gastran);
+            gastran->validate(sp);
+        }
+        th.addSpecies(sp);
     }
 
     return true;

src/transport/TransportData.cpp

@@ -0,0 +1,116 @@
+//! @file TransportData.cpp
+
+#include "cantera/transport/TransportData.h"
+#include "cantera/thermo/Species.h"
+#include "cantera/base/ctexceptions.h"
+#include "cantera/base/stringUtils.h"
+
+namespace Cantera
+{
+
+TransportData::TransportData(const std::string& name_)
+    : name(name_)
+{
+}
+
+GasTransportData::GasTransportData()
+    : diameter(0.0)
+    , well_depth(0.0)
+    , dipole(0.0)
+    , polarizability(0.0)
+    , rotational_relaxation(0.0)
+    , acentric_factor(0.0)
+{
+}
+
+GasTransportData::GasTransportData(
+        const std::string& name_, const std::string& geometry_,
+        double diameter_, double well_depth_, double dipole_,
+        double polarizability_, double rot_relax, double acentric)
+    : TransportData(name_)
+    , geometry(geometry_)
+    , diameter(diameter_)
+    , well_depth(well_depth_)
+    , dipole(dipole_)
+    , polarizability(polarizability_)
+    , rotational_relaxation(rot_relax)
+    , acentric_factor(acentric)
+{
+}
+
+void GasTransportData::setCustomaryUnits(
+        const std::string& name_, const std::string& geometry_,
+        double diameter_, double well_depth_, double dipole_,
+        double polarizability_, double rot_relax, double acentric)
+{
+    name = name_;
+    geometry = geometry_;
+    diameter = 1e-10 * diameter_; // convert from Angstroms to m
+    well_depth = Boltzmann * well_depth_; // convert from K to J
+    dipole = 1e-21 / lightSpeed * dipole_; // convert from Debye to Coulomb-m
+    polarizability = 1e-30 * polarizability_; // convert from Angstroms^3 to m^3
+    rotational_relaxation = rot_relax; // pure number
+    acentric_factor = acentric; // dimensionless
+}
+
+void GasTransportData::validate(const Species& sp)
+{
+    double nAtoms = 0;
+    for (compositionMap::const_iterator iter = sp.composition.begin();
+         iter != sp.composition.end();
+         ++iter) {
+        nAtoms += iter->second;
+    }
+
+    if (geometry == "atom") {
+        if (nAtoms != 1) {
+            throw CanteraError("GasTransportData::validate",
+                "invalid geometry for species '" + name + "'. 'atom' specified,"
+                " but species contains multiple atoms.");
+        }
+    } else if (geometry == "linear") {
+        if (nAtoms == 1) {
+            throw CanteraError("GasTransportData::validate",
+                "invalid geometry for species '" + name + "'. 'linear'"
+                " specified, but species only contains one atom.");
+        }
+    } else if (geometry == "nonlinear") {
+        if (nAtoms < 3) {
+            throw CanteraError("GasTransportData::validate",
+                "invalid geometry for species '" + name + "'. 'nonlinear'"
+                " specified, but species only contains " + fp2str(nAtoms) +
+                " atoms.");
+        }
+    } else {
+        throw CanteraError("GasTransportData::validate",
+                           "invalid geometry for species '" + name + "': '" +
+                           geometry + "'.");
+    }
+
+    if (well_depth < 0.0) {
+        throw CanteraError("GasTransportData::validate",
+                           "negative well depth for species '" + name + "'.");
+    }
+
+    if (diameter <= 0.0) {
+        throw CanteraError("GasTransportData::validate",
+            "negative or zero diameter for species '" + name + "'.");
+    }
+
+    if (dipole < 0.0) {
+        throw CanteraError("GasTransportData::validate",
+            "negative dipole moment for species '" + name + "'.");
+    }
+
+    if (polarizability < 0.0) {
+        throw CanteraError("GasTransportData::validate",
+            "negative polarizability for species '" + name + "'.");
+    }
+
+    if (rotational_relaxation < 0.0) {
+        throw CanteraError("GasTransportData::validate",
+            "negative rotation relaxation number for species '" + name + "'");
+    }
+}
+
+}