[Input] Read species Transport data from YAML / AnyMap

include/cantera/transport/TransportData.h

@@ -13,6 +13,7 @@ namespace Cantera
 
 class Species;
 class XML_Node;
+class AnyMap;
 
 //! Base class for transport data for a single species
 class TransportData
@@ -87,6 +88,9 @@ public:
 //! Create a new TransportData object from a 'transport' XML_Node.
 shared_ptr<TransportData> newTransportData(const XML_Node& transport_node);
 
+//! Create a new TransportData object from an AnyMap specification
+unique_ptr<TransportData> newTransportData(const AnyMap& node);
+
 }
 
 #endif

src/thermo/Species.cpp

@@ -98,7 +98,23 @@ unique_ptr<Species> newSpecies(const AnyMap& node)
         s->charge = -s->composition["E"];
     }
 
-    s->input = node;
+    if (node.hasKey("transport")) {
+        s->transport = newTransportData(node["transport"].as<AnyMap>());
+        s->transport->validate(*s);
+    }
+
+    // Store input parameters in the "input" map, unless they are stored in a
+    // child object
+    const static std::set<std::string> known_keys{
+        "transport"
+    };
+    s->input.applyUnits(node.units());
+    for (const auto& item : node) {
+        if (known_keys.count(item.first) == 0) {
+            s->input[item.first] = item.second;
+        }
+    }
+
     return s;
 }
 

src/transport/TransportData.cpp

@@ -154,6 +154,22 @@ void setupGasTransportData(GasTransportData& tr, const XML_Node& tr_node)
                          rot, acentric, dispersion, quad);
 }
 
+void setupGasTransportData(GasTransportData& tr, const AnyMap& node)
+{
+    std::string geometry = node["geometry"].asString();
+    double welldepth = node["well-depth"].asDouble();
+    double diameter = node["diameter"].asDouble();
+    double dipole = node.getDouble("dipole", 0.0);
+    double polar = node.getDouble("polarizability", 0.0);
+    double rot = node.getDouble("rotational-relaxation", 0.0);
+    double acentric = node.getDouble("acentric-factor", 0.0);
+    double dispersion = node.getDouble("dispersion-coefficient", 0.0);
+    double quad = node.getDouble("quadrupole-polarizability", 0.0);
+
+    tr.setCustomaryUnits(geometry, diameter, welldepth, dipole, polar,
+                         rot, acentric, dispersion, quad);
+}
+
 shared_ptr<TransportData> newTransportData(const XML_Node& transport_node)
 {
     std::string model = transport_node["model"];
@@ -167,4 +183,16 @@ shared_ptr<TransportData> newTransportData(const XML_Node& transport_node)
     }
 }
 
+unique_ptr<TransportData> newTransportData(const AnyMap& node)
+{
+    if (node.getString("model", "") == "gas") {
+        unique_ptr<GasTransportData> tr(new GasTransportData());
+        setupGasTransportData(*tr, node);
+        return unique_ptr<TransportData>(move(tr));
+    } else {
+        // Transport model not handled here
+        return unique_ptr<TransportData>(new TransportData());
+    }
+}
+
 }