From 71bf44d11f5b8b6981dc3a32fb72cee0a8d454e2 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Thu, 20 Dec 2018 17:15:31 -0500
Subject: [PATCH] [Input] Parse YAML entries for Species objects

---
 include/cantera/thermo/Species.h  |  7 +++++++
 src/thermo/Species.cpp            | 21 +++++++++++++++++++++
 test/thermo/phaseConstructors.cpp | 23 +++++++++++++++++++++++
 3 files changed, 51 insertions(+)

diff --git a/include/cantera/thermo/Species.h b/include/cantera/thermo/Species.h
index c0d028395..8c5eb8507 100644
--- a/include/cantera/thermo/Species.h
+++ b/include/cantera/thermo/Species.h
@@ -55,12 +55,19 @@ public:
     shared_ptr<SpeciesThermoInterpType> thermo;
 
     //! Extra data used for specific models
+    //! @deprecated Superseded by #input. To be removed after Cantera 2.5.
     AnyMap extra;
+
+    //! Input parameters used to define a species, e.g. from a YAML input file.
+    AnyMap input;
 };
 
 //! Create a new Species object from a 'species' XML_Node.
 shared_ptr<Species> newSpecies(const XML_Node& species_node);
 
+//! Create a new Species object from an AnyMap specification
+unique_ptr<Species> newSpecies(const AnyMap& node);
+
 //! Generate Species objects for all `<species>` nodes in an XML document.
 //!
 //! The `<species>` nodes are assumed to be children of the `<speciesData>` node
diff --git a/src/thermo/Species.cpp b/src/thermo/Species.cpp
index 08ca73490..81240a095 100644
--- a/src/thermo/Species.cpp
+++ b/src/thermo/Species.cpp
@@ -10,6 +10,7 @@
 #include "cantera/base/ctml.h"
 #include <iostream>
 #include <limits>
+#include <set>
 
 namespace Cantera {
 
@@ -81,6 +82,26 @@ shared_ptr<Species> newSpecies(const XML_Node& species_node)
     return s;
 }
 
+unique_ptr<Species> newSpecies(const AnyMap& node)
+{
+    unique_ptr<Species> s(new Species(node.at("name").asString(),
+                                      node.at("composition").asMap<double>()));
+
+    if (node.hasKey("thermo")) {
+        s->thermo = newSpeciesThermo(node.at("thermo").as<AnyMap>());
+    } else {
+        s->thermo.reset(new SpeciesThermoInterpType());
+    }
+
+    s->size = node.getDouble("sites", 1.0);
+    if (s->composition.find("E") != s->composition.end()) {
+        s->charge = -s->composition["E"];
+    }
+
+    s->input = node;
+    return s;
+}
+
 std::vector<shared_ptr<Species> > getSpecies(const XML_Node& node)
 {
     std::vector<shared_ptr<Species> > all_species;
diff --git a/test/thermo/phaseConstructors.cpp b/test/thermo/phaseConstructors.cpp
index 1c7e84412..2349e25f5 100644
--- a/test/thermo/phaseConstructors.cpp
+++ b/test/thermo/phaseConstructors.cpp
@@ -750,4 +750,27 @@ TEST(PDSS_SSVol, fromScratch)
     EXPECT_NEAR(p.entropy_mole(), 49848.48843237689, 2e-8);
 }
 
+TEST(Species, fromYaml)
+{
+    AnyMap spec = AnyMap::fromYamlString(
+        "name: NO2\n"
+        "composition: {N: 1, O: 2}\n"
+        "units: {length: cm, quantity: mol}\n"
+        "molar-volume: 0.536\n"
+        "thermo:\n"
+        "  model: NASA7\n"
+        "  temperature-ranges: [200, 1000, 6000]\n"
+        "  data:\n"
+        "  - [3.944031200E+00, -1.585429000E-03, 1.665781200E-05, -2.047542600E-08,\n"
+        "     7.835056400E-12, 2.896617900E+03, 6.311991700E+00]\n"
+        "  - [4.884754200E+00, 2.172395600E-03, -8.280690600E-07, 1.574751000E-10,\n"
+        "     -1.051089500E-14, 2.316498300E+03, -1.174169500E-01]\n");
+
+    auto S = newSpecies(spec);
+    EXPECT_DOUBLE_EQ(S->thermo->minTemp(), 200);
+    EXPECT_EQ(S->composition.at("N"), 1);
+    // Check that units directive gets propagated to `input`
+    EXPECT_DOUBLE_EQ(S->input.convert("molar-volume", "m^3/kmol"), 0.000536);
+}
+
 } // namespace Cantera