From 26bd71af539d964a1ac5dd920734e7628f5fcd6f Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Wed, 30 Jan 2019 15:24:02 -0500
Subject: [PATCH] [Input] Create Surface and Edge phases from YAML definitions

---
 include/cantera/thermo/SurfPhase.h |  1 +
 src/thermo/SurfPhase.cpp           |  9 ++++++
 src/thermo/ThermoFactory.cpp       |  2 ++
 test/data/surface-phases.yaml      | 44 ++++++++++++++++++++++++++++++
 test/thermo/thermoFromYaml.cpp     | 23 ++++++++++++++++
 5 files changed, 79 insertions(+)
 create mode 100644 test/data/surface-phases.yaml

diff --git a/include/cantera/thermo/SurfPhase.h b/include/cantera/thermo/SurfPhase.h
index 3cfc1ffb8..3b5cf04b5 100644
--- a/include/cantera/thermo/SurfPhase.h
+++ b/include/cantera/thermo/SurfPhase.h
@@ -284,6 +284,7 @@ public:
      * @endcode
      */
     virtual void setParametersFromXML(const XML_Node& thermoData);
+    virtual void initThermo();
 
     virtual bool addSpecies(shared_ptr<Species> spec);
 
diff --git a/src/thermo/SurfPhase.cpp b/src/thermo/SurfPhase.cpp
index 6c0a466a2..dac2d997e 100644
--- a/src/thermo/SurfPhase.cpp
+++ b/src/thermo/SurfPhase.cpp
@@ -323,6 +323,15 @@ void SurfPhase::setParametersFromXML(const XML_Node& eosdata)
     setSiteDensity(n);
 }
 
+void SurfPhase::initThermo()
+{
+    if (m_input.hasKey("site-density")) {
+        // Units are kmol/m^2 for surface phases or kmol/m for edge phases
+        setSiteDensity(m_input.convert("site-density",
+            Units(1.0, 0, -static_cast<double>(m_ndim), 0, 0, 0, 1)));
+    }
+}
+
 void SurfPhase::setStateFromXML(const XML_Node& state)
 {
     double t;
diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp
index aa0bec293..4934143b0 100644
--- a/src/thermo/ThermoFactory.cpp
+++ b/src/thermo/ThermoFactory.cpp
@@ -53,7 +53,9 @@ ThermoFactory::ThermoFactory()
     m_synonyms["ideal-gas"] = "IdealGas";
     reg("Incompressible", []() { return new ConstDensityThermo(); });
     reg("Surface", []() { return new SurfPhase(); });
+    m_synonyms["ideal-surface"] = "Surface";
     reg("Edge", []() { return new EdgePhase(); });
+    m_synonyms["edge"] = "Edge";
     reg("Metal", []() { return new MetalPhase(); });
     reg("StoichSubstance", []() { return new StoichSubstance(); });
     m_synonyms["fixed-stoichiometry"] = "StoichSubstance";
diff --git a/test/data/surface-phases.yaml b/test/data/surface-phases.yaml
new file mode 100644
index 000000000..0c145dd5a
--- /dev/null
+++ b/test/data/surface-phases.yaml
@@ -0,0 +1,44 @@
+phases:
+- name: Pt-surf
+  thermo: ideal-surface
+  species: [{Pt-surf-species: all}]
+  site-density: 2.7063e-9 mol/cm^2
+  state: {T: 900 K, P: 1 atm, coverages: {Pt(s): 0.5, H(s): 0.4, O(s): 0.1}}
+
+- name: TPB
+  thermo: edge
+  species: [(tpb)]
+  site-density: 5e-17 mol/cm
+  state: {T: 1073.15 K, P: 1 atm, coverages: {(tpb): 1.0}}
+
+species:
+- name: (tpb)
+  composition: {}
+  thermo:
+    model: constant-cp
+
+Pt-surf-species:
+- name: Pt(s)
+  composition: {Pt: 1}
+  thermo:
+    model: constant-cp
+- name: H(s)
+  composition: {H: 1, Pt: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300, 1000, 3000]
+    data:
+    - [-1.3029877E+00, 5.4173199E-03, 3.1277972E-07, -3.2328533E-09,
+       1.1362820E-12, -4.2277075E+03, 5.8743238E+00]
+    - [1.0696996E+00, 1.5432230E-03, -1.5500922E-07, -1.6573165E-10,
+       3.8359347E-14, -5.0546128E+03, -7.1555238E+00]
+- name: O(s)
+  composition: {O: 1, Pt: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300, 1000, 3000]
+    data:
+    - [-9.4986904E-01, 7.4042305E-03, -1.0451424E-06, -6.1120420E-09,
+       3.3787992E-12, -1.3209912E+04, 3.6137905E+00]
+    - [1.9454180E+00, 9.1761647E-04, -1.1226719E-07, -9.9099624E-11,
+       2.4307699E-14, -1.4005187E+04, -1.1531663E+01]
diff --git a/test/thermo/thermoFromYaml.cpp b/test/thermo/thermoFromYaml.cpp
index 18e4f22cc..ad410d588 100644
--- a/test/thermo/thermoFromYaml.cpp
+++ b/test/thermo/thermoFromYaml.cpp
@@ -3,6 +3,7 @@
 #include "cantera/thermo/Elements.h"
 #include "cantera/thermo/MolalityVPSSTP.h"
 #include "cantera/thermo/IdealGasPhase.h"
+#include "cantera/thermo/SurfPhase.h"
 
 using namespace Cantera;
 
@@ -86,6 +87,28 @@ TEST(ThermoFromYaml, StoichSubstance2)
     EXPECT_NEAR(thermo->density(), 1980, 0.1);
 }
 
+TEST(ThermoFromYaml, SurfPhase)
+{
+    auto thermo = newThermo("surface-phases.yaml", "Pt-surf");
+    EXPECT_EQ(thermo->type(), "Surf");
+    EXPECT_EQ(thermo->nSpecies(), (size_t) 3);
+    auto surf = std::dynamic_pointer_cast<SurfPhase>(thermo);
+    EXPECT_DOUBLE_EQ(surf->siteDensity(), 2.7063e-8);
+    vector_fp cov(surf->nSpecies());
+    surf->getCoverages(cov.data());
+    EXPECT_DOUBLE_EQ(cov[surf->speciesIndex("Pt(s)")], 0.5);
+    EXPECT_DOUBLE_EQ(cov[surf->speciesIndex("H(s)")], 0.4);
+}
+
+TEST(ThermoFromYaml, EdgePhase)
+{
+    auto thermo = newThermo("surface-phases.yaml", "TPB");
+    EXPECT_EQ(thermo->type(), "Edge");
+    EXPECT_EQ(thermo->nSpecies(), (size_t) 1);
+    auto edge = std::dynamic_pointer_cast<SurfPhase>(thermo);
+    EXPECT_DOUBLE_EQ(edge->siteDensity(), 5e-18);
+}
+
 TEST(ThermoFromYaml, WaterSSTP)
 {
     auto thermo = newThermo("thermo-models.yaml", "liquid-water");