From 37652e88c71937440d9850073b59673fc71757cb Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Wed, 14 Aug 2019 15:16:07 -0500
Subject: [PATCH 1/6] [Reactor] YAML summary of ReactorNet

* recreate ReactorNet structure
* list ReactorBase, WallBase, FlowDevice and ReactorSurface objects
* create of unique names based on
* implementation for Phase list is partial, Kinetics is missing
* names only available for ReactorBase
---
 include/cantera/zeroD/FlowDevice.h            |   5 +-
 include/cantera/zeroD/ReactorBase.h           |   8 +
 include/cantera/zeroD/ReactorNet.h            |   4 +
 include/cantera/zeroD/ReactorSurface.h        |   3 +
 include/cantera/zeroD/Wall.h                  |   5 +-
 interfaces/cython/cantera/_cantera.pxd        |   5 +
 .../cantera/examples/reactors/ic_engine.py    |  10 +-
 interfaces/cython/cantera/reactor.pyx         |  20 +++
 src/zeroD/FlowDevice.cpp                      |  20 +++
 src/zeroD/ReactorBase.cpp                     |  20 +++
 src/zeroD/ReactorNet.cpp                      | 165 ++++++++++++++++++
 src/zeroD/ReactorSurface.cpp                  |  20 +++
 src/zeroD/Wall.cpp                            |  20 +++
 13 files changed, 298 insertions(+), 7 deletions(-)

diff --git a/include/cantera/zeroD/FlowDevice.h b/include/cantera/zeroD/FlowDevice.h
index 46902db7706..e10d9a1ea4b 100644
--- a/include/cantera/zeroD/FlowDevice.h
+++ b/include/cantera/zeroD/FlowDevice.h
@@ -54,6 +54,9 @@ class FlowDevice
         return m_type;
     }
 
+    //! Generate self-documenting YAML string.
+    virtual std::string toYAML() const;
+
     //! Mass flow rate (kg/s).
     //! @deprecated The 'time' argument will be removed after Cantera 2.5.
     //!     Evaluating the mass flow rate at times other than the current time
@@ -101,7 +104,7 @@ class FlowDevice
     }
 
     //! Return a const reference to the downstream reactor.
-    const ReactorBase& out() const {
+    ReactorBase& out() const {
         return *m_out;
     }
 
diff --git a/include/cantera/zeroD/ReactorBase.h b/include/cantera/zeroD/ReactorBase.h
index 9ac35a5398e..b1af0d69c2e 100644
--- a/include/cantera/zeroD/ReactorBase.h
+++ b/include/cantera/zeroD/ReactorBase.h
@@ -101,6 +101,9 @@ class ReactorBase
         throw NotImplementedError("ReactorBase::setChemistry");
     }
 
+    //! Generate self-documenting YAML string.
+    virtual std::string toYAML() const;
+
     //! Set the energy equation on or off.
     virtual void setEnergy(int eflag = 1) {
         throw NotImplementedError("ReactorBase::setEnergy");
@@ -136,6 +139,11 @@ class ReactorBase
         return m_wall.size();
     }
 
+    //! Return the number of ReactorSurface objects connected to this reactor.
+    size_t nSurfaces() {
+        return m_surfaces.size();
+    }
+
     //! Insert a Wall between this reactor and another reactor.
     /*!
      *  `lr` = 0 if this reactor is to the left of the wall and `lr` = 1 if
diff --git a/include/cantera/zeroD/ReactorNet.h b/include/cantera/zeroD/ReactorNet.h
index af656e07311..3b48140e32f 100644
--- a/include/cantera/zeroD/ReactorNet.h
+++ b/include/cantera/zeroD/ReactorNet.h
@@ -31,6 +31,7 @@ class ReactorNet : public FuncEval
     //! @name Methods to set up a simulation.
     //@{
 
+
     //! Set initial time. Default = 0.0 s. Restarts integration from this time
     //! using the current mixture state as the initial condition.
     void setInitialTime(double time);
@@ -102,6 +103,9 @@ class ReactorNet : public FuncEval
 
     //@}
 
+    //! Generate self-documenting YAML string.
+    std::string toYAML() const;
+
     //! Add the reactor *r* to this reactor network.
     void addReactor(Reactor& r);
 
diff --git a/include/cantera/zeroD/ReactorSurface.h b/include/cantera/zeroD/ReactorSurface.h
index e3a4d3d2994..cabb9155e63 100644
--- a/include/cantera/zeroD/ReactorSurface.h
+++ b/include/cantera/zeroD/ReactorSurface.h
@@ -22,6 +22,9 @@ class ReactorSurface
     ReactorSurface(const ReactorSurface&) = delete;
     ReactorSurface& operator=(const ReactorSurface&) = delete;
 
+    //! Generate self-documenting YAML string.
+    virtual std::string toYAML() const;
+
     //! Returns the surface area [m^2]
     double area() const;
 
diff --git a/include/cantera/zeroD/Wall.h b/include/cantera/zeroD/Wall.h
index ff7fe0a4690..41e3bdef0bd 100644
--- a/include/cantera/zeroD/Wall.h
+++ b/include/cantera/zeroD/Wall.h
@@ -40,6 +40,9 @@ class WallBase
         return "WallBase";
     }
 
+    //! Generate self-documenting YAML string.
+    virtual std::string toYAML() const;
+
     //! Rate of volume change (m^3/s) for the adjacent reactors.
     /*!
      * This method is called by Reactor::evalWalls(). Base class method
@@ -95,7 +98,7 @@ class WallBase
     }
 
     //! Return a reference to the Reactor or Reservoir to the right of the wall.
-    const ReactorBase& right() {
+    ReactorBase& right() const {
         return *m_right;
     }
 
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 26ff56dcd3c..3607964a856 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -546,6 +546,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxReactorBase "Cantera::ReactorBase":
         CxxReactorBase()
         string typeStr()
+        string toYAML()
         void setThermoMgr(CxxThermoPhase&) except +translate_exception
         void restoreState() except +translate_exception
         void syncState() except +translate_exception
@@ -582,6 +583,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxWallBase "Cantera::WallBase":
         CxxWallBase()
         string type()
+        string toYAML()
         cbool install(CxxReactorBase&, CxxReactorBase&)
         double area()
         void setArea(double)
@@ -610,6 +612,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
 
     cdef cppclass CxxReactorSurface "Cantera::ReactorSurface":
         CxxReactorSurface()
+        string toYAML()
         double area()
         void setArea(double)
         void setKinetics(CxxKinetics*)
@@ -625,6 +628,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
         CxxFlowDevice()
         string typeStr()
         double massFlowRate() except +translate_exception
+        string toYAML()
         double massFlowRate(double) except +translate_exception
         cbool install(CxxReactorBase&, CxxReactorBase&) except +translate_exception
         void setPressureFunction(CxxFunc1*) except +translate_exception
@@ -652,6 +656,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxReactorNet "Cantera::ReactorNet":
         CxxReactorNet()
         void addReactor(CxxReactor&)
+        string toYAML()
         double advance(double, cbool) except +translate_exception
         double step() except +translate_exception
         void initialize() except +translate_exception
diff --git a/interfaces/cython/cantera/examples/reactors/ic_engine.py b/interfaces/cython/cantera/examples/reactors/ic_engine.py
index c1260cfd0ee..f65c5190351 100644
--- a/interfaces/cython/cantera/examples/reactors/ic_engine.py
+++ b/interfaces/cython/cantera/examples/reactors/ic_engine.py
@@ -97,12 +97,12 @@ def piston_speed(t):
 
 # define initial state and set up reactor
 gas.TPX = T_inlet, p_inlet, comp_inlet
-cyl = ct.IdealGasReactor(gas)
+cyl = ct.IdealGasReactor(gas, name='Cylinder')
 cyl.volume = V_oT
 
 # define inlet state
 gas.TPX = T_inlet, p_inlet, comp_inlet
-inlet = ct.Reservoir(gas)
+inlet = ct.Reservoir(gas, name='Inlet')
 
 # inlet valve
 inlet_valve = ct.Valve(inlet, cyl)
@@ -113,7 +113,7 @@ def piston_speed(t):
 
 # define injector state (gaseous!)
 gas.TPX = T_injector, p_injector, comp_injector
-injector = ct.Reservoir(gas)
+injector = ct.Reservoir(gas, name='Fuel')
 
 # injector is modeled as a mass flow controller
 injector_mfc = ct.MassFlowController(injector, cyl)
@@ -125,7 +125,7 @@ def piston_speed(t):
 
 # define outlet pressure (temperature and composition don't matter)
 gas.TPX = T_ambient, p_outlet, comp_ambient
-outlet = ct.Reservoir(gas)
+outlet = ct.Reservoir(gas, name='Outlet')
 
 # outlet valve
 outlet_valve = ct.Valve(cyl, outlet)
@@ -136,7 +136,7 @@ def piston_speed(t):
 
 # define ambient pressure (temperature and composition don't matter)
 gas.TPX = T_ambient, p_ambient, comp_ambient
-ambient_air = ct.Reservoir(gas)
+ambient_air = ct.Reservoir(ct.Solution('air.cti'), name='Ambient')
 
 # piston is modeled as a moving wall
 piston = ct.Wall(ambient_air, cyl)
diff --git a/interfaces/cython/cantera/reactor.pyx b/interfaces/cython/cantera/reactor.pyx
index 2bde1067d72..d1bae5d5786 100644
--- a/interfaces/cython/cantera/reactor.pyx
+++ b/interfaces/cython/cantera/reactor.pyx
@@ -63,6 +63,10 @@ cdef class ReactorBase:
         def __set__(self, name):
             self.rbase.setName(stringify(name))
 
+    def to_yaml(self):
+        """Return a YAML representation of the Reactor setup."""
+        return pystr(self.rbase.toYAML())
+
     def syncState(self):
         """
         Set the state of the Reactor to match that of the associated
@@ -414,6 +418,10 @@ cdef class ReactorSurface:
         if A is not None:
             self.area = A
 
+    def to_yaml(self):
+        """Return a YAML representation of the ReactorSurface setup."""
+        return pystr(self.surface.toYAML())
+
     def install(self, Reactor r):
         r.reactor.addSurface(self.surface)
 
@@ -542,6 +550,10 @@ cdef class WallBase:
         def __get__(self):
             return pystr(self.wall.type())
 
+    def to_yaml(self):
+        """Return a YAML representation of the WallBase setup."""
+        return pystr(self.wall.toYAML())
+
     property left:
         """ The left surface of this wall. """
         def __get__(self):
@@ -695,6 +707,10 @@ cdef class FlowDevice:
         def __get__(self):
             return pystr(self.dev.typeStr())
 
+    def to_yaml(self):
+        """Return a YAML representation of the FlowDevice setup."""
+        return pystr(self.dev.toYAML())
+
     def _install(self, ReactorBase upstream, ReactorBase downstream):
         """
         Install the device between the *upstream* (source) and *downstream*
@@ -1045,6 +1061,10 @@ cdef class ReactorNet:
         self._reactors.append(r)
         self.net.addReactor(deref(r.reactor))
 
+    def to_yaml(self):
+        """Return a YAML representation of the ReactorNet setup."""
+        return pystr(self.net.toYAML())
+
     def advance(self, double t, pybool apply_limit=True):
         """
         Advance the state of the reactor network in time from the current time
diff --git a/src/zeroD/FlowDevice.cpp b/src/zeroD/FlowDevice.cpp
index 11ed774d19e..a7ddaf2d28f 100644
--- a/src/zeroD/FlowDevice.cpp
+++ b/src/zeroD/FlowDevice.cpp
@@ -6,6 +6,7 @@
 #include "cantera/zeroD/FlowDevice.h"
 #include "cantera/zeroD/ReactorBase.h"
 #include "cantera/numerics/Func1.h"
+#include "cantera/base/yaml.h"
 
 namespace Cantera
 {
@@ -46,6 +47,25 @@ bool FlowDevice::install(ReactorBase& in, ReactorBase& out)
     return true;
 }
 
+std::string FlowDevice::toYAML() const
+{
+    YAML::Emitter yml;
+    std::stringstream out;
+
+    // object is not aware of its unique identifier
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type";
+    yml << YAML::Value << typeStr();
+    yml << YAML::Key << "in";
+    yml << YAML::Value << m_in->name();
+    yml << YAML::Key << "out";
+    yml << YAML::Value << m_out->name();
+    yml << YAML::EndMap;
+
+    out << yml.c_str();
+    return out.str();
+}
+
 void FlowDevice::setPressureFunction(Func1* f)
 {
     m_pfunc = f;
diff --git a/src/zeroD/ReactorBase.cpp b/src/zeroD/ReactorBase.cpp
index edcb7e1532c..ed9e0f334e6 100644
--- a/src/zeroD/ReactorBase.cpp
+++ b/src/zeroD/ReactorBase.cpp
@@ -7,6 +7,7 @@
 #include "cantera/zeroD/FlowDevice.h"
 #include "cantera/zeroD/ReactorNet.h"
 #include "cantera/zeroD/ReactorSurface.h"
+#include "cantera/base/yaml.h"
 
 using namespace std;
 namespace Cantera
@@ -44,6 +45,25 @@ void ReactorBase::syncState()
     }
 }
 
+std::string ReactorBase::toYAML() const
+{
+    YAML::Emitter yml;
+    std::stringstream out;
+
+    yml << YAML::BeginMap;
+    yml << YAML::Key << name();
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type";
+    yml << YAML::Value << typeStr();
+    yml << YAML::Key << "thermo";
+    yml << YAML::Value << m_thermo->name();
+    yml << YAML::EndMap;
+    yml << YAML::EndMap;
+
+    out << yml.c_str();
+    return out.str();
+}
+
 void ReactorBase::addInlet(FlowDevice& inlet)
 {
     m_inlet.push_back(&inlet);
diff --git a/src/zeroD/ReactorNet.cpp b/src/zeroD/ReactorNet.cpp
index e51627c7121..2edbc1c4a2a 100644
--- a/src/zeroD/ReactorNet.cpp
+++ b/src/zeroD/ReactorNet.cpp
@@ -6,6 +6,7 @@
 #include "cantera/zeroD/ReactorNet.h"
 #include "cantera/zeroD/FlowDevice.h"
 #include "cantera/zeroD/Wall.h"
+#include "cantera/base/yaml.h"
 
 #include <cstdio>
 
@@ -30,6 +31,170 @@ ReactorNet::ReactorNet() :
     m_integ->setProblemType(DENSE + NOJAC);
 }
 
+std::string uniqueName(void const *ptr) {
+    // use pointer address as unique name
+    std::ostringstream address;
+    address << ptr;
+    return address.str();
+}
+
+std::string ReactorNet::toYAML() const
+{
+    YAML::Emitter yml;
+    yml.SetIndent(1);
+    std::string name;
+    std::stringstream out;
+
+    // components: using generic pointers
+    std::map<std::string, ReactorBase* > reactors;
+    std::map<std::string, thermo_t* > phases;
+    std::map<std::string, Kinetics* > kinetics; // <-- needed
+    std::map<std::string, WallBase* > walls;
+    std::map<std::string, FlowDevice*> devices;
+    std::map<std::string, ReactorSurface*> surfaces;
+
+    // construct complete maps
+    for (auto r=m_reactors.begin(); r!=m_reactors.end(); r++) {
+
+        // insert reactor (emplace ensures that it remains unique)
+        ReactorBase* rb = *r;
+        reactors.emplace(uniqueName((void const *)rb), rb);
+
+        // walls
+        for (size_t i=0; i<rb->nWalls(); i++) {
+
+            // wall has reactor to left and right
+            WallBase& wall = rb->wall(i);
+            walls.emplace(uniqueName((void const *)(&wall)), &wall);
+
+            ReactorBase& rl = wall.left();
+            reactors.emplace(uniqueName((void const *)(&rl)), &rl);
+
+            ReactorBase& rr = wall.right();
+            reactors.emplace(uniqueName((void const *)(&rr)), &rr);
+        }
+
+        // inlets
+        for (size_t i=0; i<rb->nInlets(); i++) {
+
+            // flow devices at inlet have inlets
+            FlowDevice& inlet = rb->inlet(i);
+            devices.emplace(uniqueName((void const *)(&inlet)), &inlet);
+
+            ReactorBase& in = inlet.in();
+            reactors.emplace(uniqueName((void const *)(&in)), &in);
+        }
+
+        // outlets
+        for (size_t i=0; i<rb->nOutlets(); i++) {
+
+            // flow devices at outlet have outlets
+            FlowDevice& outlet = rb->outlet(i);
+            devices.emplace(uniqueName((void const *)(&outlet)), &outlet);
+
+            ReactorBase& out = outlet.out();
+            reactors.emplace(uniqueName((void const *)(&out)), &out);
+        }
+
+        // surfaces
+        for (size_t i=0; i<rb->nSurfaces(); i++) {
+
+            ReactorSurface* surface = rb->surface(i);
+            surfaces.emplace(uniqueName((void const *)surface), surface);
+
+            // missing: surface phase & kinetics
+        }
+    }
+
+    // gas phases
+    for (const auto& r : reactors) {
+
+        // missing: kinetics
+        thermo_t& contents = r.second->contents();
+        phases.emplace(uniqueName((void const *)(&contents)), &contents);
+    }
+
+    // // surface phases
+    // for (const auto& s : surfaces) {
+
+    //     missing: kinetics
+    //     SurfPhase* thermo = s.second->thermo();
+    //     phases.emplace(uniqueName((void const *)thermo), thermo);
+    // }
+
+    // header
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "ReactorNet";
+    yml << YAML::BeginMap;
+
+    // emit list of thermo phases
+    yml << YAML::Key << "t_thermo";
+    yml << YAML::Value << YAML::BeginSeq;
+    for (const auto& p : phases) {
+        yml << YAML::BeginMap;
+        yml << YAML::Key << p.first;
+        yml << YAML::BeginMap;
+        yml << YAML::Key << "type";
+        yml << YAML::Value << p.second->type();
+        yml << YAML::EndMap;
+        yml << YAML::EndMap;
+    }
+    yml << YAML::EndSeq;
+
+    // emit list of reactors
+    yml << YAML::Key << "ReactorBase";
+    yml << YAML::Value << YAML::BeginSeq;
+    for (const auto& r : reactors) {
+        yml << YAML::Load(r.second->toYAML());
+    }
+    yml << YAML::EndSeq;
+
+    // emit list of walls
+    if (walls.size()) {
+        yml << YAML::Key << "WallBase";
+        yml << YAML::Value << YAML::BeginSeq;
+        for (const auto& w : walls) {
+            yml << YAML::BeginMap;
+            yml << YAML::Key << w.first;
+            yml << YAML::Load(w.second->toYAML());
+            yml << YAML::EndMap;
+        }
+        yml << YAML::EndSeq;
+    }
+
+    // emit list of flow devices
+    if (devices.size()) {
+        yml << YAML::Key << "FlowDevice";
+        yml << YAML::Value << YAML::BeginSeq;
+        for (const auto& d : devices) {
+            yml << YAML::BeginMap;
+            yml << YAML::Key << d.first;
+            yml << YAML::Load(d.second->toYAML());
+            yml << YAML::EndMap;
+        }
+        yml << YAML::EndSeq;
+    }
+
+    // emit list of reactor surfaces
+    if (surfaces.size()) {
+        yml << YAML::Key << "ReactorSurface";
+        yml << YAML::Value << YAML::BeginSeq;
+        for (const auto& s : surfaces) {
+            yml << YAML::BeginMap;
+            yml << YAML::Key << s.first;
+            yml << YAML::Load(s.second->toYAML());
+            yml << YAML::EndMap;
+        }
+        yml << YAML::EndSeq;
+    }
+
+    // close out
+    yml << YAML::EndMap;
+    yml << YAML::EndMap;
+    out << yml.c_str();
+    return out.str();
+}
+
 void ReactorNet::setInitialTime(double time)
 {
     m_time = time;
diff --git a/src/zeroD/ReactorSurface.cpp b/src/zeroD/ReactorSurface.cpp
index 88a446ecaf7..9e1f2ebbef7 100644
--- a/src/zeroD/ReactorSurface.cpp
+++ b/src/zeroD/ReactorSurface.cpp
@@ -7,6 +7,7 @@
 #include "cantera/zeroD/ReactorNet.h"
 #include "cantera/thermo/SurfPhase.h"
 #include "cantera/kinetics/Kinetics.h"
+#include "cantera/base/yaml.h"
 
 namespace Cantera
 {
@@ -19,6 +20,25 @@ ReactorSurface::ReactorSurface()
 {
 }
 
+std::string ReactorSurface::toYAML() const
+{
+    YAML::Emitter yml;
+    std::stringstream out;
+
+    // yml << YAML::BeginMap;
+    // yml << YAML::Key << name();
+    yml << YAML::BeginMap;
+    // yml << YAML::Key << "type";
+    // yml << YAML::Value << typeStr();
+    yml << YAML::Key << "thermo";
+    yml << YAML::Value << m_thermo->name();
+    yml << YAML::EndMap;
+    //yml << YAML::EndMap;
+
+    out << yml.c_str();
+    return out.str();
+}
+
 double ReactorSurface::area() const
 {
     return m_area;
diff --git a/src/zeroD/Wall.cpp b/src/zeroD/Wall.cpp
index 6132186cd84..27aed12578d 100644
--- a/src/zeroD/Wall.cpp
+++ b/src/zeroD/Wall.cpp
@@ -7,6 +7,7 @@
 #include "cantera/numerics/Func1.h"
 #include "cantera/zeroD/Wall.h"
 #include "cantera/thermo/SurfPhase.h"
+#include "cantera/base/yaml.h"
 
 namespace Cantera
 {
@@ -28,6 +29,25 @@ bool WallBase::install(ReactorBase& rleft, ReactorBase& rright)
     return true;
 }
 
+std::string WallBase::toYAML() const
+{
+    YAML::Emitter yml;
+    std::stringstream out;
+
+    // object is not aware of its unique identifier
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type";
+    yml << YAML::Value << type();
+    yml << YAML::Key << "left";
+    yml << YAML::Value << m_left->name();
+    yml << YAML::Key << "right";
+    yml << YAML::Value << m_right->name();
+    yml << YAML::EndMap;
+
+    out << yml.c_str();
+    return out.str();
+}
+
 void WallBase::setArea(double a) {
     m_area = a;
     m_surf[0].setArea(a);

From a75bb769385c62c5b58e0109753be18147a0a64e Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Thu, 15 Aug 2019 00:21:21 -0500
Subject: [PATCH 2/6] [Reactor] streamline/update naming of zeroD objects

* pass name attributes from Cython to C++ layer for FlowDevice and
WallBase objects
* create name and type attributes for ReactorSurface objects
---
 include/cantera/zeroD/FlowDevice.h            | 14 +++++-
 include/cantera/zeroD/Reactor.h               |  3 --
 include/cantera/zeroD/ReactorBase.h           |  4 ++
 include/cantera/zeroD/ReactorSurface.h        | 20 +++++++-
 include/cantera/zeroD/Wall.h                  | 14 +++++-
 interfaces/cython/cantera/_cantera.pxd        | 11 +++--
 .../cantera/examples/reactors/ic_engine.py    |  8 ++--
 interfaces/cython/cantera/reactor.pyx         | 46 ++++++++++++++++--
 src/zeroD/FlowDevice.cpp                      | 26 +++++-----
 src/zeroD/Reactor.cpp                         |  1 -
 src/zeroD/ReactorBase.cpp                     | 16 +++++--
 src/zeroD/ReactorNet.cpp                      | 47 +------------------
 src/zeroD/ReactorSurface.cpp                  | 26 +++++-----
 src/zeroD/Wall.cpp                            | 19 ++++----
 14 files changed, 157 insertions(+), 98 deletions(-)

diff --git a/include/cantera/zeroD/FlowDevice.h b/include/cantera/zeroD/FlowDevice.h
index e10d9a1ea4b..ff9e7e3d9c7 100644
--- a/include/cantera/zeroD/FlowDevice.h
+++ b/include/cantera/zeroD/FlowDevice.h
@@ -30,7 +30,7 @@ const int Valve_Type = 3;
 class FlowDevice
 {
 public:
-    FlowDevice();
+    FlowDevice(const std::string& name = "(none)");
 
     virtual ~FlowDevice() {}
     FlowDevice(const FlowDevice&) = delete;
@@ -54,6 +54,16 @@ class FlowDevice
         return m_type;
     }
 
+    //! Return the name of this flow device
+    std::string name() const {
+        return m_name;
+    }
+
+    //! Set the name of this flow device
+    void setName(const std::string& name) {
+        m_name = name;
+    }
+
     //! Generate self-documenting YAML string.
     virtual std::string toYAML() const;
 
@@ -169,6 +179,8 @@ class FlowDevice
 
     int m_type; //!< @deprecated To be removed after Cantera 2.5.
 
+    std::string m_name; //! flow device name
+
 private:
     size_t m_nspin, m_nspout;
     ReactorBase* m_in;
diff --git a/include/cantera/zeroD/Reactor.h b/include/cantera/zeroD/Reactor.h
index 41528862b28..93c75c5f0f0 100644
--- a/include/cantera/zeroD/Reactor.h
+++ b/include/cantera/zeroD/Reactor.h
@@ -205,9 +205,6 @@ class Reactor : public ReactorBase
     //! Get initial conditions for SurfPhase objects attached to this reactor
     virtual void getSurfaceInitialConditions(double* y);
 
-    //! Pointer to the homogeneous Kinetics object that handles the reactions
-    Kinetics* m_kin;
-
     doublereal m_vdot; //!< net rate of volume change from moving walls [m^3/s]
     doublereal m_Q; //!< net heat transfer through walls [W]
     doublereal m_mass; //!< total mass
diff --git a/include/cantera/zeroD/ReactorBase.h b/include/cantera/zeroD/ReactorBase.h
index b1af0d69c2e..885c734326b 100644
--- a/include/cantera/zeroD/ReactorBase.h
+++ b/include/cantera/zeroD/ReactorBase.h
@@ -270,6 +270,10 @@ class ReactorBase
     size_t m_nsp;
 
     thermo_t* m_thermo;
+
+    //! Pointer to the homogeneous Kinetics object that handles the reactions
+    Kinetics* m_kin;
+
     doublereal m_vol;
     doublereal m_enthalpy;
     doublereal m_intEnergy;
diff --git a/include/cantera/zeroD/ReactorSurface.h b/include/cantera/zeroD/ReactorSurface.h
index cabb9155e63..b3b903817ad 100644
--- a/include/cantera/zeroD/ReactorSurface.h
+++ b/include/cantera/zeroD/ReactorSurface.h
@@ -17,11 +17,27 @@ class SurfPhase;
 class ReactorSurface
 {
 public:
-    ReactorSurface();
+    ReactorSurface(const std::string& name = "(none)");
     virtual ~ReactorSurface() {}
     ReactorSurface(const ReactorSurface&) = delete;
     ReactorSurface& operator=(const ReactorSurface&) = delete;
 
+    //! String indicating the wall model implemented. Usually
+    //! corresponds to the name of the derived class.
+    virtual std::string type() const {
+        return "ReactorSurface";
+    }
+
+    //! Return the name of this surface
+    std::string name() const {
+        return m_name;
+    }
+
+    //! Set the name of this surface
+    void setName(const std::string& name) {
+        m_name = name;
+    }
+
     //! Generate self-documenting YAML string.
     virtual std::string toYAML() const;
 
@@ -93,6 +109,8 @@ class ReactorSurface
     ReactorBase* m_reactor;
     vector_fp m_cov;
     std::vector<SensitivityParameter> m_params;
+
+    std::string m_name; //! reactor surface name
 };
 
 }
diff --git a/include/cantera/zeroD/Wall.h b/include/cantera/zeroD/Wall.h
index 41e3bdef0bd..2be60b12d8f 100644
--- a/include/cantera/zeroD/Wall.h
+++ b/include/cantera/zeroD/Wall.h
@@ -28,7 +28,7 @@ const int WallType = 1;
 class WallBase
 {
 public:
-    WallBase();
+    WallBase(const std::string& name = "(none)");
 
     virtual ~WallBase() {}
     WallBase(const WallBase&) = delete;
@@ -40,6 +40,16 @@ class WallBase
         return "WallBase";
     }
 
+    //! Return the name of this wall
+    std::string name() const {
+        return m_name;
+    }
+
+    //! Set the name of this wall
+    void setName(const std::string& name) {
+        m_name = name;
+    }
+
     //! Generate self-documenting YAML string.
     virtual std::string toYAML() const;
 
@@ -109,6 +119,8 @@ class WallBase
     std::vector<ReactorSurface> m_surf;
 
     double m_area;
+
+    std::string m_name; //! wall name
 };
 
 //! Represents a wall between between two ReactorBase objects.
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 3607964a856..1eefa9d9a3a 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -583,6 +583,8 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxWallBase "Cantera::WallBase":
         CxxWallBase()
         string type()
+        string name()
+        void setName(string)
         string toYAML()
         cbool install(CxxReactorBase&, CxxReactorBase&)
         double area()
@@ -612,6 +614,9 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
 
     cdef cppclass CxxReactorSurface "Cantera::ReactorSurface":
         CxxReactorSurface()
+        string type()
+        string name()
+        void setName(string)
         string toYAML()
         double area()
         void setArea(double)
@@ -627,8 +632,10 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxFlowDevice "Cantera::FlowDevice":
         CxxFlowDevice()
         string typeStr()
-        double massFlowRate() except +translate_exception
+        string name()
+        void setName(string)
         string toYAML()
+        double massFlowRate() except +translate_exception
         double massFlowRate(double) except +translate_exception
         cbool install(CxxReactorBase&, CxxReactorBase&) except +translate_exception
         void setPressureFunction(CxxFunc1*) except +translate_exception
@@ -1093,7 +1100,6 @@ cdef class WallBase:
     cdef object _heat_flux_func
     cdef ReactorBase _left_reactor
     cdef ReactorBase _right_reactor
-    cdef str name
 
 cdef class Wall(WallBase):
     pass
@@ -1102,7 +1108,6 @@ cdef class FlowDevice:
     cdef CxxFlowDevice* dev
     cdef Func1 _rate_func
     cdef Func1 _time_func
-    cdef str name
     cdef ReactorBase _upstream
     cdef ReactorBase _downstream
 
diff --git a/interfaces/cython/cantera/examples/reactors/ic_engine.py b/interfaces/cython/cantera/examples/reactors/ic_engine.py
index f65c5190351..f02d19b4312 100644
--- a/interfaces/cython/cantera/examples/reactors/ic_engine.py
+++ b/interfaces/cython/cantera/examples/reactors/ic_engine.py
@@ -105,7 +105,7 @@ def piston_speed(t):
 inlet = ct.Reservoir(gas, name='Inlet')
 
 # inlet valve
-inlet_valve = ct.Valve(inlet, cyl)
+inlet_valve = ct.Valve(inlet, cyl, name='InletValve')
 inlet_delta = np.mod(inlet_close - inlet_open, 4 * np.pi)
 inlet_valve.valve_coeff = inlet_valve_coeff
 inlet_valve.set_time_function(
@@ -116,7 +116,7 @@ def piston_speed(t):
 injector = ct.Reservoir(gas, name='Fuel')
 
 # injector is modeled as a mass flow controller
-injector_mfc = ct.MassFlowController(injector, cyl)
+injector_mfc = ct.MassFlowController(injector, cyl, name='Injector')
 injector_delta = np.mod(injector_close - injector_open, 4 * np.pi)
 injector_t_open = (injector_close - injector_open) / 2. / np.pi / f
 injector_mfc.mass_flow_coeff = injector_mass / injector_t_open
@@ -128,7 +128,7 @@ def piston_speed(t):
 outlet = ct.Reservoir(gas, name='Outlet')
 
 # outlet valve
-outlet_valve = ct.Valve(cyl, outlet)
+outlet_valve = ct.Valve(cyl, outlet, name='OutletValve')
 outlet_delta = np.mod(outlet_close - outlet_open, 4 * np.pi)
 outlet_valve.valve_coeff = outlet_valve_coeff
 outlet_valve.set_time_function(
@@ -139,7 +139,7 @@ def piston_speed(t):
 ambient_air = ct.Reservoir(ct.Solution('air.cti'), name='Ambient')
 
 # piston is modeled as a moving wall
-piston = ct.Wall(ambient_air, cyl)
+piston = ct.Wall(ambient_air, cyl, name='Piston')
 piston.area = A_piston
 piston.set_velocity(piston_speed)
 
diff --git a/interfaces/cython/cantera/reactor.pyx b/interfaces/cython/cantera/reactor.pyx
index d1bae5d5786..6695ee5bec8 100644
--- a/interfaces/cython/cantera/reactor.pyx
+++ b/interfaces/cython/cantera/reactor.pyx
@@ -410,7 +410,8 @@ cdef class ReactorSurface:
     def __dealloc__(self):
         del self.surface
 
-    def __init__(self, kin=None, Reactor r=None, *, A=None):
+    def __init__(self, kin=None, Reactor r=None, *, name=None, A=None):
+
         if kin is not None:
             self.kinetics = kin
         if r is not None:
@@ -418,6 +419,26 @@ cdef class ReactorSurface:
         if A is not None:
             self.area = A
 
+        if name is not None:
+            self.name = name
+        else:
+            _reactor_counts[self.__class__.__name__] += 1
+            n = _reactor_counts[self.__class__.__name__]
+            self.name = '{0}_{1}'.format(self.__class__.__name__, n)
+
+    property type:
+        """The type of the reactor."""
+        def __get__(self):
+            return pystr(self.surface.type())
+
+    property name:
+        """The name of the reactor."""
+        def __get__(self):
+            return pystr(self.surface.name())
+
+        def __set__(self, name):
+            self.surface.setName(stringify(name))
+
     def to_yaml(self):
         """Return a YAML representation of the ReactorSurface setup."""
         return pystr(self.surface.toYAML())
@@ -515,12 +536,13 @@ cdef class WallBase:
         self._heat_flux_func = None
 
         self._install(left, right)
+
         if name is not None:
             self.name = name
         else:
-            _reactor_counts['Wall'] += 1
-            n = _reactor_counts['Wall']
-            self.name = 'Wall_{0}'.format(n)
+            _reactor_counts[self.__class__.__name__] += 1
+            n = _reactor_counts[self.__class__.__name__]
+            self.name = '{0}_{1}'.format(self.__class__.__name__, n)
 
         if A is not None:
             self.area = A
@@ -550,6 +572,14 @@ cdef class WallBase:
         def __get__(self):
             return pystr(self.wall.type())
 
+    property name:
+        """The name of the reactor."""
+        def __get__(self):
+            return pystr(self.wall.name())
+
+        def __set__(self, name):
+            self.wall.setName(stringify(name))
+
     def to_yaml(self):
         """Return a YAML representation of the WallBase setup."""
         return pystr(self.wall.toYAML())
@@ -707,6 +737,14 @@ cdef class FlowDevice:
         def __get__(self):
             return pystr(self.dev.typeStr())
 
+    property name:
+        """The name of the reactor."""
+        def __get__(self):
+            return pystr(self.dev.name())
+
+        def __set__(self, name):
+            self.dev.setName(stringify(name))
+
     def to_yaml(self):
         """Return a YAML representation of the FlowDevice setup."""
         return pystr(self.dev.toYAML())
diff --git a/src/zeroD/FlowDevice.cpp b/src/zeroD/FlowDevice.cpp
index a7ddaf2d28f..83ee3b18d99 100644
--- a/src/zeroD/FlowDevice.cpp
+++ b/src/zeroD/FlowDevice.cpp
@@ -11,10 +11,15 @@
 namespace Cantera
 {
 
-FlowDevice::FlowDevice() : m_mdot(Undef), m_pfunc(0), m_tfunc(0),
-                           m_coeff(1.0), m_type(0),
-                           m_nspin(0), m_nspout(0),
-                           m_in(0), m_out(0) {}
+FlowDevice::FlowDevice(const std::string& name) :
+    m_mdot(Undef),
+    m_pfunc(0), m_tfunc(0),
+    m_coeff(1.0), m_type(0),
+    m_nspin(0), m_nspout(0),
+    m_in(0), m_out(0)
+{
+    m_name = name;
+}
 
 bool FlowDevice::install(ReactorBase& in, ReactorBase& out)
 {
@@ -52,14 +57,13 @@ std::string FlowDevice::toYAML() const
     YAML::Emitter yml;
     std::stringstream out;
 
-    // object is not aware of its unique identifier
     yml << YAML::BeginMap;
-    yml << YAML::Key << "type";
-    yml << YAML::Value << typeStr();
-    yml << YAML::Key << "in";
-    yml << YAML::Value << m_in->name();
-    yml << YAML::Key << "out";
-    yml << YAML::Value << m_out->name();
+    yml << YAML::Key << name();
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type" << YAML::Value << typeStr();
+    yml << YAML::Key << "in" << YAML::Value << m_in->name();
+    yml << YAML::Key << "out" << YAML::Value << m_out->name();
+    yml << YAML::EndMap;
     yml << YAML::EndMap;
 
     out << yml.c_str();
diff --git a/src/zeroD/Reactor.cpp b/src/zeroD/Reactor.cpp
index da3f985312b..36af26216ff 100644
--- a/src/zeroD/Reactor.cpp
+++ b/src/zeroD/Reactor.cpp
@@ -18,7 +18,6 @@ namespace bmt = boost::math::tools;
 namespace Cantera
 {
 Reactor::Reactor() :
-    m_kin(0),
     m_vdot(0.0),
     m_Q(0.0),
     m_mass(0.0),
diff --git a/src/zeroD/ReactorBase.cpp b/src/zeroD/ReactorBase.cpp
index ed9e0f334e6..815830a837a 100644
--- a/src/zeroD/ReactorBase.cpp
+++ b/src/zeroD/ReactorBase.cpp
@@ -13,8 +13,10 @@ using namespace std;
 namespace Cantera
 {
 
-ReactorBase::ReactorBase(const string& name) : m_nsp(0),
+ReactorBase::ReactorBase(const string& name) :
+    m_nsp(0),
     m_thermo(0),
+    m_kin(0),
     m_vol(1.0),
     m_enthalpy(0.0),
     m_intEnergy(0.0),
@@ -55,8 +57,16 @@ std::string ReactorBase::toYAML() const
     yml << YAML::BeginMap;
     yml << YAML::Key << "type";
     yml << YAML::Value << typeStr();
-    yml << YAML::Key << "thermo";
-    yml << YAML::Value << m_thermo->name();
+    if (m_thermo) {
+        yml << YAML::Key << "phase";
+        yml << YAML::Value << m_thermo->name();
+        yml << YAML::Key << "thermo.type";
+        yml << YAML::Value << m_thermo->type();
+    }
+    if (m_kin) {
+        yml << YAML::Key << "kinetics.type";
+        yml << YAML::Value << m_kin->kineticsType();
+    }
     yml << YAML::EndMap;
     yml << YAML::EndMap;
 
diff --git a/src/zeroD/ReactorNet.cpp b/src/zeroD/ReactorNet.cpp
index 2edbc1c4a2a..8a40f06503f 100644
--- a/src/zeroD/ReactorNet.cpp
+++ b/src/zeroD/ReactorNet.cpp
@@ -41,14 +41,10 @@ std::string uniqueName(void const *ptr) {
 std::string ReactorNet::toYAML() const
 {
     YAML::Emitter yml;
-    yml.SetIndent(1);
-    std::string name;
     std::stringstream out;
 
-    // components: using generic pointers
+    // components: maps use generic pointers
     std::map<std::string, ReactorBase* > reactors;
-    std::map<std::string, thermo_t* > phases;
-    std::map<std::string, Kinetics* > kinetics; // <-- needed
     std::map<std::string, WallBase* > walls;
     std::map<std::string, FlowDevice*> devices;
     std::map<std::string, ReactorSurface*> surfaces;
@@ -101,46 +97,14 @@ std::string ReactorNet::toYAML() const
 
             ReactorSurface* surface = rb->surface(i);
             surfaces.emplace(uniqueName((void const *)surface), surface);
-
-            // missing: surface phase & kinetics
         }
     }
 
-    // gas phases
-    for (const auto& r : reactors) {
-
-        // missing: kinetics
-        thermo_t& contents = r.second->contents();
-        phases.emplace(uniqueName((void const *)(&contents)), &contents);
-    }
-
-    // // surface phases
-    // for (const auto& s : surfaces) {
-
-    //     missing: kinetics
-    //     SurfPhase* thermo = s.second->thermo();
-    //     phases.emplace(uniqueName((void const *)thermo), thermo);
-    // }
-
     // header
     yml << YAML::BeginMap;
     yml << YAML::Key << "ReactorNet";
     yml << YAML::BeginMap;
 
-    // emit list of thermo phases
-    yml << YAML::Key << "t_thermo";
-    yml << YAML::Value << YAML::BeginSeq;
-    for (const auto& p : phases) {
-        yml << YAML::BeginMap;
-        yml << YAML::Key << p.first;
-        yml << YAML::BeginMap;
-        yml << YAML::Key << "type";
-        yml << YAML::Value << p.second->type();
-        yml << YAML::EndMap;
-        yml << YAML::EndMap;
-    }
-    yml << YAML::EndSeq;
-
     // emit list of reactors
     yml << YAML::Key << "ReactorBase";
     yml << YAML::Value << YAML::BeginSeq;
@@ -154,10 +118,7 @@ std::string ReactorNet::toYAML() const
         yml << YAML::Key << "WallBase";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& w : walls) {
-            yml << YAML::BeginMap;
-            yml << YAML::Key << w.first;
             yml << YAML::Load(w.second->toYAML());
-            yml << YAML::EndMap;
         }
         yml << YAML::EndSeq;
     }
@@ -167,10 +128,7 @@ std::string ReactorNet::toYAML() const
         yml << YAML::Key << "FlowDevice";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& d : devices) {
-            yml << YAML::BeginMap;
-            yml << YAML::Key << d.first;
             yml << YAML::Load(d.second->toYAML());
-            yml << YAML::EndMap;
         }
         yml << YAML::EndSeq;
     }
@@ -180,10 +138,7 @@ std::string ReactorNet::toYAML() const
         yml << YAML::Key << "ReactorSurface";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& s : surfaces) {
-            yml << YAML::BeginMap;
-            yml << YAML::Key << s.first;
             yml << YAML::Load(s.second->toYAML());
-            yml << YAML::EndMap;
         }
         yml << YAML::EndSeq;
     }
diff --git a/src/zeroD/ReactorSurface.cpp b/src/zeroD/ReactorSurface.cpp
index 9e1f2ebbef7..5122d30886c 100644
--- a/src/zeroD/ReactorSurface.cpp
+++ b/src/zeroD/ReactorSurface.cpp
@@ -12,12 +12,13 @@
 namespace Cantera
 {
 
-ReactorSurface::ReactorSurface()
-    : m_area(1.0)
-    , m_thermo(nullptr)
-    , m_kinetics(nullptr)
-    , m_reactor(nullptr)
+ReactorSurface::ReactorSurface(const std::string& name) :
+    m_area(1.0),
+    m_thermo(nullptr),
+    m_kinetics(nullptr),
+    m_reactor(nullptr)
 {
+    m_name = name;
 }
 
 std::string ReactorSurface::toYAML() const
@@ -25,15 +26,16 @@ std::string ReactorSurface::toYAML() const
     YAML::Emitter yml;
     std::stringstream out;
 
-    // yml << YAML::BeginMap;
-    // yml << YAML::Key << name();
     yml << YAML::BeginMap;
-    // yml << YAML::Key << "type";
-    // yml << YAML::Value << typeStr();
-    yml << YAML::Key << "thermo";
-    yml << YAML::Value << m_thermo->name();
+    yml << YAML::Key << name();
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type" << YAML::Value << type();
+    yml << YAML::Key << "reactor" << YAML::Value << m_reactor->name();
+    yml << YAML::Key << "phase" << YAML::Value << m_thermo->name();
+    yml << YAML::Key << "thermo.type" << YAML::Value << m_thermo->type();
+    yml << YAML::Key << "kinetics.type" << YAML::Value << m_kinetics->kineticsType();
+    yml << YAML::EndMap;
     yml << YAML::EndMap;
-    //yml << YAML::EndMap;
 
     out << yml.c_str();
     return out.str();
diff --git a/src/zeroD/Wall.cpp b/src/zeroD/Wall.cpp
index 27aed12578d..9aa5bd8fb8b 100644
--- a/src/zeroD/Wall.cpp
+++ b/src/zeroD/Wall.cpp
@@ -12,7 +12,11 @@
 namespace Cantera
 {
 
-WallBase::WallBase() : m_left(0), m_right(0), m_surf(2), m_area(1.0) {}
+WallBase::WallBase(const std::string& name) :
+    m_left(0), m_right(0), m_surf(2), m_area(1.0)
+{
+    m_name = name;
+}
 
 bool WallBase::install(ReactorBase& rleft, ReactorBase& rright)
 {
@@ -34,14 +38,13 @@ std::string WallBase::toYAML() const
     YAML::Emitter yml;
     std::stringstream out;
 
-    // object is not aware of its unique identifier
     yml << YAML::BeginMap;
-    yml << YAML::Key << "type";
-    yml << YAML::Value << type();
-    yml << YAML::Key << "left";
-    yml << YAML::Value << m_left->name();
-    yml << YAML::Key << "right";
-    yml << YAML::Value << m_right->name();
+    yml << YAML::Key << name();
+    yml << YAML::BeginMap;
+    yml << YAML::Key << "type" << YAML::Value << type();
+    yml << YAML::Key << "left" << YAML::Value << m_left->name();
+    yml << YAML::Key << "right" << YAML::Value << m_right->name();
+    yml << YAML::EndMap;
     yml << YAML::EndMap;
 
     out << yml.c_str();

From 74053a925be657b3e1d082333de305e568090fe6 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Thu, 15 Aug 2019 10:41:47 -0500
Subject: [PATCH 3/6] [Reactor] finalize and add unit tests

---
 include/cantera/zeroD/ReactorNet.h            |  1 -
 interfaces/cython/cantera/_cantera.pxd        |  2 +-
 interfaces/cython/cantera/reactor.pyx         | 52 ++++++++++---------
 .../cython/cantera/test/test_reactor.py       | 38 ++++++++++++++
 src/zeroD/ReactorNet.cpp                      | 24 +++++++++
 5 files changed, 90 insertions(+), 27 deletions(-)

diff --git a/include/cantera/zeroD/ReactorNet.h b/include/cantera/zeroD/ReactorNet.h
index 3b48140e32f..739357a9452 100644
--- a/include/cantera/zeroD/ReactorNet.h
+++ b/include/cantera/zeroD/ReactorNet.h
@@ -31,7 +31,6 @@ class ReactorNet : public FuncEval
     //! @name Methods to set up a simulation.
     //@{
 
-
     //! Set initial time. Default = 0.0 s. Restarts integration from this time
     //! using the current mixture state as the initial condition.
     void setInitialTime(double time);
diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 1eefa9d9a3a..439101e1045 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -663,7 +663,7 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
     cdef cppclass CxxReactorNet "Cantera::ReactorNet":
         CxxReactorNet()
         void addReactor(CxxReactor&)
-        string toYAML()
+        string toYAML() except +translate_exception
         double advance(double, cbool) except +translate_exception
         double step() except +translate_exception
         void initialize() except +translate_exception
diff --git a/interfaces/cython/cantera/reactor.pyx b/interfaces/cython/cantera/reactor.pyx
index 6695ee5bec8..80a36949080 100644
--- a/interfaces/cython/cantera/reactor.pyx
+++ b/interfaces/cython/cantera/reactor.pyx
@@ -7,6 +7,18 @@ import numbers as _numbers
 
 _reactor_counts = _defaultdict(int)
 
+
+def _unique_name(name, class_type):
+    """Generate a unique name."""
+
+    if name is not None:
+        return name
+    else:
+        _reactor_counts[class_type] += 1
+        n = _reactor_counts[class_type]
+        return '{0}_{1}'.format(class_type, n)
+
+
 # Need a pure-python class to store weakrefs to
 class _WeakrefProxy:
     pass
@@ -28,12 +40,7 @@ cdef class ReactorBase:
         if isinstance(contents, ThermoPhase):
             self.insert(contents)
 
-        if name is not None:
-            self.name = name
-        else:
-            _reactor_counts[self.reactor_type] += 1
-            n = _reactor_counts[self.reactor_type]
-            self.name = '{0}_{1}'.format(self.reactor_type, n)
+        self.name = _unique_name(name, self.type)
 
         if volume is not None:
             self.volume = volume
@@ -419,12 +426,7 @@ cdef class ReactorSurface:
         if A is not None:
             self.area = A
 
-        if name is not None:
-            self.name = name
-        else:
-            _reactor_counts[self.__class__.__name__] += 1
-            n = _reactor_counts[self.__class__.__name__]
-            self.name = '{0}_{1}'.format(self.__class__.__name__, n)
+        self.name = _unique_name(name, self.type)
 
     property type:
         """The type of the reactor."""
@@ -537,12 +539,7 @@ cdef class WallBase:
 
         self._install(left, right)
 
-        if name is not None:
-            self.name = name
-        else:
-            _reactor_counts[self.__class__.__name__] += 1
-            n = _reactor_counts[self.__class__.__name__]
-            self.name = '{0}_{1}'.format(self.__class__.__name__, n)
+        self.name = _unique_name(name, self.type)
 
         if A is not None:
             self.area = A
@@ -720,12 +717,7 @@ cdef class FlowDevice:
         assert self.dev != NULL
         self._rate_func = None
 
-        if name is not None:
-            self.name = name
-        else:
-            _reactor_counts[self.__class__.__name__] += 1
-            n = _reactor_counts[self.__class__.__name__]
-            self.name = '{0}_{1}'.format(self.__class__.__name__, n)
+        self.name = _unique_name(name, self.type)
 
         self._install(upstream, downstream)
 
@@ -1100,9 +1092,19 @@ cdef class ReactorNet:
         self.net.addReactor(deref(r.reactor))
 
     def to_yaml(self):
-        """Return a YAML representation of the ReactorNet setup."""
+        """
+        Return a YAML representation of the ReactorNet structure. To
+        print the structure to the terminal, simply call the ReactorNet object.
+        The following two statements are equivalent for the sim object::
+
+        >>> sim()
+        >>> print(sim.to_yaml())
+        """
         return pystr(self.net.toYAML())
 
+    def __call__(self):
+        print(self.to_yaml())
+
     def advance(self, double t, pybool apply_limit=True):
         """
         Advance the state of the reactor network in time from the current time
diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index 7747c1ddab9..06dd072e575 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 from .utilities import unittest
+from ruamel.yaml import YAML
 
 import cantera as ct
 from . import utilities
@@ -396,6 +397,43 @@ def v(t):
         self.assertNear(self.r1.volume, V1 + 1.0 * A, 1e-7)
         self.assertNear(self.r2.volume, V2 - 1.0 * A, 1e-7)
 
+    def test_yaml(self, **kwargs):
+        self.make_reactors()
+        self.add_wall()
+        reservoir = ct.Reservoir(self.gas1)
+        mfc = ct.MassFlowController(reservoir, self.r1)
+
+        self.assertTrue(isinstance(self.net.to_yaml(), str))
+        self.assertTrue(isinstance(self.r1.to_yaml(), str))
+        self.assertTrue(isinstance(self.r2.to_yaml(), str))
+        self.assertTrue(isinstance(self.w.to_yaml(), str))
+        self.assertTrue(isinstance(reservoir.to_yaml(), str))
+        self.assertTrue(isinstance(mfc.to_yaml(), str))
+
+        yaml = YAML()
+        yml = yaml.load(self.net.to_yaml())
+        self.assertTrue('ReactorNet' in yml)
+        net = yml['ReactorNet']
+
+        self.assertTrue('ReactorBase' in net)
+        reactors = [tuple(n)[0] for n in net['ReactorBase']]
+        self.assertTrue(self.r1.name in reactors)
+        self.assertTrue(self.r2.name in reactors)
+        self.assertTrue(reservoir.name in reactors)
+
+        self.assertTrue('WallBase' in net)
+        walls = [tuple(n)[0] for n in net['WallBase']]
+        self.assertTrue(self.w.name in walls)
+
+        self.assertTrue('FlowDevice' in net)
+        devices = [tuple(n)[0] for n in net['FlowDevice']]
+        self.assertTrue(mfc.name in devices)
+
+        self.r2.name = self.r1.name
+        with self.assertRaisesRegex(ct.CanteraError, 'names are not unique'):
+            # reactor names need to be unique
+            self.net.to_yaml()
+
     def test_disable_energy(self):
         self.make_reactors(T1=500)
         self.r1.energy_enabled = False
diff --git a/src/zeroD/ReactorNet.cpp b/src/zeroD/ReactorNet.cpp
index 8a40f06503f..039b9c1f583 100644
--- a/src/zeroD/ReactorNet.cpp
+++ b/src/zeroD/ReactorNet.cpp
@@ -42,6 +42,7 @@ std::string ReactorNet::toYAML() const
 {
     YAML::Emitter yml;
     std::stringstream out;
+    std::map<std::string, std::string> names;
 
     // components: maps use generic pointers
     std::map<std::string, ReactorBase* > reactors;
@@ -109,39 +110,62 @@ std::string ReactorNet::toYAML() const
     yml << YAML::Key << "ReactorBase";
     yml << YAML::Value << YAML::BeginSeq;
     for (const auto& r : reactors) {
+        names.emplace(r.second->name(), r.first);
         yml << YAML::Load(r.second->toYAML());
     }
     yml << YAML::EndSeq;
+    if (names.size()!=reactors.size()) {
+        // this should raise a warning, but an applicable warning system is not in place
+        throw CanteraError("ReactorNet::toYAML", "ReactorBase names are not unique.");
+    }
 
     // emit list of walls
+    names.clear();
     if (walls.size()) {
         yml << YAML::Key << "WallBase";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& w : walls) {
+            names.emplace(w.second->name(), w.first);
             yml << YAML::Load(w.second->toYAML());
         }
         yml << YAML::EndSeq;
     }
+    if (names.size()!=walls.size()) {
+        // this should raise a warning, but an applicable warning system is not in place
+        throw CanteraError("ReactorNet::toYAML", "Wall names are not unique.");
+    }
 
     // emit list of flow devices
+    names.clear();
     if (devices.size()) {
         yml << YAML::Key << "FlowDevice";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& d : devices) {
+            names.emplace(d.second->name(), d.first);
             yml << YAML::Load(d.second->toYAML());
         }
         yml << YAML::EndSeq;
     }
+    if (names.size()!=devices.size()) {
+        // this should raise a warning, but an applicable warning system is not in place
+        throw CanteraError("ReactorNet::toYAML", "FlowDevice names are not unique.");
+    }
 
     // emit list of reactor surfaces
+    names.clear();
     if (surfaces.size()) {
         yml << YAML::Key << "ReactorSurface";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& s : surfaces) {
+            names.emplace(s.second->name(), s.first);
             yml << YAML::Load(s.second->toYAML());
         }
         yml << YAML::EndSeq;
     }
+    if (names.size()!=surfaces.size()) {
+        // this should raise a warning, but an applicable warning system is not in place
+        throw CanteraError("ReactorNet::toYAML", "ReactorSurface names are not unique.");
+    }
 
     // close out
     yml << YAML::EndMap;

From 9d54e9a196d0d904be88ef1335faf49e142ac7af Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Thu, 15 Aug 2019 12:27:59 -0500
Subject: [PATCH 4/6] Fix ruamel_yaml for Travis CI on osx

---
 interfaces/cython/cantera/test/test_reactor.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index 06dd072e575..ffbf040c368 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -5,7 +5,10 @@
 
 import numpy as np
 from .utilities import unittest
-from ruamel.yaml import YAML
+try:
+    from ruamel.yaml import YAML
+except:
+    from ruamel_yaml import YAML
 
 import cantera as ct
 from . import utilities

From 34a5f9fa8c28afb56d5e5d328f4c6d2a5435cf82 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Thu, 15 Aug 2019 17:38:57 -0500
Subject: [PATCH 5/6] Replace thermo_t by ThermoPhase in ReactorBase

---
 include/cantera/zeroD/ReactorBase.h | 8 ++++----
 src/zeroD/ReactorBase.cpp           | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/cantera/zeroD/ReactorBase.h b/include/cantera/zeroD/ReactorBase.h
index 885c734326b..b80d29bf59b 100644
--- a/include/cantera/zeroD/ReactorBase.h
+++ b/include/cantera/zeroD/ReactorBase.h
@@ -89,7 +89,7 @@ class ReactorBase
     //! Specify the mixture contained in the reactor. Note that a pointer to
     //! this substance is stored, and as the integration proceeds, the state of
     //! the substance is modified.
-    virtual void setThermoMgr(thermo_t& thermo);
+    virtual void setThermoMgr(ThermoPhase& thermo);
 
     //! Specify chemical kinetics governing the reactor.
     virtual void setKineticsMgr(Kinetics& kin) {
@@ -185,7 +185,7 @@ class ReactorBase
     virtual void syncState();
 
     //! return a reference to the contents.
-    thermo_t& contents() {
+    ThermoPhase& contents() {
         if (!m_thermo) {
             throw CanteraError("ReactorBase::contents",
                                "Reactor contents not defined.");
@@ -193,7 +193,7 @@ class ReactorBase
         return *m_thermo;
     }
 
-    const thermo_t& contents() const {
+    const ThermoPhase& contents() const {
         if (!m_thermo) {
             throw CanteraError("ReactorBase::contents",
                                "Reactor contents not defined.");
@@ -269,7 +269,7 @@ class ReactorBase
     //! Number of homogeneous species in the mixture
     size_t m_nsp;
 
-    thermo_t* m_thermo;
+    ThermoPhase* m_thermo;
 
     //! Pointer to the homogeneous Kinetics object that handles the reactions
     Kinetics* m_kin;
diff --git a/src/zeroD/ReactorBase.cpp b/src/zeroD/ReactorBase.cpp
index 815830a837a..2636a890b88 100644
--- a/src/zeroD/ReactorBase.cpp
+++ b/src/zeroD/ReactorBase.cpp
@@ -26,7 +26,7 @@ ReactorBase::ReactorBase(const string& name) :
     m_name = name;
 }
 
-void ReactorBase::setThermoMgr(thermo_t& thermo)
+void ReactorBase::setThermoMgr(ThermoPhase& thermo)
 {
     m_thermo = &thermo;
     m_nsp = m_thermo->nSpecies();

From bf2eb073f071befb904729b325f115049882df9f Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lgmail.com>
Date: Sun, 18 Aug 2019 06:35:18 -0500
Subject: [PATCH 6/6] Revise structure of yaml output

---
 .../cython/cantera/test/test_reactor.py       | 16 +++---
 src/zeroD/FlowDevice.cpp                      |  4 +-
 src/zeroD/ReactorBase.cpp                     | 17 +++----
 src/zeroD/ReactorNet.cpp                      | 50 +++++++++----------
 src/zeroD/Wall.cpp                            |  4 +-
 5 files changed, 45 insertions(+), 46 deletions(-)

diff --git a/interfaces/cython/cantera/test/test_reactor.py b/interfaces/cython/cantera/test/test_reactor.py
index ffbf040c368..496347a70e2 100644
--- a/interfaces/cython/cantera/test/test_reactor.py
+++ b/interfaces/cython/cantera/test/test_reactor.py
@@ -415,21 +415,21 @@ def test_yaml(self, **kwargs):
 
         yaml = YAML()
         yml = yaml.load(self.net.to_yaml())
-        self.assertTrue('ReactorNet' in yml)
-        net = yml['ReactorNet']
+        self.assertTrue('reactor-network' in yml)
+        net = yml['reactor-network']
 
-        self.assertTrue('ReactorBase' in net)
-        reactors = [tuple(n)[0] for n in net['ReactorBase']]
+        self.assertTrue('reactors' in net)
+        reactors = [tuple(n)[0] for n in net['reactors']]
         self.assertTrue(self.r1.name in reactors)
         self.assertTrue(self.r2.name in reactors)
         self.assertTrue(reservoir.name in reactors)
 
-        self.assertTrue('WallBase' in net)
-        walls = [tuple(n)[0] for n in net['WallBase']]
+        self.assertTrue('walls' in net)
+        walls = [tuple(n)[0] for n in net['walls']]
         self.assertTrue(self.w.name in walls)
 
-        self.assertTrue('FlowDevice' in net)
-        devices = [tuple(n)[0] for n in net['FlowDevice']]
+        self.assertTrue('flow-devices' in net)
+        devices = [tuple(n)[0] for n in net['flow-devices']]
         self.assertTrue(mfc.name in devices)
 
         self.r2.name = self.r1.name
diff --git a/src/zeroD/FlowDevice.cpp b/src/zeroD/FlowDevice.cpp
index 83ee3b18d99..ce534cedee9 100644
--- a/src/zeroD/FlowDevice.cpp
+++ b/src/zeroD/FlowDevice.cpp
@@ -61,8 +61,8 @@ std::string FlowDevice::toYAML() const
     yml << YAML::Key << name();
     yml << YAML::BeginMap;
     yml << YAML::Key << "type" << YAML::Value << typeStr();
-    yml << YAML::Key << "in" << YAML::Value << m_in->name();
-    yml << YAML::Key << "out" << YAML::Value << m_out->name();
+    yml << YAML::Key << "reactors" << YAML::Flow;
+    yml << YAML::BeginSeq << m_in->name() << m_out->name() << YAML::EndSeq;
     yml << YAML::EndMap;
     yml << YAML::EndMap;
 
diff --git a/src/zeroD/ReactorBase.cpp b/src/zeroD/ReactorBase.cpp
index 2636a890b88..1df46a38c9b 100644
--- a/src/zeroD/ReactorBase.cpp
+++ b/src/zeroD/ReactorBase.cpp
@@ -1,3 +1,4 @@
+
 //! @file ReactorBase.cpp
 
 // This file is part of Cantera. See License.txt in the top-level directory or
@@ -7,6 +8,7 @@
 #include "cantera/zeroD/FlowDevice.h"
 #include "cantera/zeroD/ReactorNet.h"
 #include "cantera/zeroD/ReactorSurface.h"
+#include "cantera/thermo/SurfPhase.h"
 #include "cantera/base/yaml.h"
 
 using namespace std;
@@ -57,16 +59,13 @@ std::string ReactorBase::toYAML() const
     yml << YAML::BeginMap;
     yml << YAML::Key << "type";
     yml << YAML::Value << typeStr();
-    if (m_thermo) {
-        yml << YAML::Key << "phase";
-        yml << YAML::Value << m_thermo->name();
-        yml << YAML::Key << "thermo.type";
-        yml << YAML::Value << m_thermo->type();
-    }
-    if (m_kin) {
-        yml << YAML::Key << "kinetics.type";
-        yml << YAML::Value << m_kin->kineticsType();
+    yml << YAML::Key << "phases" << YAML::Flow;
+    yml << YAML::BeginSeq;
+    yml << m_thermo->name();
+    for (const auto& s : m_surfaces) {
+        yml << s->thermo()->name();
     }
+    yml << YAML::EndSeq;
     yml << YAML::EndMap;
     yml << YAML::EndMap;
 
diff --git a/src/zeroD/ReactorNet.cpp b/src/zeroD/ReactorNet.cpp
index 039b9c1f583..9d811c18b2a 100644
--- a/src/zeroD/ReactorNet.cpp
+++ b/src/zeroD/ReactorNet.cpp
@@ -48,7 +48,7 @@ std::string ReactorNet::toYAML() const
     std::map<std::string, ReactorBase* > reactors;
     std::map<std::string, WallBase* > walls;
     std::map<std::string, FlowDevice*> devices;
-    std::map<std::string, ReactorSurface*> surfaces;
+    // std::map<std::string, ReactorSurface*> surfaces;
 
     // construct complete maps
     for (auto r=m_reactors.begin(); r!=m_reactors.end(); r++) {
@@ -93,21 +93,21 @@ std::string ReactorNet::toYAML() const
             reactors.emplace(uniqueName((void const *)(&out)), &out);
         }
 
-        // surfaces
-        for (size_t i=0; i<rb->nSurfaces(); i++) {
+        // // surfaces
+        // for (size_t i=0; i<rb->nSurfaces(); i++) {
 
-            ReactorSurface* surface = rb->surface(i);
-            surfaces.emplace(uniqueName((void const *)surface), surface);
-        }
+        //     ReactorSurface* surface = rb->surface(i);
+        //     surfaces.emplace(uniqueName((void const *)surface), surface);
+        // }
     }
 
     // header
     yml << YAML::BeginMap;
-    yml << YAML::Key << "ReactorNet";
+    yml << YAML::Key << "reactor-network";
     yml << YAML::BeginMap;
 
     // emit list of reactors
-    yml << YAML::Key << "ReactorBase";
+    yml << YAML::Key << "reactors";
     yml << YAML::Value << YAML::BeginSeq;
     for (const auto& r : reactors) {
         names.emplace(r.second->name(), r.first);
@@ -122,7 +122,7 @@ std::string ReactorNet::toYAML() const
     // emit list of walls
     names.clear();
     if (walls.size()) {
-        yml << YAML::Key << "WallBase";
+        yml << YAML::Key << "walls";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& w : walls) {
             names.emplace(w.second->name(), w.first);
@@ -138,7 +138,7 @@ std::string ReactorNet::toYAML() const
     // emit list of flow devices
     names.clear();
     if (devices.size()) {
-        yml << YAML::Key << "FlowDevice";
+        yml << YAML::Key << "flow-devices";
         yml << YAML::Value << YAML::BeginSeq;
         for (const auto& d : devices) {
             names.emplace(d.second->name(), d.first);
@@ -151,21 +151,21 @@ std::string ReactorNet::toYAML() const
         throw CanteraError("ReactorNet::toYAML", "FlowDevice names are not unique.");
     }
 
-    // emit list of reactor surfaces
-    names.clear();
-    if (surfaces.size()) {
-        yml << YAML::Key << "ReactorSurface";
-        yml << YAML::Value << YAML::BeginSeq;
-        for (const auto& s : surfaces) {
-            names.emplace(s.second->name(), s.first);
-            yml << YAML::Load(s.second->toYAML());
-        }
-        yml << YAML::EndSeq;
-    }
-    if (names.size()!=surfaces.size()) {
-        // this should raise a warning, but an applicable warning system is not in place
-        throw CanteraError("ReactorNet::toYAML", "ReactorSurface names are not unique.");
-    }
+    // // emit list of reactor surfaces
+    // names.clear();
+    // if (surfaces.size()) {
+    //     yml << YAML::Key << "ReactorSurface";
+    //     yml << YAML::Value << YAML::BeginSeq;
+    //     for (const auto& s : surfaces) {
+    //         names.emplace(s.second->name(), s.first);
+    //         yml << YAML::Load(s.second->toYAML());
+    //     }
+    //     yml << YAML::EndSeq;
+    // }
+    // if (names.size()!=surfaces.size()) {
+    //     // this should raise a warning, but an applicable warning system is not in place
+    //     throw CanteraError("ReactorNet::toYAML", "ReactorSurface names are not unique.");
+    // }
 
     // close out
     yml << YAML::EndMap;
diff --git a/src/zeroD/Wall.cpp b/src/zeroD/Wall.cpp
index 9aa5bd8fb8b..667142c14b4 100644
--- a/src/zeroD/Wall.cpp
+++ b/src/zeroD/Wall.cpp
@@ -42,8 +42,8 @@ std::string WallBase::toYAML() const
     yml << YAML::Key << name();
     yml << YAML::BeginMap;
     yml << YAML::Key << "type" << YAML::Value << type();
-    yml << YAML::Key << "left" << YAML::Value << m_left->name();
-    yml << YAML::Key << "right" << YAML::Value << m_right->name();
+    yml << YAML::Key << "reactors" << YAML::Flow;
+    yml << YAML::BeginSeq << m_left->name() << m_right->name() << YAML::EndSeq;
     yml << YAML::EndMap;
     yml << YAML::EndMap;