Make Sim1D/Domain1D and SolutionArray usage more consistent

include/cantera/base/SolutionArray.h

@@ -129,8 +129,10 @@ class SolutionArray
     /**
      *  Check whether SolutionArray contains a component.
      *  A component is a property defining state or auxiliary variable.
+     *  @param name  name of component
+     *  @param checkAlias  if `true` (default), check alias mapping
      */
-    bool hasComponent(const string& name) const;
+    bool hasComponent(const string& name, bool checkAlias=true) const;
 
     /**
      *  Retrieve a component of the SolutionArray by name.
@@ -404,6 +406,9 @@ class SolutionArray
     vector<int> m_active; //!< Vector of locations referencing active entries
 };
 
+//! Return mapping of component alias names to standardized component names.
+const map<string, string>& _componentAliasMap();
+
 }
 
 #endif

include/cantera/oneD/Boundary1D.h

@@ -109,7 +109,7 @@ class Boundary1D : public Domain1D
 
     void setupGrid(size_t n, const double* z) override {}
 
-    void fromArray(SolutionArray& arr, double* soln) override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
 
 protected:
     //! Initialize member variables based on the adjacent domains.
@@ -173,8 +173,8 @@ class Inlet1D : public Boundary1D
     }
     void init() override;
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
-    void fromArray(SolutionArray& arr, double* soln) override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
 
 protected:
     //! A marker that indicates whether this is a left inlet or a right inlet.
@@ -216,7 +216,7 @@ class Empty1D : public Boundary1D
 
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
 
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
 };
 
 /**
@@ -245,7 +245,7 @@ class Symm1D : public Boundary1D
 
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
 
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
 };
 
 
@@ -275,7 +275,7 @@ class Outlet1D : public Boundary1D
 
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
 
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
 };
 
 
@@ -312,8 +312,8 @@ class OutletRes1D : public Boundary1D
 
     void init() override;
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
-    void fromArray(SolutionArray& arr, double* soln) override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
 
 protected:
     size_t m_nsp = 0; //!< Number of species in the adjacent flow domain
@@ -347,8 +347,8 @@ class Surf1D : public Boundary1D
 
     void init() override;
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
-    void fromArray(SolutionArray& arr, double* soln) override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
     void show(const double* x) override;
 };
 
@@ -390,8 +390,8 @@ class ReactingSurf1D : public Boundary1D
 
     void eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) override;
 
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
-    void fromArray(SolutionArray& arr, double* soln) override;
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
 
     void _getInitialSoln(double* x) override {
         m_sphase->getCoverages(x);

include/cantera/oneD/Domain1D.h

@@ -196,8 +196,23 @@ class Domain1D
         m_name[n] = name;
     }
 
-    //! index of component with name `name`.
-    virtual size_t componentIndex(const string& name) const;
+    /**
+     * Index of component with name `name`.
+     * @param name  name of component
+     * @param checkAlias  if `true` (default), check alias mapping
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual size_t componentIndex(const string& name, bool checkAlias=true) const;
+
+    /**
+     * Check whether the Domain contains a component.
+     * @param name  name of component
+     * @param checkAlias  if `true` (default), check alias mapping
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual bool hasComponent(const string& name, bool checkAlias=true) const;
 
     /**
      * Set the upper and lower bounds for a solution component, n.
@@ -348,16 +363,73 @@ class Domain1D
         return x[index(n,j)];
     }
 
+    /**
+     * Retrieve component values.
+     * @param component  Name of the component.
+     * @param[out] values  Vector of length nPoints() containing values at grid points.
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual void getValues(const string& component, vector<double>& values) const {
+        throw NotImplementedError("Domain1D::getValues", "Needs to be overloaded.");
+    }
+
+    /**
+     * Specify component values.
+     * @param component  Name of the component.
+     * @param[in] values  Vector of length nPoints() containing values at grid points.
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual void setValues(const string& component, const vector<double>& values) {
+        throw NotImplementedError("Domain1D::setValues", "Needs to be overloaded.");
+    }
+
+    /**
+     * Specify a profile for a component.
+     * @param component  Name of the component.
+     * @param[in] pos  A vector of relative positions, beginning with 0.0 at the
+     *     left of the domain, and ending with 1.0 at the right of the domain.
+     * @param[in] values  A vector of values corresponding to the relative position
+     *     locations.
+     *
+     * Note that the vector pos and values can have lengths different than the
+     * number of grid points, but their lengths must be equal. The values at
+     * the grid points will be linearly interpolated based on the (pos,
+     * values) specification.
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual void setProfile(const string& component,
+                            const vector<double>& pos, const vector<double>& values) {
+        throw NotImplementedError("Domain1D::setProfile", "Needs to be overloaded.");
+    }
+
+    /**
+     * Specify a flat profile for a component.
+     * @param component  Name of the component.
+     * @param value  Constant value.
+     *
+     * @since New in %Cantera 3.2.
+     */
+    virtual void setFlatProfile(const string& component, double v) {
+        throw NotImplementedError(
+            "Domain1D::setFlatProfile", "Needs to be overloaded.");
+    }
+
     //! Save the state of this domain as a SolutionArray.
     /*!
      * @param soln  local solution vector for this domain
      * @todo  Despite the method's name, data are copied; the intent is to access data
      *      directly in future revisions, where a non-const version will be implemented.
      *
      * @since New in %Cantera 3.0.
+     * @deprecated To be removed after %Cantera 3.2. Replaceable by toArray().
      */
-    virtual shared_ptr<SolutionArray> asArray(const double* soln) const {
-        throw NotImplementedError("Domain1D::asArray", "Needs to be overloaded.");
+    shared_ptr<SolutionArray> asArray(const double* soln) const {
+        warn_deprecated("Domain1D::asArray",
+            "To be removed after Cantera 3.2. Replaceable by 'toArray'.");
+        return toArray();
     }
 
     //! Save the state of this domain to a SolutionArray.
@@ -368,17 +440,26 @@ class Domain1D
      *
      * @since New in %Cantera 3.0.
      */
-    shared_ptr<SolutionArray> toArray(bool normalize=false) const;
+    virtual shared_ptr<SolutionArray> toArray(bool normalize=false) const {
+        throw NotImplementedError("Domain1D::toArray", "Needs to be overloaded.");
+    }
 
     //! Restore the solution for this domain from a SolutionArray
     /*!
      * @param[in] arr  SolutionArray defining the state of this domain
      * @param[out] soln  Value of the solution vector, local to this domain
      *
      * @since New in %Cantera 3.0.
+     * @deprecated To be removed after %Cantera 3.2.
+     *      Replaceable by version that does not require solution vector.
      */
-    virtual void fromArray(SolutionArray& arr, double* soln) {
-        throw NotImplementedError("Domain1D::fromArray", "Needs to be overloaded.");
+    void fromArray(SolutionArray& arr, double* soln) {
+        warn_deprecated("Domain1D::fromArray",
+            "To be removed after Cantera 3.2. Replaceable by version that does not "
+            "require solution vector.");
+        // create a shared_ptr that skips deletion of the held pointer
+        shared_ptr<SolutionArray> arr_ptr(&arr, [](SolutionArray*){});
+        fromArray(arr_ptr);
     }
 
     //! Restore the solution for this domain from a SolutionArray.
@@ -387,7 +468,9 @@ class Domain1D
      * @param arr  SolutionArray defining the state of this domain
      * @since New in %Cantera 3.0.
      */
-    void fromArray(const shared_ptr<SolutionArray>& arr);
+    virtual void fromArray(const shared_ptr<SolutionArray>& arr) {
+        throw NotImplementedError("Domain1D::fromArray", "Needs to be overloaded.");
+    }
 
     //! Return thermo/kinetics/transport manager used in the domain
     //! @since New in %Cantera 3.0.
@@ -499,6 +582,8 @@ class Domain1D
     //! @param name  Name of the component
     //! @param values  Array of length nPoints() containing the initial values
     //! @param soln  Pointer to the local portion of the system state vector
+    //! @deprecated To be removed after %Cantera 3.2.
+    //!     Replaceable by version using vectors arguments.
     void setProfile(const string& name, double* values, double* soln);
 
     //! Access the array of grid coordinates [m]

include/cantera/oneD/Flow1D.h

@@ -7,6 +7,7 @@
 #define CT_FLOW1D_H
 
 #include "Domain1D.h"
+#include "OneDim.h"
 #include "cantera/base/Array.h"
 #include "cantera/base/Solution.h"
 #include "cantera/thermo/ThermoPhase.h"
@@ -175,15 +176,23 @@ class Flow1D : public Domain1D
 
     string componentName(size_t n) const override;
 
-    size_t componentIndex(const string& name) const override;
+    size_t componentIndex(const string& name, bool checkAlias=true) const override;
+
+    bool hasComponent(const string& name, bool checkAlias=true) const override;
 
     //! Returns true if the specified component is an active part of the solver state
     virtual bool componentActive(size_t n) const;
 
     void show(const double* x) override;
 
-    shared_ptr<SolutionArray> asArray(const double* soln) const override;
-    void fromArray(SolutionArray& arr, double* soln) override;
+    void getValues(const string& component, vector<double>& values) const override;
+    void setValues(const string& component, const vector<double>& values) override;
+    void setProfile(const string& component,
+                    const vector<double>& pos, const vector<double>& values) override;
+    void setFlatProfile(const string& component, double v) override;
+
+    shared_ptr<SolutionArray> toArray(bool normalize=false) const override;
+    void fromArray(const shared_ptr<SolutionArray>& arr) override;
 
     //! Set flow configuration for freely-propagating flames, using an internal point
     //! with a fixed temperature as the condition to determine the inlet mass flux.
@@ -548,15 +557,15 @@ class Flow1D : public Domain1D
                               double rdt, size_t jmin, size_t jmax);
 
     /**
-     * Evaluate the lambda equation residual.
+     * Evaluate the radial pressure gradient equation residual.
      *
      * @f[
      *    \frac{d\Lambda}{dz} = 0
      * @f]
      *
-     * The lambda equation serves as an eigenvalue that allows the momentum
-     * equation and continuity equations to be simultaneously satisfied in
-     * axisymmetric flows. The lambda equation propagates information from
+     * The radial pressure gradient @f$ \Lambda @f$ serves as an eigenvalue that allows
+     * the momentum and continuity equations to be simultaneously satisfied in
+     * axisymmetric flows. This equation propagates information from
      * left-to-right. The default boundary condition is @f$ \Lambda = 0 @f$
      * at the left boundary. The equation is first order and so only one
      * boundary condition is needed.
@@ -571,7 +580,7 @@ class Flow1D : public Domain1D
      *
      * @f[
      *   \rho c_p u \frac{dT}{dz} =
-     *   \frac{d}{dz}\left( \lambda \frac{dT}{dz} \right)
+     *   \frac{d}{dz}\left( \Lambda \frac{dT}{dz} \right)
      *   - \sum_k h_kW_k\dot{\omega}_k
      *   - \sum_k  j_k \frac{dh_k}{dz}
      * @f]
@@ -674,7 +683,12 @@ class Flow1D : public Domain1D
 
     //! Get the radial pressure gradient [N/m⁴] at point `j` from the local state vector
     //! `x`
-    double lambda(const double* x, size_t j) const {
+    //! @deprecated To be removed after %Cantera 3.2. Renamed to Lambda().
+    double lambda(const double* x, size_t j) const;
+
+    //! Get the radial pressure gradient [N/m⁴] at point `j` from the local state vector
+    //! `x`
+    double Lambda(const double* x, size_t j) const {
         return x[index(c_offset_L, j)];
     }
 

include/cantera/oneD/OneDim.h

@@ -80,7 +80,7 @@ class OneDim : public SteadyStateSystem
     }
 
     //! Get the index of the domain named `name`.
-    size_t domainIndex(const string& name);
+    size_t domainIndex(const string& name) const;
 
     //! Check that the specified domain index is in range.
     //! Throws an exception if n is greater than nDomains()-1

include/cantera/oneD/Sim1D.h

@@ -49,6 +49,9 @@ class Sim1D : public OneDim
      *     left of the domain, and ending with 1.0 at the right of the domain.
      * @param vals  A vector of values corresponding to the relative position
      *     locations.
+     *
+     * @deprecated To be removed after %Cantera 3.2.
+     *      Replaceable by Domain1D::setProfile.
      */
     void setInitialGuess(const string& component, vector<double>& locs,
                          vector<double>& vals);
@@ -92,11 +95,16 @@ class Sim1D : public OneDim
      * number of grid points, but their lengths must be equal. The values at
      * the grid points will be linearly interpolated based on the (pos,
      * values) specification.
+     *
+     * @deprecated To be removed after %Cantera 3.2.
+     *      Replaceable by Domain1D::setProfile.
      */
     void setProfile(size_t dom, size_t comp, const vector<double>& pos,
                     const vector<double>& values);
 
     //! Set component 'comp' of domain 'dom' to value 'v' at all points.
+    //! @deprecated To be removed after %Cantera 3.2.
+    //!     Replaceable by Domain1D::setProfile.
     void setFlatProfile(size_t dom, size_t comp, double v);
 
     //! @}

interfaces/cython/cantera/_onedim.pxd

@@ -23,7 +23,14 @@ cdef extern from "cantera/oneD/Domain1D.h":
         size_t nComponents()
         size_t nPoints()
         string componentName(size_t) except +translate_exception
-        size_t componentIndex(string) except +translate_exception
+        size_t componentIndex(string&) except +translate_exception
+        cbool hasComponent(string&) except +translate_exception
+        vector[double] grid() except +translate_exception
+        void setupGrid(vector[double]&) except +translate_exception
+        void getValues(string&, vector[double]&) except +translate_exception
+        void setValues(string&, vector[double]&) except +translate_exception
+        void setProfile(string&, vector[double]&, vector[double]&) except +translate_exception
+        void setFlatProfile(string&, double) except +translate_exception
         void setBounds(size_t, double, double)
         double upperBound(size_t)
         double lowerBound(size_t)
@@ -37,8 +44,6 @@ cdef extern from "cantera/oneD/Domain1D.h":
         double steady_atol(size_t)
         double transient_rtol(size_t)
         double transient_atol(size_t)
-        double z(size_t)
-        void setupGrid(size_t, double*) except +translate_exception
         void setID(string)
         string& id()
         string domainType "type"()