Fix issues with "volume" and compressibility of SurfPhase

include/cantera/base/AnyMap.h

@@ -709,8 +709,9 @@ class InputFileError : public CanteraError
                    const std::string& message, const Args&... args)
         : CanteraError(
             procedure,
-            formatError(fmt::format(message, args...),
-                        node.m_line, node.m_column, node.m_metadata))
+            formatError(
+                (sizeof...(args) == 0) ? message : fmt::format(message, args...),
+                node.m_line, node.m_column, node.m_metadata))
         {
         }
 
@@ -723,13 +724,13 @@ class InputFileError : public CanteraError
                    const Args&... args)
         : CanteraError(
             procedure,
-            formatError2(fmt::format(message, args...),
-                         node1.m_line, node1.m_column, node1.m_metadata,
-                         node2.m_line, node2.m_column, node2.m_metadata))
+            formatError2(
+                (sizeof...(args) == 0) ? message : fmt::format(message, args...),
+                node1.m_line, node1.m_column, node1.m_metadata,
+                node2.m_line, node2.m_column, node2.m_metadata))
         {
         }
 
-
     virtual std::string getClass() const {
         return "InputFileError";
     }

include/cantera/thermo/LatticeSolidPhase.h

@@ -311,7 +311,7 @@ class LatticeSolidPhase : public ThermoPhase
         throw NotImplementedError("LatticeSolidPhase::getConcentrations");
     }
 
-    virtual doublereal concentration(int k) const {
+    virtual doublereal concentration(size_t k) const {
         throw NotImplementedError("LatticeSolidPhase::concentration");
     }
 

include/cantera/thermo/Phase.h

@@ -65,6 +65,12 @@ class Species;
  * An example of this is the function
  * Phase::setState_TRY(double t, double dens, const double* y).
  *
+ * For bulk (3-dimensional) phases, the mass density has units of kg/m^3, and the molar
+ * density and concentrations have units of kmol/m^3, and the units listed in the
+ * methods of the Phase class assume a bulk phase. However, for surface (2-dimensional)
+ * phases have units of kg/m^2 and kmol/m^2, respectively. And for edge (1-dimensional)
+ * phases, these units kg/m and kmol/m.
+ *
  * Class Phase contains methods for saving and restoring the full internal state
  * of a given phase. These are saveState() and restoreState(). These functions
  * operate on a state vector, which by default uses the first two entries for
@@ -532,7 +538,7 @@ class Phase
      *                  kmol/m^3. The length of the vector must be greater than
      *                  or equal to the number of species within the phase.
      */
-    void getConcentrations(double* const c) const;
+    virtual void getConcentrations(double* const c) const;
 
     //! Concentration of species k.
     //! If k is outside the valid range, an exception will be thrown.
@@ -541,7 +547,7 @@ class Phase
      *
      *    @returns the concentration of species k (kmol m-3).
      */
-    double concentration(const size_t k) const;
+    virtual double concentration(const size_t k) const;
 
     //! Set the concentrations to the specified values within the phase.
     //! We set the concentrations here and therefore we set the overall density
@@ -664,11 +670,11 @@ class Phase
 
     //! Molar density (kmol/m^3).
     //!     @return The molar density of the phase
-    double molarDensity() const;
+    virtual double molarDensity() const;
 
     //! Molar volume (m^3/kmol).
     //!     @return The molar volume of the phase
-    double molarVolume() const;
+    virtual double molarVolume() const;
 
     //! Set the internally stored density (kg/m^3) of the phase.
     //! Note the density of a phase is an independent variable.

include/cantera/thermo/SurfPhase.h

@@ -110,6 +110,10 @@ class SurfPhase : public ThermoPhase
         return "Surf";
     }
 
+    virtual bool isCompressible() const {
+        return false;
+    }
+
     //! Return the Molar Enthalpy. Units: J/kmol.
     /*!
      * For an ideal solution,
@@ -189,8 +193,8 @@ class SurfPhase : public ThermoPhase
      *
      * @param k Optional parameter indicating the species. The default
      *          is to assume this refers to species 0.
-     * @return
-     *   Returns the standard Concentration in units of m3 kmol-1.
+     * @return the standard concentration in units of kmol/m^2 for surface phases or
+     *     kmol/m for edge phases.
      */
     virtual doublereal standardConcentration(size_t k = 0) const;
     virtual doublereal logStandardConc(size_t k=0) const;
@@ -200,6 +204,20 @@ class SurfPhase : public ThermoPhase
 
     virtual bool addSpecies(shared_ptr<Species> spec);
 
+    //! Since interface phases have no volume, this returns 0.0.
+    virtual double molarVolume() const {
+        return 0.0;
+    }
+
+    //! Since interface phases have no volume, setting this to a value other than 0.0
+    //! raises an exception.
+    virtual void setMolarDensity(const double vm) {
+        if (vm != 0.0) {
+            throw CanteraError("SurfPhase::setMolarDensity",
+                               "The volume of an interface is zero");
+        }
+    }
+
     //! Returns the site density
     /*!
      * Site density kmol m-2
@@ -296,6 +314,8 @@ class SurfPhase : public ThermoPhase
     virtual void setState(const AnyMap& state);
 
 protected:
+    virtual void compositionChanged();
+
     //! Surface site density (kmol m-2)
     doublereal m_n0;
 

interfaces/cython/cantera/onedim.py

@@ -563,7 +563,7 @@ def write_hdf(self, filename, *args, group=None, species='X', mode='a',
         `SolutionArray.write_hdf` via `to_solution_array` and requires a working
         installation of *h5py* (``h5py`` can be installed using pip or conda).
         """
-        cols = ('extra', 'T', 'D', species)
+        cols = ('extra', 'T', 'P', species)
         meta = self.settings
         meta['date'] = formatdate(localtime=True)
         meta['cantera_version'] = __version__

interfaces/cython/cantera/thermo.pyx

@@ -691,7 +691,10 @@ cdef class ThermoPhase(_SolutionBase):
                 self._setArray1(thermo_setMoleFractions, X)
 
     property concentrations:
-        """Get/Set the species concentrations [kmol/m^3]."""
+        """
+        Get/Set the species concentrations. Units are kmol/m^3 for bulk phases, kmol/m^2
+        for surface phases, and kmol/m for edge phases.
+        """
         def __get__(self):
             return self._getArray1(thermo_getConcentrations)
         def __set__(self, C):

samples/f90/demo.f90

@@ -155,19 +155,19 @@ subroutine demo_surf(surf, nsp, nrxn)
   type(phase_t) surf
   integer :: nsp, nrxn, i
   character*40 equation
-  double precision :: kf(nrxn), ropnet(nrxn)
+  double precision :: ropf(nrxn), ropnet(nrxn)
 
   write(*,*)
   write(*,*) '********   Interface Kinetics Test   ********'
   write(*,*)
 
-  call getFwdRatesOfProgress(surf, kf)
+  call getFwdRatesOfProgress(surf, ropf)
   call getNetRatesOfProgress(surf, ropnet)
 
-  write(*,*) 'Equation                                     k_fwd        Net rate'
+  write(*,*) 'Equation                                    Fwd rate      Net rate'
   do i = 1, nrxn
     call getReactionString(surf, i, equation)
-    write(*,60) equation, kf(i), ropnet(i)
+    write(*,60) equation, ropf(i), ropnet(i)
 60  format(' ',a40, e14.5, e14.5)
   end do
 end subroutine demo_surf

src/base/Units.cpp

@@ -626,6 +626,8 @@ double UnitSystem::convert(const AnyValue& v, const std::string& dest) const
 {
     try {
         return convert(v, Units(dest));
+    } catch (InputFileError&) {
+        throw; // already have input file context from convert(AnyValue, Units)
     } catch (CanteraError& err) {
         throw InputFileError("UnitSystem::convert", v, err.getMessage());
     }

src/fortran/cantera_kinetics.f90

@@ -114,13 +114,13 @@ double precision function ctkin_productStoichCoeff(self, k, i)
       ctkin_productstoichcoeff = kin_productstoichcoeff(self%kin_id, k, i)
     end function ctkin_productstoichcoeff
 
-    integer function ctkin_getReactionType(self, i, buf)
+    subroutine ctkin_getReactionType(self, i, buf)
       implicit none
       type(phase_t), intent(inout) :: self
       integer, intent(in) :: i
       character*(*), intent(out) :: buf
       self%err = kin_getreactiontype(self%kin_id, i, buf)
-    end function ctkin_getReactionType
+    end subroutine ctkin_getReactionType
 
     subroutine ctkin_getFwdRatesOfProgress(self, fwdROP)
       implicit none

src/fortran/fct.cpp

@@ -30,6 +30,10 @@ typedef Cabinet<Transport> TransportCabinet;
 
 typedef integer status_t;
 
+template<> ThermoCabinet* ThermoCabinet::s_storage; // defined in ct.cpp
+template<> KineticsCabinet* KineticsCabinet::s_storage; // defined in ct.cpp
+template<> TransportCabinet* TransportCabinet::s_storage; // defined in ct.cpp
+
 namespace {
 
 ThermoPhase* _fph(const integer* n)

src/kinetics/solveSP.cpp

@@ -295,9 +295,14 @@ int solveSP::solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin,
 
 void solveSP::updateState(const doublereal* CSolnSP)
 {
+    vector_fp X;
     size_t loc = 0;
     for (size_t n = 0; n < m_numSurfPhases; n++) {
-        m_ptrsSurfPhase[n]->setConcentrations(CSolnSP + loc);
+        X.resize(m_nSpeciesSurfPhase[n]);
+        for (size_t k = 0; k < X.size(); k++) {
+            X[k] = CSolnSP[loc + k] / m_ptrsSurfPhase[n]->siteDensity();
+        }
+        m_ptrsSurfPhase[n]->setMoleFractions_NoNorm(X.data());
         loc += m_nSpeciesSurfPhase[n];
     }
 }

src/thermo/SurfPhase.cpp

@@ -159,9 +159,8 @@ void SurfPhase::getCp_R(doublereal* cpr) const
 
 void SurfPhase::getStandardVolumes(doublereal* vol) const
 {
-    _updateThermo();
     for (size_t k = 0; k < m_kk; k++) {
-        vol[k] = 1.0/standardConcentration(k);
+        vol[k] = 0.0;
     }
 }
 
@@ -211,39 +210,55 @@ void SurfPhase::setSiteDensity(doublereal n0)
                            "Site density must be positive. Got {}", n0);
     }
     m_n0 = n0;
+    assignDensity(n0 * meanMolecularWeight());
     m_logn0 = log(m_n0);
 }
 
 void SurfPhase::setCoverages(const doublereal* theta)
 {
     double sum = 0.0;
     for (size_t k = 0; k < m_kk; k++) {
-        sum += theta[k];
+        sum += theta[k] / size(k);
     }
     if (sum <= 0.0) {
         throw CanteraError("SurfPhase::setCoverages",
                            "Sum of Coverage fractions is zero or negative");
     }
     for (size_t k = 0; k < m_kk; k++) {
-        m_work[k] = m_n0*theta[k]/(sum*size(k));
+        m_work[k] = theta[k] / (sum * size(k));
     }
-    // Call the Phase:: class function setConcentrations.
-    setConcentrations(m_work.data());
+    setMoleFractions(m_work.data());
 }
 
 void SurfPhase::setCoveragesNoNorm(const doublereal* theta)
 {
+    double sum = 0.0;
+    double sum2 = 0.0;
     for (size_t k = 0; k < m_kk; k++) {
-        m_work[k] = m_n0*theta[k]/size(k);
+        sum += theta[k] / size(k);
+        sum2 += theta[k];
     }
-    setConcentrationsNoNorm(m_work.data());
+    if (sum <= 0.0) {
+        throw CanteraError("SurfPhase::setCoverages",
+                           "Sum of Coverage fractions is zero or negative");
+    }
+    for (size_t k = 0; k < m_kk; k++) {
+        m_work[k] = theta[k] * sum2 / (sum * size(k));
+    }
+    setMoleFractions_NoNorm(m_work.data());
 }
 
 void SurfPhase::getCoverages(doublereal* theta) const
 {
-    getConcentrations(theta);
+    double sum_X = 0.0;
+    double sum_X_s = 0.0;
+    getMoleFractions(theta);
+    for (size_t k = 0; k < m_kk; k++) {
+        sum_X += theta[k];
+        sum_X_s += theta[k] * size(k);
+    }
     for (size_t k = 0; k < m_kk; k++) {
-        theta[k] *= size(k)/m_n0;
+        theta[k] *= size(k) * sum_X / sum_X_s;
     }
 }
 
@@ -281,6 +296,12 @@ void SurfPhase::setState(const AnyMap& state) {
     ThermoPhase::setState(state);
 }
 
+void SurfPhase::compositionChanged()
+{
+    ThermoPhase::compositionChanged();
+    assignDensity(m_n0 * meanMolecularWeight());
+}
+
 void SurfPhase::_updateThermo(bool force) const
 {
     doublereal tnow = temperature();

test/data/consistency-cases.yaml

@@ -271,15 +271,12 @@ ideal-surface:
     phase: Pt-surf
     atol_v: 1e-7
     known-failures:
-      h_eq_u_plus_Pv: "Definition of volume is unclear. See GitHub Issue #1312"
       gk_eq_hk_minus_T_sk:
         "Implementation of s_k is incorrect. See GitHub Issue #1313"
       s_eq_sum_sk_Xk:
         "Implementation of s_k is incorrect. See GitHub Issue #1313"
       g_eq_sum_gk_Xk:
         "chemPotentials does not protect against inf. See GitHub Issue #1314"
-      dSdv_const_T_eq_dPdT_const_V:
-        "Compressibility of phase leads to inconsistent results. See GitHub Issue #1312"
   states:
   - {T: 800, P: 1 atm, coverages: {Pt(s): 0.5, H(s): 0.4, O(s): 0.1}}
   - {T: 800, P: 5 atm, coverages: {H(s): 1.0}}
@@ -291,10 +288,6 @@ ideal-edge:
     file: surface-phases.yaml
     phase: TPB
     atol_v: 1e3  # site density of 5e-18 kmol/m = linear molar volume of 2e17 m/kmol
-    known-failures:
-      h_eq_u_plus_Pv: "Definition of volume is unclear. See GitHub Issue #1312"
-      dSdv_const_T_eq_dPdT_const_V:
-        "Compressibility of phase leads to inconsistent results. See GitHub Issue #1312"
   states:
   - {T: 300, P: 1 atm}
   - {T: 900, P: 20 atm}

test/data/surface-phases.yaml

@@ -13,6 +13,18 @@ phases:
   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: Pt-multi-sites
+  thermo: ideal-surface
+  adjacent-phases: [gas]
+  kinetics: surface
+  reactions: [Pt-reactions, Pt-multisite-reactions]
+  species: [{Pt-surf-species: all}, {multi-site-species: all}]
+  site-density: 2.7063e-9 mol/cm^2
+  state:
+    T: 900 K
+    P: 1 atm
+    coverages: {Pt(s): 0.35, H(s): 0.4, O(s): 0.1, O2(s): 0.15}
+
 - name: TPB
   thermo: edge
   species: [{tpb-species: [(tpb)]}]
@@ -102,6 +114,19 @@ Pt-surf-species:
     - [1.9454180E+00, 9.1761647E-04, -1.1226719E-07, -9.9099624E-11,
        2.4307699E-14, -1.4005187E+04, -1.1531663E+01]
 
+multi-site-species:
+- name: O2(s)
+  composition: {O: 2, Pt: 2}
+  sites: 2
+  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]
+
 
 tpb-species:
 - name: (tpb)
@@ -120,6 +145,9 @@ Pt-reactions:
 - equation: H + Pt(s) => H(s)
   sticking-coefficient: [1.0, 0.0, 0.0]
 
+Pt-multisite-reactions:
+- equation: 2 O(s) <=> O2(s)
+  rate-constant: {A: 3.1e9 cm^2/mol/s, b: 0.0, Ea: 0.0}
 
 graphite-anode-species:
 - name: EC(e)