[oneD] Reorder content for named doxygen section

Author: ischoegl

include/cantera/oneD/Flow1D.h

@@ -171,7 +171,6 @@ class Flow1D : public Domain1D
     //! Returns true if the specified component is an active part of the solver state
     virtual bool componentActive(size_t n) const;
 
-    //! Print the solution.
     void show(const double* x) override;
 
     shared_ptr<SolutionArray> asArray(const double* soln) const override;
@@ -334,11 +333,48 @@ class Flow1D : public Domain1D
     AnyMap getMeta() const override;
     void setMeta(const AnyMap& state) override;
 
+    //! @name Updates of cached properties
+    //! These methods are called by eval() to update cached properties and data that are
+    //! used for the evaluation of the governing equations.
+    //! @{
+
     //! Update the properties (thermo, transport, and diffusion flux).
     //! This function is called in eval after the points which need
     //! to be updated are defined.
     virtual void updateProperties(size_t jg, double* x, size_t jmin, size_t jmax);
 
+    /**
+     * Update the thermodynamic properties from point j0 to point j1
+     * (inclusive), based on solution x.
+     *
+     * The gas state is set to be consistent with the solution at the
+     * points from j0 to j1.
+     *
+     * Properties that are computed and cached are:
+     * * #m_rho (density)
+     * * #m_wtm (mean molecular weight)
+     * * #m_cp (specific heat capacity)
+     * * #m_hk (species specific enthalpies)
+     * * #m_wdot (species production rates)
+     */
+    void updateThermo(const double* x, size_t j0, size_t j1) {
+        for (size_t j = j0; j <= j1; j++) {
+            setGas(x,j);
+            m_rho[j] = m_thermo->density();
+            m_wtm[j] = m_thermo->meanMolecularWeight();
+            m_cp[j] = m_thermo->cp_mass();
+            m_thermo->getPartialMolarEnthalpies(&m_hk(0, j));
+            m_kin->getNetProductionRates(&m_wdot(0, j));
+        }
+    }
+
+    //! Update the diffusive mass fluxes.
+    virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1);
+
+    //! Update the transport properties at grid points in the range from `j0`
+    //! to `j1`, based on solution `x`.
+    virtual void updateTransport(double* x, size_t j0, size_t j1);
+
     /**
      * Computes the radiative heat loss vector over points jmin to jmax and stores
      * the data in the qdotRadiation variable.
@@ -356,8 +392,11 @@ class Flow1D : public Domain1D
      */
     void computeRadiation(double* x, size_t jmin, size_t jmax);
 
+    //! @}
+
     //! @name Governing Equations
-    //! Methods are used to evaluate residuals for each of the governing equations.
+    //! Methods called by eval() to calculate residuals for individual governing
+    //! equations.
     //! @{
 
     /**
@@ -492,31 +531,6 @@ class Flow1D : public Domain1D
     //! @deprecated To be removed after Cantera 3.0.
     virtual void evalContinuity(size_t j, double* x, double* r, int* diag, double rdt);
 
-    /**
-     * Update the thermodynamic properties from point j0 to point j1
-     * (inclusive), based on solution x.
-     *
-     * The gas state is set to be consistent with the solution at the
-     * points from j0 to j1.
-     *
-     * Properties that are computed and cached are:
-     * * #m_rho (density)
-     * * #m_wtm (mean molecular weight)
-     * * #m_cp (specific heat capacity)
-     * * #m_hk (species specific enthalpies)
-     * * #m_wdot (species production rates)
-     */
-    void updateThermo(const double* x, size_t j0, size_t j1) {
-        for (size_t j = j0; j <= j1; j++) {
-            setGas(x,j);
-            m_rho[j] = m_thermo->density();
-            m_wtm[j] = m_thermo->meanMolecularWeight();
-            m_cp[j] = m_thermo->cp_mass();
-            m_thermo->getPartialMolarEnthalpies(&m_hk(0, j));
-            m_kin->getNetProductionRates(&m_wdot(0, j));
-        }
-    }
-
     //! @name Solution components
     //! @{
 
@@ -606,9 +620,6 @@ class Flow1D : public Domain1D
         return m*m_nsp*m_nsp + m_nsp*j + k;
     }
 
-    //! Update the diffusive mass fluxes.
-    virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1);
-
     //! Get the gradient of species specific molar enthalpies
     virtual void grad_hk(const double* x, size_t j);
 
@@ -690,10 +701,6 @@ class Flow1D : public Domain1D
     bool m_isFree;
     bool m_usesLambda;
 
-    //! Update the transport properties at grid points in the range from `j0`
-    //! to `j1`, based on solution `x`.
-    virtual void updateTransport(double* x, size_t j0, size_t j1);
-
 public:
     //! Location of the point where temperature is fixed
     double m_zfixed = Undef;

src/oneD/Flow1D.cpp

@@ -366,6 +366,100 @@ void Flow1D::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax)
     updateDiffFluxes(x, j0, j1);
 }
 
+void Flow1D::updateTransport(double* x, size_t j0, size_t j1)
+{
+     if (m_do_multicomponent) {
+        for (size_t j = j0; j < j1; j++) {
+            setGasAtMidpoint(x,j);
+            double wtm = m_thermo->meanMolecularWeight();
+            double rho = m_thermo->density();
+            m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0);
+            m_trans->getMultiDiffCoeffs(m_nsp, &m_multidiff[mindex(0,0,j)]);
+
+            // Use m_diff as storage for the factor outside the summation
+            for (size_t k = 0; k < m_nsp; k++) {
+                m_diff[k+j*m_nsp] = m_wt[k] * rho / (wtm*wtm);
+            }
+
+            m_tcon[j] = m_trans->thermalConductivity();
+            if (m_do_soret) {
+                m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + j*m_nsp);
+            }
+        }
+    } else { // mixture averaged transport
+        for (size_t j = j0; j < j1; j++) {
+            setGasAtMidpoint(x,j);
+            m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0);
+
+            if (m_fluxGradientBasis == ThermoBasis::molar) {
+                m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]);
+            } else {
+                m_trans->getMixDiffCoeffsMass(&m_diff[j*m_nsp]);
+            }
+
+            double rho = m_thermo->density();
+
+            if (m_fluxGradientBasis == ThermoBasis::molar) {
+                double wtm = m_thermo->meanMolecularWeight();
+                for (size_t k=0; k < m_nsp; k++) {
+                    m_diff[k+j*m_nsp] *= m_wt[k] * rho / wtm;
+                }
+            } else {
+                for (size_t k=0; k < m_nsp; k++) {
+                    m_diff[k+j*m_nsp] *= rho;
+                }
+            }
+            m_tcon[j] = m_trans->thermalConductivity();
+        }
+    }
+}
+
+void Flow1D::updateDiffFluxes(const double* x, size_t j0, size_t j1)
+{
+    if (m_do_multicomponent) {
+        for (size_t j = j0; j < j1; j++) {
+            double dz = z(j+1) - z(j);
+            for (size_t k = 0; k < m_nsp; k++) {
+                double sum = 0.0;
+                for (size_t m = 0; m < m_nsp; m++) {
+                    sum += m_wt[m] * m_multidiff[mindex(k,m,j)] * (X(x,m,j+1)-X(x,m,j));
+                }
+                m_flux(k,j) = sum * m_diff[k+j*m_nsp] / dz;
+            }
+        }
+    } else {
+        for (size_t j = j0; j < j1; j++) {
+            double sum = 0.0;
+            double dz = z(j+1) - z(j);
+            if (m_fluxGradientBasis == ThermoBasis::molar) {
+                for (size_t k = 0; k < m_nsp; k++) {
+                    m_flux(k,j) = m_diff[k+m_nsp*j] * (X(x,k,j) - X(x,k,j+1))/dz;
+                    sum -= m_flux(k,j);
+                }
+            } else {
+                for (size_t k = 0; k < m_nsp; k++) {
+                    m_flux(k,j) = m_diff[k+m_nsp*j] * (Y(x,k,j) - Y(x,k,j+1))/dz;
+                    sum -= m_flux(k,j);
+                }
+            }
+            // correction flux to insure that \sum_k Y_k V_k = 0.
+            for (size_t k = 0; k < m_nsp; k++) {
+                m_flux(k,j) += sum*Y(x,k,j);
+            }
+        }
+    }
+
+    if (m_do_soret) {
+        for (size_t m = j0; m < j1; m++) {
+            double gradlogT = 2.0 * (T(x,m+1) - T(x,m)) /
+                              ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m)));
+            for (size_t k = 0; k < m_nsp; k++) {
+                m_flux(k,m) -= m_dthermal(k,m)*gradlogT;
+            }
+        }
+    }
+}
+
 void Flow1D::computeRadiation(double* x, size_t jmin, size_t jmax)
 {
     // Variable definitions for the Planck absorption coefficient and the
@@ -622,54 +716,6 @@ void Flow1D::evalContinuity(size_t j, double* x, double* rsd, int* diag, double
         "Overloaded by StFlow; to be removed after Cantera 3.0");
 }
 
-void Flow1D::updateTransport(double* x, size_t j0, size_t j1)
-{
-     if (m_do_multicomponent) {
-        for (size_t j = j0; j < j1; j++) {
-            setGasAtMidpoint(x,j);
-            double wtm = m_thermo->meanMolecularWeight();
-            double rho = m_thermo->density();
-            m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0);
-            m_trans->getMultiDiffCoeffs(m_nsp, &m_multidiff[mindex(0,0,j)]);
-
-            // Use m_diff as storage for the factor outside the summation
-            for (size_t k = 0; k < m_nsp; k++) {
-                m_diff[k+j*m_nsp] = m_wt[k] * rho / (wtm*wtm);
-            }
-
-            m_tcon[j] = m_trans->thermalConductivity();
-            if (m_do_soret) {
-                m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + j*m_nsp);
-            }
-        }
-    } else { // mixture averaged transport
-        for (size_t j = j0; j < j1; j++) {
-            setGasAtMidpoint(x,j);
-            m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0);
-
-            if (m_fluxGradientBasis == ThermoBasis::molar) {
-                m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]);
-            } else {
-                m_trans->getMixDiffCoeffsMass(&m_diff[j*m_nsp]);
-            }
-
-            double rho = m_thermo->density();
-
-            if (m_fluxGradientBasis == ThermoBasis::molar) {
-                double wtm = m_thermo->meanMolecularWeight();
-                for (size_t k=0; k < m_nsp; k++) {
-                    m_diff[k+j*m_nsp] *= m_wt[k] * rho / wtm;
-                }
-            } else {
-                for (size_t k=0; k < m_nsp; k++) {
-                    m_diff[k+j*m_nsp] *= rho;
-                }
-            }
-            m_tcon[j] = m_trans->thermalConductivity();
-        }
-    }
-}
-
 void Flow1D::show(const double* x)
 {
     writelog("    Pressure:  {:10.4g} Pa\n", m_press);
@@ -687,52 +733,6 @@ void Flow1D::show(const double* x)
     }
 }
 
-void Flow1D::updateDiffFluxes(const double* x, size_t j0, size_t j1)
-{
-    if (m_do_multicomponent) {
-        for (size_t j = j0; j < j1; j++) {
-            double dz = z(j+1) - z(j);
-            for (size_t k = 0; k < m_nsp; k++) {
-                double sum = 0.0;
-                for (size_t m = 0; m < m_nsp; m++) {
-                    sum += m_wt[m] * m_multidiff[mindex(k,m,j)] * (X(x,m,j+1)-X(x,m,j));
-                }
-                m_flux(k,j) = sum * m_diff[k+j*m_nsp] / dz;
-            }
-        }
-    } else {
-        for (size_t j = j0; j < j1; j++) {
-            double sum = 0.0;
-            double dz = z(j+1) - z(j);
-            if (m_fluxGradientBasis == ThermoBasis::molar) {
-                for (size_t k = 0; k < m_nsp; k++) {
-                    m_flux(k,j) = m_diff[k+m_nsp*j] * (X(x,k,j) - X(x,k,j+1))/dz;
-                    sum -= m_flux(k,j);
-                }
-            } else {
-                for (size_t k = 0; k < m_nsp; k++) {
-                    m_flux(k,j) = m_diff[k+m_nsp*j] * (Y(x,k,j) - Y(x,k,j+1))/dz;
-                    sum -= m_flux(k,j);
-                }
-            }
-            // correction flux to insure that \sum_k Y_k V_k = 0.
-            for (size_t k = 0; k < m_nsp; k++) {
-                m_flux(k,j) += sum*Y(x,k,j);
-            }
-        }
-    }
-
-    if (m_do_soret) {
-        for (size_t m = j0; m < j1; m++) {
-            double gradlogT = 2.0 * (T(x,m+1) - T(x,m)) /
-                              ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m)));
-            for (size_t k = 0; k < m_nsp; k++) {
-                m_flux(k,m) -= m_dthermal(k,m)*gradlogT;
-            }
-        }
-    }
-}
-
 string Flow1D::componentName(size_t n) const
 {
     switch (n) {