Changed names of variables
Added and updated documentation
This commit is contained in:
Harry Moffat
parent
90f7898970
commit
64cc610513
3 changed files with 326 additions and 156 deletions
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@ -42,7 +42,7 @@ namespace VCSnonideal {
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m_numRxnMinorZeroed(0),
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NPhase(0),
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m_doEstimateEquil(0),
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TMoles(0.0),
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m_totalMolNum(0.0),
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m_temperature(0.0),
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m_pressurePA(0.0),
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tolmaj(0.0),
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@ -115,10 +115,144 @@ public:
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void vcs_chemPotPhase(int iph, const double *const molNum,
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double * const ac, double * const mu_i,
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bool do_deleted = false);
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void vcs_dfe(double *z, int kk, int ll, int lbot, int ltop);
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//! Calculalte the dimensionless chemical potentials of all species or
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//! of certain groups of species, at a fixed temperature and pressure.
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/*!
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* We calculate the dimensionless chemical potentials of all species
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* or certain groups of species here, at a fixed temperature and pressure,
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* for the input mole vector z[] in the parameter list.
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* Nondimensionalization is achieved by division by RT.
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*
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* Note, for multispecies phases which are currently zeroed out,
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* the chemical potential is filled out with the standard chemical
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* potential.
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*
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* For species in multispecies phases whose concentration is zero,
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* we need to set the mole fraction to a very low value.
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* It's chemical potential
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* is then calculated using the VCS_DELETE_MINORSPECIES_CUTOFF concentration
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* to keep numbers positive.
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*
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*
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* Formula:
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* ---------------
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*
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* Ideal Mixtures:
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*
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* m_feSpecies(I) = m_SSfeSpecies(I) + ln(z(I)) - ln(m_tPhaseMoles[iph])
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction onto the standard chemical
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* potential. )
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*
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* Non-Ideal Mixtures: -> molar activity formulation
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* ActivityConvention = 0:
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*
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* m_feSpecies(I) = m_SSfeSpecies(I)
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* + ln(ActCoeff[I] * z(I)) - ln(m_tPhaseMoles[iph])
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction multiplied by the activity coefficient
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* onto the standard chemical potential. )
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*
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* note: z(I)/tPhMoles_ptr[iph] = Xmol[i] is the mole fraction
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* of i in the phase.
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*
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* ActivityConvention = 1: -> molality activity formulation
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*
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* m_feSpecies(I) = m_SSfeSpecies(I)
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* + ln(ActCoeff[I] * z(I)) - ln(m_tPhaseMoles[iph])
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* - ln(Mnaught * m_units)
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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*
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* note: m_SSfeSpecies(I) is the molality based standard state.
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* However, ActCoeff[I] is the molar based activity coefficient
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* We have used the formulas;
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*
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* ActCoeff_M[I] = ActCoeff[I] / Xmol[N]
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* where Xmol[N] is the mole fraction of the solvent
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* ActCoeff_M[I] is the molality based act coeff.
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*
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* m_feSpecies(I) = m_SSfeSpecies(I)
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* + ln(ActCoeff_M[I] * m(I))
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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* where m[I] is the molality of the ith solute
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*
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* m[I] = Xmol[I] / ( Xmol[N] * Mnaught * m_units)
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*
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*
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* Handling of Small Species:
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* ------------------------------
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* As per the discussion above, for small species where the mole
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* fraction
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*
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* z(i) < VCS_DELETE_MINORSPECIES_CUTOFF
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*
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* The chemical potential is calculated as:
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*
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* m_feSpecies(I)(I) = m_SSfeSpecies(I) + ln(ActCoeff[i](VCS_DELETE_MINORSPECIES_CUTOFF))
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*
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* Handling of "Species" Representing Interfacial Voltages
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* ---------------------------------------------------------
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*
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* These species have species types of VCS_SPECIES_TYPE_INTERFACIALVOLTAGE
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* The chemical potentials for these "species" refer to electrons in
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* metal electrodes. They have the following formula
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*
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* m_feSpecies(I) = m_SSfeSpecies(I) - F z[I] / RT
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*
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* F is Faraday's constant.
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* R = gas constant
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* T = temperature
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* V = potential of the interface = phi_electrode - phi_solution
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*
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* For these species, the solution vector unknown, z[I], is V, the phase voltage, in volts.
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*
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* Input
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* --------
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* @param ll Determine which group of species gets updated
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* ll = 0: Calculate for all species
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* < 0: calculate for components and for major non-components
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* 1: calculate for components and for minor non-components
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*
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* @param lbot Restricts the calculation of the chemical potential
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* to the species between LBOT <= i < LTOP. Usually
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* LBOT and LTOP will be equal to 0 and MR, respectively.
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* @param ltop Top value of the loops
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*
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* @param z z[i] : Number of moles of species i
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* -> This can either be the current solution vector WT()
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* or the actual solution vector W()
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*
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* @param kk Determines whether z is old or new or tentative:
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* 1: Use the tentative values for the total number of
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* moles in the phases, i.e., use TG1 instead of TG etc.
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* 0: Use the base values of the total number of
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* moles in each system.
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*
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* Also needed:
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* ff : standard state chemical potentials. These are the
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* chemical potentials of the standard states at
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* the same T and P as the solution.
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* tg : Total Number of moles in the phase.
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*/
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void vcs_dfe(double const * const z, int kk, int ll, int lbot, int ltop);
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void vcs_updateVP(int place);
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int vcs_RxnStepSizes(void);
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void vcs_tmoles(void);
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//! Calculates the total number of moles of species in all phases.
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/*!
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* Calculates the total number of moles in all phases and updates
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* the variable m_totalMolNum.
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* Reconciles Phase existence flags with total moles in each phase.
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*/
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void vcs_tmoles();
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void vcs_deltag(int l, bool doDeleted);
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void vcs_switch_pos(int ifunc, int k1, int k2);
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void vcs_deltag_Phase(int iphase, bool doDeleted);
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@ -425,9 +559,15 @@ private:
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//! Alternative treatment for the update of a minor species
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/*!
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* This calculation assumes that the component basis species mole
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* numbers don't change as the minor species change. Then, it's a
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* straightforward independent calculation to find the minor species
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* concentrations.
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*
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* @param kspec Species index of the minor species
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* @param irxn Rxn index of the same minor species
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* @param do_delete
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* @param do_delete True, if the species is deleted from the mechanism
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* because the mole numbers got too small.
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*/
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double minor_alt_calc(int kspec, int irxn, int *do_delete
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#ifdef DEBUG_MODE
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@ -438,9 +578,20 @@ private:
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int force(int iti);
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int globStepDamp(int iti);
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void vcs_switch2D(double * const * const Jac, int k1, int k2);
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double l2normdg(double dg[]);
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//! Calculate the norm of a deltaGibbs free energy vector
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/*!
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* Positive DG for species which don't exist are ignored.
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*
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* @param dgLocal Vector of local delta G's.
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*/
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double l2normdg(double dg[]) const;
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#ifdef DEBUG_MODE
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void prneav(void);
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//! Print out and check the elemental abundance vector
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void prneav() const;
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void checkDelta1(double * const ds, double * const delTPhMoles, int kspec);
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#endif
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@ -706,12 +857,15 @@ public:
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*/
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std::vector<double> m_elemAbundancesGoal;
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double TMoles; /* TMoles = Total number of moles in all phases
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* This number includes the inerts.
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* -> Don't use this except for scaling
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* purposes only */
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//! Total number of kmoles in all phases
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/*!
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* This number includes the inerts.
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* -> Don't use this except for scaling
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* purposes
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*/
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double m_totalMolNum;
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//! total kmols of species in each phase
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//! Total kmols of species in each phase
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/*!
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* This contains the total number of moles of species in each phase
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*
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@ -65,7 +65,7 @@ namespace VCSnonideal {
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}
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}
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for (int iphase = 0; iphase < NPhase; iphase++) {
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double denom = MAX(TMoles, 1.0E-4);
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double denom = MAX(m_totalMolNum, 1.0E-4);
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if (!vcs_doubleEqual(dchange[iphase]/denom, delTPhMoles[iphase]/denom)) {
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plogf("checkDelta1: we have found a problem\n");
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exit(-1);
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@ -637,7 +637,7 @@ namespace VCSnonideal {
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m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx;
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} else {
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m_molNumSpecies_new[kspec] = TMoles * VCS_DELETE_PHASE_CUTOFF * 10.;
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m_molNumSpecies_new[kspec] = m_totalMolNum * VCS_DELETE_PHASE_CUTOFF * 10.;
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dx = m_molNumSpecies_new[kspec] - m_molNumSpecies_old[kspec];
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}
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m_deltaMolNumSpecies[kspec] = dx;
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@ -820,7 +820,7 @@ namespace VCSnonideal {
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* we can't call vcs_species_type() because the phase moles
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* would be wrong.
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*/
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if (m_molNumSpecies_new[kspec] < 0.005 * TMoles) {
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if (m_molNumSpecies_new[kspec] < 0.005 * m_totalMolNum) {
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iph = PhaseID[kspec];
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if (m_molNumSpecies_new[kspec] < (m_tPhaseMoles_old[iph] * 0.01)) {
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#ifdef DEBUG_MODE
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@ -1286,7 +1286,7 @@ namespace VCSnonideal {
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Vphase = VPhaseList[iph];
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if (!(Vphase->SingleSpecies)) {
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if (m_tPhaseMoles_old[iph] != 0.0 &&
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m_tPhaseMoles_old[iph]/TMoles <= VCS_DELETE_PHASE_CUTOFF) {
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m_tPhaseMoles_old[iph]/m_totalMolNum <= VCS_DELETE_PHASE_CUTOFF) {
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soldel = 1;
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for (kspec = 0; kspec < m_numSpeciesRdc; kspec++) {
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if (PhaseID[kspec] == iph && m_molNumSpecies_old[kspec] > 0.0) {
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@ -2876,9 +2876,9 @@ namespace VCSnonideal {
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*/
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iph = PhaseID[kspec];
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double tphmoles = m_tPhaseMoles_old[iph];
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double trphmoles = tphmoles / TMoles;
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double trphmoles = tphmoles / m_totalMolNum;
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if (trphmoles > VCS_DELETE_PHASE_CUTOFF) {
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m_deltaMolNumSpecies[kspec] = TMoles * VCS_SMALL_MULTIPHASE_SPECIES;
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m_deltaMolNumSpecies[kspec] = m_totalMolNum * VCS_SMALL_MULTIPHASE_SPECIES;
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#ifdef DEBUG_MODE
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sprintf(ANOTE,
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"MultSpec: small species born again DG = %11.3E",
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@ -2891,7 +2891,7 @@ namespace VCSnonideal {
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#endif
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Vphase = VPhaseList[iph];
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int numSpPhase = Vphase->NVolSpecies;
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m_deltaMolNumSpecies[kspec] = TMoles * 10.0 * VCS_DELETE_PHASE_CUTOFF / numSpPhase;
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m_deltaMolNumSpecies[kspec] = m_totalMolNum * 10.0 * VCS_DELETE_PHASE_CUTOFF / numSpPhase;
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}
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--(m_numRxnMinorZeroed);
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} else {
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@ -4131,102 +4131,133 @@ namespace VCSnonideal {
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}
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}
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}
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/*****************************************************************************/
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/*****************************************************************************/
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/*****************************************************************************/
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void VCS_SOLVE::vcs_dfe(double *z, int kk, int ll, int lbot, int ltop)
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/**************************************************************************
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*
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* vcs_dfe:
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*
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* We calculate the dimensionless chemical potentials of all species
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* or certain groups of species here, at a fixed temperature and pressure,
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* for the input mole vector z[] in the parameter list.
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* Nondimensionalization is achieved by division by RT.
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*
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* Note, for multispecies phases which are currently zeroed out,
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* the chemical potential is filled out with the standard chemical
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* potential.
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*
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* For species in multispecies phases whose concentration is zero,
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* we need to set the mole fraction to a very low value.
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* It's chemical potential
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* is then calculated using the VCS_DELETE_MINORSPECIES_CUTOFF concentration
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* to keep numbers positive.
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*
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*
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* Formula:
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* ---------------
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*
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* Ideal Mixtures:
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*
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* fe(I) = ff(I) + ln(z(I)) - ln(tPhMoles_ptr[iph])
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction onto the standard chemical
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* potential. )
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*
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* Non-Ideal Mixtures:
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* ActivityConvention = 0:
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* fe(I) = ff(I) + ln(ActCoeff[i]z(I)) - ln(tPhMoles_ptr[iph])
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction multiplied by the activity coefficient
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* onto the standard chemical potential. )
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*
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* ActivityConvention = 1: -> molality activity formulation
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* fe(I) = ff(I) + ln(ActCoeff[i]z(I)) - ln(tPhMoles_ptr[iph])
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* - ln(Mnaught * m_units)
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*
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* note: z(I)/tPhMoles_ptr[iph] = Xmol[i] is the mole fraction
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* of i in the phase.
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*
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* NOTE:
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* As per the discussion above, for small species where the mole
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* fraction
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* z(i) < VCS_DELETE_MINORSPECIES_CUTOFF
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* The chemical potential is calculated as:
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* fe(I) = ff(I) + ln(ActCoeff[i](VCS_DELETE_MINORSPECIES_CUTOFF))
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*
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* VCS_SPECIES_TYPE_INTERFACIALVOLTAGE
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*
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* These chemical potentials refer to electrons in
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* metal electrodes. They have the following formula
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*
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* fe(I) = ff(I) - F V / RT
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*
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* F is Faraday's constant.
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* R = gas constant
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* T = temperature
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* V = potential of the interface = phi_electrode - phi_solution
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*
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* For these species, the solution vector is V in volts.
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*
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* Input
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* --------
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* ll = 0: Calculate for all species
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* < 0: calculate for components and for major non-components
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* 1: calculate for components and for minor non-components
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* lbot : restricts the calculation of the chemical potential
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* ltop to the species between LBOT <= i < LTOP. Usually
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* LBOT and LTOP will be equal to 0 and MR, respectively.
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* z(i) : Number of moles of species i
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* -> This can either be the current solution vector WT()
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* or the actual solution vector W()
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* kk 1: Use the tentative values for the total number of
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* moles in the phases, i.e., use TG1 instead of TG etc.
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* 0: Use the base values of the total number of
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* moles in each system.
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* ff : standard state chemical potentials. These are the
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* chemical potentials of the standard states at
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* the same T and P as the solution.
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* tg : Total Number of moles in the phase.
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*
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*
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*************************************************************************/
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{
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// Calculalte the dimensionless chemical potentials of all species or
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// of certain groups of species, at a fixed temperature and pressure.
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/*
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* We calculate the dimensionless chemical potentials of all species
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* or certain groups of species here, at a fixed temperature and pressure,
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* for the input mole vector z[] in the parameter list.
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* Nondimensionalization is achieved by division by RT.
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*
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* Note, for multispecies phases which are currently zeroed out,
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* the chemical potential is filled out with the standard chemical
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* potential.
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*
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* For species in multispecies phases whose concentration is zero,
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* we need to set the mole fraction to a very low value.
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* It's chemical potential
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* is then calculated using the VCS_DELETE_MINORSPECIES_CUTOFF concentration
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* to keep numbers positive.
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*
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*
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* Formula:
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* ---------------
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*
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* Ideal Mixtures:
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*
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* m_feSpecies(I) = m_SSfeSpecies(I) + ln(z(I)) - ln(m_tPhaseMoles[iph])
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction onto the standard chemical
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* potential. )
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*
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* Non-Ideal Mixtures: -> molar activity formulation
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* ActivityConvention = 0:
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*
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* m_feSpecies(I) = m_SSfeSpecies(I)
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* + ln(ActCoeff[I] * z(I)) - ln(m_tPhaseMoles[iph])
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* + Charge[I] * Faraday_dim * phasePhi[iphase];
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*
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* ( This is equivalent to the adding the log of the
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* mole fraction multiplied by the activity coefficient
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* onto the standard chemical potential. )
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*
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* note: z(I)/tPhMoles_ptr[iph] = Xmol[i] is the mole fraction
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* of i in the phase.
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*
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* ActivityConvention = 1: -> molality activity formulation
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*
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* m_feSpecies(I) = m_SSfeSpecies(I)
|
||||
* + ln(ActCoeff[I] * z(I)) - ln(m_tPhaseMoles[iph])
|
||||
* - ln(Mnaught * m_units)
|
||||
* + Charge[I] * Faraday_dim * phasePhi[iphase];
|
||||
*
|
||||
* note: m_SSfeSpecies(I) is the molality based standard state.
|
||||
* However, ActCoeff[I] is the molar based activity coefficient
|
||||
* We have used the formulas;
|
||||
*
|
||||
* ActCoeff_M[I] = ActCoeff[I] / Xmol[N]
|
||||
* where Xmol[N] is the mole fraction of the solvent
|
||||
* ActCoeff_M[I] is the molality based act coeff.
|
||||
*
|
||||
* m_feSpecies(I) = m_SSfeSpecies(I)
|
||||
* + ln(ActCoeff_M[I] * m(I))
|
||||
* + Charge[I] * Faraday_dim * phasePhi[iphase];
|
||||
* where m[I] is the molality of the ith solute
|
||||
*
|
||||
* m[I] = Xmol[I] / ( Xmol[N] * Mnaught * m_units)
|
||||
*
|
||||
*
|
||||
* Handling of Small Species:
|
||||
* ------------------------------
|
||||
* As per the discussion above, for small species where the mole
|
||||
* fraction
|
||||
*
|
||||
* z(i) < VCS_DELETE_MINORSPECIES_CUTOFF
|
||||
*
|
||||
* The chemical potential is calculated as:
|
||||
*
|
||||
* m_feSpecies(I)(I) = m_SSfeSpecies(I) + ln(ActCoeff[i](VCS_DELETE_MINORSPECIES_CUTOFF))
|
||||
*
|
||||
* Handling of "Species" Representing Interfacial Voltages
|
||||
* ---------------------------------------------------------
|
||||
*
|
||||
* These species have species types of VCS_SPECIES_TYPE_INTERFACIALVOLTAGE
|
||||
* The chemical potentials for these "species" refer to electrons in
|
||||
* metal electrodes. They have the following formula
|
||||
*
|
||||
* m_feSpecies(I) = m_SSfeSpecies(I) - F z[I] / RT
|
||||
*
|
||||
* F is Faraday's constant.
|
||||
* R = gas constant
|
||||
* T = temperature
|
||||
* V = potential of the interface = phi_electrode - phi_solution
|
||||
*
|
||||
* For these species, the solution vector unknown, z[I], is V, the phase voltage, in volts.
|
||||
*
|
||||
* Input
|
||||
* --------
|
||||
* @param ll Determine which group of species gets updated
|
||||
* ll = 0: Calculate for all species
|
||||
* < 0: calculate for components and for major non-components
|
||||
* 1: calculate for components and for minor non-components
|
||||
*
|
||||
* @param lbot Restricts the calculation of the chemical potential
|
||||
* to the species between LBOT <= i < LTOP. Usually
|
||||
* LBOT and LTOP will be equal to 0 and MR, respectively.
|
||||
* @param ltop Top value of the loops
|
||||
*
|
||||
* @param z z[i] : Number of moles of species i
|
||||
* -> This can either be the current solution vector WT()
|
||||
* or the actual solution vector W()
|
||||
*
|
||||
* @param kk Determines whether z is old or new or tentative:
|
||||
* 1: Use the tentative values for the total number of
|
||||
* moles in the phases, i.e., use TG1 instead of TG etc.
|
||||
* 0: Use the base values of the total number of
|
||||
* moles in each system.
|
||||
*
|
||||
* Also needed:
|
||||
* ff : standard state chemical potentials. These are the
|
||||
* chemical potentials of the standard states at
|
||||
* the same T and P as the solution.
|
||||
* tg : Total Number of moles in the phase.
|
||||
*/
|
||||
void VCS_SOLVE::vcs_dfe(double const * const z, int kk, int ll, int lbot, int ltop) {
|
||||
int l1, l2, iph, kspec, irxn;
|
||||
int iphase;
|
||||
double *tPhMoles_ptr;
|
||||
|
|
@ -4456,22 +4487,18 @@ namespace VCSnonideal {
|
|||
checkFinite(fe[kspec]);
|
||||
}
|
||||
#endif
|
||||
} /* vcs_dfe() ***************************************************************/
|
||||
|
||||
}
|
||||
|
||||
/*****************************************************************************/
|
||||
|
||||
#ifdef DEBUG_MODE
|
||||
void VCS_SOLVE::prneav(void)
|
||||
|
||||
/*************************************************************************
|
||||
*
|
||||
* Print out and check the elemental abundance vector
|
||||
*
|
||||
*************************************************************************/
|
||||
{
|
||||
int kerr, i, j;
|
||||
//! Print out and check the elemental abundance vector
|
||||
void VCS_SOLVE::prneav() const {
|
||||
int kerr, j;
|
||||
std::vector<double> eav(m_numElemConstraints, 0.0);
|
||||
|
||||
for (j = 0; j < m_numElemConstraints; ++j) {
|
||||
for (i = 0; i < m_numSpeciesTot; ++i) {
|
||||
for (int i = 0; i < m_numSpeciesTot; ++i) {
|
||||
if (SpeciesUnknownType[i] == VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) {
|
||||
eav[j] += FormulaMatrix[j][i] * m_molNumSpecies_old[i];
|
||||
}
|
||||
|
|
@ -4495,24 +4522,20 @@ namespace VCSnonideal {
|
|||
if (kerr) {
|
||||
plogf("Element abundance check failure\n");
|
||||
}
|
||||
plogf("--------------------------------------------------\n");
|
||||
plogf("--------------------------------------------------");
|
||||
plogendl();
|
||||
}
|
||||
#endif
|
||||
|
||||
/*****************************************************************************/
|
||||
/*****************************************************************************/
|
||||
/*****************************************************************************/
|
||||
|
||||
double VCS_SOLVE::l2normdg(double dgLocal[])
|
||||
|
||||
/*************************************************************************
|
||||
*
|
||||
* l2normdg:
|
||||
*
|
||||
* Calculate the norm of the DG vector.
|
||||
* Positive DG for species which don't exist are ignored.
|
||||
************************************************************************/
|
||||
{
|
||||
// Calculate the norm of a deltaGibbs free energy vector
|
||||
/*
|
||||
* Positive DG for species which don't exist are ignored.
|
||||
*
|
||||
* @param dgLocal Vector of local delta G's.
|
||||
*/
|
||||
double VCS_SOLVE::l2normdg(double dgLocal[]) const {
|
||||
double tmp;
|
||||
int irxn;
|
||||
if (m_numRxnRdc <= 0) return 0.0;
|
||||
|
|
@ -4524,23 +4547,17 @@ namespace VCSnonideal {
|
|||
}
|
||||
}
|
||||
}
|
||||
return (sqrt(tmp / m_numRxnRdc));
|
||||
return (std::sqrt(tmp / m_numRxnRdc));
|
||||
}
|
||||
/*****************************************************************************/
|
||||
/*****************************************************************************/
|
||||
|
||||
/*****************************************************************************/
|
||||
|
||||
void VCS_SOLVE::vcs_tmoles(void)
|
||||
|
||||
/**************************************************************************
|
||||
*
|
||||
* vcs_tmoles:
|
||||
*
|
||||
* Calculates the total number of moles of species in all phases.
|
||||
* Calculates the total number of moles in all phases.
|
||||
* Reconciles Phase existence flags with total moles in each phase.
|
||||
*************************************************************************/
|
||||
{
|
||||
// Calculates the total number of moles of species in all phases.
|
||||
/*
|
||||
* Calculates the total number of moles in all phases.
|
||||
* Reconciles Phase existence flags with total moles in each phase.
|
||||
*/
|
||||
void VCS_SOLVE::vcs_tmoles() {
|
||||
int i;
|
||||
double sum;
|
||||
vcs_VolPhase *Vphase;
|
||||
|
|
@ -4568,10 +4585,9 @@ namespace VCSnonideal {
|
|||
}
|
||||
}
|
||||
}
|
||||
TMoles = sum;
|
||||
} /* vcs_tmoles() ************************************************************/
|
||||
/*****************************************************************************/
|
||||
/*****************************************************************************/
|
||||
m_totalMolNum = sum;
|
||||
}
|
||||
|
||||
/*****************************************************************************/
|
||||
|
||||
void VCS_SOLVE::vcs_updateVP (int place)
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue