This mainly involved fixing the copy and assignment operators
for the IonsFromNeutralVPSSTP operator.
Added docs for PDSS_SSVol
Turned on keyword substitution
<transport>
<speciesDiffusivity>
<velocityBasis basis="mass">
Other valid values are "mole" or a species name.
This is loaded into LiquidTransportParams and then copied into
LiquidTransport in the initLiquidTransport() method.
velocity. This allows selection of a mass-averaged, mole-averaged or
solvent specified reference velocity using the member m_velocityBasis
or the methods setVelocityBasis() and getVelocityBasis(). Parsing of
input needs to be added for this still. An enum has been added
enum VelocityBasis {
VB_MOLEAVG = -2,
VB_MASSAVG = -1 };
Other values can correspond to species indices.
In LiquidTransport, the Stefan Maxwell solve now checks to see what
the m_velocityBasis member says the reference velocity should be and
fills the matrix accordingly. To allow mass averaged we have added
members m_massfracs and m_massfracs_tran.
Added methods to extract the diffusion velocity in a similar manner to
the diffusive fluxes. The diffusion velocity will be needed to not
force the porosity/tortuosity into the Transport classes for
porous flow. These methods are getSpeciesVdiff() and
getSpeciesVdiffES().
mixing. Previously there was a LiquidTranMixingModel specification
and one or more matrices to describe interactions. For example, we had
the following for viscosity:
LiquidTranMixingModel viscMixModel;
DenseMatrix m_visc_Eij;
DenseMatrix m_visc_Sij;
The new model puts all of this into a new class
LiquidTranInteraction. This class is built in the TransportFactory
and loaded into LiquidTransport Params. In
LiquidTransport::initLiquid() pointers to these objects are
transferred to the following members:
LiquidTranInteraction *m_viscMixModel;
LiquidTranInteraction *m_lambdaMixModel;
LiquidTranInteraction *m_diffMixModel;
LiquidTranInteraction *m_radiusMixModel;
With these, the structure of methods that compute the mixture
transport properties is greatly simplified. It should be possible to
only call these interaction models (they take as arguments the vectors
of individual species models that were previously added), but I need
to check this still.
I have also removed all binary diffusion coefficient matrices except
for m_bdiff. Mainly this means that I removed the m_DiffCoeff_StefMax
member. Also removed is m_logViscSpecies[k] which was used only in the
mixture viscosity computation now handles outside.
model name.
Added new method to build LiquidTranInteraction objects.
virtual LiquidTranInteraction* newLTI( const XML_Node &trNode,
TransportPropertyList tp_ind,
LiquidTransportParams& trParam) ;
This methods calls teh new operator and the init() method for those
objects. It also call the setParameters() method for those objects
that require additional trParam access.
In TransportFactory::getLiquidInteractionsTransportData() the majority
of the work is done by a switch statement that fills the different
LiquidTranInteraction* in LiquidTransportParams by calling newLTI().
The switch statement is over the type of transport property
(i.e. viscosity). After some debugging checks we can remove the rest
of that method. (all of the XML node parsing is moved to the
LiquidTranInteraction constructor.
objects for each of the transport properties: viscosity, thermalCond,
speciesDiffusivity, electCond, hydroRadius. This should allow us to
remove the members like visc_Eij, visc_Sij, thermalCond_Aij,
diff_Dij. Also should be able to remove LiquidTranMixingModel model_*
members. This removal is pending some testing.
class LiquidTranInteraction has been further developed along with
subclasses. The list of subclasses that should be in reasonable shape
is (all should be tested)
class LTI_Solvent;
class LTI_MoleFracs;
class LTI_MassFracs;
class LTI_Log_MoleFracs;
class LTI_Pairwise_Interaction;
class LTI_StokesEinstein;
The constructor takes only the TransportPropertyList enum. The init:
virtual void init( const XML_Node &compModelNode = 0,
thermo_t* thermo = 0 );
takes the thermo object along with the XML node
<compositionDependence> which it parses. The major methods for
LiquidTranInteraction are:
virtual void setParameters( LiquidTransportParams& trParam )
that sets additional things required from trParam for some
subclasses.
virtual doublereal getMixTransProp( doublereal* speciesValues, doublereal *weightSpecies = 0 )
virtual doublereal getMixTransProp( std::vector<LTPspecies*> LTPptrs )
that get a mixture averaged transport property.
virtual DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Dij; }
that get a matrix of interaction transport properties.
class LiquidTranInteraction holds members for various types of
interactions. Some documentation of the purpose of each of these is
still required.
derivatives of the log activity coefficients as used for computing
the transport coefficients. These methods are
IonsFromNeutralVPSSTP::getdlnActCoeffdlnC()
and the internal method
IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnC()
stoichiometries. These were not allowed previously. However, if
the species with fractional stoichiometries are in single-species
phases, this is ok, and actually necessary for some solid-phase
reactions.
vector<LTPspecies*> m_viscTempDep_Ns;
Previously they were held in two objects, the first identifying the
model type
vector<LiquidTR_Model> m_viscTempDepType_Ns;
and the second holding the model coefficients
std::vector<Coeff_T_> m_coeffVisc_Ns;
This greatly simplifies the assignment of coefficients from
LiquidTransportParams in initLiquid()
This also greatly simplifies the methods
void LiquidTransport::updateCond_T()
void LiquidTransport::updateViscosity_T()
void LiquidTransport::updateHydrodynamicRadius_T()
Since the pointed-to-LTPspecies classes (subclasses actually) are
created with new in TransportFactory::newLTP, these are deleted in
~LiquidTransport()
Similar changes made to SimpleTransport.h SimpleTransport.cpp
LTPspecies_Poly classes to hole a single transport property for a
single species.
The class LiquidTransportData now holds pointers to these LTPspecies
classes. It does not need to hold the model type or the coefficients
as these are contained in the LTPspecies classes.
virtual LTPspecies*
newLTP( const XML_Node &trNode, std::string &name,
TransportPropertyList tp_ind, thermo_t* thermo) ;
This method returns a pointer to the appropriate subclass of
LTPspecies.
Added maps of TransportPropertyList and LiquidTR
std::map<std::string, TransportPropertyList> m_tranPropMap;
std::map<std::string, LiquidTR_Model> m_LTRmodelMap;
Moved the method getArrhenius() from TransportFactory.cpp to
LiquidTransportData.cpp
In TransportFactory::getLiquidSpeciesTransportData(), removed the
lines associated with parsing the XML for the individual transport
properties. This XML parsing is now carried out within the LTPspecies
subclass constructors. Instead, within
getLiquidSpeciesTransportData() we call newLTP() method that creates
these subclassed methods and returns a pointer to the new LTPspecies
object.
virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const;
to ThermoPhase, GibbsExcessVPSSTP, VPStandardStateTP and
MargulesVPSSTP classes (i.e. the whole thermo tree).
In GibbsExcessVPSSTP and above, these methods are not yet implemented.
In MargulesVPSSTP, the internal method
void s_update_dlnActCoeff_dlnX() const;
does the work and stores the result in the member dlnActCoeffdlnX_Scaled_.
getSpeciesFluxes methods. This involved changing from a
concentration-driven formulation for the Stefan-Maxwell equations to a
molefraction-driven formulation. Also, the diffusion velocities are
what is computed internally as the primary variable. It would be nice
to put these out instead of just the fluxes.
There is still work to be done regarding mass-averaged velocities,
etc. the current method uses a mole-averaged velocity at present. We
really just need to bring mass fractions into the formulation for mass
averaged.
Replaced viscosityModel_ member with m_viscMixModel.
Fixed bug in filling m_coeffVisc_Ns, etc., for the Arrhenius model.
Failed to use "push_back() to add to vector prior to this.
For temperature-dependence option LTR_MODEL_POLY, corrected the
polynomial evaluations to correctly account for number of terms in the
polynomial.
Viscosity mixture evaluations are now up to date with respect to the
use of LTR_MIXMODEL_MOLEFRACS and LTR_MIXMODEL_LOG_MOLEFRACS.
Added membersto hold activity coefficient info
vector_fp actCoeffMolar_;
vector_fp lnActCoeffMolarDelta_;
Added method
getSpeciesFluxesES(...,const doublereal* grad_Phi,doublereal* fluxes))
that takes electrostatic potential gradient in addition to other gradients.
This then calls getSpeciesFluxesExt() to do the work.
Added new version of method LiquidTransport::update_Grad_lnAC(). The
new version calls m_thermo->getdlnActCoeffdlnX( DATA_PTR(grad_lnAC) );
These routines in the thermo object need to be provided.
Filled out TransportFactory::getLiquidInteractionsTransportData to
parse interaction parameters. About 220 lines of XML node extraction
added.
LiquidTransport.h LiquidTransport.cpp
Near the end of LiquidTransport::initLiquid, added the copying of
interaction parameters from the LiquidTransportParams object to
members:
+ m_visc_Eij = tr.visc_Eij;
+ m_visc_Sij = tr.visc_Sij;
+ m_lambda_Aij = tr.thermalCond_Aij;
+ m_diff_Dij = tr.diff_Dij;
+ m_radius_Aij = tr.radius_Aij;
Note that the last member was added to allow for hydrodynamic radius
mixing rules.
