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Added back ability to get transport parameters from transport objects.

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Added back read and write of named XML array blocks.
Fixed an error in IonsFromNeutralVPSSTP.
This commit is contained in:
Harry Moffat 2012-12-21 01:18:28 +00:00
parent ea7d447864
commit eab8781ea7
7 changed files with 403 additions and 26 deletions
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90
include/cantera/base/ctml.h
View file

@ -187,6 +187,61 @@ void addFloatArray(Cantera::XML_Node& node, const std::string& titleString,
const doublereal minval = Cantera::Undef,
const doublereal maxval = Cantera::Undef);
//! This function adds a child node with the name given by the first parameter with a value
//! consisting of a comma separated list of floats
/*!
* This function will add a child node to the current XML node, with the
* name given in the list. It will have a title attribute, and the body
* of the XML node will be filled out with a comma separated list of
* integers
*
* Example:
*
* Code snipet:
* @verbatum
const XML_Node &node;
std::string titleString = "additionalTemperatures";
int n = 3;
int Tcases[3] = [273.15, 298.15, 373.15];
std::string typeString = "optional";
std::string units = "Kelvin";
addNamedFloatArray(node, titleString, n, &cases[0], typeString, units);
@endverbatum
*
* Creates the following the snippet in the XML file:
* @verbatum
<parentNode>
<additionalTemperatures type="optional" vtype="floatArray" size = "3" units="Kelvin">
273.15, 298.15, 373.15
<\additionalTemperatures>
<\parentNode>
@endverbatum
*
* @param node reference to the XML_Node object of the parent XML element
* @param name Name of the XML node
* @param n Length of the doubles vector.
* @param values Pointer to a vector of doubles
* @param unitsString String name of the Units attribute. This is an optional
* parameter. The default is to
* have an empty string.
* @param type String type. This is an optional parameter. The default
* is to have an empty string.
* @param minval Minimum allowed value of the int. This is an optional
* parameter. The default is the
* special double, Cantera::Undef, which means to ignore the
* entry.
* @param maxval Maximum allowed value of the int. This is an optional
* parameter. The default is the
* special double, Cantera::Undef, which means to ignore the
* entry.
*
*/
void addNamedFloatArray(Cantera::XML_Node& parentNode, const std::string &name, const int n,
const doublereal* const vals, const std::string units = "",
const std::string type = "",
const doublereal minval = Cantera::Undef,
const doublereal maxval = Cantera::Undef);
//! This function adds a child node with the name string with a string value
//! to the current node
/*!
@ -703,6 +758,41 @@ bool getOptionalModel(const Cantera::XML_Node& parent, const std::string& nodeNa
*/
Cantera::XML_Node* getByTitle(const Cantera::XML_Node& node, const std::string& title);
//! This function reads a child node with the name string with a specific
//! title attribute named titleString
/*!
* This function will read a child node to the current XML node with the name "string".
* It must have a title attribute, named titleString, and the body
* of the XML node will be read into the valueString output argument.
*
* If the child node is not found then the empty string is returned.
*
* Example:
*
* Code snipet:
* @verbatim
const XML_Node &node;
getString(XML_Node& node, std::string titleString, std::string valueString,
std::string typeString);
@endverbatim
*
* Reads the following the snippet in the XML file:
* @verbatim
<string title="titleString" type="typeString">
valueString
<\string>
@endverbatim
*
* @param node Reference to the XML_Node object of the parent XML element
* @param titleString String name of the title attribute of the child node
* @param valueString Value string that is found in the child node. output variable
* @param typeString String type. This is an optional output variable. It is filled
* with the attribute "type" of the XML entry.
*/
void getString(const Cantera::XML_Node& node, const std::string &titleString,
std::string& valueString, std::string& typeString);
//! This function attempts to read a named child node and returns with the contents in the value string.
//! title attribute named "titleString"
/*!

9
include/cantera/transport/MixTransport.h
View file

@ -260,7 +260,14 @@ private:
//! Update boolean for the mixture rule for the mixture thermal conductivity
bool m_condmix_ok;
public:
vector_fp m_eps;
vector_fp m_sigma;
vector_fp m_alpha;
DenseMatrix m_dipole;
vector_fp m_zrot;
vector_fp m_crot;
private:
//! Debug flag - turns on more printing
bool m_debug;
};

7
include/cantera/transport/MultiTransport.h
View file

@ -176,10 +176,15 @@ private:
//! Dense matrix for omega22
DenseMatrix m_om22;
vector_fp m_zrot;
public:
vector_fp m_crot;
vector_fp m_cinternal;
vector_fp m_zrot;
vector_fp m_eps;
vector_fp m_sigma;
vector_fp m_alpha;
DenseMatrix m_dipole;
private:
vector_fp m_sqrt_eps_k;
DenseMatrix m_log_eps_k;

289
src/base/ctml.cpp
View file

@ -234,6 +234,84 @@ void addFloatArray(Cantera::XML_Node& node, const std::string& title, const size
f.addAttribute("max",maxval);
}
}
//====================================================================================================================
// This function adds a child node with the name given by the first parameter with a value
// consisting of a comma separated list of floats
/*
* This function will add a child node to the current XML node, with the
* name given in the list. It will have a title attribute, and the body
* of the XML node will be filled out with a comma separated list of
* integers
*
* Example:
*
* Code snipet:
* @verbatum
const XML_Node &node;
std::string titleString = "additionalTemperatures";
int n = 3;
int Tcases[3] = [273.15, 298.15, 373.15];
std::string typeString = "optional";
std::string units = "Kelvin";
addNamedFloatArray(node, titleString, n, &cases[0], typeString, units);
@endverbatum
*
* Creates the following the snippet in the XML file:
* @verbatum
<parentNode>
<additionalTemperatures type="optional" vtype="floatArray" size = "3" units="Kelvin">
273.15, 298.15, 373.15
<\additionalTemperatures>
<\parentNode>
@endverbatum
*
* @param node reference to the XML_Node object of the parent XML element
* @param name Name of the XML node
* @param n Length of the doubles vector.
* @param values Pointer to a vector of doubles
* @param unitsString String name of the Units attribute. This is an optional
* parameter. The default is to
* have an empty string.
* @param type String type. This is an optional parameter. The default
* is to have an empty string.
* @param minval Minimum allowed value of the int. This is an optional
* parameter. The default is the
* special double, Cantera::Undef, which means to ignore the
* entry.
* @param maxval Maximum allowed value of the int. This is an optional
* parameter. The default is the
* special double, Cantera::Undef, which means to ignore the
* entry.
*
*/
void addNamedFloatArray(Cantera::XML_Node& node, const std::string &name, const int n,
const doublereal* const vals, const std::string units,
const std::string type, const doublereal minval,
const doublereal maxval)
{
int i;
std::string v = "";
for (i = 0; i < n; i++) {
v += fp2str(vals[i],FP_Format);
if (i == n-1) v += "\n";
else if (i > 0 && (i+1) % 3 == 0) v += ",\n";
else v += ", ";
}
XML_Node& f = node.addChild(name, v);
if (type != "") {
f.addAttribute("type",type);
}
/*
* Add vtype, which indicates the type of the value. Here we specify it as a list of floats separated
* by commas, with a length given by size attribute.
*/
f.addAttribute("vtype", "floatArray");
f.addAttribute("size", n);
if (units != "") f.addAttribute("units", units);
if (minval != Undef) f.addAttribute("min", minval);
if (maxval != Undef) f.addAttribute("max", maxval);
}
//====================================================================================================================
// This function adds a child node with the name string with a string value
@ -322,28 +400,115 @@ std::string getChildValue(const Cantera::XML_Node& parent, const std::string& na
}
return parent(nameString);
}
void getNamedStringValue(const Cantera::XML_Node& node, const std::string &nameString, std::string& valueString,
std::string& typeString)
{
//====================================================================================================================
// This function reads a child node with the name, "string", with a specific
// title attribute named "titleString"
/*
* This function will read a child node to the current XML node, with the
* name "string". It must have a title attribute, named titleString, and the body
* of the XML node will be read into the valueString output argument.
*
* Example:
*
* Code snipet:
* @verbatum
const XML_Node &node;
getString(XML_Node& node, std::string titleString, std::string valueString,
std::string typeString);
@endverbatum
*
* Reads the following the snippet in the XML file:
* @verbatum
<string title="titleString" type="typeString">
valueString
<\string>
@endverbatum
*
* @param node Reference to the XML_Node object of the parent XML element
* @param titleString String name of the title attribute of the child node
* @param valueString Value string that is found in the child node. output variable
* @param typeString String type. This is an optional output variable. It is filled
* with the attribute "type" of the XML entry.
*/
void getString(const Cantera::XML_Node& node, const std::string &titleString, std::string& valueString,
std::string& typeString) {
valueString = "";
typeString = "";
if (node.hasChild(nameString)) {
XML_Node &xc = node.child(nameString);
valueString = xc.value();
typeString = xc["type"];
} else {
XML_Node* s = getByTitle(node, nameString);
if (s) {
if (s->name() == "string") {
valueString = (*s).value();
typeString = (*s)["type"];
return;
}
XML_Node* s = getByTitle(node, titleString);
if (s)
if (s->name() == "string") {
valueString = (*s).value();
typeString = (*s)["type"];
return;
}
}
}
//=======================================================================================================================
// This function attempts to read a named child node and returns with the contents in the value string.
// title attribute named "titleString"
/*
* This function will read a child node to the current XML node, with the
* name "string". It must have a title attribute, named titleString, and the body
* of the XML node will be read into the valueString output argument.
*
* If the child node is not found then the empty string is returned.
*
* Example:
*
* Code snipet:
* @verbatum
const XML_Node &node;
std::string valueString;
std::string typeString;
std::string nameString = "timeIncrement";
getString(XML_Node& node, nameString, valueString, valueString, typeString);
@endverbatum
*
* Reads the following the snippet in the XML file:
*
* * @verbatum
<nameString type="typeString">
valueString
<\nameString>
@endverbatum
*
* or alternatively as a retrofit and special case, it also reads the following case
*
* @verbatum
<string title="nameString" type="typeString">
valueString
<\string>
@endverbatum
*
* @param node Reference to the XML_Node object of the parent XML element
* @param nameString Name of the XML Node input variable
* @param valueString Value string that is found in the child node. output variable
* @param typeString String type. This is an optional output variable. It is filled
* with the attribute "type" of the XML entry. output variable
*/
void getNamedStringValue(const Cantera::XML_Node& node, const std::string &nameString, std::string& valueString,
std::string& typeString)
{
valueString = "";
typeString = "";
if (node.hasChild(nameString)) {
XML_Node &xc = node.child(nameString);
valueString = xc.value();
typeString = xc["type"];
} else {
XML_Node* s = getByTitle(node, nameString);
if (s) {
if (s->name() == "string") {
valueString = (*s).value();
typeString = (*s)["type"];
return;
}
}
}
}
//====================================================================================================================
// Get a vector of integer values from a child element.
/*
@ -946,6 +1111,97 @@ size_t getFloatArray(const Cantera::XML_Node& node, std::vector<doublereal> & v,
return v.size();
}
//====================================================================================================================
int getNamedFloatArray(const Cantera::XML_Node& parentNode, const std::string & nodeName, std::vector<doublereal> & v,
const bool convert, const std::string unitsString) {
std::string::size_type icom;
std::string numstr;
doublereal dtmp;
std::string nn = parentNode.name();
v.clear();
const Cantera::XML_Node *readNode = parentNode.findByName(nodeName);
if (!readNode) {
return 0;
}
doublereal vmin = Undef;
doublereal vmax = Undef;
doublereal funit = 1.0;
/*
* Get the attributes field, units, from the XML node
*/
std::string units = (*readNode)["units"];
if (units != "" && convert) {
if (unitsString == "actEnergy" && units != "") {
funit = actEnergyToSI(units);
} else if (unitsString != "" && units != "") {
funit = toSI(units);
}
}
if ((*readNode)["min"] != "")
vmin = atofCheck((*readNode)["min"].c_str());
if ((*readNode)["max"] != "")
vmax = atofCheck((*readNode)["max"].c_str());
int expectedSize = 0;
nn = (*readNode)["size"];
expectedSize = atoi(nn.c_str());
nn = (*readNode)["vtype"];
if (nn != "floatArray") {
throw CanteraError("getNamedFloatArray",
"node named " + nodeName + "didn't have correct vtype");
}
doublereal vv;
std::string val = readNode->value();
while (1 > 0) {
icom = val.find(',');
if (icom != string::npos) {
numstr = val.substr(0,icom);
val = val.substr(icom+1,val.size());
dtmp = atofCheck(numstr.c_str());
v.push_back(dtmp);
}
else {
/*
* This little bit of code is to allow for the
* possibility of a comma being the last
* item in the value text. This was allowed in
* previous versions of Cantera, even though it
* would appear to be odd. So, we keep the
* possibilty in for backwards compatibility.
*/
int nlen = strlen(val.c_str());
if (nlen > 0) {
dtmp = atofCheck(val.c_str());
v.push_back(dtmp);
}
break;
}
vv = v.back();
if (vmin != Undef && vv < vmin - Tiny) {
writelog("\nWarning: value "+fp2str(vv)+
" is below lower limit of " +fp2str(vmin)+".\n");
}
if (vmax != Undef && vv > vmax + Tiny) {
writelog("\nWarning: value "+fp2str(vv)+
" is above upper limit of " +fp2str(vmin)+".\n");
}
}
int nv = v.size();
for (int n = 0; n < nv; n++) {
v[n] *= funit;
}
if (nv != expectedSize) {
throw CanteraError("getNamedFloatArray",
"node named " + nodeName + "didn't have correct number of floats"
+ int2str(expectedSize) + " vs " + int2str(nv));
}
return nv;
}
//====================================================================================================================
// This routine is used to interpret the value portions of XML
// elements that contain colon separated pairs.
@ -1183,4 +1439,5 @@ void getStringArray(const Cantera::XML_Node& node, std::vector<std::string>& v)
tokenizeString(val, v);
}
}

22
src/thermo/IonsFromNeutralVPSSTP.cpp
View file

@ -103,10 +103,10 @@ IonsFromNeutralVPSSTP::IonsFromNeutralVPSSTP(const std::string& inputFile,
}
constructPhaseFile(inputFile, id);
geThermo = dynamic_cast<GibbsExcessVPSSTP*>(neutralMoleculePhase_);
y.resize(numNeutralMoleculeSpecies_,0.0);
size_t numNeutMolSpec = geThermo->nSpecies();
dlnActCoeff_NeutralMolecule.resize(numNeutMolSpec);
dX_NeutralMolecule.resize(numNeutMolSpec);
//y.resize(numNeutralMoleculeSpecies_,0.0);
//size_t numNeutMolSpec = geThermo->nSpecies();
//dlnActCoeff_NeutralMolecule.resize(numNeutMolSpec);
//dX_NeutralMolecule.resize(numNeutMolSpec);
}
//====================================================================================================================
IonsFromNeutralVPSSTP::IonsFromNeutralVPSSTP(XML_Node& phaseRoot,
@ -201,6 +201,7 @@ operator=(const IonsFromNeutralVPSSTP& b)
GibbsExcessVPSSTP::operator=(b);
ionSolnType_ = b.ionSolnType_;
numNeutralMoleculeSpecies_ = b.numNeutralMoleculeSpecies_;
indexSpecialSpecies_ = b.indexSpecialSpecies_;
@ -215,6 +216,10 @@ operator=(const IonsFromNeutralVPSSTP& b)
passThroughList_ = b.passThroughList_;
numPassThroughSpecies_ = b.numPassThroughSpecies_;
y = b.y;
dlnActCoeff_NeutralMolecule = b.dlnActCoeff_NeutralMolecule;
dX_NeutralMolecule = b.dX_NeutralMolecule;
IOwnNThermoPhase_ = b.IOwnNThermoPhase_;
moleFractionsTmp_ = b.moleFractionsTmp_;
muNeutralMolecule_ = b.muNeutralMolecule_;
@ -224,9 +229,6 @@ operator=(const IonsFromNeutralVPSSTP& b)
dlnActCoeffdlnX_diag_NeutralMolecule_ = b.dlnActCoeffdlnX_diag_NeutralMolecule_;
dlnActCoeffdlnN_diag_NeutralMolecule_ = b.dlnActCoeffdlnN_diag_NeutralMolecule_;
dlnActCoeffdlnN_NeutralMolecule_ = b.dlnActCoeffdlnN_NeutralMolecule_;
y = b.y;
dlnActCoeff_NeutralMolecule = b.dlnActCoeff_NeutralMolecule ;
dX_NeutralMolecule = b.dX_NeutralMolecule ;
return *this;
}
@ -1162,6 +1164,11 @@ void IonsFromNeutralVPSSTP::initLengths()
dlnActCoeffdlnX_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_);
dlnActCoeffdlnN_NeutralMolecule_.resize(numNeutralMoleculeSpecies_, numNeutralMoleculeSpecies_, 0.0);
y.resize(numNeutralMoleculeSpecies_, 0.0);
dlnActCoeff_NeutralMolecule.resize(numNeutralMoleculeSpecies_, 0.0);
dX_NeutralMolecule.resize(numNeutralMoleculeSpecies_, 0.0);
}
//====================================================================================================================
//! Return the factor overlap
@ -1499,7 +1506,6 @@ void IonsFromNeutralVPSSTP::getdlnActCoeffds(const doublereal dTds, const double
return;
}
size_t numNeutMolSpec = geThermo->nSpecies();
// static vector_fp dlnActCoeff_NeutralMolecule(numNeutMolSpec);
// static vector_fp dX_NeutralMolecule(numNeutMolSpec);

8
src/transport/MixTransport.cpp
View file

@ -91,6 +91,14 @@ Transport* MixTransport::duplMyselfAsTransport() const
bool MixTransport::initGas(GasTransportParams& tr)
{
GasTransport::initGas(tr);
m_eps = tr.eps;
m_sigma = tr.sigma;
m_alpha = tr.alpha;
m_dipole = tr.dipole;
m_zrot = tr.zrot;
m_crot = tr.crot;
// copy polynomials and parameters into local storage
m_condcoeffs = tr.condcoeffs;

4
src/transport/MultiTransport.cpp
View file

@ -74,6 +74,10 @@ bool MultiTransport::initGas(GasTransportParams& tr)
m_zrot = tr.zrot;
m_crot = tr.crot;
m_eps = tr.eps;
m_sigma = tr.sigma;
m_alpha = tr.alpha;
m_dipole = tr.dipole;
m_zrot = tr.zrot;
// the L matrix
m_Lmatrix.resize(3*m_nsp, 3*m_nsp);