void Domain1D::restore(const XML_Node& dom, doublereal* soln, int loglevel)
{
vector_fp values;
vector<XML_Node*> nodes;
dom.getChildren("floatArray", nodes);
for (size_t i = 0; i < nodes.size(); i++) {
string title = nodes[i]->attrib("title");
getFloatArray(*nodes[i], values, false);
if (values.size() != nComponents()) {
throw CanteraError("Domain1D::restore", "Got an array of length " +
int2str(values.size()) + " when one of length " +
int2str(nComponents()) + "was expected.");
}
if (title == "abstol_transient") {
m_atol_ts = values;
} else if (title == "reltol_transient") {
m_rtol_ts = values;
} else if (title == "abstol_steady") {
m_atol_ss = values;
} else if (title == "reltol_steady") {
m_rtol_ss = values;
} else {
throw CanteraError("Domain1D::restore",
"Got an unexpected array, '" + title + "'");
}
}
}
void getIntegers(const XML_Node& node,
std::map<std::string, int>& v)
{
std::vector<XML_Node*> f = node.getChildren("integer");
for (size_t i = 0; i < f.size(); i++) {
const XML_Node& fi = *f[i];
if (fi["min"] != "" && fi["max"] != "") {
v[fi["title"]] = fi.int_value();
}
}
}
void Sim1D::restore(const std::string& fname, const std::string& id,
int loglevel)
{
ifstream s(fname.c_str());
if (!s)
throw CanteraError("Sim1D::restore",
"could not open input file "+fname);
XML_Node root;
root.build(s);
s.close();
XML_Node* f = root.findID(id);
if (!f) {
throw CanteraError("Sim1D::restore","No solution with id = "+id);
}
vector<XML_Node*> xd;
f->getChildren("domain", xd);
if (xd.size() != m_nd) {
throw CanteraError("Sim1D::restore", "Solution does not contain the "
" correct number of domains. Found " +
int2str(xd.size()) + "expected " +
int2str(m_nd) + ".\n");
}
size_t sz = 0;
for (size_t m = 0; m < m_nd; m++) {
if (loglevel > 0 && xd[m]->attrib("id") != domain(m).id()) {
writelog("Warning: domain names do not match: '" +
(*xd[m])["id"] + + "' and '" + domain(m).id() + "'\n");
}
sz += domain(m).nComponents() * intValue((*xd[m])["points"]);
}
m_x.resize(sz);
m_xnew.resize(sz);
for (size_t m = 0; m < m_nd; m++) {
domain(m).restore(*xd[m], DATA_PTR(m_x) + domain(m).loc(), loglevel);
}
resize();
finalize();
}
void Domain1D::restore(const XML_Node& dom, doublereal* soln, int loglevel)
{
vector_fp values;
vector<XML_Node*> nodes;
dom.getChildren("floatArray", nodes);
for (size_t i = 0; i < nodes.size(); i++) {
string title = nodes[i]->attrib("title");
getFloatArray(*nodes[i], values, false);
if (values.size() != nComponents()) {
if (loglevel > 0) {
writelog("Warning: Domain1D::restore: Got an array of length " +
int2str(values.size()) + " when one of length " +
int2str(nComponents()) + " was expected. " +
"Tolerances for individual species may not be preserved.\n");
}
// The number of components will differ when restoring from a
// mechanism with a different number of species. Assuming that
// tolerances are the same for all species, we can just copy the
// tolerance from the last species.
if (!values.empty()) {
values.resize(nComponents(), values[values.size()-1]);
} else {
// If the tolerance vector is empty, just leave the defaults
// in place.
continue;
}
}
if (title == "abstol_transient") {
m_atol_ts = values;
} else if (title == "reltol_transient") {
m_rtol_ts = values;
} else if (title == "abstol_steady") {
m_atol_ss = values;
} else if (title == "reltol_steady") {
m_rtol_ss = values;
} else {
throw CanteraError("Domain1D::restore",
"Got an unexpected array, '" + title + "'");
}
}
}
void importPhase(XML_Node& phase, ThermoPhase* th)
{
// Check the the supplied XML node in fact represents a phase.
if (phase.name() != "phase") {
throw CanteraError("importPhase",
"Current const XML_Node named, " + phase.name() +
", is not a phase element.");
}
// In this section of code, we get the reference to the phase XML tree
// within the ThermoPhase object. Then, we clear it and fill it with the
// current information that we are about to use to construct the object. We
// will then be able to resurrect the information later by calling xml().
th->setXMLdata(phase);
// set the id attribute of the phase to the 'id' attribute in the XML tree.
th->setID(phase.id());
th->setName(phase.id());
// Number of spatial dimensions. Defaults to 3 (bulk phase)
if (phase.hasAttrib("dim")) {
int idim = intValue(phase["dim"]);
if (idim < 1 || idim > 3) {
throw CanteraError("importPhase",
"phase, " + th->id() +
", has unphysical number of dimensions: " + phase["dim"]);
}
th->setNDim(idim);
} else {
th->setNDim(3); // default
}
// Set equation of state parameters. The parameters are specific to each
// subclass of ThermoPhase, so this is done by method setParametersFromXML
// in each subclass.
const XML_Node& eos = phase.child("thermo");
if (phase.hasChild("thermo")) {
th->setParametersFromXML(eos);
} else {
throw CanteraError("importPhase",
" phase, " + th->id() +
", XML_Node does not have a \"thermo\" XML_Node");
}
VPStandardStateTP* vpss_ptr = 0;
int ssConvention = th->standardStateConvention();
if (ssConvention == cSS_CONVENTION_VPSS) {
vpss_ptr = dynamic_cast <VPStandardStateTP*>(th);
if (vpss_ptr == 0) {
throw CanteraError("importPhase",
"phase, " + th->id() + ", was VPSS, but dynamic cast failed");
}
}
// Add the elements.
if (ssConvention != cSS_CONVENTION_SLAVE) {
installElements(*th, phase);
}
// Add the species.
//
// Species definitions may be imported from multiple sources. For each one,
// a speciesArray element must be present.
vector<XML_Node*> sparrays = phase.getChildren("speciesArray");
if (ssConvention != cSS_CONVENTION_SLAVE && sparrays.empty()) {
throw CanteraError("importPhase",
"phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n"
+ " There must be at least one speciesArray nodes "
"with one or more species");
}
vector<XML_Node*> dbases;
vector_int sprule(sparrays.size(),0);
// Default behavior when importing from CTI/XML is for undefined elements to
// be treated as an error
th->throwUndefinedElements();
// loop over the speciesArray elements
for (size_t jsp = 0; jsp < sparrays.size(); jsp++) {
const XML_Node& speciesArray = *sparrays[jsp];
// If the speciesArray element has a child element
//
// <skip element="undeclared">
//
// then set sprule[jsp] to 1, so that any species with an undeclared
// element will be quietly skipped when importing species. Additionally,
// if the skip node has the following attribute:
//
// <skip species="duplicate">
//
// then duplicate species names will not cause Cantera to throw an
// exception. Instead, the duplicate entry will be discarded.
if (speciesArray.hasChild("skip")) {
const XML_Node& sk = speciesArray.child("skip");
string eskip = sk["element"];
if (eskip == "undeclared") {
sprule[jsp] = 1;
}
string dskip = sk["species"];
if (dskip == "duplicate") {
sprule[jsp] += 10;
}
}
// Get a pointer to the node containing the species definitions for the
// species declared in this speciesArray element. This may be in the
// local file containing the phase element, or may be in another file.
XML_Node* db = get_XML_Node(speciesArray["datasrc"], &phase.root());
if (db == 0) {
throw CanteraError("importPhase()",
" Can not find XML node for species database: "
+ speciesArray["datasrc"]);
}
// add this node to the list of species database nodes.
dbases.push_back(db);
}
// Now, collect all the species names and all the XML_Node * pointers for
// those species in a single vector. This is where we decide what species
// are to be included in the phase. The logic is complicated enough that we
// put it in a separate routine.
std::vector<XML_Node*> spDataNodeList;
std::vector<std::string> spNamesList;
vector_int spRuleList;
formSpeciesXMLNodeList(spDataNodeList, spNamesList, spRuleList,
sparrays, dbases, sprule);
size_t nsp = spDataNodeList.size();
if (ssConvention == cSS_CONVENTION_SLAVE && nsp > 0) {
throw CanteraError("importPhase()", "For Slave standard states, "
"number of species must be zero: {}", nsp);
}
for (size_t k = 0; k < nsp; k++) {
XML_Node* s = spDataNodeList[k];
AssertTrace(s != 0);
if (spRuleList[k]) {
th->ignoreUndefinedElements();
}
th->addSpecies(newSpecies(*s));
if (vpss_ptr) {
const XML_Node* const ss = s->findByName("standardState");
std::string ss_model = (ss) ? ss->attrib("model") : "ideal-gas";
unique_ptr<PDSS> kPDSS(newPDSS(ss_model));
kPDSS->setParametersFromXML(*s);
vpss_ptr->installPDSS(k, std::move(kPDSS));
}
th->saveSpeciesData(k, s);
}
// Done adding species. Perform any required subclass-specific
// initialization.
th->initThermo();
// Perform any required subclass-specific initialization that requires the
// XML phase object
std::string id = "";
th->initThermoXML(phase, id);
}
size_t getFloatArray(const XML_Node& node, std::vector<doublereal> & v,
const bool convert, const std::string& unitsString,
const std::string& nodeName)
{
const XML_Node* readNode = &node;
if (node.name() != nodeName) {
vector<XML_Node*> ll = node.getChildren(nodeName);
if (ll.size() == 0) {
throw CanteraError("getFloatArray",
"wrong XML element type/name: was expecting "
+ nodeName + "but accessed " + node.name());
} else {
readNode = ll[0];
ll = readNode->getChildren("floatArray");
if (ll.size() > 0) {
readNode = ll[0];
}
}
}
v.clear();
doublereal vmin = Undef, vmax = Undef;
doublereal funit = 1.0;
/*
* Get the attributes field, units, from the XML node
*/
std::string units = readNode->attrib("units");
if (units != "" && convert) {
if (unitsString == "actEnergy" && units != "") {
funit = actEnergyToSI(units);
} else if (unitsString != "" && units != "") {
funit = toSI(units);
}
}
if (readNode->attrib("min") != "") {
vmin = fpValueCheck(readNode->attrib("min"));
}
if (readNode->attrib("max") != "") {
vmax = fpValueCheck(readNode->attrib("max"));
}
std::string val = readNode->value();
while (true) {
size_t icom = val.find(',');
if (icom != string::npos) {
string numstr = val.substr(0,icom);
val = val.substr(icom+1,val.size());
v.push_back(fpValueCheck(numstr));
} 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
* possibility in for backwards compatibility.
*/
if (!val.empty()) {
v.push_back(fpValueCheck(val));
}
break;
}
doublereal 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");
}
}
for (size_t n = 0; n < v.size(); n++) {
v[n] *= funit;
}
return v.size();
}
bool importPhase(XML_Node& phase, ThermoPhase* th,
SpeciesThermoFactory* spfactory)
{
// Check the the supplied XML node in fact represents a phase.
if (phase.name() != "phase") {
throw CanteraError("importPhase",
"Current const XML_Node named, " + phase.name() +
", is not a phase element.");
}
/*
* In this section of code, we get the reference to the
* phase xml tree within the ThermoPhase object. Then,
* we clear it and fill it with the current information that
* we are about to use to construct the object. We will then
* be able to resurrect the information later by calling xml().
*/
th->setXMLdata(phase);
// set the id attribute of the phase to the 'id' attribute in the XML tree.
th->setID(phase.id());
th->setName(phase.id());
// Number of spatial dimensions. Defaults to 3 (bulk phase)
if (phase.hasAttrib("dim")) {
int idim = intValue(phase["dim"]);
if (idim < 1 || idim > 3)
throw CanteraError("importPhase",
"phase, " + th->id() +
", has unphysical number of dimensions: " + phase["dim"]);
th->setNDim(idim);
} else {
th->setNDim(3); // default
}
// Set equation of state parameters. The parameters are
// specific to each subclass of ThermoPhase, so this is done
// by method setParametersFromXML in each subclass.
const XML_Node& eos = phase.child("thermo");
if (phase.hasChild("thermo")) {
th->setParametersFromXML(eos);
} else {
throw CanteraError("importPhase",
" phase, " + th->id() +
", XML_Node does not have a \"thermo\" XML_Node");
}
VPStandardStateTP* vpss_ptr = 0;
int ssConvention = th->standardStateConvention();
if (ssConvention == cSS_CONVENTION_VPSS) {
vpss_ptr = dynamic_cast <VPStandardStateTP*>(th);
if (vpss_ptr == 0) {
throw CanteraError("importPhase",
"phase, " + th->id() + ", was VPSS, but dynamic cast failed");
}
}
// if no species thermo factory was supplied, use the default one.
if (!spfactory) {
spfactory = SpeciesThermoFactory::factory();
}
/***************************************************************
* Add the elements.
***************************************************************/
if (ssConvention != cSS_CONVENTION_SLAVE) {
installElements(*th, phase);
}
/***************************************************************
* Add the species.
*
* Species definitions may be imported from multiple
* sources. For each one, a speciesArray element must be
* present.
***************************************************************/
vector<XML_Node*> sparrays;
phase.getChildren("speciesArray", sparrays);
if (ssConvention != cSS_CONVENTION_SLAVE) {
if (sparrays.empty()) {
throw CanteraError("importPhase",
"phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n"
+ " There must be at least one speciesArray nodes "
"with one or more species");
}
}
vector<XML_Node*> dbases;
vector_int sprule(sparrays.size(),0);
// loop over the speciesArray elements
for (size_t jsp = 0; jsp < sparrays.size(); jsp++) {
const XML_Node& speciesArray = *sparrays[jsp];
// If the speciesArray element has a child element
//
// <skip element="undeclared">
//
// then set sprule[jsp] to 1, so that any species with an undeclared
// element will be quietly skipped when importing species. Additionally,
// if the skip node has the following attribute:
//
// <skip species="duplicate">
//
// then duplicate species names will not cause Cantera to throw an
// exception. Instead, the duplicate entry will be discarded.
if (speciesArray.hasChild("skip")) {
const XML_Node& sk = speciesArray.child("skip");
string eskip = sk["element"];
if (eskip == "undeclared") {
sprule[jsp] = 1;
}
string dskip = sk["species"];
if (dskip == "duplicate") {
sprule[jsp] += 10;
}
}
// Get a pointer to the node containing the species
// definitions for the species declared in this
// speciesArray element. This may be in the local file
// containing the phase element, or may be in another
// file.
XML_Node* db = get_XML_Node(speciesArray["datasrc"], &phase.root());
if (db == 0) {
throw CanteraError("importPhase()",
" Can not find XML node for species database: "
+ speciesArray["datasrc"]);
}
// add this node to the list of species database nodes.
dbases.push_back(db);
}
// Now, collect all the species names and all the XML_Node * pointers
// for those species in a single vector. This is where we decide what
// species are to be included in the phase.
// The logic is complicated enough that we put it in a separate routine.
std::vector<XML_Node*> spDataNodeList;
std::vector<std::string> spNamesList;
std::vector<int> spRuleList;
formSpeciesXMLNodeList(spDataNodeList, spNamesList, spRuleList,
sparrays, dbases, sprule);
// Decide whether the the phase has a variable pressure ss or not
SpeciesThermo* spth = 0;
VPSSMgr* vp_spth = 0;
if (ssConvention == cSS_CONVENTION_TEMPERATURE) {
// Create a new species thermo manager. Function
// 'newSpeciesThermoMgr' looks at the species in the database
// to see what thermodynamic property parameterizations are
// used, and selects a class that can handle the
// parameterizations found.
spth = newSpeciesThermoMgr(spDataNodeList);
// install it in the phase object
th->setSpeciesThermo(spth);
} else if (ssConvention == cSS_CONVENTION_SLAVE) {
/*
* No species thermo manager for this type
*/
} else if (ssConvention == cSS_CONVENTION_VPSS) {
vp_spth = newVPSSMgr(vpss_ptr, &phase, spDataNodeList);
vpss_ptr->setVPSSMgr(vp_spth);
spth = vp_spth->SpeciesThermoMgr();
th->setSpeciesThermo(spth);
} else {
throw CanteraError("importPhase()", "unknown convention");
}
size_t k = 0;
size_t nsp = spDataNodeList.size();
if (ssConvention == cSS_CONVENTION_SLAVE) {
if (nsp > 0) {
throw CanteraError("importPhase()", "For Slave standard states, number of species must be zero: "
+ int2str(nsp));
}
}
for (size_t i = 0; i < nsp; i++) {
XML_Node* s = spDataNodeList[i];
AssertTrace(s != 0);
bool ok = installSpecies(k, *s, *th, spth, spRuleList[i],
&phase, vp_spth, spfactory);
if (ok) {
th->saveSpeciesData(k, s);
++k;
}
}
if (ssConvention == cSS_CONVENTION_SLAVE) {
th->installSlavePhases(&phase);
}
// Done adding species. Perform any required subclass-specific
// initialization.
th->initThermo();
// Perform any required subclass-specific initialization
// that requires the XML phase object
std::string id = "";
th->initThermoXML(phase, id);
return true;
}
bool installReactionArrays(const XML_Node& p, Kinetics& kin,
std::string default_phase, bool check_for_duplicates)
{
int itot = 0;
// Search the children of the phase element for the XML element named
// reactionArray. If we can't find it, then return signaling having not
// found any reactions. Apparently, we allow multiple reactionArray elements
// here Each one will be processed sequentially, with the end result being
// purely additive.
vector<XML_Node*> rarrays = p.getChildren("reactionArray");
if (rarrays.empty()) {
return false;
}
for (size_t n = 0; n < rarrays.size(); n++) {
// Go get a reference to the current XML element, reactionArray. We will
// process this element now.
const XML_Node& rxns = *rarrays[n];
// The reactionArray element has an attribute called, datasrc. The value
// of the attribute is the XML element comprising the top of the tree of
// reactions for the phase. Find this datasrc element starting with the
// root of the current XML node.
const XML_Node* rdata = get_XML_Node(rxns["datasrc"], &rxns.root());
// If the reactionArray element has a child element named "skip", and if
// the attribute of skip called "species" has a value of "undeclared",
// we will set rxnrule.skipUndeclaredSpecies to 'true'. rxnrule is
// passed to the routine that parses each individual reaction so that
// the parser will skip all reactions containing an undefined species
// without throwing an error.
//
// Similarly, an attribute named "third_bodies" with the value of
// "undeclared" will skip undeclared third body efficiencies (while
// retaining the reaction and any other efficiencies).
if (rxns.hasChild("skip")) {
const XML_Node& sk = rxns.child("skip");
if (sk["species"] == "undeclared") {
kin.skipUndeclaredSpecies(true);
}
if (sk["third_bodies"] == "undeclared") {
kin.skipUndeclaredThirdBodies(true);
}
}
// Search for child elements called include. We only include a reaction
// if it's tagged by one of the include fields. Or, we include all
// reactions if there are no include fields.
vector<XML_Node*> incl = rxns.getChildren("include");
vector<XML_Node*> allrxns = rdata->getChildren("reaction");
// if no 'include' directive, then include all reactions
if (incl.empty()) {
for (size_t i = 0; i < allrxns.size(); i++) {
checkElectrochemReaction(p,kin,*allrxns[i]);
kin.addReaction(newReaction(*allrxns[i]));
++itot;
}
} else {
for (size_t nii = 0; nii < incl.size(); nii++) {
const XML_Node& ii = *incl[nii];
string imin = ii["min"];
string imax = ii["max"];
string::size_type iwild = string::npos;
if (imax == imin) {
iwild = imin.find("*");
if (iwild != string::npos) {
imin = imin.substr(0,iwild);
imax = imin;
}
}
for (size_t i = 0; i < allrxns.size(); i++) {
const XML_Node* r = allrxns[i];
string rxid;
if (r) {
rxid = r->attrib("id");
if (iwild != string::npos) {
rxid = rxid.substr(0,iwild);
}
// To decide whether the reaction is included or not we
// do a lexical min max and operation. This sometimes
// has surprising results.
if ((rxid >= imin) && (rxid <= imax)) {
checkElectrochemReaction(p,kin,*r);
kin.addReaction(newReaction(*r));
++itot;
}
}
}
}
}
}
if (check_for_duplicates) {
kin.checkDuplicates();
}
return true;
}