// ## operation getMatchedFunctionalGroup(LinkedList)
public LinkedList getMatchedFunctionalGroup(LinkedList p_reactants) {
// #[ operation getMatchedFunctionalGroup(LinkedList)
LinkedList fgCollection = new LinkedList();
boolean found = false;
Iterator r_iter = p_reactants.iterator();
while (r_iter.hasNext()) {
found = false;
Object o = r_iter.next();
ChemGraph cg = null;
if (o instanceof Species) cg = ((Species) r_iter.next()).getChemGraph();
else cg = (ChemGraph) o;
Iterator t_iter = reactantTree.iterator();
while (t_iter.hasNext()) {
HierarchyTree t = (HierarchyTree) t_iter.next();
Stack s = t.findMatchedPath(cg);
if (s != null && !s.isEmpty()) {
found = true;
fgCollection.add(s);
}
}
if (!found) {
// System.out.println("can't find matched path: " + cg.toString());
// System.exit(0);
return null;
}
}
return fgCollection;
// #]
}
// ## operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
private LinkedHashMap generateSpeciesStatus(
ReactionModel p_reactionModel,
ArrayList p_speciesChemkinName,
ArrayList p_speciesConc,
ArrayList p_speciesFlux) {
// #[ operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
int size = p_speciesChemkinName.size();
if (size != p_speciesConc.size() || size != p_speciesFlux.size())
throw new InvalidSpeciesStatusException();
LinkedHashMap speStatus = new LinkedHashMap();
for (int i = 0; i < size; i++) {
String name = (String) p_speciesChemkinName.get(i);
int ID = parseIDFromChemkinName(name);
Species spe = SpeciesDictionary.getInstance().getSpeciesFromID(ID);
double conc = ((Double) p_speciesConc.get(i)).doubleValue();
double flux = ((Double) p_speciesFlux.get(i)).doubleValue();
System.out.println(
String.valueOf(spe.getID())
+ '\t'
+ spe.getName()
+ '\t'
+ String.valueOf(conc)
+ '\t'
+ String.valueOf(flux));
if (conc < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(conc) < aTol) conc = 0;
// else throw new NegativeConcentrationException("species " + spe.getName() + " has negative
// conc: " + String.valueOf(conc));
if (conc < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc));
}
SpeciesStatus ss = new SpeciesStatus(spe, 1, conc, flux);
speStatus.put(spe, ss);
}
return speStatus;
// #]
}
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
public void clearReactantTree() {
reactantTree.clear();
}
public void removeReactantTree(HierarchyTree p_HierarchyTree) {
reactantTree.remove(p_HierarchyTree);
}
public void addReactantTree(HierarchyTree p_HierarchyTree) {
reactantTree.add(p_HierarchyTree);
}
public ListIterator getReactantTree() {
ListIterator iter = reactantTree.listIterator();
return iter;
}
// ## operation getReactantTreeNumber()
public int getReactantTreeNumber() {
// #[ operation getReactantTreeNumber()
return reactantTree.size();
// #]
}