/**
* @param sourceFile File to read from
* @return List of String objects with the shas
*/
public static FileRequestFileContent readRequestFile(final File sourceFile) {
if (!sourceFile.isFile() || !(sourceFile.length() > 0)) {
return null;
}
Document d = null;
try {
d = XMLTools.parseXmlFile(sourceFile.getPath());
} catch (final Throwable t) {
logger.log(Level.SEVERE, "Exception in readRequestFile, during XML parsing", t);
return null;
}
if (d == null) {
logger.log(Level.SEVERE, "Could'nt parse the request file");
return null;
}
final Element rootNode = d.getDocumentElement();
if (rootNode.getTagName().equals(TAG_FrostFileRequestFile) == false) {
logger.severe(
"Error: xml request file does not contain the root tag '"
+ TAG_FrostFileRequestFile
+ "'");
return null;
}
final String timeStampStr = XMLTools.getChildElementsTextValue(rootNode, TAG_timestamp);
if (timeStampStr == null) {
logger.severe("Error: xml file does not contain the tag '" + TAG_timestamp + "'");
return null;
}
final long timestamp = Long.parseLong(timeStampStr);
final List<Element> nodelist = XMLTools.getChildElementsByTagName(rootNode, TAG_shaList);
if (nodelist.size() != 1) {
logger.severe("Error: xml request files must contain only one element '" + TAG_shaList + "'");
return null;
}
final Element rootShaNode = nodelist.get(0);
final List<String> shaList = new LinkedList<String>();
final List<Element> xmlKeys = XMLTools.getChildElementsByTagName(rootShaNode, TAG_sha);
for (final Element el : xmlKeys) {
final Text txtname = (Text) el.getFirstChild();
if (txtname == null) {
continue;
}
final String sha = txtname.getData();
shaList.add(sha);
}
final FileRequestFileContent content = new FileRequestFileContent(timestamp, shaList);
return content;
}
/**
* This is just a helper function for the fromXML method.
*
* @param child
*/
public void importHelper(Node child) {
if (child.getFirstChild() instanceof Text) {
Text text = (Text) child.getFirstChild();
String data = text.getData();
if (child.getNodeName().equals("description")) {
setDescription(data);
}
if (child.getNodeName().equals("refChildPattern")) {
int decID = Integer.parseInt(data.substring(1));
subPatternsID.add(decID);
}
}
}
// ## 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;
}
// #]
}
/**
* Creates nodes from index entries
*
* @param theIndexEntries index entries
* @param theTargetDocument target document
* @param theIndexEntryComparator comparator to sort the index entries. if it is null the index
* entries will be unsorted
* @return nodes for the target document
*/
private Node[] transformToNodes(
final IndexEntry[] theIndexEntries,
final Document theTargetDocument,
final Comparator<IndexEntry> theIndexEntryComparator) {
if (null != theIndexEntryComparator) {
Arrays.sort(theIndexEntries, theIndexEntryComparator);
}
final List<Element> result = new ArrayList<Element>();
for (final IndexEntry indexEntry : theIndexEntries) {
final Element indexEntryNode = createElement(theTargetDocument, "index.entry");
final Element formattedStringElement = createElement(theTargetDocument, "formatted-value");
if (indexEntry.getContents() != null) {
for (final Iterator<Node> i = indexEntry.getContents().iterator(); i.hasNext(); ) {
final Node child = i.next();
final Node clone = theTargetDocument.importNode(child, true);
if (!i.hasNext() && clone.getNodeType() == Node.TEXT_NODE) {
final Text t = (Text) clone;
t.setData(t.getData().replaceAll("[\\s\\n]+$", ""));
}
formattedStringElement.appendChild(clone);
}
} else {
final Text textNode = theTargetDocument.createTextNode(indexEntry.getFormattedString());
textNode.normalize();
formattedStringElement.appendChild(textNode);
}
indexEntryNode.appendChild(formattedStringElement);
final String[] refIDs = indexEntry.getRefIDs();
for (final String refID : refIDs) {
final Element referenceIDElement = createElement(theTargetDocument, "refID");
referenceIDElement.setAttribute("value", refID);
indexEntryNode.appendChild(referenceIDElement);
}
final String val = indexEntry.getValue();
if (null != val) {
indexEntryNode.setAttribute("value", val);
}
final String sort = indexEntry.getSortString();
if (null != sort) {
indexEntryNode.setAttribute("sort-string", sort);
}
if (indexEntry.isStartingRange()) {
indexEntryNode.setAttribute("start-range", "true");
} else if (indexEntry.isEndingRange()) {
indexEntryNode.setAttribute("end-range", "true");
}
if (indexEntry.isSuppressesThePageNumber()) {
indexEntryNode.setAttribute("no-page", "true");
} else if (indexEntry.isRestoresPageNumber()) {
indexEntryNode.setAttribute("single-page", "true");
}
final IndexEntry[] childIndexEntries = indexEntry.getChildIndexEntries();
final Node[] nodes =
transformToNodes(childIndexEntries, theTargetDocument, theIndexEntryComparator);
for (final Node node : nodes) {
indexEntryNode.appendChild(node);
}
final IndexEntry[] seeChildIndexEntries = indexEntry.getSeeChildIndexEntries();
if (seeChildIndexEntries != null) {
final Element seeElement = createElement(theTargetDocument, "see-childs");
final Node[] seeNodes =
transformToNodes(seeChildIndexEntries, theTargetDocument, theIndexEntryComparator);
for (final Node node : seeNodes) {
seeElement.appendChild(node);
}
indexEntryNode.appendChild(seeElement);
}
final IndexEntry[] seeAlsoChildIndexEntries = indexEntry.getSeeAlsoChildIndexEntries();
if (seeAlsoChildIndexEntries != null) {
final Element seeAlsoElement = createElement(theTargetDocument, "see-also-childs");
final Node[] seeAlsoNodes =
transformToNodes(seeAlsoChildIndexEntries, theTargetDocument, theIndexEntryComparator);
for (final Node node : seeAlsoNodes) {
seeAlsoElement.appendChild(node);
}
indexEntryNode.appendChild(seeAlsoElement);
}
result.add(indexEntryNode);
}
return (Node[]) result.toArray(new Node[result.size()]);
}
