// ## operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
public static void writeChemkinInputFile(
final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(p_reactionModel, p_beginStatus));
result.append(writeChemkinThermo(p_reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(
writeChemkinPdepReactions(
p_reactionModel, p_beginStatus)); // 10/26/07 gmagoon: changed to pass p_beginStatus
// result.append(writeChemkinPdepReactions(p_reactionModel));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
if (PDepRateConstant.getMode() == Mode.CHEBYSHEV
|| PDepRateConstant.getMode() == Mode.PDEPARRHENIUS
|| PDepRateConstant.getMode() == Mode.RATE) {
StringBuilder gridOfRateCoeffs = new StringBuilder();
gridOfRateCoeffs.append(writeGridOfRateCoeffs(p_reactionModel));
String newFile = "chemkin/tableOfRateCoeffs.txt";
try {
FileWriter fw = new FileWriter(newFile);
fw.write(gridOfRateCoeffs.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing tableOfRateCoeffs.txt");
System.out.println(e.getMessage());
System.exit(0);
}
}
// #]
}
public void startElement(String namespaceURI, String localName, String qName, Attributes atts)
throws ParserException {
Caller targeting = (Caller) targetMap.get(qName);
if (null == targeting) throw new ParserException("No target found for tag: " + qName + "!");
targeting = (Caller) targeting.duplicate();
XMLOp actor = (XMLOp) actionMap.get(qName);
if (null == actor) throw new ParserException("No action found for tag: " + qName + "!");
if (null == targeting.getTargetObject() && 0 < stack.size()) {
Caller parent = null;
try {
parent = (Caller) stack.peek();
} catch (Exception e) {
throw new ParserException(
"Typecast exception, unknown object placed in stack! " + e.getMessage());
}
Object targetObject = parent.parameter(0);
int idx = stack.indexOf(parent);
// climb stack for next available parent (stack may have no-ops in it.
while (null == targetObject && 0 < idx) {
{
} // System.out.println("Climbing stack for next available parent..");
try {
parent = (Caller) stack.get(--idx);
} catch (Exception e) {
throw new ParserException(
"Typecast exception, unknown object placed in stack! " + e.getMessage());
}
targetObject = parent.parameter(0);
}
targeting.setTargetObject(targetObject);
}
Object o;
try {
actor.initialize(attributeMap(qName, atts));
o = actor.process();
} catch (Exception e) {
try {
actor.initialize(attributeMap(qName, atts));
o = actor.process();
} catch (Exception r) {
throw new ParserException(
"Could not execute action for tag: " + qName + "! " + e.getMessage());
}
}
targeting.resetParameters(new Object[] {o});
stack.push(targeting);
}
// ## operation checkChemkinMessage()
public void checkChemkinMessage() {
// #[ operation checkChemkinMessage()
try {
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/chem.message";
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
String line = br.readLine().trim();
if (line.startsWith("NO ERRORS FOUND ON INPUT")) {
return;
} else if (line.startsWith("WARNING...THERE IS AN ERROR IN THE LINKING FILE")) {
System.out.println("Error in chemkin linking to reactor!");
System.exit(0);
} else {
System.out.println("Unknown message in chem.message!");
System.exit(0);
}
} catch (Exception e) {
System.out.println("Can't read chem.message!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
// ## operation runReactor()
public void runReactor() {
// #[ operation runReactor()
// run reactor
String dir = System.getProperty("RMG.workingDirectory");
try {
// system call for reactor
String[] command = {dir + "/software/reactorModel/reactor.exe"};
File runningDir = new File("chemkin");
Process reactor = Runtime.getRuntime().exec(command, null, runningDir);
InputStream ips = reactor.getInputStream();
InputStreamReader is = new InputStreamReader(ips);
BufferedReader br = new BufferedReader(is);
String line = null;
while ((line = br.readLine()) != null) {
// System.out.println(line);
}
int exitValue = reactor.waitFor();
} catch (Exception e) {
System.out.println("Error in running reactor!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
public static void writeChemkinInputFile(ReactionSystem rs) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(rs.reactionModel, rs.initialStatus));
result.append(writeChemkinThermo(rs.reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(writeChemkinPdepReactions(rs));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
private static SAXParserFactory createFastSAXParserFactory()
throws ParserConfigurationException, SAXException {
if (fastParserFactoryClass == null) {
try {
fastParserFactoryClass =
Class.forName("org.apache.crimson.jaxp.SAXParserFactoryImpl"); // NOI18N
} catch (Exception ex) {
useFastSAXParserFactory = false;
if (System.getProperty("java.version").startsWith("1.4")) { // NOI18N
ErrorManager.getDefault().notify(ErrorManager.INFORMATIONAL, ex);
}
}
}
if (fastParserFactoryClass != null) {
try {
SAXParserFactory factory = (SAXParserFactory) fastParserFactoryClass.newInstance();
return factory;
} catch (Exception ex) {
useFastSAXParserFactory = false;
throw new ParserConfigurationException(ex.getMessage());
}
}
return SAXParserFactory.newInstance();
}
private Map attributeMap(String tagName, Attributes atts) throws ParserException {
if (null == tagName || null == atts) return null;
Map mapping = null;
try {
mapping = (Map) attributeMaps.get(tagName);
} catch (Exception e) {
throw new ParserException(
"Typecast error, unknown element found in attribute list mappings! " + e.getMessage());
}
if (null == mapping) return null;
Map resultMapping = new HashMap();
for (int i = 0; i < atts.getLength(); i++) {
String xmlName = atts.getQName(i);
String value = atts.getValue(i);
TagMap.AttributeMapping aMap = null;
try {
aMap = (TagMap.AttributeMapping) mapping.get(xmlName);
} catch (Exception e) {
throw new ParserException(
"Typecast error, unknown element found in property mapping! " + e.getMessage());
}
if (null == aMap)
throw new ParserException(
"No attribute mapping specified for attribute: " + xmlName + " in tag: " + tagName);
String propertyName = aMap.getPropertyName();
try {
resultMapping.put(propertyName, aMap.convertValue(value));
} catch (Exception e) {
throw new ParserException(
"Can not convert given value: \""
+ value
+ "\" to specified type: "
+ aMap.getType()
+ " for attribute: "
+ xmlName
+ " in tag: "
+ tagName
+ "! "
+ e.getMessage());
}
}
checkForRequiredAttributes(tagName, resultMapping, mapping);
addDefaultValues(resultMapping, mapping);
return resultMapping;
}
public void endElement(String namespaceURI, String localName, String qName)
throws ParserException {
{
} // System.out.println("end Element");
Caller targeting = (Caller) stack.pop();
try {
targeting.process();
} catch (Exception e) {
throw new ParserException("Could not place " + qName + " into system!\n" + e.getMessage());
}
}
/**
* Get the named properties for this resource and (potentially) its children.
*
* @param names an arrary of property names to retrieve
* @return a MultiStatus of PropertyResponses
* @exception com.ibm.webdav.WebDAVException
*/
public MultiStatus getProperties(PropertyName[] names) throws WebDAVException {
MultiStatus multiStatus = resource.getProperties(resource.getContext());
MultiStatus newMultiStatus = new MultiStatus();
Enumeration responses = multiStatus.getResponses();
while (responses.hasMoreElements()) {
PropertyResponse response = (PropertyResponse) responses.nextElement();
PropertyResponse newResponse = new PropertyResponse(response.getResource());
newResponse.setDescription(response.getDescription());
newMultiStatus.addResponse(newResponse);
Hashtable properties = (Hashtable) response.getPropertiesByPropName();
// Hashtable newProperties = (Hashtable) newResponse.getProperties();
for (int i = 0; i < names.length; i++) {
if (properties.containsKey(names[i])) {
PropertyValue srcval = response.getProperty(names[i]);
newResponse.setProperty(names[i], srcval);
// newProperties.put(names[i], properties.get(names[i]));
} else {
Document factory = null;
try {
factory = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
} catch (Exception e) {
throw new WebDAVException(WebDAVStatus.SC_INTERNAL_SERVER_ERROR, e.getMessage());
}
// we'll create an xml element with no value because that's
// what webdav will need to return for most methods... even if the
// property doesn't exist. That's because the
// distinction between a propertyname and propertyvalue
// is fuzzy in WebDAV xml. A property name is
// essentially an empty property value because
// all property values have their property
// name stuck on.
// if we decide to set reviewStatus to null instead (as
// we did previously, then the code for MultiStatus.asXML()
// needs to be updated to expect null values.
// (jlc 990520)
Element elTm = factory.createElementNS("X", "X:" + names[i].getLocal());
elTm.setAttribute("xmlns:X", names[i].getNamespace());
newResponse.addProperty(names[i], elTm, WebDAVStatus.SC_NOT_FOUND);
}
}
}
return newMultiStatus;
}
@Override
public VPackage parse() {
logger.debug("Starting parsing package: " + xmlFile.getAbsolutePath());
long startParsing = System.currentTimeMillis();
try {
Document document = getDocument();
Element root = document.getDocumentElement();
_package = new VPackage(xmlFile);
Node name = root.getElementsByTagName(EL_NAME).item(0);
_package.setName(name.getTextContent());
Node descr = root.getElementsByTagName(EL_DESCRIPTION).item(0);
_package.setDescription(descr.getTextContent());
NodeList list = root.getElementsByTagName(EL_CLASS);
boolean initPainters = false;
for (int i = 0; i < list.getLength(); i++) {
PackageClass pc = parseClass((Element) list.item(i));
if (pc.getPainterName() != null) {
initPainters = true;
}
}
if (initPainters) {
_package.initPainters();
}
logger.info(
"Parsing the package '{}' finished in {}ms.\n",
_package.getName(),
(System.currentTimeMillis() - startParsing));
} catch (Exception e) {
collector.collectDiagnostic(e.getMessage(), true);
if (RuntimeProperties.isLogDebugEnabled()) {
e.printStackTrace();
}
}
try {
checkProblems("Error parsing package file " + xmlFile.getName());
} catch (Exception e) {
return null;
}
return _package;
}
public void save(String filename) {
try {
Document document = element.getOwnerDocument();
document.getDocumentElement().normalize();
TransformerFactory tFactory = TransformerFactory.newInstance();
tFactory.setAttribute("indent-number", new Integer(4));
Transformer transformer = tFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(document);
File file = new File(filename);
StreamResult result = new StreamResult(file);
transformer.transform(source, result);
} catch (Exception e) {
severe("Could not save XML file: " + e.getMessage());
}
}
private static Document getDocument(String docString) {
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setIgnoringComments(true);
factory.setIgnoringElementContentWhitespace(true);
factory.setValidating(true);
DocumentBuilder builder = factory.newDocumentBuilder();
return builder.parse(docString);
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
return null;
}
public static void main(String[] args) {
try {
// open existing file
File xmlFile = new File(userFile);
DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
DocumentBuilder dbuild = dbfac.newDocumentBuilder();
Document doc = dbuild.parse(xmlFile);
// DocumentBuilderFactory dbfac2 = DocumentBuilderFactory.newInstance();
// DocumentBuilder docBuilder = dbfac2.newDocumentBuilder();
// Document doc2 = docBuilder.parse(xmlFile);
// doc.getDocumentElement().normalize();
} catch (Exception e) {
System.err.println(e.getMessage());
}
}
public XMLHelper(String filename, String root) {
this();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
try {
Document document = builder.parse(new File(filename));
setElement((Element) document.getElementsByTagName(root).item(0));
} catch (Exception e) {
Document document = builder.newDocument();
setElement((Element) document.appendChild(document.createElement(root)));
warning("Could not load XML file: " + e.getMessage());
}
} catch (ParserConfigurationException e) {
// Not quite sure when this would happen
severe("Could not extantiate XML builder: " + e.getMessage());
}
}
private static Element readXmlFile(GenericFile file) {
try {
BufferedReader reader = new BufferedReader(file.getReader());
StringBuilder sBuilder = new StringBuilder();
for (String line = reader.readLine(); line != null; line = reader.readLine()) {
sBuilder.append(line);
sBuilder.append("\n");
}
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(new ByteArrayInputStream(sBuilder.toString().getBytes()));
doc.getDocumentElement().normalize();
return doc.getDocumentElement();
} catch (Exception e) {
e.printStackTrace();
System.err.println(e.getMessage());
return null;
}
}
public Command executeStep(Element stepRow) throws Exception {
Command command = new Command();
NodeList stepFields = stepRow.getElementsByTagName("td");
String cmd = stepFields.item(0).getTextContent().trim();
command.cmd = cmd;
ArrayList<String> argList = new ArrayList<String>();
if (stepFields.getLength() == 1) {
// skip comments
command.result = "OK";
return command;
}
for (int i = 1; i < stepFields.getLength(); i++) {
String content = stepFields.item(i).getTextContent();
content = content.replaceAll(" +", " ");
content = content.replace('\u00A0', ' ');
content = content.trim();
argList.add(content);
}
String args[] = argList.toArray(new String[0]);
command.args = args;
if (this.verbose) {
System.out.println(cmd + " " + Arrays.asList(args));
}
try {
command.result = this.commandProcessor.doCommand(cmd, args);
command.error = false;
} catch (Exception e) {
command.result = e.getMessage();
command.error = true;
}
command.failure = command.error && !cmd.startsWith("verify");
if (this.verbose) {
System.out.println(command.result);
}
return command;
}
@Override
public HashSet<ScoredAnnotation> solveSa2W(String text) throws AnnotationException {
HashSet<ScoredAnnotation> res;
try {
res = new HashSet<ScoredAnnotation>();
lastTime = Calendar.getInstance().getTimeInMillis();
URL wikiApi = new URL(url);
String parameters =
"references=true&repeatMode=all&minProbability=0.0&source="
+ URLEncoder.encode(text, "UTF-8");
HttpURLConnection slConnection = (HttpURLConnection) wikiApi.openConnection();
slConnection.setRequestProperty("accept", "text/xml");
slConnection.setDoOutput(true);
slConnection.setDoInput(true);
slConnection.setRequestMethod("POST");
slConnection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");
slConnection.setRequestProperty("charset", "utf-8");
slConnection.setRequestProperty(
"Content-Length", "" + Integer.toString(parameters.getBytes().length));
slConnection.setUseCaches(false);
DataOutputStream wr = new DataOutputStream(slConnection.getOutputStream());
wr.writeBytes(parameters);
wr.flush();
wr.close();
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(slConnection.getInputStream());
/* URL wikiApi = new URL(url+"?references=true&repeatMode=all&minProbability=0.0&source="+URLEncoder.encode(text, "UTF-8"));
URLConnection wikiConnection = wikiApi.openConnection();
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(wikiConnection.getInputStream());
*/
lastTime = Calendar.getInstance().getTimeInMillis() - lastTime;
XPathFactory xPathfactory = XPathFactory.newInstance();
XPath xpath = xPathfactory.newXPath();
XPathExpression idExpr = xpath.compile("//detectedTopic/@id");
XPathExpression weightExpr = xpath.compile("//detectedTopic/@weight");
XPathExpression referenceExpr = xpath.compile("//detectedTopic/references");
NodeList ids = (NodeList) idExpr.evaluate(doc, XPathConstants.NODESET);
NodeList weights = (NodeList) weightExpr.evaluate(doc, XPathConstants.NODESET);
NodeList references = (NodeList) referenceExpr.evaluate(doc, XPathConstants.NODESET);
for (int i = 0; i < weights.getLength(); i++) {
if (weights.item(i).getNodeType() != Node.TEXT_NODE) {
int id = Integer.parseInt(ids.item(i).getNodeValue());
float weight = Float.parseFloat(weights.item(i).getNodeValue());
// System.out.println("ID="+ids.item(i).getNodeValue()+" weight="+weight);
XPathExpression startExpr =
xpath.compile("//detectedTopic[@id=" + id + "]/references/reference/@start");
XPathExpression endExpr =
xpath.compile("//detectedTopic[@id=" + id + "]/references/reference/@end");
NodeList starts =
(NodeList) startExpr.evaluate(references.item(i), XPathConstants.NODESET);
NodeList ends = (NodeList) endExpr.evaluate(references.item(i), XPathConstants.NODESET);
for (int j = 0; j < starts.getLength(); j++) {
int start = Integer.parseInt(starts.item(j).getNodeValue());
int end = Integer.parseInt(ends.item(j).getNodeValue());
int len = end - start;
res.add(new ScoredAnnotation(start, len, id, weight));
}
}
}
} catch (Exception e) {
e.printStackTrace();
throw new AnnotationException(
"An error occurred while querying Wikipedia Miner API. Message: " + e.getMessage());
}
return res;
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
// ## operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
public boolean writeReactorInputFile(
ReactionModel p_reactionModel,
ReactionTime p_beginTime,
ReactionTime p_endTime,
SystemSnapshot p_beginStatus) {
// #[ operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
// construct "input" string
String input = "<?xml version=\"1.0\" standalone=\"no\"?>" + "\n";
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
String dtd = dir + "software/reactorModel/documentTypeDefinitions/reactorInput.dtd";
input += "<!DOCTYPE reactorinput SYSTEM \"" + dtd + "\">" + "\n";
input += "<reactorinput>" + "\n";
input += "<header>" + "\n";
input += "<title>Reactor Input File</title>" + "\n";
input +=
"<description>RMG-generated file used to call an external reactor model</description>"
+ "\n";
input += "</header>" + "\n";
input += "<inputvalues>" + "\n";
input += "<integrationparameters>" + "\n";
input += "<reactortype>" + reactorType + "</reactortype>" + "\n";
input +=
"<starttime units=\""
+ p_beginTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_beginTime.getTime(), 15, 6)
+ "</starttime>"
+ "\n";
input +=
"<endtime units=\""
+ p_endTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_endTime.getTime(), 15, 6)
+ "</endtime>"
+ "\n";
// input += "<starttime units=\"" + p_beginTime.unit + "\">" +
// MathTool.formatDouble(p_beginTime.time,15,6) + "</starttime>" + "\n";
// input += "<endtime units=\"" + p_endTime.unit + "\">" +
// MathTool.formatDouble(p_endTime.time,15,6) + "</endtime>" + "\n";
input += "<rtol>" + rtol + "</rtol>" + "\n";
input += "<atol>" + atol + "</atol>" + "\n";
input += "</integrationparameters>" + "\n";
input += "<chemistry>" + "\n";
input += "</chemistry>" + "\n";
input += "<systemstate>" + "\n";
input +=
"<temperature units=\"K\">"
+ MathTool.formatDouble(p_beginStatus.getTemperature().getK(), 15, 6)
+ "</temperature>"
+ "\n";
input +=
"<pressure units=\"Pa\">"
+ MathTool.formatDouble(p_beginStatus.getPressure().getPa(), 15, 6)
+ "</pressure>"
+ "\n";
for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) {
SpeciesStatus spcStatus = (SpeciesStatus) iter.next();
Species thisSpecies = spcStatus.getSpecies();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
if (cerm.containsAsReactedSpecies(thisSpecies)) {
String spcChemkinName = thisSpecies.getChemkinName();
double concentration = spcStatus.getConcentration();
input +=
"<amount units=\"molPerCm3\" speciesid=\""
+ spcChemkinName
+ "\">"
+ concentration
+ "</amount>"
+ "\n";
}
}
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
double conc = p_beginStatus.getInertGas(name);
if (conc != 0.0)
input +=
"<amount units=\"molPerCm3\" speciesid=\"" + name + "\">" + conc + "</amount>" + "\n";
}
input += "</systemstate>" + "\n";
input += "</inputvalues>" + "\n";
input += "</reactorinput>" + "\n";
// write "input" string to file
try {
String file = "chemkin/reactorInput.xml";
FileWriter fw = new FileWriter(file);
fw.write(input);
fw.close();
return true;
} catch (Exception e) {
System.out.println("Error in writing reactorInput.xml!");
System.out.println(e.getMessage());
return false;
}
// #]
}
public void saveUnsaved() throws SaveAbortedException {
if (!saved) {
int option = 0;
if (loadedFile == null)
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to UNTITLED?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
else
option =
JOptionPane.showConfirmDialog(
this,
new JLabel("Save changes to " + loadedFile.getName() + "?"),
"Warning",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.WARNING_MESSAGE);
if (option == JOptionPane.YES_OPTION) {
if (loadedFile == null) // SAVE NEW FILE
{
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
throw new SaveAbortedException();
}
fileChooser.setFileFilter(filter);
int option2 = fileChooser.showSaveDialog(this);
if (option2 == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this,
new JLabel("Error: " + ex.getMessage()),
"Error",
JOptionPane.ERROR_MESSAGE);
}
} else throw new SaveAbortedException();
;
} else // save LOADED FILE
{
try {
PrintStream stream = new PrintStream(new FileOutputStream(loadedFile), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (option == JOptionPane.CANCEL_OPTION) throw new SaveAbortedException();
;
}
}
// реализуем метод парсинга
@Override
public List<Root.News> parse(File fileToParse) {
try {
// создаем фабрику документов, в наш документ парсим файл
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
// парсим файл в документ
dom = db.parse(fileToParse);
} catch (SAXException e1) {
e1.printStackTrace();
} catch (IOException e1) {
e1.printStackTrace();
} catch (Exception e) {
System.out.println(e.getMessage());
}
// root элемент
Element root = dom.getDocumentElement();
// NodeList новостей
NodeList elementsNodeList = root.getElementsByTagName("news").item(0).getChildNodes();
// перебираем все элементы
for (int i = 0; i < elementsNodeList.getLength(); i++) {
Node item = elementsNodeList.item(i);
if (item.getNodeType() != Node.ELEMENT_NODE) { // если вернуло что-то не то
continue;
}
Element element = (Element) item;
Root.News myNews = new Root.News();
// дата
String tempDate = element.getElementsByTagName("date").item(0).getTextContent();
SimpleDateFormat format = new SimpleDateFormat(Constants.DATE_FORMAT_IN);
Date date = null;
try {
date = format.parse(tempDate);
} catch (ParseException e) {
e.printStackTrace();
}
// описание
String description = element.getElementsByTagName("description").item(0).getTextContent();
// id
int id = Integer.parseInt(element.getElementsByTagName("id").item(0).getTextContent());
// ключевые слова
List<String> keywordsList = new ArrayList<String>();
// перебираем ключевые слова
NodeList keywords = element.getElementsByTagName("keywords").item(0).getChildNodes();
for (int j = 0; j < keywords.getLength(); j++) {
Node itemKey = keywords.item(j);
if (itemKey.getNodeType() != Node.ELEMENT_NODE) { // если вернуло что-то не то
continue;
}
keywordsList.add(itemKey.getFirstChild().getTextContent());
}
// заголовок
String title = element.getElementsByTagName("title").item(0).getTextContent();
// буленовская переменная
boolean isVisible =
Boolean.parseBoolean(element.getElementsByTagName("visible").item(0).getTextContent());
// записываем данные в экземпляр новости
myNews.setDescription(description);
myNews.setDate(date);
myNews.setTitle(title);
myNews.setId(id);
myNews.setKeywords(keywordsList);
myNews.setVisible(isVisible);
// добавляем новость в список
news.add(myNews);
}
System.out.println("---> Парсинг файла " + "\"" + fileToParse + "\" завершен!");
return news;
}
// ## 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 actionPerformed(ActionEvent e) {
JButton b = (JButton) e.getSource();
if (b.getText() == "PLAY") {
if (scoreP != null) scoreP.playScale(sp.getScale(), tempoP.getValue());
} else if (b.getText() == "New") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
sp.notes.removeAllElements();
sp.repaint();
nameTF.setText("");
loadedFile = null;
} else if (b.getText() == "Save") {
if (nameTF.getText().equals("")) {
JOptionPane.showMessageDialog(
this,
new JLabel("Please type in the Scale Name"),
"Warning",
JOptionPane.WARNING_MESSAGE);
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showSaveDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
File target = fileChooser.getSelectedFile();
if (target.getName().indexOf(".scl") == -1) target = new File(target.getPath() + ".scl");
try {
PrintStream stream = new PrintStream(new FileOutputStream(target), true);
save(stream);
stream.close();
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, new JLabel("Error: " + ex.getMessage()), "Error", JOptionPane.ERROR_MESSAGE);
}
}
} else if (b.getText() == "Load") {
try {
saveUnsaved();
} catch (SaveAbortedException ex) {
return;
}
fileChooser.setFileFilter(filter);
int option = fileChooser.showOpenDialog(this);
if (option == JFileChooser.APPROVE_OPTION) {
loadedFile = fileChooser.getSelectedFile();
SAXParserFactory factory = SAXParserFactory.newInstance();
ScaleParser handler = new ScaleParser(false);
try {
SAXParser parser = factory.newSAXParser();
parser.parse(loadedFile, handler);
// System.out.println("success");
} catch (Exception ex) {
// System.out.println("no!!!!!! exception: "+e);
// System.out.println(ex.getMessage());
ex.printStackTrace();
}
// -----now :P:P---------------
System.out.println("name: " + handler.getName());
nameTF.setText(handler.getName());
sp.notes.removeAllElements();
int[] scale = handler.getScale();
for (int i = 0; i < scale.length; i++) {
sp.addNote(scale[i]);
}
sp.repaint();
} else loadedFile = null;
}
}