Ejemplo n.º 1
0
  // ## 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);
      }
    }

    // #]
  }
Ejemplo n.º 2
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);
  }
Ejemplo n.º 3
0
  // ## 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);
    }

    // #]
  }
Ejemplo n.º 4
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);
    }

    // #]
  }
Ejemplo n.º 5
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);
    }

    // #]
  }
Ejemplo n.º 6
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();
  }
Ejemplo n.º 7
0
 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;
 }
Ejemplo n.º 8
0
 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;
  }
Ejemplo n.º 10
0
  @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;
  }
Ejemplo n.º 11
0
 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());
   }
 }
Ejemplo n.º 12
0
  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;
  }
Ejemplo n.º 13
0
  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());
    }
  }
Ejemplo n.º 14
0
 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());
   }
 }
Ejemplo n.º 15
0
  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;
  }
Ejemplo n.º 18
0
  /**
   * 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);
          }
        }
      }
    }
  }
Ejemplo n.º 19
0
  // ## 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;
    }

    // #]
  }
Ejemplo n.º 20
0
 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();
     ;
   }
 }
Ejemplo n.º 21
0
  // 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;
  }
Ejemplo n.º 22
0
  // ## 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;
    }

    // #]
  }
Ejemplo n.º 23
0
  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;
    }
  }