コード例 #1
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 // Constructors
 // ## operation StructureTemplate(Matchable,Matchable)
 public StructureTemplate(Matchable p_reactant1, Matchable p_reactant2) {
   {
     reactantTree = new ArrayList();
   }
   // #[ operation StructureTemplate(Matchable,Matchable)
   reactants.add(p_reactant1);
   if (p_reactant2 != null) reactants.add(p_reactant2);
   // #]
 }
コード例 #2
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 // ## 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;
   // #]
 }
コード例 #3
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 // ## operation generateReverse(ReactionAdjList)
 public StructureTemplate generateReverse(ReactionAdjList p_reactionAdjList) {
   // #[ operation generateReverse(ReactionAdjList)
   int r_num = getReactantNumber();
   Matchable r1 = getAllowedFunctionalGroupAt(1);
   LinkedList reactant = new LinkedList();
   reactant.add(r1);
   if (r_num == 2) {
     Matchable r2 = getAllowedFunctionalGroupAt(2);
     reactant.add(r2);
   }
   LinkedList reverse = p_reactionAdjList.reactFunctionalGroup(reactant);
   StructureTemplate reverseRT = new StructureTemplate(reverse);
   reverseRT.reactantTree = this.reactantTree;
   return reverseRT;
   // #]
 }
コード例 #4
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 // ## operation StructureTemplate(Matchable)
 public StructureTemplate(Matchable p_reactant) {
   {
     reactantTree = new ArrayList();
   }
   // #[ operation StructureTemplate(Matchable)
   reactants.add(p_reactant);
   // #]
 }
コード例 #5
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ファイル: Chemkin.java プロジェクト: ecintron/RMG-Java
  public static String writeGridOfRateCoeffs(ReactionModel p_reactionModel) {

    StringBuilder result = new StringBuilder();

    LinkedList pDepList = new LinkedList();
    CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;

    for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
      PDepNetwork pdn = (PDepNetwork) iter.next();
      for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
        PDepReaction rxn = (PDepReaction) pdniter.next();
        if (cerm.categorizeReaction(rxn) != 1) continue;
        // check if this reaction is not already in the list and also check if this reaction has a
        // reverse reaction
        // which is already present in the list.
        if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();
        if (!rxn.reactantEqualsProduct()
            && !pDepList.contains(rxn)
            && !pDepList.contains(rxn.getReverseReaction())) {
          pDepList.add(rxn);
        }
      }
    }

    Temperature[] tempsUsedInFame = PDepRateConstant.getTemperatures();
    int numTemps = tempsUsedInFame.length;
    Pressure[] pressUsedInFame = PDepRateConstant.getPressures();
    int numPress = pressUsedInFame.length;

    for (int i = 0; i < numTemps; i++) {
      for (int j = 0; j < numPress; j++) {
        result.append(
            "T=" + tempsUsedInFame[i].getK() + "K,P=" + pressUsedInFame[j].getBar() + "bar\t");
      }
      result.append("\n");
    }
    result.append("\n");

    for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
      PDepReaction r = (PDepReaction) iter.next();
      result.append(r.toString() + "\n");
      double[][] rates = new double[numTemps][numPress];
      rates = r.getPDepRate().getRateConstants();
      for (int i = 0; i < numTemps; i++) {
        for (int j = 0; j < numPress; j++) {
          result.append(rates[i][j] + "\t");
        }
        result.append("\n");
      }
      result.append("\n");
    }
    return result.toString();
  }
コード例 #6
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ファイル: Chemkin.java プロジェクト: ecintron/RMG-Java
  // ## operation writeChemkinReactions(ReactionModel)
  public static String writeChemkinPdepReactions(
      ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
    // #[ operation writeChemkinReactions(ReactionModel)

    StringBuilder result = new StringBuilder();
    //      result.append("REACTIONS	KCAL/MOLE\n");

    String reactionHeader = "";

    String units4Ea = ArrheniusKinetics.getEaUnits();
    if (units4Ea.equals("cal/mol")) reactionHeader = "CAL/MOL\t";
    else if (units4Ea.equals("kcal/mol")) reactionHeader = "KCAL/MOL\t";
    else if (units4Ea.equals("J/mol")) reactionHeader = "JOULES/MOL\t";
    else if (units4Ea.equals("kJ/mol")) reactionHeader = "KJOULES/MOL\t";
    else if (units4Ea.equals("Kelvins")) reactionHeader = "KELVINS\t";

    String units4A = ArrheniusKinetics.getAUnits();
    if (units4A.equals("moles")) reactionHeader += "MOLES\n";
    else if (units4A.equals("molecules")) reactionHeader += "MOLECULES\n";

    result.append("REACTIONS\t" + reactionHeader);

    LinkedList pDepList = new LinkedList();
    LinkedList nonPDepList = new LinkedList();
    LinkedList duplicates = new LinkedList();

    CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
    // first get troe and thirdbodyreactions
    for (Iterator iter = cerm.getReactionSet().iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      /*
       * 1Jul2009-MRH:
       * 	Added extra set of parenthesis.  Before, if the rxn was reverse but an instance of
       * 		TROEReaction, it would also be added to the pDepList, resulting in RMG reporting
       * 		both rxns (forward and reverse) in the chem.inp file, w/o a DUP tag.  Furthermore,
       * 		both rxns were given the same set of Arrhenius parameters.  Running this in
       * 		Chemkin-v4.1.1 resulted in an error.
       */
      if (r.isForward()
          && (r instanceof ThirdBodyReaction
              || r instanceof TROEReaction
              || r instanceof LindemannReaction)) {
        pDepList.add(r);
      }
    }

    for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
      PDepNetwork pdn = (PDepNetwork) iter.next();
      for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
        PDepReaction rxn = (PDepReaction) pdniter.next();
        if (cerm.categorizeReaction(rxn) != 1) continue;

        // check if this reaction is not already in the list and also check if this reaction has a
        // reverse reaction
        // which is already present in the list.
        if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();

        if (!rxn.reactantEqualsProduct()
            && !pDepList.contains(rxn)
            && !pDepList.contains(rxn.getReverseReaction())) {
          pDepList.add(rxn);
        }
      }
    }
    LinkedList removeReactions = new LinkedList();
    for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();

      boolean presentInPDep = false;
      if (r.isForward()
          && !(r instanceof ThirdBodyReaction)
          && !(r instanceof TROEReaction)
          && !(r instanceof LindemannReaction)) {
        Iterator r_iter = pDepList.iterator();
        while (r_iter.hasNext()) {
          Reaction pDepr = (Reaction) r_iter.next();
          if (pDepr.equals(r)) {
            //      				removeReactions.add(pDepr);
            //      				duplicates.add(pDepr);
            //      				if (!r.hasAdditionalKinetics()){
            //      					duplicates.add(r);
            //      					presentInPDep = true;
            //      				}
            presentInPDep = true;
            nonPDepList.add(r);
          }
        }
        if (!presentInPDep) nonPDepList.add(r);
      }
    }

    for (Iterator iter = removeReactions.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      pDepList.remove(r);
    }

    for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      // 6Jul2009-MRH:
      //	Pass both system temperature and pressure to function toChemkinString.
      //		The only PDepKineticsModel that uses the passed pressure is RATE
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
              + "\n"); // 10/26/07 gmagoon: eliminating use of Global.temperature; **** I use
                       // beginStatus here, which may or may not be appropriate
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = nonPDepList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = duplicates.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
              + "\n\tDUP\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n\tDUP\n");
    }

    result.append("END\n");

    return result.toString();

    // #]
  }
コード例 #7
0
 // ## operation setReactant(int,LinkedHashSet)
 public void setReactant(int p_position, LinkedHashSet p_reactantFGSet) {
   // #[ operation setReactant(int,LinkedHashSet)
   reactants.add(p_position, p_reactantFGSet);
   // #]
 }