Esempio n. 1
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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;
   // #]
 }
Esempio n. 2
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  public static String writeChemkinPdepReactions(ReactionSystem rs) {
    // #[ operation writeChemkinReactions(ReactionModel)

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

    LinkedList rList = new LinkedList();
    LinkedList troeList = new LinkedList();
    LinkedList tbrList = new LinkedList();
    LinkedList duplicates = new LinkedList();
    LinkedList lindeList = new LinkedList();

    if (rs.dynamicSimulator instanceof JDASPK) {
      rList = ((JDASPK) rs.dynamicSimulator).rList;
      troeList = ((JDASPK) rs.dynamicSimulator).troeList;
      tbrList = ((JDASPK) rs.dynamicSimulator).thirdBodyList;
      duplicates = ((JDASPK) rs.dynamicSimulator).duplicates;
      lindeList = ((JDASPK) rs.dynamicSimulator).lindemannList;
    } else if (rs.dynamicSimulator instanceof JDASSL) {
      rList = ((JDASSL) rs.dynamicSimulator).rList;
      troeList = ((JDASSL) rs.dynamicSimulator).troeList;
      tbrList = ((JDASSL) rs.dynamicSimulator).thirdBodyList;
      duplicates = ((JDASSL) rs.dynamicSimulator).duplicates;
      lindeList = ((JDASSL) rs.dynamicSimulator).lindemannList;
    }

    for (Iterator iter = rList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      // 10/26/07 gmagoon: changed to avoid use of Global.temperature; I am using
      // getPresentTemperature for the time being; it is possible that
      // getInitialStatus.getTemperature or something similar may be more appropriate
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = troeList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = tbrList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = duplicates.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n\tDUP\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n\tDUP\n");
    }
    for (Iterator iter = lindeList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
    }

    result.append("END\n");

    return result.toString();

    // #]
  }
Esempio n. 3
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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);
   // #]
 }
Esempio n. 4
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  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();
  }
Esempio n. 5
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 // ## operation getAllowedFunctionalGroupAt(int)
 public Matchable getAllowedFunctionalGroupAt(int p_index) {
   // #[ operation getAllowedFunctionalGroupAt(int)
   Matchable t = (Matchable) (reactants.get(p_index - 1));
   if (t == null) return null;
   return t;
   // #]
 }
Esempio n. 6
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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;
   // #]
 }
Esempio n. 7
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 // ## operation StructureTemplate(Matchable)
 public StructureTemplate(Matchable p_reactant) {
   {
     reactantTree = new ArrayList();
   }
   // #[ operation StructureTemplate(Matchable)
   reactants.add(p_reactant);
   // #]
 }
Esempio n. 8
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  // ## operation generateReverseForBackwardReaction()
  private TemplateReaction generateReverseForBackwardReaction(Structure fs, Structure fsSp) {
    // #[ operation generateReverseForBackwardReaction()
    // we need to only generate reverse reaction for backward reaction, so that we wont be stuck
    // into a self loop.
    if (!this.isBackward()) {
      return null;
    }
    ReactionTemplate fRT = getReactionTemplate();
    ReactionTemplate rRT = null;

    if (fRT.isForward()) {
      return null;
    } else if (fRT.isNeutral()) {
      rRT = fRT;
    } else if (fRT.isBackward()) {
      rRT = fRT.getReverseReactionTemplate();
    } else {
      throw new InvalidReactionTemplateDirectionException(); // Structure fs = getStructure();
    }
    LinkedList freactant = fs.getReactantList();
    LinkedList fproduct = fs.getProductList();
    Structure rs = new Structure(fproduct, freactant, -1 * this.getDirection());
    Structure rsSp = new Structure(fsSp.products, fsSp.reactants, -1 * this.getDirection());
    // If it's in the reverse ReactionTemplate.reactionDictionaryByStructure then just return that
    // one.
    TemplateReaction rr = rRT.getReactionFromStructure(rsSp);
    if (rr != null) {
      rr.setReverseReaction(this);
      return rr;
    }
    int rNum = fproduct.size();

    Kinetics[] k = rRT.findReverseRateConstant(rs);

    // If that didnt work, what to do....

    if (k == null && rRT.name.equals("R_Recombination")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();
      Node n = (Node) g.getCentralNodeAt(2);
      if (n == null) {
        cg = ((ChemGraph) fproduct.get(1));
        g = cg.getGraph();
        n = (Node) g.getCentralNodeAt(2);
      }
      g.clearCentralNode();
      g.setCentralNode(1, n);
      k = rRT.findRateConstant(rs);
    } else if (k == null && rRT.name.equals("H_Abstraction")) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      Graph g1 = cg1.getGraph();
      Node n3 = (Node) g1.getCentralNodeAt(3);
      if (n3 == null) {
        cg1 = ((ChemGraph) fproduct.get(1));
        g1 = cg1.getGraph();
        n3 = (Node) g1.getCentralNodeAt(3);
        Node n2 = (Node) g1.getCentralNodeAt(2);
        g1.clearCentralNode();
        g1.setCentralNode(1, n3);
        g1.setCentralNode(2, n2);
        ChemGraph cg2 = ((ChemGraph) fproduct.get(0));
        Graph g2 = cg2.getGraph();
        Node n1 = (Node) g2.getCentralNodeAt(1);
        g2.clearCentralNode();
        g2.setCentralNode(3, n1);
      } else {
        Node n2 = (Node) g1.getCentralNodeAt(2);
        g1.clearCentralNode();
        g1.setCentralNode(1, n3);
        g1.setCentralNode(2, n2);
        ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
        Graph g2 = cg2.getGraph();
        Node n1 = (Node) g2.getCentralNodeAt(1);
        g2.clearCentralNode();
        g2.setCentralNode(3, n1);
      }
      k = rRT.findRateConstant(rs);
    }
    /*
     * Added by MRH on 27-Aug-2009 This hard-coding is necessary for rxn family templates that are labeled
     * "thermo_consistence". After the chemgraphs are mutated, the central nodes for the products are not correct
     * (see example below). These hard-coded portions are necessary for RMG to find Kinetics for the structure.
     * Example: CH4 + H CH4 1 *1 C 0 {2,S} {3,S} {4,S} {5,S} 2 *2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} 5 H 0 {1,S} H 1
     * *3 H 1 After RMG has "reactChemGraph" and "mutate" the chemgraphs of the reactants, the products would look
     * as such: prod1 1 *1 C 1 {2,S} {3,S} {4,S} 2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} prod2 1 *3 H 0 {2,S} 2 *2 H 0
     * {1,S} Assuming the reaction as written (CH4+H=CH3+H2) is endothermic at 298K, RMG will label this structure
     * as direction=-1 (backward). When attempting to find Kinetics for the backward reaction, RMG will try to match
     * the prod1 graph against the generic graphs X_H and Y_rad_birad. It cannot match Y_rad_birad (because there is
     * no *3 node) and it cannot match X_H (because there is no *2 node). Thus, a "null" Kinetics will be returned
     * from the findReverseRateConstant call. We then relabel the central nodes on prod1 and prod2 and attempt to
     * get Kinetics for this structure. I am adding the following bit of code to work with the new reaction family
     * Aaron Vandeputte is adding to RMG: "".
     */
    else if (k == null && rRT.name.equals("intra_substitutionS_isomerization")) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      Graph g1 = cg1.getGraph();
      Node n1 = (Node) g1.getCentralNodeAt(1);
      Node n2 = (Node) g1.getCentralNodeAt(2);
      Node n3 = (Node) g1.getCentralNodeAt(3);
      Node n4 = (Node) g1.getCentralNodeAt(4);
      Node n5 = (Node) g1.getCentralNodeAt(5);
      Node n6 = (Node) g1.getCentralNodeAt(6);
      Node n7 = (Node) g1.getCentralNodeAt(7);
      g1.clearCentralNode();
      g1.setCentralNode(1, n1);
      g1.setCentralNode(2, n3);
      g1.setCentralNode(3, n2);
      if (n7 != null) {
        g1.setCentralNode(7, n4);
        g1.setCentralNode(6, n5);
        g1.setCentralNode(5, n6);
        g1.setCentralNode(4, n7);
      } else if (n6 != null) {
        g1.setCentralNode(6, n4);
        g1.setCentralNode(5, n5);
        g1.setCentralNode(4, n6);
      } else if (n5 != null) {
        g1.setCentralNode(5, n4);
        g1.setCentralNode(4, n5);
      } else if (n4 != null) g1.setCentralNode(4, n4);
      k = rRT.findRateConstant(rs);
    }
    // Adding another elseif statement for Aaron Vandeputte rxn family
    // RMG expects to find *1 and *2 in the same ChemGraph (for this rxn family)
    // but will instead find *1 and *3 in the same ChemGraph (if we've reached this far)
    // Need to switch *2 and *3
    else if (k == null && (rRT.name.equals("substitutionS") || rRT.name.equals("Substitution_O"))) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
      Graph g1 = cg1.getGraph();
      Graph g2 = cg2.getGraph();
      Node n3 = (Node) g1.getCentralNodeAt(3);
      if (n3 == null) {
        // Switch the identities of cg1/g1 and cg2/g2
        cg1 = ((ChemGraph) fproduct.get(1));
        g1 = cg1.getGraph();
        cg2 = ((ChemGraph) fproduct.get(0));
        g2 = cg2.getGraph();
        n3 = (Node) g1.getCentralNodeAt(3);
      }
      Node n1 = (Node) g1.getCentralNodeAt(1);
      g1.clearCentralNode();
      g1.setCentralNode(2, n3);
      g1.setCentralNode(1, n1);
      Node n2 = (Node) g2.getCentralNodeAt(2);
      g2.clearCentralNode();
      g2.setCentralNode(3, n2);
      k = rRT.findRateConstant(rs);
    } else if (k == null && rRT.name.equals("intra_H_migration")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();

      // Current max is 8 identified nodes
      Node n1 = (Node) g.getCentralNodeAt(1);
      Node n2 = (Node) g.getCentralNodeAt(2);
      Node n3 = (Node) g.getCentralNodeAt(3);
      Node n4 = (Node) g.getCentralNodeAt(4);
      Node n5 = (Node) g.getCentralNodeAt(5);
      Node n6 = (Node) g.getCentralNodeAt(6);
      Node n7 = (Node) g.getCentralNodeAt(7);
      Node n8 = (Node) g.getCentralNodeAt(8);

      g.clearCentralNode();
      // Swap the locations of the central nodes 1 and 2
      g.setCentralNode(1, n2);
      g.setCentralNode(2, n1);
      // Retain the location of the central node at 3
      g.setCentralNode(3, n3);

      if (n8 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n8);
        g.setCentralNode(7, n7);
        g.setCentralNode(8, n6);
      } else if (n7 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n7);
        g.setCentralNode(7, n6);
      } else if (n6 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n6);
      } else if (n5 != null) { // Swap the locations of the central nodes 4 and 5, if node 5 exists
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
      } else if (n4 != null) { // if only central node 4 exists, retain that location
        g.setCentralNode(4, n4);
      }

      k = rRT.findRateConstant(rs);
      //            rr = rRT.calculateForwardRateConstant(cg, rs);
      //            if (!rr.isForward()) {
      //                String err = "Backward:"
      //                        + structure.toString()
      //                        + String.valueOf(structure
      //                                .calculateKeq(new Temperature(298, "K")))
      //                        + '\n';
      //                err = err
      //                        + "Forward:"
      //                        + rr.structure.toString()
      //                        + String.valueOf(rr.structure
      //                                .calculateKeq(new Temperature(298, "K")));
      //                throw new InvalidReactionDirectionException(err);
      //            }
      //           rr.setReverseReaction(this);
      //           rRT.addReaction(rr);
      //           return rr;

    } else if (k == null && rRT.name.equals("H_shift_cyclopentadiene")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();

      // Current max is 6 identified nodes
      Node n1 = (Node) g.getCentralNodeAt(1);
      Node n2 = (Node) g.getCentralNodeAt(2);
      Node n3 = (Node) g.getCentralNodeAt(3);
      Node n4 = (Node) g.getCentralNodeAt(4);
      Node n5 = (Node) g.getCentralNodeAt(5);
      Node n6 = (Node) g.getCentralNodeAt(6);

      g.clearCentralNode();

      // Swap the locations of the central nodes 1 to 6
      g.setCentralNode(1, n2);
      g.setCentralNode(2, n1);
      g.setCentralNode(3, n5);
      g.setCentralNode(4, n4);
      g.setCentralNode(5, n3);
      g.setCentralNode(6, n6);
      k = rRT.findRateConstant(rs);
    }
    if (k == null) {
      Logger.error(
          "Couldn't find the rate constant for reaction: "
              + rs.toChemkinString(true)
              + " with "
              + rRT.name);
      // System.exit(0);
      return null;
    }
    rr = new TemplateReaction(rsSp, k, rRT);
    if (!rr.isForward()) {
      String err =
          "Backward:"
              + structure.toString()
              + String.valueOf(structure.calculateKeq(new Temperature(298, "K")))
              + '\n';
      err =
          err
              + "Forward:"
              + rr.structure.toString()
              + String.valueOf(rr.structure.calculateKeq(new Temperature(298, "K")));
      throw new InvalidReactionDirectionException(err);
    }
    rr.setReverseReaction(this);
    rRT.addReaction(rr);
    return rr;
    // #]
  }
Esempio n. 9
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  // ## 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();

    // #]
  }
Esempio n. 10
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 // ## operation setReactant(int,LinkedHashSet)
 public void setReactant(int p_position, LinkedHashSet p_reactantFGSet) {
   // #[ operation setReactant(int,LinkedHashSet)
   reactants.add(p_position, p_reactantFGSet);
   // #]
 }
Esempio n. 11
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 // ## operation getReactants()
 public Iterator getReactants() {
   // #[ operation getReactants()
   Iterator iter = reactants.iterator();
   return iter;
   // #]
 }
Esempio n. 12
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 // ## operation getReactantNumber()
 public int getReactantNumber() {
   // #[ operation getReactantNumber()
   return reactants.size();
   // #]
 }