// ## 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; } // #] }
// ## 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(); // #] }