// ## operation writeChemkinSpecies(ReactionModel,SystemSnapshot) public static String writeChemkinSpecies( ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) { // #[ operation writeChemkinSpecies(ReactionModel,SystemSnapshot) StringBuilder result = new StringBuilder(); result.append("SPECIES\n"); CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel; // write inert gas for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) { String name = (String) iter.next(); result.append('\t' + name + '\n'); } // write species for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) { Species spe = (Species) iter.next(); result.append('\t' + spe.getChemkinName() + '\n'); } result.append("END\n"); return result.toString(); // #] }
// ## operation writeChemkinReactions(ReactionModel) // 10/26/07 gmagoon: changed to take temperature as parameter (it doesn't seem like this method is // currently used anywhere) public static String writeChemkinReactions( ReactionModel p_reactionModel, Temperature p_temperature) { // #[ operation writeChemkinReactions(ReactionModel) StringBuilder result = new StringBuilder(); result.append("REACTIONS KCAL/MOLE\n"); CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel; LinkedHashSet all = cerm.getReactedReactionSet(); HashSet hs = new HashSet(); int numfor = 0; int numrev = 0; int numdup = 0; int numnorev = 0; for (Iterator iter = all.iterator(); iter.hasNext(); ) { Reaction rxn = (Reaction) iter.next(); if (rxn.isForward()) { result.append( " " + rxn.toChemkinString(p_temperature) + "\n"); // 10/26/07 gmagoon: changed to avoid use of Global.temperature // result.append(" " + rxn.toChemkinString(Global.temperature) + "\n"); } } result.append("END\n"); return result.toString(); // #] }
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(); }
// ## 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 writeChemkinThermo(ReactionModel) public static String writeChemkinThermo(ReactionModel p_reactionModel) { // #[ operation writeChemkinThermo(ReactionModel) /* String thermoHeader = "! neon added by pey (20/6/04) - used thermo for Ar\n"; thermoHeader += "Ne 120186Ne 1 G 0300.00 5000.00 1000.00 1\n"; thermoHeader += " 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n"; thermoHeader += "-0.07453750E+04 0.04366001E+02 0.02500000E+02 0.00000000E+00 0.00000000E+00 3\n"; thermoHeader += " 0.00000000E+00 0.00000000E+00-0.07453750E+04 0.04366001E+02 4\n"; thermoHeader += "N2 121286N 2 G 0300.00 5000.00 1000.00 1\n"; thermoHeader += " 0.02926640e+02 0.01487977e-01-0.05684761e-05 0.01009704e-08-0.06753351e-13 2\n"; thermoHeader += "-0.09227977e+04 0.05980528e+02 0.03298677e+02 0.01408240e-01-0.03963222e-04 3\n"; thermoHeader += " 0.05641515e-07-0.02444855e-10-0.01020900e+05 0.03950372e+02 4\n"; thermoHeader += "Ar 120186Ar 1 G 0300.00 5000.00 1000.00 1\n"; thermoHeader += " 0.02500000e+02 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 2\n"; thermoHeader += "-0.07453750e+04 0.04366001e+02 0.02500000e+02 0.00000000e+00 0.00000000e+00 3\n"; thermoHeader += " 0.00000000e+00 0.00000000e+00-0.07453750e+04 0.04366001e+02 4\n"; */ // #] String thermoHeader = "! The first four sets of polynomial coefficients (Ar, N2, Ne, He) are from \n"; thermoHeader += "! THIRD MILLENIUM IDEAL GAS AND CONDENSED PHASE THERMOCHEMICAL DATABASE FOR \n"; thermoHeader += "! COMBUSTION WITH UPDATES FROM ACTIVE THERMOCHENICAL TABLES \n"; thermoHeader += "! Authors: Alexander Burcat and Branko Ruscic \n"; thermoHeader += "! \n"; thermoHeader += "! The rest of the species are estimated by RMG (http://rmg.mit.edu/) \n"; // thermoHeader += "! Ar HF298=0. REF=C.E. Moore 'Atomic Energy Levels' NSRDS-NBS 35 (1971) // p.211 \n"; // thermoHeader += "! NASA Glen (former Lewis) Research Center (1988) // \n"; thermoHeader += "Ar L 6/88Ar 1 G 200.000 6000.000 1000. 1\n"; thermoHeader += " 0.25000000E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n"; thermoHeader += "-0.74537500E+03 0.43796749E+01 0.25000000E+01 0.00000000E+00 0.00000000E+00 3\n"; thermoHeader += " 0.00000000E+00 0.00000000E+00-0.74537500E+03 0.43796749E+01 4\n"; // thermoHeader += "! N2 HF298= 0.0 KJ REF=TSIV Max Lst Sq Error Cp @ 6000 K 0.29% // \n"; thermoHeader += "N2 G 8/02N 2 G 200.000 6000.000 1000. 1\n"; thermoHeader += " 2.95257637E+00 1.39690040E-03-4.92631603E-07 7.86010195E-11-4.60755204E-15 2\n"; thermoHeader += "-9.23948688E+02 5.87188762E+00 3.53100528E+00-1.23660988E-04-5.02999433E-07 3\n"; thermoHeader += " 2.43530612E-09-1.40881235E-12-1.04697628E+03 2.96747038E+00 4\n"; // thermoHeader += "!Ne HF298= 0.0 KJ REF=McBride, Heimel, Ehlers & Gordon // \n"; // thermoHeader += "! 'Thermodynamic Properties to 6000 K...' NASA SP-3001 // (1963) \n"; thermoHeader += "Ne L10/90Ne 1 G 200.0 6000.00 1000.0 1\n"; thermoHeader += " 0.25000000E 01 0.00000000E 00 0.00000000E 00 0.00000000E 00 0.00000000E 00 2\n"; thermoHeader += "-0.74537500E 03 0.33553227E 01 0.25000000E 01 0.00000000E 00 0.00000000E 00 3\n"; thermoHeader += " 0.00000000E 00 0.00000000E 00-0.74537498E 03 0.33553227E 01 4\n"; // thermoHeader += "7440-59-7 // \n"; // thermoHeader += "He HF298=0.0 KJ REF=McBride, Heimel, Ehlers & Gordon "Thermodynamic // Properties\n"; // thermoHeader += "to 6000K ..." NASA SP-3001 1963. // \n"; thermoHeader += "He REF ELEMENT L10/90HE 1. 0. 0. 0.G 200.000 6000.000 B 4.00260 1\n"; thermoHeader += " 2.50000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n"; thermoHeader += "-7.45375000E+02 9.28723974E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3\n"; thermoHeader += " 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28723974E-01 0.00000000E+00 4\n\n"; StringBuilder result = new StringBuilder(); result.append("THERMO ALL\n"); result.append(" 300.000 1000.000 5000.000\n"); result.append(thermoHeader); CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel; for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) { Species spe = (Species) iter.next(); if (spe.getNasaThermoSource() != null) { result.append("!" + spe.getNasaThermoSource() + "\n"); } result.append(spe.getNasaThermoData() + "\n"); } result.append("END\n"); // Added by Amrit for Richard's liquid phase chemkin code 05/21/2009 result.append("\n"); return result.toString(); // #] }
// ## 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(); // #] }
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(); // #] }