// ## 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();
// #]
}
private static Kinetics[] getReactionKinetics(Reaction r) {
Kinetics[] allKinetics;
if (r.isForward()) {
allKinetics = r.getKinetics();
} else if (r.isBackward()) {
allKinetics = r.getFittedReverseKinetics();
} else {
allKinetics = r.getKinetics();
}
return allKinetics;
}
// ## 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 writeOutputString(Reaction r, TemplateReactionGenerator rtLibrary) {
String listOfReactions = "";
Temperature stdtemp = new Temperature(298, "K");
double Hrxn = r.calculateHrxn(stdtemp);
// If r Reaction is from Reaction Library add it to list of reaction append its kinetics and
// return
String source = r.getKineticsSource(0);
if (source == null) {
// If source is null I am assuming that its not a Reaction from Reaction Library or Seed
// Mechanism
source = "TemplateReaction:";
}
StringTokenizer st = new StringTokenizer(source, ":");
String reaction_type = st.nextToken();
// Reactions from Reaction Libraries:
if (reaction_type.equals("ReactionLibrary")) {
// We will get the forward reaction
if (r.isBackward()) {
r = r.getReverseReaction();
Hrxn = -Hrxn; // Reversing the heat of reaction
}
Kinetics[] allKinetics = getReactionKinetics(r);
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
return listOfReactions;
}
// Reactions NOT from Reaction Libraries are from Templates:
if (r.isForward()) {
Kinetics[] allKinetics = r.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
} else if (r.isBackward()) {
LinkedHashSet reverseReactions = new LinkedHashSet();
Iterator iter2 = r.getStructure().getProducts();
Species species1 = (Species) iter2.next();
Species species2 = species1;
while (iter2.hasNext()) species2 = (Species) iter2.next();
String rxnFamilyName = "";
if (r instanceof TemplateReaction) {
rxnFamilyName = ((TemplateReaction) r.getReverseReaction()).getReactionTemplate().getName();
}
LinkedHashSet speciesHashSet = new LinkedHashSet();
speciesHashSet.add(species1);
reverseReactions = rtLibrary.react(speciesHashSet, species2, rxnFamilyName);
for (Iterator iter3 = reverseReactions.iterator(); iter3.hasNext(); ) {
Reaction currentRxn = (Reaction) iter3.next();
if (currentRxn.getStructure() == r.getReverseReaction().getStructure()) {
Kinetics[] allKinetics = currentRxn.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
currentRxn.toString()
+ "\t"
+ getFormattedKinetics(allKinetics[numKinetics], -Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
}
}
} else {
Kinetics[] allKinetics = r.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
}
return listOfReactions;
}
