// ## 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();
// #]
}
/**
* Enrich portClassHier with class/interface names that map to a list of parent
* classes/interfaces. For any class encountered, find its parents too.<br>
* Also find the port types which have assignable schema classes.
*
* @param oper Operator to work on
* @param portClassHierarchy In-Out param that contains a mapping of class/interface to its
* parents
* @param portTypesWithSchemaClasses Json that will contain all the ports which have any schema
* classes.
*/
public void buildAdditionalPortInfo(
JSONObject oper, JSONObject portClassHierarchy, JSONObject portTypesWithSchemaClasses) {
try {
JSONArray ports = oper.getJSONArray(OperatorDiscoverer.PORT_TYPE_INFO_KEY);
for (int i = 0; i < ports.length(); i++) {
JSONObject port = ports.getJSONObject(i);
String portType = port.optString("type");
if (portType == null) {
// skipping if port type is null
continue;
}
if (typeGraph.size() == 0) {
buildTypeGraph();
}
try {
// building port class hierarchy
LinkedList<String> queue = Lists.newLinkedList();
queue.add(portType);
while (!queue.isEmpty()) {
String currentType = queue.remove();
if (portClassHierarchy.has(currentType)) {
// already present in the json so we skip.
continue;
}
List<String> immediateParents = typeGraph.getParents(currentType);
if (immediateParents == null) {
portClassHierarchy.put(currentType, Lists.<String>newArrayList());
continue;
}
portClassHierarchy.put(currentType, immediateParents);
queue.addAll(immediateParents);
}
} catch (JSONException e) {
LOG.warn("building port type hierarchy {}", portType, e);
}
// finding port types with schema classes
if (portTypesWithSchemaClasses.has(portType)) {
// already present in the json so skipping
continue;
}
if (portType.equals("byte")
|| portType.equals("short")
|| portType.equals("char")
|| portType.equals("int")
|| portType.equals("long")
|| portType.equals("float")
|| portType.equals("double")
|| portType.equals("java.lang.String")
|| portType.equals("java.lang.Object")) {
// ignoring primitives, strings and object types as this information is needed only for
// complex types.
continue;
}
if (port.has("typeArgs")) {
// ignoring any type with generics
continue;
}
boolean hasSchemaClasses = false;
List<String> instantiableDescendants = typeGraph.getInstantiableDescendants(portType);
if (instantiableDescendants != null) {
for (String descendant : instantiableDescendants) {
try {
if (typeGraph.isInstantiableBean(descendant)) {
hasSchemaClasses = true;
break;
}
} catch (JSONException ex) {
LOG.warn("checking descendant is instantiable {}", descendant);
}
}
}
portTypesWithSchemaClasses.put(portType, hasSchemaClasses);
}
} catch (JSONException e) {
// should not reach this
LOG.error("JSON Exception {}", e);
throw new RuntimeException(e);
}
}