// ## 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 void main(String[] args) {
// Initialize the logger (saves to RMG.log file).
Logger.initialize();
initializeSystemProperties();
try {
ChemGraph.readForbiddenStructure();
} catch (IOException e1) {
System.err.println("PopulateReactions cannot locate forbiddenStructures.txt file");
e1.printStackTrace();
}
ArrheniusKinetics.setAUnits("moles");
ArrheniusKinetics.setEaUnits("kcal/mol");
// Creating a new ReactionModelGenerator so I can set the variable temp4BestKinetics
// and call the new readAndMakePTL and readAndMakePRL methods
ReactionModelGenerator rmg = new ReactionModelGenerator();
rmg.setSpeciesSeed(new LinkedHashSet());
// Set Global.lowTemp and Global.highTemp
// The values of the low/highTemp are not used in the function
// (to the best of my knowledge).
// They are necessary for the instances of additionalKinetics,
// e.g. H2C*-CH2-CH2-CH3 -> H3C-CH2-*CH-CH3
/*
* 7Apr2010: The input file will now ask the user for a TemperatureModel and PressureModel (same as the RMG
* module). The Global .lowTemperature and .highTemperature will automatically be determined
*/
// Global.lowTemperature = new Temperature(300,"K");
// Global.highTemperature = new Temperature(1500,"K");
// Define variable 'speciesSet' to store the species contained in the input file
LinkedHashSet speciesSet = new LinkedHashSet();
// Define variable 'reactions' to store all possible rxns between the species in speciesSet
LinkedHashSet reactions = new LinkedHashSet();
// Define two string variables 'listOfReactions' and 'listOfSpecies'
// These strings will hold the list of rxns (including the structure,
// modified Arrhenius parameters, and source/comments) and the list of
// species (including the chemkin name and graph), respectively
String listOfReactions =
"Arrhenius 'A' parameter has units of: "
+ ArrheniusEPKinetics.getAUnits()
+ ",cm3,s\n"
+ "Arrhenius 'n' parameter is unitless and assumes Tref = 1K\n"
+ "Arrhenius 'E' parameter has units of: "
+ ArrheniusEPKinetics.getEaUnits()
+ "\n\n";
String listOfSpecies = "";
// Open and read the input file
try {
FileReader fr_input = new FileReader(args[0]);
BufferedReader br_input = new BufferedReader(fr_input);
// Read in the Database field
String line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("database")) {
RMG.extractAndSetDatabasePath(line);
} else {
System.err.println("PopulateReactions: Could not" + " locate the Database field");
System.exit(0);
}
// Read in the first line of the input file
// This line should hold the temperature of the system, e.g.
// Temperature: 500 (K)
line = ChemParser.readMeaningfulLine(br_input, true);
/*
* Read max atom types (if they exist)
*/
line = rmg.readMaxAtomTypes(line, br_input);
/*
* Read primary thermo libraries (if they exist)
*/
if (line.toLowerCase().startsWith("primarythermolibrary")) {
rmg.readAndMakePTL(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryThermoLibrary field.\n"
+ "Line read was: "
+ line);
System.exit(0);
}
line = ChemParser.readMeaningfulLine(br_input, true);
// Read primary transport library
if (line.toLowerCase().startsWith("primarytransportlibrary"))
rmg.readAndMakePTransL(br_input);
else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryTransportLibrary field.\n"
+ "Line read was: "
+ line);
System.exit(0);
}
/*
* Read the temperature model (must be of length one)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
rmg.createTModel(line);
if (rmg.getTempList().size() > 1) {
System.out.println("Please list only one temperature in the TemperatureModel field.");
System.exit(0);
}
// Set the user's input temperature
LinkedList tempList = rmg.getTempList();
systemTemp = ((ConstantTM) tempList.get(0)).getTemperature();
rmg.setTemp4BestKinetics(systemTemp);
/*
* Read the pressure model (must be of length 1)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
rmg.createPModel(line);
if (rmg.getPressList().size() > 1) {
System.out.println("Please list only one pressure in the PressureModel field.");
System.exit(0);
}
/*
* Read the solvation field (if present)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
StringTokenizer st = new StringTokenizer(line);
// The first line should start with "Solvation", otherwise do nothing and display a message to
// the user
if (st.nextToken().startsWith("Solvation")) {
line = st.nextToken().toLowerCase();
// The options for the "Solvation" field are "on" or "off" (as of 18May2009), otherwise do
// nothing and
// display a message to the user
// Note: I use "Species.useInChI" because the "Species.useSolvation" updates were not yet
// committed.
if (line.equals("on")) {
Species.useSolvation = true;
// rmg.setUseDiffusion(true);
listOfReactions += "Solution-phase chemistry!\n\n";
} else if (line.equals("off")) {
Species.useSolvation = false;
// rmg.setUseDiffusion(false);
listOfReactions += "Gas-phase chemistry.\n\n";
} else {
System.out.println(
"Error in reading input.txt file:\nThe field 'Solvation' has the options 'on' or 'off'."
+ "\nPopulateReactions does not recognize: "
+ line);
return;
}
line = ChemParser.readMeaningfulLine(br_input, true);
}
/*
* Read in the species (name, concentration, adjacency list)
*/
if (line.toLowerCase().startsWith("speciesstatus")) {
LinkedHashMap lhm = new LinkedHashMap();
lhm = rmg.populateInitialStatusListWithReactiveSpecies(br_input);
speciesSet.addAll(lhm.values());
}
/*
* Read in the inert gas (name, concentration)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("bathgas")) {
rmg.populateInitialStatusListWithInertSpecies(br_input);
}
/*
* Read in the p-dep options
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("spectroscopicdata")) {
rmg.setSpectroscopicDataMode(line);
line = ChemParser.readMeaningfulLine(br_input, true);
line = rmg.setPressureDependenceOptions(line, br_input);
}
/*
* Read primary kinetic libraries (if they exist)
*/
if (line.toLowerCase().startsWith("primarykineticlibrary")) {
rmg.readAndMakePKL(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryKineticLibrary field."
+ "Line read was: "
+ line);
System.exit(0);
}
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("reactionlibrary")) {
rmg.readAndMakeReactionLibrary(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the ReactionLibrary field."
+ "Line read was: "
+ line);
System.exit(0);
}
/*
* Read in verbosity field (if it exists)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line != null && line.toLowerCase().startsWith("verbose")) {
StringTokenizer st2 = new StringTokenizer(line);
String tempString = st2.nextToken();
tempString = st2.nextToken();
tempString = tempString.toLowerCase();
if (tempString.equals("on") || tempString.equals("true") || tempString.equals("yes"))
ArrheniusKinetics.setVerbose(true);
}
TemplateReactionGenerator rtLibrary = new TemplateReactionGenerator();
// / THE SERVERY BIT
ServerSocket Server = new ServerSocket(5000);
Logger.info("TCPServer Waiting for client on port 5000");
Logger.info("Switching to quiet mode - only WARNINGS and above will be logged...");
Logger.setConsoleLevel(jing.rxnSys.Logger.WARNING);
Logger.setFileLevel(jing.rxnSys.Logger.WARNING);
while (true) {
Socket connected = Server.accept();
Logger.warning(
" THE CLIENT"
+ " "
+ connected.getInetAddress()
+ ":"
+ connected.getPort()
+ " IS CONNECTED ");
BufferedReader inFromClient =
new BufferedReader(new InputStreamReader(connected.getInputStream()));
inFromClient.mark(4096); // so you can reset up to 4096 characters back.
PrintWriter outToClient = new PrintWriter(connected.getOutputStream(), true);
try {
listOfReactions =
"Arrhenius 'A' parameter has units of: "
+ ArrheniusEPKinetics.getAUnits()
+ ",cm3,s\n"
+ "Arrhenius 'n' parameter is unitless and assumes Tref = 1K\n"
+ "Arrhenius 'E' parameter has units of: "
+ ArrheniusEPKinetics.getEaUnits()
+ "\n\n";
listOfSpecies = "";
// clear old things
speciesSet.clear();
reactions.clear();
/*
* Read in the species (name, concentration, adjacency list)
*/
LinkedHashMap lhm = new LinkedHashMap();
lhm = rmg.populateInitialStatusListWithReactiveSpecies(inFromClient);
speciesSet.addAll(lhm.values());
// Check Reaction Library
ReactionLibrary RL = rmg.getReactionLibrary();
LibraryReactionGenerator lrg1 = new LibraryReactionGenerator(RL);
reactions = lrg1.react(speciesSet);
if (RL != null) {
System.out.println("Checking Reaction Library " + RL.getName() + " for reactions.");
Iterator ReactionIter = reactions.iterator();
while (ReactionIter.hasNext()) {
Reaction current_reaction = (Reaction) ReactionIter.next();
System.out.println("Library Reaction: " + current_reaction.toString());
}
}
// Add all reactions found from RMG template reaction generator
reactions.addAll(rtLibrary.react(speciesSet));
System.out.println("FINISHED generating template reactions");
if (!(rmg.getReactionModelEnlarger() instanceof RateBasedRME)) {
// NOT an instance of RateBasedRME therefore assume RateBasedPDepRME and we're doing
// pressure
// dependence
CoreEdgeReactionModel cerm = new CoreEdgeReactionModel(speciesSet, reactions);
rmg.setReactionModel(cerm);
rmg.setReactionGenerator(rtLibrary);
ReactionSystem rs =
new ReactionSystem(
(TemperatureModel) rmg.getTempList().get(0),
(PressureModel) rmg.getPressList().get(0),
rmg.getReactionModelEnlarger(),
new FinishController(),
null,
rmg.getPrimaryKineticLibrary(),
rmg.getReactionGenerator(),
speciesSet,
(InitialStatus) rmg.getInitialStatusList().get(0),
rmg.getReactionModel(),
rmg.getLibraryReactionGenerator(),
0,
"GasPhase");
PDepNetwork.reactionModel = rmg.getReactionModel();
PDepNetwork.reactionSystem = rs;
// If the reaction structure is A + B = C + D, we are not concerned w/pdep
Iterator iter = reactions.iterator();
LinkedHashSet nonPdepReactions = new LinkedHashSet();
while (iter.hasNext()) {
Reaction r = (Reaction) iter.next();
if (FastMasterEqn.isReactionPressureDependent(r)) {
cerm.categorizeReaction(r.getStructure());
PDepNetwork.addReactionToNetworks(r);
} else {
nonPdepReactions.add(r);
}
}
// Run fame calculation
PDepKineticsEstimator pDepKineticsEstimator =
((RateBasedPDepRME) rmg.getReactionModelEnlarger()).getPDepKineticsEstimator();
BathGas bathGas = new BathGas(rs);
for (int numNetworks = 0;
numNetworks < PDepNetwork.getNetworks().size();
++numNetworks) {
LinkedHashSet allSpeciesInNetwork = new LinkedHashSet();
PDepNetwork pdepnetwork = PDepNetwork.getNetworks().get(numNetworks);
LinkedList isomers = pdepnetwork.getIsomers();
for (int numIsomers = 0; numIsomers < isomers.size(); ++numIsomers) {
PDepIsomer currentIsomer = (PDepIsomer) isomers.get(numIsomers);
if (currentIsomer.getNumSpecies() == 2)
pdepnetwork.makeIsomerIncluded(currentIsomer);
}
pDepKineticsEstimator.runPDepCalculation(pdepnetwork, rs, cerm);
if (pdepnetwork.getNetReactions().size() > 0) {
String formatSpeciesName = "%1$-16s\t";
listOfReactions +=
"!PDepNetwork\n"
+ "!\tdeltaEdown = "
+ bathGas.getDeltaEdown().getAlpha()
+ "(T / "
+ bathGas.getDeltaEdown().getT0()
+ ")^"
+ bathGas.getDeltaEdown().getN()
+ " kJ/mol\n"
+ "!\tbathgas MW = "
+ bathGas.getMolecularWeight()
+ " amu\n"
+ "!\tbathgas LJ sigma = "
+ bathGas.getLJSigma()
+ " meters\n"
+ "!\tbathgas LJ epsilon = "
+ bathGas.getLJEpsilon()
+ " Joules\n"
+ "!Here are the species and their thermochemistry:\n";
LinkedList<PDepIsomer> allpdepisomers = pdepnetwork.getIsomers();
for (int numIsomers = 0; numIsomers < allpdepisomers.size(); ++numIsomers) {
LinkedList species = allpdepisomers.get(numIsomers).getSpeciesList();
for (int numSpecies = 0; numSpecies < species.size(); ++numSpecies) {
Species currentSpec = (Species) species.get(numSpecies);
if (!allSpeciesInNetwork.contains(currentSpec)) {
listOfReactions +=
"!\t"
+ String.format(formatSpeciesName, currentSpec.getFullName())
+ currentSpec.getThermoData().toString()
+ currentSpec.getThermoData().getSource()
+ "\n";
allSpeciesInNetwork.add(currentSpec);
}
}
speciesSet.addAll(species);
}
String formatRxnName = "%1$-32s\t";
listOfReactions +=
"!Here are the path reactions and their high-P limit kinetics:\n";
LinkedList<PDepReaction> pathRxns = pdepnetwork.getPathReactions();
for (int numPathRxns = 0; numPathRxns < pathRxns.size(); numPathRxns++) {
Kinetics[] currentKinetics = pathRxns.get(numPathRxns).getKinetics();
for (int numKinetics = 0; numKinetics < currentKinetics.length; ++numKinetics) {
listOfReactions +=
"!\t"
+ String.format(
formatRxnName,
pathRxns.get(numPathRxns).getStructure().toRestartString(true))
+ currentKinetics[numKinetics].toChemkinString(
pathRxns
.get(numPathRxns)
.calculateHrxn(new Temperature(298.0, "K")),
new Temperature(298.0, "K"),
false)
+ "\n";
}
}
listOfReactions += "\n";
LinkedList<PDepReaction> indivPDepRxns = pdepnetwork.getNetReactions();
for (int numPDepRxns = 0; numPDepRxns < indivPDepRxns.size(); numPDepRxns++) {
listOfReactions += indivPDepRxns.get(numPDepRxns).toRestartString(systemTemp);
}
LinkedList<PDepReaction> nonIncludedRxns = pdepnetwork.getNonincludedReactions();
for (int numNonRxns = 0; numNonRxns < nonIncludedRxns.size(); ++numNonRxns) {
listOfReactions += nonIncludedRxns.get(numNonRxns).toRestartString(systemTemp);
}
}
}
reactions = nonPdepReactions;
}
// Some of the reactions may be duplicates of one another
// (e.g. H+CH4=CH3+H2 as a forward reaction and reverse reaction)
// Create new LinkedHashSet which will store the non-duplicate rxns
LinkedHashSet nonDuplicateRxns = new LinkedHashSet();
int Counter = 0;
Iterator iter_rxns = reactions.iterator();
while (iter_rxns.hasNext()) {
++Counter;
Reaction r = (Reaction) iter_rxns.next();
// The first reaction is not a duplicate of any previous reaction
if (Counter == 1) {
nonDuplicateRxns.add(r);
listOfReactions += writeOutputString(r, rtLibrary);
speciesSet.addAll(r.getProductList());
}
// Check whether the current reaction (or its reverse) has the same structure
// of any reactions already reported in the output
else {
Iterator iterOverNonDup = nonDuplicateRxns.iterator();
boolean dupRxn = false;
while (iterOverNonDup.hasNext()) {
Reaction temp_Reaction = (Reaction) iterOverNonDup.next();
if (r.getStructure() == temp_Reaction.getStructure()) {
dupRxn = true;
break;
} else if (r.hasReverseReaction()) {
if (r.getReverseReaction().getStructure() == temp_Reaction.getStructure()) {
dupRxn = true;
break;
}
}
}
if (!dupRxn) {
nonDuplicateRxns.add(r);
// If Reaction is Not a Library Reaction
listOfReactions += writeOutputString(r, rtLibrary);
speciesSet.addAll(r.getProductList());
}
}
}
Iterator iter_species = speciesSet.iterator();
// Define dummy integer 'i' so our getChemGraph().toString()
// call only returns the graph
int i = 0;
while (iter_species.hasNext()) {
Species species = (Species) iter_species.next();
listOfSpecies +=
species.getFullName() + "\n" + species.getChemGraph().toStringWithoutH(i) + "\n";
}
// Write the output files
try {
File rxns = new File("PopRxnsOutput_rxns.txt");
FileWriter fw_rxns = new FileWriter(rxns);
fw_rxns.write(listOfReactions);
fw_rxns.close();
File spcs = new File("PopRxnsOutput_spcs.txt");
FileWriter fw_spcs = new FileWriter(spcs);
fw_spcs.write(listOfSpecies);
fw_spcs.close();
} catch (IOException e) {
System.err.println("Could not write PopRxnsOutput*.txt files");
}
// Display to the user that the program was successful and also
// inform them where the results may be located
System.out.println(
"Reaction population complete. "
+ "Results are stored in PopRxnsOutput_rxns.txt and PopRxnsOutput_spcs.txt");
// send output to client
System.out.println("SENDING RESPONSE TO CLIENT");
outToClient.println(listOfSpecies);
outToClient.println(listOfReactions);
} catch (Throwable t) {
Logger.error("Error in PopulateReactionsServer");
try {
inFromClient.reset();
Logger.error("Input:");
while (inFromClient.ready()) {
Logger.error(inFromClient.readLine());
}
} catch (IOException e) {
Logger.error("Couldn't read input stream");
}
Logger.logStackTrace(t);
outToClient.println("Error in PopulateReactionsServer");
t.printStackTrace(outToClient);
}
connected.close();
System.out.println("SOCKET CLOSED");
}
} catch (FileNotFoundException e) {
System.err.println("File was not found!\n");
} catch (IOException e) {
System.err.println(
"IOException: Something maybe wrong with ChemParser.readChemGraph.\n" + e.toString());
}
}