public MPSModulesClosure reset() {
modules.clear();
languagesWithRuntime.clear();
SetSequence.fromSet(devkits).clear();
skipExternalModules = false;
trackDevkits = false;
return this;
}
/**
* Insert the method's description here. Creation date: (21.12.2000 22:24:23)
*
* @return boolean
* @param object com.cosylab.vdct.graphics.objects.VisibleObject
* @param zoomOnHilited sets the option whether the hilited object should be zoomed in
*/
public boolean setAsHilited(VisibleObject object, boolean zoomOnHilited) {
this.zoomOnHilited = zoomOnHilited;
if (zoomOnHilited) {
DrawingSurface.getInstance().repaint();
hilitedObjects.clear();
if (hilitedObject != null) {
hilitedObjects.add(hilitedObject);
}
}
if (object == null) {
hilitedObjects.clear();
hilitedObject = null;
return false;
}
if (object != hilitedObject || hilitedObjects.size() == 1) {
hilitedObject = object;
// initialization
hilitedObjects.clear();
hilitedObjects.add(hilitedObject);
Object obj = hilitedObject;
// inlinks
Vector outlinks = null;
if (obj instanceof MultiInLink) {
outlinks = ((MultiInLink) obj).getOutlinks();
} else if (obj instanceof InLink) {
outlinks = new Vector();
outlinks.add(((InLink) obj).getOutput());
}
if (!zoomOnHilited) {
if (outlinks != null)
for (int i = 0; i < outlinks.size(); i++) {
obj = outlinks.elementAt(i);
hilitedObjects.add(obj);
while (obj instanceof InLink) {
obj = ((InLink) obj).getOutput();
hilitedObjects.add(obj);
}
}
// outLinks
obj = hilitedObject;
while (obj instanceof OutLink) {
obj = ((OutLink) obj).getInput();
hilitedObjects.add(obj);
}
}
return true;
} else return false;
}
@SuppressWarnings("rawtypes")
private boolean addOrderedElement(Ordered adding) {
boolean added = false;
E[] tempUnorderedElements = (E[]) this.toArray();
if (super.contains(adding)) {
return false;
}
super.clear();
if (tempUnorderedElements.length == 0) {
added = super.add((E) adding);
} else {
Set tempSet = new LinkedHashSet();
for (E current : tempUnorderedElements) {
if (current instanceof Ordered) {
if (this.comparator.compare(adding, current) < 0) {
added = super.add((E) adding);
super.add(current);
} else {
super.add(current);
}
} else {
tempSet.add(current);
}
}
if (!added) {
added = super.add((E) adding);
}
for (Object object : tempSet) {
super.add((E) object);
}
}
return added;
}
/** java.util.LinkedHashSet#clear() */
public void test_clear() {
// Test for method void java.util.LinkedHashSet.clear()
Set orgSet = (Set) hs.clone();
hs.clear();
Iterator i = orgSet.iterator();
assertEquals("Returned non-zero size after clear", 0, hs.size());
while (i.hasNext()) assertTrue("Failed to clear set", !hs.contains(i.next()));
}
void removeAllCustomGraphics() {
synchronized (CG_LOCK) {
if (orderedCustomGraphicLayers != null) {
orderedCustomGraphicLayers.clear();
graphicsPositions.clear();
}
}
// ensureContentChanged();
}
public void destroy() {
synchronized (lock) {
if (destroyed) {
return;
}
destroyed = true;
uris.clear();
for (ResourceLocation resourceLocation : classPath.values()) {
resourceLocation.close();
}
classPath.clear();
}
}
public static void main(String a[]) {
LinkedHashSet<String> lhs = new LinkedHashSet<String>();
// add elements to HashSet
lhs.add("first");
lhs.add("second");
lhs.add("third");
System.out.println("My LinkedHashSet content:");
System.out.println(lhs);
System.out.println("Clearing LinkedHashSet:");
lhs.clear();
System.out.println("Content After clear:");
System.out.println(lhs);
}
/** {@inheritDoc} */
public void okClicked() {
// Check that at least one checkbox is selected.
selectedAttributes.clear();
int i = 0;
for (T attribute : monitoringAttributes) {
if (checkboxes[i].isSelected()) {
selectedAttributes.add(attribute);
}
i++;
}
if (selectedAttributes.isEmpty()) {
super.displayErrorDialog(newArrayList(INFO_CTRL_PANEL_NO_OPERATION_SELECTED.get()));
} else {
isCanceled = false;
super.closeClicked();
}
}
/** Method to clear the LinkedHashSet */
public void clear() {
if (ownerOP != null && ownerOP.getExecutionContext().getManageRelations()) {
// Relationship management
Iterator iter = delegate.iterator();
RelationshipManager relMgr = ownerOP.getExecutionContext().getRelationshipManager(ownerOP);
while (iter.hasNext()) {
relMgr.relationRemove(ownerMmd.getAbsoluteFieldNumber(), iter.next());
}
}
if (ownerOP != null && !delegate.isEmpty()) {
// Cascade delete
if (SCOUtils.useQueuedUpdate(ownerOP)) {
// Queue the cascade delete
Iterator iter = delegate.iterator();
while (iter.hasNext()) {
ownerOP
.getExecutionContext()
.addOperationToQueue(
new CollectionRemoveOperation(
ownerOP, ownerMmd.getAbsoluteFieldNumber(), iter.next(), true));
}
} else if (SCOUtils.hasDependentElement(ownerMmd)) {
// Perform the cascade delete
Iterator iter = delegate.iterator();
while (iter.hasNext()) {
ownerOP.getExecutionContext().deleteObjectInternal(iter.next());
}
}
}
delegate.clear();
makeDirty();
if (ownerOP != null && !ownerOP.getExecutionContext().getTransaction().isActive()) {
ownerOP.getExecutionContext().processNontransactionalUpdate();
}
}
public static Props resolveProps(Props props) {
if (props == null) return null;
Props resolvedProps = new Props();
LinkedHashSet<String> visitedVariables = new LinkedHashSet<String>();
for (String key : props.getKeySet()) {
String value = props.get(key);
visitedVariables.add(key);
String replacedValue = resolveVariableReplacement(value, props, visitedVariables);
visitedVariables.clear();
resolvedProps.put(key, replacedValue);
}
for (String key : resolvedProps.getKeySet()) {
String value = resolvedProps.get(key);
String expressedValue = resolveVariableExpression(value);
resolvedProps.put(key, expressedValue);
}
return resolvedProps;
};
// somewhat similar to Outgoing.findCommonWithRemote()
public List<BranchChain> calculateMissingBranches() throws HgRemoteConnectionException {
List<Nodeid> remoteHeads = remoteRepo.heads();
LinkedList<Nodeid> common = new LinkedList<Nodeid>(); // these remotes are known in local
LinkedHashSet<Nodeid> toQuery =
new LinkedHashSet<Nodeid>(); // these need further queries to find common
for (Nodeid rh : remoteHeads) {
if (localRepo.knownNode(rh)) {
common.add(rh);
} else {
toQuery.add(rh);
}
}
if (toQuery.isEmpty()) {
return Collections.emptyList(); // no incoming changes
}
LinkedList<BranchChain> branches2load = new LinkedList<BranchChain>(); // return value
// detailed comments are in Outgoing.findCommonWithRemote
LinkedList<RemoteBranch> checkUp2Head = new LinkedList<RemoteBranch>();
// records relation between branch head and its parent branch, if any
HashMap<Nodeid, BranchChain> head2chain = new HashMap<Nodeid, BranchChain>();
while (!toQuery.isEmpty()) {
List<RemoteBranch> remoteBranches =
remoteRepo.branches(
new ArrayList<Nodeid>(toQuery)); // head, root, first parent, second parent
toQuery.clear();
while (!remoteBranches.isEmpty()) {
RemoteBranch rb = remoteBranches.remove(0);
BranchChain chainElement = head2chain.get(rb.head);
if (chainElement == null) {
chainElement = new BranchChain(rb.head);
// record this unknown branch to download later
branches2load.add(chainElement);
// the only chance we'll need chainElement in the head2chain is when we know this branch's
// root
head2chain.put(rb.head, chainElement);
}
if (localRepo.knownNode(rb.root)) {
// we known branch start, common head is somewhere in its descendants line
checkUp2Head.add(rb);
} else {
chainElement.branchRoot = rb.root;
// dig deeper in the history, if necessary
boolean hasP1 = !rb.p1.isNull(), hasP2 = !rb.p2.isNull();
if (hasP1 && !localRepo.knownNode(rb.p1)) {
toQuery.add(rb.p1);
// we might have seen parent node already, and recorded it as a branch chain
// we shall reuse existing BC to get it completely initialized (head2chain map
// on second put with the same key would leave first BC uninitialized.
// It seems there's no reason to be afraid (XXX although shall double-check)
// that BC's chain would get corrupt (its p1 and p2 fields assigned twice with different
// values)
// as parents are always the same (and likely, BC that is common would be the last
// unknown)
BranchChain bc = head2chain.get(rb.p1);
if (bc == null) {
head2chain.put(rb.p1, bc = new BranchChain(rb.p1));
}
chainElement.p1 = bc;
}
if (hasP2 && !localRepo.knownNode(rb.p2)) {
toQuery.add(rb.p2);
BranchChain bc = head2chain.get(rb.p2);
if (bc == null) {
head2chain.put(rb.p2, bc = new BranchChain(rb.p2));
}
chainElement.p2 = bc;
}
if (!hasP1 && !hasP2) {
// special case, when we do incoming against blank repository, chainElement.branchRoot
// is first unknown element (revision 0). We need to add another fake BranchChain
// to fill the promise that terminal BranchChain has branchRoot that is known both
// locally and remotely
BranchChain fake = new BranchChain(NULL);
fake.branchRoot = NULL;
chainElement.p1 = chainElement.p2 = fake;
}
}
}
}
for (RemoteBranch rb : checkUp2Head) {
Nodeid h = rb.head;
Nodeid r = rb.root;
int watchdog = 1000;
assert head2chain.containsKey(h);
BranchChain bc = head2chain.get(h);
assert bc != null : h.toString();
// if we know branch root locally, there could be no parent branch chain elements.
assert bc.p1 == null;
assert bc.p2 == null;
do {
List<Nodeid> between = remoteRepo.between(h, r);
if (between.isEmpty()) {
bc.branchRoot = r;
break;
} else {
Collections.reverse(between);
for (Nodeid n : between) {
if (localRepo.knownNode(n)) {
r = n;
} else {
h = n;
break;
}
}
Nodeid lastInBetween = between.get(between.size() - 1);
if (r.equals(lastInBetween)) {
bc.branchRoot = r;
break;
} else if (h.equals(
lastInBetween)) { // the only chance for current head pointer to point to the sequence
// tail
// is when r is second from the between list end (iow, head,1,[2],4,8...,root)
bc.branchRoot = r;
break;
}
}
} while (--watchdog > 0);
if (watchdog == 0) {
throw new HgInvalidStateException(
String.format(
"Can't narrow down branch [%s, %s]",
rb.head.shortNotation(), rb.root.shortNotation()));
}
}
if (debug) {
System.out.println("calculateMissingBranches:");
for (BranchChain bc : branches2load) {
bc.dump();
}
}
return branches2load;
}
@Override
public void invoke(@NotNull final Project project, final Editor editor, final PsiFile file)
throws IncorrectOperationException {
if (!FileModificationService.getInstance().prepareFileForWrite(file)) return;
PsiMethod[] constructors = myClass.getConstructors();
if (constructors.length == 0) {
final AddDefaultConstructorFix defaultConstructorFix = new AddDefaultConstructorFix(myClass);
ApplicationManager.getApplication()
.runWriteAction(
new Runnable() {
@Override
public void run() {
defaultConstructorFix.invoke(project, editor, file);
}
});
constructors = myClass.getConstructors();
}
Arrays.sort(
constructors,
new Comparator<PsiMethod>() {
@Override
public int compare(PsiMethod c1, PsiMethod c2) {
final PsiMethod cc1 = RefactoringUtil.getChainedConstructor(c1);
final PsiMethod cc2 = RefactoringUtil.getChainedConstructor(c2);
if (cc1 == c2) return 1;
if (cc2 == c1) return -1;
if (cc1 == null) {
return cc2 == null ? 0 : compare(c1, cc2);
} else {
return cc2 == null ? compare(cc1, c2) : compare(cc1, cc2);
}
}
});
final ArrayList<PsiMethod> constrs =
filterConstructorsIfFieldAlreadyAssigned(constructors, getField());
if (constrs.size() > 1) {
final PsiMethodMember[] members = new PsiMethodMember[constrs.size()];
int i = 0;
for (PsiMethod constructor : constrs) {
members[i++] = new PsiMethodMember(constructor);
}
final List<PsiMethodMember> elements;
if (ApplicationManager.getApplication().isUnitTestMode()) {
elements = Arrays.asList(members);
} else {
final MemberChooser<PsiMethodMember> chooser =
new MemberChooser<PsiMethodMember>(members, false, true, project);
chooser.setTitle("Choose constructors to add parameter to");
chooser.show();
elements = chooser.getSelectedElements();
if (elements == null) return;
}
for (PsiMethodMember member : elements) {
if (!addParameterToConstructor(
project, file, editor, member.getElement(), new PsiField[] {getField()})) break;
}
} else if (!constrs.isEmpty()) {
final Collection<SmartPsiElementPointer<PsiField>> fieldsToFix = getFieldsToFix();
try {
final PsiMethod constructor = constrs.get(0);
final LinkedHashSet<PsiField> fields = new LinkedHashSet<PsiField>();
getFieldsToFix().add(myField);
for (SmartPsiElementPointer<PsiField> elementPointer : fieldsToFix) {
final PsiField field = elementPointer.getElement();
if (field != null
&& isAvailable(field)
&& filterConstructorsIfFieldAlreadyAssigned(new PsiMethod[] {constructor}, field)
.contains(constructor)) {
fields.add(field);
}
}
if (constrs.size() == constructors.length
&& fields.size() > 1
&& !ApplicationManager.getApplication().isUnitTestMode()) {
PsiFieldMember[] members = new PsiFieldMember[fields.size()];
int i = 0;
for (PsiField field : fields) {
members[i++] = new PsiFieldMember(field);
}
MemberChooser<PsiElementClassMember> chooser =
new MemberChooser<PsiElementClassMember>(members, false, true, project);
chooser.setTitle("Choose Fields to Generate Constructor Parameters for");
chooser.show();
if (chooser.getExitCode() != DialogWrapper.OK_EXIT_CODE) return;
final List<PsiElementClassMember> selectedElements = chooser.getSelectedElements();
if (selectedElements == null) return;
fields.clear();
for (PsiElementClassMember member : selectedElements) {
fields.add((PsiField) member.getElement());
}
}
addParameterToConstructor(
project,
file,
editor,
constructor,
constrs.size() == constructors.length
? fields.toArray(new PsiField[fields.size()])
: new PsiField[] {getField()});
} finally {
fieldsToFix.clear();
}
}
}
public void reset() {
m_entries.addAll(m_added);
m_added.clear();
m_removed.clear();
}
/** java.util.LinkedHashSet#size() */
public void test_size() {
// Test for method int java.util.LinkedHashSet.size()
assertTrue("Returned incorrect size", hs.size() == (objArray.length + 1));
hs.clear();
assertEquals("Cleared set returned non-zero size", 0, hs.size());
}
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());
}
}
/**
* run any deferred post-commit triggers.
*
* @see com.yahoo.elide.annotation.CreatePermission
*/
public void runCommitTriggers() {
new ArrayList<>(commitTriggers).forEach(Runnable::run);
commitTriggers.clear();
}
public void clearProcedures() {
m_procedures.clear();
m_procInfoOverrides.clear();
m_prefetchQueries.clear();
}
public List<Repository> getMappedRepositories(
Repository repository, ResourceStoreRequest request, List<Repository> resolvedRepositories)
throws NoSuchRepositoryException {
if (!compiled) {
compile();
}
// NEXUS-2852: to make our life easier, we will work with repository IDs,
// and will fill the result with Repositories at the end
LinkedHashSet<String> reposIdSet = new LinkedHashSet<String>(resolvedRepositories.size());
for (Repository resolvedRepositorty : resolvedRepositories) {
reposIdSet.add(resolvedRepositorty.getId());
}
// for tracking what is applied
ArrayList<RepositoryPathMapping> appliedMappings = new ArrayList<RepositoryPathMapping>();
// if include found, add it to the list.
boolean firstAdd = true;
for (RepositoryPathMapping mapping : blockings) {
if (mapping.matches(repository, request)) {
if (getLogger().isDebugEnabled()) {
getLogger()
.debug(
"The request path ["
+ request.toString()
+ "] is blocked by rule "
+ mapping.toString());
}
return Collections.emptyList();
}
}
// include, if found a match
// NEXUS-2852: watch to not add multiple times same repository
// ie. you have different inclusive rules that are triggered by same request
// and contains some repositories. This is now solved using LinkedHashSet and using repo IDs.
for (RepositoryPathMapping mapping : inclusions) {
if (mapping.matches(repository, request)) {
appliedMappings.add(mapping);
if (firstAdd) {
reposIdSet.clear();
firstAdd = false;
}
// add only those that are in initial resolvedRepositories list and that are non-user
// managed
// (preserve ordering)
if (mapping.getMappedRepositories().size() == 1
&& "*".equals(mapping.getMappedRepositories().get(0))) {
for (Repository repo : resolvedRepositories) {
reposIdSet.add(repo.getId());
}
} else {
for (Repository repo : resolvedRepositories) {
if (mapping.getMappedRepositories().contains(repo.getId()) || !repo.isUserManaged()) {
reposIdSet.add(repo.getId());
}
}
}
}
}
// then, if exlude found, remove those
for (RepositoryPathMapping mapping : exclusions) {
if (mapping.matches(repository, request)) {
appliedMappings.add(mapping);
if (mapping.getMappedRepositories().size() == 1
&& "*".equals(mapping.getMappedRepositories().get(0))) {
reposIdSet.clear();
break;
}
for (String repositoryId : mapping.getMappedRepositories()) {
Repository mappedRepository = repositoryRegistry.getRepository(repositoryId);
// but only if is user managed
if (mappedRepository.isUserManaged()) {
reposIdSet.remove(mappedRepository.getId());
}
}
}
}
// store the applied mappings to request context
ArrayList<String> appliedMappingsList = new ArrayList<String>(appliedMappings.size());
for (RepositoryPathMapping mapping : appliedMappings) {
appliedMappingsList.add(mapping.toString());
}
request.addAppliedMappingsList(repository, appliedMappingsList);
// log it if needed
if (getLogger().isDebugEnabled()) {
if (appliedMappings.isEmpty()) {
getLogger().debug("No mapping exists for request path [" + request.toString() + "]");
} else {
StringBuilder sb =
new StringBuilder(
"Request for path \""
+ request.toString()
+ "\" with the initial list of processable repositories of \""
+ ResourceStoreUtils.getResourceStoreListAsString(resolvedRepositories)
+ "\" got these mappings applied:\n");
for (RepositoryPathMapping mapping : appliedMappings) {
sb.append(" * ").append(mapping.toString()).append("\n");
}
getLogger().debug(sb.toString());
if (reposIdSet.size() == 0) {
getLogger()
.debug(
"Mapping for path ["
+ request.toString()
+ "] excluded all storages from servicing the request.");
} else {
getLogger()
.debug(
"Request path for ["
+ request.toString()
+ "] is MAPPED to reposes: "
+ reposIdSet);
}
}
}
ArrayList<Repository> result = new ArrayList<Repository>(reposIdSet.size());
try {
for (String repoId : reposIdSet) {
result.add(repositoryRegistry.getRepository(repoId));
}
} catch (NoSuchRepositoryException e) {
getLogger()
.error(
"Some of the Routes contains references to non-existant repositories! Please check the following mappings: \""
+ appliedMappingsList.toString()
+ "\".");
throw e;
}
return result;
}
/** Removes all picked elements. */
public final void removeAllElements() {
LinkedHashSet<String> elements = (LinkedHashSet<String>) selection.getValue();
elements.clear();
markDirty();
}
public synchronized void drainTo(List<T> list) {
list.addAll(items);
items.clear();
}