// ## 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();
// #]
}
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();
// #]
}
// convert coordinates to relative coordinates with the top-left one as (0,0)
public void convertToRelativePositions() {
LayoutBox box = getExactLayoutBox();
// System.out.println("Box
// ("+box.topleft.x+","+box.topleft.y+");("+(box.topleft.x+box.width)+","+(box.topleft.y+box.height));
Iterator<NodeLayout> e = nodes.iterator();
NodeLayout nl;
while (e.hasNext()) {
nl = e.next();
/* Debug code
if(nl.x<box.topleft.x || nl.y<box.topleft.y || nl.x>(box.topleft.x+box.width) || nl.y>(box.topleft.y+box.height)){
System.out.println("Invalid node "+nl.x+","+nl.y);
}
//*/
nl.x = nl.x - box.topleft.x;
nl.y = nl.y - box.topleft.y;
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = lp.x - box.topleft.x;
lp.y = lp.y - box.topleft.y;
}
}
}
public void flipLayoutLeftRight() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (nl.processID.equals("null")) {
nl.x =
box.topleft.x
+ (box.width - (nl.x - box.topleft.x))
- 60; // minus 60 which is the width of process node's box, since using upperleft
// coor
} else if (isSecondary(nl)) {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 60;
} else {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = box.topleft.x + (box.width - (lp.x - box.topleft.x));
}
}
}
public void selectNext() {
Iterator i = new SelectionIterator(this);
if (m_actives.size() == 1) {
boolean isFound = false;
// loop the iterator in reverse order of drawing
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (m_actives.isSelected(object)) {
isFound = true;
continue;
} // if
if (!isFound) {
continue;
} // if
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // while i
} // if
i = new SelectionIterator(this);
if (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // if
}
/**
* @return exact rectangle box bounding all the center points of the nodes and all the bend
* points.
*/
public LayoutBox getExactLayoutBox() {
Iterator<NodeLayout> e = nodes.iterator();
double tlx = 0, tly = 0, brx = 0, bry = 0; // top left, bottom right
NodeLayout nl;
if (e.hasNext()) {
nl = e.next();
tlx = nl.x;
tly = nl.y;
brx = nl.x;
bry = nl.y;
}
while (e.hasNext()) {
nl = e.next();
if (nl.x < tlx) {
tlx = nl.x;
}
if (nl.x > brx) {
brx = nl.x;
}
if (nl.y < tly) {
tly = nl.y;
}
if (nl.y > bry) {
bry = nl.y;
}
}
Iterator<EdgeLayout> ee = edges.iterator();
Iterator<LayoutPoint> be;
LayoutPoint lp;
EdgeLayout el;
while (ee.hasNext()) {
el = ee.next();
be = el.bends.iterator();
while (be.hasNext()) {
lp = be.next();
if (lp.x < tlx) {
tlx = lp.x;
}
if (lp.x > brx) {
brx = lp.x;
}
if (lp.y < tly) {
tly = lp.y;
}
if (lp.y > bry) {
bry = lp.y;
}
}
}
return new LayoutBox(tlx, tly, brx - tlx, bry - tly);
}
public String toString() {
if (isEmpty()) {
return "";
}
StringBuffer sb = new StringBuffer();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) sb.append((e.next()).toString());
sb.append("\n");
Iterator<EdgeLayout> ee = edges.iterator();
while (ee.hasNext()) sb.append((ee.next()).toString());
return sb.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 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 void display(Graphics2D g, AffineTransform a_trans) {
Iterator i = createIterator();
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
object.display(g, a_trans);
} // while
}
/**
* Reload the composite nodes of the circuit, this is recursive
*
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public void reloadCompositeNodes(Graphics g) throws CircuitLoadingException {
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.COMPOSITE) ((CompositeNode) n).reload(g);
}
}
public String toBeautifiedString() {
StringBuffer sb = new StringBuffer();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) sb.append((e.next()).toBeautifiedString());
sb.append("\n");
Iterator<EdgeLayout> ee = edges.iterator();
while (ee.hasNext()) {
sb.append((ee.next()).toBeautifiedString());
}
sb.append("\n\nNumber of Nodes: ");
sb.append(nodes.size());
sb.append("\nNumber of Edges: ");
sb.append(edges.size() + "\n");
return sb.toString();
}
// convert coordinates to shifted coordinates with the top-left one as (xs,ys)
public void convertToShiftedPositions(double xs, double ys) {
convertToRelativePositions();
Iterator<NodeLayout> e = nodes.iterator();
NodeLayout nl;
while (e.hasNext()) {
nl = e.next();
nl.x += xs;
nl.y += ys;
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x += xs;
lp.y += ys;
}
}
}
public EdgeLayout getEdgeLayouts(String spid, String sid, String tpid, String tid) {
Iterator<EdgeLayout> ee = edges.iterator();
EdgeLayout el;
while (ee.hasNext()) {
el = ee.next();
if (el.sourceNode.equals(sid) && el.targetNode.equals(tid)) {
return el;
}
}
return null;
} // */
/**
* Get the inputable nodes of the circuit
*
* @return an hashset of the inputable nodes of the circuit
*/
public HashSet<Inputable> getInputables() {
HashSet<Inputable> inputs = new HashSet<Inputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.INPUT) inputs.add((Inputable) n);
}
return inputs;
}
protected void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
try {
DateFormat df = DateFormat.getDateTimeInstance();
String titleStr = "C3P0 Status - " + df.format(new Date());
DocumentBuilderFactory fact = DocumentBuilderFactory.newInstance();
DocumentBuilder db = fact.newDocumentBuilder();
Document doc = db.newDocument();
Element htmlElem = doc.createElement("html");
Element headElem = doc.createElement("head");
Element titleElem = doc.createElement("title");
titleElem.appendChild(doc.createTextNode(titleStr));
Element bodyElem = doc.createElement("body");
Element h1Elem = doc.createElement("h1");
h1Elem.appendChild(doc.createTextNode(titleStr));
Element h3Elem = doc.createElement("h3");
h3Elem.appendChild(doc.createTextNode("PooledDataSources"));
Element pdsDlElem = doc.createElement("dl");
pdsDlElem.setAttribute("class", "PooledDataSources");
for (Iterator ii = C3P0Registry.getPooledDataSources().iterator(); ii.hasNext(); ) {
PooledDataSource pds = (PooledDataSource) ii.next();
StatusReporter sr = findStatusReporter(pds, doc);
pdsDlElem.appendChild(sr.reportDtElem());
pdsDlElem.appendChild(sr.reportDdElem());
}
headElem.appendChild(titleElem);
htmlElem.appendChild(headElem);
bodyElem.appendChild(h1Elem);
bodyElem.appendChild(h3Elem);
bodyElem.appendChild(pdsDlElem);
htmlElem.appendChild(bodyElem);
res.setContentType("application/xhtml+xml");
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
Source src = new DOMSource(doc);
Result result = new StreamResult(res.getOutputStream());
transformer.transform(src, result);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new ServletException(e);
}
}
/**
* Get the outputable nodes of the circuit
*
* @return an hashset of the outputable nodes of the circuit
*/
public HashSet<Outputable> getOutputables() {
HashSet<Outputable> outputs = new HashSet<Outputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.OUTPUT) outputs.add((Outputable) n);
}
return outputs;
}
public void flipLayoutUpDown() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (isSecondary(nl)) {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 12;
} else {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.y = box.topleft.y + (box.height - (lp.y - box.topleft.y));
}
}
}
public void filpLayoutUpDown() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (nl.cofactor.equalsIgnoreCase("true")) {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 12;
} else {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.y = box.topleft.y + (box.height - (lp.y - box.topleft.y));
}
}
}
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(sourcepid + "," + sourceNode + "," + targetpid + "," + targetNode + ",");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(b.x + "," + b.y + ",");
}
sb.append("\n");
return sb.toString();
}
// Return the shared nodes(with the same node id) with the other LayoutInfo
public LinkedHashMap<NodeLayout, NodeLayout> sharedNodes(LayoutInfo info2) {
LinkedHashMap<NodeLayout, NodeLayout> shared = new LinkedHashMap<NodeLayout, NodeLayout>();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) {
NodeLayout nl = e.next();
if (nl.cofactor.equalsIgnoreCase("true")) {
continue;
}
NodeLayout nl2;
Iterator<NodeLayout> e2 = info2.nodes.iterator();
while (e2.hasNext()) {
nl2 = e2.next();
if (nl2.cofactor.equalsIgnoreCase("true")) {
continue;
}
if (nl.nodeID.equals(nl2.nodeID)) {
shared.put(nl, nl2);
}
}
}
return shared;
}
/**
* Make the circuit for simulation
*
* @return the equivalent circuit
*/
public Circuit makeSimulationCircuit() {
this.circuit = new Circuit();
this.wirestable = new Hashtable<Link, Wire>();
this.inputstable = new Hashtable<Node, Input>();
this.outputstable = new Hashtable<Node, Output>();
for (iterLinks = this.links.iterator(); iterLinks.hasNext(); )
this.wirestable.put(iterLinks.next(), new Wire(this.circuit));
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
Actor a = n.makeSimulationNode(this);
if (a instanceof Input) {
this.inputstable.put(n, (Input) a);
this.circuit.addInput((Input) a);
} else if (n instanceof OutputUI) {
this.outputstable.put(n, (Output) a);
this.circuit.addOutput((Output) a);
}
}
return this.circuit;
}
public String toBeautifiedString() {
StringBuffer sb = new StringBuffer();
sb.append("sourcePID: " + sourcepid);
sb.append(" sourceNodeId: " + sourceNode + "\n");
sb.append(" targetPID: " + targetpid);
sb.append(" targetNodeId: " + targetNode + "\n");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(" Bend Points: " + b.x + "," + b.y + " ");
}
sb.append("\n\n");
return sb.toString();
}
/**
* converts this glyph into Shape. It could be called for root's preview mode or by include
* invoke. Pushing either this GlyphFile or DIncludeInvoke should be handled before this.
*/
public Shape toShape(AffineTransform a_trans) {
int ppem = k_defaultPixelSize;
GeneralPath retval = new GeneralPath();
Iterator i = createIterator();
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (object instanceof EContourPoint || object instanceof EHint) {
continue;
} // if
retval.append(object.toShape(a_trans, ppem), false);
} // if
return retval;
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
private boolean hitObjects(Rectangle2D a_rect, boolean a_isSelectOnlyOne) {
boolean retval = false;
Iterator i = new SelectionIterator(this);
// loop the iterator in reverse order of drawing
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (!object.hit(a_rect, new AffineTransform())) {
continue;
} // if
retval = true;
if (a_isSelectOnlyOne) {
return true;
} // if
} // while i
return retval;
}
// ## 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();
// #]
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}
// ## 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();
// #]
}