/**
* If the outbound level is BINARY, convert the string field to binary, then pad to the left with
* the appropriate number of zero bits to reach a number of bits specified by the bitLength
* attribute of the TDT definition file.
*/
private void binaryPadding(Map<String, String> extraparams, Field tdtfield) {
String fieldname = tdtfield.getName();
int reqbitlength = tdtfield.getBitLength();
String value;
String binaryValue = fieldToBinary(tdtfield, extraparams);
if (binaryValue.length() < reqbitlength) {
int extraBitLength = reqbitlength - binaryValue.length();
StringBuilder zeroPaddedBinaryValue = new StringBuilder("");
for (int i = 0; i < extraBitLength; i++) {
zeroPaddedBinaryValue.append("0");
}
zeroPaddedBinaryValue.append(binaryValue);
value = zeroPaddedBinaryValue.toString();
} else {
if (binaryValue.length() > reqbitlength)
throw new TDTException(
"Binary value ["
+ binaryValue
+ "] for field "
+ fieldname
+ " exceeds maximum allowed "
+ reqbitlength
+ " bits. Decimal value was "
+ extraparams.get(fieldname));
value = binaryValue;
}
extraparams.put(fieldname, value);
}
private Node[] processIndexNode(
final Node theNode,
final Document theTargetDocument,
final IndexEntryFoundListener theIndexEntryFoundListener) {
theNode.normalize();
boolean ditastyle = false;
String textNode = null;
final NodeList childNodes = theNode.getChildNodes();
final StringBuilder textBuf = new StringBuilder();
final List<Node> contents = new ArrayList<Node>();
for (int i = 0; i < childNodes.getLength(); i++) {
final Node child = childNodes.item(i);
if (checkElementName(child)) {
ditastyle = true;
break;
} else if (child.getNodeType() == Node.ELEMENT_NODE) {
textBuf.append(XMLUtils.getStringValue((Element) child));
contents.add(child);
} else if (child.getNodeType() == Node.TEXT_NODE) {
textBuf.append(child.getNodeValue());
contents.add(child);
}
}
textNode = IndexStringProcessor.normalizeTextValue(textBuf.toString());
if (textNode.length() == 0) {
textNode = null;
}
if (theNode.getAttributes().getNamedItem(elIndexRangeStartName) != null
|| theNode.getAttributes().getNamedItem(elIndexRangeEndName) != null) {
ditastyle = true;
}
final ArrayList<Node> res = new ArrayList<Node>();
if ((ditastyle)) {
final IndexEntry[] indexEntries = indexDitaProcessor.processIndexDitaNode(theNode, "");
for (final IndexEntry indexEntrie : indexEntries) {
theIndexEntryFoundListener.foundEntry(indexEntrie);
}
final Node[] nodes = transformToNodes(indexEntries, theTargetDocument, null);
for (final Node node : nodes) {
res.add(node);
}
} else if (textNode != null) {
final Node[] nodes =
processIndexString(textNode, contents, theTargetDocument, theIndexEntryFoundListener);
for (final Node node : nodes) {
res.add(node);
}
} else {
return new Node[0];
}
return (Node[]) res.toArray(new Node[res.size()]);
}
private String unirMapeos(LinkedHashMap<String, String> mapa, Object[] descripciones) {
// mapa(llave,punto)
// descripciones en el mismo orden que el mapeo
String comillas = "\"";
StringBuilder builder = new StringBuilder();
Iterator<String> iterador = mapa.keySet().iterator();
int indice = 0;
while (iterador.hasNext()) {
String llave = iterador.next();
String puntaje = mapa.get(llave);
String descripcion =
descripciones[indice].toString().equals("null") ? "" : descripciones[indice].toString();
builder.append(comillas + descripcion + comillas + "," + comillas + puntaje + comillas + ",");
indice++;
}
return builder.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();
// #]
}
private void initExecute(Element executeRoot) throws XmlaException {
Element[] childElems = XmlaUtil.filterChildElements(executeRoot, NS_XMLA, "Command");
if (childElems.length != 1) {
StringBuilder buf = new StringBuilder(100);
buf.append(MSG_INVALID_XMLA);
buf.append(": Wrong number of Command elements: ");
buf.append(childElems.length);
throw new XmlaException(
CLIENT_FAULT_FC,
HSB_BAD_COMMAND_CODE,
HSB_BAD_COMMAND_FAULT_FS,
Util.newError(buf.toString()));
}
initCommand(childElems[0]); // <Command><Statement>
childElems = XmlaUtil.filterChildElements(executeRoot, NS_XMLA, "Properties");
if (childElems.length != 1) {
StringBuilder buf = new StringBuilder(100);
buf.append(MSG_INVALID_XMLA);
buf.append(": Wrong number of Properties elements: ");
buf.append(childElems.length);
throw new XmlaException(
CLIENT_FAULT_FC,
HSB_BAD_PROPERTIES_CODE,
HSB_BAD_PROPERTIES_FAULT_FS,
Util.newError(buf.toString()));
}
initProperties(childElems[0]); // <Properties><PropertyList>
}
private static String normalisedVersion(String version, String sep, int maxWidth) {
String[] split = Pattern.compile(sep, Pattern.LITERAL).split(version);
StringBuilder sb = new StringBuilder();
for (String s : split) {
sb.append(String.format("%" + maxWidth + 's', s));
}
return sb.toString();
}
private static String encodeChar(char c) {
StringBuilder buf = new StringBuilder();
buf.append("_x");
String str = Integer.toHexString(c);
for (int i = 4 - str.length(); i > 0; i--) {
buf.append("0");
}
return buf.append(str).append("_").toString();
}
/**
* Returns a string representation of all found arguments.
*
* @param args array with arguments
* @return string representation
*/
static String foundArgs(final Value[] args) {
// compose found arguments
final StringBuilder sb = new StringBuilder();
for (final Value v : args) {
if (sb.length() != 0) sb.append(", ");
sb.append(v instanceof Jav ? Util.className(((Jav) v).toJava()) : v.seqType());
}
return sb.toString();
}
private static String dump(Collection<ProtocolConfiguration> configs) {
StringBuilder sb = new StringBuilder();
String indent = " ";
sb.append("<config>\n");
for (ProtocolConfiguration cfg : configs) {
sb.append(indent).append("<").append(cfg.getProtocolName());
Map<String, String> props = cfg.getProperties();
if (props.isEmpty()) {
sb.append(" />\n");
} else {
sb.append("\n").append(indent).append(indent);
for (Map.Entry<String, String> entry : props.entrySet()) {
String key = entry.getKey();
String val = entry.getValue();
key = trim(key);
val = trim(val);
sb.append(key).append("=\"").append(val).append("\" ");
}
sb.append(" />\n");
}
}
sb.append("</config>\n");
return sb.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();
// #]
}
/** Converts a binary string input into a byte string, using 8-bits per character byte */
private String bytestring2bin(String bytestring) {
String binary;
StringBuilder buffer = new StringBuilder("");
int len = bytestring.length();
byte[] bytes = bytestring.getBytes();
for (int i = 0; i < len; i++) {
buffer.append(padBinary(dec2bin(Integer.toString(bytes[i])), 8));
}
binary = buffer.toString();
return binary;
}
/** Converts a byte string input into a binary string, using 8-bits per character byte */
private String bin2bytestring(String binary) {
String bytestring;
StringBuilder buffer = new StringBuilder("");
int len = binary.length();
for (int i = 0; i < len; i += 8) {
int j = Integer.parseInt(bin2dec(padBinary(binary.substring(i, i + 8), 8)));
buffer.append((char) j);
}
bytestring = buffer.toString();
return bytestring;
}
/**
* Converts an upper case character string input into a binary string, using 5-bit compaction of
* each ASCII byte
*/
private String uppercasefive2bin(String uppercasefive) {
String binary;
StringBuilder buffer = new StringBuilder("");
int len = uppercasefive.length();
byte[] bytes = uppercasefive.getBytes();
for (int i = 0; i < len; i++) {
buffer.append(padBinary(dec2bin(Integer.toString(bytes[i] % 32)), 8).substring(3, 8));
}
binary = buffer.toString();
return binary;
}
private static <T> String toString(List<T> list) {
StringBuilder buf = new StringBuilder();
int k = -1;
for (T t : list) {
if (++k > 0) {
buf.append(", ");
}
buf.append(t);
}
return buf.toString();
}
/**
* Converts an ASCII string input into a binary string, using 7-bit compaction of each ASCII byte
*/
private String asciiseven2bin(String asciiseven) {
String binary;
StringBuilder buffer = new StringBuilder("");
int len = asciiseven.length();
byte[] bytes = asciiseven.getBytes();
for (int i = 0; i < len; i++) {
buffer.append(padBinary(dec2bin(Integer.toString(bytes[i] % 128)), 8).substring(1, 8));
}
binary = buffer.toString();
return binary;
}
/**
* Converts a binary string input into a character string output, assuming that 5-bit compaction
* was used
*/
private String bin2uppercasefive(String binary) {
String uppercasefive;
StringBuilder buffer = new StringBuilder("");
int len = binary.length();
for (int i = 0; i < len; i += 5) {
int j = Integer.parseInt(bin2dec(padBinary(binary.substring(i, i + 5), 8)));
buffer.append((char) (j + 64));
}
uppercasefive = buffer.toString();
return uppercasefive;
}
/**
* Converts an alphanumeric string input into a binary string, using 6-bit compaction of each
* ASCII byte
*/
private String alphanumsix2bin(String alphanumsix) {
String binary;
StringBuilder buffer = new StringBuilder("");
int len = alphanumsix.length();
byte[] bytes = alphanumsix.getBytes();
for (int i = 0; i < len; i++) {
buffer.append(padBinary(dec2bin(Integer.toString(bytes[i] % 64)), 8).substring(2, 8));
}
binary = buffer.toString();
return binary;
}
/**
* Converts a binary string input into an ASCII string output, assuming that 7-bit compaction was
* used
*/
private String bin2asciiseven(String binary) {
String asciiseven;
StringBuilder buffer = new StringBuilder("");
int len = binary.length();
for (int i = 0; i < len; i += 7) {
int j = Integer.parseInt(bin2dec(padBinary(binary.substring(i, i + 7), 8)));
buffer.append((char) j);
}
asciiseven = buffer.toString();
return asciiseven;
}
public String getPath() {
StringBuilder builder = new StringBuilder();
Node current = node;
while (current != null && current instanceof Element) {
if (current != node) {
builder.insert(0, "/");
}
builder.insert(0, current.getNodeName());
current = current.getParentNode();
}
return builder.toString();
}
/**
* Pads a binary value supplied as a string first parameter to the left with leading zeros in
* order to reach a required number of bits, as expressed by the second parameter, reqlen. Returns
* a string value corresponding to the binary value left padded to the required number of bits.
*/
private String padBinary(String binary, int reqlen) {
String rv;
int l = binary.length();
int pad = (reqlen - (l % reqlen)) % reqlen;
StringBuilder buffer = new StringBuilder("");
for (int i = 0; i < pad; i++) {
buffer.append("0");
}
buffer.append(binary);
rv = buffer.toString();
return rv;
}
// ## operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
public static void writeChemkinInputFile(
final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(p_reactionModel, p_beginStatus));
result.append(writeChemkinThermo(p_reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(
writeChemkinPdepReactions(
p_reactionModel, p_beginStatus)); // 10/26/07 gmagoon: changed to pass p_beginStatus
// result.append(writeChemkinPdepReactions(p_reactionModel));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
if (PDepRateConstant.getMode() == Mode.CHEBYSHEV
|| PDepRateConstant.getMode() == Mode.PDEPARRHENIUS
|| PDepRateConstant.getMode() == Mode.RATE) {
StringBuilder gridOfRateCoeffs = new StringBuilder();
gridOfRateCoeffs.append(writeGridOfRateCoeffs(p_reactionModel));
String newFile = "chemkin/tableOfRateCoeffs.txt";
try {
FileWriter fw = new FileWriter(newFile);
fw.write(gridOfRateCoeffs.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing tableOfRateCoeffs.txt");
System.out.println(e.getMessage());
System.exit(0);
}
}
// #]
}
/**
* Encodes an XML element name.
*
* <p>This function is mainly for encode element names in result of Drill Through execute, because
* its element names come from database, we cannot make sure they are valid XML contents.
*
* <p>Quoth the <a href="http://xmla.org">XML/A specification</a>, version 1.1:
*
* <blockquote>
*
* XML does not allow certain characters as element and attribute names. XML for Analysis supports
* encoding as defined by SQL Server 2000 to address this XML constraint. For column names that
* contain invalid XML name characters (according to the XML 1.0 specification), the nonvalid
* Unicode characters are encoded using the corresponding hexadecimal values. These are escaped as
* _x<i>HHHH_</i> where <i>HHHH</i> stands for the four-digit hexadecimal UCS-2 code for the
* character in most-significant bit first order. For example, the name "Order Details" is encoded
* as Order_<i>x0020</i>_Details, where the space character is replaced by the corresponding
* hexadecimal code.
*
* </blockquote>
*
* @param name Name of XML element
* @return encoded name
*/
private static String encodeElementName(String name) {
StringBuilder buf = new StringBuilder();
char[] nameChars = name.toCharArray();
for (char ch : nameChars) {
String encodedStr = (ch >= CHAR_TABLE.length ? null : CHAR_TABLE[ch]);
if (encodedStr == null) {
buf.append(ch);
} else {
buf.append(encodedStr);
}
}
return buf.toString();
}
public static String textInElement(Element elem) {
StringBuilder buf = new StringBuilder(100);
elem.normalize();
NodeList nlst = elem.getChildNodes();
for (int i = 0, nlen = nlst.getLength(); i < nlen; i++) {
Node n = nlst.item(i);
if (n instanceof Text) {
final String data = ((Text) n).getData();
buf.append(data);
}
}
return buf.toString();
}
/**
* Returns a string built using a particular grammar. Single-quotes strings are counted as literal
* strings, whereas all other strings appearing in the grammar require substitution with the
* corresponding value from the extraparams hashmap.
*/
private String buildGrammar(String grammar, Map<String, String> extraparams) {
StringBuilder outboundstring = new StringBuilder();
String[] fields = Pattern.compile("\\s+").split(grammar);
for (int i = 0; i < fields.length; i++) {
if (fields[i].substring(0, 1).equals("'")) {
outboundstring.append(fields[i].substring(1, fields[i].length() - 1));
} else {
outboundstring.append(extraparams.get(fields[i]));
}
}
return outboundstring.toString();
}
/**
* Converts a binary string input into a character string output, assuming that 6-bit compaction
* was used
*/
private String bin2alphanumsix(String binary) {
String alphanumsix;
StringBuilder buffer = new StringBuilder("");
int len = binary.length();
for (int i = 0; i < len; i += 6) {
int j = Integer.parseInt(bin2dec(padBinary(binary.substring(i, i + 6), 8)));
if (j < 32) {
j += 64;
}
buffer.append((char) j);
}
alphanumsix = buffer.toString();
return alphanumsix;
}
private String obtenerNombre(Element raiz) {
String comillas = "\"";
StringBuilder nombre = new StringBuilder(comillas);
String[] vars = {"CliApePat", "CliApeMat", "CliNom"};
for (String s : vars) {
nombre.append(raiz.getElementsByTagName(s).item(0).getTextContent() + " ");
}
nombre.append(comillas);
return nombre.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();
}
private void initCommand(Element commandRoot) throws XmlaException {
Element[] childElems = XmlaUtil.filterChildElements(commandRoot, NS_XMLA, "Statement");
if (childElems.length != 1) {
StringBuilder buf = new StringBuilder(100);
buf.append(MSG_INVALID_XMLA);
buf.append(": Wrong number of Statement elements: ");
buf.append(childElems.length);
throw new XmlaException(
CLIENT_FAULT_FC,
HSB_BAD_STATEMENT_CODE,
HSB_BAD_STATEMENT_FAULT_FS,
Util.newError(buf.toString()));
}
statement = XmlaUtil.textInElement(childElems[0]).replaceAll("\\r", "");
drillthrough = statement.toUpperCase().indexOf("DRILLTHROUGH") != -1;
}
public static String replace(String input, final String expr, String replacement) {
StringBuilder sb = new StringBuilder();
int new_index = 0, index = 0, len = expr.length(), input_len = input.length();
while (true) {
new_index = input.indexOf(expr, index);
if (new_index == -1) {
sb.append(input.substring(index, input_len));
break;
}
sb.append(input.substring(index, new_index));
sb.append(replacement);
index = new_index + len;
}
return sb.toString();
}
public static void writeChemkinInputFile(ReactionSystem rs) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(rs.reactionModel, rs.initialStatus));
result.append(writeChemkinThermo(rs.reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(writeChemkinPdepReactions(rs));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
