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);
}
// #]
}
// ## 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);
}
}
// #]
}
public static TemplateReaction makeTemplateReaction(
Structure p_structureSp,
Kinetics[] p_kinetics,
ReactionTemplate p_template,
Structure p_structure) {
double PT = System.currentTimeMillis();
// Look for pre-existing reaction in Template's reactionDictionaryByStructure.
TemplateReaction reaction = p_template.getReactionFromStructure(p_structureSp);
Global.getReacFromStruc =
Global.getReacFromStruc + (System.currentTimeMillis() - PT) / 1000 / 60;
if (reaction == null) {
// Create a new reaction.
reaction = new TemplateReaction(p_structureSp, p_kinetics, p_template);
if (reaction.isBackward()) {
Logger.info(
"Created new reverse " + p_template.getName() + " reaction: " + reaction.toString());
TemplateReaction reverse =
reaction.generateReverseForBackwardReaction(p_structure, p_structureSp);
if (reverse == null) return null;
reaction.setReverseReaction(reverse);
} else {
Logger.info(
"Created new forwards " + p_template.getName() + " reaction: " + reaction.toString());
ReactionTemplate fRT = reaction.getReactionTemplate();
ReactionTemplate rRT = null;
if (fRT.isNeutral()) rRT = fRT;
else rRT = fRT.getReverseReactionTemplate();
if (rRT != null) {
TemplateReaction reverse =
new TemplateReaction(p_structureSp.generateReverseStructure(), p_kinetics, rRT);
reaction.setReverseReaction(reverse);
reverse.setReverseReaction(reaction);
rRT.addReaction(reverse);
}
}
if (!reaction.repOk()) {
throw new InvalidTemplateReactionException();
}
p_template.addReaction(reaction);
}
Global.makeTR += (System.currentTimeMillis() - PT) / 1000 / 60;
if (!reaction.repOk()) {
throw new InvalidTemplateReactionException();
}
return reaction;
}